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
|
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
0PJ 0PJ 'N-[(S)-({[(benzyloxy)carbonyl]amino}' non-polymer 65 32 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_0PJ
#
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
0PJ OXT O OC -0.500 0.000 0.000 0.000
0PJ CC C C 0.000 -1.064 0.535 -0.384
0PJ O3 O OC -0.500 -1.202 1.776 -0.311
0PJ CA1 C CH1 0.000 -2.178 -0.315 -0.937
0PJ HA1 H H 0.000 -2.504 -1.034 -0.172
0PJ CB1 C CH2 0.000 -1.679 -1.073 -2.169
0PJ HB21 H H 0.000 -0.795 -1.656 -1.903
0PJ HB31 H H 0.000 -1.420 -0.360 -2.954
0PJ CG1 C CH1 0.000 -2.778 -2.010 -2.671
0PJ HG1 H H 0.000 -3.700 -1.436 -2.841
0PJ CD21 C CH3 0.000 -3.039 -3.097 -1.626
0PJ HD26 H H 0.000 -3.801 -3.747 -1.974
0PJ HD25 H H 0.000 -2.151 -3.651 -1.462
0PJ HD24 H H 0.000 -3.347 -2.648 -0.718
0PJ CD11 C CH3 0.000 -2.334 -2.662 -3.983
0PJ HD16 H H 0.000 -1.495 -3.283 -3.803
0PJ HD15 H H 0.000 -3.127 -3.245 -4.375
0PJ HD14 H H 0.000 -2.072 -1.909 -4.681
0PJ N2 N NH1 0.000 -3.306 0.541 -1.314
0PJ H3 H H 0.000 -3.402 0.859 -2.268
0PJ C9 C C 0.000 -4.215 0.904 -0.388
0PJ O O O 0.000 -4.101 0.521 0.757
0PJ CA C CH1 0.000 -5.375 1.785 -0.776
0PJ HA H H 0.000 -5.971 1.285 -1.553
0PJ CB C CH2 0.000 -4.846 3.115 -1.316
0PJ HB2 H H 0.000 -4.162 2.925 -2.145
0PJ HB3 H H 0.000 -4.314 3.644 -0.522
0PJ CG C CH1 0.000 -6.018 3.969 -1.804
0PJ HG H H 0.000 -6.756 4.074 -0.996
0PJ CD2 C CH3 0.000 -6.674 3.294 -3.010
0PJ HD23 H H 0.000 -7.485 3.885 -3.349
0PJ HD22 H H 0.000 -5.963 3.192 -3.789
0PJ HD21 H H 0.000 -7.029 2.336 -2.730
0PJ CD1 C CH3 0.000 -5.507 5.353 -2.210
0PJ HD13 H H 0.000 -6.318 5.945 -2.548
0PJ HD12 H H 0.000 -5.052 5.822 -1.375
0PJ HD11 H H 0.000 -4.795 5.253 -2.988
0PJ N1 N NH1 0.000 -6.216 2.035 0.403
0PJ H H H 0.000 -6.041 2.756 1.088
0PJ P P P 0.000 -7.508 0.958 0.459
0PJ O11 O O 0.000 -8.402 1.199 -0.696
0PJ O21 O OH1 0.000 -6.953 -0.552 0.402
0PJ HO2 H H 0.000 -6.351 -0.872 1.088
0PJ C C CH2 0.000 -8.438 1.204 2.008
0PJ H1 H H 0.000 -8.814 2.229 2.047
0PJ H2 H H 0.000 -7.778 1.028 2.860
0PJ N N NH1 0.000 -9.563 0.268 2.058
0PJ HN2 H H 0.000 -10.437 0.504 1.610
0PJ C1 C C 0.000 -9.432 -0.909 2.701
0PJ O1 O O 0.000 -8.380 -1.193 3.241
0PJ O2 O O2 0.000 -10.468 -1.767 2.751
0PJ C2 C CH2 0.000 -10.257 -3.013 3.466
0PJ H21 H H 0.000 -10.003 -2.797 4.506
0PJ H22 H H 0.000 -9.438 -3.566 3.001
0PJ C3 C CR6 0.000 -11.516 -3.841 3.417
0PJ C8 C CR16 0.000 -12.470 -3.708 4.409
0PJ H81 H H 0.000 -12.311 -3.012 5.223
0PJ C7 C CR16 0.000 -13.627 -4.463 4.360
0PJ H71 H H 0.000 -14.377 -4.353 5.133
0PJ C6 C CR16 0.000 -13.825 -5.358 3.326
0PJ H61 H H 0.000 -14.730 -5.952 3.290
0PJ C5 C CR16 0.000 -12.869 -5.494 2.337
0PJ H51 H H 0.000 -13.025 -6.195 1.526
0PJ C4 C CR16 0.000 -11.714 -4.735 2.383
0PJ H41 H H 0.000 -10.965 -4.842 1.608
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
0PJ OXT n/a CC START
0PJ CC OXT CA1 .
0PJ O3 CC . .
0PJ CA1 CC N2 .
0PJ HA1 CA1 . .
0PJ CB1 CA1 CG1 .
0PJ HB21 CB1 . .
0PJ HB31 CB1 . .
0PJ CG1 CB1 CD11 .
0PJ HG1 CG1 . .
0PJ CD21 CG1 HD24 .
0PJ HD26 CD21 . .
0PJ HD25 CD21 . .
0PJ HD24 CD21 . .
0PJ CD11 CG1 HD14 .
0PJ HD16 CD11 . .
0PJ HD15 CD11 . .
0PJ HD14 CD11 . .
0PJ N2 CA1 C9 .
0PJ H3 N2 . .
0PJ C9 N2 CA .
0PJ O C9 . .
0PJ CA C9 N1 .
0PJ HA CA . .
0PJ CB CA CG .
0PJ HB2 CB . .
0PJ HB3 CB . .
0PJ CG CB CD1 .
0PJ HG CG . .
0PJ CD2 CG HD21 .
0PJ HD23 CD2 . .
0PJ HD22 CD2 . .
0PJ HD21 CD2 . .
0PJ CD1 CG HD11 .
0PJ HD13 CD1 . .
0PJ HD12 CD1 . .
0PJ HD11 CD1 . .
0PJ N1 CA P .
0PJ H N1 . .
0PJ P N1 C .
0PJ O11 P . .
0PJ O21 P HO2 .
0PJ HO2 O21 . .
0PJ C P N .
0PJ H1 C . .
0PJ H2 C . .
0PJ N C C1 .
0PJ HN2 N . .
0PJ C1 N O2 .
0PJ O1 C1 . .
0PJ O2 C1 C2 .
0PJ C2 O2 C3 .
0PJ H21 C2 . .
0PJ H22 C2 . .
0PJ C3 C2 C8 .
0PJ C8 C3 C7 .
0PJ H81 C8 . .
0PJ C7 C8 C6 .
0PJ H71 C7 . .
0PJ C6 C7 C5 .
0PJ H61 C6 . .
0PJ C5 C6 C4 .
0PJ H51 C5 . .
0PJ C4 C5 H41 .
0PJ H41 C4 . END
0PJ C3 C4 . 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
0PJ O1 C1 double 1.220 0.020
0PJ O2 C1 single 1.454 0.020
0PJ C2 O2 single 1.426 0.020
0PJ C3 C2 single 1.511 0.020
0PJ H21 C2 single 1.092 0.020
0PJ H22 C2 single 1.092 0.020
0PJ C3 C4 double 1.390 0.020
0PJ C8 C3 single 1.390 0.020
0PJ C4 C5 single 1.390 0.020
0PJ H41 C4 single 1.083 0.020
0PJ C5 C6 double 1.390 0.020
0PJ H51 C5 single 1.083 0.020
0PJ C6 C7 single 1.390 0.020
0PJ H61 C6 single 1.083 0.020
0PJ C7 C8 double 1.390 0.020
0PJ H71 C7 single 1.083 0.020
0PJ H81 C8 single 1.083 0.020
0PJ N C single 1.450 0.020
0PJ HN2 N single 1.010 0.020
0PJ C P single 1.812 0.020
0PJ H1 C single 1.092 0.020
0PJ H2 C single 1.092 0.020
0PJ O11 P double 1.480 0.020
0PJ O21 P single 1.610 0.020
0PJ HO2 O21 single 0.967 0.020
0PJ N1 CA single 1.450 0.020
0PJ H N1 single 1.010 0.020
0PJ CA C9 single 1.500 0.020
0PJ CB CA single 1.524 0.020
0PJ HA CA single 1.099 0.020
0PJ O C9 double 1.220 0.020
0PJ CG CB single 1.524 0.020
0PJ HB2 CB single 1.092 0.020
0PJ HB3 CB single 1.092 0.020
0PJ CD1 CG single 1.524 0.020
0PJ CD2 CG single 1.524 0.020
0PJ HG CG single 1.099 0.020
0PJ HD11 CD1 single 1.059 0.020
0PJ HD12 CD1 single 1.059 0.020
0PJ HD13 CD1 single 1.059 0.020
0PJ HD21 CD2 single 1.059 0.020
0PJ HD22 CD2 single 1.059 0.020
0PJ HD23 CD2 single 1.059 0.020
0PJ N2 CA1 single 1.450 0.020
0PJ H3 N2 single 1.010 0.020
0PJ CA1 CC single 1.500 0.020
0PJ CB1 CA1 single 1.524 0.020
0PJ HA1 CA1 single 1.099 0.020
0PJ O3 CC deloc 1.250 0.020
0PJ CC OXT deloc 1.250 0.020
0PJ CG1 CB1 single 1.524 0.020
0PJ HB21 CB1 single 1.092 0.020
0PJ HB31 CB1 single 1.092 0.020
0PJ CD11 CG1 single 1.524 0.020
0PJ CD21 CG1 single 1.524 0.020
0PJ HG1 CG1 single 1.099 0.020
0PJ HD14 CD11 single 1.059 0.020
0PJ HD15 CD11 single 1.059 0.020
0PJ HD16 CD11 single 1.059 0.020
0PJ HD24 CD21 single 1.059 0.020
0PJ HD25 CD21 single 1.059 0.020
0PJ HD26 CD21 single 1.059 0.020
0PJ C1 N single 1.330 0.020
0PJ P N1 single 1.750 0.020
0PJ C9 N2 single 1.330 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
0PJ OXT CC O3 123.000 3.000
0PJ OXT CC CA1 118.500 3.000
0PJ O3 CC CA1 118.500 3.000
0PJ CC CA1 HA1 108.810 3.000
0PJ CC CA1 CB1 109.470 3.000
0PJ CC CA1 N2 111.600 3.000
0PJ HA1 CA1 CB1 108.340 3.000
0PJ HA1 CA1 N2 108.550 3.000
0PJ CB1 CA1 N2 110.000 3.000
0PJ CA1 CB1 HB21 109.470 3.000
0PJ CA1 CB1 HB31 109.470 3.000
0PJ CA1 CB1 CG1 111.000 3.000
0PJ HB21 CB1 HB31 107.900 3.000
0PJ HB21 CB1 CG1 109.470 3.000
0PJ HB31 CB1 CG1 109.470 3.000
0PJ CB1 CG1 HG1 108.340 3.000
0PJ CB1 CG1 CD21 111.000 3.000
0PJ CB1 CG1 CD11 111.000 3.000
0PJ HG1 CG1 CD21 108.340 3.000
0PJ HG1 CG1 CD11 108.340 3.000
0PJ CD21 CG1 CD11 111.000 3.000
0PJ CG1 CD21 HD26 109.470 3.000
0PJ CG1 CD21 HD25 109.470 3.000
0PJ CG1 CD21 HD24 109.470 3.000
0PJ HD26 CD21 HD25 109.470 3.000
0PJ HD26 CD21 HD24 109.470 3.000
0PJ HD25 CD21 HD24 109.470 3.000
0PJ CG1 CD11 HD16 109.470 3.000
0PJ CG1 CD11 HD15 109.470 3.000
0PJ CG1 CD11 HD14 109.470 3.000
0PJ HD16 CD11 HD15 109.470 3.000
0PJ HD16 CD11 HD14 109.470 3.000
0PJ HD15 CD11 HD14 109.470 3.000
0PJ CA1 N2 H3 118.500 3.000
0PJ CA1 N2 C9 121.500 3.000
0PJ H3 N2 C9 120.000 3.000
0PJ N2 C9 O 123.000 3.000
0PJ N2 C9 CA 116.500 3.000
0PJ O C9 CA 120.500 3.000
0PJ C9 CA HA 108.810 3.000
0PJ C9 CA CB 109.470 3.000
0PJ C9 CA N1 111.600 3.000
0PJ HA CA CB 108.340 3.000
0PJ HA CA N1 108.550 3.000
0PJ CB CA N1 110.000 3.000
0PJ CA CB HB2 109.470 3.000
0PJ CA CB HB3 109.470 3.000
0PJ CA CB CG 111.000 3.000
0PJ HB2 CB HB3 107.900 3.000
0PJ HB2 CB CG 109.470 3.000
0PJ HB3 CB CG 109.470 3.000
0PJ CB CG HG 108.340 3.000
0PJ CB CG CD2 111.000 3.000
0PJ CB CG CD1 111.000 3.000
0PJ HG CG CD2 108.340 3.000
0PJ HG CG CD1 108.340 3.000
0PJ CD2 CG CD1 111.000 3.000
0PJ CG CD2 HD23 109.470 3.000
0PJ CG CD2 HD22 109.470 3.000
0PJ CG CD2 HD21 109.470 3.000
0PJ HD23 CD2 HD22 109.470 3.000
0PJ HD23 CD2 HD21 109.470 3.000
0PJ HD22 CD2 HD21 109.470 3.000
0PJ CG CD1 HD13 109.470 3.000
0PJ CG CD1 HD12 109.470 3.000
0PJ CG CD1 HD11 109.470 3.000
0PJ HD13 CD1 HD12 109.470 3.000
0PJ HD13 CD1 HD11 109.470 3.000
0PJ HD12 CD1 HD11 109.470 3.000
0PJ CA N1 H 118.500 3.000
0PJ CA N1 P 120.000 3.000
0PJ H N1 P 120.000 3.000
0PJ N1 P O11 109.500 3.000
0PJ N1 P O21 109.500 3.000
0PJ N1 P C 109.500 3.000
0PJ O11 P O21 109.500 3.000
0PJ O11 P C 109.500 3.000
0PJ O21 P C 109.500 3.000
0PJ P O21 HO2 120.000 3.000
0PJ P C H1 109.500 3.000
0PJ P C H2 109.500 3.000
0PJ P C N 109.500 3.000
0PJ H1 C H2 107.900 3.000
0PJ H1 C N 109.470 3.000
0PJ H2 C N 109.470 3.000
0PJ C N HN2 118.500 3.000
0PJ C N C1 121.500 3.000
0PJ HN2 N C1 120.000 3.000
0PJ N C1 O1 123.000 3.000
0PJ N C1 O2 118.000 3.000
0PJ O1 C1 O2 119.000 3.000
0PJ C1 O2 C2 120.000 3.000
0PJ O2 C2 H21 109.470 3.000
0PJ O2 C2 H22 109.470 3.000
0PJ O2 C2 C3 109.470 3.000
0PJ H21 C2 H22 107.900 3.000
0PJ H21 C2 C3 109.470 3.000
0PJ H22 C2 C3 109.470 3.000
0PJ C2 C3 C8 120.000 3.000
0PJ C2 C3 C4 120.000 3.000
0PJ C8 C3 C4 120.000 3.000
0PJ C3 C8 H81 120.000 3.000
0PJ C3 C8 C7 120.000 3.000
0PJ H81 C8 C7 120.000 3.000
0PJ C8 C7 H71 120.000 3.000
0PJ C8 C7 C6 120.000 3.000
0PJ H71 C7 C6 120.000 3.000
0PJ C7 C6 H61 120.000 3.000
0PJ C7 C6 C5 120.000 3.000
0PJ H61 C6 C5 120.000 3.000
0PJ C6 C5 H51 120.000 3.000
0PJ C6 C5 C4 120.000 3.000
0PJ H51 C5 C4 120.000 3.000
0PJ C5 C4 H41 120.000 3.000
0PJ C5 C4 C3 120.000 3.000
0PJ H41 C4 C3 120.000 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
0PJ var_1 OXT CC CA1 N2 -179.991 20.000 3
0PJ var_2 CC CA1 CB1 CG1 176.038 20.000 3
0PJ var_3 CA1 CB1 CG1 CD11 174.283 20.000 3
0PJ var_4 CB1 CG1 CD21 HD24 60.000 20.000 3
0PJ var_5 CB1 CG1 CD11 HD14 -55.120 20.000 3
0PJ var_6 CC CA1 N2 C9 -84.949 20.000 3
0PJ CONST_1 CA1 N2 C9 CA 180.000 0.000 0
0PJ var_7 N2 C9 CA N1 179.987 20.000 3
0PJ var_8 C9 CA CB CG 175.932 20.000 3
0PJ var_9 CA CB CG CD1 174.240 20.000 3
0PJ var_10 CB CG CD2 HD21 60.018 20.000 3
0PJ var_11 CB CG CD1 HD11 60.015 20.000 3
0PJ var_12 C9 CA N1 P -95.834 20.000 3
0PJ var_13 CA N1 P C 175.013 20.000 1
0PJ var_14 N1 P O21 HO2 59.955 20.000 1
0PJ var_15 N1 P C N -179.999 20.000 1
0PJ var_16 P C N C1 94.994 20.000 3
0PJ CONST_2 C N C1 O2 180.000 0.000 0
0PJ var_17 N C1 O2 C2 -179.707 20.000 1
0PJ var_18 C1 O2 C2 C3 179.976 20.000 1
0PJ var_19 O2 C2 C3 C8 -90.304 20.000 2
0PJ CONST_3 C2 C3 C4 C5 180.000 0.000 0
0PJ CONST_4 C2 C3 C8 C7 180.000 0.000 0
0PJ CONST_5 C3 C8 C7 C6 0.000 0.000 0
0PJ CONST_6 C8 C7 C6 C5 0.000 0.000 0
0PJ CONST_7 C7 C6 C5 C4 0.000 0.000 0
0PJ CONST_8 C6 C5 C4 C3 0.000 0.000 0
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
0PJ chir_01 CA N1 C9 CB positiv
0PJ chir_02 CG CB CD1 CD2 negativ
0PJ chir_03 CA1 N2 CC CB1 positiv
0PJ chir_04 CG1 CB1 CD11 CD21 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
0PJ plan-1 C1 0.020
0PJ plan-1 O1 0.020
0PJ plan-1 O2 0.020
0PJ plan-1 N 0.020
0PJ plan-1 HN2 0.020
0PJ plan-2 C3 0.020
0PJ plan-2 C2 0.020
0PJ plan-2 C4 0.020
0PJ plan-2 C8 0.020
0PJ plan-2 C5 0.020
0PJ plan-2 C6 0.020
0PJ plan-2 C7 0.020
0PJ plan-2 H41 0.020
0PJ plan-2 H51 0.020
0PJ plan-2 H61 0.020
0PJ plan-2 H71 0.020
0PJ plan-2 H81 0.020
0PJ plan-3 N 0.020
0PJ plan-3 C1 0.020
0PJ plan-3 C 0.020
0PJ plan-3 HN2 0.020
0PJ plan-4 N1 0.020
0PJ plan-4 P 0.020
0PJ plan-4 CA 0.020
0PJ plan-4 H 0.020
0PJ plan-5 C9 0.020
0PJ plan-5 CA 0.020
0PJ plan-5 O 0.020
0PJ plan-5 N2 0.020
0PJ plan-5 H3 0.020
0PJ plan-6 N2 0.020
0PJ plan-6 C9 0.020
0PJ plan-6 CA1 0.020
0PJ plan-6 H3 0.020
0PJ plan-7 CC 0.020
0PJ plan-7 CA1 0.020
0PJ plan-7 O3 0.020
0PJ plan-7 OXT 0.020
# ------------------------------------------------------
|
