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
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
|
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
PVB PVB 'PURVALANOL B ' non-polymer 54 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PVB
#
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
PVB OX2 O OC -0.500 0.000 0.000 0.000
PVB CX C C 0.000 -0.414 0.933 0.723
PVB OX1 O OC -0.500 0.370 1.509 1.511
PVB C4A C CR6 0.000 -1.824 1.354 0.648
PVB C3A C CR16 0.000 -2.288 2.396 1.456
PVB H3A H H 0.000 -1.611 2.895 2.139
PVB C2A C CR16 0.000 -3.606 2.787 1.384
PVB H2A H H 0.000 -3.966 3.593 2.011
PVB C5A C CR6 0.000 -2.701 0.710 -0.232
PVB CL1 CL CL 0.000 -2.131 -0.583 -1.238
PVB C6A C CR16 0.000 -4.020 1.104 -0.295
PVB H6A H H 0.000 -4.703 0.602 -0.970
PVB C1A C CR6 0.000 -4.477 2.146 0.506
PVB N6 N NH1 0.000 -5.808 2.544 0.436
PVB H6 H H 0.000 -6.051 3.516 0.565
PVB C6 C CR6 0.000 -6.799 1.608 0.190
PVB N1 N NRD6 0.000 -6.516 0.312 0.164
PVB C5 C CR56 0.000 -8.127 2.011 -0.037
PVB N7 N NRD5 0.000 -8.763 3.208 -0.084
PVB C8 C CR15 0.000 -10.026 3.017 -0.335
PVB H8 H H 0.000 -10.767 3.801 -0.428
PVB N9 N NR5 0.000 -10.277 1.682 -0.465
PVB C9 C CH1 0.000 -11.578 1.070 -0.750
PVB H9 H H 0.000 -11.466 -0.022 -0.796
PVB C10 C CH3 0.000 -12.102 1.586 -2.092
PVB H103 H H 0.000 -13.042 1.143 -2.299
PVB H102 H H 0.000 -12.211 2.639 -2.049
PVB H101 H H 0.000 -11.418 1.334 -2.860
PVB C11 C CH3 0.000 -12.567 1.434 0.359
PVB H113 H H 0.000 -13.507 0.991 0.154
PVB H112 H H 0.000 -12.204 1.078 1.288
PVB H111 H H 0.000 -12.676 2.487 0.404
PVB C4 C CR56 0.000 -9.090 1.019 -0.281
PVB N3 N NRD6 0.000 -8.720 -0.257 -0.288
PVB C2 C CR6 0.000 -7.459 -0.593 -0.070
PVB N2 N NH1 0.000 -7.110 -1.933 -0.088
PVB H2 H H 0.000 -6.141 -2.204 -0.004
PVB C12 C CH1 0.000 -8.148 -2.958 -0.228
PVB H12 H H 0.000 -9.009 -2.536 -0.764
PVB C15 C CH2 0.000 -7.589 -4.145 -1.016
PVB H151 H H 0.000 -7.193 -3.793 -1.970
PVB H152 H H 0.000 -8.387 -4.867 -1.199
PVB O1 O OH1 0.000 -6.545 -4.766 -0.263
PVB H1 H H 0.000 -6.192 -5.516 -0.761
PVB C13 C CH1 0.000 -8.591 -3.428 1.158
PVB H13 H H 0.000 -7.716 -3.782 1.722
PVB C14 C CH3 0.000 -9.599 -4.571 1.012
PVB H143 H H 0.000 -9.979 -4.832 1.966
PVB H142 H H 0.000 -10.397 -4.261 0.387
PVB H141 H H 0.000 -9.121 -5.412 0.581
PVB C16 C CH3 0.000 -9.244 -2.265 1.908
PVB H163 H H 0.000 -9.495 -2.573 2.890
PVB H162 H H 0.000 -8.568 -1.450 1.956
PVB H161 H H 0.000 -10.123 -1.963 1.398
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
PVB OX2 n/a CX START
PVB CX OX2 C4A .
PVB OX1 CX . .
PVB C4A CX C5A .
PVB C3A C4A C2A .
PVB H3A C3A . .
PVB C2A C3A H2A .
PVB H2A C2A . .
PVB C5A C4A C6A .
PVB CL1 C5A . .
PVB C6A C5A C1A .
PVB H6A C6A . .
PVB C1A C6A N6 .
PVB N6 C1A C6 .
PVB H6 N6 . .
PVB C6 N6 C5 .
PVB N1 C6 . .
PVB C5 C6 C4 .
PVB N7 C5 C8 .
PVB C8 N7 N9 .
PVB H8 C8 . .
PVB N9 C8 C9 .
PVB C9 N9 C11 .
PVB H9 C9 . .
PVB C10 C9 H101 .
PVB H103 C10 . .
PVB H102 C10 . .
PVB H101 C10 . .
PVB C11 C9 H111 .
PVB H113 C11 . .
PVB H112 C11 . .
PVB H111 C11 . .
PVB C4 C5 N3 .
PVB N3 C4 C2 .
PVB C2 N3 N2 .
PVB N2 C2 C12 .
PVB H2 N2 . .
PVB C12 N2 C13 .
PVB H12 C12 . .
PVB C15 C12 O1 .
PVB H151 C15 . .
PVB H152 C15 . .
PVB O1 C15 H1 .
PVB H1 O1 . .
PVB C13 C12 C16 .
PVB H13 C13 . .
PVB C14 C13 H141 .
PVB H143 C14 . .
PVB H142 C14 . .
PVB H141 C14 . .
PVB C16 C13 H161 .
PVB H163 C16 . .
PVB H162 C16 . .
PVB H161 C16 . END
PVB N1 C2 . ADD
PVB N9 C4 . ADD
PVB C1A C2A . 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
PVB N1 C2 single 1.350 0.020
PVB N1 C6 double 1.350 0.020
PVB C9 N9 single 1.485 0.020
PVB C11 C9 single 1.524 0.020
PVB C10 C9 single 1.524 0.020
PVB N9 C4 single 1.337 0.020
PVB N9 C8 single 1.337 0.020
PVB N3 C4 single 1.355 0.020
PVB C4 C5 double 1.490 0.020
PVB C2 N3 double 1.350 0.020
PVB N2 C2 single 1.350 0.020
PVB C5 C6 single 1.490 0.020
PVB C6 N6 single 1.350 0.020
PVB N7 C5 single 1.350 0.020
PVB C8 N7 double 1.350 0.020
PVB N6 C1A single 1.350 0.020
PVB C1A C2A double 1.390 0.020
PVB C1A C6A single 1.390 0.020
PVB C2A C3A single 1.390 0.020
PVB C3A C4A double 1.390 0.020
PVB C5A C4A single 1.487 0.020
PVB C4A CX single 1.500 0.020
PVB CL1 C5A single 1.795 0.020
PVB C6A C5A double 1.390 0.020
PVB OX1 CX deloc 1.250 0.020
PVB CX OX2 deloc 1.250 0.020
PVB C12 N2 single 1.450 0.020
PVB C13 C12 single 1.524 0.020
PVB C15 C12 single 1.524 0.020
PVB C16 C13 single 1.524 0.020
PVB C14 C13 single 1.524 0.020
PVB O1 C15 single 1.432 0.020
PVB H9 C9 single 1.099 0.020
PVB H111 C11 single 1.059 0.020
PVB H112 C11 single 1.059 0.020
PVB H113 C11 single 1.059 0.020
PVB H101 C10 single 1.059 0.020
PVB H102 C10 single 1.059 0.020
PVB H103 C10 single 1.059 0.020
PVB H8 C8 single 1.083 0.020
PVB H2 N2 single 1.010 0.020
PVB H6 N6 single 1.010 0.020
PVB H2A C2A single 1.083 0.020
PVB H6A C6A single 1.083 0.020
PVB H3A C3A single 1.083 0.020
PVB H12 C12 single 1.099 0.020
PVB H13 C13 single 1.099 0.020
PVB H151 C15 single 1.092 0.020
PVB H152 C15 single 1.092 0.020
PVB H161 C16 single 1.059 0.020
PVB H162 C16 single 1.059 0.020
PVB H163 C16 single 1.059 0.020
PVB H141 C14 single 1.059 0.020
PVB H142 C14 single 1.059 0.020
PVB H143 C14 single 1.059 0.020
PVB H1 O1 single 0.967 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
PVB OX2 CX OX1 123.000 3.000
PVB OX2 CX C4A 120.000 3.000
PVB OX1 CX C4A 120.000 3.000
PVB CX C4A C3A 120.000 3.000
PVB CX C4A C5A 120.000 3.000
PVB C3A C4A C5A 120.000 3.000
PVB C4A C3A H3A 120.000 3.000
PVB C4A C3A C2A 120.000 3.000
PVB H3A C3A C2A 120.000 3.000
PVB C3A C2A H2A 120.000 3.000
PVB C3A C2A C1A 120.000 3.000
PVB H2A C2A C1A 120.000 3.000
PVB C4A C5A CL1 120.000 3.000
PVB C4A C5A C6A 120.000 3.000
PVB CL1 C5A C6A 120.000 3.000
PVB C5A C6A H6A 120.000 3.000
PVB C5A C6A C1A 120.000 3.000
PVB H6A C6A C1A 120.000 3.000
PVB C6A C1A N6 120.000 3.000
PVB C6A C1A C2A 120.000 3.000
PVB N6 C1A C2A 120.000 3.000
PVB C1A N6 H6 120.000 3.000
PVB C1A N6 C6 120.000 3.000
PVB H6 N6 C6 120.000 3.000
PVB N6 C6 N1 120.000 3.000
PVB N6 C6 C5 120.000 3.000
PVB N1 C6 C5 120.000 3.000
PVB C6 N1 C2 120.000 3.000
PVB C6 C5 N7 132.000 3.000
PVB C6 C5 C4 120.000 3.000
PVB N7 C5 C4 108.000 3.000
PVB C5 N7 C8 108.000 3.000
PVB N7 C8 H8 126.000 3.000
PVB N7 C8 N9 108.000 3.000
PVB H8 C8 N9 126.000 3.000
PVB C8 N9 C9 126.000 3.000
PVB C8 N9 C4 108.000 3.000
PVB C9 N9 C4 126.000 3.000
PVB N9 C9 H9 109.470 3.000
PVB N9 C9 C10 109.500 3.000
PVB N9 C9 C11 109.500 3.000
PVB H9 C9 C10 108.340 3.000
PVB H9 C9 C11 108.340 3.000
PVB C10 C9 C11 111.000 3.000
PVB C9 C10 H103 109.470 3.000
PVB C9 C10 H102 109.470 3.000
PVB C9 C10 H101 109.470 3.000
PVB H103 C10 H102 109.470 3.000
PVB H103 C10 H101 109.470 3.000
PVB H102 C10 H101 109.470 3.000
PVB C9 C11 H113 109.470 3.000
PVB C9 C11 H112 109.470 3.000
PVB C9 C11 H111 109.470 3.000
PVB H113 C11 H112 109.470 3.000
PVB H113 C11 H111 109.470 3.000
PVB H112 C11 H111 109.470 3.000
PVB C5 C4 N3 120.000 3.000
PVB C5 C4 N9 108.000 3.000
PVB N3 C4 N9 132.000 3.000
PVB C4 N3 C2 120.000 3.000
PVB N3 C2 N2 120.000 3.000
PVB N3 C2 N1 120.000 3.000
PVB N2 C2 N1 120.000 3.000
PVB C2 N2 H2 120.000 3.000
PVB C2 N2 C12 120.000 3.000
PVB H2 N2 C12 118.500 3.000
PVB N2 C12 H12 108.550 3.000
PVB N2 C12 C15 110.000 3.000
PVB N2 C12 C13 110.000 3.000
PVB H12 C12 C15 108.340 3.000
PVB H12 C12 C13 108.340 3.000
PVB C15 C12 C13 111.000 3.000
PVB C12 C15 H151 109.470 3.000
PVB C12 C15 H152 109.470 3.000
PVB C12 C15 O1 109.470 3.000
PVB H151 C15 H152 107.900 3.000
PVB H151 C15 O1 109.470 3.000
PVB H152 C15 O1 109.470 3.000
PVB C15 O1 H1 109.470 3.000
PVB C12 C13 H13 108.340 3.000
PVB C12 C13 C14 111.000 3.000
PVB C12 C13 C16 111.000 3.000
PVB H13 C13 C14 108.340 3.000
PVB H13 C13 C16 108.340 3.000
PVB C14 C13 C16 111.000 3.000
PVB C13 C14 H143 109.470 3.000
PVB C13 C14 H142 109.470 3.000
PVB C13 C14 H141 109.470 3.000
PVB H143 C14 H142 109.470 3.000
PVB H143 C14 H141 109.470 3.000
PVB H142 C14 H141 109.470 3.000
PVB C13 C16 H163 109.470 3.000
PVB C13 C16 H162 109.470 3.000
PVB C13 C16 H161 109.470 3.000
PVB H163 C16 H162 109.470 3.000
PVB H163 C16 H161 109.470 3.000
PVB H162 C16 H161 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
PVB var_1 OX2 CX C4A C5A 0.026 20.000 1
PVB CONST_1 CX C4A C3A C2A 180.000 0.000 0
PVB CONST_2 C4A C3A C2A C1A 0.000 0.000 0
PVB CONST_3 CX C4A C5A C6A 180.000 0.000 0
PVB CONST_4 C4A C5A C6A C1A 0.000 0.000 0
PVB CONST_5 C5A C6A C1A N6 180.000 0.000 0
PVB CONST_6 C6A C1A C2A C3A 0.000 0.000 0
PVB var_2 C6A C1A N6 C6 33.839 20.000 1
PVB var_3 C1A N6 C6 C5 -172.615 20.000 1
PVB CONST_7 N6 C6 N1 C2 180.000 0.000 0
PVB CONST_8 C6 N1 C2 N3 0.000 0.000 0
PVB CONST_9 N6 C6 C5 C4 180.000 0.000 0
PVB CONST_10 C6 C5 N7 C8 180.000 0.000 0
PVB CONST_11 C5 N7 C8 N9 0.000 0.000 0
PVB CONST_12 N7 C8 N9 C9 180.000 0.000 0
PVB CONST_13 C8 N9 C4 C5 0.000 0.000 0
PVB var_4 C8 N9 C9 C11 -60.047 20.000 1
PVB var_5 N9 C9 C10 H101 59.955 20.000 3
PVB var_6 N9 C9 C11 H111 60.051 20.000 3
PVB CONST_14 C6 C5 C4 N3 0.000 0.000 0
PVB CONST_15 C5 C4 N3 C2 0.000 0.000 0
PVB CONST_16 C4 N3 C2 N2 180.000 0.000 0
PVB var_7 N3 C2 N2 C12 -5.343 20.000 1
PVB var_8 C2 N2 C12 C13 -93.258 20.000 3
PVB var_9 N2 C12 C15 O1 65.057 20.000 3
PVB var_10 C12 C15 O1 H1 179.971 20.000 1
PVB var_11 N2 C12 C13 C16 64.127 20.000 3
PVB var_12 C12 C13 C14 H141 65.620 20.000 3
PVB var_13 C12 C13 C16 H161 63.581 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
PVB chir_01 C9 N9 C11 C10 negativ
PVB chir_02 C12 N2 C13 C15 positiv
PVB chir_03 C13 C12 C16 C14 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
PVB plan-1 N1 0.020
PVB plan-1 C2 0.020
PVB plan-1 C6 0.020
PVB plan-1 N3 0.020
PVB plan-1 C4 0.020
PVB plan-1 N2 0.020
PVB plan-1 C5 0.020
PVB plan-1 N6 0.020
PVB plan-1 N7 0.020
PVB plan-1 C8 0.020
PVB plan-1 N9 0.020
PVB plan-1 H8 0.020
PVB plan-1 C9 0.020
PVB plan-1 H2 0.020
PVB plan-1 H6 0.020
PVB plan-2 N6 0.020
PVB plan-2 C6 0.020
PVB plan-2 C1A 0.020
PVB plan-2 H6 0.020
PVB plan-3 C1A 0.020
PVB plan-3 N6 0.020
PVB plan-3 C2A 0.020
PVB plan-3 C6A 0.020
PVB plan-3 C3A 0.020
PVB plan-3 C4A 0.020
PVB plan-3 C5A 0.020
PVB plan-3 H2A 0.020
PVB plan-3 H3A 0.020
PVB plan-3 CX 0.020
PVB plan-3 CL1 0.020
PVB plan-3 H6A 0.020
PVB plan-3 H6 0.020
PVB plan-4 CX 0.020
PVB plan-4 C4A 0.020
PVB plan-4 OX1 0.020
PVB plan-4 OX2 0.020
PVB plan-5 N2 0.020
PVB plan-5 C2 0.020
PVB plan-5 C12 0.020
PVB plan-5 H2 0.020
# ------------------------------------------------------
|
