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
|
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
IRF IRF '1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO' non-polymer 44 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_IRF
#
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
IRF I8 I I 0.000 0.000 0.000 0.000
IRF C8 C CR6 0.000 0.395 -0.534 -1.987
IRF C7 C CR6 0.000 0.818 0.398 -2.925
IRF C7M C CH3 0.000 1.025 1.839 -2.592
IRF H7M3 H H 0.000 0.468 2.083 -1.726
IRF H7M2 H H 0.000 2.054 2.013 -2.413
IRF H7M1 H H 0.000 0.701 2.436 -3.403
IRF C6 C CR16 0.000 1.067 -0.008 -4.232
IRF H6 H H 0.000 1.397 0.719 -4.965
IRF C9 C CR16 0.000 0.220 -1.870 -2.355
IRF H9 H H 0.000 -0.112 -2.586 -1.613
IRF C9A C CR66 0.000 0.465 -2.305 -3.672
IRF C5A C CR66 0.000 0.894 -1.348 -4.614
IRF N5 N NRD6 0.000 1.164 -1.682 -5.950
IRF N10 N NR6 0.000 0.303 -3.643 -4.095
IRF C10 C CR66 0.000 0.565 -3.995 -5.414
IRF C4A C CR66 0.000 1.019 -2.905 -6.346
IRF C4 C CR6 0.000 1.325 -3.187 -7.780
IRF O4 O O 0.000 1.692 -2.292 -8.524
IRF N3 N NR16 0.000 1.138 -4.512 -8.094
IRF H3 H H 0.000 1.329 -4.796 -9.076
IRF C2 C CR6 0.000 0.716 -5.511 -7.216
IRF O2 O O 0.000 0.588 -6.665 -7.634
IRF N1 N NRD6 0.000 0.448 -5.195 -5.901
IRF "C1'" C CH2 0.000 -0.144 -4.630 -3.112
IRF "H1'1" H H 0.000 -0.717 -5.409 -3.620
IRF "H1'2" H H 0.000 -0.777 -4.137 -2.371
IRF "C2'" C CH1 0.000 1.068 -5.259 -2.413
IRF "H2'" H H 0.000 1.641 -4.464 -1.914
IRF "O2'" O OH1 0.000 1.897 -5.870 -3.403
IRF HA H H 0.000 2.432 -5.192 -3.838
IRF "C3'" C CH1 0.000 0.666 -6.315 -1.364
IRF "H3'" H H 0.000 0.104 -7.112 -1.871
IRF "O3'" O OH1 0.000 -0.181 -5.718 -0.383
IRF HB H H 0.000 0.173 -5.898 0.499
IRF "C4'" C CH1 0.000 1.876 -6.947 -0.652
IRF "H4'" H H 0.000 2.493 -7.473 -1.395
IRF "O4'" O OH1 0.000 1.408 -7.891 0.313
IRF HC H H 0.000 2.076 -8.578 0.442
IRF "C5'" C CH2 0.000 2.738 -5.909 0.063
IRF "H5'1" H H 0.000 2.150 -5.409 0.835
IRF "H5'2" H H 0.000 3.098 -5.170 -0.655
IRF "O5'" O OH1 0.000 3.848 -6.570 0.664
IRF "H5'" H H 0.000 3.918 -7.466 0.308
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
IRF I8 n/a C8 START
IRF C8 I8 C9 .
IRF C7 C8 C6 .
IRF C7M C7 H7M1 .
IRF H7M3 C7M . .
IRF H7M2 C7M . .
IRF H7M1 C7M . .
IRF C6 C7 H6 .
IRF H6 C6 . .
IRF C9 C8 C9A .
IRF H9 C9 . .
IRF C9A C9 N10 .
IRF C5A C9A N5 .
IRF N5 C5A . .
IRF N10 C9A "C1'" .
IRF C10 N10 N1 .
IRF C4A C10 C4 .
IRF C4 C4A N3 .
IRF O4 C4 . .
IRF N3 C4 C2 .
IRF H3 N3 . .
IRF C2 N3 O2 .
IRF O2 C2 . .
IRF N1 C10 . .
IRF "C1'" N10 "C2'" .
IRF "H1'1" "C1'" . .
IRF "H1'2" "C1'" . .
IRF "C2'" "C1'" "C3'" .
IRF "H2'" "C2'" . .
IRF "O2'" "C2'" HA .
IRF HA "O2'" . .
IRF "C3'" "C2'" "C4'" .
IRF "H3'" "C3'" . .
IRF "O3'" "C3'" HB .
IRF HB "O3'" . .
IRF "C4'" "C3'" "C5'" .
IRF "H4'" "C4'" . .
IRF "O4'" "C4'" HC .
IRF HC "O4'" . .
IRF "C5'" "C4'" "O5'" .
IRF "H5'1" "C5'" . .
IRF "H5'2" "C5'" . .
IRF "O5'" "C5'" "H5'" .
IRF "H5'" "O5'" . END
IRF N1 C2 . ADD
IRF C4A N5 . ADD
IRF C5A C6 . 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
IRF N1 C2 single 1.350 0.020
IRF N1 C10 double 1.350 0.020
IRF O2 C2 double 1.250 0.020
IRF C2 N3 single 1.337 0.020
IRF N3 C4 single 1.337 0.020
IRF H3 N3 single 1.040 0.020
IRF O4 C4 double 1.250 0.020
IRF C4 C4A single 1.490 0.020
IRF C4A N5 double 1.350 0.020
IRF C4A C10 single 1.490 0.020
IRF N5 C5A single 1.350 0.020
IRF C5A C6 single 1.390 0.020
IRF C5A C9A double 1.490 0.020
IRF C6 C7 double 1.390 0.020
IRF H6 C6 single 1.083 0.020
IRF C7M C7 single 1.506 0.020
IRF C7 C8 single 1.487 0.020
IRF H7M1 C7M single 1.059 0.020
IRF H7M2 C7M single 1.059 0.020
IRF H7M3 C7M single 1.059 0.020
IRF C9 C8 double 1.390 0.020
IRF C8 I8 single 2.090 0.020
IRF C9A C9 single 1.390 0.020
IRF H9 C9 single 1.083 0.020
IRF N10 C9A single 1.410 0.020
IRF C10 N10 single 1.410 0.020
IRF "C1'" N10 single 1.465 0.020
IRF "C2'" "C1'" single 1.524 0.020
IRF "H1'1" "C1'" single 1.092 0.020
IRF "H1'2" "C1'" single 1.092 0.020
IRF "O2'" "C2'" single 1.432 0.020
IRF "C3'" "C2'" single 1.524 0.020
IRF "H2'" "C2'" single 1.099 0.020
IRF HA "O2'" single 0.967 0.020
IRF "O3'" "C3'" single 1.432 0.020
IRF "C4'" "C3'" single 1.524 0.020
IRF "H3'" "C3'" single 1.099 0.020
IRF HB "O3'" single 0.967 0.020
IRF "O4'" "C4'" single 1.432 0.020
IRF "C5'" "C4'" single 1.524 0.020
IRF "H4'" "C4'" single 1.099 0.020
IRF HC "O4'" single 0.967 0.020
IRF "O5'" "C5'" single 1.432 0.020
IRF "H5'1" "C5'" single 1.092 0.020
IRF "H5'2" "C5'" single 1.092 0.020
IRF "H5'" "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
IRF I8 C8 C7 120.000 3.000
IRF I8 C8 C9 120.000 3.000
IRF C7 C8 C9 120.000 3.000
IRF C8 C7 C7M 120.000 3.000
IRF C8 C7 C6 120.000 3.000
IRF C7M C7 C6 120.000 3.000
IRF C7 C7M H7M3 109.470 3.000
IRF C7 C7M H7M2 109.470 3.000
IRF C7 C7M H7M1 109.470 3.000
IRF H7M3 C7M H7M2 109.470 3.000
IRF H7M3 C7M H7M1 109.470 3.000
IRF H7M2 C7M H7M1 109.470 3.000
IRF C7 C6 H6 120.000 3.000
IRF C7 C6 C5A 120.000 3.000
IRF H6 C6 C5A 120.000 3.000
IRF C8 C9 H9 120.000 3.000
IRF C8 C9 C9A 120.000 3.000
IRF H9 C9 C9A 120.000 3.000
IRF C9 C9A C5A 120.000 3.000
IRF C9 C9A N10 120.000 3.000
IRF C5A C9A N10 120.000 3.000
IRF C9A C5A N5 120.000 3.000
IRF C9A C5A C6 120.000 3.000
IRF N5 C5A C6 120.000 3.000
IRF C5A N5 C4A 120.000 3.000
IRF C9A N10 C10 120.000 3.000
IRF C9A N10 "C1'" 120.000 3.000
IRF C10 N10 "C1'" 120.000 3.000
IRF N10 C10 C4A 120.000 3.000
IRF N10 C10 N1 120.000 3.000
IRF C4A C10 N1 120.000 3.000
IRF C10 C4A C4 120.000 3.000
IRF C10 C4A N5 120.000 3.000
IRF C4 C4A N5 120.000 3.000
IRF C4A C4 O4 120.000 3.000
IRF C4A C4 N3 120.000 3.000
IRF O4 C4 N3 120.000 3.000
IRF C4 N3 H3 120.000 3.000
IRF C4 N3 C2 120.000 3.000
IRF H3 N3 C2 120.000 3.000
IRF N3 C2 O2 120.000 3.000
IRF N3 C2 N1 120.000 3.000
IRF O2 C2 N1 120.000 3.000
IRF C10 N1 C2 120.000 3.000
IRF N10 "C1'" "H1'1" 109.470 3.000
IRF N10 "C1'" "H1'2" 109.470 3.000
IRF N10 "C1'" "C2'" 109.470 3.000
IRF "H1'1" "C1'" "H1'2" 107.900 3.000
IRF "H1'1" "C1'" "C2'" 109.470 3.000
IRF "H1'2" "C1'" "C2'" 109.470 3.000
IRF "C1'" "C2'" "H2'" 108.340 3.000
IRF "C1'" "C2'" "O2'" 109.470 3.000
IRF "C1'" "C2'" "C3'" 111.000 3.000
IRF "H2'" "C2'" "O2'" 109.470 3.000
IRF "H2'" "C2'" "C3'" 108.340 3.000
IRF "O2'" "C2'" "C3'" 109.470 3.000
IRF "C2'" "O2'" HA 109.470 3.000
IRF "C2'" "C3'" "H3'" 108.340 3.000
IRF "C2'" "C3'" "O3'" 109.470 3.000
IRF "C2'" "C3'" "C4'" 111.000 3.000
IRF "H3'" "C3'" "O3'" 109.470 3.000
IRF "H3'" "C3'" "C4'" 108.340 3.000
IRF "O3'" "C3'" "C4'" 109.470 3.000
IRF "C3'" "O3'" HB 109.470 3.000
IRF "C3'" "C4'" "H4'" 108.340 3.000
IRF "C3'" "C4'" "O4'" 109.470 3.000
IRF "C3'" "C4'" "C5'" 111.000 3.000
IRF "H4'" "C4'" "O4'" 109.470 3.000
IRF "H4'" "C4'" "C5'" 108.340 3.000
IRF "O4'" "C4'" "C5'" 109.470 3.000
IRF "C4'" "O4'" HC 109.470 3.000
IRF "C4'" "C5'" "H5'1" 109.470 3.000
IRF "C4'" "C5'" "H5'2" 109.470 3.000
IRF "C4'" "C5'" "O5'" 109.470 3.000
IRF "H5'1" "C5'" "H5'2" 107.900 3.000
IRF "H5'1" "C5'" "O5'" 109.470 3.000
IRF "H5'2" "C5'" "O5'" 109.470 3.000
IRF "C5'" "O5'" "H5'" 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
IRF CONST_1 I8 C8 C7 C6 180.000 0.000 0
IRF var_1 C8 C7 C7M H7M1 -141.812 20.000 1
IRF CONST_2 C8 C7 C6 C5A 0.000 0.000 0
IRF CONST_3 I8 C8 C9 C9A 180.000 0.000 0
IRF CONST_4 C8 C9 C9A N10 180.000 0.000 0
IRF CONST_5 C9 C9A C5A N5 180.000 0.000 0
IRF CONST_6 C9A C5A C6 C7 0.000 0.000 0
IRF CONST_7 C9A C5A N5 C4A 0.000 0.000 0
IRF CONST_8 C9 C9A N10 "C1'" 0.000 0.000 0
IRF CONST_9 C9A N10 C10 N1 180.000 0.000 0
IRF CONST_10 N10 C10 C4A C4 180.000 0.000 0
IRF CONST_11 C10 C4A N5 C5A 0.000 0.000 0
IRF CONST_12 C10 C4A C4 N3 0.000 0.000 0
IRF CONST_13 C4A C4 N3 C2 0.000 0.000 0
IRF CONST_14 C4 N3 C2 O2 180.000 0.000 0
IRF CONST_15 N10 C10 N1 C2 180.000 0.000 0
IRF CONST_16 C10 N1 C2 N3 0.000 0.000 0
IRF var_2 C9A N10 "C1'" "C2'" -89.987 20.000 1
IRF var_3 N10 "C1'" "C2'" "C3'" -179.800 20.000 3
IRF var_4 "C1'" "C2'" "O2'" HA 79.663 20.000 1
IRF var_5 "C1'" "C2'" "C3'" "C4'" -179.728 20.000 3
IRF var_6 "C2'" "C3'" "O3'" HB -127.502 20.000 1
IRF var_7 "C2'" "C3'" "C4'" "C5'" 58.637 20.000 3
IRF var_8 "C3'" "C4'" "O4'" HC 152.052 20.000 1
IRF var_9 "C3'" "C4'" "C5'" "O5'" -178.544 20.000 3
IRF var_10 "C4'" "C5'" "O5'" "H5'" 13.558 20.000 1
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
IRF chir_01 "C2'" "C1'" "O2'" "C3'" positiv
IRF chir_02 "C3'" "C2'" "O3'" "C4'" positiv
IRF chir_03 "C4'" "C3'" "O4'" "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
IRF plan-1 N1 0.020
IRF plan-1 C2 0.020
IRF plan-1 C10 0.020
IRF plan-1 N3 0.020
IRF plan-1 C4 0.020
IRF plan-1 O2 0.020
IRF plan-1 H3 0.020
IRF plan-1 O4 0.020
IRF plan-1 C4A 0.020
IRF plan-1 N5 0.020
IRF plan-1 N10 0.020
IRF plan-1 C5A 0.020
IRF plan-1 C6 0.020
IRF plan-1 C9A 0.020
IRF plan-1 C7 0.020
IRF plan-1 C8 0.020
IRF plan-1 C9 0.020
IRF plan-1 H6 0.020
IRF plan-1 C7M 0.020
IRF plan-1 I8 0.020
IRF plan-1 H9 0.020
IRF plan-1 "C1'" 0.020
# ------------------------------------------------------
|
