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
|
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
PRD PRD 'N6-(2,5-DIMETHOXY-BENZYL)-N6-METHYL-' non-polymer 45 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PRD
#
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
PRD "N2'" N NH2 0.000 0.000 0.000 0.000
PRD HN21 H H 0.000 0.769 -0.639 0.174
PRD HN22 H H 0.000 0.205 0.972 -0.207
PRD C2B C CR6 0.000 -1.307 -0.447 0.045
PRD "N1'" N NRD6 0.000 -2.278 0.417 -0.185
PRD "N3'" N NRD6 0.000 -1.532 -1.727 0.321
PRD C4B C CR6 0.000 -2.765 -2.212 0.379
PRD "N4'" N NH2 0.000 -2.989 -3.542 0.666
PRD HN42 H H 0.000 -3.934 -3.907 0.708
PRD HN41 H H 0.000 -2.210 -4.169 0.837
PRD C4A C CR66 0.000 -3.846 -1.329 0.139
PRD C5B C CR16 0.000 -5.178 -1.757 0.186
PRD "H5'" H H 0.000 -5.427 -2.786 0.414
PRD C6B C CR6 0.000 -6.168 -0.822 -0.067
PRD C7B C CR16 0.000 -5.812 0.499 -0.347
PRD "H7'" H H 0.000 -6.592 1.226 -0.540
PRD "N8'" N NRD6 0.000 -4.557 0.882 -0.380
PRD C8A C CR66 0.000 -3.561 0.026 -0.151
PRD "N6'" N N 0.000 -7.515 -1.197 -0.038
PRD C61 C CH3 0.000 -7.883 -2.584 0.255
PRD HC63 H H 0.000 -7.456 -3.226 -0.471
PRD HC62 H H 0.000 -7.522 -2.851 1.216
PRD HC61 H H 0.000 -8.938 -2.683 0.236
PRD "C7'" C CH2 0.000 -8.558 -0.202 -0.300
PRD HC71 H H 0.000 -9.422 -0.692 -0.755
PRD HC72 H H 0.000 -8.172 0.559 -0.982
PRD "C1'" C CR6 0.000 -8.971 0.446 0.996
PRD "C6'" C CR16 0.000 -8.368 0.068 2.179
PRD "HC6'" H H 0.000 -7.597 -0.692 2.175
PRD "C5'" C CR6 0.000 -8.752 0.662 3.372
PRD "O5'" O O2 0.000 -8.163 0.286 4.539
PRD C51 C CH3 0.000 -8.759 1.070 5.574
PRD HC53 H H 0.000 -8.590 2.098 5.381
PRD HC52 H H 0.000 -9.801 0.884 5.603
PRD HC51 H H 0.000 -8.329 0.811 6.507
PRD "C4'" C CR16 0.000 -9.733 1.642 3.376
PRD "HC4'" H H 0.000 -10.030 2.108 4.307
PRD "C3'" C CR16 0.000 -10.332 2.024 2.191
PRD "HC3'" H H 0.000 -11.097 2.791 2.193
PRD "C2'" C CR6 0.000 -9.953 1.426 0.999
PRD "O2'" O O2 0.000 -10.542 1.802 -0.168
PRD C21 C CH3 0.000 -11.494 2.815 0.159
PRD HC23 H H 0.000 -12.211 2.423 0.833
PRD HC22 H H 0.000 -10.998 3.635 0.609
PRD HC21 H H 0.000 -11.982 3.140 -0.724
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
PRD "N2'" n/a C2B START
PRD HN21 "N2'" . .
PRD HN22 "N2'" . .
PRD C2B "N2'" "N3'" .
PRD "N1'" C2B . .
PRD "N3'" C2B C4B .
PRD C4B "N3'" C4A .
PRD "N4'" C4B HN41 .
PRD HN42 "N4'" . .
PRD HN41 "N4'" . .
PRD C4A C4B C5B .
PRD C5B C4A C6B .
PRD "H5'" C5B . .
PRD C6B C5B "N6'" .
PRD C7B C6B "N8'" .
PRD "H7'" C7B . .
PRD "N8'" C7B C8A .
PRD C8A "N8'" . .
PRD "N6'" C6B "C7'" .
PRD C61 "N6'" HC61 .
PRD HC63 C61 . .
PRD HC62 C61 . .
PRD HC61 C61 . .
PRD "C7'" "N6'" "C1'" .
PRD HC71 "C7'" . .
PRD HC72 "C7'" . .
PRD "C1'" "C7'" "C6'" .
PRD "C6'" "C1'" "C5'" .
PRD "HC6'" "C6'" . .
PRD "C5'" "C6'" "C4'" .
PRD "O5'" "C5'" C51 .
PRD C51 "O5'" HC51 .
PRD HC53 C51 . .
PRD HC52 C51 . .
PRD HC51 C51 . .
PRD "C4'" "C5'" "C3'" .
PRD "HC4'" "C4'" . .
PRD "C3'" "C4'" "C2'" .
PRD "HC3'" "C3'" . .
PRD "C2'" "C3'" "O2'" .
PRD "O2'" "C2'" C21 .
PRD C21 "O2'" HC21 .
PRD HC23 C21 . .
PRD HC22 C21 . .
PRD HC21 C21 . END
PRD C4A C8A . ADD
PRD C8A "N1'" . ADD
PRD "C1'" "C2'" . 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
PRD C4A C8A double 1.490 0.020
PRD C5B C4A single 1.390 0.020
PRD C4A C4B single 1.490 0.020
PRD C8A "N1'" single 1.350 0.020
PRD C8A "N8'" single 1.350 0.020
PRD "N1'" C2B double 1.350 0.020
PRD "N8'" C7B double 1.337 0.020
PRD C7B C6B single 1.390 0.020
PRD "H7'" C7B single 1.083 0.020
PRD "N6'" C6B single 1.400 0.020
PRD C6B C5B double 1.390 0.020
PRD C61 "N6'" single 1.455 0.020
PRD "C7'" "N6'" single 1.455 0.020
PRD HC61 C61 single 1.059 0.020
PRD HC62 C61 single 1.059 0.020
PRD HC63 C61 single 1.059 0.020
PRD "H5'" C5B single 1.083 0.020
PRD "N4'" C4B single 1.355 0.020
PRD C4B "N3'" double 1.350 0.020
PRD HN41 "N4'" single 1.010 0.020
PRD HN42 "N4'" single 1.010 0.020
PRD "N3'" C2B single 1.350 0.020
PRD C2B "N2'" single 1.355 0.020
PRD HN21 "N2'" single 1.010 0.020
PRD HN22 "N2'" single 1.010 0.020
PRD "C1'" "C7'" single 1.511 0.020
PRD HC71 "C7'" single 1.092 0.020
PRD HC72 "C7'" single 1.092 0.020
PRD "C1'" "C2'" double 1.487 0.020
PRD "C6'" "C1'" single 1.390 0.020
PRD "C2'" "C3'" single 1.390 0.020
PRD "O2'" "C2'" single 1.370 0.020
PRD "C3'" "C4'" double 1.390 0.020
PRD "HC3'" "C3'" single 1.083 0.020
PRD "C4'" "C5'" single 1.390 0.020
PRD "HC4'" "C4'" single 1.083 0.020
PRD "C5'" "C6'" double 1.390 0.020
PRD "O5'" "C5'" single 1.370 0.020
PRD "HC6'" "C6'" single 1.083 0.020
PRD C21 "O2'" single 1.426 0.020
PRD HC21 C21 single 1.059 0.020
PRD HC22 C21 single 1.059 0.020
PRD HC23 C21 single 1.059 0.020
PRD C51 "O5'" single 1.426 0.020
PRD HC51 C51 single 1.059 0.020
PRD HC52 C51 single 1.059 0.020
PRD HC53 C51 single 1.059 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
PRD HN21 "N2'" HN22 120.000 3.000
PRD HN21 "N2'" C2B 120.000 3.000
PRD HN22 "N2'" C2B 120.000 3.000
PRD "N2'" C2B "N1'" 120.000 3.000
PRD "N2'" C2B "N3'" 120.000 3.000
PRD "N1'" C2B "N3'" 120.000 3.000
PRD C2B "N1'" C8A 120.000 3.000
PRD C2B "N3'" C4B 120.000 3.000
PRD "N3'" C4B "N4'" 120.000 3.000
PRD "N3'" C4B C4A 120.000 3.000
PRD "N4'" C4B C4A 120.000 3.000
PRD C4B "N4'" HN42 120.000 3.000
PRD C4B "N4'" HN41 120.000 3.000
PRD HN42 "N4'" HN41 120.000 3.000
PRD C4B C4A C5B 120.000 3.000
PRD C4B C4A C8A 120.000 3.000
PRD C5B C4A C8A 120.000 3.000
PRD C4A C5B "H5'" 120.000 3.000
PRD C4A C5B C6B 120.000 3.000
PRD "H5'" C5B C6B 120.000 3.000
PRD C5B C6B C7B 120.000 3.000
PRD C5B C6B "N6'" 120.000 3.000
PRD C7B C6B "N6'" 120.000 3.000
PRD C6B C7B "H7'" 120.000 3.000
PRD C6B C7B "N8'" 120.000 3.000
PRD "H7'" C7B "N8'" 120.000 3.000
PRD C7B "N8'" C8A 120.000 3.000
PRD "N8'" C8A C4A 120.000 3.000
PRD "N8'" C8A "N1'" 120.000 3.000
PRD C4A C8A "N1'" 120.000 3.000
PRD C6B "N6'" C61 120.000 3.000
PRD C6B "N6'" "C7'" 120.000 3.000
PRD C61 "N6'" "C7'" 120.000 3.000
PRD "N6'" C61 HC63 109.470 3.000
PRD "N6'" C61 HC62 109.470 3.000
PRD "N6'" C61 HC61 109.470 3.000
PRD HC63 C61 HC62 109.470 3.000
PRD HC63 C61 HC61 109.470 3.000
PRD HC62 C61 HC61 109.470 3.000
PRD "N6'" "C7'" HC71 109.470 3.000
PRD "N6'" "C7'" HC72 109.470 3.000
PRD "N6'" "C7'" "C1'" 109.470 3.000
PRD HC71 "C7'" HC72 107.900 3.000
PRD HC71 "C7'" "C1'" 109.470 3.000
PRD HC72 "C7'" "C1'" 109.470 3.000
PRD "C7'" "C1'" "C6'" 120.000 3.000
PRD "C7'" "C1'" "C2'" 120.000 3.000
PRD "C6'" "C1'" "C2'" 120.000 3.000
PRD "C1'" "C6'" "HC6'" 120.000 3.000
PRD "C1'" "C6'" "C5'" 120.000 3.000
PRD "HC6'" "C6'" "C5'" 120.000 3.000
PRD "C6'" "C5'" "O5'" 120.000 3.000
PRD "C6'" "C5'" "C4'" 120.000 3.000
PRD "O5'" "C5'" "C4'" 120.000 3.000
PRD "C5'" "O5'" C51 120.000 3.000
PRD "O5'" C51 HC53 109.470 3.000
PRD "O5'" C51 HC52 109.470 3.000
PRD "O5'" C51 HC51 109.470 3.000
PRD HC53 C51 HC52 109.470 3.000
PRD HC53 C51 HC51 109.470 3.000
PRD HC52 C51 HC51 109.470 3.000
PRD "C5'" "C4'" "HC4'" 120.000 3.000
PRD "C5'" "C4'" "C3'" 120.000 3.000
PRD "HC4'" "C4'" "C3'" 120.000 3.000
PRD "C4'" "C3'" "HC3'" 120.000 3.000
PRD "C4'" "C3'" "C2'" 120.000 3.000
PRD "HC3'" "C3'" "C2'" 120.000 3.000
PRD "C3'" "C2'" "O2'" 120.000 3.000
PRD "C3'" "C2'" "C1'" 120.000 3.000
PRD "O2'" "C2'" "C1'" 120.000 3.000
PRD "C2'" "O2'" C21 120.000 3.000
PRD "O2'" C21 HC23 109.470 3.000
PRD "O2'" C21 HC22 109.470 3.000
PRD "O2'" C21 HC21 109.470 3.000
PRD HC23 C21 HC22 109.470 3.000
PRD HC23 C21 HC21 109.470 3.000
PRD HC22 C21 HC21 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
PRD CONST_1 HN22 "N2'" C2B "N3'" -179.947 0.000 0
PRD CONST_2 "N2'" C2B "N1'" C8A 180.000 0.000 0
PRD CONST_3 "N2'" C2B "N3'" C4B 180.000 0.000 0
PRD CONST_4 C2B "N3'" C4B C4A 0.000 0.000 0
PRD CONST_5 "N3'" C4B "N4'" HN41 0.007 0.000 0
PRD CONST_6 "N3'" C4B C4A C5B 180.000 0.000 0
PRD CONST_7 C4B C4A C8A "N8'" 180.000 0.000 0
PRD CONST_8 C4B C4A C5B C6B 180.000 0.000 0
PRD CONST_9 C4A C5B C6B "N6'" 180.000 0.000 0
PRD CONST_10 C5B C6B C7B "N8'" 0.000 0.000 0
PRD CONST_11 C6B C7B "N8'" C8A 0.000 0.000 0
PRD CONST_12 C7B "N8'" C8A C4A 0.000 0.000 0
PRD CONST_13 "N8'" C8A "N1'" C2B 180.000 0.000 0
PRD var_1 C5B C6B "N6'" "C7'" 179.666 20.000 1
PRD var_2 C6B "N6'" C61 HC61 179.968 20.000 1
PRD var_3 C6B "N6'" "C7'" "C1'" -89.992 20.000 1
PRD var_4 "N6'" "C7'" "C1'" "C6'" 0.303 20.000 2
PRD CONST_14 "C7'" "C1'" "C2'" "C3'" 180.000 0.000 0
PRD CONST_15 "C7'" "C1'" "C6'" "C5'" 180.000 0.000 0
PRD CONST_16 "C1'" "C6'" "C5'" "C4'" 0.000 0.000 0
PRD var_5 "C6'" "C5'" "O5'" C51 179.770 20.000 1
PRD var_6 "C5'" "O5'" C51 HC51 -179.976 20.000 1
PRD CONST_17 "C6'" "C5'" "C4'" "C3'" 0.000 0.000 0
PRD CONST_18 "C5'" "C4'" "C3'" "C2'" 0.000 0.000 0
PRD CONST_19 "C4'" "C3'" "C2'" "O2'" 180.000 0.000 0
PRD var_7 "C3'" "C2'" "O2'" C21 -0.016 20.000 1
PRD var_8 "C2'" "O2'" C21 HC21 -179.964 20.000 1
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
PRD plan-1 C4A 0.020
PRD plan-1 C8A 0.020
PRD plan-1 C5B 0.020
PRD plan-1 C4B 0.020
PRD plan-1 "N8'" 0.020
PRD plan-1 C7B 0.020
PRD plan-1 C6B 0.020
PRD plan-1 "N1'" 0.020
PRD plan-1 C2B 0.020
PRD plan-1 "N3'" 0.020
PRD plan-1 "H7'" 0.020
PRD plan-1 "N6'" 0.020
PRD plan-1 "H5'" 0.020
PRD plan-1 "N4'" 0.020
PRD plan-1 "N2'" 0.020
PRD plan-1 HN42 0.020
PRD plan-1 HN41 0.020
PRD plan-1 HN21 0.020
PRD plan-1 HN22 0.020
PRD plan-2 "N6'" 0.020
PRD plan-2 C6B 0.020
PRD plan-2 C61 0.020
PRD plan-2 "C7'" 0.020
PRD plan-3 "N4'" 0.020
PRD plan-3 C4B 0.020
PRD plan-3 HN41 0.020
PRD plan-3 HN42 0.020
PRD plan-4 "N2'" 0.020
PRD plan-4 C2B 0.020
PRD plan-4 HN21 0.020
PRD plan-4 HN22 0.020
PRD plan-5 "C1'" 0.020
PRD plan-5 "C7'" 0.020
PRD plan-5 "C2'" 0.020
PRD plan-5 "C6'" 0.020
PRD plan-5 "C3'" 0.020
PRD plan-5 "C4'" 0.020
PRD plan-5 "C5'" 0.020
PRD plan-5 "O2'" 0.020
PRD plan-5 "HC3'" 0.020
PRD plan-5 "HC4'" 0.020
PRD plan-5 "O5'" 0.020
PRD plan-5 "HC6'" 0.020
# ------------------------------------------------------
|
