; ########################################################################
; # #
; # ffamber ports for GROMACS 3.3 - Nov. 2005 #
; # Eric J. Sorin & Sanghyun Park - Stanford University #
; # please cite: Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. #
; # for additional information, tools, and updates #
; # please consult http://folding.stanford.edu/ffamber/ #
; # #
; ########################################################################
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove impropers over the same bond as a proper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1 1 3 1 0
; first are tip3p, heavy tip3p, tip4p, tip4p-EW, and tip5p; then ion definitions, urea, and terminal caps
;tip3p
[ HOH ]
[ atoms ]
OW amber99_42 -0.834 0
HW1 amber99_27 0.417 0
HW2 amber99_27 0.417 0
[ bonds ]
OW HW1
OW HW2
[ T3P ]
[ atoms ]
OW amber99_42 -0.834 0
HW1 amber99_27 0.417 0
HW2 amber99_27 0.417 0
[ bonds ]
OW HW1
OW HW2
;tip3p (heavy)
[ T3H ]
[ atoms ]
OW amber99_67 -0.834 0
HW1 amber99_66 0.417 0
HW2 amber99_66 0.417 0
[ bonds ]
OW HW1
OW HW2
;tip4p
[ T4P ]
[ atoms ]
OW amber99_63 0.000 0
HW2 amber99_62 0.520 0
HW3 amber99_62 0.520 0
MW4 MW -1.040 0
[ bonds ]
OW HW1
OW HW2
;tip4p-EW
[ T4E ]
[ atoms ]
OW amber99_61 0.000 0
HW1 amber99_60 0.52422 0
HW2 amber99_60 0.52422 0
MW MW -1.04844 0
[ bonds ]
OW HW1
OW HW2
;tip5p
[ T5P ]
[ atoms ]
OW amber99_65 0.000 0
HW1 amber99_64 0.241 0
HW2 amber99_64 0.241 0
LP1 MW -0.241 0
LP2 MW -0.241 0
[ bonds ]
OW HW1
OW HW2
[ IB+ ] ; big positive ion
[ atoms ]
IB amber99_32 1.00000 1
[ Ca+ ]
[ atoms ]
Ca amber99_15 2.00000 1
[ Cl- ]
[ atoms ]
Cl amber99_30 -1.00000 1
[ Na+ ]
[ atoms ]
Na amber99_31 1.00000 1
[ Mg+ ]
[ atoms ]
Mg amber99_33 2.00000 1
[ K+ ]
[ atoms ]
K amber99_51 1.00000 1
[ Rb+ ]
[ atoms ]
Rb amber99_52 1.00000 1
[ Cs+ ]
[ atoms ]
CS amber99_53 1.00000 1
[ Li+ ]
[ atoms ]
Li amber99_56 1.00000 1
[ Zn+ ]
[ atoms ]
Zn amber99_57 2.00000 1
[ Sr+ ] ; ponder/tinker amber
[ atoms ]
Sr amber99_58 2.00000 1
[ Ba+ ] ; ponder/tinker amber
[ atoms ]
Ba amber99_59 2.00000 1
[ URE ] ; added in by EJS, resp charges by Jim Caldwell
[ atoms ]
C amber99_2 0.880229 1
O amber99_41 -0.613359 2
N1 amber99_34 -0.923545 3
H11 amber99_17 0.395055 4
H12 amber99_17 0.395055 5
N2 amber99_34 -0.923545 6
H21 amber99_17 0.395055 7
H22 amber99_17 0.395055 8
[ bonds ]
C N1
C N2
C O
N1 H11
N1 H12
N2 H21
N2 H22
[ dihedrals ]
O C N1 H11 backbone_prop_2
O C N1 H12 backbone_prop_2
O C N2 H21 backbone_prop_2
O C N2 H22 backbone_prop_2
N1 C N2 H21 backbone_prop_1
N1 C N2 H22 backbone_prop_1
N2 C N1 H11 backbone_prop_1
N2 C N1 H12 backbone_prop_1
[ impropers ]
N1 N2 C O urea_improper_1
C H11 N1 H12
C H21 N2 H22
[ ACE ]
[ atoms ]
HH31 amber99_18 0.11230 1
CH3 amber99_11 -0.36620 2
HH32 amber99_18 0.11230 3
HH33 amber99_18 0.11230 4
C amber99_2 0.59720 5
O amber99_41 -0.56790 6
[ bonds ]
HH31 CH3
CH3 HH32
CH3 HH33
CH3 C
C O
[ dihedrals ]
CH3 C +N +CA backbone_prop_1
CH3 C +N +H backbone_prop_1
O C +N +CA backbone_prop_1
O C +N +H backbone_prop_2
[ impropers ]
CH3 +N C O
[ NME ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CH3 amber99_11 -0.14900 3
HH31 amber99_19 0.09760 4
HH32 amber99_19 0.09760 5
HH33 amber99_19 0.09760 6
[ bonds ]
N H
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
-C N
[ dihedrals ]
-O -C N CH3 backbone_prop_1
-CA -C N CH3 backbone_prop_1
[ impropers ]
-C CH3 N H
[ NHE ]
[ atoms ]
N amber99_34 -0.46300 1
H1 amber99_17 0.23150 2
H2 amber99_17 0.23150 3
[ bonds ]
N H1
N H2
-C N
[ dihedrals ]
-CA -C N H1 backbone_prop_1
-CA -C N H2 backbone_prop_1
-O -C N H1 backbone_prop_2
-O -C N H2 backbone_prop_2
[ impropers ]
-C H1 N H2
[ NH2 ]
[ atoms ]
N amber99_34 -0.46300 1
H1 amber99_17 0.23150 2
H2 amber99_17 0.23150 3
[ bonds ]
N H1
N H2
-C N
[ dihedrals ]
-CA -C N H1 backbone_prop_1
-CA -C N H2 backbone_prop_1
-O -C N H1 backbone_prop_2
-O -C N H2 backbone_prop_2
[ impropers ]
-C H1 N H2
; Next are non-terminal AA's
[ ALA ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.03370 3
HA amber99_19 0.08230 4
CB amber99_11 -0.18250 5
HB1 amber99_18 0.06030 6
HB2 amber99_18 0.06030 7
HB3 amber99_18 0.06030 8
C amber99_2 0.59730 9
O amber99_41 -0.56790 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ GLY ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.02520 3
HA1 amber99_19 0.06980 4
HA2 amber99_19 0.06980 5
C amber99_2 0.59730 6
O amber99_41 -0.56790 7
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ SER ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.02490 3
HA amber99_19 0.08430 4
CB amber99_11 0.21170 5
HB1 amber99_19 0.03520 6
HB2 amber99_19 0.03520 7
OG amber99_43 -0.65460 8
HG amber99_25 0.42750 9
C amber99_2 0.59730 10
O amber99_41 -0.56790 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ THR ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.03890 3
HA amber99_19 0.10070 4
CB amber99_11 0.36540 5
HB amber99_19 0.00430 6
CG2 amber99_11 -0.24380 7
HG21 amber99_18 0.06420 8
HG22 amber99_18 0.06420 9
HG23 amber99_18 0.06420 10
OG1 amber99_43 -0.67610 11
HG1 amber99_25 0.41020 12
C amber99_2 0.59730 13
O amber99_41 -0.56790 14
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG2
CB OG1
CG2 HG21
CG2 HG22
CG2 HG23
OG1 HG1
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ LEU ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.05180 3
HA amber99_19 0.09220 4
CB amber99_11 -0.11020 5
HB1 amber99_18 0.04570 6
HB2 amber99_18 0.04570 7
CG amber99_11 0.35310 8
HG amber99_18 -0.03610 9
CD1 amber99_11 -0.41210 10
HD11 amber99_18 0.10000 11
HD12 amber99_18 0.10000 12
HD13 amber99_18 0.10000 13
CD2 amber99_11 -0.41210 14
HD21 amber99_18 0.10000 15
HD22 amber99_18 0.10000 16
HD23 amber99_18 0.10000 17
C amber99_2 0.59730 18
O amber99_41 -0.56790 19
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ ILE ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.05970 3
HA amber99_19 0.08690 4
CB amber99_11 0.13030 5
HB amber99_18 0.01870 6
CG2 amber99_11 -0.32040 7
HG21 amber99_18 0.08820 8
HG22 amber99_18 0.08820 9
HG23 amber99_18 0.08820 10
CG1 amber99_11 -0.04300 11
HG11 amber99_18 0.02360 12
HG12 amber99_18 0.02360 13
CD amber99_11 -0.06600 14
HD1 amber99_18 0.01860 15
HD2 amber99_18 0.01860 16
HD3 amber99_18 0.01860 17
C amber99_2 0.59730 18
O amber99_41 -0.56790 19
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG2
CB CG1
CG2 HG21
CG2 HG22
CG2 HG23
CG1 HG11
CG1 HG12
CG1 CD
CD HD1
CD HD2
CD HD3
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ VAL ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.08750 3
HA amber99_19 0.09690 4
CB amber99_11 0.29850 5
HB amber99_18 -0.02970 6
CG1 amber99_11 -0.31920 7
HG11 amber99_18 0.07910 8
HG12 amber99_18 0.07910 9
HG13 amber99_18 0.07910 10
CG2 amber99_11 -0.31920 11
HG21 amber99_18 0.07910 12
HG22 amber99_18 0.07910 13
HG23 amber99_18 0.07910 14
C amber99_2 0.59730 15
O amber99_41 -0.56790 16
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ ASN ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.01430 3
HA amber99_19 0.10480 4
CB amber99_11 -0.20410 5
HB1 amber99_18 0.07970 6
HB2 amber99_18 0.07970 7
CG amber99_2 0.71300 8
OD1 amber99_41 -0.59310 9
ND2 amber99_34 -0.91910 10
HD21 amber99_17 0.41960 11
HD22 amber99_17 0.41960 12
C amber99_2 0.59730 13
O amber99_41 -0.56790 14
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG ND2
ND2 HD21
ND2 HD22
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CB CG ND2 HD21 backbone_prop_1
CB CG ND2 HD22 backbone_prop_1
OD1 CG ND2 HD21 backbone_prop_2
OD1 CG ND2 HD22 backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
CB ND2 CG OD1
CG HD21 ND2 HD22
[ GLN ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.00310 3
HA amber99_19 0.08500 4
CB amber99_11 -0.00360 5
HB1 amber99_18 0.01710 6
HB2 amber99_18 0.01710 7
CG amber99_11 -0.06450 8
HG1 amber99_18 0.03520 9
HG2 amber99_18 0.03520 10
CD amber99_2 0.69510 11
OE1 amber99_41 -0.60860 12
NE2 amber99_34 -0.94070 13
HE21 amber99_17 0.42510 14
HE22 amber99_17 0.42510 15
C amber99_2 0.59730 16
O amber99_41 -0.56790 17
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD NE2
NE2 HE21
NE2 HE22
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CG CD NE2 HE21 backbone_prop_1
CG CD NE2 HE22 backbone_prop_1
OE1 CD NE2 HE21 backbone_prop_2
OE1 CD NE2 HE22 backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
CG NE2 CD OE1
CD HE21 NE2 HE22
[ ARG ]
[ atoms ]
N amber99_34 -0.34790 1
H amber99_17 0.27470 2
CA amber99_11 -0.26370 3
HA amber99_19 0.15600 4
CB amber99_11 -0.00070 5
HB1 amber99_18 0.03270 6
HB2 amber99_18 0.03270 7
CG amber99_11 0.03900 8
HG1 amber99_18 0.02850 9
HG2 amber99_18 0.02850 10
CD amber99_11 0.04860 11
HD1 amber99_19 0.06870 12
HD2 amber99_19 0.06870 13
NE amber99_38 -0.52950 14
HE amber99_17 0.34560 15
CZ amber99_3 0.80760 16
NH1 amber99_38 -0.86270 17
HH11 amber99_17 0.44780 18
HH12 amber99_17 0.44780 19
NH2 amber99_38 -0.86270 20
HH21 amber99_17 0.44780 21
HH22 amber99_17 0.44780 22
C amber99_2 0.73410 23
O amber99_41 -0.58940 24
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
HH12 NH1 CZ NH2 sidechain_prop_1
HH11 NH1 CZ NH2 sidechain_prop_1
HE NE CZ NH1 sidechain_prop_1
HE NE CZ NH2 sidechain_prop_1
NE CZ NH1 HH11 sidechain_prop_1
NE CZ NH1 HH12 sidechain_prop_1
CD NE CZ NH1 sidechain_prop_1
CD NE CZ NH2 sidechain_prop_1
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
NE NH1 CZ NH2
CD CZ NE HE
CZ HH11 NH1 HH12
CZ HH21 NH2 HH22
[ HID ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.01880 3
HA amber99_19 0.08810 4
CB amber99_11 -0.04620 5
HB1 amber99_18 0.04020 6
HB2 amber99_18 0.04020 7
CG amber99_5 -0.02660 8
ND1 amber99_35 -0.38110 9
HD1 amber99_17 0.36490 10
CE1 amber99_10 0.20570 11
HE1 amber99_24 0.13920 12
NE2 amber99_36 -0.57270 13
CD2 amber99_12 0.12920 14
HD2 amber99_23 0.11470 15
C amber99_2 0.59730 16
O amber99_41 -0.56790 17
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CE1 HE1
CE1 NE2
NE2 CD2
CD2 HD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG ND1 HD1 aromatic_prop_3
HD1 ND1 CE1 HE1 aromatic_prop_5
NE2 CE1 ND1 HD1 aromatic_prop_5
HD1 ND1 CG CD2 aromatic_prop_3
CB CG ND1 CE1 aromatic_prop_3
CB CG CD2 HD2 aromatic_prop_6a
CB CG CD2 NE2 aromatic_prop_6a
CG ND1 CE1 HE1 aromatic_prop_5
CG ND1 CE1 NE2 aromatic_prop_5
ND1 CE1 NE2 CD2 aromatic_prop_5a
ND1 CG CD2 HD2 aromatic_prop_6a
ND1 CG CD2 NE2 aromatic_prop_6a
CE1 NE2 CD2 HD2 aromatic_prop_4a
CE1 NE2 CD2 CG aromatic_prop_4a
HE1 CE1 NE2 CD2 aromatic_prop_5a
CD2 CG ND1 CE1 aromatic_prop_3
[ impropers ]
-C CA N H
CA +N C O
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ HIE ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.05810 3
HA amber99_19 0.13600 4
CB amber99_11 -0.00740 5
HB1 amber99_18 0.03670 6
HB2 amber99_18 0.03670 7
CG amber99_5 0.18680 8
ND1 amber99_36 -0.54320 9
CE1 amber99_10 0.16350 10
HE1 amber99_24 0.14350 11
NE2 amber99_35 -0.27950 12
HE2 amber99_17 0.33390 13
CD2 amber99_13 -0.22070 14
HD2 amber99_23 0.18620 15
C amber99_2 0.59730 16
O amber99_41 -0.56790 17
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB2
CB HB1
CB CG
CG ND1
CG CD2
ND1 CE1
CE1 HE1
CE1 NE2
NE2 HE2
NE2 CD2
CD2 HD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CG CD2 NE2 HE2 aromatic_prop_4
HE1 CE1 NE2 HE2 aromatic_prop_5
HD2 CD2 NE2 HE2 aromatic_prop_4
ND1 CE1 NE2 HE2 aromatic_prop_5
CB CG ND1 CE1 aromatic_prop_3a
CB CG CD2 HD2 aromatic_prop_6
CB CG CD2 NE2 aromatic_prop_6
CG ND1 CE1 HE1 aromatic_prop_5a
CG ND1 CE1 NE2 aromatic_prop_5a
ND1 CE1 NE2 CD2 aromatic_prop_5
HE1 CE1 NE2 CD2 aromatic_prop_5
ND1 CG CD2 HD2 aromatic_prop_6
ND1 CG CD2 NE2 aromatic_prop_6
CE1 NE2 CD2 CG aromatic_prop_4
CE1 NE2 CD2 HD2 aromatic_prop_4
CD2 CG ND1 CE1 aromatic_prop_3a
[ impropers ]
-C CA N H
CA +N C O
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ HIP ]
[ atoms ]
N amber99_34 -0.34790 1
H amber99_17 0.27470 2
CA amber99_11 -0.13540 3
HA amber99_19 0.12120 4
CB amber99_11 -0.04140 5
HB1 amber99_18 0.08100 6
HB2 amber99_18 0.08100 7
CG amber99_5 -0.00120 8
ND1 amber99_35 -0.15130 9
HD1 amber99_17 0.38660 10
CE1 amber99_10 -0.01700 11
HE1 amber99_24 0.26810 12
NE2 amber99_35 -0.17180 13
HE2 amber99_17 0.39110 14
CD2 amber99_13 -0.11410 15
HD2 amber99_23 0.23170 16
C amber99_2 0.73410 17
O amber99_41 -0.58940 18
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CE1 HE1
CE1 NE2
NE2 HE2
NE2 CD2
CD2 HD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG ND1 HD1 aromatic_prop_3
CG CD2 NE2 HE2 aromatic_prop_4
HD1 ND1 CE1 HE1 aromatic_prop_5
HE1 CE1 NE2 HE2 aromatic_prop_5
HD2 CD2 NE2 HE2 aromatic_prop_4
ND1 CE1 NE2 HE2 aromatic_prop_5
NE2 CE1 ND1 HD1 aromatic_prop_5
HD1 ND1 CG CD2 aromatic_prop_3
CB CG ND1 CE1 aromatic_prop_3
CB CG CD2 HD2 aromatic_prop_6
CB CG CD2 NE2 aromatic_prop_6
CG ND1 CE1 HE1 aromatic_prop_5
CG ND1 CE1 NE2 aromatic_prop_5
CG CD2 NE2 CE1 aromatic_prop_4
ND1 CE1 NE2 CD2 aromatic_prop_5
ND1 CG CD2 HD2 aromatic_prop_6
ND1 CG CD2 NE2 aromatic_prop_6
CE1 NE2 CD2 HD2 aromatic_prop_4
HE1 CE1 NE2 CD2 aromatic_prop_5
CD2 CG ND1 CE1 aromatic_prop_3
[ impropers ]
-C CA N H
CA +N C O
CG CE1 ND1 HD1
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ TRP ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.02750 3
HA amber99_19 0.11230 4
CB amber99_11 -0.00500 5
HB1 amber99_18 0.03390 6
HB2 amber99_18 0.03390 7
CG amber99_14 -0.14150 8
CD1 amber99_13 -0.16380 9
HD1 amber99_23 0.20620 10
NE1 amber99_35 -0.34180 11
HE1 amber99_17 0.34120 12
CE2 amber99_8 0.13800 13
CZ2 amber99_3 -0.26010 14
HZ2 amber99_22 0.15720 15
CH2 amber99_3 -0.11340 16
HH2 amber99_22 0.14170 17
CZ3 amber99_3 -0.19720 18
HZ3 amber99_22 0.14470 19
CE3 amber99_3 -0.23870 20
HE3 amber99_22 0.17000 21
CD2 amber99_4 0.12430 22
C amber99_2 0.59730 23
O amber99_41 -0.56790 24
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 NE1
NE1 HE1
NE1 CE2
CE2 CZ2
CE2 CD2
CZ2 HZ2
CZ2 CH2
CH2 HH2
CH2 CZ3
CZ3 HZ3
CZ3 CE3
CE3 HE3
CE3 CD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG CD1 HD1 aromatic_prop_7
CB CG CD1 NE1 aromatic_prop_7
CB CG CD2 CE2 aromatic_prop_8
CB CG CD2 CE3 aromatic_prop_8
CG CD1 NE1 HE1 aromatic_prop_4
CG CD1 NE1 CE2 aromatic_prop_4
CG CD2 CE2 NE1 aromatic_prop_10
CG CD2 CE2 CZ2 aromatic_prop_10
CG CD2 CE3 HE3 aromatic_prop_12
CG CD2 CE3 CZ3 aromatic_prop_12
CD1 CG CD2 CE2 aromatic_prop_8
CD1 CG CD2 CE3 aromatic_prop_8
CD1 NE1 CE2 CD2 aromatic_prop_9
CD1 NE1 CE2 CZ2 aromatic_prop_9
HD1 CD1 NE1 HE1 aromatic_prop_4
HD1 CD1 NE1 CE2 aromatic_prop_4
HD1 CD1 CG CD2 aromatic_prop_7
HE1 NE1 CE2 CD2 aromatic_prop_9
HE1 NE1 CE2 CZ2 aromatic_prop_9
NE1 CD1 CG CD2 aromatic_prop_7
NE1 CE2 CD2 CE3 aromatic_prop_10
NE1 CE2 CZ2 HZ2 aromatic_prop_11
NE1 CE2 CZ2 CH2 aromatic_prop_11
CE2 CD2 CE3 HE3 aromatic_prop_12
CE2 CD2 CE3 CZ3 aromatic_prop_12
CE2 CZ2 CH2 HH2 aromatic_prop_1
CE2 CZ2 CH2 CZ3 aromatic_prop_1
CZ2 CH2 CZ3 HZ3 aromatic_prop_1
CZ2 CH2 CZ3 CE3 aromatic_prop_1
CZ2 CE2 CD2 CE3 aromatic_prop_10
HZ2 CZ2 CH2 HH2 aromatic_prop_1
HZ2 CZ2 CH2 CZ3 aromatic_prop_1
CH2 CZ2 CE2 CD2 aromatic_prop_11
CH2 CZ3 CE3 HE3 aromatic_prop_1
CH2 CZ3 CE3 CD2 aromatic_prop_1
HH2 CH2 CZ3 HZ3 aromatic_prop_1
HH2 CH2 CZ3 CE3 aromatic_prop_1
HZ3 CZ3 CE3 HE3 aromatic_prop_1
HZ3 CZ3 CE3 CD2 aromatic_prop_1
[ impropers ]
-C CA N H
CA +N C O
CD1 CE2 NE1 HE1
CE2 CH2 CZ2 HZ2
CZ2 CZ3 CH2 HH2
CH2 CE3 CZ3 HZ3
CZ3 CD2 CE3 HE3
CG NE1 CD1 HD1
CD1 CD2 CG CB
[ PHE ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.00240 3
HA amber99_19 0.09780 4
CB amber99_11 -0.03430 5
HB1 amber99_18 0.02950 6
HB2 amber99_18 0.02950 7
CG amber99_3 0.01180 8
CD1 amber99_3 -0.12560 9
HD1 amber99_22 0.13300 10
CE1 amber99_3 -0.17040 11
HE1 amber99_22 0.14300 12
CZ amber99_3 -0.10720 13
HZ amber99_22 0.12970 14
CE2 amber99_3 -0.17040 15
HE2 amber99_22 0.14300 16
CD2 amber99_3 -0.12560 17
HD2 amber99_22 0.13300 18
C amber99_2 0.59730 19
O amber99_41 -0.56790 20
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ HZ
CZ CE2
CE2 HE2
CE2 CD2
CD2 HD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG CD1 HD1 aromatic_prop_1
CB CG CD2 HD2 aromatic_prop_1
CB CG CD1 CE1 aromatic_prop_1
CB CG CD2 CE2 aromatic_prop_1
CG CD1 CE1 HE1 aromatic_prop_1
CG CD2 CE2 HE2 aromatic_prop_1
CG CD1 CE1 CZ aromatic_prop_1
CG CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ HZ aromatic_prop_1
CD1 CE1 CZ CE2 aromatic_prop_1
CD2 CE2 CZ HZ aromatic_prop_1
CD2 CE2 CZ CE1 aromatic_prop_1
CE1 CZ CE2 HE2 aromatic_prop_1
CE2 CZ CE1 HE1 aromatic_prop_1
HD1 CD1 CE1 HE1 aromatic_prop_1
HD2 CD2 CE2 HE2 aromatic_prop_1
HE1 CE1 CZ HZ aromatic_prop_1
HE2 CE2 CZ HZ aromatic_prop_1
HD1 CD1 CE1 CZ aromatic_prop_1
HD2 CD2 CE2 CZ aromatic_prop_1
HD1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 HD2 aromatic_prop_1
CE1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 CE2 aromatic_prop_1
[ impropers ]
-C CA N H
CA +N C O
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CE1 CE2 CZ HZ
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
[ TYR ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.00140 3
HA amber99_19 0.08760 4
CB amber99_11 -0.01520 5
HB1 amber99_18 0.02950 6
HB2 amber99_18 0.02950 7
CG amber99_3 -0.00110 8
CD1 amber99_3 -0.19060 9
HD1 amber99_22 0.16990 10
CE1 amber99_3 -0.23410 11
HE1 amber99_22 0.16560 12
CZ amber99_2 0.32260 13
OH amber99_43 -0.55790 14
HH amber99_25 0.39920 15
CE2 amber99_3 -0.23410 16
HE2 amber99_22 0.16560 17
CD2 amber99_3 -0.19060 18
HD2 amber99_22 0.16990 19
C amber99_2 0.59730 20
O amber99_41 -0.56790 21
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ OH
CZ CE2
OH HH
CE2 HE2
CE2 CD2
CD2 HD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG CD1 HD1 aromatic_prop_1
CB CG CD2 HD2 aromatic_prop_1
CB CG CD1 CE1 aromatic_prop_1
CB CG CD2 CE2 aromatic_prop_1
CG CD1 CE1 HE1 aromatic_prop_1
CG CD2 CE2 HE2 aromatic_prop_1
CG CD1 CE1 CZ aromatic_prop_1
CG CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ CE2 aromatic_prop_1
CD2 CE2 CZ CE1 aromatic_prop_1
CE1 CZ CE2 HE2 aromatic_prop_1
CE2 CZ CE1 HE1 aromatic_prop_1
HD1 CD1 CE1 HE1 aromatic_prop_1
HD2 CD2 CE2 HE2 aromatic_prop_1
HD1 CD1 CE1 CZ aromatic_prop_1
HD2 CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ OH aromatic_prop_1
CD2 CE2 CZ OH aromatic_prop_1
HE1 CE1 CZ OH aromatic_prop_1
HE2 CE2 CZ OH aromatic_prop_1
CE1 CZ OH HH aromatic_prop_2
CE2 CZ OH HH aromatic_prop_2
HD1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 HD2 aromatic_prop_1
CE1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 CE2 aromatic_prop_1
[ impropers ]
-C CA N H
CA +N C O
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
CE1 CE2 CZ OH
[ GLU ]
[ atoms ]
N amber99_34 -0.51630 1
H amber99_17 0.29360 2
CA amber99_11 0.03970 3
HA amber99_19 0.11050 4
CB amber99_11 0.05600 5
HB1 amber99_18 -0.01730 6
HB2 amber99_18 -0.01730 7
CG amber99_11 0.01360 8
HG1 amber99_18 -0.04250 9
HG2 amber99_18 -0.04250 10
CD amber99_2 0.80540 11
OE1 amber99_45 -0.81880 12
OE2 amber99_45 -0.81880 13
C amber99_2 0.53660 14
O amber99_41 -0.58190 15
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
CG OE1 CD OE2
[ ASP ]
[ atoms ]
N amber99_34 -0.51630 1
H amber99_17 0.29360 2
CA amber99_11 0.03810 3
HA amber99_19 0.08800 4
CB amber99_11 -0.03030 5
HB1 amber99_18 -0.01220 6
HB2 amber99_18 -0.01220 7
CG amber99_2 0.79940 8
OD1 amber99_45 -0.80140 9
OD2 amber99_45 -0.80140 10
C amber99_2 0.53660 11
O amber99_41 -0.58190 12
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
CB OD1 CG OD2
[ LYP ]
[ atoms ]
N amber99_34 -0.34790 1
H amber99_17 0.27470 2
CA amber99_11 -0.24000 3
HA amber99_19 0.14260 4
CB amber99_11 -0.00940 5
HB1 amber99_18 0.03620 6
HB2 amber99_18 0.03620 7
CG amber99_11 0.01870 8
HG1 amber99_18 0.01030 9
HG2 amber99_18 0.01030 10
CD amber99_11 -0.04790 11
HD1 amber99_18 0.06210 12
HD2 amber99_18 0.06210 13
CE amber99_11 -0.01430 14
HE1 amber99_28 0.11350 15
HE2 amber99_28 0.11350 16
NZ amber99_39 -0.38540 17
HZ1 amber99_17 0.34000 18
HZ2 amber99_17 0.34000 19
HZ3 amber99_17 0.34000 20
C amber99_2 0.73410 21
O amber99_41 -0.58940 22
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
NZ HZ3
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ ORN ] ; charges taken from amber99.prm of tinker 4.0
[ atoms ]
N amber99_34 -0.34790 1
H amber99_17 0.27470 2
CA amber99_11 -0.24000 3
HA amber99_19 0.14260 4
CB amber99_11 0.00990 5
HB1 amber99_18 0.03620 6
HB2 amber99_18 0.03620 7
CG amber99_11 -0.02790 8
HG1 amber99_18 0.06210 9
HG2 amber99_18 0.06210 10
CD amber99_11 -0.01430 11
HD1 amber99_28 0.11350 12
HD2 amber99_28 0.11350 13
NE amber99_39 -0.38540 14
HE1 amber99_17 0.34000 15
HE2 amber99_17 0.34000 16
HE3 amber99_17 0.34000 17
C amber99_2 0.73410 18
O amber99_41 -0.58940 19
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE1
NE HE2
NE HE3
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ DAB ] ; sidechain charges fit to maintain heavy atom charge group trend LYS -> ORN -> DAB
[ atoms ]
N amber99_34 -0.34790 1
H amber99_17 0.27470 2
CA amber99_11 -0.24000 3
HA amber99_19 0.14260 4
CB amber99_11 0.02920 5
HB1 amber99_18 0.07470 6
HB2 amber99_18 0.07470 7
CG amber99_11 -0.01430 8
HG1 amber99_28 0.11350 9
HG2 amber99_28 0.11350 10
ND amber99_39 -0.38540 11
HD1 amber99_17 0.34000 12
HD2 amber99_17 0.34000 13
HD3 amber99_17 0.34000 14
C amber99_2 0.73410 15
O amber99_41 -0.58940 16
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG ND
ND HD1
ND HD2
ND HD3
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ LYN ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.07206 3
HA amber99_19 0.09940 4
CB amber99_11 -0.04845 5
HB1 amber99_18 0.03400 6
HB2 amber99_18 0.03400 7
CG amber99_11 0.06612 8
HG1 amber99_18 0.01041 9
HG2 amber99_18 0.01041 10
CD amber99_11 -0.03768 11
HD1 amber99_18 0.01155 12
HD2 amber99_18 0.01155 13
CE amber99_11 0.32604 14
HE1 amber99_28 -0.03358 15
HE2 amber99_28 -0.03358 16
NZ amber99_39 -1.03581 17
HZ1 amber99_17 0.38604 18
HZ2 amber99_17 0.38604 19
C amber99_2 0.59730 20
O amber99_41 -0.56790 21
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ PRO ]
[ atoms ]
N amber99_34 -0.25480 1
CD amber99_11 0.01920 2
HD1 amber99_19 0.03910 3
HD2 amber99_19 0.03910 4
CG amber99_11 0.01890 5
HG1 amber99_18 0.02130 6
HG2 amber99_18 0.02130 7
CB amber99_11 -0.00700 8
HB1 amber99_18 0.02530 9
HB2 amber99_18 0.02530 10
CA amber99_11 -0.02660 11
HA amber99_19 0.06410 12
C amber99_2 0.58960 13
O amber99_41 -0.57480 14
[ bonds ]
N CD
N CA
CD HD1
CD HD2
CD CG
CG HG1
CG HG2
CG CB
CB HB1
CB HB2
CB CA
CA HA
CA C
C O
-C N
[ dihedrals ]
-CA -C N CD backbone_prop_1
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
-CH3 -C N CD backbone_prop_1
-O -C N CD backbone_prop_1
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
-C N CD CG proline_prop_1
[ impropers ]
CA +N C O
-C CD N CA
[ HYP ] ; S Park, R J Radmer, T E Klein & V S Pande (submitted).
[ atoms ]
N amber99_34 -0.25480 1
CD2 amber99_11 0.05950 2
HD21 amber99_19 0.07000 3
HD22 amber99_19 0.07000 4
CG amber99_11 0.04000 5
HG amber99_19 0.04160 6
OD1 amber99_43 -0.61340 7
HD1 amber99_25 0.38510 8
CB amber99_11 0.02030 9
HB1 amber99_18 0.04260 10
HB2 amber99_18 0.04260 11
CA amber99_11 0.00470 12
HA amber99_19 0.07700 13
C amber99_2 0.58960 14
O amber99_41 -0.57480 15
[ bonds ]
N CD2
N CA
CD2 HD21
CD2 HD22
CD2 CG
CG HG
CG OD1
CG CB
OD1 HD1
CB HB1
CB HB2
CB CA
CA HA
CA C
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
-CH3 -C N CD2 backbone_prop_1
-O -C N CD2 backbone_prop_1
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
-C N CD2 CG proline_prop_1
N CD2 CG OD1 hyp_prop_1
-CA -C N CD2 backbone_prop_1
[ impropers ]
CA +N C O
-C CD2 N CA
[ CYN ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.02130 3
HA amber99_19 0.11240 4
CB amber99_11 -0.12310 5
HB1 amber99_19 0.11120 6
HB2 amber99_19 0.11120 7
SG amber99_48 -0.31190 8
HG amber99_26 0.19330 9
C amber99_2 0.59730 10
O amber99_41 -0.56790 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ CYM ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.03510 3
HA amber99_19 0.05080 4
CB amber99_11 -0.24130 5
HB1 amber99_19 0.11220 6
HB2 amber99_19 0.11220 7
SG amber99_48 -0.88440 8
C amber99_2 0.59730 9
O amber99_41 -0.56790 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ CYX ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.04290 3
HA amber99_19 0.07660 4
CB amber99_11 -0.07900 5
HB1 amber99_19 0.09100 6
HB2 amber99_19 0.09100 7
SG amber99_47 -0.10810 8
C amber99_2 0.59730 9
O amber99_41 -0.56790 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ CYS2 ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.04290 3
HA amber99_19 0.07660 4
CB amber99_11 -0.07900 5
HB1 amber99_19 0.09100 6
HB2 amber99_19 0.09100 7
SG amber99_47 -0.10810 8
C amber99_2 0.59730 9
O amber99_41 -0.56790 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
[ MET ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.02370 3
HA amber99_19 0.08800 4
CB amber99_11 0.03420 5
HB1 amber99_18 0.02410 6
HB2 amber99_18 0.02410 7
CG amber99_11 0.00180 8
HG1 amber99_19 0.04400 9
HG2 amber99_19 0.04400 10
SD amber99_47 -0.27370 11
CE amber99_11 -0.05360 12
HE1 amber99_19 0.06840 13
HE2 amber99_19 0.06840 14
HE3 amber99_19 0.06840 15
C amber99_2 0.59730 16
O amber99_41 -0.56790 17
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG SD
SD CE
CE HE1
CE HE2
CE HE3
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
; non-terminal acidic AA's
[ ASH ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.03410 3
HA amber99_19 0.08640 4
CB amber99_11 -0.03160 5
HB1 amber99_18 0.04880 6
HB2 amber99_18 0.04880 7
CG amber99_2 0.64620 8
OD1 amber99_41 -0.55540 9
OD2 amber99_43 -0.63760 10
HD2 amber99_25 0.47470 11
C amber99_2 0.59730 12
O amber99_41 -0.56790 13
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
OD2 HD2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
CB OD1 CG OD2
[ GLH ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 0.01450 3
HA amber99_19 0.07790 4
CB amber99_11 -0.00710 5
HB1 amber99_18 0.02560 6
HB2 amber99_18 0.02560 7
CG amber99_11 -0.01740 8
HG1 amber99_18 0.04300 9
HG2 amber99_18 0.04300 10
CD amber99_2 0.68010 11
OE1 amber99_41 -0.58380 12
OE2 amber99_43 -0.65110 13
HE2 amber99_25 0.46410 14
C amber99_2 0.59730 15
O amber99_41 -0.56790 16
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
OE2 HE2
C O
-C N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
-C CA N H
CA +N C O
CG OE1 CD OE2
; C-terminal AA's
[ CALA ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.17470 3
HA amber99_19 0.10670 4
CB amber99_11 -0.20930 5
HB1 amber99_18 0.07640 6
HB2 amber99_18 0.07640 7
HB3 amber99_18 0.07640 8
C amber99_2 0.77310 9
OC1 amber99_45 -0.80550 10
OC2 amber99_45 -0.80550 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CGLY ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.24930 3
HA1 amber99_19 0.10560 4
HA2 amber99_19 0.10560 5
C amber99_2 0.72310 6
OC1 amber99_45 -0.78550 7
OC2 amber99_45 -0.78550 8
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CSER ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.27220 3
HA amber99_19 0.13040 4
CB amber99_11 0.11230 5
HB1 amber99_19 0.08130 6
HB2 amber99_19 0.08130 7
OG amber99_43 -0.65140 8
HG amber99_25 0.44740 9
C amber99_2 0.81130 10
OC1 amber99_45 -0.81320 11
OC2 amber99_45 -0.81320 12
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CTHR ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.24200 3
HA amber99_19 0.12070 4
CB amber99_11 0.30250 5
HB amber99_19 0.00780 6
CG2 amber99_11 -0.18530 7
HG21 amber99_18 0.05860 8
HG22 amber99_18 0.05860 9
HG23 amber99_18 0.05860 10
OG1 amber99_43 -0.64960 11
HG1 amber99_25 0.41190 12
C amber99_2 0.78100 13
OC1 amber99_45 -0.80440 14
OC2 amber99_45 -0.80440 15
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG2
CB OG1
CG2 HG21
CG2 HG22
CG2 HG23
OG1 HG1
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CLEU ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.28470 3
HA amber99_19 0.13460 4
CB amber99_11 -0.24690 5
HB1 amber99_18 0.09740 6
HB2 amber99_18 0.09740 7
CG amber99_11 0.37060 8
HG amber99_18 -0.03740 9
CD1 amber99_11 -0.41630 10
HD11 amber99_18 0.10380 11
HD12 amber99_18 0.10380 12
HD13 amber99_18 0.10380 13
CD2 amber99_11 -0.41630 14
HD21 amber99_18 0.10380 15
HD22 amber99_18 0.10380 16
HD23 amber99_18 0.10380 17
C amber99_2 0.83260 18
OC1 amber99_45 -0.81990 19
OC2 amber99_45 -0.81990 20
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CILE ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.31000 3
HA amber99_19 0.13750 4
CB amber99_11 0.03630 5
HB amber99_18 0.07660 6
CG2 amber99_11 -0.34980 7
HG21 amber99_18 0.10210 8
HG22 amber99_18 0.10210 9
HG23 amber99_18 0.10210 10
CG1 amber99_11 -0.03230 11
HG11 amber99_18 0.03210 12
HG12 amber99_18 0.03210 13
CD amber99_11 -0.06990 14
HD1 amber99_18 0.01960 15
HD2 amber99_18 0.01960 16
HD3 amber99_18 0.01960 17
C amber99_2 0.83430 18
OC1 amber99_45 -0.81900 19
OC2 amber99_45 -0.81900 20
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG2
CB CG1
CG2 HG21
CG2 HG22
CG2 HG23
CG1 HG11
CG1 HG12
CG1 CD
CD HD1
CD HD2
CD HD3
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CVAL ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.34380 3
HA amber99_19 0.14380 4
CB amber99_11 0.19400 5
HB amber99_18 0.03080 6
CG1 amber99_11 -0.30640 7
HG11 amber99_18 0.08360 8
HG12 amber99_18 0.08360 9
HG13 amber99_18 0.08360 10
CG2 amber99_11 -0.30640 11
HG21 amber99_18 0.08360 12
HG22 amber99_18 0.08360 13
HG23 amber99_18 0.08360 14
C amber99_2 0.83500 15
OC1 amber99_45 -0.81730 16
OC2 amber99_45 -0.81730 17
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CASN ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.20800 3
HA amber99_19 0.13580 4
CB amber99_11 -0.22990 5
HB1 amber99_18 0.10230 6
HB2 amber99_18 0.10230 7
CG amber99_2 0.71530 8
OD1 amber99_41 -0.60100 9
ND2 amber99_34 -0.90840 10
HD21 amber99_17 0.41500 11
HD22 amber99_17 0.41500 12
C amber99_2 0.80500 13
OC1 amber99_45 -0.81470 14
OC2 amber99_45 -0.81470 15
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG ND2
ND2 HD21
ND2 HD22
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CB CG ND2 HD21 backbone_prop_1
CB CG ND2 HD22 backbone_prop_1
OD1 CG ND2 HD21 backbone_prop_2
OD1 CG ND2 HD22 backbone_prop_2
[ impropers ]
-C CA N H
CA OC1 C OC2
CB ND2 CG OD1
CG HD21 ND2 HD22
[ CGLN ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.22480 3
HA amber99_19 0.12320 4
CB amber99_11 -0.06640 5
HB1 amber99_18 0.04520 6
HB2 amber99_18 0.04520 7
CG amber99_11 -0.02100 8
HG1 amber99_18 0.02030 9
HG2 amber99_18 0.02030 10
CD amber99_2 0.70930 11
OE1 amber99_41 -0.60980 12
NE2 amber99_34 -0.95740 13
HE21 amber99_17 0.43040 14
HE22 amber99_17 0.43040 15
C amber99_2 0.77750 16
OC1 amber99_45 -0.80420 17
OC2 amber99_45 -0.80420 18
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD NE2
NE2 HE21
NE2 HE22
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CG CD NE2 HE21 backbone_prop_1
CG CD NE2 HE22 backbone_prop_1
OE1 CD NE2 HE21 backbone_prop_2
OE1 CD NE2 HE22 backbone_prop_2
[ impropers ]
-C CA N H
CA OC1 C OC2
CG NE2 CD OE1
CD HE21 NE2 HE22
[ CARG ]
[ atoms ]
N amber99_34 -0.34810 1
H amber99_17 0.27640 2
CA amber99_11 -0.30680 3
HA amber99_19 0.14470 4
CB amber99_11 -0.03740 5
HB1 amber99_18 0.03710 6
HB2 amber99_18 0.03710 7
CG amber99_11 0.07440 8
HG1 amber99_18 0.01850 9
HG2 amber99_18 0.01850 10
CD amber99_11 0.11140 11
HD1 amber99_19 0.04680 12
HD2 amber99_19 0.04680 13
NE amber99_38 -0.55640 14
HE amber99_17 0.34790 15
CZ amber99_3 0.83680 16
NH1 amber99_38 -0.87370 17
HH11 amber99_17 0.44930 18
HH12 amber99_17 0.44930 19
NH2 amber99_38 -0.87370 20
HH21 amber99_17 0.44930 21
HH22 amber99_17 0.44930 22
C amber99_2 0.85570 23
OC1 amber99_45 -0.82660 24
OC2 amber99_45 -0.82660 25
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
HH12 NH1 CZ NH2 sidechain_prop_1
HH11 NH1 CZ NH2 sidechain_prop_1
HE NE CZ NH1 sidechain_prop_1
HE NE CZ NH2 sidechain_prop_1
NE CZ NH1 HH11 sidechain_prop_1
NE CZ NH1 HH12 sidechain_prop_1
CD NE CZ NH1 sidechain_prop_1
CD NE CZ NH2 sidechain_prop_1
[ impropers ]
-C CA N H
CA OC1 C OC2
NE NH1 CZ NH2
CD CZ NE HE
CZ HH11 NH1 HH12
CZ HH21 NH2 HH22
[ CHID ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.17390 3
HA amber99_19 0.11000 4
CB amber99_11 -0.10460 5
HB1 amber99_18 0.05650 6
HB2 amber99_18 0.05650 7
CG amber99_5 0.02930 8
ND1 amber99_35 -0.38920 9
HD1 amber99_17 0.37550 10
CE1 amber99_10 0.19250 11
HE1 amber99_24 0.14180 12
NE2 amber99_36 -0.56290 13
CD2 amber99_12 0.10010 14
HD2 amber99_23 0.12410 15
C amber99_2 0.76150 16
OC1 amber99_45 -0.80160 17
OC2 amber99_45 -0.80160 18
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CE1 HE1
CE1 NE2
NE2 CD2
CD2 HD2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CB CG ND1 HD1 aromatic_prop_3
HD1 ND1 CE1 HE1 aromatic_prop_5
NE2 CE1 ND1 HD1 aromatic_prop_5
HD1 ND1 CG CD2 aromatic_prop_3
CB CG ND1 CE1 aromatic_prop_3
CB CG CD2 HD2 aromatic_prop_6a
CB CG CD2 NE2 aromatic_prop_6a
CG ND1 CE1 HE1 aromatic_prop_5
CG ND1 CE1 NE2 aromatic_prop_5
ND1 CE1 NE2 CD2 aromatic_prop_5a
ND1 CG CD2 HD2 aromatic_prop_6a
ND1 CG CD2 NE2 aromatic_prop_6a
CE1 NE2 CD2 HD2 aromatic_prop_4a
CE1 NE2 CD2 CG aromatic_prop_4a
HE1 CE1 NE2 CD2 aromatic_prop_5a
CD2 CG ND1 CE1 aromatic_prop_3
[ impropers ]
-C CA N H
CA OC1 C OC2
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ CHIE ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.26990 3
HA amber99_19 0.16500 4
CB amber99_11 -0.10680 5
HB1 amber99_18 0.06200 6
HB2 amber99_18 0.06200 7
CG amber99_5 0.27240 8
ND1 amber99_36 -0.55170 9
CE1 amber99_10 0.15580 10
HE1 amber99_24 0.14480 11
NE2 amber99_35 -0.26700 12
HE2 amber99_17 0.33190 13
CD2 amber99_13 -0.25880 14
HD2 amber99_23 0.19570 15
C amber99_2 0.79160 16
OC1 amber99_45 -0.80650 17
OC2 amber99_45 -0.80650 18
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 CE1
CE1 HE1
CE1 NE2
NE2 HE2
NE2 CD2
CD2 HD2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CG CD2 NE2 HE2 aromatic_prop_4
HE1 CE1 NE2 HE2 aromatic_prop_5
HD2 CD2 NE2 HE2 aromatic_prop_4
ND1 CE1 NE2 HE2 aromatic_prop_5
CB CG ND1 CE1 aromatic_prop_3a
CB CG CD2 HD2 aromatic_prop_6
CB CG CD2 NE2 aromatic_prop_6
CG ND1 CE1 HE1 aromatic_prop_5a
CG ND1 CE1 NE2 aromatic_prop_5a
ND1 CE1 NE2 CD2 aromatic_prop_5
HE1 CE1 NE2 CD2 aromatic_prop_5
ND1 CG CD2 HD2 aromatic_prop_6
ND1 CG CD2 NE2 aromatic_prop_6
CE1 NE2 CD2 CG aromatic_prop_4
CE1 NE2 CD2 HD2 aromatic_prop_4
CD2 CG ND1 CE1 aromatic_prop_3a
[ impropers ]
-C CA N H
CA OC1 C OC2
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ CHIP ]
[ atoms ]
N amber99_34 -0.34810 1
H amber99_17 0.27640 2
CA amber99_11 -0.14450 3
HA amber99_19 0.11150 4
CB amber99_11 -0.08000 5
HB1 amber99_18 0.08680 6
HB2 amber99_18 0.08680 7
CG amber99_5 0.02980 8
ND1 amber99_35 -0.15010 9
HD1 amber99_17 0.38830 10
CE1 amber99_10 -0.02510 11
HE1 amber99_24 0.26940 12
NE2 amber99_35 -0.16830 13
HE2 amber99_17 0.39130 14
CD2 amber99_13 -0.12560 15
HD2 amber99_23 0.23360 16
C amber99_2 0.80320 17
OC1 amber99_45 -0.81770 18
OC2 amber99_45 -0.81770 19
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CE1 HE1
CE1 NE2
NE2 HE2
NE2 CD2
CD2 HD2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CB CG ND1 HD1 aromatic_prop_3
CG CD2 NE2 HE2 aromatic_prop_4
HD1 ND1 CE1 HE1 aromatic_prop_5
HE1 CE1 NE2 HE2 aromatic_prop_5
HD2 CD2 NE2 HE2 aromatic_prop_4
ND1 CE1 NE2 HE2 aromatic_prop_5
NE2 CE1 ND1 HD1 aromatic_prop_5
HD1 ND1 CG CD2 aromatic_prop_3
CB CG ND1 CE1 aromatic_prop_3
CB CG CD2 HD2 aromatic_prop_6
CB CG CD2 NE2 aromatic_prop_6
CG ND1 CE1 HE1 aromatic_prop_5
CG ND1 CE1 NE2 aromatic_prop_5
CG CD2 NE2 CE1 aromatic_prop_4
ND1 CE1 NE2 CD2 aromatic_prop_5
ND1 CG CD2 HD2 aromatic_prop_6
ND1 CG CD2 NE2 aromatic_prop_6
CE1 NE2 CD2 HD2 aromatic_prop_4
HE1 CE1 NE2 CD2 aromatic_prop_5
CD2 CG ND1 CE1 aromatic_prop_3
[ impropers ]
-C CA N H
CA OC1 C OC2
CG CE1 ND1 HD1
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ CTRP ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.20840 3
HA amber99_19 0.12720 4
CB amber99_11 -0.07420 5
HB1 amber99_18 0.04970 6
HB2 amber99_18 0.04970 7
CG amber99_14 -0.07960 8
CD1 amber99_13 -0.18080 9
HD1 amber99_23 0.20430 10
NE1 amber99_35 -0.33160 11
HE1 amber99_17 0.34130 12
CE2 amber99_8 0.12220 13
CZ2 amber99_3 -0.25940 14
HZ2 amber99_22 0.15670 15
CH2 amber99_3 -0.10200 16
HH2 amber99_22 0.14010 17
CZ3 amber99_3 -0.22870 18
HZ3 amber99_22 0.15070 19
CE3 amber99_3 -0.18370 20
HE3 amber99_22 0.14910 21
CD2 amber99_4 0.10780 22
C amber99_2 0.76580 23
OC1 amber99_45 -0.80110 24
OC2 amber99_45 -0.80110 25
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 NE1
NE1 HE1
NE1 CE2
CE2 CZ2
CE2 CD2
CZ2 HZ2
CZ2 CH2
CH2 HH2
CH2 CZ3
CZ3 HZ3
CZ3 CE3
CE3 HE3
CE3 CD2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CB CG CD1 HD1 aromatic_prop_7
CB CG CD1 NE1 aromatic_prop_7
CB CG CD2 CE2 aromatic_prop_8
CB CG CD2 CE3 aromatic_prop_8
CG CD1 NE1 HE1 aromatic_prop_4
CG CD1 NE1 CE2 aromatic_prop_4
CG CD2 CE2 NE1 aromatic_prop_10
CG CD2 CE2 CZ2 aromatic_prop_10
CG CD2 CE3 HE3 aromatic_prop_12
CG CD2 CE3 CZ3 aromatic_prop_12
CD1 CG CD2 CE2 aromatic_prop_8
CD1 CG CD2 CE3 aromatic_prop_8
CD1 NE1 CE2 CD2 aromatic_prop_9
CD1 NE1 CE2 CZ2 aromatic_prop_9
HD1 CD1 NE1 HE1 aromatic_prop_4
HD1 CD1 NE1 CE2 aromatic_prop_4
HD1 CD1 CG CD2 aromatic_prop_7
HE1 NE1 CE2 CD2 aromatic_prop_9
HE1 NE1 CE2 CZ2 aromatic_prop_9
NE1 CD1 CG CD2 aromatic_prop_7
NE1 CE2 CD2 CE3 aromatic_prop_10
NE1 CE2 CZ2 HZ2 aromatic_prop_11
NE1 CE2 CZ2 CH2 aromatic_prop_11
CE2 CD2 CE3 HE3 aromatic_prop_12
CE2 CD2 CE3 CZ3 aromatic_prop_12
CE2 CZ2 CH2 HH2 aromatic_prop_1
CE2 CZ2 CH2 CZ3 aromatic_prop_1
CZ2 CH2 CZ3 HZ3 aromatic_prop_1
CZ2 CH2 CZ3 CE3 aromatic_prop_1
CZ2 CE2 CD2 CE3 aromatic_prop_10
HZ2 CZ2 CH2 HH2 aromatic_prop_1
HZ2 CZ2 CH2 CZ3 aromatic_prop_1
CH2 CZ2 CE2 CD2 aromatic_prop_11
CH2 CZ3 CE3 HE3 aromatic_prop_1
CH2 CZ3 CE3 CD2 aromatic_prop_1
HH2 CH2 CZ3 HZ3 aromatic_prop_1
HH2 CH2 CZ3 CE3 aromatic_prop_1
HZ3 CZ3 CE3 HE3 aromatic_prop_1
HZ3 CZ3 CE3 CD2 aromatic_prop_1
[ impropers ]
-C CA N H
CA OC1 C OC2
CD1 CE2 NE1 HE1
CE2 CH2 CZ2 HZ2
CZ2 CZ3 CH2 HH2
CH2 CE3 CZ3 HZ3
CZ3 CD2 CE3 HE3
CG NE1 CD1 HD1
CD1 CD2 CG CB
[ CPHE ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.18250 3
HA amber99_19 0.10980 4
CB amber99_11 -0.09590 5
HB1 amber99_18 0.04430 6
HB2 amber99_18 0.04430 7
CG amber99_3 0.05520 8
CD1 amber99_3 -0.13000 9
HD1 amber99_22 0.14080 10
CE1 amber99_3 -0.18470 11
HE1 amber99_22 0.14610 12
CZ amber99_3 -0.09440 13
HZ amber99_22 0.12800 14
CE2 amber99_3 -0.18470 15
HE2 amber99_22 0.14610 16
CD2 amber99_3 -0.13000 17
HD2 amber99_22 0.14080 18
C amber99_2 0.76600 19
OC1 amber99_45 -0.80260 20
OC2 amber99_45 -0.80260 21
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ HZ
CZ CE2
CE2 HE2
CE2 CD2
CD2 HD2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CB CG CD1 HD1 aromatic_prop_1
CB CG CD2 HD2 aromatic_prop_1
CB CG CD1 CE1 aromatic_prop_1
CB CG CD2 CE2 aromatic_prop_1
CG CD1 CE1 HE1 aromatic_prop_1
CG CD2 CE2 HE2 aromatic_prop_1
CG CD1 CE1 CZ aromatic_prop_1
CG CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ HZ aromatic_prop_1
CD1 CE1 CZ CE2 aromatic_prop_1
CD2 CE2 CZ HZ aromatic_prop_1
CD2 CE2 CZ CE1 aromatic_prop_1
CE1 CZ CE2 HE2 aromatic_prop_1
CE2 CZ CE1 HE1 aromatic_prop_1
HD1 CD1 CE1 HE1 aromatic_prop_1
HD2 CD2 CE2 HE2 aromatic_prop_1
HE1 CE1 CZ HZ aromatic_prop_1
HE2 CE2 CZ HZ aromatic_prop_1
HD1 CD1 CE1 CZ aromatic_prop_1
HD2 CD2 CE2 CZ aromatic_prop_1
HD1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 HD2 aromatic_prop_1
CE1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 CE2 aromatic_prop_1
[ impropers ]
-C CA N H
CA OC1 C OC2
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CE1 CE2 CZ HZ
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
[ CTYR ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.20150 3
HA amber99_19 0.10920 4
CB amber99_11 -0.07520 5
HB1 amber99_18 0.04900 6
HB2 amber99_18 0.04900 7
CG amber99_3 0.02430 8
CD1 amber99_3 -0.19220 9
HD1 amber99_22 0.17800 10
CE1 amber99_3 -0.24580 11
HE1 amber99_22 0.16730 12
CZ amber99_2 0.33950 13
OH amber99_43 -0.56430 14
HH amber99_25 0.40170 15
CE2 amber99_3 -0.24580 16
HE2 amber99_22 0.16730 17
CD2 amber99_3 -0.19220 18
HD2 amber99_22 0.17800 19
C amber99_2 0.78170 20
OC1 amber99_45 -0.80700 21
OC2 amber99_45 -0.80700 22
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ OH
CZ CE2
OH HH
CE2 HE2
CE2 CD2
CD2 HD2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
CB CG CD1 HD1 aromatic_prop_1
CB CG CD2 HD2 aromatic_prop_1
CB CG CD1 CE1 aromatic_prop_1
CB CG CD2 CE2 aromatic_prop_1
CG CD1 CE1 HE1 aromatic_prop_1
CG CD2 CE2 HE2 aromatic_prop_1
CG CD1 CE1 CZ aromatic_prop_1
CG CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ CE2 aromatic_prop_1
CD2 CE2 CZ CE1 aromatic_prop_1
CE1 CZ CE2 HE2 aromatic_prop_1
CE2 CZ CE1 HE1 aromatic_prop_1
HD1 CD1 CE1 HE1 aromatic_prop_1
HD2 CD2 CE2 HE2 aromatic_prop_1
HD1 CD1 CE1 CZ aromatic_prop_1
HD2 CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ OH aromatic_prop_1
CD2 CE2 CZ OH aromatic_prop_1
HE1 CE1 CZ OH aromatic_prop_1
HE2 CE2 CZ OH aromatic_prop_1
CE1 CZ OH HH aromatic_prop_2
CE2 CZ OH HH aromatic_prop_2
HD1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 HD2 aromatic_prop_1
CE1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 CE2 aromatic_prop_1
[ impropers ]
-C CA N H
CA OC1 C OC2
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
CE1 CE2 CZ OH
[ CGLU ]
[ atoms ]
N amber99_34 -0.51920 1
H amber99_17 0.30550 2
CA amber99_11 -0.20590 3
HA amber99_19 0.13990 4
CB amber99_11 0.00710 5
HB1 amber99_18 -0.00780 6
HB2 amber99_18 -0.00780 7
CG amber99_11 0.06750 8
HG1 amber99_18 -0.05480 9
HG2 amber99_18 -0.05480 10
CD amber99_2 0.81830 11
OE1 amber99_45 -0.82200 12
OE2 amber99_45 -0.82200 13
C amber99_2 0.74200 14
OC1 amber99_45 -0.79300 15
OC2 amber99_45 -0.79300 16
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
CG OE1 CD OE2
[ CASP ]
[ atoms ]
N amber99_34 -0.51920 1
H amber99_17 0.30550 2
CA amber99_11 -0.18170 3
HA amber99_19 0.10460 4
CB amber99_11 -0.06770 5
HB1 amber99_18 -0.02120 6
HB2 amber99_18 -0.02120 7
CG amber99_2 0.88510 8
OD1 amber99_45 -0.81620 9
OD2 amber99_45 -0.81620 10
C amber99_2 0.72560 11
OC1 amber99_45 -0.78870 12
OC2 amber99_45 -0.78870 13
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
CB OD1 CG OD2
[ CLYP ]
[ atoms ]
N amber99_34 -0.34810 1
H amber99_17 0.27640 2
CA amber99_11 -0.29030 3
HA amber99_19 0.14380 4
CB amber99_11 -0.05380 5
HB1 amber99_18 0.04820 6
HB2 amber99_18 0.04820 7
CG amber99_11 0.02270 8
HG1 amber99_18 0.01340 9
HG2 amber99_18 0.01340 10
CD amber99_11 -0.03920 11
HD1 amber99_18 0.06110 12
HD2 amber99_18 0.06110 13
CE amber99_11 -0.01760 14
HE1 amber99_28 0.11210 15
HE2 amber99_28 0.11210 16
NZ amber99_39 -0.37410 17
HZ1 amber99_17 0.33740 18
HZ2 amber99_17 0.33740 19
HZ3 amber99_17 0.33740 20
C amber99_2 0.84880 21
OC1 amber99_45 -0.82520 22
OC2 amber99_45 -0.82520 23
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
NZ HZ3
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CPRO ]
[ atoms ]
N amber99_34 -0.28020 1
CD amber99_11 0.04340 2
HD1 amber99_19 0.03310 3
HD2 amber99_19 0.03310 4
CG amber99_11 0.04660 5
HG1 amber99_18 0.01720 6
HG2 amber99_18 0.01720 7
CB amber99_11 -0.05430 8
HB1 amber99_18 0.03810 9
HB2 amber99_18 0.03810 10
CA amber99_11 -0.13360 11
HA amber99_19 0.07760 12
C amber99_2 0.66310 13
OC1 amber99_45 -0.76970 14
OC2 amber99_45 -0.76970 15
[ bonds ]
N CD
N CA
CD HD1
CD HD2
CD CG
CG HG1
CG HG2
CG CB
CB HB1
CB HB2
CB CA
CA HA
CA C
C OC1
C OC2
-C N
[ dihedrals ]
-CA -C N CD backbone_prop_1
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
-CH3 -C N CD backbone_prop_1
-O -C N CD backbone_prop_1
-C N CD CG proline_prop_1
[ impropers ]
CA OC1 C OC2
-C CD N CA
[ CCYN ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.16350 3
HA amber99_19 0.13960 4
CB amber99_11 -0.19960 5
HB1 amber99_19 0.14370 6
HB2 amber99_19 0.14370 7
SG amber99_48 -0.31020 8
HG amber99_26 0.20680 9
C amber99_2 0.74970 10
OC1 amber99_45 -0.79810 11
OC2 amber99_45 -0.79810 12
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CCYX ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.13180 3
HA amber99_19 0.09380 4
CB amber99_11 -0.19430 5
HB1 amber99_19 0.12280 6
HB2 amber99_19 0.12280 7
SG amber99_47 -0.05290 8
C amber99_2 0.76180 9
OC1 amber99_45 -0.80410 10
OC2 amber99_45 -0.80410 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CMET ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.25970 3
HA amber99_19 0.12770 4
CB amber99_11 -0.02360 5
HB1 amber99_18 0.04800 6
HB2 amber99_18 0.04800 7
CG amber99_11 0.04920 8
HG1 amber99_19 0.03170 9
HG2 amber99_19 0.03170 10
SD amber99_47 -0.26920 11
CE amber99_11 -0.03760 12
HE1 amber99_19 0.06250 13
HE2 amber99_19 0.06250 14
HE3 amber99_19 0.06250 15
C amber99_2 0.80130 16
OC1 amber99_45 -0.81050 17
OC2 amber99_45 -0.81050 18
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG SD
SD CE
CE HE1
CE HE2
CE HE3
C OC1
C OC2
-C N
[ dihedrals ]
-C N CA CB backbone_prop_3
-C N CA C backbone_prop_4
[ impropers ]
-C CA N H
CA OC1 C OC2
; N-terminal AA's
[ NALA ]
[ atoms ]
N amber99_39 0.14140 1
H1 amber99_17 0.19970 2
H2 amber99_17 0.19970 3
H3 amber99_17 0.19970 4
CA amber99_11 0.09620 5
HA amber99_28 0.08890 6
CB amber99_11 -0.05970 7
HB1 amber99_18 0.03000 8
HB2 amber99_18 0.03000 9
HB3 amber99_18 0.03000 10
C amber99_2 0.61630 11
O amber99_41 -0.57220 12
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NGLY ]
[ atoms ]
N amber99_39 0.29430 1
H1 amber99_17 0.16420 2
H2 amber99_17 0.16420 3
H3 amber99_17 0.16420 4
CA amber99_11 -0.01000 5
HA1 amber99_28 0.08950 6
HA2 amber99_28 0.08950 7
C amber99_2 0.61630 8
O amber99_41 -0.57220 9
[ bonds ]
N H1
N H2
N H3
N CA
CA HA1
CA HA2
CA C
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NSER ]
[ atoms ]
N amber99_39 0.18490 1
H1 amber99_17 0.18980 2
H2 amber99_17 0.18980 3
H3 amber99_17 0.18980 4
CA amber99_11 0.05670 5
HA amber99_28 0.07820 6
CB amber99_11 0.25960 7
HB1 amber99_19 0.02730 8
HB2 amber99_19 0.02730 9
OG amber99_43 -0.67140 10
HG amber99_25 0.42390 11
C amber99_2 0.61630 12
O amber99_41 -0.57220 13
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NTHR ]
[ atoms ]
N amber99_39 0.18120 1
H1 amber99_17 0.19340 2
H2 amber99_17 0.19340 3
H3 amber99_17 0.19340 4
CA amber99_11 0.00340 5
HA amber99_28 0.10870 6
CB amber99_11 0.45140 7
HB amber99_19 -0.03230 8
CG2 amber99_11 -0.25540 9
HG21 amber99_18 0.06270 10
HG22 amber99_18 0.06270 11
HG23 amber99_18 0.06270 12
OG1 amber99_43 -0.67640 13
HG1 amber99_25 0.40700 14
C amber99_2 0.61630 15
O amber99_41 -0.57220 16
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB
CB CG2
CB OG1
CG2 HG21
CG2 HG22
CG2 HG23
OG1 HG1
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NLEU ]
[ atoms ]
N amber99_39 0.10100 1
H1 amber99_17 0.21480 2
H2 amber99_17 0.21480 3
H3 amber99_17 0.21480 4
CA amber99_11 0.01040 5
HA amber99_28 0.10530 6
CB amber99_11 -0.02440 7
HB1 amber99_18 0.02560 8
HB2 amber99_18 0.02560 9
CG amber99_11 0.34210 10
HG amber99_18 -0.03800 11
CD1 amber99_11 -0.41060 12
HD11 amber99_18 0.09800 13
HD12 amber99_18 0.09800 14
HD13 amber99_18 0.09800 15
CD2 amber99_11 -0.41040 16
HD21 amber99_18 0.09800 17
HD22 amber99_18 0.09800 18
HD23 amber99_18 0.09800 19
C amber99_2 0.61230 20
O amber99_41 -0.57130 21
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NILE ]
[ atoms ]
N amber99_39 0.03110 1
H1 amber99_17 0.23290 2
H2 amber99_17 0.23290 3
H3 amber99_17 0.23290 4
CA amber99_11 0.02570 5
HA amber99_28 0.10310 6
CB amber99_11 0.18850 7
HB amber99_18 0.02130 8
CG2 amber99_11 -0.37200 9
HG21 amber99_18 0.09470 10
HG22 amber99_18 0.09470 11
HG23 amber99_18 0.09470 12
CG1 amber99_11 -0.03870 13
HG11 amber99_18 0.02010 14
HG12 amber99_18 0.02010 15
CD amber99_11 -0.09080 16
HD1 amber99_18 0.02260 17
HD2 amber99_18 0.02260 18
HD3 amber99_18 0.02260 19
C amber99_2 0.61230 20
O amber99_41 -0.57130 21
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB
CB CG2
CB CG1
CG2 HG21
CG2 HG22
CG2 HG23
CG1 HG11
CG1 HG12
CG1 CD
CD HD1
CD HD2
CD HD3
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NVAL ]
[ atoms ]
N amber99_39 0.05770 1
H1 amber99_17 0.22720 2
H2 amber99_17 0.22720 3
H3 amber99_17 0.22720 4
CA amber99_11 -0.00540 5
HA amber99_28 0.10930 6
CB amber99_11 0.31960 7
HB amber99_18 -0.02210 8
CG1 amber99_11 -0.31290 9
HG11 amber99_18 0.07350 10
HG12 amber99_18 0.07350 11
HG13 amber99_18 0.07350 12
CG2 amber99_11 -0.31290 13
HG21 amber99_18 0.07350 14
HG22 amber99_18 0.07350 15
HG23 amber99_18 0.07350 16
C amber99_2 0.61630 17
O amber99_41 -0.57220 18
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NASN ]
[ atoms ]
N amber99_39 0.18010 1
H1 amber99_17 0.19210 2
H2 amber99_17 0.19210 3
H3 amber99_17 0.19210 4
CA amber99_11 0.03680 5
HA amber99_28 0.12310 6
CB amber99_11 -0.02830 7
HB1 amber99_18 0.05150 8
HB2 amber99_18 0.05150 9
CG amber99_2 0.58330 10
OD1 amber99_41 -0.57440 11
ND2 amber99_34 -0.86340 12
HD21 amber99_17 0.40970 13
HD22 amber99_17 0.40970 14
C amber99_2 0.61630 15
O amber99_41 -0.57220 16
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG ND2
ND2 HD21
ND2 HD22
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CB CG ND2 HD21 backbone_prop_1
CB CG ND2 HD22 backbone_prop_1
OD1 CG ND2 HD21 backbone_prop_2
OD1 CG ND2 HD22 backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
CB ND2 CG OD1
CG HD21 ND2 HD22
[ NGLN ]
[ atoms ]
N amber99_39 0.14930 1
H1 amber99_17 0.19960 2
H2 amber99_17 0.19960 3
H3 amber99_17 0.19960 4
CA amber99_11 0.05360 5
HA amber99_28 0.10150 6
CB amber99_11 0.06510 7
HB1 amber99_18 0.00500 8
HB2 amber99_18 0.00500 9
CG amber99_11 -0.09030 10
HG1 amber99_18 0.03310 11
HG2 amber99_18 0.03310 12
CD amber99_2 0.73540 13
OE1 amber99_41 -0.61330 14
NE2 amber99_34 -1.00310 15
HE21 amber99_17 0.44290 16
HE22 amber99_17 0.44290 17
C amber99_2 0.61230 18
O amber99_41 -0.57130 19
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD NE2
NE2 HE21
NE2 HE22
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CG CD NE2 HE21 backbone_prop_1
CG CD NE2 HE22 backbone_prop_1
OE1 CD NE2 HE21 backbone_prop_2
OE1 CD NE2 HE22 backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
CG NE2 CD OE1
CD HE21 NE2 HE22
[ NARG ]
[ atoms ]
N amber99_39 0.13050 1
H1 amber99_17 0.20830 2
H2 amber99_17 0.20830 3
H3 amber99_17 0.20830 4
CA amber99_11 -0.02230 5
HA amber99_28 0.12420 6
CB amber99_11 0.01180 7
HB1 amber99_18 0.02260 8
HB2 amber99_18 0.02260 9
CG amber99_11 0.02360 10
HG1 amber99_18 0.03090 11
HG2 amber99_18 0.03090 12
CD amber99_11 0.09350 13
HD1 amber99_19 0.05270 14
HD2 amber99_19 0.05270 15
NE amber99_38 -0.56500 16
HE amber99_17 0.35920 17
CZ amber99_3 0.82810 18
NH1 amber99_38 -0.86930 19
HH11 amber99_17 0.44940 20
HH12 amber99_17 0.44940 21
NH2 amber99_38 -0.86930 22
HH21 amber99_17 0.44940 23
HH22 amber99_17 0.44940 24
C amber99_2 0.72140 25
O amber99_41 -0.60130 26
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
HH12 NH1 CZ NH2 sidechain_prop_1
HH11 NH1 CZ NH2 sidechain_prop_1
HE NE CZ NH1 sidechain_prop_1
HE NE CZ NH2 sidechain_prop_1
NE CZ NH1 HH11 sidechain_prop_1
NE CZ NH1 HH12 sidechain_prop_1
CD NE CZ NH1 sidechain_prop_1
CD NE CZ NH2 sidechain_prop_1
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
NE NH1 CZ NH2
CD CZ NE HE
CZ HH11 NH1 HH12
CZ HH21 NH2 HH22
[ NHID ]
[ atoms ]
N amber99_39 0.15420 1
H1 amber99_17 0.19630 2
H2 amber99_17 0.19630 3
H3 amber99_17 0.19630 4
CA amber99_11 0.09640 5
HA amber99_28 0.09580 6
CB amber99_11 0.02590 7
HB1 amber99_18 0.02090 8
HB2 amber99_18 0.02090 9
CG amber99_5 -0.03990 10
ND1 amber99_35 -0.38190 11
HD1 amber99_17 0.36320 12
CE1 amber99_10 0.21270 13
HE1 amber99_24 0.13850 14
NE2 amber99_36 -0.57110 15
CD2 amber99_12 0.10460 16
HD2 amber99_23 0.12990 17
C amber99_2 0.61230 18
O amber99_41 -0.57130 19
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CE1 HE1
CE1 NE2
NE2 CD2
CD2 HD2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG ND1 HD1 aromatic_prop_3
HD1 ND1 CE1 HE1 aromatic_prop_5
NE2 CE1 ND1 HD1 aromatic_prop_5
HD1 ND1 CG CD2 aromatic_prop_3
CB CG ND1 CE1 aromatic_prop_3
CB CG CD2 HD2 aromatic_prop_6a
CB CG CD2 NE2 aromatic_prop_6a
CG ND1 CE1 HE1 aromatic_prop_5
CG ND1 CE1 NE2 aromatic_prop_5
ND1 CE1 NE2 CD2 aromatic_prop_5a
ND1 CG CD2 HD2 aromatic_prop_6a
ND1 CG CD2 NE2 aromatic_prop_6a
CE1 NE2 CD2 HD2 aromatic_prop_4a
CE1 NE2 CD2 CG aromatic_prop_4a
HE1 CE1 NE2 CD2 aromatic_prop_5a
CD2 CG ND1 CE1 aromatic_prop_3
[ impropers ]
CA +N C O
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ NHIE ]
[ atoms ]
N amber99_39 0.14720 1
H1 amber99_17 0.20160 2
H2 amber99_17 0.20160 3
H3 amber99_17 0.20160 4
CA amber99_11 0.02360 5
HA amber99_28 0.13800 6
CB amber99_11 0.04890 7
HB1 amber99_18 0.02230 8
HB2 amber99_18 0.02230 9
CG amber99_5 0.17400 10
ND1 amber99_36 -0.55790 11
CE1 amber99_10 0.18040 12
HE1 amber99_24 0.13970 13
NE2 amber99_35 -0.27810 14
HE2 amber99_17 0.33240 15
CD2 amber99_13 -0.23490 16
HD2 amber99_23 0.19630 17
C amber99_2 0.61230 18
O amber99_41 -0.57130 19
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 CE1
CE1 HE1
CE1 NE2
NE2 HE2
NE2 CD2
CD2 HD2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CG CD2 NE2 HE2 aromatic_prop_4
HE1 CE1 NE2 HE2 aromatic_prop_5
HD2 CD2 NE2 HE2 aromatic_prop_4
ND1 CE1 NE2 HE2 aromatic_prop_5
CB CG ND1 CE1 aromatic_prop_3a
CB CG CD2 HD2 aromatic_prop_6
CB CG CD2 NE2 aromatic_prop_6
CG ND1 CE1 HE1 aromatic_prop_5a
CG ND1 CE1 NE2 aromatic_prop_5a
ND1 CE1 NE2 CD2 aromatic_prop_5
HE1 CE1 NE2 CD2 aromatic_prop_5
ND1 CG CD2 HD2 aromatic_prop_6
ND1 CG CD2 NE2 aromatic_prop_6
CE1 NE2 CD2 CG aromatic_prop_4
CE1 NE2 CD2 HD2 aromatic_prop_4
CD2 CG ND1 CE1 aromatic_prop_3a
[ impropers ]
CA +N C O
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ NHIP ]
[ atoms ]
N amber99_39 0.25600 1
H1 amber99_17 0.17040 2
H2 amber99_17 0.17040 3
H3 amber99_17 0.17040 4
CA amber99_11 0.05810 5
HA amber99_28 0.10470 6
CB amber99_11 0.04840 7
HB1 amber99_18 0.05310 8
HB2 amber99_18 0.05310 9
CG amber99_5 -0.02360 10
ND1 amber99_35 -0.15100 11
HD1 amber99_17 0.38210 12
CE1 amber99_10 -0.00110 13
HE1 amber99_24 0.26450 14
NE2 amber99_35 -0.17390 15
HE2 amber99_17 0.39210 16
CD2 amber99_13 -0.14330 17
HD2 amber99_23 0.24950 18
C amber99_2 0.72140 19
O amber99_41 -0.60130 20
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CE1 HE1
CE1 NE2
NE2 HE2
NE2 CD2
CD2 HD2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG ND1 HD1 aromatic_prop_3
CG CD2 NE2 HE2 aromatic_prop_4
HD1 ND1 CE1 HE1 aromatic_prop_5
HE1 CE1 NE2 HE2 aromatic_prop_5
HD2 CD2 NE2 HE2 aromatic_prop_4
ND1 CE1 NE2 HE2 aromatic_prop_5
NE2 CE1 ND1 HD1 aromatic_prop_5
HD1 ND1 CG CD2 aromatic_prop_3
CB CG ND1 CE1 aromatic_prop_3
CB CG CD2 HD2 aromatic_prop_6
CB CG CD2 NE2 aromatic_prop_6
CG ND1 CE1 HE1 aromatic_prop_5
CG ND1 CE1 NE2 aromatic_prop_5
CG CD2 NE2 CE1 aromatic_prop_4
ND1 CE1 NE2 CD2 aromatic_prop_5
ND1 CG CD2 HD2 aromatic_prop_6
ND1 CG CD2 NE2 aromatic_prop_6
CE1 NE2 CD2 HD2 aromatic_prop_4
HE1 CE1 NE2 CD2 aromatic_prop_5
CD2 CG ND1 CE1 aromatic_prop_3
[ impropers ]
CA +N C O
CG CE1 ND1 HD1
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ NTRP ]
[ atoms ]
N amber99_39 0.19130 1
H1 amber99_17 0.18880 2
H2 amber99_17 0.18880 3
H3 amber99_17 0.18880 4
CA amber99_11 0.04210 5
HA amber99_28 0.11620 6
CB amber99_11 0.05430 7
HB1 amber99_18 0.02220 8
HB2 amber99_18 0.02220 9
CG amber99_14 -0.16540 10
CD1 amber99_13 -0.17880 11
HD1 amber99_23 0.21950 12
NE1 amber99_35 -0.34440 13
HE1 amber99_17 0.34120 14
CE2 amber99_8 0.15750 15
CZ2 amber99_3 -0.27100 16
HZ2 amber99_22 0.15890 17
CH2 amber99_3 -0.10800 18
HH2 amber99_22 0.14110 19
CZ3 amber99_3 -0.20340 20
HZ3 amber99_22 0.14580 21
CE3 amber99_3 -0.22650 22
HE3 amber99_22 0.16460 23
CD2 amber99_4 0.11320 24
C amber99_2 0.61230 25
O amber99_41 -0.57130 26
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 NE1
NE1 HE1
NE1 CE2
CE2 CZ2
CE2 CD2
CZ2 HZ2
CZ2 CH2
CH2 HH2
CH2 CZ3
CZ3 HZ3
CZ3 CE3
CE3 HE3
CE3 CD2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG CD1 HD1 aromatic_prop_7
CB CG CD1 NE1 aromatic_prop_7
CB CG CD2 CE2 aromatic_prop_8
CB CG CD2 CE3 aromatic_prop_8
CG CD1 NE1 HE1 aromatic_prop_4
CG CD1 NE1 CE2 aromatic_prop_4
CG CD2 CE2 NE1 aromatic_prop_10
CG CD2 CE2 CZ2 aromatic_prop_10
CG CD2 CE3 HE3 aromatic_prop_12
CG CD2 CE3 CZ3 aromatic_prop_12
CD1 CG CD2 CE2 aromatic_prop_8
CD1 CG CD2 CE3 aromatic_prop_8
CD1 NE1 CE2 CD2 aromatic_prop_9
CD1 NE1 CE2 CZ2 aromatic_prop_9
HD1 CD1 NE1 HE1 aromatic_prop_4
HD1 CD1 NE1 CE2 aromatic_prop_4
HD1 CD1 CG CD2 aromatic_prop_7
HE1 NE1 CE2 CD2 aromatic_prop_9
HE1 NE1 CE2 CZ2 aromatic_prop_9
NE1 CD1 CG CD2 aromatic_prop_7
NE1 CE2 CD2 CE3 aromatic_prop_10
NE1 CE2 CZ2 HZ2 aromatic_prop_11
NE1 CE2 CZ2 CH2 aromatic_prop_11
CE2 CD2 CE3 HE3 aromatic_prop_12
CE2 CD2 CE3 CZ3 aromatic_prop_12
CE2 CZ2 CH2 HH2 aromatic_prop_1
CE2 CZ2 CH2 CZ3 aromatic_prop_1
CZ2 CH2 CZ3 HZ3 aromatic_prop_1
CZ2 CH2 CZ3 CE3 aromatic_prop_1
CZ2 CE2 CD2 CE3 aromatic_prop_10
HZ2 CZ2 CH2 HH2 aromatic_prop_1
HZ2 CZ2 CH2 CZ3 aromatic_prop_1
CH2 CZ2 CE2 CD2 aromatic_prop_11
CH2 CZ3 CE3 HE3 aromatic_prop_1
CH2 CZ3 CE3 CD2 aromatic_prop_1
HH2 CH2 CZ3 HZ3 aromatic_prop_1
HH2 CH2 CZ3 CE3 aromatic_prop_1
HZ3 CZ3 CE3 HE3 aromatic_prop_1
HZ3 CZ3 CE3 CD2 aromatic_prop_1
[ impropers ]
CA +N C O
CD1 CE2 NE1 HE1
CE2 CH2 CZ2 HZ2
CZ2 CZ3 CH2 HH2
CH2 CE3 CZ3 HZ3
CZ3 CD2 CE3 HE3
CG NE1 CD1 HD1
CD1 CD2 CG CB
[ NPHE ]
[ atoms ]
N amber99_39 0.17370 1
H1 amber99_17 0.19210 2
H2 amber99_17 0.19210 3
H3 amber99_17 0.19210 4
CA amber99_11 0.07330 5
HA amber99_28 0.10410 6
CB amber99_11 0.03300 7
HB1 amber99_18 0.01040 8
HB2 amber99_18 0.01040 9
CG amber99_3 0.00310 10
CD1 amber99_3 -0.13920 11
HD1 amber99_22 0.13740 12
CE1 amber99_3 -0.16020 13
HE1 amber99_22 0.14330 14
CZ amber99_3 -0.12080 15
HZ amber99_22 0.13290 16
CE2 amber99_3 -0.16030 17
HE2 amber99_22 0.14330 18
CD2 amber99_3 -0.13910 19
HD2 amber99_22 0.13740 20
C amber99_2 0.61230 21
O amber99_41 -0.57130 22
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ HZ
CZ CE2
CE2 HE2
CE2 CD2
CD2 HD2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG CD1 HD1 aromatic_prop_1
CB CG CD2 HD2 aromatic_prop_1
CB CG CD1 CE1 aromatic_prop_1
CB CG CD2 CE2 aromatic_prop_1
CG CD1 CE1 HE1 aromatic_prop_1
CG CD2 CE2 HE2 aromatic_prop_1
CG CD1 CE1 CZ aromatic_prop_1
CG CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ HZ aromatic_prop_1
CD1 CE1 CZ CE2 aromatic_prop_1
CD2 CE2 CZ HZ aromatic_prop_1
CD2 CE2 CZ CE1 aromatic_prop_1
CE1 CZ CE2 HE2 aromatic_prop_1
CE2 CZ CE1 HE1 aromatic_prop_1
HD1 CD1 CE1 HE1 aromatic_prop_1
HD2 CD2 CE2 HE2 aromatic_prop_1
HE1 CE1 CZ HZ aromatic_prop_1
HE2 CE2 CZ HZ aromatic_prop_1
HD1 CD1 CE1 CZ aromatic_prop_1
HD2 CD2 CE2 CZ aromatic_prop_1
HD1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 HD2 aromatic_prop_1
CE1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 CE2 aromatic_prop_1
[ impropers ]
CA +N C O
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CE1 CE2 CZ HZ
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
[ NTYR ]
[ atoms ]
N amber99_39 0.19400 1
H1 amber99_17 0.18730 2
H2 amber99_17 0.18730 3
H3 amber99_17 0.18730 4
CA amber99_11 0.05700 5
HA amber99_28 0.09830 6
CB amber99_11 0.06590 7
HB1 amber99_18 0.01020 8
HB2 amber99_18 0.01020 9
CG amber99_3 -0.02050 10
CD1 amber99_3 -0.20020 11
HD1 amber99_22 0.17200 12
CE1 amber99_3 -0.22390 13
HE1 amber99_22 0.16500 14
CZ amber99_2 0.31390 15
OH amber99_43 -0.55780 16
HH amber99_25 0.40010 17
CE2 amber99_3 -0.22390 18
HE2 amber99_22 0.16500 19
CD2 amber99_3 -0.20020 20
HD2 amber99_22 0.17200 21
C amber99_2 0.61230 22
O amber99_41 -0.57130 23
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ OH
CZ CE2
OH HH
CE2 HE2
CE2 CD2
CD2 HD2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
CB CG CD1 HD1 aromatic_prop_1
CB CG CD2 HD2 aromatic_prop_1
CB CG CD1 CE1 aromatic_prop_1
CB CG CD2 CE2 aromatic_prop_1
CG CD1 CE1 HE1 aromatic_prop_1
CG CD2 CE2 HE2 aromatic_prop_1
CG CD1 CE1 CZ aromatic_prop_1
CG CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ CE2 aromatic_prop_1
CD2 CE2 CZ CE1 aromatic_prop_1
CE1 CZ CE2 HE2 aromatic_prop_1
CE2 CZ CE1 HE1 aromatic_prop_1
HD1 CD1 CE1 HE1 aromatic_prop_1
HD2 CD2 CE2 HE2 aromatic_prop_1
HD1 CD1 CE1 CZ aromatic_prop_1
HD2 CD2 CE2 CZ aromatic_prop_1
CD1 CE1 CZ OH aromatic_prop_1
CD2 CE2 CZ OH aromatic_prop_1
HE1 CE1 CZ OH aromatic_prop_1
HE2 CE2 CZ OH aromatic_prop_1
CE1 CZ OH HH aromatic_prop_2
CE2 CZ OH HH aromatic_prop_2
HD1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 HD2 aromatic_prop_1
CE1 CD1 CG CD2 aromatic_prop_1
CD1 CG CD2 CE2 aromatic_prop_1
[ impropers ]
CA +N C O
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
CE1 CE2 CZ OH
[ NGLU ]
[ atoms ]
N amber99_39 0.00170 1
H1 amber99_17 0.23910 2
H2 amber99_17 0.23910 3
H3 amber99_17 0.23910 4
CA amber99_11 0.05880 5
HA amber99_28 0.12020 6
CB amber99_11 0.09090 7
HB1 amber99_18 -0.02320 8
HB2 amber99_18 -0.02320 9
CG amber99_11 -0.02360 10
HG1 amber99_18 -0.03150 11
HG2 amber99_18 -0.03150 12
CD amber99_2 0.80870 13
OE1 amber99_45 -0.81890 14
OE2 amber99_45 -0.81890 15
C amber99_2 0.56210 16
O amber99_41 -0.58890 17
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
CG OE1 CD OE2
[ NASP ]
[ atoms ]
N amber99_39 0.07820 1
H1 amber99_17 0.22000 2
H2 amber99_17 0.22000 3
H3 amber99_17 0.22000 4
CA amber99_11 0.02920 5
HA amber99_28 0.11410 6
CB amber99_11 -0.02350 7
HB1 amber99_18 -0.01690 8
HB2 amber99_18 -0.01690 9
CG amber99_2 0.81940 10
OD1 amber99_45 -0.80840 11
OD2 amber99_45 -0.80840 12
C amber99_2 0.56210 13
O amber99_41 -0.58890 14
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
CB OD1 CG OD2
[ NLYP ]
[ atoms ]
N amber99_39 0.09660 1
H1 amber99_17 0.21650 2
H2 amber99_17 0.21650 3
H3 amber99_17 0.21650 4
CA amber99_11 -0.00150 5
HA amber99_28 0.11800 6
CB amber99_11 0.02120 7
HB1 amber99_18 0.02830 8
HB2 amber99_18 0.02830 9
CG amber99_11 -0.00480 10
HG1 amber99_18 0.01210 11
HG2 amber99_18 0.01210 12
CD amber99_11 -0.06080 13
HD1 amber99_18 0.06330 14
HD2 amber99_18 0.06330 15
CE amber99_11 -0.01810 16
HE1 amber99_28 0.11710 17
HE2 amber99_28 0.11710 18
NZ amber99_39 -0.37640 19
HZ1 amber99_17 0.33820 20
HZ2 amber99_17 0.33820 21
HZ3 amber99_17 0.33820 22
C amber99_2 0.72140 23
O amber99_41 -0.60130 24
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
NZ HZ3
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NPRO ]
[ atoms ]
N amber99_39 -0.20200 1
H1 amber99_17 0.31200 2
H2 amber99_17 0.31200 3
CD amber99_11 -0.01200 4
HD1 amber99_28 0.10000 5
HD2 amber99_28 0.10000 6
CG amber99_11 -0.12100 7
HG1 amber99_18 0.10000 8
HG2 amber99_18 0.10000 9
CB amber99_11 -0.11500 10
HB1 amber99_18 0.10000 11
HB2 amber99_18 0.10000 12
CA amber99_11 0.10000 13
HA amber99_28 0.10000 14
C amber99_2 0.52600 15
O amber99_41 -0.50000 16
[ bonds ]
N H1
N H2
N CD
N CA
CD HD1
CD HD2
CD CG
CG HG1
CG HG2
CG CB
CB HB1
CB HB2
CB CA
CA HA
CA C
C O
C +N
[ dihedrals ]
-CA -C N CD backbone_prop_1
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
-C N CA CB backbone_prop_3
-CH3 -C N CD backbone_prop_1
-O -C N CD backbone_prop_1
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NCYN ]
[ atoms ]
N amber99_39 0.13250 1
H1 amber99_17 0.20230 2
H2 amber99_17 0.20230 3
H3 amber99_17 0.20230 4
CA amber99_11 0.09270 5
HA amber99_28 0.14110 6
CB amber99_11 -0.11950 7
HB1 amber99_19 0.11880 8
HB2 amber99_19 0.11880 9
SG amber99_48 -0.32980 10
HG amber99_26 0.19750 11
C amber99_2 0.61230 12
O amber99_41 -0.57130 13
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NCYX ]
[ atoms ]
N amber99_39 0.20690 1
H1 amber99_17 0.18150 2
H2 amber99_17 0.18150 3
H3 amber99_17 0.18150 4
CA amber99_11 0.10550 5
HA amber99_28 0.09220 6
CB amber99_11 -0.02770 7
HB1 amber99_19 0.06800 8
HB2 amber99_19 0.06800 9
SG amber99_47 -0.09840 10
C amber99_2 0.61230 11
O amber99_41 -0.57130 12
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB2
CB HB1
CB SG
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
[ NMET ]
[ atoms ]
N amber99_39 0.15920 1
H1 amber99_17 0.19840 2
H2 amber99_17 0.19840 3
H3 amber99_17 0.19840 4
CA amber99_11 0.02210 5
HA amber99_28 0.11160 6
CB amber99_11 0.08650 7
HB1 amber99_18 0.01250 8
HB2 amber99_18 0.01250 9
CG amber99_11 0.03340 10
HG1 amber99_19 0.02920 11
HG2 amber99_19 0.02920 12
SD amber99_47 -0.27740 13
CE amber99_11 -0.03410 14
HE1 amber99_19 0.05970 15
HE2 amber99_19 0.05970 16
HE3 amber99_19 0.05970 17
C amber99_2 0.61230 18
O amber99_41 -0.57130 19
[ bonds ]
N H1
N H2
N H3
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG SD
SD CE
CE HE1
CE HE2
CE HE3
C O
C +N
[ dihedrals ]
CA C +N +H backbone_prop_1
O C +N +H backbone_prop_2
CA C +N +CA backbone_prop_1
O C +N +CA backbone_prop_1
[ impropers ]
CA +N C O
; now 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's
[ DA5 ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 0.04310 9
H1' amber99_20 0.18380 10
N9 amber99_40 -0.02680 11
C8 amber99_6 0.16070 12
H8 amber99_24 0.18770 13
N7 amber99_36 -0.61750 14
C5 amber99_4 0.07250 15
C6 amber99_3 0.68970 16
N6 amber99_38 -0.91230 17
H61 amber99_17 0.41670 18
H62 amber99_17 0.41670 19
N1 amber99_37 -0.76240 20
C2 amber99_9 0.57160 21
H2 amber99_24 0.05980 22
N3 amber99_37 -0.74170 23
C4 amber99_4 0.38000 24
C3' amber99_11 0.07130 25
H3' amber99_19 0.09850 26
C2' amber99_11 -0.08540 27
H2'1 amber99_18 0.07180 28
H2'2 amber99_18 0.07180 29
O3' amber99_44 -0.52320 30
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C8 C4 N9 C1'
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N1 C6 N6
[ DA ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 0.04310 11
H1' amber99_20 0.18380 12
N9 amber99_40 -0.02680 13
C8 amber99_6 0.16070 14
H8 amber99_24 0.18770 15
N7 amber99_36 -0.61750 16
C5 amber99_4 0.07250 17
C6 amber99_3 0.68970 18
N6 amber99_38 -0.91230 19
H61 amber99_17 0.41670 20
H62 amber99_17 0.41670 21
N1 amber99_37 -0.76240 22
C2 amber99_9 0.57160 23
H2 amber99_24 0.05980 24
N3 amber99_37 -0.74170 25
C4 amber99_4 0.38000 26
C3' amber99_11 0.07130 27
H3' amber99_19 0.09850 28
C2' amber99_11 -0.08540 29
H2'1 amber99_18 0.07180 30
H2'2 amber99_18 0.07180 31
O3' amber99_44 -0.52320 32
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H62 N6 C6 N1 proper_X_CA_N2_X
H61 N6 C6 N1 proper_X_CA_N2_X
C5 C6 N6 H61 proper_X_CA_N2_X
C5 C6 N6 H62 proper_X_CA_N2_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N6 C6 N1 nucleic_imp_11
[ DA3 ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 0.04310 11
H1' amber99_20 0.18380 12
N9 amber99_40 -0.02680 13
C8 amber99_6 0.16070 14
H8 amber99_24 0.18770 15
N7 amber99_36 -0.61750 16
C5 amber99_4 0.07250 17
C6 amber99_3 0.68970 18
N6 amber99_38 -0.91230 19
H61 amber99_17 0.41670 20
H62 amber99_17 0.41670 21
N1 amber99_37 -0.76240 22
C2 amber99_9 0.57160 23
H2 amber99_24 0.05980 24
N3 amber99_37 -0.74170 25
C4 amber99_4 0.38000 26
C3' amber99_11 0.07130 27
H3' amber99_19 0.09850 28
C2' amber99_11 -0.08540 29
H2'1 amber99_18 0.07180 30
H2'2 amber99_18 0.07180 31
O3' amber99_43 -0.65490 32
H3T amber99_25 0.43960 33
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H62 N6 C6 N1 proper_X_CA_N2_X
H61 N6 C6 N1 proper_X_CA_N2_X
C5 C6 N6 H61 proper_X_CA_N2_X
C5 C6 N6 H62 proper_X_CA_N2_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N6 C6 N1 nucleic_imp_11
[ DAN ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 0.04310 9
H1' amber99_20 0.18380 10
N9 amber99_40 -0.02680 11
C8 amber99_6 0.16070 12
H8 amber99_24 0.18770 13
N7 amber99_36 -0.61750 14
C5 amber99_4 0.07250 15
C6 amber99_3 0.68970 16
N6 amber99_38 -0.91230 17
H61 amber99_17 0.41670 18
H62 amber99_17 0.41670 19
N1 amber99_37 -0.76240 20
C2 amber99_9 0.57160 21
H2 amber99_24 0.05980 22
N3 amber99_37 -0.74170 23
C4 amber99_4 0.38000 24
C3' amber99_11 0.07130 25
H3' amber99_19 0.09850 26
C2' amber99_11 -0.08540 27
H2'1 amber99_18 0.07180 28
H2'2 amber99_18 0.07180 29
O3' amber99_43 -0.65490 30
H3T amber99_25 0.43960 31
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
[ impropers ]
C8 C4 N9 C1'
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N1 C6 N6
[ RA5 ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.03940 9
H1' amber99_20 0.20070 10
N9 amber99_40 -0.02510 11
C8 amber99_6 0.20060 12
H8 amber99_24 0.15530 13
N7 amber99_36 -0.60730 14
C5 amber99_4 0.05150 15
C6 amber99_3 0.70090 16
N6 amber99_38 -0.90190 17
H61 amber99_17 0.41150 18
H62 amber99_17 0.41150 19
N1 amber99_37 -0.76150 20
C2 amber99_9 0.58750 21
H2 amber99_24 0.04730 22
N3 amber99_37 -0.69970 23
C4 amber99_4 0.30530 24
C3' amber99_11 0.20220 25
H3' amber99_19 0.06150 26
C2' amber99_11 0.06700 27
H2'1 amber99_19 0.09720 28
O2' amber99_43 -0.61390 29
HO'2 amber99_25 0.41860 30
O3' amber99_44 -0.52460 31
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C8 C4 N9 C1'
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N1 C6 N6
[ RA ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.03940 11
H1' amber99_20 0.20070 12
N9 amber99_40 -0.02510 13
C8 amber99_6 0.20060 14
H8 amber99_24 0.15530 15
N7 amber99_36 -0.60730 16
C5 amber99_4 0.05150 17
C6 amber99_3 0.70090 18
N6 amber99_38 -0.90190 19
H61 amber99_17 0.41150 20
H62 amber99_17 0.41150 21
N1 amber99_37 -0.76150 22
C2 amber99_9 0.58750 23
H2 amber99_24 0.04730 24
N3 amber99_37 -0.69970 25
C4 amber99_4 0.30530 26
C3' amber99_11 0.20220 27
H3' amber99_19 0.06150 28
C2' amber99_11 0.06700 29
H2'1 amber99_19 0.09720 30
O2' amber99_43 -0.61390 31
HO'2 amber99_25 0.41860 32
O3' amber99_44 -0.52460 33
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H62 N6 C6 N1 proper_X_CA_N2_X
H61 N6 C6 N1 proper_X_CA_N2_X
C5 C6 N6 H61 proper_X_CA_N2_X
C5 C6 N6 H62 proper_X_CA_N2_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N6 C6 N1 nucleic_imp_11
[ RA3 ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.03940 11
H1' amber99_20 0.20070 12
N9 amber99_40 -0.02510 13
C8 amber99_6 0.20060 14
H8 amber99_24 0.15530 15
N7 amber99_36 -0.60730 16
C5 amber99_4 0.05150 17
C6 amber99_3 0.70090 18
N6 amber99_38 -0.90190 19
H61 amber99_17 0.41150 20
H62 amber99_17 0.41150 21
N1 amber99_37 -0.76150 22
C2 amber99_9 0.58750 23
H2 amber99_24 0.04730 24
N3 amber99_37 -0.69970 25
C4 amber99_4 0.30530 26
C3' amber99_11 0.20220 27
H3' amber99_19 0.06150 28
C2' amber99_11 0.06700 29
H2'1 amber99_19 0.09720 30
O2' amber99_43 -0.61390 31
HO'2 amber99_25 0.41860 32
O3' amber99_43 -0.65410 33
H3T amber99_25 0.43760 34
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H62 N6 C6 N1 proper_X_CA_N2_X
H61 N6 C6 N1 proper_X_CA_N2_X
C5 C6 N6 H61 proper_X_CA_N2_X
C5 C6 N6 H62 proper_X_CA_N2_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N6 C6 N1 nucleic_imp_11
[ RAN ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.03940 9
H1' amber99_20 0.20070 10
N9 amber99_40 -0.02510 11
C8 amber99_6 0.20060 12
H8 amber99_24 0.15530 13
N7 amber99_36 -0.60730 14
C5 amber99_4 0.05150 15
C6 amber99_3 0.70090 16
N6 amber99_38 -0.90190 17
H61 amber99_17 0.41150 18
H62 amber99_17 0.41150 19
N1 amber99_37 -0.76150 20
C2 amber99_9 0.58750 21
H2 amber99_24 0.04730 22
N3 amber99_37 -0.69970 23
C4 amber99_4 0.30530 24
C3' amber99_11 0.20220 25
H3' amber99_19 0.06150 26
C2' amber99_11 0.06700 27
H2'1 amber99_19 0.09720 28
O2' amber99_43 -0.61390 29
HO'2 amber99_25 0.41860 30
O3' amber99_43 -0.65410 31
H3T amber99_25 0.43760 32
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 N6
C6 N1
N6 H61
N6 H62
N1 C2
C2 H2
C2 N3
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 C2 proper_X_CA_NC_X
N6 C6 N1 C2 proper_X_CA_NC_X
N1 C2 N3 C4 proper_X_CQ_NC_X
H2 C2 N3 C4 proper_X_CQ_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
O5' C5' C4' H4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
H3' C3' C2' O2' proper_H_CT_CT_O
[ impropers ]
C8 C4 N9 C1'
C6 H61 N6 H62
N9 N7 C8 H8
N1 N3 C2 H2 nucleic_imp_11
C5 N1 C6 N6
[ DT5 ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 0.06800 9
H1' amber99_20 0.18040 10
N1 amber99_40 -0.02390 11
C6 amber99_7 -0.22090 12
H6 amber99_23 0.26070 13
C5 amber99_7 0.00250 14
C7 amber99_11 -0.22690 15
H71 amber99_18 0.07700 16
H72 amber99_18 0.07700 17
H73 amber99_18 0.07700 18
C4 amber99_2 0.51940 19
O4 amber99_41 -0.55630 20
N3 amber99_35 -0.43400 21
H3 amber99_17 0.34200 22
C2 amber99_2 0.56770 23
O amber99_41 -0.58810 24
C3' amber99_11 0.07130 25
H3' amber99_19 0.09850 26
C2' amber99_11 -0.08540 27
H2'1 amber99_18 0.07180 28
H2'2 amber99_18 0.07180 29
O3' amber99_44 -0.52320 30
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 C7
C5 C4
C7 H71
C7 H72
C7 H73
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 C7 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C7 H71 proper_HC_CT_CM_CM
C6 C5 C7 H72 proper_HC_CT_CM_CM
C6 C5 C7 H73 proper_HC_CT_CM_CM
H6 C6 C5 C7 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
C7 C5 C4 O4 proper_X_C_CM_X
C7 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C6 C2 N1 C1'
C6 C4 C5 C7
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ DT ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 0.06800 11
H1' amber99_20 0.18040 12
N1 amber99_40 -0.02390 13
C6 amber99_7 -0.22090 14
H6 amber99_23 0.26070 15
C5 amber99_7 0.00250 16
C7 amber99_11 -0.22690 17
H71 amber99_18 0.07700 18
H72 amber99_18 0.07700 19
H73 amber99_18 0.07700 20
C4 amber99_2 0.51940 21
O4 amber99_41 -0.55630 22
N3 amber99_35 -0.43400 23
H3 amber99_17 0.34200 24
C2 amber99_2 0.56770 25
O amber99_41 -0.58810 26
C3' amber99_11 0.07130 27
H3' amber99_19 0.09850 28
C2' amber99_11 -0.08540 29
H2'1 amber99_18 0.07180 30
H2'2 amber99_18 0.07180 31
O3' amber99_44 -0.52320 32
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 C7
C5 C4
C7 H71
C7 H72
C7 H73
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 C7 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C7 H71 proper_HC_CT_CM_CM
C6 C5 C7 H72 proper_HC_CT_CM_CM
C6 C5 C7 H73 proper_HC_CT_CM_CM
H6 C6 C5 C7 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
C7 C5 C4 O4 proper_X_C_CM_X
C7 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
C4 C6 C5 C7
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ DT3 ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 0.06800 11
H1' amber99_20 0.18040 12
N1 amber99_40 -0.02390 13
C6 amber99_7 -0.22090 14
H6 amber99_23 0.26070 15
C5 amber99_7 0.00250 16
C7 amber99_11 -0.22690 17
H71 amber99_18 0.07700 18
H72 amber99_18 0.07700 19
H73 amber99_18 0.07700 20
C4 amber99_2 0.51940 21
O4 amber99_41 -0.55630 22
N3 amber99_35 -0.43400 23
H3 amber99_17 0.34200 24
C2 amber99_2 0.56770 25
O amber99_41 -0.58810 26
C3' amber99_11 0.07130 27
H3' amber99_19 0.09850 28
C2' amber99_11 -0.08540 29
H2'1 amber99_18 0.07180 30
H2'2 amber99_18 0.07180 31
O3' amber99_43 -0.65490 32
H3T amber99_25 0.43960 33
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 C7
C5 C4
C7 H71
C7 H72
C7 H73
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 C7 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C7 H71 proper_HC_CT_CM_CM
C6 C5 C7 H72 proper_HC_CT_CM_CM
C6 C5 C7 H73 proper_HC_CT_CM_CM
H6 C6 C5 C7 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
C7 C5 C4 O4 proper_X_C_CM_X
C7 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
C4 C6 C5 C7
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ DTN ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 0.06800 9
H1' amber99_20 0.18040 10
N1 amber99_40 -0.02390 11
C6 amber99_7 -0.22090 12
H6 amber99_23 0.26070 13
C5 amber99_7 0.00250 14
C7 amber99_11 -0.22690 15
H71 amber99_18 0.07700 16
H72 amber99_18 0.07700 17
H73 amber99_18 0.07700 18
C4 amber99_2 0.51940 19
O4 amber99_41 -0.55630 20
N3 amber99_35 -0.43400 21
H3 amber99_17 0.34200 22
C2 amber99_2 0.56770 23
O amber99_41 -0.58810 24
C3' amber99_11 0.07130 25
H3' amber99_19 0.09850 26
C2' amber99_11 -0.08540 27
H2'1 amber99_18 0.07180 28
H2'2 amber99_18 0.07180 29
O3' amber99_43 -0.65490 30
H3T amber99_25 0.43960 31
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 C7
C5 C4
C7 H71
C7 H72
C7 H73
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 C7 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C7 H71 proper_HC_CT_CM_CM
C6 C5 C7 H72 proper_HC_CT_CM_CM
C6 C5 C7 H73 proper_HC_CT_CM_CM
H6 C6 C5 C7 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
C7 C5 C4 O4 proper_X_C_CM_X
C7 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
[ impropers ]
C6 C2 N1 C1'
C6 C4 C5 C7
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ RU5 ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.06740 9
H1' amber99_20 0.18240 10
N1 amber99_40 0.04180 11
C6 amber99_7 -0.11260 12
H6 amber99_23 0.21880 13
C5 amber99_7 -0.36350 14
H5 amber99_22 0.18110 15
C4 amber99_2 0.59520 16
O4 amber99_41 -0.57610 17
N3 amber99_35 -0.35490 18
H3 amber99_17 0.31540 19
C2 amber99_2 0.46870 20
O amber99_41 -0.54770 21
C3' amber99_11 0.20220 22
H3' amber99_19 0.06150 23
C2' amber99_11 0.06700 24
H2'1 amber99_19 0.09720 25
O2' amber99_43 -0.61390 26
HO'2 amber99_25 0.41860 27
O3' amber99_44 -0.52460 28
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
H5 C5 C4 O4 proper_X_C_CM_X
H5 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C6 C2 N1 C1'
C6 C4 C5 H5
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ RU ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.06740 11
H1' amber99_20 0.18240 12
N1 amber99_40 0.04180 13
C6 amber99_7 -0.11260 14
H6 amber99_23 0.21880 15
C5 amber99_7 -0.36350 16
H5 amber99_22 0.18110 17
C4 amber99_2 0.59520 18
O4 amber99_41 -0.57610 19
N3 amber99_35 -0.35490 20
H3 amber99_17 0.31540 21
C2 amber99_2 0.46870 22
O amber99_41 -0.54770 23
C3' amber99_11 0.20220 24
H3' amber99_19 0.06150 25
C2' amber99_11 0.06700 26
H2'1 amber99_19 0.09720 27
O2' amber99_43 -0.61390 28
HO'2 amber99_25 0.41860 29
O3' amber99_44 -0.52460 30
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
H5 C5 C4 O4 proper_X_C_CM_X
H5 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
C6 C4 C5 H5
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ RU3 ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.06740 11
H1' amber99_20 0.18240 12
N1 amber99_40 0.04180 13
C6 amber99_7 -0.11260 14
H6 amber99_23 0.21880 15
C5 amber99_7 -0.36350 16
H5 amber99_22 0.18110 17
C4 amber99_2 0.59520 18
O4 amber99_41 -0.57610 19
N3 amber99_35 -0.35490 20
H3 amber99_17 0.31540 21
C2 amber99_2 0.46870 22
O amber99_41 -0.54770 23
C3' amber99_11 0.20220 24
H3' amber99_19 0.06150 25
C2' amber99_11 0.06700 26
H2'1 amber99_19 0.09720 27
O2' amber99_43 -0.61390 28
HO'2 amber99_25 0.41860 29
O3' amber99_43 -0.65410 30
H3T amber99_25 0.43760 31
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
H5 C5 C4 O4 proper_X_C_CM_X
H5 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
C6 C4 C5 H5
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ RUN ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.06740 9
H1' amber99_20 0.18240 10
N1 amber99_40 0.04180 11
C6 amber99_7 -0.11260 12
H6 amber99_23 0.21880 13
C5 amber99_7 -0.36350 14
H5 amber99_22 0.18110 15
C4 amber99_2 0.59520 16
O4 amber99_41 -0.57610 17
N3 amber99_35 -0.35490 18
H3 amber99_17 0.31540 19
C2 amber99_2 0.46870 20
O amber99_41 -0.54770 21
C3' amber99_11 0.20220 22
H3' amber99_19 0.06150 23
C2' amber99_11 0.06700 24
H2'1 amber99_19 0.09720 25
O2' amber99_43 -0.61390 26
HO'2 amber99_25 0.41860 27
O3' amber99_43 -0.65410 28
H3T amber99_25 0.43760 29
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 O4
C4 N3
N3 H3
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
C5 C4 N3 H3 proper_X_C_NA_X
C5 C4 N3 C2 proper_X_C_NA_X
C4 N3 C2 N1 proper_X_C_NA_X
C4 N3 C2 O proper_X_C_NA_X
O4 C4 N3 H3 proper_X_C_NA_X
O4 C4 N3 C2 proper_X_C_NA_X
H3 N3 C2 N1 proper_X_C_NA_X
H3 N3 C2 O proper_X_C_NA_X
H5 C5 C4 O4 proper_X_C_CM_X
H5 C5 C4 N3 proper_X_C_CM_X
C6 C5 C4 O4 proper_CM_CM_C_O
C6 C5 C4 N3 proper_X_C_CM_X
O5' C5' C4' H4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
H3' C3' C2' O2' proper_H_CT_CT_O
[ impropers ]
C6 C2 N1 C1'
C6 C4 C5 H5
N1 N3 C2 O
C5 N3 C4 O4
C4 C2 N3 H3 nucleic_imp_10
N1 C5 C6 H6
[ DG5 ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 0.03580 9
H1' amber99_20 0.17460 10
N9 amber99_40 0.05770 11
C8 amber99_6 0.07360 12
H8 amber99_24 0.19970 13
N7 amber99_36 -0.57250 14
C5 amber99_4 0.19910 15
C6 amber99_2 0.49180 16
O6 amber99_41 -0.56990 17
N1 amber99_35 -0.50530 18
H1 amber99_17 0.35200 19
C2 amber99_3 0.74320 20
N2 amber99_38 -0.92300 21
H21 amber99_17 0.42350 22
H22 amber99_17 0.42350 23
N3 amber99_37 -0.66360 24
C4 amber99_4 0.18140 25
C3' amber99_11 0.07130 26
H3' amber99_19 0.09850 27
C2' amber99_11 -0.08540 28
H2'1 amber99_18 0.07180 29
H2'2 amber99_18 0.07180 30
O3' amber99_44 -0.52320 31
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C8 C4 N9 C1'
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N1 N3 C2 N2
[ DG ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 0.03580 11
H1' amber99_20 0.17460 12
N9 amber99_40 0.05770 13
C8 amber99_6 0.07360 14
H8 amber99_24 0.19970 15
N7 amber99_36 -0.57250 16
C5 amber99_4 0.19910 17
C6 amber99_2 0.49180 18
O6 amber99_41 -0.56990 19
N1 amber99_35 -0.50530 20
H1 amber99_17 0.35200 21
C2 amber99_3 0.74320 22
N2 amber99_38 -0.92300 23
H21 amber99_17 0.42350 24
H22 amber99_17 0.42350 25
N3 amber99_37 -0.66360 26
C4 amber99_4 0.18140 27
C3' amber99_11 0.07130 28
H3' amber99_19 0.09850 29
C2' amber99_11 -0.08540 30
H2'1 amber99_18 0.07180 31
H2'2 amber99_18 0.07180 32
O3' amber99_44 -0.52320 33
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N2 N1 C2 N3 nucleic_imp_11
[ DG3 ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 0.03580 11
H1' amber99_20 0.17460 12
N9 amber99_40 0.05770 13
C8 amber99_6 0.07360 14
H8 amber99_24 0.19970 15
N7 amber99_36 -0.57250 16
C5 amber99_4 0.19910 17
C6 amber99_2 0.49180 18
O6 amber99_41 -0.56990 19
N1 amber99_35 -0.50530 20
H1 amber99_17 0.35200 21
C2 amber99_3 0.74320 22
N2 amber99_38 -0.92300 23
H21 amber99_17 0.42350 24
H22 amber99_17 0.42350 25
N3 amber99_37 -0.66360 26
C4 amber99_4 0.18140 27
C3' amber99_11 0.07130 28
H3' amber99_19 0.09850 29
C2' amber99_11 -0.08540 30
H2'1 amber99_18 0.07180 31
H2'2 amber99_18 0.07180 32
O3' amber99_43 -0.65490 33
H3T amber99_25 0.43960 34
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N2 N1 C2 N3 nucleic_imp_11
[ DGN ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 0.03580 9
H1' amber99_20 0.17460 10
N9 amber99_40 0.05770 11
C8 amber99_6 0.07360 12
H8 amber99_24 0.19970 13
N7 amber99_36 -0.57250 14
C5 amber99_4 0.19910 15
C6 amber99_2 0.49180 16
O6 amber99_41 -0.56990 17
N1 amber99_35 -0.50530 18
H1 amber99_17 0.35200 19
C2 amber99_3 0.74320 20
N2 amber99_38 -0.92300 21
H21 amber99_17 0.42350 22
H22 amber99_17 0.42350 23
N3 amber99_37 -0.66360 24
C4 amber99_4 0.18140 25
C3' amber99_11 0.07130 26
H3' amber99_19 0.09850 27
C2' amber99_11 -0.08540 28
H2'1 amber99_18 0.07180 29
H2'2 amber99_18 0.07180 30
O3' amber99_43 -0.65490 31
H3T amber99_25 0.43960 32
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
[ impropers ]
C8 C4 N9 C1'
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N1 N3 C2 N2
[ RG5 ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.01910 9
H1' amber99_20 0.20060 10
N9 amber99_40 0.04920 11
C8 amber99_6 0.13740 12
H8 amber99_24 0.16400 13
N7 amber99_36 -0.57090 14
C5 amber99_4 0.17440 15
C6 amber99_2 0.47700 16
O6 amber99_41 -0.55970 17
N1 amber99_35 -0.47870 18
H1 amber99_17 0.34240 19
C2 amber99_3 0.76570 20
N2 amber99_38 -0.96720 21
H21 amber99_17 0.43640 22
H22 amber99_17 0.43640 23
N3 amber99_37 -0.63230 24
C4 amber99_4 0.12220 25
C3' amber99_11 0.20220 26
H3' amber99_19 0.06150 27
C2' amber99_11 0.06700 28
H2'1 amber99_19 0.09720 29
O2' amber99_43 -0.61390 30
HO'2 amber99_25 0.41860 31
O3' amber99_44 -0.52460 32
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C8 C4 N9 C1'
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N1 N3 C2 N2
[ RG ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.01910 11
H1' amber99_20 0.20060 12
N9 amber99_40 0.04920 13
C8 amber99_6 0.13740 14
H8 amber99_24 0.16400 15
N7 amber99_36 -0.57090 16
C5 amber99_4 0.17440 17
C6 amber99_2 0.47700 18
O6 amber99_41 -0.55970 19
N1 amber99_35 -0.47870 20
H1 amber99_17 0.34240 21
C2 amber99_3 0.76570 22
N2 amber99_38 -0.96720 23
H21 amber99_17 0.43640 24
H22 amber99_17 0.43640 25
N3 amber99_37 -0.63230 26
C4 amber99_4 0.12220 27
C3' amber99_11 0.20220 28
H3' amber99_19 0.06150 29
C2' amber99_11 0.06700 30
H2'1 amber99_19 0.09720 31
O2' amber99_43 -0.61390 32
HO'2 amber99_25 0.41860 33
O3' amber99_44 -0.52460 34
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N2 N1 C2 N3 nucleic_imp_11
[ RG3 ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.01910 11
H1' amber99_20 0.20060 12
N9 amber99_40 0.04920 13
C8 amber99_6 0.13740 14
H8 amber99_24 0.16400 15
N7 amber99_36 -0.57090 16
C5 amber99_4 0.17440 17
C6 amber99_2 0.47700 18
O6 amber99_41 -0.55970 19
N1 amber99_35 -0.47870 20
H1 amber99_17 0.34240 21
C2 amber99_3 0.76570 22
N2 amber99_38 -0.96720 23
H21 amber99_17 0.43640 24
H22 amber99_17 0.43640 25
N3 amber99_37 -0.63230 26
C4 amber99_4 0.12220 27
C3' amber99_11 0.20220 28
H3' amber99_19 0.06150 29
C2' amber99_11 0.06700 30
H2'1 amber99_19 0.09720 31
O2' amber99_43 -0.61390 32
HO'2 amber99_25 0.41860 33
O3' amber99_43 -0.65410 34
H3T amber99_25 0.43760 35
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
H8 C8 N9 C4 proper_X_CK_N*_X
N7 C8 N9 C4 proper_X_CK_N*_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C4 C8 N9 C1' nucleic_imp_10
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N2 N1 C2 N3 nucleic_imp_11
[ RGN ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.01910 9
H1' amber99_20 0.20060 10
N9 amber99_40 0.04920 11
C8 amber99_6 0.13740 12
H8 amber99_24 0.16400 13
N7 amber99_36 -0.57090 14
C5 amber99_4 0.17440 15
C6 amber99_2 0.47700 16
O6 amber99_41 -0.55970 17
N1 amber99_35 -0.47870 18
H1 amber99_17 0.34240 19
C2 amber99_3 0.76570 20
N2 amber99_38 -0.96720 21
H21 amber99_17 0.43640 22
H22 amber99_17 0.43640 23
N3 amber99_37 -0.63230 24
C4 amber99_4 0.12220 25
C3' amber99_11 0.20220 26
H3' amber99_19 0.06150 27
C2' amber99_11 0.06700 28
H2'1 amber99_19 0.09720 29
O2' amber99_43 -0.61390 30
HO'2 amber99_25 0.41860 31
O3' amber99_43 -0.65410 32
H3T amber99_25 0.43760 33
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N9
C1' C2'
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C5 C6
C5 C4
C6 O6
C6 N1
N1 H1
N1 C2
C2 N2
C2 N3
N2 H21
N2 H22
N3 C4
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N9 C4 proper_X_CT_N*_X
C1' N9 C8 H8 proper_X_CK_N*_X
C1' N9 C8 N7 proper_X_CK_N*_X
C1' N9 C4 C5 proper_X_CB_N*_X
C1' N9 C4 N3 proper_X_CB_N*_X
H1' C1' N9 C8 proper_X_CT_N*_X
H1' C1' N9 C4 proper_X_CT_N*_X
C8 N9 C4 C5 proper_X_CB_N*_X
C8 N9 C4 N3 proper_X_CB_N*_X
C5 C6 N1 H1 proper_X_C_NA_X
C5 C6 N1 C2 proper_X_C_NA_X
C6 N1 C2 N2 proper_X_CA_NA_X
C6 N1 C2 N3 proper_X_CA_NA_X
O6 C6 N1 H1 proper_X_C_NA_X
O6 C6 N1 C2 proper_X_C_NA_X
N1 C2 N3 C4 proper_X_CA_NC_X
H1 N1 C2 N2 proper_X_CA_NA_X
H1 N1 C2 N3 proper_X_CA_NA_X
N2 C2 N3 C4 proper_X_CA_NC_X
H8 C8 N7 C5 proper_X_CK_NB_X
N9 C8 N7 C5 proper_X_CK_NB_X
O5' C5' C4' H4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
H3' C3' C2' O2' proper_H_CT_CT_O
[ impropers ]
C8 C4 N9 C1'
C5 N1 C6 O6
C6 C2 N1 H1 nucleic_imp_10
C2 H21 N2 H22
N9 N7 C8 H8
N1 N3 C2 N2
[ DC5 ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 -0.01160 9
H1' amber99_20 0.19630 10
N1 amber99_40 -0.03390 11
C6 amber99_7 -0.01830 12
H6 amber99_23 0.22930 13
C5 amber99_7 -0.52220 14
H5 amber99_22 0.18630 15
C4 amber99_3 0.84390 16
N4 amber99_38 -0.97730 17
H41 amber99_17 0.43140 18
H42 amber99_17 0.43140 19
N3 amber99_37 -0.77480 20
C2 amber99_2 0.79590 21
O amber99_41 -0.65480 22
C3' amber99_11 0.07130 23
H3' amber99_19 0.09850 24
C2' amber99_11 -0.08540 25
H2'1 amber99_18 0.07180 26
H2'2 amber99_18 0.07180 27
O3' amber99_44 -0.52320 28
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C6 C2 N1 C1'
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
N3 C5 C4 N4
[ DC ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 -0.01160 11
H1' amber99_20 0.19630 12
N1 amber99_40 -0.03390 13
C6 amber99_7 -0.01830 14
H6 amber99_23 0.22930 15
C5 amber99_7 -0.52220 16
H5 amber99_22 0.18630 17
C4 amber99_3 0.84390 18
N4 amber99_38 -0.97730 19
H41 amber99_17 0.43140 20
H42 amber99_17 0.43140 21
N3 amber99_37 -0.77480 22
C2 amber99_2 0.79590 23
O amber99_41 -0.65480 24
C3' amber99_11 0.07130 25
H3' amber99_19 0.09850 26
C2' amber99_11 -0.08540 27
H2'1 amber99_18 0.07180 28
H2'2 amber99_18 0.07180 29
O3' amber99_44 -0.52320 30
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
C5 C4 N4 H41 proper_X_CA_N2_X
C5 C4 N4 H42 proper_X_CA_N2_X
H42 N4 C4 N3 proper_X_CA_N2_X
H41 N4 C4 N3 proper_X_CA_N2_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
C5 N4 C4 N3 nucleic_imp_11
[ DC3 ]
[ atoms ]
P amber99_46 1.16590 1
O1P amber99_45 -0.77610 2
O2P amber99_45 -0.77610 3
O5' amber99_44 -0.49540 4
C5' amber99_11 -0.00690 5
H5'1 amber99_19 0.07540 6
H5'2 amber99_19 0.07540 7
C4' amber99_11 0.16290 8
H4' amber99_19 0.11760 9
O4' amber99_44 -0.36910 10
C1' amber99_11 -0.01160 11
H1' amber99_20 0.19630 12
N1 amber99_40 -0.03390 13
C6 amber99_7 -0.01830 14
H6 amber99_23 0.22930 15
C5 amber99_7 -0.52220 16
H5 amber99_22 0.18630 17
C4 amber99_3 0.84390 18
N4 amber99_38 -0.97730 19
H41 amber99_17 0.43140 20
H42 amber99_17 0.43140 21
N3 amber99_37 -0.77480 22
C2 amber99_2 0.79590 23
O amber99_41 -0.65480 24
C3' amber99_11 0.07130 25
H3' amber99_19 0.09850 26
C2' amber99_11 -0.08540 27
H2'1 amber99_18 0.07180 28
H2'2 amber99_18 0.07180 29
O3' amber99_43 -0.65490 30
H3T amber99_25 0.43960 31
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
C5 C4 N4 H41 proper_X_CA_N2_X
C5 C4 N4 H42 proper_X_CA_N2_X
H42 N4 C4 N3 proper_X_CA_N2_X
H41 N4 C4 N3 proper_X_CA_N2_X
O4' C1' C2' H2'1 proper_H_CT_CT_O
O4' C1' C2' H2'2 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
C5 N4 C4 N3 nucleic_imp_11
[ DCN ]
[ atoms ]
H5T amber99_25 0.44220 1
O5' amber99_43 -0.63180 2
C5' amber99_11 -0.00690 3
H5'1 amber99_19 0.07540 4
H5'2 amber99_19 0.07540 5
C4' amber99_11 0.16290 6
H4' amber99_19 0.11760 7
O4' amber99_44 -0.36910 8
C1' amber99_11 -0.01160 9
H1' amber99_20 0.19630 10
N1 amber99_40 -0.03390 11
C6 amber99_7 -0.01830 12
H6 amber99_23 0.22930 13
C5 amber99_7 -0.52220 14
H5 amber99_22 0.18630 15
C4 amber99_3 0.84390 16
N4 amber99_38 -0.97730 17
H41 amber99_17 0.43140 18
H42 amber99_17 0.43140 19
N3 amber99_37 -0.77480 20
C2 amber99_2 0.79590 21
O amber99_41 -0.65480 22
C3' amber99_11 0.07130 23
H3' amber99_19 0.09850 24
C2' amber99_11 -0.08540 25
H2'1 amber99_18 0.07180 26
H2'2 amber99_18 0.07180 27
O3' amber99_43 -0.65490 28
H3T amber99_25 0.43960 29
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' H2'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
[ impropers ]
C6 C2 N1 C1'
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
N3 C5 C4 N4
[ RC5 ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.00660 9
H1' amber99_20 0.20290 10
N1 amber99_40 -0.04840 11
C6 amber99_7 0.00530 12
H6 amber99_23 0.19580 13
C5 amber99_7 -0.52150 14
H5 amber99_22 0.19280 15
C4 amber99_3 0.81850 16
N4 amber99_38 -0.95300 17
H41 amber99_17 0.42340 18
H42 amber99_17 0.42340 19
N3 amber99_37 -0.75840 20
C2 amber99_2 0.75380 21
O amber99_41 -0.62520 22
C3' amber99_11 0.20220 23
H3' amber99_19 0.06150 24
C2' amber99_11 0.06700 25
H2'1 amber99_19 0.09720 26
O2' amber99_43 -0.61390 27
HO'2 amber99_25 0.41860 28
O3' amber99_44 -0.52460 29
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C6 C2 N1 C1'
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
N3 C5 C4 N4
[ RC ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.00660 11
H1' amber99_20 0.20290 12
N1 amber99_40 -0.04840 13
C6 amber99_7 0.00530 14
H6 amber99_23 0.19580 15
C5 amber99_7 -0.52150 16
H5 amber99_22 0.19280 17
C4 amber99_3 0.81850 18
N4 amber99_38 -0.95300 19
H41 amber99_17 0.42340 20
H42 amber99_17 0.42340 21
N3 amber99_37 -0.75840 22
C2 amber99_2 0.75380 23
O amber99_41 -0.62520 24
C3' amber99_11 0.20220 25
H3' amber99_19 0.06150 26
C2' amber99_11 0.06700 27
H2'1 amber99_19 0.09720 28
O2' amber99_43 -0.61390 29
HO'2 amber99_25 0.41860 30
O3' amber99_44 -0.52460 31
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
H42 N4 C4 N3 proper_X_CA_N2_X
H41 N4 C4 N3 proper_X_CA_N2_X
C5 C4 N4 H41 proper_X_CA_N2_X
C5 C4 N4 H42 proper_X_CA_N2_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
O3' C3' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
C5 N4 C4 N3 nucleic_imp_11
[ RC3 ]
[ atoms ]
P amber99_46 1.16620 1
O1P amber99_45 -0.77600 2
O2P amber99_45 -0.77600 3
O5' amber99_44 -0.49890 4
C5' amber99_11 0.05580 5
H5'1 amber99_19 0.06790 6
H5'2 amber99_19 0.06790 7
C4' amber99_11 0.10650 8
H4' amber99_19 0.11740 9
O4' amber99_44 -0.35480 10
C1' amber99_11 0.00660 11
H1' amber99_20 0.20290 12
N1 amber99_40 -0.04840 13
C6 amber99_7 0.00530 14
H6 amber99_23 0.19580 15
C5 amber99_7 -0.52150 16
H5 amber99_22 0.19280 17
C4 amber99_3 0.81850 18
N4 amber99_38 -0.95300 19
H41 amber99_17 0.42340 20
H42 amber99_17 0.42340 21
N3 amber99_37 -0.75840 22
C2 amber99_2 0.75380 23
O amber99_41 -0.62520 24
C3' amber99_11 0.20220 25
H3' amber99_19 0.06150 26
C2' amber99_11 0.06700 27
H2'1 amber99_19 0.09720 28
O2' amber99_43 -0.61390 29
HO'2 amber99_25 0.41860 30
O3' amber99_43 -0.65410 31
H3T amber99_25 0.43760 32
[ bonds ]
P O1P
P O2P
P O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
H42 N4 C4 N3 proper_X_CA_N2_X
H41 N4 C4 N3 proper_X_CA_N2_X
C5 C4 N4 H41 proper_X_CA_N2_X
C5 C4 N4 H42 proper_X_CA_N2_X
H6 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 H6 proper_X_N*_CM_X
C5 C6 N1 C2 proper_X_N*_CM_X
C1' N1 C6 C5 proper_X_N*_CM_X
O5' C5' C4' H4' proper_H_CT_CT_O
H5'1 C5' C4' O4' proper_H_CT_CT_O
H5'2 C5' C4' O4' proper_H_CT_CT_O
O4' C4' C3' H3' proper_H_CT_CT_O
O4' C1' C2' H2'1 proper_H_CT_CT_O
[ impropers ]
C2 C6 N1 C1' nucleic_imp_10
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
C5 N4 C4 N3 nucleic_imp_11
[ RCN ]
[ atoms ]
H5T amber99_25 0.42950 1
O5' amber99_43 -0.62230 2
C5' amber99_11 0.05580 3
H5'1 amber99_19 0.06790 4
H5'2 amber99_19 0.06790 5
C4' amber99_11 0.10650 6
H4' amber99_19 0.11740 7
O4' amber99_44 -0.35480 8
C1' amber99_11 0.00660 9
H1' amber99_20 0.20290 10
N1 amber99_40 -0.04840 11
C6 amber99_7 0.00530 12
H6 amber99_23 0.19580 13
C5 amber99_7 -0.52150 14
H5 amber99_22 0.19280 15
C4 amber99_3 0.81850 16
N4 amber99_38 -0.95300 17
H41 amber99_17 0.42340 18
H42 amber99_17 0.42340 19
N3 amber99_37 -0.75840 20
C2 amber99_2 0.75380 21
O amber99_41 -0.62520 22
C3' amber99_11 0.20220 23
H3' amber99_19 0.06150 24
C2' amber99_11 0.06700 25
H2'1 amber99_19 0.09720 26
O2' amber99_43 -0.61390 27
HO'2 amber99_25 0.41860 28
O3' amber99_43 -0.65410 29
H3T amber99_25 0.43760 30
[ bonds ]
H5T O5'
O5' C5'
C5' H5'1
C5' H5'2
C5' C4'
C4' H4'
C4' O4'
C4' C3'
O4' C1'
C1' H1'
C1' N1
C1' C2'
N1 C6
N1 C2
C6 H6
C6 C5
C5 H5
C5 C4
C4 N4
C4 N3
N4 H41
N4 H42
N3 C2
C2 O
C3' H3'
C3' C2'
C3' O3'
C2' H2'1
C2' O2'
O2' HO'2
O3' H3T
-O3' P
[ dihedrals ]
O4' C1' N1 C2 proper_X_CT_N*_X
C1' N1 C2 N3 proper_X_C_N*_X
C1' N1 C2 O proper_X_C_N*_X
H1' C1' N1 C6 proper_X_CT_N*_X
H1' C1' N1 C2 proper_X_CT_N*_X
N1 C6 C5 H5 proper_X_CM_CM_X
N1 C6 C5 C4 proper_X_CM_CM_X
C6 N1 C2 N3 proper_X_C_N*_X
C6 N1 C2 O proper_X_C_N*_X
C6 C5 C4 N4 proper_X_CA_CM_X
C6 C5 C4 N3 proper_X_CA_CM_X
H6 C6 C5 H5 proper_X_CM_CM_X
H6 C6 C5 C4 proper_X_CM_CM_X
H5 C5 C4 N4 proper_X_CA_CM_X
H5 C5 C4 N3 proper_X_CA_CM_X
C4 N3 C2 N1 proper_X_C_NC_X
C4 N3 C2 O proper_X_C_NC_X
O5' C5' C4' H4' proper_H_CT_CT_O
H4' C4' C3' O3' proper_H_CT_CT_O
H3' C3' C2' O2' proper_H_CT_CT_O
[ impropers ]
C6 C2 N1 C1'
N1 N3 C2 O
C4 H41 N4 H42
N1 C5 C6 H6
C6 C4 C5 H5
N3 C5 C4 N4
distrib
>
Mandriva
>
2008.1
>
x86_64
>
media
>
contrib-release
>
by-pkgid
>
0300a44d46b1dcd30fdf6e83931f63bd
>
files
>
54
