/usr/share/gromacs/top/amber03.ff/aminoacids.rtp is in gromacs-data 5.0.2-1.
This file is owned by root:root, with mode 0o644.
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3422 3423 3424 | [ bondedtypes ]
; Column 1 : default bondtype
; Column 2 : default angletype
; Column 3 : default proper dihedraltype
; Column 4 : default improper dihedraltype
; Column 5 : This controls the generation of dihedrals from the bonding.
; All possible dihedrals are generated automatically. A value of
; 1 here means that all these are retained. A value of
; 0 here requires generated dihedrals be removed if
; * there are any dihedrals on the same central atoms
; specified in the residue topology, or
; * there are other identical generated dihedrals
; sharing the same central atoms, or
; * there are other generated dihedrals sharing the
; same central bond that have fewer hydrogen atoms
; Column 6 : number of neighbors to exclude from non-bonded interactions
; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
; 0 = do not generate such
; Column 8 : 1 = remove proper dihedrals if found centered on the same
; bond as an improper dihedral
; 0 = do not generate such
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 9 4 1 3 1 0
; now: water, ions, urea, terminal caps, AA's and terminal AA's
; tip3p
[ HOH ]
[ atoms ]
OW OW -0.834 0
HW1 HW 0.417 0
HW2 HW 0.417 0
[ bonds ]
OW HW1
OW HW2
; tip4p
[ HO4 ]
[ atoms ]
OW OW_tip4p 0.00 0
HW1 HW 0.52 0
HW2 HW 0.52 0
MW MW -1.04 0
[ bonds ]
OW HW1
OW HW2
[ IB+ ] ; big positive ion
[ atoms ]
IB IB 1.00000 1
[ CA ]
[ atoms ]
CA C0 2.00000 1
[ CL ]
[ atoms ]
CL Cl -1.00000 1
[ NA ]
[ atoms ]
NA Na 1.00000 1
[ MG ]
[ atoms ]
MG MG 2.00000 1
[ K ]
[ atoms ]
K K 1.00000 1
[ RB ]
[ atoms ]
RB Rb 1.00000 1
[ CS ]
[ atoms ]
CS Cs 1.00000 1
[ LI ]
[ atoms ]
LI Li 1.00000 1
[ ZN ]
[ atoms ]
ZN Zn 2.00000 1
[ URE ] ; urea added in by EJS, resp charges by Jim Caldwell
[ atoms ]
C C 0.880229 1
O O -0.613359 2
N1 N -0.923545 3
H11 H 0.395055 4
H12 H 0.395055 5
N2 N -0.923545 6
H21 H 0.395055 7
H22 H 0.395055 8
[ bonds ]
C N1
C N2
C O
N1 H11
N1 H12
N2 H21
N2 H22
[ impropers ]
N1 N2 C O
C H11 N1 H12
C H21 N2 H22
[ ACE ]
[ atoms ]
HH31 HC 0.076010 1
CH3 CT -0.190264 2
HH32 HC 0.076011 3
HH33 HC 0.076010 4
C C 0.512403 5
O O -0.550170 6
[ bonds ]
HH31 CH3
CH3 HH32
CH3 HH33
CH3 C
C O
[ impropers ]
CH3 +N C O
[ NME ]
[ atoms ]
N N -0.423888 1
H H 0.290111 2
CH3 CT -0.054293 3
HH31 H1 0.062690 4
HH32 H1 0.062690 5
HH33 H1 0.062690 6
[ bonds ]
N H
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
-C N
[ impropers ]
-C CH3 N H
[ NHE ]
[ atoms ]
N N -0.46300 1
H1 H 0.23150 2
H2 H 0.23150 3
[ bonds ]
N H1
N H2
-C N
[ impropers ]
-C H1 N H2
[ NH2 ]
[ atoms ]
N N -0.46300 1
H1 H 0.23150 2
H2 H 0.23150 3
[ bonds ]
N H1
N H2
-C N
[ impropers ]
-C H1 N H2
; Next are non-terminal AA's
[ ALA ]
[ atoms ]
N N -0.404773 1
H H 0.294276 2
CA CT -0.027733 3
HA H1 0.120802 4
CB CT -0.229951 5
HB1 HC 0.077428 6
HB2 HC 0.077428 7
HB3 HC 0.077428 8
C C 0.570224 9
O O -0.555129 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
[ GLY ] ; HAx atoms assigned new ff03 atom type
[ atoms ]
N N -0.374282 1
H H 0.253981 2
CA CT -0.128844 3
HA1 H0 0.088859 4
HA2 H0 0.088859 5
C C 0.580584 6
O O -0.509157 7
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C O
-C N
[ dihedrals ]
CA C +N +H
O C +N +H
-C N CA CB
-C N CA C
CA C +N +CA
O C +N +CA
-C N CA HA1
-C N CA HA2
HA1 CA C +N
HA2 CA C +N
[ impropers ]
-C CA N H
CA +N C O
[ SER ]
[ atoms ]
N N -0.541430 1
H H 0.345415 2
CA CT 0.118140 3
HA H1 0.142177 4
CB CT 0.146998 5
HB1 H1 0.040081 6
HB2 H1 0.040081 7
OG OH -0.640312 8
HG HO 0.446255 9
C C 0.483424 10
O O -0.580829 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
[ THR ]
[ atoms ]
N N -0.245382 1
H H 0.255339 2
CA CT -0.271249 3
HA H1 0.163757 4
CB CT 0.237868 5
HB H1 0.044688 6
CG2 CT -0.176489 7
HG21 HC 0.060019 8
HG22 HC 0.060019 9
HG23 HC 0.060019 10
OG1 OH -0.601931 11
HG1 HO 0.405484 12
C C 0.559878 13
O O -0.552020 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
[ impropers ]
-C CA N H
CA +N C O
[ LEU ]
[ atoms ]
N N -0.355153 1
H H 0.262417 2
CA CT -0.101497 3
HA H1 0.136951 4
CB CT -0.144399 5
HB1 HC 0.052533 6
HB2 HC 0.052533 7
CG CT 0.191982 8
HG HC 0.000825 9
CD1 CT -0.123036 10
HD11 HC 0.022376 11
HD12 HC 0.022376 12
HD13 HC 0.022376 13
CD2 CT -0.123036 14
HD21 HC 0.022376 15
HD22 HC 0.022376 16
HD23 HC 0.022376 17
C C 0.573471 18
O O -0.557847 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
[ impropers ]
-C CA N H
CA +N C O
[ ILE ]
[ atoms ]
N N -0.451047 1
H H 0.328831 2
CA CT -0.101874 3
HA H1 0.174193 4
CB CT 0.062238 5
HB HC 0.061662 6
CG2 CT -0.129989 7
HG21 HC 0.030227 8
HG22 HC 0.030227 9
HG23 HC 0.030227 10
CG1 CT 0.022230 11
HG11 HC 0.011551 12
HG12 HC 0.011551 13
CD CT -0.101251 14
HD1 HC 0.023792 15
HD2 HC 0.023792 16
HD3 HC 0.023792 17
C C 0.569383 18
O O -0.619535 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
[ impropers ]
-C CA N H
CA +N C O
[ VAL ]
[ atoms ]
N N -0.450087 1
H H 0.440048 2
CA CT -0.051858 3
HA H1 -0.026204 4
CB CT 0.395217 5
HB HC -0.115672 6
CG1 CT -0.090132 7
HG11 HC -0.008985 8
HG12 HC -0.008985 9
HG13 HC -0.008985 10
CG2 CT -0.090132 11
HG21 HC -0.008985 12
HG22 HC -0.008985 13
HG23 HC -0.008985 14
C C 0.447359 15
O O -0.404629 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
[ impropers ]
-C CA N H
CA +N C O
[ ASN ]
[ atoms ]
N N -0.430106 1
H H 0.254543 2
CA CT 0.044609 3
HA H1 0.059601 4
CB CT -0.093650 5
HB1 HC 0.043321 6
HB2 HC 0.043321 7
CG C 0.583519 8
OD1 O -0.526813 9
ND2 N -0.781735 10
HD21 H 0.355079 11
HD22 H 0.355079 12
C C 0.617141 13
O O -0.523909 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
[ impropers ]
-C CA N H
CA +N C O
CB ND2 CG OD1
CG HD21 ND2 HD22
[ GLN ]
[ atoms ]
N N -0.387353 1
H H 0.300605 2
CA CT 0.037470 3
HA H1 0.152255 4
CB CT -0.032112 5
HB1 HC 0.030995 6
HB2 HC 0.030995 7
CG CT -0.020264 8
HG1 HC 0.030791 9
HG2 HC 0.030791 10
CD C 0.667812 11
OE1 O -0.628483 12
NE2 N -0.883393 13
HE21 H 0.408312 14
HE22 H 0.408312 15
C C 0.418577 16
O O -0.565310 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
[ impropers ]
-C CA N H
CA +N C O
CG NE2 CD OE1
CD HE21 NE2 HE22
[ ARG ]
[ atoms ]
N N -0.300879 1
H H 0.233693 2
CA CT -0.131381 3
HA H1 0.053266 4
CB CT 0.036707 5
HB1 HC 0.028012 6
HB2 HC 0.028012 7
CG CT 0.012454 8
HG1 HC 0.002964 9
HG2 HC 0.002964 10
CD CT 0.126329 11
HD1 H1 0.068148 12
HD2 H1 0.068148 13
NE N2 -0.464890 14
HE H 0.326274 15
CZ CA 0.565543 16
NH1 N2 -0.685774 17
HH11 H 0.391052 18
HH12 H 0.391052 19
NH2 N2 -0.685774 20
HH21 H 0.391052 21
HH22 H 0.391052 22
C C 0.730308 23
O O -0.578332 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
[ 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 N -0.506799 1
H H 0.351021 2
CA CT 0.119066 3
HA H1 0.137761 4
CB CT -0.122638 5
HB1 HC 0.086329 6
HB2 HC 0.086329 7
CG CC -0.001547 8
ND1 NA -0.205785 9
HD1 H 0.318273 10
CE1 CR 0.147273 11
HE1 H5 0.122182 12
NE2 NB -0.601482 13
CD2 CV 0.043744 14
HD2 H4 0.110157 15
C C 0.515947 16
O O -0.599831 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
[ 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 N -0.528120 1
H H 0.281695 2
CA CT 0.031249 3
HA H1 0.085175 4
CB CT -0.152267 5
HB1 HC 0.054608 6
HB2 HC 0.054608 7
CG CC 0.278406 8
ND1 NB -0.423316 9
CE1 CR 0.025960 10
HE1 H5 0.126832 11
NE2 NA -0.097984 12
HE2 H 0.266865 13
CD2 CW -0.297563 14
HD2 H4 0.160413 15
C C 0.662405 16
O O -0.528966 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
[ 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 N -0.150599 1
H H 0.174903 2
CA CT -0.139355 3
HA H1 0.103647 4
CB CT -0.105724 5
HB1 HC 0.102146 6
HB2 HC 0.102146 7
CG CC 0.051128 8
ND1 NA 0.002100 9
HD1 H 0.258443 10
CE1 CR -0.033333 11
HE1 H5 0.218884 12
NE2 NA -0.140978 13
HE2 H 0.353373 14
CD2 CW -0.143848 15
HD2 H4 0.213519 16
C C 0.675645 17
O O -0.542097 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
[ 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 N -0.427579 1
H H 0.241716 2
CA CT -0.020082 3
HA H1 0.106629 4
CB CT -0.098364 5
HB1 HC 0.065424 6
HB2 HC 0.065424 7
CG C* -0.099797 8
CD1 CW -0.174053 9
HD1 H4 0.170633 10
NE1 NA -0.298433 11
HE1 H 0.322375 12
CE2 CN 0.141523 13
CZ2 CA -0.210701 14
HZ2 HA 0.125512 15
CH2 CA -0.133022 16
HH2 HA 0.119467 17
CZ3 CA -0.164054 18
HZ3 HA 0.119250 19
CE3 CA -0.153992 20
HE3 HA 0.123084 21
CD2 CB 0.089641 22
C C 0.584129 23
O O -0.494730 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
[ 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 CG CB CD2
[ PHE ]
[ atoms ]
N N -0.371290 1
H H 0.234053 2
CA CT -0.030057 3
HA H1 0.102448 4
CB CT -0.098720 5
HB1 HC 0.060989 6
HB2 HC 0.060989 7
CG CA 0.021313 8
CD1 CA -0.083109 9
HD1 HA 0.098466 10
CE1 CA -0.156974 11
HE1 HA 0.123731 12
CZ CA -0.099824 13
HZ HA 0.114679 14
CE2 CA -0.156974 15
HE2 HA 0.123731 16
CD2 CA -0.083109 17
HD2 HA 0.098466 18
C C 0.547987 19
O O -0.506795 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
[ 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 N -0.487560 1
H H 0.263521 2
CA CT 0.009614 3
HA H1 0.095501 4
CB CT -0.051853 5
HB1 HC 0.019145 6
HB2 HC 0.019145 7
CG CA 0.112601 8
CD1 CA -0.183461 9
HD1 HA 0.132715 10
CE1 CA -0.181823 11
HE1 HA 0.137303 12
CZ C 0.206277 13
OH OH -0.421233 14
HH HO 0.329691 15
CE2 CA -0.181823 16
HE2 HA 0.137303 17
CD2 CA -0.183461 18
HD2 HA 0.132715 19
C C 0.622290 20
O O -0.526607 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
[ 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 N -0.423392 1
H H 0.306811 2
CA CT 0.031633 3
HA H1 0.065100 4
CB CT 0.074772 5
HB1 HC -0.003535 6
HB2 HC -0.003535 7
CG CT -0.033909 8
HG1 HC -0.004135 9
HG2 HC -0.004135 10
CD C 0.765188 11
OE1 O2 -0.824035 12
OE2 O2 -0.824035 13
C C 0.469735 14
O O -0.592528 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
[ impropers ]
-C CA N H
CA +N C O
CG OE1 CD OE2
[ ASP ]
[ atoms ]
N N -0.558201 1
H H 0.319676 2
CA CT 0.007225 3
HA H1 0.082375 4
CB CT -0.047555 5
HB1 HC -0.014836 6
HB2 HC -0.014836 7
CG C 0.745168 8
OD1 O2 -0.730385 9
OD2 O2 -0.730385 10
C C 0.443199 11
O O -0.501445 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
[ impropers ]
-C CA N H
CA +N C O
CB OD1 CG OD2
[ LYS ]
[ atoms ]
N N -0.435875 1
H H 0.251302 2
CA CT -0.038773 3
HA H1 0.129478 4
CB CT -0.108273 5
HB1 HC 0.045214 6
HB2 HC 0.045214 7
CG CT 0.033341 8
HG1 HC 0.010208 9
HG2 HC 0.010208 10
CD CT -0.047841 11
HD1 HC 0.070715 12
HD2 HC 0.070715 13
CE CT -0.069974 14
HE1 HP 0.119522 15
HE2 HP 0.119522 16
NZ N3 -0.250358 17
HZ1 H 0.294561 18
HZ2 H 0.294561 19
HZ3 H 0.294561 20
C C 0.725129 21
O O -0.563157 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
[ impropers ]
-C CA N H
CA +N C O
[ ORN ] ; charges taken from amber99.prm of tinker 4.0
[ atoms ]
N N -0.34790 1
H H 0.27470 2
CA CT -0.24000 3
HA H1 0.14260 4
CB CT 0.00990 5
HB1 HC 0.03620 6
HB2 HC 0.03620 7
CG CT -0.02790 8
HG1 HC 0.06210 9
HG2 HC 0.06210 10
CD CT -0.01430 11
HD1 HP 0.11350 12
HD2 HP 0.11350 13
NE N3 -0.38540 14
HE1 H 0.34000 15
HE2 H 0.34000 16
HE3 H 0.34000 17
C C 0.73410 18
O O -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
[ 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 N -0.34790 1
H H 0.27470 2
CA CT -0.24000 3
HA H1 0.14260 4
CB CT 0.02920 5
HB1 HC 0.07470 6
HB2 HC 0.07470 7
CG CT -0.01430 8
HG1 HP 0.11350 9
HG2 HP 0.11350 10
ND N3 -0.38540 11
HD1 H 0.34000 12
HD2 H 0.34000 13
HD3 H 0.34000 14
C C 0.73410 15
O O -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
[ impropers ]
-C CA N H
CA +N C O
[ LYN ]
[ atoms ]
N N -0.415700 1
H H 0.271900 2
CA CT -0.072060 3
HA H1 0.099400 4
CB CT -0.048450 5
HB1 HC 0.034000 6
HB2 HC 0.034000 7
CG CT 0.066120 8
HG1 HC 0.010410 9
HG2 HC 0.010410 10
CD CT -0.037680 11
HD1 HC 0.011550 12
HD2 HC 0.011550 13
CE CT 0.326040 14
HE1 HP -0.033580 15
HE2 HP -0.033580 16
NZ N3 -1.035810 17
HZ1 H 0.386040 18
HZ2 H 0.386040 19
C C 0.597300 20
O O -0.567900 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
[ impropers ]
-C CA N H
CA +N C O
[ PRO ]
[ atoms ]
N N -0.088116 1
CD CT -0.011906 2
HD1 H1 0.043951 3
HD2 H1 0.043950 4
CG CT 0.013059 5
HG1 HC 0.019574 6
HG2 HC 0.019574 7
CB CT -0.003351 8
HB1 HC 0.019352 9
HB2 HC 0.019352 10
CA CT -0.034577 11
HA H1 0.059977 12
C C 0.333720 13
O O -0.434559 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
[ impropers ]
CA +N C O
-C CD N CA
[ HYP ] ; S Park, R J Radmer, T E Klein & V S Pande (submitted).
[ atoms ]
N N -0.25480 1
CD2 CT 0.05950 2
HD21 H1 0.07000 3
HD22 H1 0.07000 4
CG CT 0.04000 5
HG H1 0.04160 6
OD1 OH -0.61340 7
HD1 HO 0.38510 8
CB CT 0.02030 9
HB1 HC 0.04260 10
HB2 HC 0.04260 11
CA CT 0.00470 12
HA H1 0.07700 13
C C 0.58960 14
O O -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
[ impropers ]
CA +N C O
-C CD2 N CA
[ CYS ]
[ atoms ]
N N -0.396165 1
H H 0.295187 2
CA CT -0.073501 3
HA H1 0.140510 4
CB CT -0.221371 5
HB1 H1 0.146537 6
HB2 H1 0.146537 7
SG SH -0.285182 8
HG HS 0.189274 9
C C 0.643035 10
O O -0.584861 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
[ CYM ]
[ atoms ]
N N -0.415700 1
H H 0.271900 2
CA CT -0.035100 3
HA H1 0.050800 4
CB CT -0.241300 5
HB1 H1 0.112200 6
HB2 H1 0.112200 7
SG SH -0.884400 8
C C 0.597300 9
O O -0.567900 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
[ CYX ]
[ atoms ]
N N -0.435921 1
H H 0.290077 2
CA CT -0.030547 3
HA H1 0.132146 4
CB CT -0.033006 5
HB1 H1 0.078951 6
HB2 H1 0.078951 7
SG S -0.132272 8
C C 0.624788 9
O O -0.573167 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
[ MET ]
[ atoms ]
N N -0.394918 1
H H 0.280537 2
CA CT -0.087681 3
HA H1 0.123080 4
CB CT 0.019227 5
HB1 HC 0.048840 6
HB2 HC 0.048840 7
CG CT -0.208167 8
HG1 H1 0.124228 9
HG2 H1 0.124228 10
SD S -0.211958 11
CE CT -0.284698 12
HE1 H1 0.128394 13
HE2 H1 0.128394 14
HE3 H1 0.128394 15
C C 0.599684 16
O O -0.566424 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
[ impropers ]
-C CA N H
CA +N C O
; non-terminal acidic AA's
[ ASH ]
[ atoms ]
N N -0.392069 1
H H 0.282413 2
CA CT -0.035317 3
HA H1 0.094292 4
CB CT -0.121405 5
HB1 HC 0.069032 6
HB2 HC 0.069032 7
CG C 0.678640 8
OD1 O -0.550940 9
OD2 OH -0.587163 10
HD2 HO 0.438035 11
C C 0.620495 12
O O -0.565045 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
[ impropers ]
-C CA N H
CA +N C O
CB OD1 CG OD2
[ GLH ]
[ atoms ]
N N -0.384536 1
H H 0.263963 2
CA CT -0.060898 3
HA H1 0.109620 4
CB CT -0.018753 5
HB1 HC 0.034966 6
HB2 HC 0.034966 7
CG CT -0.038364 8
HG1 HC 0.048444 9
HG2 HC 0.048444 10
CD C 0.638937 11
OE1 O -0.559031 12
OE2 OH -0.588722 13
HE2 HO 0.447661 14
C C 0.587056 15
O O -0.563753 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
[ impropers ]
-C CA N H
CA +N C O
CG OE1 CD OE2
; C-terminal AA's
[ CALA ]
[ atoms ]
N N -0.622202 1
H H 0.359784 2
CA CT -0.054102 3
HA H1 0.123283 4
CB CT -0.185718 5
HB1 HC 0.069652 6
HB2 HC 0.069652 7
HB3 HC 0.069652 8
C C 0.664014 9
OC1 O2 -0.747007 10
OC2 O2 -0.747007 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C OC1
C OC2
-C N
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CGLY ]
[ atoms ]
N N -0.523362 1
H H 0.349622 2
CA CT -0.316659 3
HA1 H1 0.160200 4
HA2 H1 0.160200 5
C C 0.661797 6
OC1 O2 -0.745899 7
OC2 O2 -0.745899 8
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C OC1
C OC2
-C N
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CSER ]
[ atoms ]
N N -0.676281 1
H H 0.369239 2
CA CT -0.072385 3
HA H1 0.158185 4
CB CT 0.132964 5
HB1 H1 0.048008 6
HB2 H1 0.048008 7
OG OH -0.580479 8
HG HO 0.402742 9
C C 0.594367 10
OC1 O2 -0.712184 11
OC2 O2 -0.712184 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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CTHR ]
[ atoms ]
N N -0.351668 1
H H 0.299320 2
CA CT -0.500569 3
HA H1 0.237658 4
CB CT 0.294422 5
HB H1 0.031148 6
CG2 CT -0.137163 7
HG21 HC 0.051258 8
HG22 HC 0.051258 9
HG23 HC 0.051258 10
OG1 OH -0.605568 11
HG1 HO 0.408646 12
C C 0.681669 13
OC1 O2 -0.755835 14
OC2 O2 -0.755835 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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CLEU ]
[ atoms ]
N N -0.556595 1
H H 0.338672 2
CA CT -0.229880 3
HA H1 0.190710 4
CB CT -0.102213 5
HB1 HC 0.054816 6
HB2 HC 0.054816 7
CG CT 0.195714 8
HG HC 0.005286 9
CD1 CT -0.136225 10
HD11 HC 0.025188 11
HD12 HC 0.025188 12
HD13 HC 0.025188 13
CD2 CT -0.136225 14
HD21 HC 0.025188 15
HD22 HC 0.025188 16
HD23 HC 0.025188 17
C C 0.598427 18
OC1 O2 -0.714214 19
OC2 O2 -0.714214 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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CILE ]
[ atoms ]
N N -0.509270 1
H H 0.314575 2
CA CT -0.227333 3
HA H1 0.143304 4
CB CT 0.044365 5
HB HC 0.064001 6
CG2 CT -0.162378 7
HG21 HC 0.040070 8
HG22 HC 0.040070 9
HG23 HC 0.040070 10
CG1 CT 0.058658 11
HG11 HC 0.008847 12
HG12 HC 0.008847 13
CD CT -0.101376 14
HD1 HC 0.022516 15
HD2 HC 0.022516 16
HD3 HC 0.022516 17
C C 0.671034 18
OC1 O2 -0.750517 19
OC2 O2 -0.750517 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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CVAL ]
[ atoms ]
N N -0.217054 1
H H 0.243122 2
CA CT -0.374120 3
HA H1 0.097720 4
CB CT 0.202309 5
HB HC -0.022953 6
CG1 CT -0.137796 7
HG11 HC 0.029428 8
HG12 HC 0.029428 9
HG13 HC 0.029428 10
CG2 CT -0.137796 11
HG21 HC 0.029428 12
HG22 HC 0.029428 13
HG23 HC 0.029428 14
C C 0.525616 15
OC1 O2 -0.677808 16
OC2 O2 -0.677808 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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CASN ]
[ atoms ]
N N -0.626530 1
H H 0.343242 2
CA CT 0.014405 3
HA H1 0.085796 4
CB CT -0.029468 5
HB1 HC 0.045738 6
HB2 HC 0.045738 7
CG C 0.551512 8
OD1 O -0.567440 9
ND2 N -0.766241 10
HD21 H 0.366624 11
HD22 H 0.366624 12
C C 0.607381 13
OC1 O2 -0.718691 14
OC2 O2 -0.718691 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
[ impropers ]
-C CA N H
CA OC1 C OC2
CB ND2 CG OD1
CG HD21 ND2 HD22
[ CGLN ]
[ atoms ]
N N -0.515135 1
H H 0.324299 2
CA CT -0.235630 3
HA H1 0.164628 4
CB CT 0.004813 5
HB1 HC 0.030788 6
HB2 HC 0.030788 7
CG CT -0.024848 8
HG1 HC 0.034840 9
HG2 HC 0.034840 10
CD C 0.662321 11
OE1 O -0.588799 12
NE2 N -0.883570 13
HE21 H 0.395334 14
HE22 H 0.395334 15
C C 0.600448 16
OC1 O2 -0.715224 17
OC2 O2 -0.715224 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
[ impropers ]
-C CA N H
CA OC1 C OC2
CG NE2 CD OE1
CD HE21 NE2 HE22
[ CARG ]
[ atoms ]
N N -0.495340 1
H H 0.313864 2
CA CT -0.122265 3
HA H1 0.093073 4
CB CT 0.015820 5
HB1 HC 0.040376 6
HB2 HC 0.040376 7
CG CT 0.013697 8
HG1 HC -0.001366 9
HG2 HC -0.001366 10
CD CT 0.183324 11
HD1 H1 0.048691 12
HD2 H1 0.048691 13
NE N2 -0.468682 14
HE H 0.343094 15
CZ CA 0.577784 16
NH1 N2 -0.712318 17
HH11 H 0.406216 18
HH12 H 0.406216 19
NH2 N2 -0.712318 20
HH21 H 0.406216 21
HH22 H 0.406216 22
C C 0.648763 23
OC1 O2 -0.739382 24
OC2 O2 -0.739382 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
[ 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 N -0.692510 1
H H 0.357784 2
CA CT 0.113471 3
HA H1 0.070490 4
CB CT -0.032237 5
HB1 HC 0.047858 6
HB2 HC 0.047858 7
CG CC -0.034691 8
ND1 NA -0.218767 9
HD1 H 0.294104 10
CE1 CR 0.152151 11
HE1 H5 0.108726 12
NE2 NB -0.552887 13
CD2 CV 0.073505 14
HD2 H4 0.095147 15
C C 0.622331 16
OC1 O2 -0.726166 17
OC2 O2 -0.726166 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
[ 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 N -0.678107 1
H H 0.378617 2
CA CT -0.045762 3
HA H1 0.135589 4
CB CT -0.088284 5
HB1 HC 0.068197 6
HB2 HC 0.068197 7
CG CC 0.197858 8
ND1 NB -0.476371 9
CE1 CR 0.048815 10
HE1 H5 0.126861 11
NE2 NA -0.084778 12
HE2 H 0.280364 13
CD2 CW -0.254856 14
HD2 H4 0.153659 15
C C 0.585209 16
OC1 O2 -0.707605 17
OC2 O2 -0.707605 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
[ 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 N -0.464193 1
H H 0.315351 2
CA CT -0.076871 3
HA H1 0.125219 4
CB CT -0.062807 5
HB1 HC 0.092794 6
HB2 HC 0.092794 7
CG CC 0.057843 8
ND1 NA -0.015072 9
HD1 H 0.276076 10
CE1 CR -0.033413 11
HE1 H5 0.226049 12
NE2 NA -0.129808 13
HE2 H 0.369253 14
CD2 CW -0.163636 15
HD2 H4 0.220420 16
C C 0.513757 17
OC1 O2 -0.671879 18
OC2 O2 -0.671879 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
[ 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 N -0.629974 1
H H 0.341228 2
CA CT -0.044250 3
HA H1 0.128436 4
CB CT -0.058372 5
HB1 HC 0.069590 6
HB2 HC 0.069590 7
CG C* -0.146344 8
CD1 CW -0.168076 9
HD1 H4 0.178686 10
NE1 NA -0.301970 11
HE1 H 0.344032 12
CE2 CN 0.143447 13
CZ2 CA -0.223194 14
HZ2 HA 0.136724 15
CH2 CA -0.137673 16
HH2 HA 0.122474 17
CZ3 CA -0.173223 18
HZ3 HA 0.121634 19
CE3 CA -0.187847 20
HE3 HA 0.143053 21
CD2 CB 0.102028 22
C C 0.615569 23
OC1 O2 -0.722785 24
OC2 O2 -0.722785 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
[ 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 CG CB CD2
[ CPHE ]
[ atoms ]
N N -0.625562 1
H H 0.349898 2
CA CT -0.088182 3
HA H1 0.134954 4
CB CT -0.057583 5
HB1 HC 0.064041 6
HB2 HC 0.064041 7
CG CA 0.007991 8
CD1 CA -0.098964 9
HD1 HA 0.112120 10
CE1 CA -0.161136 11
HE1 HA 0.128127 12
CZ CA -0.097375 13
HZ HA 0.117481 14
CE2 CA -0.161136 15
HE2 HA 0.128127 16
CD2 CA -0.098964 17
HD2 HA 0.112120 18
C C 0.595519 19
OC1 O2 -0.712760 20
OC2 O2 -0.712760 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
[ 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 N -0.675628 1
H H 0.350448 2
CA CT -0.012728 3
HA H1 0.146871 4
CB CT -0.058078 5
HB1 HC 0.016619 6
HB2 HC 0.016619 7
CG CA 0.133018 8
CD1 CA -0.194675 9
HD1 HA 0.149917 10
CE1 CA -0.218820 11
HE1 HA 0.148692 12
CZ C 0.247734 13
OH OH -0.475120 14
HH HO 0.370016 15
CE2 CA -0.218820 16
HE2 HA 0.148692 17
CD2 CA -0.194675 18
HD2 HA 0.149917 19
C C 0.665555 20
OC1 O2 -0.747778 21
OC2 O2 -0.747778 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
[ 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 N -0.748778 1
H H 0.396125 2
CA CT -0.133159 3
HA H1 0.105730 4
CB CT 0.185749 5
HB1 HC -0.045957 6
HB2 HC -0.045957 7
CG CT -0.033125 8
HG1 HC -0.011832 9
HG2 HC -0.011832 10
CD C 0.757964 11
OE1 O2 -0.792463 12
OE2 O2 -0.792463 13
C C 0.731186 14
OC1 O2 -0.780593 15
OC2 O2 -0.780593 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
[ impropers ]
-C CA N H
CA OC1 C OC2
CG OE1 CD OE2
[ CASP ]
[ atoms ]
N N -0.649462 1
H H 0.426853 2
CA CT -0.306286 3
HA H1 0.183181 4
CB CT -0.078986 5
HB1 HC 0.018648 6
HB2 HC 0.018648 7
CG C 0.844830 8
OD1 O2 -0.813714 9
OD2 O2 -0.813714 10
C C 0.732350 11
OC1 O2 -0.781175 12
OC2 O2 -0.781175 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
[ impropers ]
-C CA N H
CA OC1 C OC2
CB OD1 CG OD2
[ CLYS ]
[ atoms ]
N N -0.629569 1
H H 0.357460 2
CA CT -0.053541 3
HA H1 0.138544 4
CB CT -0.046022 5
HB1 HC 0.042912 6
HB2 HC 0.042912 7
CG CT 0.020231 8
HG1 HC 0.010971 9
HG2 HC 0.010971 10
CD CT -0.046165 11
HD1 HC 0.061437 12
HD2 HC 0.061437 13
CE CT -0.032772 14
HE1 HP 0.101654 15
HE2 HP 0.101654 16
NZ N3 -0.168623 17
HZ1 H 0.285503 18
HZ2 H 0.285503 19
HZ3 H 0.285503 20
C C 0.541818 21
OC1 O2 -0.685909 22
OC2 O2 -0.685909 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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CPRO ]
[ atoms ]
N N -0.268742 1
CD CT 0.062285 2
HD1 H1 0.034717 3
HD2 H1 0.034717 4
CG CT 0.059879 5
HG1 HC 0.007548 6
HG2 HC 0.007548 7
CB CT 0.065773 8
HB1 HC 0.016889 9
HB2 HC 0.016889 10
CA CT -0.385442 11
HA H1 0.177938 12
C C 0.643321 13
OC1 O2 -0.736661 14
OC2 O2 -0.736661 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
[ impropers ]
CA OC1 C OC2
-C CD N CA
[ CCYS ]
[ atoms ]
N N -0.555037 1
H H 0.345483 2
CA CT -0.110929 3
HA H1 0.147206 4
CB CT -0.162428 5
HB1 H1 0.131999 6
HB2 H1 0.131999 7
SG SH -0.290711 8
HG HS 0.192419 9
C C 0.671942 10
OC1 O2 -0.750971 11
OC2 O2 -0.750971 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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CCYX ]
[ atoms ]
N N -0.38210 1
H H 0.26810 2
CA CT -0.13180 3
HA H1 0.09380 4
CB CT -0.19430 5
HB1 H1 0.12280 6
HB2 H1 0.12280 7
SG S -0.05290 8
C C 0.76180 9
OC1 O2 -0.80410 10
OC2 O2 -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
[ impropers ]
-C CA N H
CA OC1 C OC2
[ CMET ]
[ atoms ]
N N -0.564246 1
H H 0.334412 2
CA CT -0.159882 3
HA H1 0.142833 4
CB CT 0.058364 5
HB1 HC 0.052479 6
HB2 HC 0.052479 7
CG CT -0.230352 8
HG1 H1 0.127983 9
HG2 H1 0.127983 10
SD S -0.218570 11
CE CT -0.262571 12
HE1 H1 0.123031 13
HE2 H1 0.123031 14
HE3 H1 0.123031 15
C C 0.664918 16
OC1 O2 -0.747459 17
OC2 O2 -0.747459 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
[ impropers ]
-C CA N H
CA OC1 C OC2
; N-terminal AA's
[ NALA ]
[ atoms ]
N N3 -0.589266 1
H1 H 0.446422 2
H2 H 0.446422 3
H3 H 0.446422 4
CA CT 0.113871 5
HA HP 0.067150 6
CB CT -0.204113 7
HB1 HC 0.063056 8
HB2 HC 0.063056 9
HB3 HC 0.063056 10
C C 0.676687 11
O O -0.592764 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
[ impropers ]
CA +N C O
[ NGLY ]
[ atoms ]
N N3 -0.600766 1
H1 H 0.450255 2
H2 H 0.450255 3
H3 H 0.450255 4
CA CT 0.126891 5
HA1 HP 0.036849 6
HA2 HP 0.036849 7
C C 0.648768 8
O O -0.599357 9
[ bonds ]
N H1
N H2
N H3
N CA
CA HA1
CA HA2
CA C
C O
C +N
[ impropers ]
CA +N C O
[ NSER ]
[ atoms ]
N N3 -0.664403 1
H1 H 0.471468 2
H2 H 0.471468 3
H3 H 0.471468 4
CA CT 0.140290 5
HA HP 0.091150 6
CB CT 0.111987 7
HB1 H1 0.039285 8
HB2 H1 0.039285 9
OG OH -0.593805 10
HG HO 0.407492 11
C C 0.592480 12
O O -0.578162 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
[ impropers ]
CA +N C O
[ NTHR ]
[ atoms ]
N N3 -0.570235 1
H1 H 0.440078 2
H2 H 0.440078 3
H3 H 0.440078 4
CA CT 0.028754 5
HA HP 0.078538 6
CB CT 0.270941 7
HB H1 -0.014476 8
CG2 CT -0.160657 9
HG21 HC 0.053833 10
HG22 HC 0.053833 11
HG23 HC 0.053833 12
OG1 OH -0.621934 13
HG1 HO 0.409167 14
C C 0.709968 15
O O -0.611797 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
[ impropers ]
CA +N C O
[ NLEU ]
[ atoms ]
N N3 -0.624705 1
H1 H 0.458235 2
H2 H 0.458235 3
H3 H 0.458235 4
CA CT 0.069804 5
HA HP 0.092394 6
CB CT -0.118019 7
HB1 HC 0.037615 8
HB2 HC 0.037615 9
CG CT 0.177099 10
HG HC 0.013272 11
CD1 CT -0.157414 12
HD11 HC 0.031964 13
HD12 HC 0.031964 14
HD13 HC 0.031964 15
CD2 CT -0.157414 16
HD21 HC 0.031964 17
HD22 HC 0.031964 18
HD23 HC 0.031964 19
C C 0.656583 20
O O -0.593318 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
[ impropers ]
CA +N C O
[ NILE ]
[ atoms ]
N N3 -0.605757 1
H1 H 0.451919 2
H2 H 0.451919 3
H3 H 0.451919 4
CA CT 0.025768 5
HA HP 0.062754 6
CB CT 0.044198 7
HB HC 0.038704 8
CG2 CT -0.172672 9
HG21 HC 0.038544 10
HG22 HC 0.038544 11
HG23 HC 0.038544 12
CG1 CT 0.058447 13
HG11 HC 0.003617 14
HG12 HC 0.003617 15
CD CT -0.111609 16
HD1 HC 0.025639 17
HD2 HC 0.025639 18
HD3 HC 0.025639 19
C C 0.733445 20
O O -0.628820 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
[ impropers ]
CA +N C O
[ NVAL ]
[ atoms ]
N N3 -0.737450 1
H1 H 0.495817 2
H2 H 0.495817 3
H3 H 0.495817 4
CA CT -0.082837 5
HA HP 0.017007 6
CB CT 0.240887 7
HB HC -0.034674 8
CG1 CT -0.209130 9
HG11 HC 0.043124 10
HG12 HC 0.043124 11
HG13 HC 0.043124 12
CG2 CT -0.209130 13
HG21 HC 0.043124 14
HG22 HC 0.043124 15
HG23 HC 0.043124 16
C C 0.890641 17
O O -0.621511 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
[ impropers ]
CA +N C O
[ NASN ]
[ atoms ]
N N3 -0.669106 1
H1 H 0.473035 2
H2 H 0.473035 3
H3 H 0.473035 4
CA CT 0.256684 5
HA HP 0.013306 6
CB CT -0.062106 7
HB1 HC 0.038289 8
HB2 HC 0.038289 9
CG C 0.554932 10
OD1 O -0.568797 11
ND2 N -0.784547 12
HD21 H 0.372344 13
HD22 H 0.372344 14
C C 0.602554 15
O O -0.583293 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
[ impropers ]
CA +N C O
CB ND2 CG OD1
CG HD21 ND2 HD22
[ NGLN ]
[ atoms ]
N N3 -0.603779 1
H1 H 0.451260 2
H2 H 0.451260 3
H3 H 0.451260 4
CA CT 0.201127 5
HA HP 0.028930 6
CB CT -0.013277 7
HB1 HC 0.001827 8
HB2 HC 0.001827 9
CG CT -0.030707 10
HG1 HC 0.024665 11
HG2 HC 0.024665 12
CD C 0.669568 13
OE1 O -0.585802 14
NE2 N -0.889652 15
HE21 H 0.397306 16
HE22 H 0.397306 17
C C 0.606634 18
O O -0.584415 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
[ impropers ]
CA +N C O
CG NE2 CD OE1
CD HE21 NE2 HE22
[ NARG ]
[ atoms ]
N N3 -0.670515 1
H1 H 0.473505 2
H2 H 0.473505 3
H3 H 0.473505 4
CA CT 0.093903 5
HA HP 0.024998 6
CB CT 0.029171 7
HB1 HC 0.028728 8
HB2 HC 0.028728 9
CG CT -0.016208 10
HG1 HC 0.002044 11
HG2 HC 0.002044 12
CD CT 0.176568 13
HD1 H1 0.048477 14
HD2 H1 0.048477 15
NE N2 -0.450568 16
HE H 0.338467 17
CZ CA 0.561360 18
NH1 N2 -0.706473 19
HH11 H 0.405927 20
HH12 H 0.405927 21
NH2 N2 -0.706473 22
HH21 H 0.405927 23
HH22 H 0.405927 24
C C 0.770284 25
O O -0.647234 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
[ impropers ]
CA +N C O
NE NH1 CZ NH2
CD CZ NE HE
CZ HH11 NH1 HH12
CZ HH21 NH2 HH22
[ NHID ]
[ atoms ]
N N3 -0.702202 1
H1 H 0.484067 2
H2 H 0.484067 3
H3 H 0.484067 4
CA CT 0.270112 5
HA HP 0.023946 6
CB CT -0.066199 7
HB1 HC 0.045493 8
HB2 HC 0.045493 9
CG CC -0.029295 10
ND1 NA -0.217584 11
HD1 H 0.293840 12
CE1 CR 0.147532 13
HE1 H5 0.110099 14
NE2 NB -0.551585 15
CD2 CV 0.071109 16
HD2 H4 0.096199 17
C C 0.590651 18
O O -0.579809 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
[ impropers ]
CA +N C O
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ NHIE ]
[ atoms ]
N N3 -0.697797 1
H1 H 0.482599 2
H2 H 0.482599 3
H3 H 0.482599 4
CA CT 0.181926 5
HA HP 0.060125 6
CB CT -0.114822 7
HB1 HC 0.057721 8
HB2 HC 0.057721 9
CG CC 0.209925 10
ND1 NB -0.486658 11
CE1 CR 0.055422 12
HE1 H5 0.126178 13
NE2 NA -0.090417 14
HE2 H 0.281999 15
CD2 CW -0.258671 16
HD2 H4 0.154335 17
C C 0.601906 18
O O -0.586694 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
[ impropers ]
CA +N C O
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
[ NHIP ]
[ atoms ]
N N3 -0.745211 1
H1 H 0.498404 2
H2 H 0.498404 3
H3 H 0.498404 4
CA CT 0.223794 5
HA HP 0.029571 6
CB CT -0.063494 7
HB1 HC 0.089473 8
HB2 HC 0.089473 9
CG CC -0.005485 10
ND1 NA -0.014619 11
HD1 H 0.275668 12
CE1 CR -0.020417 13
HE1 H5 0.220661 14
NE2 NA -0.119388 15
HE2 H 0.363590 16
CD2 CW -0.156771 17
HD2 H4 0.221434 18
C C 0.737512 19
O O -0.621000 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
[ 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 N3 -0.621979 1
H1 H 0.457326 2
H2 H 0.457326 3
H3 H 0.457326 4
CA CT 0.117919 5
HA HP 0.073247 6
CB CT -0.053219 7
HB1 HC 0.055273 8
HB2 HC 0.055273 9
CG C* -0.144090 10
CD1 CW -0.172104 11
HD1 H4 0.179500 12
NE1 NA -0.300089 13
HE1 H 0.343546 14
CE2 CN 0.145233 15
CZ2 CA -0.220933 16
HZ2 HA 0.135970 17
CH2 CA -0.139029 18
HH2 HA 0.123118 19
CZ3 CA -0.177371 20
HZ3 HA 0.122346 21
CE3 CA -0.170285 22
HE3 HA 0.135963 23
CD2 CB 0.083829 24
C C 0.626460 25
O O -0.570557 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
[ 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 CG CB CD2
[ NPHE ]
[ atoms ]
N N3 -0.629494 1
H1 H 0.459831 2
H2 H 0.459831 3
H3 H 0.459831 4
CA CT 0.175018 5
HA HP 0.051530 6
CB CT -0.056597 7
HB1 HC 0.044331 8
HB2 HC 0.044331 9
CG CA 0.000827 10
CD1 CA -0.101529 11
HD1 HA 0.108610 12
CE1 CA -0.156341 13
HE1 HA 0.128346 14
CZ CA -0.104791 15
HZ HA 0.119084 16
CE2 CA -0.156341 17
HE2 HA 0.128346 18
CD2 CA -0.101529 19
HD2 HA 0.108610 20
C C 0.596118 21
O O -0.578021 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
[ 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 N3 -0.592849 1
H1 H 0.447616 2
H2 H 0.447616 3
H3 H 0.447616 4
CA CT 0.090652 5
HA HP 0.113265 6
CB CT -0.050705 7
HB1 HC 0.006441 8
HB2 HC 0.006441 9
CG CA 0.130909 10
CD1 CA -0.198282 11
HD1 HA 0.148246 12
CE1 CA -0.213863 13
HE1 HA 0.148090 14
CZ C 0.242629 15
OH OH -0.475387 16
HH HO 0.370782 17
CE2 CA -0.213863 18
HE2 HA 0.148090 19
CD2 CA -0.198282 20
HD2 HA 0.148246 21
C C 0.620893 22
O O -0.574301 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
[ 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 N3 -0.465328 1
H1 H 0.405109 2
H2 H 0.405109 3
H3 H 0.405109 4
CA CT 0.127199 5
HA HP 0.023038 6
CB CT 0.088282 7
HB1 HC -0.034219 8
HB2 HC -0.034219 9
CG CT -0.009673 10
HG1 HC -0.021524 11
HG2 HC -0.021524 12
CD C 0.740015 13
OE1 O2 -0.780545 14
OE2 O2 -0.780545 15
C C 0.552551 16
O O -0.598835 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
[ impropers ]
CA +N C O
CG OE1 CD OE2
[ NASP ]
[ atoms ]
N N3 -0.588807 1
H1 H 0.446269 2
H2 H 0.446269 3
H3 H 0.446269 4
CA CT 0.015024 5
HA HP 0.090798 6
CB CT -0.071792 7
HB1 HC 0.002802 8
HB2 HC 0.002802 9
CG C 0.770432 10
OD1 O2 -0.787966 11
OD2 O2 -0.787966 12
C C 0.602072 13
O O -0.586206 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
[ impropers ]
CA +N C O
CB OD1 CG OD2
[ NLYS ]
[ atoms ]
N N3 -0.743778 1
H1 H 0.497926 2
H2 H 0.497926 3
H3 H 0.497926 4
CA CT 0.163115 5
HA HP 0.070671 6
CB CT -0.044702 7
HB1 HC 0.023815 8
HB2 HC 0.023815 9
CG CT 0.007065 10
HG1 HC 0.017881 11
HG2 HC 0.017881 12
CD CT -0.061357 13
HD1 HC 0.065779 14
HD2 HC 0.065779 15
CE CT -0.029056 16
HE1 HP 0.102772 17
HE2 HP 0.102772 18
NZ N3 -0.181839 19
HZ1 H 0.289529 20
HZ2 H 0.289529 21
HZ3 H 0.289529 22
C C 0.633667 23
O O -0.596645 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
[ impropers ]
CA +N C O
[ NPRO ]
[ atoms ]
N N3 -0.421739 1
H1 H 0.471857 2
H2 H 0.471857 3
CD CT 0.048486 4
HD1 HP 0.039901 5
HD2 HP 0.039901 6
CG CT 0.106081 7
HG1 HC -0.000632 8
HG2 HC -0.000632 9
CB CT -0.123305 10
HB1 HC 0.028355 11
HB2 HC 0.028355 12
CA CT 0.251986 13
HA HP -0.021715 14
C C 0.680470 15
O O -0.599226 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
[ impropers ]
CA +N C O
[ NCYS ]
[ atoms ]
N N3 -0.610355 1
H1 H 0.453452 2
H2 H 0.453452 3
H3 H 0.453452 4
CA CT 0.072150 5
HA HP 0.083203 6
CB CT -0.155113 7
HB1 H1 0.113742 8
HB2 H1 0.113742 9
SG SH -0.293380 10
HG HS 0.190705 11
C C 0.747857 12
O O -0.622908 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
[ impropers ]
CA +N C O
[ NCYX ]
[ atoms ]
N N3 0.20690 1
H1 H 0.18150 2
H2 H 0.18150 3
H3 H 0.18150 4
CA CT 0.10550 5
HA HP 0.09220 6
CB CT -0.02770 7
HB1 H1 0.06800 8
HB2 H1 0.06800 9
SG S -0.09840 10
C C 0.61230 11
O O -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
[ impropers ]
CA +N C O
[ NMET ]
[ atoms ]
N N3 -0.597213 1
H1 H 0.449071 2
H2 H 0.449071 3
H3 H 0.449071 4
CA CT 0.060906 5
HA HP 0.075421 6
CB CT 0.051523 7
HB1 HC 0.038926 8
HB2 HC 0.038926 9
CG CT -0.254386 10
HG1 H1 0.129517 11
HG2 H1 0.129517 12
SD S -0.206852 13
CE CT -0.284358 14
HE1 H1 0.128754 15
HE2 H1 0.128754 16
HE3 H1 0.128754 17
C C 0.683639 18
O O -0.599042 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
[ impropers ]
CA +N C O
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