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
|
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
PDN PDN '17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11' non-polymer 52 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDN
#
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
PDN O2 O O 0.000 0.000 0.000 0.000
PDN C11 C C 0.000 -1.121 -0.414 0.177
PDN C9 C CH1 0.000 -2.106 -0.447 -0.962
PDN HC9 H H 0.000 -2.247 -1.487 -1.290
PDN C10 C CT 0.000 -1.599 0.389 -2.136
PDN C19 C CH3 0.000 -1.439 1.834 -1.656
PDN H193 H H 0.000 -2.376 2.206 -1.330
PDN H192 H H 0.000 -0.750 1.866 -0.852
PDN H191 H H 0.000 -1.080 2.435 -2.452
PDN C5 C CR6 0.000 -2.633 0.381 -3.221
PDN C4 C CR16 0.000 -2.364 0.059 -4.478
PDN HC4 H H 0.000 -3.152 0.093 -5.220
PDN C3 C CR6 0.000 -1.007 -0.345 -4.875
PDN O1 O O 0.000 -0.749 -0.602 -6.036
PDN C2 C CR16 0.000 0.032 -0.432 -3.835
PDN HC2 H H 0.000 1.029 -0.769 -4.091
PDN C1 C CR16 0.000 -0.256 -0.099 -2.587
PDN HC1 H H 0.000 0.528 -0.184 -1.845
PDN C12 C CH2 0.000 -1.549 -0.907 1.550
PDN H121 H H 0.000 -0.809 -0.643 2.308
PDN H122 H H 0.000 -1.696 -1.989 1.547
PDN C13 C CT 0.000 -2.866 -0.217 1.864
PDN C18 C CH3 0.000 -2.667 1.299 1.885
PDN H183 H H 0.000 -3.604 1.777 2.012
PDN H182 H H 0.000 -2.027 1.562 2.687
PDN H181 H H 0.000 -2.233 1.612 0.971
PDN C17 C CT 0.000 -3.556 -0.668 3.148
PDN O3 O OH1 0.000 -3.180 -2.011 3.462
PDN HO3 H H 0.000 -3.659 -2.303 4.249
PDN C20 C C 0.000 -3.216 0.251 4.292
PDN O4 O OH1 0.000 -3.482 1.581 4.199
PDN HO4 H H 0.000 -3.206 2.030 5.013
PDN C21 C C1 0.000 -2.659 -0.235 5.386
PDN HC12 H H 0.000 -2.448 -1.288 5.461
PDN O5 O OH1 0.000 -2.351 0.595 6.419
PDN HO5 H H 0.000 -1.940 0.245 7.228
PDN C16 C CH2 0.000 -5.094 -0.596 2.832
PDN H161 H H 0.000 -5.589 0.142 3.467
PDN H162 H H 0.000 -5.568 -1.570 2.971
PDN C15 C CH2 0.000 -5.217 -0.167 1.346
PDN H151 H H 0.000 -5.336 0.913 1.231
PDN H152 H H 0.000 -6.031 -0.679 0.829
PDN C14 C CH1 0.000 -3.873 -0.602 0.746
PDN HC41 H H 0.000 -3.862 -1.688 0.578
PDN C8 C CH1 0.000 -3.459 0.131 -0.512
PDN HC8 H H 0.000 -3.346 1.202 -0.293
PDN C7 C CH2 0.000 -4.481 -0.055 -1.632
PDN HC71 H H 0.000 -5.462 0.282 -1.290
PDN HC72 H H 0.000 -4.535 -1.110 -1.905
PDN C6 C CH2 0.000 -4.052 0.770 -2.851
PDN HC62 H H 0.000 -4.088 1.834 -2.611
PDN HC61 H H 0.000 -4.718 0.565 -3.691
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
PDN O2 n/a C11 START
PDN C11 O2 C12 .
PDN C9 C11 C10 .
PDN HC9 C9 . .
PDN C10 C9 C1 .
PDN C19 C10 H191 .
PDN H193 C19 . .
PDN H192 C19 . .
PDN H191 C19 . .
PDN C5 C10 C4 .
PDN C4 C5 C3 .
PDN HC4 C4 . .
PDN C3 C4 C2 .
PDN O1 C3 . .
PDN C2 C3 HC2 .
PDN HC2 C2 . .
PDN C1 C10 HC1 .
PDN HC1 C1 . .
PDN C12 C11 C13 .
PDN H121 C12 . .
PDN H122 C12 . .
PDN C13 C12 C17 .
PDN C18 C13 H181 .
PDN H183 C18 . .
PDN H182 C18 . .
PDN H181 C18 . .
PDN C17 C13 C16 .
PDN O3 C17 HO3 .
PDN HO3 O3 . .
PDN C20 C17 C21 .
PDN O4 C20 HO4 .
PDN HO4 O4 . .
PDN C21 C20 O5 .
PDN HC12 C21 . .
PDN O5 C21 HO5 .
PDN HO5 O5 . .
PDN C16 C17 C15 .
PDN H161 C16 . .
PDN H162 C16 . .
PDN C15 C16 C14 .
PDN H151 C15 . .
PDN H152 C15 . .
PDN C14 C15 C8 .
PDN HC41 C14 . .
PDN C8 C14 C7 .
PDN HC8 C8 . .
PDN C7 C8 C6 .
PDN HC71 C7 . .
PDN HC72 C7 . .
PDN C6 C7 HC61 .
PDN HC62 C6 . .
PDN HC61 C6 . END
PDN C1 C2 . ADD
PDN C5 C6 . ADD
PDN C8 C9 . ADD
PDN C13 C14 . 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
PDN C1 C2 double 1.390 0.020
PDN C1 C10 single 1.457 0.020
PDN HC1 C1 single 1.083 0.020
PDN C2 C3 single 1.390 0.020
PDN HC2 C2 single 1.083 0.020
PDN C3 C4 single 1.390 0.020
PDN O1 C3 double 1.250 0.020
PDN C4 C5 double 1.390 0.020
PDN HC4 C4 single 1.083 0.020
PDN C5 C6 single 1.511 0.020
PDN C5 C10 single 1.500 0.020
PDN C6 C7 single 1.524 0.020
PDN HC61 C6 single 1.092 0.020
PDN HC62 C6 single 1.092 0.020
PDN C7 C8 single 1.524 0.020
PDN HC71 C7 single 1.092 0.020
PDN HC72 C7 single 1.092 0.020
PDN C8 C9 single 1.524 0.020
PDN C8 C14 single 1.524 0.020
PDN HC8 C8 single 1.099 0.020
PDN C10 C9 single 1.524 0.020
PDN C9 C11 single 1.500 0.020
PDN HC9 C9 single 1.099 0.020
PDN C19 C10 single 1.524 0.020
PDN C12 C11 single 1.510 0.020
PDN C11 O2 double 1.220 0.020
PDN C13 C12 single 1.524 0.020
PDN H121 C12 single 1.092 0.020
PDN H122 C12 single 1.092 0.020
PDN C13 C14 single 1.524 0.020
PDN C17 C13 single 1.524 0.020
PDN C18 C13 single 1.524 0.020
PDN C14 C15 single 1.524 0.020
PDN HC41 C14 single 1.099 0.020
PDN C15 C16 single 1.524 0.020
PDN H151 C15 single 1.092 0.020
PDN H152 C15 single 1.092 0.020
PDN C16 C17 single 1.524 0.020
PDN H161 C16 single 1.092 0.020
PDN H162 C16 single 1.092 0.020
PDN C20 C17 single 1.507 0.020
PDN O3 C17 single 1.432 0.020
PDN H181 C18 single 1.059 0.020
PDN H182 C18 single 1.059 0.020
PDN H183 C18 single 1.059 0.020
PDN H191 C19 single 1.059 0.020
PDN H192 C19 single 1.059 0.020
PDN H193 C19 single 1.059 0.020
PDN C21 C20 double 1.340 0.020
PDN O4 C20 single 1.330 0.020
PDN O5 C21 single 1.330 0.020
PDN HC12 C21 single 1.077 0.020
PDN HO3 O3 single 0.967 0.020
PDN HO4 O4 single 0.967 0.020
PDN HO5 O5 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
PDN O2 C11 C9 120.500 3.000
PDN O2 C11 C12 120.500 3.000
PDN C9 C11 C12 120.000 3.000
PDN C11 C9 HC9 108.810 3.000
PDN C11 C9 C10 109.470 3.000
PDN C11 C9 C8 109.470 3.000
PDN HC9 C9 C10 108.340 3.000
PDN HC9 C9 C8 108.340 3.000
PDN C10 C9 C8 111.000 3.000
PDN C9 C10 C19 111.000 3.000
PDN C9 C10 C5 109.500 3.000
PDN C9 C10 C1 109.500 3.000
PDN C19 C10 C5 109.500 3.000
PDN C19 C10 C1 109.500 3.000
PDN C5 C10 C1 109.500 3.000
PDN C10 C19 H193 109.470 3.000
PDN C10 C19 H192 109.470 3.000
PDN C10 C19 H191 109.470 3.000
PDN H193 C19 H192 109.470 3.000
PDN H193 C19 H191 109.470 3.000
PDN H192 C19 H191 109.470 3.000
PDN C10 C5 C4 120.000 3.000
PDN C10 C5 C6 120.000 3.000
PDN C4 C5 C6 120.000 3.000
PDN C5 C4 HC4 120.000 3.000
PDN C5 C4 C3 120.000 3.000
PDN HC4 C4 C3 120.000 3.000
PDN C4 C3 O1 120.000 3.000
PDN C4 C3 C2 120.000 3.000
PDN O1 C3 C2 120.000 3.000
PDN C3 C2 HC2 120.000 3.000
PDN C3 C2 C1 120.000 3.000
PDN HC2 C2 C1 120.000 3.000
PDN C10 C1 HC1 120.000 3.000
PDN C10 C1 C2 120.000 3.000
PDN HC1 C1 C2 120.000 3.000
PDN C11 C12 H121 109.470 3.000
PDN C11 C12 H122 109.470 3.000
PDN C11 C12 C13 109.470 3.000
PDN H121 C12 H122 107.900 3.000
PDN H121 C12 C13 109.470 3.000
PDN H122 C12 C13 109.470 3.000
PDN C12 C13 C18 111.000 3.000
PDN C12 C13 C17 111.000 3.000
PDN C12 C13 C14 111.000 3.000
PDN C18 C13 C17 111.000 3.000
PDN C18 C13 C14 111.000 3.000
PDN C17 C13 C14 111.000 3.000
PDN C13 C18 H183 109.470 3.000
PDN C13 C18 H182 109.470 3.000
PDN C13 C18 H181 109.470 3.000
PDN H183 C18 H182 109.470 3.000
PDN H183 C18 H181 109.470 3.000
PDN H182 C18 H181 109.470 3.000
PDN C13 C17 C20 111.000 3.000
PDN C13 C17 O3 109.470 3.000
PDN C13 C17 C16 111.000 3.000
PDN C20 C17 O3 109.470 3.000
PDN C20 C17 C16 109.470 3.000
PDN O3 C17 C16 109.470 3.000
PDN C17 C20 O4 120.000 3.000
PDN C17 C20 C21 120.000 3.000
PDN O4 C20 C21 120.000 3.000
PDN C20 O4 HO4 109.470 3.000
PDN C20 C21 HC12 120.000 3.000
PDN C20 C21 O5 120.000 3.000
PDN HC12 C21 O5 120.000 3.000
PDN C21 O5 HO5 120.000 3.000
PDN C17 O3 HO3 109.470 3.000
PDN C17 C16 H161 109.470 3.000
PDN C17 C16 H162 109.470 3.000
PDN C17 C16 C15 111.000 3.000
PDN H161 C16 H162 107.900 3.000
PDN H161 C16 C15 109.470 3.000
PDN H162 C16 C15 109.470 3.000
PDN C16 C15 H151 109.470 3.000
PDN C16 C15 H152 109.470 3.000
PDN C16 C15 C14 111.000 3.000
PDN H151 C15 H152 107.900 3.000
PDN H151 C15 C14 109.470 3.000
PDN H152 C15 C14 109.470 3.000
PDN C15 C14 HC41 108.340 3.000
PDN C15 C14 C8 111.000 3.000
PDN C15 C14 C13 111.000 3.000
PDN HC41 C14 C8 108.340 3.000
PDN HC41 C14 C13 108.340 3.000
PDN C8 C14 C13 111.000 3.000
PDN C14 C8 HC8 108.340 3.000
PDN C14 C8 C7 111.000 3.000
PDN C14 C8 C9 111.000 3.000
PDN HC8 C8 C7 108.340 3.000
PDN HC8 C8 C9 108.340 3.000
PDN C7 C8 C9 111.000 3.000
PDN C8 C7 HC71 109.470 3.000
PDN C8 C7 HC72 109.470 3.000
PDN C8 C7 C6 111.000 3.000
PDN HC71 C7 HC72 107.900 3.000
PDN HC71 C7 C6 109.470 3.000
PDN HC72 C7 C6 109.470 3.000
PDN C7 C6 HC62 109.470 3.000
PDN C7 C6 HC61 109.470 3.000
PDN C7 C6 C5 109.470 3.000
PDN HC62 C6 HC61 107.900 3.000
PDN HC62 C6 C5 109.470 3.000
PDN HC61 C6 C5 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
PDN var_1 O2 C11 C9 C10 0.000 20.000 3
PDN var_2 C11 C9 C10 C1 60.000 20.000 1
PDN var_3 C9 C10 C19 H191 179.515 20.000 1
PDN CONST_1 C9 C10 C5 C4 -120.000 0.000 0
PDN var_4 C10 C5 C6 C7 -60.000 20.000 2
PDN CONST_2 C10 C5 C4 C3 0.000 0.000 0
PDN CONST_3 C5 C4 C3 C2 0.000 0.000 0
PDN CONST_4 C4 C3 C2 C1 0.000 0.000 0
PDN CONST_5 C9 C10 C1 C2 120.000 0.000 0
PDN CONST_6 C10 C1 C2 C3 0.000 0.000 0
PDN var_5 O2 C11 C12 C13 120.000 20.000 3
PDN var_6 C11 C12 C13 C17 180.000 20.000 1
PDN var_7 C12 C13 C14 C15 180.000 20.000 1
PDN var_8 C12 C13 C18 H181 54.586 20.000 1
PDN var_9 C12 C13 C17 C16 -150.000 20.000 1
PDN var_10 C13 C17 C20 C21 -122.682 20.000 1
PDN var_11 C17 C20 O4 HO4 179.965 20.000 1
PDN CONST_7 C17 C20 C21 O5 179.988 0.000 0
PDN var_12 C20 C21 O5 HO5 -179.918 20.000 1
PDN var_13 C13 C17 O3 HO3 -176.942 20.000 1
PDN var_14 C13 C17 C16 C15 0.000 20.000 1
PDN var_15 C17 C16 C15 C14 30.000 20.000 3
PDN var_16 C16 C15 C14 C8 -150.000 20.000 3
PDN var_17 C15 C14 C8 C7 -60.000 20.000 3
PDN var_18 C14 C8 C9 C11 -60.000 20.000 3
PDN var_19 C14 C8 C7 C6 180.000 20.000 3
PDN var_20 C8 C7 C6 C5 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
PDN chir_01 C8 C7 C9 C14 positiv
PDN chir_02 C9 C8 C10 C11 negativ
PDN chir_03 C10 C1 C5 C9 negativ
PDN chir_04 C13 C12 C14 C17 negativ
PDN chir_05 C14 C8 C13 C15 negativ
PDN chir_06 C17 C13 C16 C20 positiv
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
PDN plan-1 C1 0.020
PDN plan-1 C2 0.020
PDN plan-1 C10 0.020
PDN plan-1 HC1 0.020
PDN plan-1 C3 0.020
PDN plan-1 C4 0.020
PDN plan-1 C5 0.020
PDN plan-1 HC2 0.020
PDN plan-1 O1 0.020
PDN plan-1 HC4 0.020
PDN plan-1 C6 0.020
PDN plan-2 C11 0.020
PDN plan-2 C9 0.020
PDN plan-2 C12 0.020
PDN plan-2 O2 0.020
PDN plan-3 C20 0.020
PDN plan-3 C17 0.020
PDN plan-3 C21 0.020
PDN plan-3 O4 0.020
PDN plan-3 O5 0.020
PDN plan-3 HC12 0.020
# ------------------------------------------------------
|
