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
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
|
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
P13 P13 'N-[2-(3-AMINOPROPOXY)-5-(1H-INDOL-5-' non-polymer 63 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_P13
#
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
P13 N N NH2 0.000 0.000 0.000 0.000
P13 HN1A H H 0.000 0.000 0.000 0.000
P13 HN2 H H 0.000 0.000 0.000 0.000
P13 CB C CH2 0.000 0.000 0.000 0.000
P13 HB1 H H 0.000 0.000 0.000 0.000
P13 HB2 H H 0.000 0.000 0.000 0.000
P13 CA C CH2 0.000 0.000 0.000 0.000
P13 HA1 H H 0.000 0.000 0.000 0.000
P13 HA2 H H 0.000 0.000 0.000 0.000
P13 C C CH2 0.000 0.000 0.000 0.000
P13 HC1 H H 0.000 0.000 0.000 0.000
P13 HC2 H H 0.000 0.000 0.000 0.000
P13 O O O2 0.000 0.000 0.000 0.000
P13 C5 C CR6 0.000 0.000 0.000 0.000
P13 C6 C CR16 0.000 0.000 0.000 0.000
P13 H6 H H 0.000 0.000 0.000 0.000
P13 C1 C CR16 0.000 0.000 0.000 0.000
P13 H1 H H 0.000 0.000 0.000 0.000
P13 C4 C CR6 0.000 0.000 0.000 0.000
P13 C3 C CR16 0.000 0.000 0.000 0.000
P13 H3 H H 0.000 0.000 0.000 0.000
P13 C2 C CR6 0.000 0.000 0.000 0.000
P13 C51 C CR6 0.000 0.000 0.000 0.000
P13 C61 C CR16 0.000 0.000 0.000 0.000
P13 H61 H H 0.000 0.000 0.000 0.000
P13 C71 C CR16 0.000 0.000 0.000 0.000
P13 H7 H H 0.000 0.000 0.000 0.000
P13 C81 C CR56 0.000 0.000 0.000 0.000
P13 C91 C CR56 0.000 0.000 0.000 0.000
P13 C41 C CR16 0.000 0.000 0.000 0.000
P13 H4 H H 0.000 0.000 0.000 0.000
P13 C31 C CR15 0.000 0.000 0.000 0.000
P13 H31 H H 0.000 0.000 0.000 0.000
P13 C21 C CR15 0.000 0.000 0.000 0.000
P13 H2 H H 0.000 0.000 0.000 0.000
P13 N1 N NR15 0.000 0.000 0.000 0.000
P13 HN1 H H 0.000 0.000 0.000 0.000
P13 CA1 C CH2 0.000 0.000 0.000 0.000
P13 HA11 H H 0.000 0.000 0.000 0.000
P13 HA12 H H 0.000 0.000 0.000 0.000
P13 NB N NH1 0.000 0.000 0.000 0.000
P13 HB11 H H 0.000 0.000 0.000 0.000
P13 CG C CH2 0.000 0.000 0.000 0.000
P13 HG1 H H 0.000 0.000 0.000 0.000
P13 HG2 H H 0.000 0.000 0.000 0.000
P13 CD C CH2 0.000 0.000 0.000 0.000
P13 HD1 H H 0.000 0.000 0.000 0.000
P13 HD2 H H 0.000 0.000 0.000 0.000
P13 NE N N 0.000 0.000 0.000 0.000
P13 CH2 C CH2 0.000 0.000 0.000 0.000
P13 HH21 H H 0.000 0.000 0.000 0.000
P13 HH22 H H 0.000 0.000 0.000 0.000
P13 CI2 C CH2 0.000 0.000 0.000 0.000
P13 HI21 H H 0.000 0.000 0.000 0.000
P13 HI22 H H 0.000 0.000 0.000 0.000
P13 NJ N NH1 0.000 0.000 0.000 0.000
P13 HJ1 H H 0.000 0.000 0.000 0.000
P13 CI1 C CH2 0.000 0.000 0.000 0.000
P13 HI11 H H 0.000 0.000 0.000 0.000
P13 HI12 H H 0.000 0.000 0.000 0.000
P13 CH1 C CH2 0.000 0.000 0.000 0.000
P13 HH12 H H 0.000 0.000 0.000 0.000
P13 HH11 H H 0.000 0.000 0.000 0.000
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
P13 N n/a CB START
P13 HN1A N . .
P13 HN2 N . .
P13 CB N CA .
P13 HB1 CB . .
P13 HB2 CB . .
P13 CA CB C .
P13 HA1 CA . .
P13 HA2 CA . .
P13 C CA O .
P13 HC1 C . .
P13 HC2 C . .
P13 O C C5 .
P13 C5 O C4 .
P13 C6 C5 C1 .
P13 H6 C6 . .
P13 C1 C6 H1 .
P13 H1 C1 . .
P13 C4 C5 CA1 .
P13 C3 C4 C2 .
P13 H3 C3 . .
P13 C2 C3 C51 .
P13 C51 C2 C61 .
P13 C61 C51 C71 .
P13 H61 C61 . .
P13 C71 C61 C81 .
P13 H7 C71 . .
P13 C81 C71 N1 .
P13 C91 C81 C31 .
P13 C41 C91 H4 .
P13 H4 C41 . .
P13 C31 C91 C21 .
P13 H31 C31 . .
P13 C21 C31 H2 .
P13 H2 C21 . .
P13 N1 C81 HN1 .
P13 HN1 N1 . .
P13 CA1 C4 NB .
P13 HA11 CA1 . .
P13 HA12 CA1 . .
P13 NB CA1 CG .
P13 HB11 NB . .
P13 CG NB CD .
P13 HG1 CG . .
P13 HG2 CG . .
P13 CD CG NE .
P13 HD1 CD . .
P13 HD2 CD . .
P13 NE CD CH2 .
P13 CH2 NE CI2 .
P13 HH21 CH2 . .
P13 HH22 CH2 . .
P13 CI2 CH2 NJ .
P13 HI21 CI2 . .
P13 HI22 CI2 . .
P13 NJ CI2 CI1 .
P13 HJ1 NJ . .
P13 CI1 NJ CH1 .
P13 HI11 CI1 . .
P13 HI12 CI1 . .
P13 CH1 CI1 HH11 .
P13 HH12 CH1 . .
P13 HH11 CH1 . END
P13 C1 C2 . ADD
P13 NE CH1 . ADD
P13 N1 C21 . ADD
P13 C41 C51 . 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
P13 C1 C2 double 1.390 0.020
P13 C1 C6 single 1.390 0.020
P13 H1 C1 single 1.083 0.020
P13 C2 C3 single 1.390 0.020
P13 C51 C2 single 1.487 0.020
P13 C3 C4 double 1.390 0.020
P13 H3 C3 single 1.083 0.020
P13 C4 C5 single 1.487 0.020
P13 CA1 C4 single 1.511 0.020
P13 C6 C5 double 1.390 0.020
P13 C5 O single 1.370 0.020
P13 H6 C6 single 1.083 0.020
P13 CB N single 1.450 0.020
P13 HN1A N single 1.010 0.020
P13 HN2 N single 1.010 0.020
P13 CA CB single 1.524 0.020
P13 HB1 CB single 1.092 0.020
P13 HB2 CB single 1.092 0.020
P13 C CA single 1.524 0.020
P13 HA1 CA single 1.092 0.020
P13 HA2 CA single 1.092 0.020
P13 O C single 1.426 0.020
P13 HC1 C single 1.092 0.020
P13 HC2 C single 1.092 0.020
P13 NB CA1 single 1.450 0.020
P13 HA11 CA1 single 1.092 0.020
P13 HA12 CA1 single 1.092 0.020
P13 CG NB single 1.450 0.020
P13 HB11 NB single 1.010 0.020
P13 CD CG single 1.524 0.020
P13 HG1 CG single 1.092 0.020
P13 HG2 CG single 1.092 0.020
P13 NE CD single 1.455 0.020
P13 HD1 CD single 1.092 0.020
P13 HD2 CD single 1.092 0.020
P13 NE CH1 single 1.455 0.020
P13 CH2 NE single 1.455 0.020
P13 CH1 CI1 single 1.524 0.020
P13 HH11 CH1 single 1.092 0.020
P13 HH12 CH1 single 1.092 0.020
P13 CI1 NJ single 1.450 0.020
P13 HI11 CI1 single 1.092 0.020
P13 HI12 CI1 single 1.092 0.020
P13 NJ CI2 single 1.450 0.020
P13 HJ1 NJ single 1.010 0.020
P13 CI2 CH2 single 1.524 0.020
P13 HI21 CI2 single 1.092 0.020
P13 HI22 CI2 single 1.092 0.020
P13 HH21 CH2 single 1.092 0.020
P13 HH22 CH2 single 1.092 0.020
P13 N1 C21 single 1.350 0.020
P13 N1 C81 single 1.340 0.020
P13 HN1 N1 single 1.040 0.020
P13 C21 C31 double 1.380 0.020
P13 H2 C21 single 1.083 0.020
P13 C31 C91 single 1.440 0.020
P13 H31 C31 single 1.083 0.020
P13 C41 C51 double 1.390 0.020
P13 C41 C91 single 1.390 0.020
P13 H4 C41 single 1.083 0.020
P13 C61 C51 single 1.390 0.020
P13 C71 C61 double 1.390 0.020
P13 H61 C61 single 1.083 0.020
P13 C81 C71 single 1.390 0.020
P13 H7 C71 single 1.083 0.020
P13 C91 C81 double 1.490 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
P13 HN1A N HN2 120.000 3.000
P13 HN1A N CB 120.000 3.000
P13 HN2 N CB 120.000 3.000
P13 N CB HB1 109.470 3.000
P13 N CB HB2 109.470 3.000
P13 N CB CA 109.470 3.000
P13 HB1 CB HB2 107.900 3.000
P13 HB1 CB CA 109.470 3.000
P13 HB2 CB CA 109.470 3.000
P13 CB CA HA1 109.470 3.000
P13 CB CA HA2 109.470 3.000
P13 CB CA C 111.000 3.000
P13 HA1 CA HA2 107.900 3.000
P13 HA1 CA C 109.470 3.000
P13 HA2 CA C 109.470 3.000
P13 CA C HC1 109.470 3.000
P13 CA C HC2 109.470 3.000
P13 CA C O 109.470 3.000
P13 HC1 C HC2 107.900 3.000
P13 HC1 C O 109.470 3.000
P13 HC2 C O 109.470 3.000
P13 C O C5 120.000 3.000
P13 O C5 C6 120.000 3.000
P13 O C5 C4 120.000 3.000
P13 C6 C5 C4 120.000 3.000
P13 C5 C6 H6 120.000 3.000
P13 C5 C6 C1 120.000 3.000
P13 H6 C6 C1 120.000 3.000
P13 C6 C1 H1 120.000 3.000
P13 C6 C1 C2 120.000 3.000
P13 H1 C1 C2 120.000 3.000
P13 C5 C4 C3 120.000 3.000
P13 C5 C4 CA1 120.000 3.000
P13 C3 C4 CA1 120.000 3.000
P13 C4 C3 H3 120.000 3.000
P13 C4 C3 C2 120.000 3.000
P13 H3 C3 C2 120.000 3.000
P13 C3 C2 C51 120.000 3.000
P13 C3 C2 C1 120.000 3.000
P13 C51 C2 C1 120.000 3.000
P13 C2 C51 C61 120.000 3.000
P13 C2 C51 C41 120.000 3.000
P13 C61 C51 C41 120.000 3.000
P13 C51 C61 H61 120.000 3.000
P13 C51 C61 C71 120.000 3.000
P13 H61 C61 C71 120.000 3.000
P13 C61 C71 H7 120.000 3.000
P13 C61 C71 C81 120.000 3.000
P13 H7 C71 C81 120.000 3.000
P13 C71 C81 C91 120.000 3.000
P13 C71 C81 N1 132.000 3.000
P13 C91 C81 N1 108.000 3.000
P13 C81 C91 C41 120.000 3.000
P13 C81 C91 C31 120.000 3.000
P13 C41 C91 C31 126.000 3.000
P13 C91 C41 H4 120.000 3.000
P13 C91 C41 C51 120.000 3.000
P13 H4 C41 C51 120.000 3.000
P13 C91 C31 H31 108.000 3.000
P13 C91 C31 C21 108.000 3.000
P13 H31 C31 C21 126.000 3.000
P13 C31 C21 H2 126.000 3.000
P13 C31 C21 N1 108.000 3.000
P13 H2 C21 N1 126.000 3.000
P13 C81 N1 HN1 126.000 3.000
P13 C81 N1 C21 108.000 3.000
P13 HN1 N1 C21 126.000 3.000
P13 C4 CA1 HA11 109.470 3.000
P13 C4 CA1 HA12 109.470 3.000
P13 C4 CA1 NB 109.500 3.000
P13 HA11 CA1 HA12 107.900 3.000
P13 HA11 CA1 NB 109.470 3.000
P13 HA12 CA1 NB 109.470 3.000
P13 CA1 NB HB11 118.500 3.000
P13 CA1 NB CG 120.000 3.000
P13 HB11 NB CG 118.500 3.000
P13 NB CG HG1 109.470 3.000
P13 NB CG HG2 109.470 3.000
P13 NB CG CD 112.000 3.000
P13 HG1 CG HG2 107.900 3.000
P13 HG1 CG CD 109.470 3.000
P13 HG2 CG CD 109.470 3.000
P13 CG CD HD1 109.470 3.000
P13 CG CD HD2 109.470 3.000
P13 CG CD NE 105.000 3.000
P13 HD1 CD HD2 107.900 3.000
P13 HD1 CD NE 109.470 3.000
P13 HD2 CD NE 109.470 3.000
P13 CD NE CH2 120.000 3.000
P13 CD NE CH1 120.000 3.000
P13 CH2 NE CH1 120.000 3.000
P13 NE CH2 HH21 109.470 3.000
P13 NE CH2 HH22 109.470 3.000
P13 NE CH2 CI2 105.000 3.000
P13 HH21 CH2 HH22 107.900 3.000
P13 HH21 CH2 CI2 109.470 3.000
P13 HH22 CH2 CI2 109.470 3.000
P13 CH2 CI2 HI21 109.470 3.000
P13 CH2 CI2 HI22 109.470 3.000
P13 CH2 CI2 NJ 112.000 3.000
P13 HI21 CI2 HI22 107.900 3.000
P13 HI21 CI2 NJ 109.470 3.000
P13 HI22 CI2 NJ 109.470 3.000
P13 CI2 NJ HJ1 118.500 3.000
P13 CI2 NJ CI1 120.000 3.000
P13 HJ1 NJ CI1 118.500 3.000
P13 NJ CI1 HI11 109.470 3.000
P13 NJ CI1 HI12 109.470 3.000
P13 NJ CI1 CH1 112.000 3.000
P13 HI11 CI1 HI12 107.900 3.000
P13 HI11 CI1 CH1 109.470 3.000
P13 HI12 CI1 CH1 109.470 3.000
P13 CI1 CH1 HH12 109.470 3.000
P13 CI1 CH1 HH11 109.470 3.000
P13 CI1 CH1 NE 105.000 3.000
P13 HH12 CH1 HH11 107.900 3.000
P13 HH12 CH1 NE 109.470 3.000
P13 HH11 CH1 NE 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
P13 var_1 HN2 N CB CA 0.000 20.000 1
P13 var_2 N CB CA C 0.000 20.000 3
P13 var_3 CB CA C O 0.000 20.000 3
P13 var_4 CA C O C5 0.000 20.000 1
P13 var_5 C O C5 C4 0.000 20.000 1
P13 CONST_1 O C5 C6 C1 0.000 0.000 0
P13 CONST_2 C5 C6 C1 C2 0.000 0.000 0
P13 CONST_3 C6 C1 C2 C3 0.000 0.000 0
P13 CONST_4 O C5 C4 CA1 0.000 0.000 0
P13 CONST_5 C5 C4 C3 C2 0.000 0.000 0
P13 CONST_6 C4 C3 C2 C51 0.000 0.000 0
P13 CONST_7 C3 C2 C51 C61 0.000 0.000 0
P13 CONST_8 C2 C51 C61 C71 0.000 0.000 0
P13 CONST_9 C51 C61 C71 C81 0.000 0.000 0
P13 CONST_10 C61 C71 C81 N1 0.000 0.000 0
P13 CONST_11 C71 C81 C91 C31 0.000 0.000 0
P13 CONST_12 C81 C91 C41 C51 0.000 0.000 0
P13 CONST_13 C91 C41 C51 C2 0.000 0.000 0
P13 CONST_14 C81 C91 C31 C21 0.000 0.000 0
P13 CONST_15 C91 C31 C21 N1 0.000 0.000 0
P13 CONST_16 C71 C81 N1 C21 0.000 0.000 0
P13 CONST_17 C81 N1 C21 C31 0.000 0.000 0
P13 var_6 C5 C4 CA1 NB 0.000 20.000 2
P13 var_7 C4 CA1 NB CG 0.000 20.000 3
P13 var_8 CA1 NB CG CD 0.000 20.000 3
P13 var_9 NB CG CD NE 0.000 20.000 3
P13 var_10 CG CD NE CH2 0.000 20.000 1
P13 var_11 CD NE CH1 CI1 0.000 20.000 1
P13 var_12 CD NE CH2 CI2 0.000 20.000 1
P13 var_13 NE CH2 CI2 NJ 0.000 20.000 3
P13 var_14 CH2 CI2 NJ CI1 0.000 20.000 3
P13 var_15 CI2 NJ CI1 CH1 0.000 20.000 3
P13 var_16 NJ CI1 CH1 NE 0.000 20.000 3
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
P13 plan-1 C1 0.020
P13 plan-1 C2 0.020
P13 plan-1 C6 0.020
P13 plan-1 H1 0.020
P13 plan-1 C3 0.020
P13 plan-1 C4 0.020
P13 plan-1 C5 0.020
P13 plan-1 C51 0.020
P13 plan-1 H3 0.020
P13 plan-1 CA1 0.020
P13 plan-1 O 0.020
P13 plan-1 H6 0.020
P13 plan-2 N 0.020
P13 plan-2 CB 0.020
P13 plan-2 HN1A 0.020
P13 plan-2 HN2 0.020
P13 plan-3 NB 0.020
P13 plan-3 CA1 0.020
P13 plan-3 CG 0.020
P13 plan-3 HB11 0.020
P13 plan-4 NE 0.020
P13 plan-4 CD 0.020
P13 plan-4 CH1 0.020
P13 plan-4 CH2 0.020
P13 plan-5 NJ 0.020
P13 plan-5 CI1 0.020
P13 plan-5 CI2 0.020
P13 plan-5 HJ1 0.020
P13 plan-6 N1 0.020
P13 plan-6 C21 0.020
P13 plan-6 C81 0.020
P13 plan-6 HN1 0.020
P13 plan-6 C31 0.020
P13 plan-6 H2 0.020
P13 plan-6 C91 0.020
P13 plan-6 H31 0.020
P13 plan-6 C41 0.020
P13 plan-6 C51 0.020
P13 plan-6 H4 0.020
P13 plan-6 C61 0.020
P13 plan-6 C71 0.020
P13 plan-6 C2 0.020
P13 plan-6 H61 0.020
P13 plan-6 H7 0.020
# ------------------------------------------------------
|
