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
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
|
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
OPD OPD '9R,13R-12-OXOPHYTODIENOIC ACID ' non-polymer 48 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_OPD
#
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
OPD O19 O OC -0.500 0.000 0.000 0.000
OPD C18 C C 0.000 -0.247 1.060 0.617
OPD O20 O OC -0.500 0.641 1.804 1.089
OPD C17 C CH2 0.000 -1.639 1.576 0.880
OPD H171 H H 0.000 -1.708 2.581 0.459
OPD H172 H H 0.000 -1.778 1.625 1.962
OPD C16 C CH2 0.000 -2.719 0.689 0.267
OPD H161 H H 0.000 -2.567 -0.312 0.674
OPD H162 H H 0.000 -2.534 0.675 -0.810
OPD C15 C CH2 0.000 -4.162 1.138 0.534
OPD H151 H H 0.000 -4.275 2.140 0.114
OPD H152 H H 0.000 -4.295 1.182 1.617
OPD C14 C CH2 0.000 -5.212 0.207 -0.075
OPD H141 H H 0.000 -5.053 -0.787 0.349
OPD H142 H H 0.000 -5.036 0.175 -1.152
OPD C13 C CH2 0.000 -6.654 0.655 0.196
OPD H131 H H 0.000 -6.763 1.665 -0.204
OPD H132 H H 0.000 -6.791 0.677 1.279
OPD C12 C CH2 0.000 -7.706 -0.262 -0.434
OPD H121 H H 0.000 -7.554 -1.264 -0.027
OPD H122 H H 0.000 -7.526 -0.277 -1.511
OPD C11 C CH2 0.000 -9.143 0.188 -0.161
OPD H111 H H 0.000 -9.255 1.189 -0.583
OPD H112 H H 0.000 -9.269 0.235 0.923
OPD C4 C CH1 0.000 -10.195 -0.735 -0.756
OPD H41 H H 0.000 -10.059 -1.744 -0.340
OPD C3 C C1 0.000 -10.047 -0.801 -2.251
OPD H31 H H 0.000 -9.163 -1.197 -2.723
OPD C2 C C1 0.000 -11.080 -0.337 -2.953
OPD H21 H H 0.000 -11.162 -0.274 -4.025
OPD C1 C C 0.000 -12.083 0.069 -1.962
OPD O6 O O 0.000 -13.134 0.613 -2.268
OPD C5 C CH1 0.000 -11.665 -0.309 -0.560
OPD H51 H H 0.000 -12.243 -1.193 -0.254
OPD C6 C CH2 0.000 -11.939 0.807 0.434
OPD H61 H H 0.000 -11.410 1.703 0.102
OPD H62 H H 0.000 -11.557 0.501 1.411
OPD C7 C C1 0.000 -13.406 1.101 0.538
OPD H71 H H 0.000 -14.065 0.298 0.823
OPD C8 C C1 0.000 -13.945 2.305 0.297
OPD H81 H H 0.000 -13.288 3.106 0.005
OPD C9 C CH2 0.000 -15.411 2.600 0.412
OPD H91 H H 0.000 -15.531 3.645 0.707
OPD H92 H H 0.000 -15.834 1.954 1.185
OPD C10 C CH3 0.000 -16.132 2.358 -0.904
OPD H103 H H 0.000 -17.160 2.591 -0.794
OPD H102 H H 0.000 -15.711 2.972 -1.658
OPD H101 H H 0.000 -16.031 1.340 -1.182
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
OPD O19 n/a C18 START
OPD C18 O19 C17 .
OPD O20 C18 . .
OPD C17 C18 C16 .
OPD H171 C17 . .
OPD H172 C17 . .
OPD C16 C17 C15 .
OPD H161 C16 . .
OPD H162 C16 . .
OPD C15 C16 C14 .
OPD H151 C15 . .
OPD H152 C15 . .
OPD C14 C15 C13 .
OPD H141 C14 . .
OPD H142 C14 . .
OPD C13 C14 C12 .
OPD H131 C13 . .
OPD H132 C13 . .
OPD C12 C13 C11 .
OPD H121 C12 . .
OPD H122 C12 . .
OPD C11 C12 C4 .
OPD H111 C11 . .
OPD H112 C11 . .
OPD C4 C11 C5 .
OPD H41 C4 . .
OPD C3 C4 C2 .
OPD H31 C3 . .
OPD C2 C3 C1 .
OPD H21 C2 . .
OPD C1 C2 O6 .
OPD O6 C1 . .
OPD C5 C4 C6 .
OPD H51 C5 . .
OPD C6 C5 C7 .
OPD H61 C6 . .
OPD H62 C6 . .
OPD C7 C6 C8 .
OPD H71 C7 . .
OPD C8 C7 C9 .
OPD H81 C8 . .
OPD C9 C8 C10 .
OPD H91 C9 . .
OPD H92 C9 . .
OPD C10 C9 H101 .
OPD H103 C10 . .
OPD H102 C10 . .
OPD H101 C10 . END
OPD C5 C1 . 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
OPD C8 C7 double 1.330 0.020
OPD C9 C8 single 1.510 0.020
OPD H81 C8 single 1.077 0.020
OPD C7 C6 single 1.510 0.020
OPD H71 C7 single 1.077 0.020
OPD C5 C1 single 1.500 0.020
OPD C5 C4 single 1.524 0.020
OPD C6 C5 single 1.524 0.020
OPD H51 C5 single 1.099 0.020
OPD O6 C1 double 1.220 0.020
OPD C1 C2 single 1.475 0.020
OPD C2 C3 double 1.330 0.020
OPD H21 C2 single 1.077 0.020
OPD C3 C4 single 1.510 0.020
OPD H31 C3 single 1.077 0.020
OPD C4 C11 single 1.524 0.020
OPD H41 C4 single 1.099 0.020
OPD C11 C12 single 1.524 0.020
OPD H111 C11 single 1.092 0.020
OPD H112 C11 single 1.092 0.020
OPD C12 C13 single 1.524 0.020
OPD H121 C12 single 1.092 0.020
OPD H122 C12 single 1.092 0.020
OPD C13 C14 single 1.524 0.020
OPD H131 C13 single 1.092 0.020
OPD H132 C13 single 1.092 0.020
OPD C14 C15 single 1.524 0.020
OPD H141 C14 single 1.092 0.020
OPD H142 C14 single 1.092 0.020
OPD C15 C16 single 1.524 0.020
OPD H151 C15 single 1.092 0.020
OPD H152 C15 single 1.092 0.020
OPD C16 C17 single 1.524 0.020
OPD H161 C16 single 1.092 0.020
OPD H162 C16 single 1.092 0.020
OPD C17 C18 single 1.510 0.020
OPD H171 C17 single 1.092 0.020
OPD H172 C17 single 1.092 0.020
OPD O20 C18 deloc 1.250 0.020
OPD C18 O19 deloc 1.250 0.020
OPD H61 C6 single 1.092 0.020
OPD H62 C6 single 1.092 0.020
OPD C10 C9 single 1.513 0.020
OPD H91 C9 single 1.092 0.020
OPD H92 C9 single 1.092 0.020
OPD H101 C10 single 1.059 0.020
OPD H102 C10 single 1.059 0.020
OPD H103 C10 single 1.059 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
OPD O19 C18 O20 123.000 3.000
OPD O19 C18 C17 118.500 3.000
OPD O20 C18 C17 118.500 3.000
OPD C18 C17 H171 109.470 3.000
OPD C18 C17 H172 109.470 3.000
OPD C18 C17 C16 109.470 3.000
OPD H171 C17 H172 107.900 3.000
OPD H171 C17 C16 109.470 3.000
OPD H172 C17 C16 109.470 3.000
OPD C17 C16 H161 109.470 3.000
OPD C17 C16 H162 109.470 3.000
OPD C17 C16 C15 111.000 3.000
OPD H161 C16 H162 107.900 3.000
OPD H161 C16 C15 109.470 3.000
OPD H162 C16 C15 109.470 3.000
OPD C16 C15 H151 109.470 3.000
OPD C16 C15 H152 109.470 3.000
OPD C16 C15 C14 111.000 3.000
OPD H151 C15 H152 107.900 3.000
OPD H151 C15 C14 109.470 3.000
OPD H152 C15 C14 109.470 3.000
OPD C15 C14 H141 109.470 3.000
OPD C15 C14 H142 109.470 3.000
OPD C15 C14 C13 111.000 3.000
OPD H141 C14 H142 107.900 3.000
OPD H141 C14 C13 109.470 3.000
OPD H142 C14 C13 109.470 3.000
OPD C14 C13 H131 109.470 3.000
OPD C14 C13 H132 109.470 3.000
OPD C14 C13 C12 111.000 3.000
OPD H131 C13 H132 107.900 3.000
OPD H131 C13 C12 109.470 3.000
OPD H132 C13 C12 109.470 3.000
OPD C13 C12 H121 109.470 3.000
OPD C13 C12 H122 109.470 3.000
OPD C13 C12 C11 111.000 3.000
OPD H121 C12 H122 107.900 3.000
OPD H121 C12 C11 109.470 3.000
OPD H122 C12 C11 109.470 3.000
OPD C12 C11 H111 109.470 3.000
OPD C12 C11 H112 109.470 3.000
OPD C12 C11 C4 111.000 3.000
OPD H111 C11 H112 107.900 3.000
OPD H111 C11 C4 109.470 3.000
OPD H112 C11 C4 109.470 3.000
OPD C11 C4 H41 108.340 3.000
OPD C11 C4 C3 109.470 3.000
OPD C11 C4 C5 111.000 3.000
OPD H41 C4 C3 108.810 3.000
OPD H41 C4 C5 108.340 3.000
OPD C3 C4 C5 109.470 3.000
OPD C4 C3 H31 120.000 3.000
OPD C4 C3 C2 120.000 3.000
OPD H31 C3 C2 120.000 3.000
OPD C3 C2 H21 120.000 3.000
OPD C3 C2 C1 120.000 3.000
OPD H21 C2 C1 120.000 3.000
OPD C2 C1 O6 120.500 3.000
OPD C2 C1 C5 120.000 3.000
OPD O6 C1 C5 120.500 3.000
OPD C4 C5 H51 108.340 3.000
OPD C4 C5 C6 111.000 3.000
OPD C4 C5 C1 109.470 3.000
OPD H51 C5 C6 108.340 3.000
OPD H51 C5 C1 108.810 3.000
OPD C6 C5 C1 109.470 3.000
OPD C5 C6 H61 109.470 3.000
OPD C5 C6 H62 109.470 3.000
OPD C5 C6 C7 109.470 3.000
OPD H61 C6 H62 107.900 3.000
OPD H61 C6 C7 109.470 3.000
OPD H62 C6 C7 109.470 3.000
OPD C6 C7 H71 120.000 3.000
OPD C6 C7 C8 120.000 3.000
OPD H71 C7 C8 120.000 3.000
OPD C7 C8 H81 120.000 3.000
OPD C7 C8 C9 120.000 3.000
OPD H81 C8 C9 120.000 3.000
OPD C8 C9 H91 109.470 3.000
OPD C8 C9 H92 109.470 3.000
OPD C8 C9 C10 109.500 3.000
OPD H91 C9 H92 107.900 3.000
OPD H91 C9 C10 109.470 3.000
OPD H92 C9 C10 109.470 3.000
OPD C9 C10 H103 109.470 3.000
OPD C9 C10 H102 109.470 3.000
OPD C9 C10 H101 109.470 3.000
OPD H103 C10 H102 109.470 3.000
OPD H103 C10 H101 109.470 3.000
OPD H102 C10 H101 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
OPD var_1 O19 C18 C17 C16 -2.109 20.000 3
OPD var_2 C18 C17 C16 C15 178.310 20.000 3
OPD var_3 C17 C16 C15 C14 -178.823 20.000 3
OPD var_4 C16 C15 C14 C13 179.837 20.000 3
OPD var_5 C15 C14 C13 C12 178.943 20.000 3
OPD var_6 C14 C13 C12 C11 -179.996 20.000 3
OPD var_7 C13 C12 C11 C4 -178.650 20.000 3
OPD var_8 C12 C11 C4 C5 -177.871 20.000 3
OPD var_9 C11 C4 C3 C2 -120.000 20.000 1
OPD var_10 C4 C3 C2 C1 0.000 20.000 1
OPD var_11 C3 C2 C1 O6 180.000 20.000 1
OPD var_12 C11 C4 C5 C6 0.000 20.000 3
OPD var_13 C4 C5 C1 C2 0.000 20.000 3
OPD var_14 C4 C5 C6 C7 -179.104 20.000 3
OPD var_15 C5 C6 C7 C8 -122.114 20.000 1
OPD CONST_1 C6 C7 C8 C9 -179.498 0.000 0
OPD var_16 C7 C8 C9 C10 -89.975 20.000 1
OPD var_17 C8 C9 C10 H101 60.989 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
OPD chir_01 C5 C1 C4 C6 negativ
OPD chir_02 C4 C5 C3 C11 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
OPD plan-1 C8 0.020
OPD plan-1 C7 0.020
OPD plan-1 C9 0.020
OPD plan-1 H81 0.020
OPD plan-1 C6 0.020
OPD plan-1 H71 0.020
OPD plan-2 C1 0.020
OPD plan-2 C5 0.020
OPD plan-2 O6 0.020
OPD plan-2 C2 0.020
OPD plan-2 H21 0.020
OPD plan-3 C2 0.020
OPD plan-3 C1 0.020
OPD plan-3 C3 0.020
OPD plan-3 H21 0.020
OPD plan-3 H31 0.020
OPD plan-4 C3 0.020
OPD plan-4 C2 0.020
OPD plan-4 C4 0.020
OPD plan-4 H31 0.020
OPD plan-4 H21 0.020
OPD plan-5 C18 0.020
OPD plan-5 C17 0.020
OPD plan-5 O20 0.020
OPD plan-5 O19 0.020
# ------------------------------------------------------
|
