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
|
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
DF9 DF9 '(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d' non-polymer 49 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DF9
#
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
DF9 "O3'" O OH1 0.000 0.000 0.000 0.000
DF9 "HO3'" H H 0.000 0.757 -0.042 0.600
DF9 "C3'" C CH1 0.000 -1.185 -0.383 0.701
DF9 "H3'" H H 0.000 -1.107 -1.418 1.060
DF9 "C2'" C CH2 0.000 -1.461 0.583 1.873
DF9 "H2'A" H H 0.000 -0.952 1.536 1.712
DF9 "H2'" H H 0.000 -1.126 0.147 2.816
DF9 "C4'" C CH1 0.000 -2.435 -0.206 -0.199
DF9 "H4'" H H 0.000 -2.333 0.677 -0.845
DF9 "C5'" C CH2 0.000 -2.695 -1.465 -1.030
DF9 "H5'" H H 0.000 -2.946 -2.294 -0.365
DF9 "H5'A" H H 0.000 -1.797 -1.716 -1.599
DF9 "S6'" S S2 0.000 -4.072 -1.164 -2.171
DF9 "C7'" C CH2 0.000 -4.224 -2.742 -3.053
DF9 "H7'" H H 0.000 -4.437 -3.539 -2.337
DF9 "H7'A" H H 0.000 -3.288 -2.961 -3.571
DF9 C21 C CR6 0.000 -5.346 -2.652 -4.054
DF9 C22 C CR16 0.000 -6.631 -3.003 -3.687
DF9 H22 H H 0.000 -6.832 -3.347 -2.679
DF9 C23 C CR16 0.000 -7.661 -2.917 -4.605
DF9 H23 H H 0.000 -8.669 -3.187 -4.315
DF9 C24 C CR16 0.000 -7.404 -2.485 -5.893
DF9 H24 H H 0.000 -8.211 -2.418 -6.613
DF9 C25 C CR16 0.000 -6.117 -2.139 -6.263
DF9 H25 H H 0.000 -5.915 -1.803 -7.272
DF9 C26 C CR16 0.000 -5.089 -2.222 -5.343
DF9 H26 H H 0.000 -4.081 -1.949 -5.632
DF9 "C1'" C CH2 0.000 -3.553 0.003 0.853
DF9 "H1'" H H 0.000 -3.902 -0.946 1.267
DF9 "H1'A" H H 0.000 -4.401 0.553 0.439
DF9 "N1'" N NT 0.000 -2.918 0.804 1.922
DF9 C10 C CH2 0.000 -3.460 0.447 3.240
DF9 H10 H H 0.000 -3.110 -0.549 3.519
DF9 H10A H H 0.000 -4.551 0.450 3.197
DF9 C9 C CR5 0.000 -2.994 1.450 4.264
DF9 C4 C CR56 0.000 -3.557 2.775 4.500
DF9 N3 N NRD6 0.000 -4.555 3.484 3.965
DF9 C2 C CR16 0.000 -4.826 4.691 4.407
DF9 H2 H H 0.000 -5.641 5.243 3.954
DF9 N1 N NRD6 0.000 -4.140 5.257 5.385
DF9 C8 C CR15 0.000 -1.970 1.298 5.124
DF9 H8 H H 0.000 -1.340 0.419 5.193
DF9 N7 N NR15 0.000 -1.843 2.415 5.896
DF9 HN7 H H 0.000 -1.133 2.547 6.644
DF9 C5 C CR56 0.000 -2.797 3.339 5.539
DF9 C6 C CR6 0.000 -3.130 4.626 5.976
DF9 N6 N NH2 0.000 -2.420 5.231 7.000
DF9 HN6A H H 0.000 -1.649 4.747 7.450
DF9 HN6 H H 0.000 -2.661 6.167 7.312
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
DF9 "O3'" n/a "C3'" START
DF9 "HO3'" "O3'" . .
DF9 "C3'" "O3'" "C4'" .
DF9 "H3'" "C3'" . .
DF9 "C2'" "C3'" "H2'" .
DF9 "H2'A" "C2'" . .
DF9 "H2'" "C2'" . .
DF9 "C4'" "C3'" "C1'" .
DF9 "H4'" "C4'" . .
DF9 "C5'" "C4'" "S6'" .
DF9 "H5'" "C5'" . .
DF9 "H5'A" "C5'" . .
DF9 "S6'" "C5'" "C7'" .
DF9 "C7'" "S6'" C21 .
DF9 "H7'" "C7'" . .
DF9 "H7'A" "C7'" . .
DF9 C21 "C7'" C22 .
DF9 C22 C21 C23 .
DF9 H22 C22 . .
DF9 C23 C22 C24 .
DF9 H23 C23 . .
DF9 C24 C23 C25 .
DF9 H24 C24 . .
DF9 C25 C24 C26 .
DF9 H25 C25 . .
DF9 C26 C25 H26 .
DF9 H26 C26 . .
DF9 "C1'" "C4'" "N1'" .
DF9 "H1'" "C1'" . .
DF9 "H1'A" "C1'" . .
DF9 "N1'" "C1'" C10 .
DF9 C10 "N1'" C9 .
DF9 H10 C10 . .
DF9 H10A C10 . .
DF9 C9 C10 C8 .
DF9 C4 C9 N3 .
DF9 N3 C4 C2 .
DF9 C2 N3 N1 .
DF9 H2 C2 . .
DF9 N1 C2 . .
DF9 C8 C9 N7 .
DF9 H8 C8 . .
DF9 N7 C8 C5 .
DF9 HN7 N7 . .
DF9 C5 N7 C6 .
DF9 C6 C5 N6 .
DF9 N6 C6 HN6 .
DF9 HN6A N6 . .
DF9 HN6 N6 . END
DF9 C6 N1 . ADD
DF9 C5 C4 . ADD
DF9 "N1'" "C2'" . ADD
DF9 C21 C26 . 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
DF9 N6 C6 single 1.355 0.020
DF9 C6 N1 double 1.350 0.020
DF9 C6 C5 single 1.490 0.020
DF9 N1 C2 single 1.337 0.020
DF9 C2 N3 double 1.337 0.020
DF9 N3 C4 single 1.355 0.020
DF9 C5 C4 double 1.490 0.020
DF9 C5 N7 single 1.340 0.020
DF9 C4 C9 single 1.490 0.020
DF9 N7 C8 single 1.350 0.020
DF9 C8 C9 double 1.387 0.020
DF9 C9 C10 single 1.510 0.020
DF9 C10 "N1'" single 1.469 0.020
DF9 "N1'" "C2'" single 1.469 0.020
DF9 "N1'" "C1'" single 1.469 0.020
DF9 "C2'" "C3'" single 1.524 0.020
DF9 "C3'" "O3'" single 1.432 0.020
DF9 "C4'" "C3'" single 1.524 0.020
DF9 "C1'" "C4'" single 1.524 0.020
DF9 "C5'" "C4'" single 1.524 0.020
DF9 "S6'" "C5'" single 1.762 0.020
DF9 "C7'" "S6'" single 1.762 0.020
DF9 C21 "C7'" single 1.511 0.020
DF9 C21 C26 double 1.390 0.020
DF9 C22 C21 single 1.390 0.020
DF9 C26 C25 single 1.390 0.020
DF9 C25 C24 double 1.390 0.020
DF9 C24 C23 single 1.390 0.020
DF9 C23 C22 double 1.390 0.020
DF9 HN6 N6 single 1.010 0.020
DF9 HN6A N6 single 1.010 0.020
DF9 H2 C2 single 1.083 0.020
DF9 HN7 N7 single 1.040 0.020
DF9 H8 C8 single 1.083 0.020
DF9 H10 C10 single 1.092 0.020
DF9 H10A C10 single 1.092 0.020
DF9 "H2'" "C2'" single 1.092 0.020
DF9 "H2'A" "C2'" single 1.092 0.020
DF9 "H3'" "C3'" single 1.099 0.020
DF9 "HO3'" "O3'" single 0.967 0.020
DF9 "H1'" "C1'" single 1.092 0.020
DF9 "H1'A" "C1'" single 1.092 0.020
DF9 "H4'" "C4'" single 1.099 0.020
DF9 "H5'" "C5'" single 1.092 0.020
DF9 "H5'A" "C5'" single 1.092 0.020
DF9 "H7'" "C7'" single 1.092 0.020
DF9 "H7'A" "C7'" single 1.092 0.020
DF9 H26 C26 single 1.083 0.020
DF9 H25 C25 single 1.083 0.020
DF9 H24 C24 single 1.083 0.020
DF9 H23 C23 single 1.083 0.020
DF9 H22 C22 single 1.083 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
DF9 "HO3'" "O3'" "C3'" 109.470 3.000
DF9 "O3'" "C3'" "H3'" 109.470 3.000
DF9 "O3'" "C3'" "C2'" 109.470 3.000
DF9 "O3'" "C3'" "C4'" 109.470 3.000
DF9 "H3'" "C3'" "C2'" 108.340 3.000
DF9 "H3'" "C3'" "C4'" 108.340 3.000
DF9 "C2'" "C3'" "C4'" 111.000 3.000
DF9 "C3'" "C2'" "H2'A" 109.470 3.000
DF9 "C3'" "C2'" "H2'" 109.470 3.000
DF9 "C3'" "C2'" "N1'" 109.500 3.000
DF9 "H2'A" "C2'" "H2'" 107.900 3.000
DF9 "H2'A" "C2'" "N1'" 109.470 3.000
DF9 "H2'" "C2'" "N1'" 109.470 3.000
DF9 "C3'" "C4'" "H4'" 108.340 3.000
DF9 "C3'" "C4'" "C5'" 111.000 3.000
DF9 "C3'" "C4'" "C1'" 111.000 3.000
DF9 "H4'" "C4'" "C5'" 108.340 3.000
DF9 "H4'" "C4'" "C1'" 108.340 3.000
DF9 "C5'" "C4'" "C1'" 109.470 3.000
DF9 "C4'" "C5'" "H5'" 109.470 3.000
DF9 "C4'" "C5'" "H5'A" 109.470 3.000
DF9 "C4'" "C5'" "S6'" 109.500 3.000
DF9 "H5'" "C5'" "H5'A" 107.900 3.000
DF9 "H5'" "C5'" "S6'" 109.500 3.000
DF9 "H5'A" "C5'" "S6'" 109.500 3.000
DF9 "C5'" "S6'" "C7'" 102.997 3.000
DF9 "S6'" "C7'" "H7'" 109.500 3.000
DF9 "S6'" "C7'" "H7'A" 109.500 3.000
DF9 "S6'" "C7'" C21 109.500 3.000
DF9 "H7'" "C7'" "H7'A" 107.900 3.000
DF9 "H7'" "C7'" C21 109.470 3.000
DF9 "H7'A" "C7'" C21 109.470 3.000
DF9 "C7'" C21 C22 120.000 3.000
DF9 "C7'" C21 C26 120.000 3.000
DF9 C22 C21 C26 120.000 3.000
DF9 C21 C22 H22 120.000 3.000
DF9 C21 C22 C23 120.000 3.000
DF9 H22 C22 C23 120.000 3.000
DF9 C22 C23 H23 120.000 3.000
DF9 C22 C23 C24 120.000 3.000
DF9 H23 C23 C24 120.000 3.000
DF9 C23 C24 H24 120.000 3.000
DF9 C23 C24 C25 120.000 3.000
DF9 H24 C24 C25 120.000 3.000
DF9 C24 C25 H25 120.000 3.000
DF9 C24 C25 C26 120.000 3.000
DF9 H25 C25 C26 120.000 3.000
DF9 C25 C26 H26 120.000 3.000
DF9 C25 C26 C21 120.000 3.000
DF9 H26 C26 C21 120.000 3.000
DF9 "C4'" "C1'" "H1'" 109.470 3.000
DF9 "C4'" "C1'" "H1'A" 109.470 3.000
DF9 "C4'" "C1'" "N1'" 109.500 3.000
DF9 "H1'" "C1'" "H1'A" 107.900 3.000
DF9 "H1'" "C1'" "N1'" 109.470 3.000
DF9 "H1'A" "C1'" "N1'" 109.470 3.000
DF9 "C1'" "N1'" C10 109.470 3.000
DF9 "C1'" "N1'" "C2'" 109.470 3.000
DF9 C10 "N1'" "C2'" 109.470 3.000
DF9 "N1'" C10 H10 109.470 3.000
DF9 "N1'" C10 H10A 109.470 3.000
DF9 "N1'" C10 C9 109.500 3.000
DF9 H10 C10 H10A 107.900 3.000
DF9 H10 C10 C9 109.470 3.000
DF9 H10A C10 C9 109.470 3.000
DF9 C10 C9 C4 126.000 3.000
DF9 C10 C9 C8 126.000 3.000
DF9 C4 C9 C8 108.000 3.000
DF9 C9 C4 N3 120.000 3.000
DF9 C9 C4 C5 108.000 3.000
DF9 N3 C4 C5 120.000 3.000
DF9 C4 N3 C2 120.000 3.000
DF9 N3 C2 H2 120.000 3.000
DF9 N3 C2 N1 120.000 3.000
DF9 H2 C2 N1 120.000 3.000
DF9 C2 N1 C6 120.000 3.000
DF9 C9 C8 H8 126.000 3.000
DF9 C9 C8 N7 108.000 3.000
DF9 H8 C8 N7 126.000 3.000
DF9 C8 N7 HN7 126.000 3.000
DF9 C8 N7 C5 108.000 3.000
DF9 HN7 N7 C5 126.000 3.000
DF9 N7 C5 C6 132.000 3.000
DF9 N7 C5 C4 108.000 3.000
DF9 C6 C5 C4 120.000 3.000
DF9 C5 C6 N6 120.000 3.000
DF9 C5 C6 N1 120.000 3.000
DF9 N6 C6 N1 120.000 3.000
DF9 C6 N6 HN6A 120.000 3.000
DF9 C6 N6 HN6 120.000 3.000
DF9 HN6A N6 HN6 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
DF9 var_1 "HO3'" "O3'" "C3'" "C4'" 175.029 20.000 1
DF9 var_2 "O3'" "C3'" "C2'" "N1'" 150.000 20.000 3
DF9 var_3 "O3'" "C3'" "C4'" "C1'" -150.000 20.000 3
DF9 var_4 "C3'" "C4'" "C5'" "S6'" -175.023 20.000 3
DF9 var_5 "C4'" "C5'" "S6'" "C7'" 179.978 20.000 1
DF9 var_6 "C5'" "S6'" "C7'" C21 179.989 20.000 1
DF9 var_7 "S6'" "C7'" C21 C22 -90.247 20.000 2
DF9 CONST_1 "C7'" C21 C26 C25 180.000 0.000 0
DF9 CONST_2 "C7'" C21 C22 C23 180.000 0.000 0
DF9 CONST_3 C21 C22 C23 C24 0.000 0.000 0
DF9 CONST_4 C22 C23 C24 C25 0.000 0.000 0
DF9 CONST_5 C23 C24 C25 C26 0.000 0.000 0
DF9 CONST_6 C24 C25 C26 C21 0.000 0.000 0
DF9 var_8 "C3'" "C4'" "C1'" "N1'" 30.000 20.000 3
DF9 var_9 "C4'" "C1'" "N1'" C10 -150.000 20.000 1
DF9 var_10 "C1'" "N1'" "C2'" "C3'" 0.000 20.000 1
DF9 var_11 "C1'" "N1'" C10 C9 -169.258 20.000 1
DF9 var_12 "N1'" C10 C9 C8 -99.220 20.000 2
DF9 CONST_7 C10 C9 C4 N3 0.000 0.000 0
DF9 CONST_8 C9 C4 N3 C2 180.000 0.000 0
DF9 CONST_9 C4 N3 C2 N1 0.000 0.000 0
DF9 CONST_10 N3 C2 N1 C6 0.000 0.000 0
DF9 CONST_11 C10 C9 C8 N7 180.000 0.000 0
DF9 CONST_12 C9 C8 N7 C5 0.000 0.000 0
DF9 CONST_13 C8 N7 C5 C6 180.000 0.000 0
DF9 CONST_14 N7 C5 C4 C9 0.000 0.000 0
DF9 CONST_15 N7 C5 C6 N6 0.000 0.000 0
DF9 CONST_16 C5 C6 N1 C2 0.000 0.000 0
DF9 CONST_17 C5 C6 N6 HN6 179.708 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
DF9 chir_01 "N1'" C10 "C2'" "C1'" negativ
DF9 chir_02 "C3'" "C2'" "O3'" "C4'" positiv
DF9 chir_03 "C4'" "C3'" "C1'" "C5'" 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
DF9 plan-1 N6 0.020
DF9 plan-1 C6 0.020
DF9 plan-1 HN6 0.020
DF9 plan-1 HN6A 0.020
DF9 plan-2 C6 0.020
DF9 plan-2 N6 0.020
DF9 plan-2 N1 0.020
DF9 plan-2 C5 0.020
DF9 plan-2 C2 0.020
DF9 plan-2 N3 0.020
DF9 plan-2 H2 0.020
DF9 plan-2 C4 0.020
DF9 plan-2 N7 0.020
DF9 plan-2 C8 0.020
DF9 plan-2 C9 0.020
DF9 plan-2 HN7 0.020
DF9 plan-2 H8 0.020
DF9 plan-2 C10 0.020
DF9 plan-2 HN6A 0.020
DF9 plan-2 HN6 0.020
DF9 plan-3 C21 0.020
DF9 plan-3 "C7'" 0.020
DF9 plan-3 C26 0.020
DF9 plan-3 C22 0.020
DF9 plan-3 C25 0.020
DF9 plan-3 C24 0.020
DF9 plan-3 C23 0.020
DF9 plan-3 H26 0.020
DF9 plan-3 H25 0.020
DF9 plan-3 H24 0.020
DF9 plan-3 H23 0.020
DF9 plan-3 H22 0.020
# ------------------------------------------------------
|
