1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
|
global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
PCE PCE '2-(3-AMINO-4-CYCLOHEXYL-2-HYDROXY-BU' non-polymer 43 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PCE
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
PCE OXT O OC -0.500 0.000 0.000 0.000
PCE C C C 0.000 -1.110 0.576 0.003
PCE O O OC -0.500 -1.355 1.457 0.857
PCE CA2 C CH1 0.000 -2.153 0.210 -1.021
PCE HA2 H H 0.000 -1.978 -0.818 -1.370
PCE CB2 C CH2 0.000 -2.065 1.172 -2.205
PCE HB21 H H 0.000 -2.239 2.192 -1.858
PCE HB22 H H 0.000 -2.822 0.906 -2.946
PCE CG2 C CSP 0.000 -0.727 1.080 -2.813
PCE CD3 C CSP1 0.000 0.340 1.008 -3.298
PCE HD31 H H 0.000 1.192 0.950 -3.685
PCE CM C CH2 0.000 -3.544 0.303 -0.390
PCE HM1 H H 0.000 -3.749 1.341 -0.117
PCE HM2 H H 0.000 -3.578 -0.320 0.506
PCE CH C CH1 0.000 -4.593 -0.180 -1.390
PCE HH H H 0.000 -4.504 0.396 -2.322
PCE OH O OH1 0.000 -4.384 -1.566 -1.666
PCE HO H H 0.000 -4.400 -2.065 -0.838
PCE CA C CH1 0.000 -5.990 0.017 -0.802
PCE HA H H 0.000 -6.080 -0.559 0.130
PCE N N NH2 0.000 -6.205 1.442 -0.518
PCE H2 H H 0.000 -6.401 1.752 0.426
PCE H H H 0.000 -6.158 2.125 -1.266
PCE CB C CH2 0.000 -7.040 -0.467 -1.804
PCE HB2 H H 0.000 -6.879 -1.526 -2.015
PCE HB3 H H 0.000 -6.950 0.106 -2.729
PCE CG C CH1 0.000 -8.437 -0.270 -1.213
PCE HG H H 0.000 -8.597 0.796 -1.001
PCE CD2 C CH2 0.000 -8.562 -1.071 0.082
PCE HD23 H H 0.000 -7.812 -0.726 0.796
PCE HD22 H H 0.000 -8.402 -2.130 -0.130
PCE CE2 C CH2 0.000 -9.960 -0.873 0.673
PCE HE23 H H 0.000 -10.119 0.187 0.884
PCE HE22 H H 0.000 -10.048 -1.445 1.599
PCE CZ C CH2 0.000 -11.009 -1.358 -0.330
PCE HZ2 H H 0.000 -12.007 -1.219 0.092
PCE HZ3 H H 0.000 -10.849 -2.418 -0.540
PCE CE1 C CH2 0.000 -10.885 -0.556 -1.626
PCE HE12 H H 0.000 -11.047 0.503 -1.415
PCE HE13 H H 0.000 -11.635 -0.902 -2.341
PCE CD1 C CH2 0.000 -9.487 -0.753 -2.216
PCE HD13 H H 0.000 -9.399 -0.180 -3.141
PCE HD12 H H 0.000 -9.328 -1.813 -2.429
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
PCE OXT n/a C START
PCE C OXT CA2 .
PCE O C . .
PCE CA2 C CM .
PCE HA2 CA2 . .
PCE CB2 CA2 CG2 .
PCE HB21 CB2 . .
PCE HB22 CB2 . .
PCE CG2 CB2 CD3 .
PCE CD3 CG2 HD31 .
PCE HD31 CD3 . .
PCE CM CA2 CH .
PCE HM1 CM . .
PCE HM2 CM . .
PCE CH CM CA .
PCE HH CH . .
PCE OH CH HO .
PCE HO OH . .
PCE CA CH CB .
PCE HA CA . .
PCE N CA H .
PCE H2 N . .
PCE H N . .
PCE CB CA CG .
PCE HB2 CB . .
PCE HB3 CB . .
PCE CG CB CD2 .
PCE HG CG . .
PCE CD2 CG CE2 .
PCE HD23 CD2 . .
PCE HD22 CD2 . .
PCE CE2 CD2 CZ .
PCE HE23 CE2 . .
PCE HE22 CE2 . .
PCE CZ CE2 CE1 .
PCE HZ2 CZ . .
PCE HZ3 CZ . .
PCE CE1 CZ CD1 .
PCE HE12 CE1 . .
PCE HE13 CE1 . .
PCE CD1 CE1 HD12 .
PCE HD13 CD1 . .
PCE HD12 CD1 . END
PCE CG CD1 . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
PCE N CA single 1.450 0.020
PCE H N single 1.010 0.020
PCE H2 N single 1.010 0.020
PCE CB CA single 1.524 0.020
PCE CA CH single 1.524 0.020
PCE HA CA single 1.099 0.020
PCE CG CB single 1.524 0.020
PCE HB2 CB single 1.092 0.020
PCE HB3 CB single 1.092 0.020
PCE CG CD1 single 1.524 0.020
PCE CD2 CG single 1.524 0.020
PCE HG CG single 1.099 0.020
PCE CD1 CE1 single 1.524 0.020
PCE HD12 CD1 single 1.092 0.020
PCE HD13 CD1 single 1.092 0.020
PCE CE2 CD2 single 1.524 0.020
PCE HD23 CD2 single 1.092 0.020
PCE HD22 CD2 single 1.092 0.020
PCE CE1 CZ single 1.524 0.020
PCE HE12 CE1 single 1.092 0.020
PCE HE13 CE1 single 1.092 0.020
PCE CZ CE2 single 1.524 0.020
PCE HE23 CE2 single 1.092 0.020
PCE HE22 CE2 single 1.092 0.020
PCE HZ2 CZ single 1.092 0.020
PCE HZ3 CZ single 1.092 0.020
PCE OH CH single 1.432 0.020
PCE CH CM single 1.524 0.020
PCE HH CH single 1.099 0.020
PCE HO OH single 0.967 0.020
PCE CM CA2 single 1.524 0.020
PCE HM1 CM single 1.092 0.020
PCE HM2 CM single 1.092 0.020
PCE CB2 CA2 single 1.524 0.020
PCE CA2 C single 1.500 0.020
PCE HA2 CA2 single 1.099 0.020
PCE CG2 CB2 single 1.470 0.020
PCE HB21 CB2 single 1.092 0.020
PCE HB22 CB2 single 1.092 0.020
PCE CD3 CG2 triple 1.278 0.020
PCE HD31 CD3 single 1.022 0.020
PCE O C deloc 1.250 0.020
PCE C OXT deloc 1.250 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
PCE OXT C O 123.000 3.000
PCE OXT C CA2 118.500 3.000
PCE O C CA2 118.500 3.000
PCE C CA2 HA2 108.810 3.000
PCE C CA2 CB2 109.470 3.000
PCE C CA2 CM 109.470 3.000
PCE HA2 CA2 CB2 108.340 3.000
PCE HA2 CA2 CM 108.340 3.000
PCE CB2 CA2 CM 109.470 3.000
PCE CA2 CB2 HB21 109.470 3.000
PCE CA2 CB2 HB22 109.470 3.000
PCE CA2 CB2 CG2 109.500 3.000
PCE HB21 CB2 HB22 107.900 3.000
PCE HB21 CB2 CG2 109.500 3.000
PCE HB22 CB2 CG2 109.500 3.000
PCE CB2 CG2 CD3 180.000 3.000
PCE CG2 CD3 HD31 180.000 3.000
PCE CA2 CM HM1 109.470 3.000
PCE CA2 CM HM2 109.470 3.000
PCE CA2 CM CH 111.000 3.000
PCE HM1 CM HM2 107.900 3.000
PCE HM1 CM CH 109.470 3.000
PCE HM2 CM CH 109.470 3.000
PCE CM CH HH 108.340 3.000
PCE CM CH OH 109.470 3.000
PCE CM CH CA 111.000 3.000
PCE HH CH OH 109.470 3.000
PCE HH CH CA 108.340 3.000
PCE OH CH CA 109.470 3.000
PCE CH OH HO 109.470 3.000
PCE CH CA HA 108.340 3.000
PCE CH CA N 109.470 3.000
PCE CH CA CB 111.000 3.000
PCE HA CA N 109.470 3.000
PCE HA CA CB 108.340 3.000
PCE N CA CB 109.470 3.000
PCE CA N H2 120.000 3.000
PCE CA N H 120.000 3.000
PCE H2 N H 120.000 3.000
PCE CA CB HB2 109.470 3.000
PCE CA CB HB3 109.470 3.000
PCE CA CB CG 111.000 3.000
PCE HB2 CB HB3 107.900 3.000
PCE HB2 CB CG 109.470 3.000
PCE HB3 CB CG 109.470 3.000
PCE CB CG HG 108.340 3.000
PCE CB CG CD2 109.470 3.000
PCE CB CG CD1 109.470 3.000
PCE HG CG CD2 108.340 3.000
PCE HG CG CD1 108.340 3.000
PCE CD2 CG CD1 109.470 3.000
PCE CG CD2 HD23 109.470 3.000
PCE CG CD2 HD22 109.470 3.000
PCE CG CD2 CE2 111.000 3.000
PCE HD23 CD2 HD22 107.900 3.000
PCE HD23 CD2 CE2 109.470 3.000
PCE HD22 CD2 CE2 109.470 3.000
PCE CD2 CE2 HE23 109.470 3.000
PCE CD2 CE2 HE22 109.470 3.000
PCE CD2 CE2 CZ 111.000 3.000
PCE HE23 CE2 HE22 107.900 3.000
PCE HE23 CE2 CZ 109.470 3.000
PCE HE22 CE2 CZ 109.470 3.000
PCE CE2 CZ HZ2 109.470 3.000
PCE CE2 CZ HZ3 109.470 3.000
PCE CE2 CZ CE1 111.000 3.000
PCE HZ2 CZ HZ3 107.900 3.000
PCE HZ2 CZ CE1 109.470 3.000
PCE HZ3 CZ CE1 109.470 3.000
PCE CZ CE1 HE12 109.470 3.000
PCE CZ CE1 HE13 109.470 3.000
PCE CZ CE1 CD1 111.000 3.000
PCE HE12 CE1 HE13 107.900 3.000
PCE HE12 CE1 CD1 109.470 3.000
PCE HE13 CE1 CD1 109.470 3.000
PCE CE1 CD1 HD13 109.470 3.000
PCE CE1 CD1 HD12 109.470 3.000
PCE CE1 CD1 CG 111.000 3.000
PCE HD13 CD1 HD12 107.900 3.000
PCE HD13 CD1 CG 109.470 3.000
PCE HD12 CD1 CG 109.470 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
PCE var_1 OXT C CA2 CM 145.053 20.000 3
PCE var_2 C CA2 CB2 CG2 60.017 20.000 3
PCE var_3 CA2 CB2 CG2 CD3 -106.186 20.000 1
PCE var_4 CB2 CG2 CD3 HD31 -96.718 20.000 1
PCE var_5 C CA2 CM CH -175.308 20.000 3
PCE var_6 CA2 CM CH CA -175.547 20.000 3
PCE var_7 CM CH OH HO 56.028 20.000 1
PCE var_8 CM CH CA CB -179.980 20.000 3
PCE var_9 CH CA N H 60.001 20.000 1
PCE var_10 CH CA CB CG 179.964 20.000 3
PCE var_11 CA CB CG CD2 -60.000 20.000 3
PCE var_12 CB CG CD1 CE1 180.000 20.000 3
PCE var_13 CB CG CD2 CE2 180.000 20.000 3
PCE var_14 CG CD2 CE2 CZ 60.000 20.000 3
PCE var_15 CD2 CE2 CZ CE1 -60.000 20.000 3
PCE var_16 CE2 CZ CE1 CD1 60.000 20.000 3
PCE var_17 CZ CE1 CD1 CG -60.000 20.000 3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
PCE chir_01 CA N CB CH negativ
PCE chir_02 CG CB CD1 CD2 negativ
PCE chir_03 CH CA OH CM positiv
PCE chir_04 CA2 CM CB2 C negativ
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
PCE plan-1 N 0.020
PCE plan-1 CA 0.020
PCE plan-1 H 0.020
PCE plan-1 H2 0.020
PCE plan-2 C 0.020
PCE plan-2 CA2 0.020
PCE plan-2 O 0.020
PCE plan-2 OXT 0.020
# ------------------------------------------------------
|
