1770 lines
71 KiB
Plaintext
1770 lines
71 KiB
Plaintext
*>>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<
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*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
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*>>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
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* All comments to the CHARMM web site: www.charmm.org
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* parameter set discussion forum
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*
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36 1
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AUTOGENERATE ANGLE DIHE
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!references
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!
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!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P.
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!Mittal, J., Feig, M. and MacKerell, A.D., Jr. "Optimization of the
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!additive CHARMM all-atom protein force field targeting improved
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!sampling of the backbone phi, psi and sidechain chi1 and chi2
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!dihedral angles," JCTC, 8: 3257-3273, 2013, PMC3549273
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!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved
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!treatment of the protein backbone in empirical force fields," Journal
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!of the American Chemical Society, 126: 698-699, 2004
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!
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!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
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!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
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!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
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!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
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!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
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!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
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!empirical potential for molecular modeling and dynamics Studies of
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!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
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!
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MASS -1 H 1.00800 ! polar H
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MASS -1 HC 1.00800 ! N-ter H
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MASS -1 HA 1.00800 ! nonpolar H
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MASS -1 HP 1.00800 ! aromatic H
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MASS -1 HB1 1.00800 ! backbone H
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MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2
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MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2
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MASS -1 HR2 1.00800 ! (+) his HE1
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MASS -1 HR3 1.00800 ! neutral his HG, HD2
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MASS -1 HS 1.00800 ! thiol hydrogen
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MASS -1 HE1 1.00800 ! for alkene; RHC=CR
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MASS -1 HE2 1.00800 ! for alkene; H2C=CR
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MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
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MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
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MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
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MASS -1 C 12.01100 ! carbonyl C, peptide backbone
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MASS -1 CA 12.01100 ! aromatic C
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MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens
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MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH
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MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2
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MASS -1 CT2A 12.01100 ! from CT2 (asp, glu, hsp chi1/chi2 fitting)
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MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3
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MASS -1 CPH1 12.01100 ! his CG and CD2 carbons
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MASS -1 CPH2 12.01100 ! his CE1 carbon
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MASS -1 CPT 12.01100 ! trp C between rings
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MASS -1 CY 12.01100 ! TRP C in pyrrole ring
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MASS -1 CP1 12.01100 ! tetrahedral C (proline CA)
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MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG)
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MASS -1 CP3 12.01100 ! tetrahedral C (proline CD)
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MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2
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MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1
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MASS -1 CS 12.01100 ! thiolate carbon
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MASS -1 CE1 12.01100 ! for alkene; RHC=CR
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MASS -1 CE2 12.01100 ! for alkene; H2C=CR
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MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp
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MASS -1 C3 12.01100 ! cyclopropane carbon
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MASS -1 N 14.00700 ! proline N
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MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen
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MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen
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MASS -1 NR3 14.00700 ! charged his ring nitrogen
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MASS -1 NH1 14.00700 ! peptide nitrogen
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MASS -1 NH2 14.00700 ! amide nitrogen
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MASS -1 NH3 14.00700 ! ammonium nitrogen
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MASS -1 NC2 14.00700 ! guanidinium nitrogen
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MASS -1 NY 14.00700 ! TRP N in pyrrole ring
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MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal)
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MASS -1 O 15.99940 ! carbonyl oxygen
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MASS -1 OB 15.99940 ! carbonyl oxygen in acetic acid
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MASS -1 OC 15.99940 ! carboxylate oxygen
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MASS -1 OH1 15.99940 ! hydroxyl oxygen
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MASS -1 OS 15.99940 ! ester oxygen
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MASS -1 S 32.06000 ! sulphur
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MASS -1 SM 32.06000 ! sulfur C-S-S-C type
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MASS -1 SS 32.06000 ! thiolate sulfur
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DECL -CA
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DECL -C
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DECL -O
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DECL +N
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DECL +HN
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DECL +CA
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DEFA FIRS NTER LAST CTER
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AUTO ANGLES DIHE PATCH
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RESI ALA 0.00
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GROUP
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ATOM N NH1 -0.47 ! |
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ATOM HN H 0.31 ! HN-N
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ATOM CA CT1 0.07 ! | HB1
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ATOM HA HB1 0.09 ! | /
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GROUP ! HA-CA--CB-HB2
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ATOM CB CT3 -0.27 ! | \
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ATOM HB1 HA3 0.09 ! | HB3
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ATOM HB2 HA3 0.09 ! O=C
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ATOM HB3 HA3 0.09 ! |
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GROUP !
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ATOM C C 0.51
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ATOM O O -0.51
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BOND CB CA N HN N CA
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BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
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DOUBLE O C
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IMPR N -C CA HN C CA +N O
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CMAP -C N CA C N CA C +N
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DONOR HN N
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ACCEPTOR O C
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IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
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IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390
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IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558
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IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
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IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
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IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
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IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
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IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
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IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
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IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
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RESI ARG 1.00
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GROUP
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ATOM N NH1 -0.47 ! | HH11
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ATOM HN H 0.31 ! HN-N |
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ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12
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ATOM HA HB1 0.09 ! | | | | | //(+)
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GROUP ! HA-CA--CB--CG--CD--NE--CZ
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ATOM CB CT2 -0.18 ! | | | | \
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ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 NH2-HH22
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ATOM HB2 HA2 0.09 ! O=C |
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GROUP ! | HH21
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ATOM CG CT2 -0.18
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ATOM HG1 HA2 0.09
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ATOM HG2 HA2 0.09
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GROUP
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ATOM CD CT2 0.20
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ATOM HD1 HA2 0.09
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ATOM HD2 HA2 0.09
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ATOM NE NC2 -0.70
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ATOM HE HC 0.44
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ATOM CZ C 0.64
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ATOM NH1 NC2 -0.80
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ATOM HH11 HC 0.46
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ATOM HH12 HC 0.46
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ATOM NH2 NC2 -0.80
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ATOM HH21 HC 0.46
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ATOM HH22 HC 0.46
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GROUP
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ATOM C C 0.51
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ATOM O O -0.51
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BOND CB CA CG CB CD CG NE CD CZ NE
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BOND NH2 CZ N HN N CA
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BOND C CA C +N CA HA CB HB1
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BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2
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BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22
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DOUBLE O C CZ NH1
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IMPR N -C CA HN C CA +N O
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IMPR CZ NH1 NH2 NE
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IMPR NH1 HH11 HH12 CZ
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IMPR NH2 HH21 HH22 CZ
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CMAP -C N CA C N CA C +N
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DONOR HN N
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DONOR HE NE
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DONOR HH11 NH1
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DONOR HH12 NH1
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DONOR HH21 NH2
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DONOR HH22 NH2
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ACCEPTOR O C
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IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973
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IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227
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IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511
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IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271
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IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565
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IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552
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IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836
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IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475
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IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163
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IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124
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IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384
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IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121
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IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143
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IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034
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IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143
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IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150
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IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401
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IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065
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IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311
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IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903
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IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023
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IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292
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IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899
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IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914
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RESI ASN 0.00
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GROUP
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ATOM N NH1 -0.47 ! |
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ATOM HN H 0.31 ! HN-N
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ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1)
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ATOM HA HB1 0.09 ! | | || /
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GROUP ! HA-CA--CB--CG--ND2
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ATOM CB CT2 -0.18 ! | | \
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ATOM HB1 HA2 0.09 ! | HB2 HD22 (trans to OD1)
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ATOM HB2 HA2 0.09 ! O=C
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GROUP ! |
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ATOM CG CC 0.55
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ATOM OD1 O -0.55
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GROUP
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ATOM ND2 NH2 -0.62
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ATOM HD21 H 0.32
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ATOM HD22 H 0.30
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GROUP
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ATOM C C 0.51
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ATOM O O -0.51
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BOND CB CA CG CB ND2 CG
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BOND N HN N CA C CA C +N
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BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22
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DOUBLE C O CG OD1
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IMPR N -C CA HN C CA +N O
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IMPR CG ND2 CB OD1 CG CB ND2 OD1
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IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21
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CMAP -C N CA C N CA C +N
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DONOR HN N
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DONOR HD21 ND2
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DONOR HD22 ND2
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ACCEPTOR OD1 CG
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ACCEPTOR O C
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IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992
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IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245
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IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467
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IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282
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IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528
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IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627
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IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848
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IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319
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IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120
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IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091
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IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323
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IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521
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IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963
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IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951
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RESI ASP -1.00
|
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GROUP
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ATOM N NH1 -0.47 ! |
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|
ATOM HN H 0.31 ! HN-N
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ATOM CA CT1 0.07 ! | HB1 OD1
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|
ATOM HA HB1 0.09 ! | | //
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GROUP ! HA-CA--CB--CG
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|
ATOM CB CT2A -0.28 ! | | \
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|
ATOM HB1 HA2 0.09 ! | HB2 OD2(-)
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ATOM HB2 HA2 0.09 ! O=C
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|
ATOM CG CC 0.62 ! |
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|
ATOM OD1 OC -0.76
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|
ATOM OD2 OC -0.76
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GROUP
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|
ATOM C C 0.51
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|
ATOM O O -0.51
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|
BOND CB CA CG CB OD2 CG
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|
BOND N HN N CA C CA C +N
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|
BOND CA HA CB HB1 CB HB2
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|
DOUBLE O C CG OD1
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|
IMPR N -C CA HN C CA +N O
|
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IMPR CG CB OD2 OD1
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|
CMAP -C N CA C N CA C +N
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|
DONOR HN N
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|
ACCEPTOR OD1 CG
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ACCEPTOR OD2 CG
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ACCEPTOR O C
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|
IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966
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IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315
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|
IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478
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|
IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330
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|
IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484
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|
IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619
|
|
IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841
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|
IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218
|
|
IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086
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|
IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080
|
|
IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565
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|
IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541
|
|
|
|
RESI CYS 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | HB1
|
|
ATOM HA HB1 0.09 ! | |
|
|
GROUP ! HA-CA--CB--SG
|
|
ATOM CB CT2 -0.11 ! | | \
|
|
ATOM HB1 HA2 0.09 ! | HB2 HG1
|
|
ATOM HB2 HA2 0.09 ! O=C
|
|
ATOM SG S -0.23 ! |
|
|
ATOM HG1 HS 0.16
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA SG CB N HN N CA
|
|
BOND C CA C +N CA HA CB HB1
|
|
BOND CB HB2 SG HG1
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HG1 SG
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
|
|
IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
|
|
IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
|
|
IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
|
|
IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
|
|
IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
|
|
IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
|
|
IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
|
|
IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
|
|
IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
|
|
IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341
|
|
|
|
RESI GLN 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1)
|
|
ATOM HA HB1 0.09 ! | | | || /
|
|
GROUP ! HA-CA--CB--CG--CD--NE2
|
|
ATOM CB CT2 -0.18 ! | | | \
|
|
ATOM HB1 HA2 0.09 ! | HB2 HG2 HE22 (trans to OE1)
|
|
ATOM HB2 HA2 0.09 ! O=C
|
|
GROUP ! |
|
|
ATOM CG CT2 -0.18
|
|
ATOM HG1 HA2 0.09
|
|
ATOM HG2 HA2 0.09
|
|
GROUP
|
|
ATOM CD CC 0.55
|
|
ATOM OE1 O -0.55
|
|
GROUP
|
|
ATOM NE2 NH2 -0.62
|
|
ATOM HE21 H 0.32
|
|
ATOM HE22 H 0.30
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB CD CG NE2 CD
|
|
BOND N HN N CA C CA
|
|
BOND C +N CA HA CB HB1 CB HB2 CG HG1
|
|
BOND CG HG2 NE2 HE21 NE2 HE22
|
|
DOUBLE O C CD OE1
|
|
IMPR N -C CA HN C CA +N O
|
|
IMPR CD NE2 CG OE1 CD CG NE2 OE1
|
|
IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HE21 NE2
|
|
DONOR HE22 NE2
|
|
ACCEPTOR OE1 CD
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984
|
|
IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180
|
|
IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463
|
|
IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291
|
|
IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461
|
|
IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538
|
|
IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832
|
|
IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534
|
|
IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147
|
|
IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140
|
|
IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320
|
|
IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112
|
|
IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094
|
|
IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294
|
|
IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530
|
|
IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959
|
|
IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943
|
|
|
|
RESI GLU -1.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | HB1 HG1 OE1
|
|
ATOM HA HB1 0.09 ! | | | //
|
|
GROUP ! HA-CA--CB--CG--CD
|
|
ATOM CB CT2A -0.18 ! | | | \
|
|
ATOM HB1 HA2 0.09 ! | HB2 HG2 OE2(-)
|
|
ATOM HB2 HA2 0.09 ! O=C
|
|
GROUP ! |
|
|
ATOM CG CT2 -0.28
|
|
ATOM HG1 HA2 0.09
|
|
ATOM HG2 HA2 0.09
|
|
ATOM CD CC 0.62
|
|
ATOM OE1 OC -0.76
|
|
ATOM OE2 OC -0.76
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB CD CG OE2 CD
|
|
BOND N HN N CA C CA
|
|
BOND C +N CA HA CB HB1 CB HB2 CG HG1
|
|
BOND CG HG2
|
|
DOUBLE O C CD OE1
|
|
IMPR N -C CA HN C CA +N O
|
|
IMPR CD CG OE2 OE1
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR OE1 CD
|
|
ACCEPTOR OE2 CD
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961
|
|
IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216
|
|
IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501
|
|
IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306
|
|
IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530
|
|
IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516
|
|
IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828
|
|
IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557
|
|
IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
|
|
IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
|
|
IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307
|
|
IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053
|
|
IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081
|
|
IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590
|
|
IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532
|
|
|
|
RESI GLY 0.00
|
|
!GROUP
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! N-H
|
|
ATOM CA CT2 -0.02 ! |
|
|
ATOM HA1 HB2 0.09 ! |
|
|
ATOM HA2 HB2 0.09 ! HA1-CA-HA2
|
|
GROUP ! |
|
|
ATOM C C 0.51 ! |
|
|
ATOM O O -0.51 ! C=O
|
|
! |
|
|
BOND N HN N CA C CA
|
|
BOND C +N CA HA1 CA HA2
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992
|
|
IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971
|
|
IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479
|
|
IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289
|
|
IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560
|
|
IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814
|
|
IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817
|
|
PATCHING FIRS GLYP
|
|
|
|
RESI HSD 0.00 ! neutral HIS, proton on ND1
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HD1 HE1
|
|
ATOM HN H 0.31 ! HN-N | /
|
|
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
|
|
ATOM HA HB1 0.09 ! | | / ||
|
|
GROUP ! HA-CA--CB--CG ||
|
|
ATOM CB CT2 -0.09 ! | | \\ ||
|
|
ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2
|
|
ATOM HB2 HA2 0.09 ! O=C |
|
|
ATOM ND1 NR1 -0.36 ! | HD2
|
|
ATOM HD1 H 0.32
|
|
ATOM CG CPH1 -0.05
|
|
GROUP
|
|
ATOM CE1 CPH2 0.25
|
|
ATOM HE1 HR1 0.13
|
|
ATOM NE2 NR2 -0.70
|
|
ATOM CD2 CPH1 0.22
|
|
ATOM HD2 HR3 0.10
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB ND1 CG CE1 ND1
|
|
BOND NE2 CD2 N HN N CA
|
|
BOND C CA C +N CA HA CB HB1
|
|
BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1
|
|
DOUBLE O C CG CD2 CE1 NE2
|
|
IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
|
|
IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HD1 ND1
|
|
ACCEPTOR NE2
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988
|
|
IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166
|
|
IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509
|
|
IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273
|
|
IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545
|
|
IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519
|
|
IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830
|
|
IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041
|
|
IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118
|
|
IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121
|
|
IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783
|
|
IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597
|
|
IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549
|
|
IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817
|
|
IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932
|
|
IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005
|
|
IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834
|
|
|
|
RESI HSE 0.00 ! neutral His, proton on NE2
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HE1
|
|
ATOM HN H 0.31 ! HN-N __ /
|
|
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
|
|
ATOM HA HB1 0.09 ! | | / |
|
|
GROUP ! HA-CA--CB--CG |
|
|
ATOM CB CT2 -0.08 ! | | \\ |
|
|
ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2
|
|
ATOM HB2 HA2 0.09 ! O=C | \
|
|
ATOM ND1 NR2 -0.70 ! | HD2 HE2
|
|
ATOM CG CPH1 0.22
|
|
ATOM CE1 CPH2 0.25
|
|
ATOM HE1 HR1 0.13
|
|
GROUP
|
|
ATOM NE2 NR1 -0.36
|
|
ATOM HE2 H 0.32
|
|
ATOM CD2 CPH1 -0.05
|
|
ATOM HD2 HR3 0.09
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB ND1 CG
|
|
BOND NE2 CD2 N HN N CA
|
|
BOND C CA C +N NE2 CE1 CA HA CB HB1
|
|
BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1
|
|
DOUBLE O C CD2 CG CE1 ND1
|
|
IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
|
|
IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HE2 NE2
|
|
ACCEPTOR ND1
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991
|
|
IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166
|
|
IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446
|
|
IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290
|
|
IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505
|
|
IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578
|
|
IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833
|
|
IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109
|
|
IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114
|
|
IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101
|
|
IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859
|
|
IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596
|
|
IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170
|
|
IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782
|
|
IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929
|
|
IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996
|
|
IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809
|
|
|
|
RESI HSP 1.00 ! Protonated His
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HD1 HE1
|
|
ATOM HN H 0.31 ! HN-N | /
|
|
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
|
|
ATOM HA HB1 0.09 ! | | / ||
|
|
GROUP ! HA-CA--CB--CG ||
|
|
ATOM CB CT2A -0.05 ! | | \\ ||
|
|
ATOM HB1 HA2 0.09 ! | HB2 CD2--NE2(+)
|
|
ATOM HB2 HA2 0.09 ! O=C | \
|
|
ATOM CD2 CPH1 0.19 ! | HD2 HE2
|
|
ATOM HD2 HR1 0.13
|
|
ATOM CG CPH1 0.19
|
|
GROUP
|
|
ATOM NE2 NR3 -0.51
|
|
ATOM HE2 H 0.44
|
|
ATOM ND1 NR3 -0.51
|
|
ATOM HD1 H 0.44
|
|
ATOM CE1 CPH2 0.32
|
|
ATOM HE1 HR2 0.18
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB ND1 CG CE1 ND1
|
|
BOND NE2 CD2 N HN N CA
|
|
BOND C CA C +N CA HA CB HB1
|
|
BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1
|
|
DOUBLE O C CD2 CG NE2 CE1
|
|
IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1
|
|
IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HD1 ND1
|
|
DONOR HE2 NE2
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041
|
|
IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225
|
|
IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464
|
|
IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284
|
|
IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521
|
|
IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533
|
|
IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832
|
|
IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168
|
|
IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116
|
|
IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132
|
|
IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718
|
|
IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549
|
|
IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262
|
|
IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727
|
|
IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799
|
|
IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020
|
|
IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018
|
|
IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867
|
|
|
|
RESI ILE 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HG21 HG22
|
|
ATOM HN H 0.31 ! HN-N | /
|
|
ATOM CA CT1 0.07 ! | CG2--HG23
|
|
ATOM HA HB1 0.09 ! | /
|
|
GROUP ! HA-CA--CB-HB HD1
|
|
ATOM CB CT1 -0.09 ! | \ /
|
|
ATOM HB HA1 0.09 ! | CG1--CD--HD2
|
|
GROUP ! O=C / \ \
|
|
ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3
|
|
ATOM HG21 HA3 0.09
|
|
ATOM HG22 HA3 0.09
|
|
ATOM HG23 HA3 0.09
|
|
GROUP
|
|
ATOM CG1 CT2 -0.18
|
|
ATOM HG11 HA2 0.09
|
|
ATOM HG12 HA2 0.09
|
|
GROUP
|
|
ATOM CD CT3 -0.27
|
|
ATOM HD1 HA3 0.09
|
|
ATOM HD2 HA3 0.09
|
|
ATOM HD3 HA3 0.09
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG1 CB CG2 CB CD CG1
|
|
BOND N HN N CA C CA C +N
|
|
BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21
|
|
BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978
|
|
IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190
|
|
IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465
|
|
IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300
|
|
IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467
|
|
IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681
|
|
IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826
|
|
IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498
|
|
IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195
|
|
IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452
|
|
IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100
|
|
IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102
|
|
IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105
|
|
IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381
|
|
IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130
|
|
IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141
|
|
IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115
|
|
IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113
|
|
IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103
|
|
|
|
RESI LEU 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HD11 HD12
|
|
ATOM HN H 0.31 ! HN-N | /
|
|
ATOM CA CT1 0.07 ! | HB1 CD1--HD13
|
|
ATOM HA HB1 0.09 ! | | /
|
|
GROUP ! HA-CA--CB--CG-HG
|
|
ATOM CB CT2 -0.18 ! | | \
|
|
ATOM HB1 HA2 0.09 ! | HB2 CD2--HD23
|
|
ATOM HB2 HA2 0.09 ! O=C | \
|
|
GROUP ! | HD21 HD22
|
|
ATOM CG CT1 -0.09
|
|
ATOM HG HA1 0.09
|
|
GROUP
|
|
ATOM CD1 CT3 -0.27
|
|
ATOM HD11 HA3 0.09
|
|
ATOM HD12 HA3 0.09
|
|
ATOM HD13 HA3 0.09
|
|
GROUP
|
|
ATOM CD2 CT3 -0.27
|
|
ATOM HD21 HA3 0.09
|
|
ATOM HD22 HA3 0.09
|
|
ATOM HD23 HA3 0.09
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB CD1 CG CD2 CG
|
|
BOND N HN N CA C CA C +N
|
|
BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11
|
|
BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979
|
|
IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184
|
|
IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463
|
|
IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299
|
|
IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467
|
|
IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543
|
|
IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824
|
|
IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472
|
|
IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145
|
|
IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126
|
|
IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361
|
|
IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360
|
|
IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168
|
|
IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111
|
|
IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112
|
|
IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108
|
|
IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116
|
|
IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086
|
|
IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115
|
|
|
|
RESI LYS 1.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1
|
|
ATOM HA HB1 0.09 ! | | | | | /
|
|
GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2
|
|
ATOM CB CT2 -0.18 ! | | | | | \
|
|
ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 HE2 HZ3
|
|
ATOM HB2 HA2 0.09 ! O=C
|
|
GROUP ! |
|
|
ATOM CG CT2 -0.18
|
|
ATOM HG1 HA2 0.09
|
|
ATOM HG2 HA2 0.09
|
|
GROUP
|
|
ATOM CD CT2 -0.18
|
|
ATOM HD1 HA2 0.09
|
|
ATOM HD2 HA2 0.09
|
|
GROUP
|
|
ATOM CE CT2 0.21
|
|
ATOM HE1 HA2 0.05
|
|
ATOM HE2 HA2 0.05
|
|
ATOM NZ NH3 -0.30
|
|
ATOM HZ1 HC 0.33
|
|
ATOM HZ2 HC 0.33
|
|
ATOM HZ3 HC 0.33
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB CD CG CE CD NZ CE
|
|
BOND N HN N CA C CA
|
|
BOND C +N CA HA CB HB1 CB HB2 CG HG1
|
|
BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2
|
|
DOUBLE O C
|
|
BOND NZ HZ1 NZ HZ2 NZ HZ3
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HZ1 NZ
|
|
DONOR HZ2 NZ
|
|
DONOR HZ3 NZ
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988
|
|
IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187
|
|
IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478
|
|
IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277
|
|
IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487
|
|
IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568
|
|
IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833
|
|
IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435
|
|
IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146
|
|
IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131
|
|
IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397
|
|
IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138
|
|
IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143
|
|
IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350
|
|
IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141
|
|
IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146
|
|
IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604
|
|
IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128
|
|
IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123
|
|
IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404
|
|
IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402
|
|
IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401
|
|
|
|
RESI MET 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | HB1 HG1 HE1
|
|
ATOM HA HB1 0.09 ! | | | |
|
|
GROUP ! HA-CA--CB--CG--SD--CE--HE3
|
|
ATOM CB CT2 -0.18 ! | | | |
|
|
ATOM HB1 HA2 0.09 ! | HB2 HG2 HE2
|
|
ATOM HB2 HA2 0.09 ! O=C
|
|
GROUP ! |
|
|
ATOM CG CT2 -0.14
|
|
ATOM HG1 HA2 0.09
|
|
ATOM HG2 HA2 0.09
|
|
ATOM SD S -0.09
|
|
ATOM CE CT3 -0.22
|
|
ATOM HE1 HA3 0.09
|
|
ATOM HE2 HA3 0.09
|
|
ATOM HE3 HA3 0.09
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB SD CG CE SD
|
|
BOND N HN N CA C CA C +N
|
|
BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2
|
|
BOND CE HE1 CE HE2 CE HE3
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978
|
|
IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195
|
|
IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471
|
|
IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288
|
|
IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471
|
|
IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546
|
|
IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832
|
|
IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460
|
|
IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153
|
|
IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129
|
|
IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219
|
|
IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106
|
|
IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119
|
|
IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206
|
|
IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111
|
|
IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115
|
|
IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112
|
|
|
|
RESI PHE 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HD1 HE1
|
|
ATOM HN H 0.31 ! HN-N | |
|
|
ATOM CA CT1 0.07 ! | HB1 CD1--CE1
|
|
ATOM HA HB1 0.09 ! | | // \\
|
|
GROUP ! HA-CA--CB--CG CZ--HZ
|
|
ATOM CB CT2 -0.18 ! | | \ __ /
|
|
ATOM HB1 HA2 0.09 ! | HB2 CD2--CE2
|
|
ATOM HB2 HA2 0.09 ! O=C | |
|
|
GROUP ! | HD2 HE2
|
|
ATOM CG CA 0.00
|
|
GROUP
|
|
ATOM CD1 CA -0.115
|
|
ATOM HD1 HP 0.115
|
|
GROUP
|
|
ATOM CE1 CA -0.115
|
|
ATOM HE1 HP 0.115
|
|
GROUP
|
|
ATOM CZ CA -0.115
|
|
ATOM HZ HP 0.115
|
|
GROUP
|
|
ATOM CD2 CA -0.115
|
|
ATOM HD2 HP 0.115
|
|
GROUP
|
|
ATOM CE2 CA -0.115
|
|
ATOM HE2 HP 0.115
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB CD2 CG CE1 CD1
|
|
BOND CZ CE2 N HN
|
|
BOND N CA C CA C +N CA HA
|
|
BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1
|
|
DOUBLE O C CD1 CG CZ CE1 CE2 CD2
|
|
BOND CE2 HE2 CZ HZ
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987
|
|
IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229
|
|
IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483
|
|
IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287
|
|
IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523
|
|
IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594
|
|
IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832
|
|
IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109
|
|
IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119
|
|
IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113
|
|
IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059
|
|
IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062
|
|
IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006
|
|
IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814
|
|
IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002
|
|
IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811
|
|
IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004
|
|
IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808
|
|
IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811
|
|
IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807
|
|
|
|
RESI PRO 0.00
|
|
GROUP ! HD1 HD2
|
|
ATOM N N -0.29 ! | \ /
|
|
ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02
|
|
ATOM HD1 HA2 0.09 ! | \ /
|
|
ATOM HD2 HA2 0.09 ! | CG
|
|
ATOM CA CP1 0.02 ! | / \
|
|
ATOM HA HB1 0.09 ! HA-CA--CB HG2
|
|
GROUP ! | / \
|
|
ATOM CB CP2 -0.18 ! | HB1 HB2
|
|
ATOM HB1 HA2 0.09 ! O=C
|
|
ATOM HB2 HA2 0.09 ! |
|
|
GROUP
|
|
ATOM CG CP2 -0.18
|
|
ATOM HG1 HA2 0.09
|
|
ATOM HG2 HA2 0.09
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND C CA C +N
|
|
BOND N CA CA CB CB CG CG CD N CD
|
|
BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB
|
|
DOUBLE O C
|
|
IMPR N -C CA CD
|
|
IMPR C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
ACCEPTOR O C
|
|
IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624
|
|
IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399
|
|
IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569
|
|
IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316
|
|
IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517
|
|
IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399
|
|
IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837
|
|
IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322
|
|
IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317
|
|
IC CA CG *CB HB1 1.4585 102.5600 120.0000 109.0200 1.1131
|
|
IC CA CG *CB HB2 1.4585 102.5600 -120.0000 109.0200 1.1131
|
|
IC CB CD *CG HG1 1.5399 104.3900 120.0000 112.9500 1.1077
|
|
IC CB CD *CG HG2 1.5399 104.3900 -120.0000 109.2200 1.1143
|
|
IC N CG *CD HD1 1.5322 103.2100 120.0000 110.0300 1.1137
|
|
IC N CG *CD HD2 1.5322 103.2100 -120.0000 110.0000 1.1144
|
|
PATCHING FIRS PROP
|
|
|
|
RESI SER 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | HB1
|
|
ATOM HA HB1 0.09 ! | |
|
|
GROUP ! HA-CA--CB--OG
|
|
ATOM CB CT2 0.05 ! | | \
|
|
ATOM HB1 HA2 0.09 ! | HB2 HG1
|
|
ATOM HB2 HA2 0.09 ! O=C
|
|
ATOM OG OH1 -0.66 ! |
|
|
ATOM HG1 H 0.43
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA OG CB N HN N CA
|
|
BOND C CA C +N CA HA CB HB1
|
|
BOND CB HB2 OG HG1
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HG1 OG
|
|
ACCEPTOR OG
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999
|
|
IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166
|
|
IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448
|
|
IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290
|
|
IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529
|
|
IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585
|
|
IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821
|
|
IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341
|
|
IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140
|
|
IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136
|
|
IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655
|
|
|
|
RESI THR 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | OG1--HG1
|
|
ATOM HA HB1 0.09 ! | /
|
|
GROUP ! HA-CA--CB-HB
|
|
ATOM CB CT1 0.14 ! | \
|
|
ATOM HB HA1 0.09 ! | CG2--HG21
|
|
ATOM OG1 OH1 -0.66 ! O=C / \
|
|
ATOM HG1 H 0.43 ! | HG21 HG22
|
|
GROUP
|
|
ATOM CG2 CT3 -0.27
|
|
ATOM HG21 HA3 0.09
|
|
ATOM HG22 HA3 0.09
|
|
ATOM HG23 HA3 0.09
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA OG1 CB CG2 CB N HN
|
|
BOND N CA C CA C +N CA HA
|
|
BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HG1 OG1
|
|
ACCEPTOR OG1
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995
|
|
IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162
|
|
IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449
|
|
IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294
|
|
IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525
|
|
IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693
|
|
IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817
|
|
IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252
|
|
IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174
|
|
IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324
|
|
IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633
|
|
IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104
|
|
IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109
|
|
IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113
|
|
|
|
RESI TRP 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HE3
|
|
ATOM HN H 0.31 ! HN-N |
|
|
ATOM CA CT1 0.07 ! | HB1 CE3
|
|
ATOM HA HB1 0.09 ! | | / \\
|
|
GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3
|
|
ATOM CB CT2 -0.18 ! | | || || |
|
|
ATOM HB1 HA2 0.09 ! | HB2 CD1 CE2 CH2-HH2
|
|
ATOM HB2 HA2 0.09 ! O=C / \ / \ //
|
|
GROUP ! | HD1 NE1 CZ2
|
|
ATOM CG CY -0.03 ! | |
|
|
ATOM CD1 CA -0.15 ! HE1 HZ2
|
|
ATOM HD1 HP 0.22
|
|
ATOM NE1 NY -0.51
|
|
ATOM HE1 H 0.37
|
|
ATOM CE2 CPT 0.24
|
|
ATOM CD2 CPT 0.11
|
|
ATOM CE3 CAI -0.25
|
|
ATOM HE3 HP 0.17
|
|
ATOM CZ3 CA -0.20
|
|
ATOM HZ3 HP 0.14
|
|
ATOM CZ2 CAI -0.27
|
|
ATOM HZ2 HP 0.16
|
|
ATOM CH2 CA -0.14
|
|
ATOM HH2 HP 0.14
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB CD2 CG NE1 CD1
|
|
BOND CZ2 CE2
|
|
BOND N HN N CA C CA C +N
|
|
BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1
|
|
BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2
|
|
BOND CZ3 HZ3 CH2 HH2
|
|
DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HE1 NE1
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972
|
|
IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202
|
|
IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505
|
|
IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304
|
|
IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526
|
|
IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560
|
|
IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835
|
|
IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233
|
|
IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127
|
|
IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118
|
|
IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407
|
|
IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679
|
|
IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126
|
|
IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746
|
|
IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011
|
|
IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017
|
|
IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019
|
|
IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030
|
|
IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815
|
|
IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811
|
|
IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811
|
|
IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790
|
|
IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767
|
|
IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820
|
|
|
|
RESI TYR 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HD1 HE1
|
|
ATOM HN H 0.31 ! HN-N | |
|
|
ATOM CA CT1 0.07 ! | HB1 CD1--CE1
|
|
ATOM HA HB1 0.09 ! | | // \\
|
|
GROUP ! HA-CA--CB--CG CZ--OH
|
|
ATOM CB CT2 -0.18 ! | | \ __ / \
|
|
ATOM HB1 HA2 0.09 ! | HB2 CD2--CE2 HH
|
|
ATOM HB2 HA2 0.09 ! O=C | |
|
|
GROUP ! | HD2 HE2
|
|
ATOM CG CA 0.00
|
|
GROUP
|
|
ATOM CD1 CA -0.115
|
|
ATOM HD1 HP 0.115
|
|
GROUP
|
|
ATOM CE1 CA -0.115
|
|
ATOM HE1 HP 0.115
|
|
GROUP
|
|
ATOM CZ CA 0.11
|
|
ATOM OH OH1 -0.54
|
|
ATOM HH H 0.43
|
|
GROUP
|
|
ATOM CD2 CA -0.115
|
|
ATOM HD2 HP 0.115
|
|
GROUP
|
|
ATOM CE2 CA -0.115
|
|
ATOM HE2 HP 0.115
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG CB CD2 CG CE1 CD1
|
|
BOND CZ CE2 OH CZ
|
|
BOND N HN N CA C CA C +N
|
|
BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2
|
|
BOND CE1 HE1 CE2 HE2 OH HH
|
|
DOUBLE O C CD1 CG CE1 CZ CE2 CD2
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
DONOR HH OH
|
|
ACCEPTOR OH
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986
|
|
IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232
|
|
IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484
|
|
IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287
|
|
IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513
|
|
IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606
|
|
IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833
|
|
IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113
|
|
IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119
|
|
IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115
|
|
IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064
|
|
IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068
|
|
IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026
|
|
IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814
|
|
IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022
|
|
IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813
|
|
IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978
|
|
IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799
|
|
IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798
|
|
IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063
|
|
IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594
|
|
|
|
RESI VAL 0.00
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! | HG11 HG12
|
|
ATOM HN H 0.31 ! HN-N | /
|
|
ATOM CA CT1 0.07 ! | CG1--HG13
|
|
ATOM HA HB1 0.09 ! | /
|
|
GROUP ! HA-CA--CB-HB
|
|
ATOM CB CT1 -0.09 ! | \
|
|
ATOM HB HA1 0.09 ! | CG2--HG21
|
|
GROUP ! O=C / \
|
|
ATOM CG1 CT3 -0.27 ! | HG21 HG22
|
|
ATOM HG11 HA3 0.09
|
|
ATOM HG12 HA3 0.09
|
|
ATOM HG13 HA3 0.09
|
|
GROUP
|
|
ATOM CG2 CT3 -0.27
|
|
ATOM HG21 HA3 0.09
|
|
ATOM HG22 HA3 0.09
|
|
ATOM HG23 HA3 0.09
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA CG1 CB CG2 CB N HN
|
|
BOND N CA C CA C +N CA HA
|
|
BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21
|
|
BOND CG2 HG22 CG2 HG23
|
|
DOUBLE O C
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR O C
|
|
IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966
|
|
IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180
|
|
IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471
|
|
IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297
|
|
IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471
|
|
IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660
|
|
IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828
|
|
IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441
|
|
IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414
|
|
IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178
|
|
IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114
|
|
IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097
|
|
IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110
|
|
IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108
|
|
IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115
|
|
IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098
|
|
|
|
RESI ALAD 0.00 ! Alanine dipeptide
|
|
GROUP
|
|
ATOM CL CT3 -0.27
|
|
ATOM HL1 HA3 0.09
|
|
ATOM HL2 HA3 0.09
|
|
ATOM HL3 HA3 0.09
|
|
GROUP
|
|
ATOM CLP C 0.51
|
|
ATOM OL O -0.51
|
|
GROUP
|
|
ATOM NL NH1 -0.47
|
|
ATOM HL H 0.31
|
|
ATOM CA CT1 0.07
|
|
ATOM HA HB1 0.09
|
|
GROUP
|
|
ATOM CB CT3 -0.27 ! HL1 OL OR HR1
|
|
ATOM HB1 HA3 0.09 ! \ || HL HA || HR /
|
|
ATOM HB2 HA3 0.09 ! \ || | | || | /
|
|
ATOM HB3 HA3 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2
|
|
GROUP ! / | \
|
|
ATOM CRP C 0.51 ! / HB1--CB--HB3 \
|
|
ATOM OR O -0.51 ! HL3 | HR3
|
|
GROUP ! HB2
|
|
ATOM NR NH1 -0.47
|
|
ATOM HR H 0.31
|
|
ATOM CR CT3 -0.11
|
|
ATOM HR1 HA3 0.09
|
|
ATOM HR2 HA3 0.09
|
|
ATOM HR3 HA3 0.09
|
|
|
|
BOND CL CLP CLP NL NL CA
|
|
BOND CA CRP CRP NR NR CR
|
|
DOUBLE CLP OL CRP OR
|
|
BOND NL HL NR HR
|
|
BOND CA HA CA CB
|
|
BOND CL HL1 CL HL2 CL HL3
|
|
BOND CB HB1 CB HB2 CB HB3
|
|
BOND CR HR1 CR HR2 CR HR3
|
|
IMPR CLP CL NL OL NL CLP CA HL
|
|
IMPR CRP CA NR OR NR CRP CR HR
|
|
|
|
CMAP CLP NL CA CRP NL CA CRP NR
|
|
|
|
ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi
|
|
ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0
|
|
ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0
|
|
ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi
|
|
ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0
|
|
ic nl ca crp or 0.0 0.0 0.0 0.0 0.0
|
|
ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left
|
|
ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0
|
|
ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0
|
|
ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right
|
|
ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0
|
|
ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0
|
|
ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0
|
|
ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0
|
|
ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0
|
|
ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0
|
|
ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0
|
|
ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0
|
|
ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0
|
|
ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0
|
|
ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0
|
|
ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0
|
|
ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0
|
|
ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0
|
|
ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0
|
|
ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0
|
|
ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0
|
|
ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0
|
|
ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0
|
|
patch first none last none
|
|
|
|
PRES NTER 1.00 ! standard N-terminus
|
|
GROUP ! use in generate statement
|
|
ATOM N NH3 -0.30 !
|
|
ATOM HT1 HC 0.33 ! HT1
|
|
ATOM HT2 HC 0.33 ! (+)/
|
|
ATOM HT3 HC 0.33 ! --CA--N--HT2
|
|
ATOM CA CT1 0.21 ! | \
|
|
ATOM HA HB1 0.10 ! HA HT3
|
|
DELETE ATOM HN
|
|
BOND HT1 N HT2 N HT3 N
|
|
DONOR HT1 N
|
|
DONOR HT2 N
|
|
DONOR HT3 N
|
|
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
|
|
PRES GLYP 1.00 ! Glycine N-terminus
|
|
GROUP ! use in generate statement
|
|
ATOM N NH3 -0.30 !
|
|
ATOM HT1 HC 0.33 ! HA1 HT1
|
|
ATOM HT2 HC 0.33 ! | (+)/
|
|
ATOM HT3 HC 0.33 ! --CA--N--HT2
|
|
ATOM CA CT2 0.13 ! | \
|
|
ATOM HA1 HB2 0.09 ! HA2 HT3
|
|
ATOM HA2 HB2 0.09 !
|
|
DELETE ATOM HN
|
|
BOND HT1 N HT2 N HT3 N
|
|
DONOR HT1 N
|
|
DONOR HT2 N
|
|
DONOR HT3 N
|
|
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
|
|
PRES PROP 1.00 ! Proline N-Terminal
|
|
GROUP ! use in generate statement
|
|
ATOM N NP -0.07 ! HA
|
|
ATOM HN1 HC 0.24 ! |
|
|
ATOM HN2 HC 0.24 ! -CA HN1
|
|
ATOM CD CP3 0.16 ! / \ /
|
|
ATOM HD1 HA2 0.09 ! N(+)
|
|
ATOM HD2 HA2 0.09 ! / \
|
|
ATOM CA CP1 0.16 ! -CD HN2
|
|
ATOM HA HB1 0.09 ! | \
|
|
BOND HN1 N HN2 N ! HD1 HD2
|
|
DONOR HN1 N
|
|
DONOR HN2 N
|
|
IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
|
|
PRES ACE 0.00 ! acetylated N-terminus
|
|
! do NOT use to create dipeptides, see ACED
|
|
GROUP ! use in generate statement
|
|
ATOM CAY CT3 -0.27 !
|
|
ATOM HY1 HA3 0.09 ! HY1 HY2 HY3
|
|
ATOM HY2 HA3 0.09 ! \ | /
|
|
ATOM HY3 HA3 0.09 ! CAY
|
|
GROUP ! |
|
|
ATOM CY C 0.51 ! CY=OY
|
|
ATOM OY O -0.51 ! |
|
|
!
|
|
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
|
|
DOUBLE OY CY
|
|
IMPR CY CAY N OY
|
|
IMPR N CY CA HN
|
|
CMAP CY N CA C N CA C +N
|
|
ACCEPTOR OY CY
|
|
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
|
|
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
|
|
PRES ACED 0.00 ! acetylated N-terminus (to create dipeptide)
|
|
GROUP ! use in generate statement
|
|
ATOM CAY CT3 -0.27 !
|
|
ATOM HY1 HA3 0.09 ! HY1 HY2 HY3
|
|
ATOM HY2 HA3 0.09 ! \ | /
|
|
ATOM HY3 HA3 0.09 ! CAY
|
|
GROUP ! |
|
|
ATOM CY C 0.51 ! CY=OY
|
|
ATOM OY O -0.51 ! |
|
|
!
|
|
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
|
|
DOUBLE OY CY
|
|
IMPR CY CAY N OY
|
|
IMPR N CY CA HN
|
|
CMAP CY N CA C N CA C NT
|
|
ACCEPTOR OY CY
|
|
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
|
|
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
|
|
PRES ACP 0.00 ! acetylated N-terminus for proline
|
|
! do NOT use to create dipeptide, see ACPD
|
|
GROUP ! use in generate statement
|
|
ATOM CAY CT3 -0.27 !
|
|
ATOM HY1 HA3 0.09 ! HY1 HY2 HY3
|
|
ATOM HY2 HA3 0.09 ! \ | /
|
|
ATOM HY3 HA3 0.09 ! CAY
|
|
GROUP ! |
|
|
ATOM CY C 0.51 ! CY=OY
|
|
ATOM OY O -0.51 ! |
|
|
!
|
|
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
|
|
DOUBLE OY CY
|
|
IMPR CY CAY N OY
|
|
IMPR N CY CA CD
|
|
CMAP CY N CA C N CA C +N
|
|
ACCEPTOR OY CY
|
|
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
|
|
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
|
|
PRES ACPD 0.00 ! acetylated N-terminus for proline (to create dipeptide)
|
|
GROUP ! use in generate statement
|
|
ATOM CAY CT3 -0.27 !
|
|
ATOM HY1 HA3 0.09 ! HY1 HY2 HY3
|
|
ATOM HY2 HA3 0.09 ! \ | /
|
|
ATOM HY3 HA3 0.09 ! CAY
|
|
GROUP ! |
|
|
ATOM CY C 0.51 ! CY=OY
|
|
ATOM OY O -0.51 ! |
|
|
!
|
|
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
|
|
DOUBLE OY CY
|
|
IMPR CY CAY N OY
|
|
IMPR N CY CA CD
|
|
CMAP CY N CA C N CA C NT
|
|
ACCEPTOR OY CY
|
|
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
|
|
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
|
|
PRES NNEU 0.00 ! neutral N-terminus; charges from LSN
|
|
GROUP ! use in generate statement
|
|
ATOM N NH2 -0.96 !
|
|
ATOM HT1 H 0.34 ! HT1
|
|
ATOM HT2 H 0.34 ! /
|
|
! --CA--N--HT2
|
|
ATOM CA CT1 0.19 ! | ! change to CT2 for neutral N terminal glycine
|
|
ATOM HA HB1 0.09 ! HA ! change to HA1 and HB2 and add HA2 atom for N terminal glycine
|
|
DELETE ATOM HN
|
|
BOND HT1 N HT2 N
|
|
DONOR HT1 N
|
|
DONOR HT2 N
|
|
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
|
|
PRES NGNE 0.00 ! neutral N-terminal glycine; charges from LSN
|
|
GROUP ! use in generate statement
|
|
ATOM N NH2 -0.96 !
|
|
ATOM HT1 H 0.34 ! HA1 HT1
|
|
ATOM HT2 H 0.34 ! | /
|
|
! --CA--N--HT2
|
|
ATOM CA CT2 0.10 ! | ! change to CT2 for neutral N terminal glycine
|
|
ATOM HA1 HB2 0.09 ! HA2 ! change to HA1 and HB2 and add HA2 atom for N terminal glycine
|
|
ATOM HA2 HB2 0.09 ! HA2 ! change to HA1 and HB2 and add HA2 atom for N terminal glycine
|
|
DELETE ATOM HN
|
|
BOND HT1 N HT2 N
|
|
DONOR HT1 N
|
|
DONOR HT2 N
|
|
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
|
|
PRES CTER -1.00 ! standard C-terminus
|
|
GROUP ! use in generate statement
|
|
ATOM C CC 0.34 ! OT2(-)
|
|
ATOM OT1 OC -0.67 ! /
|
|
ATOM OT2 OC -0.67 ! -C
|
|
DELETE ATOM O ! \\
|
|
BOND C OT2 ! OT1
|
|
DOUBLE C OT1
|
|
IMPR C CA OT2 OT1
|
|
ACCEPTOR OT1 C
|
|
ACCEPTOR OT2 C
|
|
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
PRES CNEU 0.00 ! protonated (neutral) C-terminu, charges from ASPP
|
|
GROUP ! use in generate statement; C reduced to balance charges
|
|
ATOM C CD 0.72 ! OT2-HT2
|
|
ATOM OT1 OB -0.55 ! /
|
|
ATOM OT2 OH1 -0.61 ! -C
|
|
ATOM HT2B H 0.44 ! \\
|
|
DELETE ATOM O ! OT1
|
|
BOND C OT2 OT2 HT2B
|
|
DOUBLE C OT1
|
|
IMPR C CA OT2 OT1
|
|
ACCEPTOR OT1 C
|
|
ACCEPTOR OT2 C
|
|
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CA C OT2 HT2B 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
PRES PCTE 0.00 ! protonated C-terminus (previously CTP)
|
|
GROUP ! use in generate statement
|
|
ATOM C CD 0.72 ! OT2--HT2
|
|
ATOM OT1 OB -0.55 ! /
|
|
ATOM OT2 OH1 -0.61 ! -C
|
|
ATOM HT2 H 0.44 ! \\
|
|
DELETE ATOM O ! OT1
|
|
BOND C OT2 OT2 HT2 !
|
|
DOUBLE C OT1
|
|
IMPR C CA OT2 OT1
|
|
ACCEPTOR OT1 C
|
|
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
PRES CT1 0.00 ! methylated C-terminus from methyl acetate
|
|
GROUP ! use in generate statement
|
|
ATOM N NH1 -0.47 ! don't use with Gly or Pro
|
|
ATOM HN H 0.31 ! OT1
|
|
ATOM CA CT1 0.17 ! | //
|
|
ATOM HA HB1 0.09 ! -N--CA--C HT1
|
|
ATOM C CD 0.63 ! | | \ /
|
|
ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
|
|
ATOM OT2 OS -0.34 ! \
|
|
ATOM CT CT3 -0.14 ! HT3
|
|
ATOM HT1 HA3 0.09 !
|
|
ATOM HT2 HA3 0.09 !
|
|
ATOM HT3 HA3 0.09 !
|
|
DELETE ATOM O
|
|
BOND C OT2 OT2 CT
|
|
BOND CT HT1 CT HT2 CT HT3
|
|
DOUBLE C OT1
|
|
IMPR C CA OT2 OT1
|
|
ACCEPTOR OT1 C
|
|
ACCEPTOR OT2 C
|
|
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000
|
|
IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000
|
|
IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000
|
|
|
|
PRES CT2 0.00 ! amidated C-terminus
|
|
GROUP ! use in generate statement
|
|
ATOM C CC 0.55 !
|
|
ATOM O O -0.55 ! |
|
|
GROUP ! O=C
|
|
ATOM NT NH2 -0.62 ! |
|
|
ATOM HT1 H 0.32 ! NT
|
|
ATOM HT2 H 0.30 ! / \
|
|
BOND C NT ! HT1 HT2 (HT1 is cis to O)
|
|
BOND NT HT1 NT HT2 !
|
|
IMPR C NT CA O C CA NT O
|
|
IMPR NT C HT1 HT2 NT C HT2 HT1
|
|
DONOR HT1 NT
|
|
DONOR HT2 NT
|
|
IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
PRES CT3 0.00 ! N-Methylamide C-terminus
|
|
GROUP ! use in generate statement
|
|
ATOM C C 0.51 !
|
|
ATOM O O -0.51 ! |
|
|
GROUP ! C=O
|
|
ATOM NT NH1 -0.47 ! |
|
|
ATOM HNT H 0.31 ! NT-HNT
|
|
ATOM CAT CT3 -0.11 ! |
|
|
ATOM HT1 HA3 0.09 ! HT1-CAT-HT3
|
|
ATOM HT2 HA3 0.09 ! |
|
|
ATOM HT3 HA3 0.09 ! HT2
|
|
!
|
|
BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3
|
|
IMPR NT C CAT HNT C CA NT O
|
|
CMAP -C N CA C N CA C NT
|
|
!CMAP CY N CA C N CA C NT
|
|
DONOR HNT NT
|
|
IC N CA C NT 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000
|
|
IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000
|
|
|
|
PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2
|
|
! via acetic acid, use in a patch statement and
|
|
! follow with AUTOgenerate ANGLes DIHEdrals command
|
|
GROUP
|
|
ATOM CB CT2 -0.21 !
|
|
ATOM HB1 HA2 0.09 ! HB1 OD1
|
|
ATOM HB2 HA2 0.09 ! | //
|
|
ATOM CG CD 0.75 ! -CB--CG
|
|
ATOM OD1 OB -0.55 ! | \
|
|
ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2
|
|
ATOM HD2 H 0.44 !
|
|
BOND OD2 HD2
|
|
DONOR HD2 OD2
|
|
IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000
|
|
|
|
PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2
|
|
! via acetic acid, use in a patch statement and
|
|
! follow with AUTOgenerate ANGLes DIHEdrals command
|
|
GROUP
|
|
ATOM CG CT2 -0.21 !
|
|
ATOM HG1 HA2 0.09 ! HG1 OE1
|
|
ATOM HG2 HA2 0.09 ! | //
|
|
ATOM CD CD 0.75 ! -CG--CD
|
|
ATOM OE1 OB -0.55 ! | \
|
|
ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2
|
|
ATOM HE2 H 0.44 !
|
|
BOND OE2 HE2
|
|
DONOR HE2 OE2
|
|
IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000
|
|
|
|
PRES LSN 0.00 ! patch for neutral lysine based on methylamine
|
|
! use in a patch statement
|
|
! follow with AUTOgenerate ANGLes DIHEdrals command
|
|
!delete atom and reassign charges
|
|
DELETE ATOM HZ3
|
|
GROUP
|
|
ATOM CE CT2 0.13
|
|
ATOM HE1 HA2 0.075
|
|
ATOM HE2 HA2 0.075
|
|
ATOM NZ NH2 -0.96
|
|
ATOM HZ1 HC 0.34
|
|
ATOM HZ2 HC 0.34
|
|
|
|
RESI CYM -1.00 ! Anionic Cysteine
|
|
! Thiolate form based on RESI MES1 & ES1 (adm jr.)
|
|
! in toppar_*_prot_model.str
|
|
! Foloppe, N., J. Sagemark, K. Nordstrand, K.D. Berndt, and L. Nilsson
|
|
! (2001). J. Mol. Biol. 310:449-470.
|
|
! Ported to CHARMM36 by kevo and beta hydrogens changed
|
|
! from HA to HA2 based on other AA and RESI ES1
|
|
GROUP
|
|
ATOM N NH1 -0.47 ! |
|
|
ATOM HN H 0.31 ! HN-N
|
|
ATOM CA CT1 0.07 ! | HB1
|
|
ATOM HA HB1 0.09 ! | | -
|
|
GROUP ! HA-CA--CB--SG (thiolate)
|
|
ATOM CB CS -0.38 ! | |
|
|
ATOM HB1 HA2 0.09 ! | HB2
|
|
ATOM HB2 HA2 0.09 ! O=C
|
|
ATOM SG SS -0.80 ! |
|
|
GROUP
|
|
ATOM C C 0.51
|
|
ATOM O O -0.51
|
|
BOND CB CA SG CB N HN N CA
|
|
BOND O C C CA C +N CA HA CB HB1 CB HB2
|
|
IMPR N -C CA HN C CA +N O
|
|
CMAP -C N CA C N CA C +N
|
|
DONOR HN N
|
|
ACCEPTOR O C
|
|
! IC table copied by kevo from RESI CYS
|
|
IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
|
|
IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
|
|
IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
|
|
IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
|
|
IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
|
|
IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
|
|
IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
|
|
IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
|
|
IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
|
|
IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
|
|
|
|
PRES CYSD -1.00 ! patch to deprotonate cysteine by kevo
|
|
DELETE ATOM HG1 ! from RESI ES1 in toppar_*_prot_model.str
|
|
ATOM CB CS -0.38
|
|
ATOM HB1 HA2 0.09
|
|
ATOM HB2 HA2 0.09
|
|
ATOM SG SS -0.80
|
|
! Doesn't require AUTOgenerate.
|
|
|
|
PRES SERD -1.00 ! patch to deprotonate serine by kevo
|
|
DELETE ATOM HG1 ! from RESI ETO in toppar_*_prot_model.str
|
|
ATOM CB CT2 -0.30
|
|
ATOM HB1 HA2 0.11
|
|
ATOM HB2 HA2 0.11
|
|
ATOM OG OC -0.92
|
|
! That's all, folks! Doesn't even need AUTOgenerate.
|
|
|
|
PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS.
|
|
! use in a patch statement
|
|
! follow with AUTOgenerate ANGLes DIHEdrals command
|
|
GROUP
|
|
ATOM 1CB CT2 -0.10 !
|
|
ATOM 1SG SM -0.08 ! 2SG--2CB--
|
|
GROUP ! /
|
|
ATOM 2SG SM -0.08 ! -1CB--1SG
|
|
ATOM 2CB CT2 -0.10 !
|
|
DELETE ATOM 1HG1
|
|
DELETE ATOM 2HG1
|
|
BOND 1SG 2SG
|
|
IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000
|
|
IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2
|
|
! use in a patch statement
|
|
! follow with AUTOgenerate ANGLes DIHEdrals command
|
|
GROUP
|
|
ATOM CE1 CPH2 0.25 ! HE1
|
|
ATOM HE1 HR1 0.13 ! /
|
|
ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1
|
|
ATOM CG CPH1 0.22 ! | / |
|
|
ATOM CB CT2 -0.08 ! -CB--CG |
|
|
ATOM HB1 HA2 0.09 ! | \ |
|
|
ATOM HB2 HA2 0.09 ! HB2 CD2--NE2
|
|
GROUP ! | \
|
|
ATOM NE2 NR1 -0.36 ! HD2 HE2
|
|
ATOM HE2 H 0.32
|
|
ATOM CD2 CPH1 -0.05
|
|
ATOM HD2 HR3 0.09
|
|
DELETE ATOM HD1
|
|
DELETE ACCE NE2
|
|
BOND NE2 HE2
|
|
IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
|
|
DONOR HE2 NE2
|
|
ACCEPTOR ND1
|
|
IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
! patches for cyclic peptides
|
|
! updated 2019_8 to include CMAP. requires specification of 4 residues
|
|
! to include the necessary atoms for the CMAP. LIG2 and LIG3 deleted
|
|
|
|
PRES LIG1 0.00 ! linkage for cyclic peptide
|
|
! 1 refers to the residue prior to the C terminus
|
|
! 2 refers to the C terminus
|
|
! 3 refers to the N terminus
|
|
! 4 refers to the residue following the N terminus
|
|
! use in a patch statement, perform initial
|
|
! generation using first NONE last NONE
|
|
! follow with AUTOgenerate ANGLes DIHEdrals command
|
|
BOND 2C 3N
|
|
IMPR 3N 2C 3CA 3HN 2C 2CA 3N 2O
|
|
CMAP 1C 2N 2CA 2C 2N 2CA 2C 3N ! former C-terminal residue CMAP
|
|
CMAP 2C 3N 3CA 3C 3N 3CA 3C 4N ! former N-terminal residue CMAP
|
|
IC 2N 2CA 2C 3N 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 3N 2CA *2C 2O 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 2CA 2C 3N 3CA 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 2C 3N 3CA 3C 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 2C 3CA *3N 3HN 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
PRES LINK 0.00 ! peptide linkage for IMAGES or for joining segments
|
|
! 1 refers to the residue prior to the C terminus
|
|
! 2 refers to the C terminus
|
|
! 3 refers to the N terminus
|
|
! 4 refers to the residue following the N terminus
|
|
! use in a patch statement, perform initial
|
|
! generation using first NONE last NONE
|
|
! When using this patch for a single residue with IMPATCH
|
|
! (i.e. an infinite chain repeating just one residue),
|
|
! do NOT specify the 4th residue and use the WARN option,
|
|
! and make sure to use IMALL for image updating.
|
|
!omit angles and dihedrals once image autogenerate is complete.
|
|
! ! follow with AUTOgenerate ANGLes DIHEdrals command
|
|
BOND 2C 3N
|
|
!the need for the explicit specification of angles and dihedrals in
|
|
!patches linking images has not been tested
|
|
ANGLE 2C 3N 3CA 2CA 2C 3N
|
|
ANGLE 2O 2C 3N 2C 3N 3HN
|
|
DIHE 2C 3N 3CA 3C 2C 3N 3CA 3HA 2C 3N 3CA 3CB
|
|
DIHE 2HA 2CA 2C 3N 2N 2CA 2C 3N 2CB 2CA 2C 3N
|
|
DIHE 2CA 2C 3N 3HN 2CA 2C 3N 3CA
|
|
DIHE 2O 2C 3N 3HN 2O 2C 3N 3CA
|
|
IMPR 3N 2C 3CA 3HN 2C 2CA 3N 2O
|
|
CMAP 1C 2N 2CA 2C 2N 2CA 2C 3N ! former C-terminal residue CMAP
|
|
CMAP 2C 3N 3CA 3C 3N 3CA 3C 4N ! former N-terminal residue CMAP
|
|
IC 2N 2CA 2C 3N 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 3N 2CA *2C 2O 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 2CA 2C 3N 3CA 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 2C 3N 3CA 3C 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
IC 2C 3CA *3N 3HN 0.0000 0.0000 180.0000 0.0000 0.0000
|
|
|
|
END
|
|
|