packmol-memgen-minimal 1.1.16__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (71) hide show
  1. packmol_memgen/__init__.py +2 -0
  2. packmol_memgen/__version__.py +34 -0
  3. packmol_memgen/data/LICENSE.Apache-2.0 +201 -0
  4. packmol_memgen/data/extra_solvents.lib +789 -0
  5. packmol_memgen/data/frcmod.lipid_ext +97 -0
  6. packmol_memgen/data/frcmod.solvents +129 -0
  7. packmol_memgen/data/insane_lipids.txt +138 -0
  8. packmol_memgen/data/insane_solvents.txt +45 -0
  9. packmol_memgen/data/leaprc.extra_solvents +42 -0
  10. packmol_memgen/data/leaprc.lipid_ext +48 -0
  11. packmol_memgen/data/lipid_ext.lib +12312 -0
  12. packmol_memgen/data/martini_v3.0.0.itp +356605 -0
  13. packmol_memgen/data/memgen.parm +4082 -0
  14. packmol_memgen/data/pdbs.tar.gz +0 -0
  15. packmol_memgen/data/solvent.parm +14 -0
  16. packmol_memgen/example/example.sh +31 -0
  17. packmol_memgen/lib/__init__.py +0 -0
  18. packmol_memgen/lib/amber.py +77 -0
  19. packmol_memgen/lib/charmmlipid2amber/__init__.py +0 -0
  20. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv +7164 -0
  21. packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py +225 -0
  22. packmol_memgen/lib/pdbremix/LICENSE +21 -0
  23. packmol_memgen/lib/pdbremix/__init__.py +0 -0
  24. packmol_memgen/lib/pdbremix/_version.py +1 -0
  25. packmol_memgen/lib/pdbremix/amber.py +1103 -0
  26. packmol_memgen/lib/pdbremix/asa.py +227 -0
  27. packmol_memgen/lib/pdbremix/data/aminoacid.pdb +334 -0
  28. packmol_memgen/lib/pdbremix/data/binaries.json +26 -0
  29. packmol_memgen/lib/pdbremix/data/charmm22.parameter +2250 -0
  30. packmol_memgen/lib/pdbremix/data/charmm22.topology +1635 -0
  31. packmol_memgen/lib/pdbremix/data/color_b.py +682 -0
  32. packmol_memgen/lib/pdbremix/data/hin.lib +130 -0
  33. packmol_memgen/lib/pdbremix/data/hydroxide.lib +88 -0
  34. packmol_memgen/lib/pdbremix/data/make_chi.py +92 -0
  35. packmol_memgen/lib/pdbremix/data/opls.parameter +1108 -0
  36. packmol_memgen/lib/pdbremix/data/opls.topology +1869 -0
  37. packmol_memgen/lib/pdbremix/data/phd.frcmod +82 -0
  38. packmol_memgen/lib/pdbremix/data/phd.leaprc +4 -0
  39. packmol_memgen/lib/pdbremix/data/phd.prepin +35 -0
  40. packmol_memgen/lib/pdbremix/data/template.pdb +334 -0
  41. packmol_memgen/lib/pdbremix/data/znb.frcmod +24 -0
  42. packmol_memgen/lib/pdbremix/data/znb.leaprc +7 -0
  43. packmol_memgen/lib/pdbremix/data/znb.lib +69 -0
  44. packmol_memgen/lib/pdbremix/data.py +264 -0
  45. packmol_memgen/lib/pdbremix/fetch.py +102 -0
  46. packmol_memgen/lib/pdbremix/force.py +627 -0
  47. packmol_memgen/lib/pdbremix/gromacs.py +978 -0
  48. packmol_memgen/lib/pdbremix/lib/__init__.py +0 -0
  49. packmol_memgen/lib/pdbremix/lib/docopt.py +579 -0
  50. packmol_memgen/lib/pdbremix/lib/pyqcprot.py +305 -0
  51. packmol_memgen/lib/pdbremix/namd.py +1078 -0
  52. packmol_memgen/lib/pdbremix/pdbatoms.py +543 -0
  53. packmol_memgen/lib/pdbremix/pdbtext.py +120 -0
  54. packmol_memgen/lib/pdbremix/protein.py +311 -0
  55. packmol_memgen/lib/pdbremix/pymol.py +480 -0
  56. packmol_memgen/lib/pdbremix/rmsd.py +203 -0
  57. packmol_memgen/lib/pdbremix/simulate.py +420 -0
  58. packmol_memgen/lib/pdbremix/spacehash.py +73 -0
  59. packmol_memgen/lib/pdbremix/trajectory.py +286 -0
  60. packmol_memgen/lib/pdbremix/util.py +273 -0
  61. packmol_memgen/lib/pdbremix/v3.py +16 -0
  62. packmol_memgen/lib/pdbremix/v3array.py +482 -0
  63. packmol_memgen/lib/pdbremix/v3numpy.py +350 -0
  64. packmol_memgen/lib/pdbremix/volume.py +155 -0
  65. packmol_memgen/lib/utils.py +1017 -0
  66. packmol_memgen/main.py +2827 -0
  67. packmol_memgen_minimal-1.1.16.dist-info/METADATA +664 -0
  68. packmol_memgen_minimal-1.1.16.dist-info/RECORD +71 -0
  69. packmol_memgen_minimal-1.1.16.dist-info/WHEEL +4 -0
  70. packmol_memgen_minimal-1.1.16.dist-info/entry_points.txt +2 -0
  71. packmol_memgen_minimal-1.1.16.dist-info/licenses/LICENSE +338 -0
packmol_memgen/lib/pdbremix/data/charmm22.topology ADDED
@@ -0,0 +1,1635 @@
1
+ *>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
2
+ *>>>>>>>>>>>>>>>>>>>>> December 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
3
+ * All comments to ADM jr. via the CHARMM web site: www.charmm.org
4
+ * parameter set discussion forum
5
+ *
6
+ 22 1
7
+
8
+ !includes revised aliphatic carbon parameters see (CT*x) for use with
9
+ !trifluoroethanol
10
+
11
+ !
12
+ !
13
+ ! references
14
+ !
15
+ !PROTEINS
16
+ !
17
+ !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
18
+ !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
19
+ !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
20
+ !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
21
+ !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
22
+ !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
23
+ !empirical potential for molecular modeling and dynamics Studies of
24
+ !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
25
+ !
26
+ !IONS (see lipid and nucleic acid topology and parameter files for
27
+ !additional ions
28
+ !
29
+ !ZINC
30
+ !
31
+ !Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
32
+ !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
33
+ !Structure, Function, and Genetics 23:12-31 (1995)
34
+ !
35
+
36
+ MASS 1 H 1.00800 H ! polar H
37
+ MASS 2 HC 1.00800 H ! N-ter H
38
+ MASS 3 HA 1.00800 H ! nonpolar H
39
+ MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
40
+ MASS 5 HP 1.00800 H ! aromatic H
41
+ MASS 6 HB 1.00800 H ! backbone H
42
+ MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2
43
+ MASS 8 HR2 1.00800 H ! (+) his HE1
44
+ MASS 9 HR3 1.00800 H ! neutral his HG, HD2
45
+ MASS 10 HS 1.00800 H ! thiol hydrogen
46
+ MASS 11 HE1 1.00800 H ! for alkene; RHC=CR
47
+ MASS 12 HE2 1.00800 H ! for alkene; H2C=CR
48
+ MASS 13 HA1 1.00800 H ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
49
+ MASS 14 HA2 1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
50
+ MASS 15 HA3 1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
51
+ MASS 16 HF1 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
52
+ MASS 17 HF2 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
53
+ MASS 20 C 12.01100 C ! carbonyl C, peptide backbone
54
+ MASS 21 CA 12.01100 C ! aromatic C
55
+ MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH
56
+ MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2
57
+ MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3
58
+ MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons
59
+ MASS 26 CPH2 12.01100 C ! his CE1 carbon
60
+ MASS 27 CPT 12.01100 C ! trp C between rings
61
+ MASS 28 CY 12.01100 C ! TRP C in pyrrole ring
62
+ MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA)
63
+ MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG)
64
+ MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD)
65
+ MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2
66
+ MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1
67
+ MASS 34 CPA 12.01100 C ! heme alpha-C
68
+ MASS 35 CPB 12.01100 C ! heme beta-C
69
+ MASS 36 CPM 12.01100 C ! heme meso-C
70
+ MASS 37 CM 12.01100 C ! heme CO carbon
71
+ MASS 38 CS 12.01100 C ! thiolate carbon
72
+ MASS 39 CE1 12.01100 C ! for alkene; RHC=CR
73
+ MASS 40 CE2 12.01100 C ! for alkene; H2C=CR
74
+ MASS 41 CST 12.01100 C ! CO2 carbon
75
+ MASS 42 CT 12.01100 C ! aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str)
76
+ MASS 43 CT1x 12.01100 C ! aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
77
+ MASS 44 CT2x 12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
78
+ MASS 45 CT3x 12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
79
+ MASS 46 CN 12.01100 C ! C for cyano group (see toppar_all22_prot_pyridines.str)
80
+ MASS 47 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str)
81
+ MASS 48 COA 12.01100 C ! carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str)
82
+ MASS 50 N 14.00700 N ! proline N
83
+ MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen
84
+ MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen
85
+ MASS 53 NR3 14.00700 N ! charged his ring nitrogen
86
+ MASS 54 NH1 14.00700 N ! peptide nitrogen
87
+ MASS 55 NH2 14.00700 N ! amide nitrogen
88
+ MASS 56 NH3 14.00700 N ! ammonium nitrogen
89
+ MASS 57 NC2 14.00700 N ! guanidinium nitroogen
90
+ MASS 58 NY 14.00700 N ! TRP N in pyrrole ring
91
+ MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal)
92
+ MASS 60 NPH 14.00700 N ! heme pyrrole N
93
+ MASS 61 NC 14.00700 N ! N for cyano group (see toppar_all22_prot_pyridines.str)
94
+ MASS 70 O 15.99900 O ! carbonyl oxygen
95
+ MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid
96
+ MASS 72 OC 15.99900 O ! carboxylate oxygen
97
+ MASS 73 OH1 15.99900 O ! hydroxyl oxygen
98
+ MASS 74 OS 15.99940 O ! ester oxygen
99
+ MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN
100
+ MASS 76 OM 15.99900 O ! heme CO/O2 oxygen
101
+ MASS 77 OST 15.99900 O ! CO2 oxygen
102
+ MASS 78 OCA 15.99900 O ! carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str)
103
+ MASS 81 S 32.06000 S ! sulphur
104
+ MASS 82 SM 32.06000 S ! sulfur C-S-S-C type
105
+ MASS 83 SS 32.06000 S ! thiolate sulfur
106
+ MASS 85 HE 4.00260 HE ! helium
107
+ MASS 86 NE 20.17970 NE ! neon
108
+ MASS 87 CF1 12.01100 C ! monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
109
+ MASS 88 CF2 12.01100 C ! difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
110
+ MASS 89 CF3 12.01100 C ! trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
111
+ MASS 90 FE 55.84700 Fe ! heme iron 56
112
+ MASS 91 CLAL 35.45300 CL ! Chlorine Atom (see toppar_all22_prot_aldehydes.str)
113
+ MASS 92 FA 18.99800 F ! aromatic flourine (see toppar_all22_prot_pyridines.str)
114
+ MASS 93 F1 18.99800 F ! Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str)
115
+ MASS 94 F2 18.99800 F ! Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str)
116
+ MASS 95 F3 18.99800 F ! Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str)
117
+ MASS 99 DUM 0.00000 H ! dummy atom
118
+ MASS 100 SOD 22.989770 NA ! Sodium Ion
119
+ MASS 101 MG 24.305000 MG ! Magnesium Ion
120
+ MASS 102 POT 39.102000 K ! Potassium Ion! check masses
121
+ MASS 103 CES 132.900000 CS ! Cesium Ion
122
+ MASS 104 CAL 40.080000 CA ! Calcium Ion
123
+ MASS 105 CLA 35.450000 CL ! Chloride Ion
124
+ MASS 106 ZN 65.370000 ZN ! zinc (II) cation
125
+
126
+ DECL -CA
127
+ DECL -C
128
+ DECL -O
129
+ DECL +N
130
+ DECL +HN
131
+ DECL +CA
132
+ DEFA FIRS NTER LAST CTER
133
+ AUTO ANGLES DIHE
134
+
135
+ RESI ALA 0.00
136
+ GROUP
137
+ ATOM N NH1 -0.47 ! |
138
+ ATOM HN H 0.31 ! HN-N
139
+ ATOM CA CT1 0.07 ! | HB1
140
+ ATOM HA HB 0.09 ! | /
141
+ GROUP ! HA-CA--CB-HB2
142
+ ATOM CB CT3 -0.27 ! | \
143
+ ATOM HB1 HA 0.09 ! | HB3
144
+ ATOM HB2 HA 0.09 ! O=C
145
+ ATOM HB3 HA 0.09 ! |
146
+ GROUP !
147
+ ATOM C C 0.51
148
+ ATOM O O -0.51
149
+ BOND CB CA N HN N CA
150
+ BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
151
+ DOUBLE O C
152
+ IMPR N -C CA HN C CA +N O
153
+ DONOR HN N
154
+ ACCEPTOR O C
155
+ IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
156
+ IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390
157
+ IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558
158
+ IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
159
+ IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
160
+ IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
161
+ IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
162
+ IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
163
+ IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
164
+ IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
165
+
166
+ RESI ARG 1.00
167
+ GROUP
168
+ ATOM N NH1 -0.47 ! | HH11
169
+ ATOM HN H 0.31 ! HN-N |
170
+ ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12
171
+ ATOM HA HB 0.09 ! | | | | | //(+)
172
+ GROUP ! HA-CA--CB--CG--CD--NE--CZ
173
+ ATOM CB CT2 -0.18 ! | | | | \
174
+ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22
175
+ ATOM HB2 HA 0.09 ! O=C |
176
+ GROUP ! | HH21
177
+ ATOM CG CT2 -0.18
178
+ ATOM HG1 HA 0.09
179
+ ATOM HG2 HA 0.09
180
+ GROUP
181
+ ATOM CD CT2 0.20
182
+ ATOM HD1 HA 0.09
183
+ ATOM HD2 HA 0.09
184
+ ATOM NE NC2 -0.70
185
+ ATOM HE HC 0.44
186
+ ATOM CZ C 0.64
187
+ ATOM NH1 NC2 -0.80
188
+ ATOM HH11 HC 0.46
189
+ ATOM HH12 HC 0.46
190
+ ATOM NH2 NC2 -0.80
191
+ ATOM HH21 HC 0.46
192
+ ATOM HH22 HC 0.46
193
+ GROUP
194
+ ATOM C C 0.51
195
+ ATOM O O -0.51
196
+ BOND CB CA CG CB CD CG NE CD CZ NE
197
+ BOND NH2 CZ N HN N CA
198
+ BOND C CA C +N CA HA CB HB1
199
+ BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2
200
+ BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22
201
+ DOUBLE O C CZ NH1
202
+ IMPR N -C CA HN C CA +N O
203
+ IMPR CZ NH1 NH2 NE
204
+ DONOR HN N
205
+ DONOR HE NE
206
+ DONOR HH11 NH1
207
+ DONOR HH12 NH1
208
+ DONOR HH21 NH2
209
+ DONOR HH22 NH2
210
+ ACCEPTOR O C
211
+ IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973
212
+ IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227
213
+ IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511
214
+ IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271
215
+ IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565
216
+ IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552
217
+ IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836
218
+ IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475
219
+ IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163
220
+ IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124
221
+ IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384
222
+ IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121
223
+ IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143
224
+ IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034
225
+ IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143
226
+ IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150
227
+ IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401
228
+ IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065
229
+ IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311
230
+ IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903
231
+ IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023
232
+ IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292
233
+ IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899
234
+ IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914
235
+
236
+ RESI ASN 0.00
237
+ GROUP
238
+ ATOM N NH1 -0.47 ! |
239
+ ATOM HN H 0.31 ! HN-N
240
+ ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1)
241
+ ATOM HA HB 0.09 ! | | || /
242
+ GROUP ! HA-CA--CB--CG--ND2
243
+ ATOM CB CT2 -0.18 ! | | \
244
+ ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1)
245
+ ATOM HB2 HA 0.09 ! O=C
246
+ GROUP ! |
247
+ ATOM CG CC 0.55
248
+ ATOM OD1 O -0.55
249
+ GROUP
250
+ ATOM ND2 NH2 -0.62
251
+ ATOM HD21 H 0.32
252
+ ATOM HD22 H 0.30
253
+ GROUP
254
+ ATOM C C 0.51
255
+ ATOM O O -0.51
256
+ BOND CB CA CG CB ND2 CG
257
+ BOND N HN N CA C CA C +N
258
+ BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22
259
+ DOUBLE C O CG OD1
260
+ IMPR N -C CA HN C CA +N O
261
+ IMPR CG ND2 CB OD1 CG CB ND2 OD1
262
+ IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21
263
+ DONOR HN N
264
+ DONOR HD21 ND2
265
+ DONOR HD22 ND2
266
+ ACCEPTOR OD1 CG
267
+ ACCEPTOR O C
268
+ IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992
269
+ IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245
270
+ IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467
271
+ IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282
272
+ IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528
273
+ IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627
274
+ IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848
275
+ IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319
276
+ IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120
277
+ IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091
278
+ IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323
279
+ IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521
280
+ IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963
281
+ IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951
282
+
283
+ RESI ASP -1.00
284
+ GROUP
285
+ ATOM N NH1 -0.47 ! |
286
+ ATOM HN H 0.31 ! HN-N
287
+ ATOM CA CT1 0.07 ! | HB1 OD1
288
+ ATOM HA HB 0.09 ! | | //
289
+ GROUP ! HA-CA--CB--CG
290
+ ATOM CB CT2 -0.28 ! | | \
291
+ ATOM HB1 HA 0.09 ! | HB2 OD2(-)
292
+ ATOM HB2 HA 0.09 ! O=C
293
+ ATOM CG CC 0.62 ! |
294
+ ATOM OD1 OC -0.76
295
+ ATOM OD2 OC -0.76
296
+ GROUP
297
+ ATOM C C 0.51
298
+ ATOM O O -0.51
299
+ BOND CB CA CG CB OD2 CG
300
+ BOND N HN N CA C CA C +N
301
+ BOND CA HA CB HB1 CB HB2
302
+ DOUBLE O C CG OD1
303
+ IMPR N -C CA HN C CA +N O
304
+ !IMPR OD1 CB OD2 CG
305
+ IMPR CG CB OD2 OD1
306
+ DONOR HN N
307
+ ACCEPTOR OD1 CG
308
+ ACCEPTOR OD2 CG
309
+ ACCEPTOR O C
310
+ IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966
311
+ IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315
312
+ IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478
313
+ IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330
314
+ IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484
315
+ IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619
316
+ IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841
317
+ IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218
318
+ IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086
319
+ IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080
320
+ IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565
321
+ IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541
322
+
323
+ RESI CYS 0.00
324
+ GROUP
325
+ ATOM N NH1 -0.47 ! |
326
+ ATOM HN H 0.31 ! HN-N
327
+ ATOM CA CT1 0.07 ! | HB1
328
+ ATOM HA HB 0.09 ! | |
329
+ GROUP ! HA-CA--CB--SG
330
+ ATOM CB CT2 -0.11 ! | | \
331
+ ATOM HB1 HA 0.09 ! | HB2 HG1
332
+ ATOM HB2 HA 0.09 ! O=C
333
+ ATOM SG S -0.23 ! |
334
+ ATOM HG1 HS 0.16
335
+ GROUP
336
+ ATOM C C 0.51
337
+ ATOM O O -0.51
338
+ BOND CB CA SG CB N HN N CA
339
+ BOND C CA C +N CA HA CB HB1
340
+ BOND CB HB2 SG HG1
341
+ DOUBLE O C
342
+ IMPR N -C CA HN C CA +N O
343
+ DONOR HN N
344
+ DONOR HG1 SG
345
+ ACCEPTOR O C
346
+ IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
347
+ IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
348
+ IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
349
+ IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
350
+ IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
351
+ IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
352
+ IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
353
+ IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
354
+ IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
355
+ IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
356
+ IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341
357
+
358
+ RESI GLN 0.00
359
+ GROUP
360
+ ATOM N NH1 -0.47 ! |
361
+ ATOM HN H 0.31 ! HN-N
362
+ ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1)
363
+ ATOM HA HB 0.09 ! | | | || /
364
+ GROUP ! HA-CA--CB--CG--CD--NE2
365
+ ATOM CB CT2 -0.18 ! | | | \
366
+ ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1)
367
+ ATOM HB2 HA 0.09 ! O=C
368
+ GROUP ! |
369
+ ATOM CG CT2 -0.18
370
+ ATOM HG1 HA 0.09
371
+ ATOM HG2 HA 0.09
372
+ GROUP
373
+ ATOM CD CC 0.55
374
+ ATOM OE1 O -0.55
375
+ GROUP
376
+ ATOM NE2 NH2 -0.62
377
+ ATOM HE21 H 0.32
378
+ ATOM HE22 H 0.30
379
+ GROUP
380
+ ATOM C C 0.51
381
+ ATOM O O -0.51
382
+ BOND CB CA CG CB CD CG NE2 CD
383
+ BOND N HN N CA C CA
384
+ BOND C +N CA HA CB HB1 CB HB2 CG HG1
385
+ BOND CG HG2 NE2 HE21 NE2 HE22
386
+ DOUBLE O C CD OE1
387
+ IMPR N -C CA HN C CA +N O
388
+ IMPR CD NE2 CG OE1 CD CG NE2 OE1
389
+ IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21
390
+ DONOR HN N
391
+ DONOR HE21 NE2
392
+ DONOR HE22 NE2
393
+ ACCEPTOR OE1 CD
394
+ ACCEPTOR O C
395
+ IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984
396
+ IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180
397
+ IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463
398
+ IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291
399
+ IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461
400
+ IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538
401
+ IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832
402
+ IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534
403
+ IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147
404
+ IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140
405
+ IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320
406
+ IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112
407
+ IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094
408
+ IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294
409
+ IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530
410
+ IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959
411
+ IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943
412
+
413
+ RESI GLU -1.00
414
+ GROUP
415
+ ATOM N NH1 -0.47 ! |
416
+ ATOM HN H 0.31 ! HN-N
417
+ ATOM CA CT1 0.07 ! | HB1 HG1 OE1
418
+ ATOM HA HB 0.09 ! | | | //
419
+ GROUP ! HA-CA--CB--CG--CD
420
+ ATOM CB CT2 -0.18 ! | | | \
421
+ ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-)
422
+ ATOM HB2 HA 0.09 ! O=C
423
+ GROUP ! |
424
+ ATOM CG CT2 -0.28
425
+ ATOM HG1 HA 0.09
426
+ ATOM HG2 HA 0.09
427
+ ATOM CD CC 0.62
428
+ ATOM OE1 OC -0.76
429
+ ATOM OE2 OC -0.76
430
+ GROUP
431
+ ATOM C C 0.51
432
+ ATOM O O -0.51
433
+ BOND CB CA CG CB CD CG OE2 CD
434
+ BOND N HN N CA C CA
435
+ BOND C +N CA HA CB HB1 CB HB2 CG HG1
436
+ BOND CG HG2
437
+ DOUBLE O C CD OE1
438
+ IMPR N -C CA HN C CA +N O
439
+ !IMPR OE1 CG OE2 CD
440
+ IMPR CD CG OE2 OE1
441
+ DONOR HN N
442
+ ACCEPTOR OE1 CD
443
+ ACCEPTOR OE2 CD
444
+ ACCEPTOR O C
445
+ IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961
446
+ IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216
447
+ IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501
448
+ IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306
449
+ IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530
450
+ IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516
451
+ IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828
452
+ IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557
453
+ IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
454
+ IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
455
+ IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307
456
+ IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053
457
+ IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081
458
+ IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590
459
+ IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532
460
+
461
+ RESI GLY 0.00
462
+ GROUP
463
+ ATOM N NH1 -0.47 ! |
464
+ ATOM HN H 0.31 ! N-H
465
+ ATOM CA CT2 -0.02 ! |
466
+ ATOM HA1 HB 0.09 ! |
467
+ ATOM HA2 HB 0.09 ! HA1-CA-HA2
468
+ GROUP ! |
469
+ ATOM C C 0.51 ! |
470
+ ATOM O O -0.51 ! C=O
471
+ ! |
472
+ BOND N HN N CA C CA
473
+ BOND C +N CA HA1 CA HA2
474
+ DOUBLE O C
475
+ IMPR N -C CA HN C CA +N O
476
+ DONOR HN N
477
+ ACCEPTOR O C
478
+ IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992
479
+ IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971
480
+ IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479
481
+ IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289
482
+ IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560
483
+ IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814
484
+ IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817
485
+ PATCHING FIRS GLYP
486
+
487
+ RESI HSD 0.00 ! neutral HIS, proton on ND1
488
+ GROUP
489
+ ATOM N NH1 -0.47 ! | HD1 HE1
490
+ ATOM HN H 0.31 ! HN-N | /
491
+ ATOM CA CT1 0.07 ! | HB1 ND1--CE1
492
+ ATOM HA HB 0.09 ! | | / ||
493
+ GROUP ! HA-CA--CB--CG ||
494
+ ATOM CB CT2 -0.09 ! | | \\ ||
495
+ ATOM HB1 HA 0.09 ! | HB2 CD2--NE2
496
+ ATOM HB2 HA 0.09 ! O=C |
497
+ ATOM ND1 NR1 -0.36 ! | HD2
498
+ ATOM HD1 H 0.32
499
+ ATOM CG CPH1 -0.05
500
+ GROUP
501
+ ATOM CE1 CPH2 0.25
502
+ ATOM HE1 HR1 0.13
503
+ ATOM NE2 NR2 -0.70
504
+ ATOM CD2 CPH1 0.22
505
+ ATOM HD2 HR3 0.10
506
+ GROUP
507
+ ATOM C C 0.51
508
+ ATOM O O -0.51
509
+ BOND CB CA CG CB ND1 CG CE1 ND1
510
+ BOND NE2 CD2 N HN N CA
511
+ BOND C CA C +N CA HA CB HB1
512
+ BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1
513
+ DOUBLE O C CG CD2 CE1 NE2
514
+ IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
515
+ IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
516
+ IMPR N -C CA HN C CA +N O
517
+ DONOR HN N
518
+ DONOR HD1 ND1
519
+ ACCEPTOR NE2
520
+ ACCEPTOR O C
521
+ IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988
522
+ IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166
523
+ IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509
524
+ IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273
525
+ IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545
526
+ IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519
527
+ IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830
528
+ IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041
529
+ IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118
530
+ IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121
531
+ IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783
532
+ IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597
533
+ IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549
534
+ IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817
535
+ IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932
536
+ IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005
537
+ IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834
538
+
539
+ RESI HSE 0.00 ! neutral His, proton on NE2
540
+ GROUP
541
+ ATOM N NH1 -0.47 ! | HE1
542
+ ATOM HN H 0.31 ! HN-N __ /
543
+ ATOM CA CT1 0.07 ! | HB1 ND1--CE1
544
+ ATOM HA HB 0.09 ! | | / |
545
+ GROUP ! HA-CA--CB--CG |
546
+ ATOM CB CT2 -0.08 ! | | \\ |
547
+ ATOM HB1 HA 0.09 ! | HB2 CD2--NE2
548
+ ATOM HB2 HA 0.09 ! O=C | \
549
+ ATOM ND1 NR2 -0.70 ! | HD2 HE2
550
+ ATOM CG CPH1 0.22
551
+ ATOM CE1 CPH2 0.25
552
+ ATOM HE1 HR1 0.13
553
+ GROUP
554
+ ATOM NE2 NR1 -0.36
555
+ ATOM HE2 H 0.32
556
+ ATOM CD2 CPH1 -0.05
557
+ ATOM HD2 HR3 0.09
558
+ GROUP
559
+ ATOM C C 0.51
560
+ ATOM O O -0.51
561
+ BOND CB CA CG CB ND1 CG
562
+ BOND NE2 CD2 N HN N CA
563
+ BOND C CA C +N NE2 CE1 CA HA CB HB1
564
+ BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1
565
+ DOUBLE O C CD2 CG CE1 ND1
566
+ IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
567
+ IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
568
+ IMPR N -C CA HN C CA +N O
569
+ DONOR HN N
570
+ DONOR HE2 NE2
571
+ ACCEPTOR ND1
572
+ ACCEPTOR O C
573
+ IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991
574
+ IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166
575
+ IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446
576
+ IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290
577
+ IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505
578
+ IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578
579
+ IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833
580
+ IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109
581
+ IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114
582
+ IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101
583
+ IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859
584
+ IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596
585
+ IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170
586
+ IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782
587
+ IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929
588
+ IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996
589
+ IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809
590
+
591
+ RESI HSP 1.00 ! Protonated His
592
+ GROUP
593
+ ATOM N NH1 -0.47 ! | HD1 HE1
594
+ ATOM HN H 0.31 ! HN-N | /
595
+ ATOM CA CT1 0.07 ! | HB1 ND1--CE1
596
+ ATOM HA HB 0.09 ! | | / ||
597
+ GROUP ! HA-CA--CB--CG ||
598
+ ATOM CB CT2 -0.05 ! | | \\ ||
599
+ ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+)
600
+ ATOM HB2 HA 0.09 ! O=C | \
601
+ ATOM CD2 CPH1 0.19 ! | HD2 HE2
602
+ ATOM HD2 HR1 0.13
603
+ ATOM CG CPH1 0.19
604
+ GROUP
605
+ ATOM NE2 NR3 -0.51
606
+ ATOM HE2 H 0.44
607
+ ATOM ND1 NR3 -0.51
608
+ ATOM HD1 H 0.44
609
+ ATOM CE1 CPH2 0.32
610
+ ATOM HE1 HR2 0.18
611
+ GROUP
612
+ ATOM C C 0.51
613
+ ATOM O O -0.51
614
+ BOND CB CA CG CB ND1 CG CE1 ND1
615
+ BOND NE2 CD2 N HN N CA
616
+ BOND C CA C +N CA HA CB HB1
617
+ BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1
618
+ DOUBLE O C CD2 CG NE2 CE1
619
+ IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1
620
+ IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
621
+ IMPR N -C CA HN C CA +N O
622
+ DONOR HN N
623
+ DONOR HD1 ND1
624
+ DONOR HE2 NE2
625
+ ACCEPTOR O C
626
+ IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041
627
+ IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225
628
+ IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464
629
+ IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284
630
+ IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521
631
+ IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533
632
+ IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832
633
+ IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168
634
+ IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116
635
+ IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132
636
+ IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718
637
+ IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549
638
+ IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262
639
+ IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727
640
+ IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799
641
+ IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020
642
+ IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018
643
+ IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867
644
+
645
+ RESI ILE 0.00
646
+ GROUP
647
+ ATOM N NH1 -0.47 ! | HG21 HG22
648
+ ATOM HN H 0.31 ! HN-N | /
649
+ ATOM CA CT1 0.07 ! | CG2--HG23
650
+ ATOM HA HB 0.09 ! | /
651
+ GROUP ! HA-CA--CB-HB HD1
652
+ ATOM CB CT1 -0.09 ! | \ /
653
+ ATOM HB HA 0.09 ! | CG1--CD--HD2
654
+ GROUP ! O=C / \ \
655
+ ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3
656
+ ATOM HG21 HA 0.09
657
+ ATOM HG22 HA 0.09
658
+ ATOM HG23 HA 0.09
659
+ GROUP
660
+ ATOM CG1 CT2 -0.18
661
+ ATOM HG11 HA 0.09
662
+ ATOM HG12 HA 0.09
663
+ GROUP
664
+ ATOM CD CT3 -0.27
665
+ ATOM HD1 HA 0.09
666
+ ATOM HD2 HA 0.09
667
+ ATOM HD3 HA 0.09
668
+ GROUP
669
+ ATOM C C 0.51
670
+ ATOM O O -0.51
671
+ BOND CB CA CG1 CB CG2 CB CD CG1
672
+ BOND N HN N CA C CA C +N
673
+ BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21
674
+ BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3
675
+ DOUBLE O C
676
+ IMPR N -C CA HN C CA +N O
677
+ DONOR HN N
678
+ ACCEPTOR O C
679
+ IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978
680
+ IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190
681
+ IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465
682
+ IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300
683
+ IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467
684
+ IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681
685
+ IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826
686
+ IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498
687
+ IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195
688
+ IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452
689
+ IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100
690
+ IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102
691
+ IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105
692
+ IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381
693
+ IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130
694
+ IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141
695
+ IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115
696
+ IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113
697
+ IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103
698
+
699
+ RESI LEU 0.00
700
+ GROUP
701
+ ATOM N NH1 -0.47 ! | HD11 HD12
702
+ ATOM HN H 0.31 ! HN-N | /
703
+ ATOM CA CT1 0.07 ! | HB1 CD1--HD13
704
+ ATOM HA HB 0.09 ! | | /
705
+ GROUP ! HA-CA--CB--CG-HG
706
+ ATOM CB CT2 -0.18 ! | | \
707
+ ATOM HB1 HA 0.09 ! | HB2 CD2--HD23
708
+ ATOM HB2 HA 0.09 ! O=C | \
709
+ GROUP ! | HD21 HD22
710
+ ATOM CG CT1 -0.09
711
+ ATOM HG HA 0.09
712
+ GROUP
713
+ ATOM CD1 CT3 -0.27
714
+ ATOM HD11 HA 0.09
715
+ ATOM HD12 HA 0.09
716
+ ATOM HD13 HA 0.09
717
+ GROUP
718
+ ATOM CD2 CT3 -0.27
719
+ ATOM HD21 HA 0.09
720
+ ATOM HD22 HA 0.09
721
+ ATOM HD23 HA 0.09
722
+ GROUP
723
+ ATOM C C 0.51
724
+ ATOM O O -0.51
725
+ BOND CB CA CG CB CD1 CG CD2 CG
726
+ BOND N HN N CA C CA C +N
727
+ BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11
728
+ BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23
729
+ DOUBLE O C
730
+ IMPR N -C CA HN C CA +N O
731
+ DONOR HN N
732
+ ACCEPTOR O C
733
+ IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979
734
+ IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184
735
+ IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463
736
+ IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299
737
+ IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467
738
+ IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543
739
+ IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824
740
+ IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472
741
+ IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145
742
+ IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126
743
+ IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361
744
+ IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360
745
+ IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168
746
+ IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111
747
+ IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112
748
+ IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108
749
+ IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116
750
+ IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086
751
+ IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115
752
+
753
+ RESI LYS 1.00
754
+ GROUP
755
+ ATOM N NH1 -0.47 ! |
756
+ ATOM HN H 0.31 ! HN-N
757
+ ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1
758
+ ATOM HA HB 0.09 ! | | | | | /
759
+ GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2
760
+ ATOM CB CT2 -0.18 ! | | | | | \
761
+ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3
762
+ ATOM HB2 HA 0.09 ! O=C
763
+ GROUP ! |
764
+ ATOM CG CT2 -0.18
765
+ ATOM HG1 HA 0.09
766
+ ATOM HG2 HA 0.09
767
+ GROUP
768
+ ATOM CD CT2 -0.18
769
+ ATOM HD1 HA 0.09
770
+ ATOM HD2 HA 0.09
771
+ GROUP
772
+ ATOM CE CT2 0.21
773
+ ATOM HE1 HA 0.05
774
+ ATOM HE2 HA 0.05
775
+ ATOM NZ NH3 -0.30
776
+ ATOM HZ1 HC 0.33
777
+ ATOM HZ2 HC 0.33
778
+ ATOM HZ3 HC 0.33
779
+ GROUP
780
+ ATOM C C 0.51
781
+ ATOM O O -0.51
782
+ BOND CB CA CG CB CD CG CE CD NZ CE
783
+ BOND N HN N CA C CA
784
+ BOND C +N CA HA CB HB1 CB HB2 CG HG1
785
+ BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2
786
+ DOUBLE O C
787
+ BOND NZ HZ1 NZ HZ2 NZ HZ3
788
+ IMPR N -C CA HN C CA +N O
789
+ DONOR HN N
790
+ DONOR HZ1 NZ
791
+ DONOR HZ2 NZ
792
+ DONOR HZ3 NZ
793
+ ACCEPTOR O C
794
+ IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988
795
+ IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187
796
+ IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478
797
+ IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277
798
+ IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487
799
+ IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568
800
+ IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833
801
+ IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435
802
+ IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146
803
+ IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131
804
+ IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397
805
+ IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138
806
+ IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143
807
+ IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350
808
+ IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141
809
+ IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146
810
+ IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604
811
+ IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128
812
+ IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123
813
+ IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404
814
+ IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402
815
+ IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401
816
+
817
+ RESI MET 0.00
818
+ GROUP
819
+ ATOM N NH1 -0.47 ! |
820
+ ATOM HN H 0.31 ! HN-N
821
+ ATOM CA CT1 0.07 ! | HB1 HG1 HE1
822
+ ATOM HA HB 0.09 ! | | | |
823
+ GROUP ! HA-CA--CB--CG--SD--CE--HE3
824
+ ATOM CB CT2 -0.18 ! | | | |
825
+ ATOM HB1 HA 0.09 ! | HB2 HG2 HE2
826
+ ATOM HB2 HA 0.09 ! O=C
827
+ GROUP ! |
828
+ ATOM CG CT2 -0.14
829
+ ATOM HG1 HA 0.09
830
+ ATOM HG2 HA 0.09
831
+ ATOM SD S -0.09
832
+ ATOM CE CT3 -0.22
833
+ ATOM HE1 HA 0.09
834
+ ATOM HE2 HA 0.09
835
+ ATOM HE3 HA 0.09
836
+ GROUP
837
+ ATOM C C 0.51
838
+ ATOM O O -0.51
839
+ BOND CB CA CG CB SD CG CE SD
840
+ BOND N HN N CA C CA C +N
841
+ BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2
842
+ BOND CE HE1 CE HE2 CE HE3
843
+ DOUBLE O C
844
+ IMPR N -C CA HN C CA +N O
845
+ DONOR HN N
846
+ ACCEPTOR O C
847
+ IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978
848
+ IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195
849
+ IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471
850
+ IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288
851
+ IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471
852
+ IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546
853
+ IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832
854
+ IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460
855
+ IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153
856
+ IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129
857
+ IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219
858
+ IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106
859
+ IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119
860
+ IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206
861
+ IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111
862
+ IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115
863
+ IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112
864
+
865
+ RESI PHE 0.00
866
+ GROUP
867
+ ATOM N NH1 -0.47 ! | HD1 HE1
868
+ ATOM HN H 0.31 ! HN-N | |
869
+ ATOM CA CT1 0.07 ! | HB1 CD1--CE1
870
+ ATOM HA HB 0.09 ! | | // \\
871
+ GROUP ! HA-CA--CB--CG CZ--HZ
872
+ ATOM CB CT2 -0.18 ! | | \ __ /
873
+ ATOM HB1 HA 0.09 ! | HB2 CD2--CE2
874
+ ATOM HB2 HA 0.09 ! O=C | |
875
+ GROUP ! | HD2 HE2
876
+ ATOM CG CA 0.00
877
+ GROUP
878
+ ATOM CD1 CA -0.115
879
+ ATOM HD1 HP 0.115
880
+ GROUP
881
+ ATOM CE1 CA -0.115
882
+ ATOM HE1 HP 0.115
883
+ GROUP
884
+ ATOM CZ CA -0.115
885
+ ATOM HZ HP 0.115
886
+ GROUP
887
+ ATOM CD2 CA -0.115
888
+ ATOM HD2 HP 0.115
889
+ GROUP
890
+ ATOM CE2 CA -0.115
891
+ ATOM HE2 HP 0.115
892
+ GROUP
893
+ ATOM C C 0.51
894
+ ATOM O O -0.51
895
+ BOND CB CA CG CB CD2 CG CE1 CD1
896
+ BOND CZ CE2 N HN
897
+ BOND N CA C CA C +N CA HA
898
+ BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1
899
+ DOUBLE O C CD1 CG CZ CE1 CE2 CD2
900
+ BOND CE2 HE2 CZ HZ
901
+ IMPR N -C CA HN C CA +N O
902
+ DONOR HN N
903
+ ACCEPTOR O C
904
+ IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987
905
+ IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229
906
+ IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483
907
+ IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287
908
+ IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523
909
+ IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594
910
+ IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832
911
+ IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109
912
+ IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119
913
+ IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113
914
+ IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059
915
+ IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062
916
+ IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006
917
+ IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814
918
+ IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002
919
+ IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811
920
+ IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004
921
+ IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808
922
+ IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811
923
+ IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807
924
+
925
+ RESI PRO 0.00
926
+ GROUP ! HD1 HD2
927
+ ATOM N N -0.29 ! | \ /
928
+ ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02
929
+ ATOM HD1 HA 0.09 ! | \ /
930
+ ATOM HD2 HA 0.09 ! | CG
931
+ ATOM CA CP1 0.02 ! | / \
932
+ ATOM HA HB 0.09 ! HA-CA--CB HG2
933
+ GROUP ! | / \
934
+ ATOM CB CP2 -0.18 ! | HB1 HB2
935
+ ATOM HB1 HA 0.09 ! O=C
936
+ ATOM HB2 HA 0.09 ! |
937
+ GROUP
938
+ ATOM CG CP2 -0.18
939
+ ATOM HG1 HA 0.09
940
+ ATOM HG2 HA 0.09
941
+ GROUP
942
+ ATOM C C 0.51
943
+ ATOM O O -0.51
944
+ BOND C CA C +N
945
+ BOND N CA CA CB CB CG CG CD N CD
946
+ BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB
947
+ DOUBLE O C
948
+ IMPR N -C CA CD
949
+ IMPR C CA +N O
950
+ ACCEPTOR O C
951
+ IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624
952
+ IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399
953
+ IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569
954
+ IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316
955
+ IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517
956
+ IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399
957
+ IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837
958
+ IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322
959
+ IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317
960
+ IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131
961
+ IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088
962
+ IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077
963
+ IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143
964
+ IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137
965
+ IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144
966
+ PATCHING FIRS PROP
967
+
968
+ RESI SER 0.00
969
+ GROUP
970
+ ATOM N NH1 -0.47 ! |
971
+ ATOM HN H 0.31 ! HN-N
972
+ ATOM CA CT1 0.07 ! | HB1
973
+ ATOM HA HB 0.09 ! | |
974
+ GROUP ! HA-CA--CB--OG
975
+ ATOM CB CT2 0.05 ! | | \
976
+ ATOM HB1 HA 0.09 ! | HB2 HG1
977
+ ATOM HB2 HA 0.09 ! O=C
978
+ ATOM OG OH1 -0.66 ! |
979
+ ATOM HG1 H 0.43
980
+ GROUP
981
+ ATOM C C 0.51
982
+ ATOM O O -0.51
983
+ BOND CB CA OG CB N HN N CA
984
+ BOND C CA C +N CA HA CB HB1
985
+ BOND CB HB2 OG HG1
986
+ DOUBLE O C
987
+ IMPR N -C CA HN C CA +N O
988
+ DONOR HN N
989
+ DONOR HG1 OG
990
+ ACCEPTOR OG
991
+ ACCEPTOR O C
992
+ IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999
993
+ IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166
994
+ IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448
995
+ IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290
996
+ IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529
997
+ IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585
998
+ IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821
999
+ IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341
1000
+ IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140
1001
+ IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136
1002
+ IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655
1003
+
1004
+ RESI THR 0.00
1005
+ GROUP
1006
+ ATOM N NH1 -0.47 ! |
1007
+ ATOM HN H 0.31 ! HN-N
1008
+ ATOM CA CT1 0.07 ! | OG1--HG1
1009
+ ATOM HA HB 0.09 ! | /
1010
+ GROUP ! HA-CA--CB-HB
1011
+ ATOM CB CT1 0.14 ! | \
1012
+ ATOM HB HA 0.09 ! | CG2--HG21
1013
+ ATOM OG1 OH1 -0.66 ! O=C / \
1014
+ ATOM HG1 H 0.43 ! | HG21 HG22
1015
+ GROUP
1016
+ ATOM CG2 CT3 -0.27
1017
+ ATOM HG21 HA 0.09
1018
+ ATOM HG22 HA 0.09
1019
+ ATOM HG23 HA 0.09
1020
+ GROUP
1021
+ ATOM C C 0.51
1022
+ ATOM O O -0.51
1023
+ BOND CB CA OG1 CB CG2 CB N HN
1024
+ BOND N CA C CA C +N CA HA
1025
+ BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23
1026
+ DOUBLE O C
1027
+ IMPR N -C CA HN C CA +N O
1028
+ DONOR HN N
1029
+ DONOR HG1 OG1
1030
+ ACCEPTOR OG1
1031
+ ACCEPTOR O C
1032
+ IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995
1033
+ IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162
1034
+ IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449
1035
+ IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294
1036
+ IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525
1037
+ IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693
1038
+ IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817
1039
+ IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252
1040
+ IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174
1041
+ IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324
1042
+ IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633
1043
+ IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104
1044
+ IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109
1045
+ IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113
1046
+
1047
+ RESI TRP 0.00
1048
+ GROUP
1049
+ ATOM N NH1 -0.47 ! | HE3
1050
+ ATOM HN H 0.31 ! HN-N |
1051
+ ATOM CA CT1 0.07 ! | HB1 CE3
1052
+ ATOM HA HB 0.09 ! | | / \\
1053
+ GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3
1054
+ ATOM CB CT2 -0.18 ! | | || || |
1055
+ ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2
1056
+ ATOM HB2 HA 0.09 ! O=C / \ / \ //
1057
+ GROUP ! | HD1 NE1 CZ2
1058
+ ATOM CG CY -0.03 ! | |
1059
+ ATOM CD1 CA 0.035 ! HE1 HZ2
1060
+ ATOM HD1 HP 0.115
1061
+ ATOM NE1 NY -0.61
1062
+ ATOM HE1 H 0.38
1063
+ ATOM CE2 CPT 0.13
1064
+ ATOM CD2 CPT -0.02
1065
+ GROUP
1066
+ ATOM CE3 CA -0.115
1067
+ ATOM HE3 HP 0.115
1068
+ GROUP
1069
+ ATOM CZ3 CA -0.115
1070
+ ATOM HZ3 HP 0.115
1071
+ GROUP
1072
+ ATOM CZ2 CA -0.115
1073
+ ATOM HZ2 HP 0.115
1074
+ GROUP
1075
+ ATOM CH2 CA -0.115
1076
+ ATOM HH2 HP 0.115
1077
+ GROUP
1078
+ ATOM C C 0.51
1079
+ ATOM O O -0.51
1080
+ BOND CB CA CG CB CD2 CG NE1 CD1
1081
+ BOND CZ2 CE2
1082
+ BOND N HN N CA C CA C +N
1083
+ BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1
1084
+ BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2
1085
+ BOND CZ3 HZ3 CH2 HH2
1086
+ DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2
1087
+ IMPR N -C CA HN C CA +N O
1088
+ DONOR HN N
1089
+ DONOR HE1 NE1
1090
+ ACCEPTOR O C
1091
+ IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972
1092
+ IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202
1093
+ IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505
1094
+ IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304
1095
+ IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526
1096
+ IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560
1097
+ IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835
1098
+ IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233
1099
+ IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127
1100
+ IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118
1101
+ IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407
1102
+ IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679
1103
+ IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126
1104
+ IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746
1105
+ IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011
1106
+ IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017
1107
+ IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019
1108
+ IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030
1109
+ IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815
1110
+ IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811
1111
+ IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811
1112
+ IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790
1113
+ IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767
1114
+ IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820
1115
+
1116
+ RESI TYR 0.00
1117
+ GROUP
1118
+ ATOM N NH1 -0.47 ! | HD1 HE1
1119
+ ATOM HN H 0.31 ! HN-N | |
1120
+ ATOM CA CT1 0.07 ! | HB1 CD1--CE1
1121
+ ATOM HA HB 0.09 ! | | // \\
1122
+ GROUP ! HA-CA--CB--CG CZ--OH
1123
+ ATOM CB CT2 -0.18 ! | | \ __ / \
1124
+ ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH
1125
+ ATOM HB2 HA 0.09 ! O=C | |
1126
+ GROUP ! | HD2 HE2
1127
+ ATOM CG CA 0.00
1128
+ GROUP
1129
+ ATOM CD1 CA -0.115
1130
+ ATOM HD1 HP 0.115
1131
+ GROUP
1132
+ ATOM CE1 CA -0.115
1133
+ ATOM HE1 HP 0.115
1134
+ GROUP
1135
+ ATOM CZ CA 0.11
1136
+ ATOM OH OH1 -0.54
1137
+ ATOM HH H 0.43
1138
+ GROUP
1139
+ ATOM CD2 CA -0.115
1140
+ ATOM HD2 HP 0.115
1141
+ GROUP
1142
+ ATOM CE2 CA -0.115
1143
+ ATOM HE2 HP 0.115
1144
+ GROUP
1145
+ ATOM C C 0.51
1146
+ ATOM O O -0.51
1147
+ BOND CB CA CG CB CD2 CG CE1 CD1
1148
+ BOND CZ CE2 OH CZ
1149
+ BOND N HN N CA C CA C +N
1150
+ BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2
1151
+ BOND CE1 HE1 CE2 HE2 OH HH
1152
+ DOUBLE O C CD1 CG CE1 CZ CE2 CD2
1153
+ IMPR N -C CA HN C CA +N O
1154
+ DONOR HN N
1155
+ DONOR HH OH
1156
+ ACCEPTOR OH
1157
+ ACCEPTOR O C
1158
+ IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986
1159
+ IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232
1160
+ IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484
1161
+ IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287
1162
+ IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513
1163
+ IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606
1164
+ IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833
1165
+ IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113
1166
+ IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119
1167
+ IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115
1168
+ IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064
1169
+ IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068
1170
+ IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026
1171
+ IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814
1172
+ IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022
1173
+ IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813
1174
+ IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978
1175
+ IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799
1176
+ IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798
1177
+ IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063
1178
+ IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594
1179
+
1180
+ RESI VAL 0.00
1181
+ GROUP
1182
+ ATOM N NH1 -0.47 ! | HG11 HG12
1183
+ ATOM HN H 0.31 ! HN-N | /
1184
+ ATOM CA CT1 0.07 ! | CG1--HG13
1185
+ ATOM HA HB 0.09 ! | /
1186
+ GROUP ! HA-CA--CB-HB
1187
+ ATOM CB CT1 -0.09 ! | \
1188
+ ATOM HB HA 0.09 ! | CG2--HG21
1189
+ GROUP ! O=C / \
1190
+ ATOM CG1 CT3 -0.27 ! | HG21 HG22
1191
+ ATOM HG11 HA 0.09
1192
+ ATOM HG12 HA 0.09
1193
+ ATOM HG13 HA 0.09
1194
+ GROUP
1195
+ ATOM CG2 CT3 -0.27
1196
+ ATOM HG21 HA 0.09
1197
+ ATOM HG22 HA 0.09
1198
+ ATOM HG23 HA 0.09
1199
+ GROUP
1200
+ ATOM C C 0.51
1201
+ ATOM O O -0.51
1202
+ BOND CB CA CG1 CB CG2 CB N HN
1203
+ BOND N CA C CA C +N CA HA
1204
+ BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21
1205
+ BOND CG2 HG22 CG2 HG23
1206
+ DOUBLE O C
1207
+ IMPR N -C CA HN C CA +N O
1208
+ DONOR HN N
1209
+ ACCEPTOR O C
1210
+ IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966
1211
+ IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180
1212
+ IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471
1213
+ IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297
1214
+ IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471
1215
+ IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660
1216
+ IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828
1217
+ IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441
1218
+ IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414
1219
+ IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178
1220
+ IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114
1221
+ IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097
1222
+ IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110
1223
+ IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108
1224
+ IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115
1225
+ IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098
1226
+
1227
+ RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
1228
+ GROUP
1229
+ ATOM OH2 OT -0.834
1230
+ ATOM H1 HT 0.417
1231
+ ATOM H2 HT 0.417
1232
+ BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
1233
+ ANGLE H1 OH2 H2 ! required
1234
+ ACCEPTOR OH2
1235
+ PATCHING FIRS NONE LAST NONE
1236
+
1237
+ RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p
1238
+ GROUP
1239
+ ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup
1240
+ ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup
1241
+ ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup
1242
+ BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p
1243
+ ANGLE H1 OH2 H2 ! required
1244
+ ACCEPTOR OH2
1245
+ PATCHING FIRS NONE LAST NONE
1246
+
1247
+ ! Ion parameters from Benoit Roux and Coworkers
1248
+ ! As of 8/98 no NBFIX terms required
1249
+ !
1250
+ RESI SOD 1.00 ! Sodium Ion
1251
+ GROUP
1252
+ ATOM SOD SOD 1.00
1253
+ PATCHING FIRST NONE LAST NONE
1254
+
1255
+ RESI MG 2.00 ! Magnesium Ion
1256
+ GROUP
1257
+ ATOM MG MG 2.00
1258
+ PATCHING FIRST NONE LAST NONE
1259
+
1260
+ RESI POT 1.00 ! Potassium Ion
1261
+ GROUP
1262
+ ATOM POT POT 1.00
1263
+ PATCHING FIRST NONE LAST NONE
1264
+
1265
+ RESI CES 1.00 ! Cesium Ion
1266
+ GROUP
1267
+ ATOM CES CES 1.00
1268
+ PATCHING FIRST NONE LAST NONE
1269
+
1270
+ RESI CAL 2.00 ! Calcium Ion
1271
+ GROUP
1272
+ ATOM CAL CAL 2.00
1273
+ PATCHING FIRST NONE LAST NONE
1274
+
1275
+ RESI CLA -1.00 ! Chloride Ion
1276
+ GROUP
1277
+ ATOM CLA CLA -1.00
1278
+ PATCHING FIRST NONE LAST NONE
1279
+
1280
+ RESI ZN2 2.00 ! Zinc ion, Roland Stote
1281
+ GROUP
1282
+ ATOM ZN ZN 2.00
1283
+ PATCHING FIRST NONE LAST NONE
1284
+
1285
+ PRES NTER 1.00 ! standard N-terminus
1286
+ GROUP ! use in generate statement
1287
+ ATOM N NH3 -0.30 !
1288
+ ATOM HT1 HC 0.33 ! HT1
1289
+ ATOM HT2 HC 0.33 ! (+)/
1290
+ ATOM HT3 HC 0.33 ! --CA--N--HT2
1291
+ ATOM CA CT1 0.21 ! | \
1292
+ ATOM HA HB 0.10 ! HA HT3
1293
+ DELETE ATOM HN
1294
+ BOND HT1 N HT2 N HT3 N
1295
+ DONOR HT1 N
1296
+ DONOR HT2 N
1297
+ DONOR HT3 N
1298
+ IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
1299
+ IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
1300
+ IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
1301
+
1302
+ PRES GLYP 1.00 ! Glycine N-terminus
1303
+ GROUP ! use in generate statement
1304
+ ATOM N NH3 -0.30 !
1305
+ ATOM HT1 HC 0.33 ! HA1 HT1
1306
+ ATOM HT2 HC 0.33 ! | (+)/
1307
+ ATOM HT3 HC 0.33 ! --CA--N--HT2
1308
+ ATOM CA CT2 0.13 ! | \
1309
+ ATOM HA1 HB 0.09 ! HA2 HT3
1310
+ ATOM HA2 HB 0.09 !
1311
+ DELETE ATOM HN
1312
+ BOND HT1 N HT2 N HT3 N
1313
+ DONOR HT1 N
1314
+ DONOR HT2 N
1315
+ DONOR HT3 N
1316
+ IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
1317
+ IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
1318
+ IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
1319
+
1320
+ PRES PROP 1.00 ! Proline N-Terminal
1321
+ GROUP ! use in generate statement
1322
+ ATOM N NP -0.07 ! HA
1323
+ ATOM HN1 HC 0.24 ! |
1324
+ ATOM HN2 HC 0.24 ! -CA HN1
1325
+ ATOM CD CP3 0.16 ! / \ /
1326
+ ATOM HD1 HA 0.09 ! N(+)
1327
+ ATOM HD2 HA 0.09 ! / \
1328
+ ATOM CA CP1 0.16 ! -CD HN2
1329
+ ATOM HA HB 0.09 ! | \
1330
+ BOND HN1 N HN2 N ! HD1 HD2
1331
+ DONOR HN1 N
1332
+ DONOR HN2 N
1333
+ IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000
1334
+ IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000
1335
+
1336
+ PRES ACE 0.00 ! acetylated N-terminus
1337
+ GROUP ! use in generate statement
1338
+ ATOM CAY CT3 -0.27 !
1339
+ ATOM HY1 HA 0.09 ! HY1 HY2 HY3
1340
+ ATOM HY2 HA 0.09 ! \ | /
1341
+ ATOM HY3 HA 0.09 ! CAY
1342
+ GROUP ! |
1343
+ ATOM CY C 0.51 ! CY=OY
1344
+ ATOM OY O -0.51 ! |
1345
+ !
1346
+ BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
1347
+ DOUBLE OY CY
1348
+ IMPR CY CAY N OY
1349
+ IMPR N CY CA HN
1350
+ ACCEPTOR OY CY
1351
+ IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
1352
+ IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000
1353
+ IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
1354
+ IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
1355
+ IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
1356
+ IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
1357
+ IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
1358
+
1359
+ PRES ACP 0.00 ! acetylated N-terminus for proline
1360
+ GROUP ! use in generate statement
1361
+ ATOM CAY CT3 -0.27 !
1362
+ ATOM HY1 HA 0.09 ! HY1 HY2 HY3
1363
+ ATOM HY2 HA 0.09 ! \ | /
1364
+ ATOM HY3 HA 0.09 ! CAY
1365
+ GROUP ! |
1366
+ ATOM CY C 0.51 ! CY=OY
1367
+ ATOM OY O -0.51 ! |
1368
+ !
1369
+ BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
1370
+ DOUBLE OY CY
1371
+ IMPR CY CAY N OY
1372
+ IMPR N CY CA CD
1373
+ ACCEPTOR OY CY
1374
+ IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
1375
+ IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000
1376
+ IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
1377
+ IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
1378
+ IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
1379
+ IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
1380
+ IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
1381
+
1382
+ PRES CTER -1.00 ! standard C-terminus
1383
+ GROUP ! use in generate statement
1384
+ ATOM C CC 0.34 ! OT2(-)
1385
+ ATOM OT1 OC -0.67 ! /
1386
+ ATOM OT2 OC -0.67 ! -C
1387
+ DELETE ATOM O ! \\
1388
+ BOND C OT2 ! OT1
1389
+ DOUBLE C OT1
1390
+ !IMPR OT1 CA OT2 C
1391
+ IMPR C CA OT2 OT1
1392
+ ACCEPTOR OT1 C
1393
+ ACCEPTOR OT2 C
1394
+ IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
1395
+ IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
1396
+
1397
+ PRES CT1 0.00 ! methylated C-terminus from methyl acetate
1398
+ GROUP ! use in generate statement
1399
+ ATOM N NH1 -0.47 !
1400
+ ATOM HN H 0.31 ! OT1
1401
+ ATOM CA CT1 0.17 ! | //
1402
+ ATOM HA HB 0.09 ! -N--CA--C HT1
1403
+ ATOM C CD 0.63 ! | | \ /
1404
+ ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
1405
+ ATOM OT2 OS -0.34 ! \
1406
+ ATOM CT CT3 -0.14 ! HT3
1407
+ ATOM HT1 HA 0.09 !
1408
+ ATOM HT2 HA 0.09 !
1409
+ ATOM HT3 HA 0.09 !
1410
+ DELETE ATOM O
1411
+ BOND C OT2 OT2 CT
1412
+ BOND CT HT1 CT HT2 CT HT3
1413
+ DOUBLE C OT1
1414
+ IMPR C CA OT2 OT1
1415
+ ACCEPTOR OT1 C
1416
+ ACCEPTOR OT2 C
1417
+ IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
1418
+ IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
1419
+ IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000
1420
+ IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000
1421
+ IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000
1422
+ IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000
1423
+
1424
+ PRES CT2 0.00 ! amidated C-terminus
1425
+ GROUP ! use in generate statement
1426
+ ATOM C CC 0.55 !
1427
+ ATOM O O -0.55 ! |
1428
+ GROUP ! O=C
1429
+ ATOM NT NH2 -0.62 ! |
1430
+ ATOM HT1 H 0.32 ! NT
1431
+ ATOM HT2 H 0.30 ! / \
1432
+ BOND C NT ! HT1 HT2
1433
+ BOND NT HT1 NT HT2 !
1434
+ DIHE CA C NT HT2 ! (HT1 is cis to O)
1435
+ IMPR C NT CA O C CA NT O
1436
+ IMPR NT C HT1 HT2 NT C HT2 HT1
1437
+ DONOR HT1 NT
1438
+ DONOR HT2 NT
1439
+ IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
1440
+ IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
1441
+ IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000
1442
+ IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
1443
+
1444
+ PRES CT3 0.00 ! N-Methylamide C-terminus
1445
+ GROUP ! use in generate statement
1446
+ ATOM C C 0.51 !
1447
+ ATOM O O -0.51 ! |
1448
+ GROUP ! C=O
1449
+ ATOM NT NH1 -0.47 ! |
1450
+ ATOM HNT H 0.31 ! NT-HNT
1451
+ ATOM CAT CT3 -0.11 ! |
1452
+ ATOM HT1 HA 0.09 ! HT1-CAT-HT3
1453
+ ATOM HT2 HA 0.09 ! |
1454
+ ATOM HT3 HA 0.09 ! HT2
1455
+ !
1456
+ BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3
1457
+ DIHE CA C NT CAT
1458
+ IMPR NT C CAT HNT C CA NT O
1459
+ DONOR HNT NT
1460
+ IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
1461
+ IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
1462
+ IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000
1463
+ IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000
1464
+ IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000
1465
+ IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
1466
+ IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000
1467
+
1468
+ PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2
1469
+ GROUP ! via acetic acid, use in a patch statementand
1470
+ ! follow with AUTOgenerate ANGLes DIHEdrals command
1471
+ ATOM CB CT2 -0.21 !
1472
+ ATOM HB1 HA 0.09 ! HB1 OD1
1473
+ ATOM HB2 HA 0.09 ! | //
1474
+ ATOM CG CD 0.75 ! -CB--CG
1475
+ ATOM OD1 OB -0.55 ! | \
1476
+ ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2
1477
+ ATOM HD2 H 0.44 !
1478
+ BOND OD2 HD2
1479
+ DONOR HD2 OD2
1480
+ IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000
1481
+
1482
+ PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2
1483
+ GROUP ! via acetic acid, use in a patch statement and
1484
+ ! follow with AUTOgenerate ANGLes DIHEdrals command
1485
+ ATOM CG CT2 -0.21 !
1486
+ ATOM HG1 HA 0.09 ! HG1 OE1
1487
+ ATOM HG2 HA 0.09 ! | //
1488
+ ATOM CD CD 0.75 ! -CG--CD
1489
+ ATOM OE1 OB -0.55 ! | \
1490
+ ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2
1491
+ ATOM HE2 H 0.44 !
1492
+ BOND OE2 HE2
1493
+ DONOR HE2 OE2
1494
+ IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000
1495
+
1496
+ PRES LSN 0.00 ! patch for neutral lysine based on methylamine
1497
+ ! use in a patch statement
1498
+ !delete atom and reassign charges
1499
+ DELETE ATOM HZ3
1500
+ GROUP
1501
+ ATOM CE CT2 0.13
1502
+ ATOM HE1 HA 0.075
1503
+ ATOM HE2 HA 0.075
1504
+ ATOM NZ NH2 -0.96
1505
+ ATOM HZ1 HC 0.34
1506
+ ATOM HZ2 HC 0.34
1507
+
1508
+ PRES LINK 0.00 ! linkage for IMAGES or for joining segments
1509
+ ! 1 refers to previous (N terminal)
1510
+ ! 2 refers to next (C terminal)
1511
+ ! use in a patch statement
1512
+ BOND 1C 2N
1513
+ ANGLE 1C 2N 2CA 1CA 1C 2N
1514
+ ANGLE 1O 1C 2N 1C 2N 2HN
1515
+ DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
1516
+ DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
1517
+ DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
1518
+ DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
1519
+ IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
1520
+ IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
1521
+ IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
1522
+ IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
1523
+ IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
1524
+ IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
1525
+
1526
+ PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS.
1527
+ GROUP ! use in a patch statement
1528
+ ATOM 1CB CT2 -0.10 !
1529
+ ATOM 1SG SM -0.08 ! 2SG--2CB--
1530
+ GROUP ! /
1531
+ ATOM 2SG SM -0.08 ! -1CB--1SG
1532
+ ATOM 2CB CT2 -0.10 !
1533
+ DELETE ATOM 1HG1
1534
+ DELETE ATOM 2HG1
1535
+ BOND 1SG 2SG
1536
+ ANGLE 1CB 1SG 2SG 1SG 2SG 2CB
1537
+ DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG
1538
+ DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG
1539
+ DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA
1540
+ DIHE 1CB 1SG 2SG 2CB
1541
+ !DIHE 1CB 1SG 2SG 2CB
1542
+ IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000
1543
+ IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000
1544
+ IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
1545
+
1546
+ PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2
1547
+ GROUP ! use in a patch statement
1548
+ ATOM CE1 CPH2 0.25 ! HE1
1549
+ ATOM HE1 HR1 0.13 ! /
1550
+ ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1
1551
+ ATOM CG CPH1 0.22 ! | / |
1552
+ ATOM CB CT2 -0.08 ! -CB--CG |
1553
+ ATOM HB1 HA 0.09 ! | \ |
1554
+ ATOM HB2 HA 0.09 ! HB2 CD2--NE2
1555
+ GROUP ! | \
1556
+ ATOM NE2 NR1 -0.36 ! HD2 HE2
1557
+ ATOM HE2 H 0.32
1558
+ ATOM CD2 CPH1 -0.05
1559
+ ATOM HD2 HR3 0.09
1560
+ DELETE ATOM HD1
1561
+ DELETE ACCE NE2
1562
+ BOND NE2 HE2
1563
+ ANGLE CD2 NE2 HE2 CE1 NE2 HE2
1564
+ DIHE HE2 NE2 CE1 HE1 HE2 NE2 CE1 ND1 HE2 NE2 CD2 HD2
1565
+ DIHE HE2 NE2 CD2 CG
1566
+ IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
1567
+ DONOR HE2 NE2
1568
+ ACCEPTOR ND1
1569
+ IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000
1570
+
1571
+ ! patches for cyclic peptides
1572
+ PRES LIG1 0.00000 ! linkage for cyclic peptide
1573
+ ! 1 refers to the C terminus which is a glycine
1574
+ ! 2 refers to the N terminus
1575
+ ! use in a patch statement, perform initial
1576
+ ! generation using first NONE last NONE
1577
+ BOND 1C 2N
1578
+ ANGLE 1C 2N 2CA 1CA 1C 2N
1579
+ ANGLE 1O 1C 2N 1C 2N 2HN
1580
+ DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
1581
+ DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N
1582
+ DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
1583
+ DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
1584
+ DIHE 1CA 1C 2N 2CA
1585
+ IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
1586
+ IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
1587
+ IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
1588
+ IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
1589
+ IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
1590
+ IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
1591
+
1592
+ PRES LIG2 0.00000 ! linkage for cyclic peptide
1593
+ ! 1 refers to the C terminus
1594
+ ! 2 refers to the N terminus which is a glycine
1595
+ ! use in a patch statement, perform initial
1596
+ ! generation using first NONE last NONE
1597
+ BOND 1C 2N
1598
+ ANGLE 1C 2N 2CA 1CA 1C 2N
1599
+ ANGLE 1O 1C 2N 1C 2N 2HN
1600
+ DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2
1601
+ DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
1602
+ DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
1603
+ DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
1604
+ DIHE 1CA 1C 2N 2CA
1605
+ IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
1606
+ IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
1607
+ IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
1608
+ IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
1609
+ IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
1610
+ IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
1611
+
1612
+ PRES LIG3 0.00000 ! linkage for cyclic peptide
1613
+ ! 1 refers to the C terminus which is a glycine
1614
+ ! 2 refers to the N terminus which is a glycine
1615
+ ! use in a patch statement, perform initial
1616
+ ! generation using first NONE last NONE
1617
+ BOND 1C 2N
1618
+ ANGLE 1C 2N 2CA 1CA 1C 2N
1619
+ ANGLE 1O 1C 2N 1C 2N 2HN
1620
+ DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2
1621
+ DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N
1622
+ DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
1623
+ DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
1624
+ DIHE 1CA 1C 2N 2CA
1625
+ IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
1626
+ IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
1627
+ IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
1628
+ IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
1629
+ IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
1630
+ IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
1631
+
1632
+ END
1633
+
1634
+
1635
+