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
|
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
7MG 7MG '7N-METHYL-8-HYDROGUANOSINE-5'-MONOPH' RNA 41 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_7MG
#
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
7MG OP3 O OP -0.666 0.000 0.000 0.000
7MG P P P 0.000 -0.915 -0.685 0.991
7MG OP1 O OP -0.666 -1.198 0.249 2.147
7MG OP2 O OP -0.666 -0.246 -1.939 1.509
7MG "O5'" O O2 0.000 -2.297 -1.075 0.264
7MG "C5'" C CH2 0.000 -2.878 0.144 -0.201
7MG "H5'" H H 0.000 -2.193 0.628 -0.900
7MG "H5''" H H 0.000 -3.058 0.807 0.648
7MG "C4'" C CH1 0.000 -4.202 -0.156 -0.905
7MG "H4'" H H 0.000 -4.034 -0.812 -1.770
7MG "C3'" C CH1 0.000 -4.888 1.154 -1.350
7MG "H3'" H H 0.000 -4.550 1.996 -0.730
7MG "C2'" C CH1 0.000 -6.394 0.885 -1.125
7MG "H2'" H H 0.000 -6.805 1.594 -0.392
7MG "O2'" O OH1 0.000 -7.108 0.974 -2.359
7MG "HO2'" H H 0.000 -7.017 1.866 -2.720
7MG "C1'" C CH1 0.000 -6.437 -0.554 -0.568
7MG "H1'" H H 0.000 -6.614 -1.273 -1.380
7MG "O4'" O O2 0.000 -5.134 -0.766 0.015
7MG N9 N NR5 0.000 -7.478 -0.674 0.456
7MG C4 C CR56 0.000 -7.563 0.065 1.623
7MG C5 C CR56 0.000 -8.681 -0.315 2.347
7MG N7 N NR5 0.000 -9.368 -1.340 1.662
7MG CM7 C CH3 0.000 -10.595 -2.012 2.097
7MG HM73 H H 0.000 -11.352 -1.855 1.375
7MG HM72 H H 0.000 -10.408 -3.048 2.198
7MG HM71 H H 0.000 -10.901 -1.613 3.027
7MG C8 C CH2 0.000 -8.618 -1.597 0.426
7MG H82 H H 0.000 -9.228 -1.397 -0.458
7MG H81 H H 0.000 -8.254 -2.626 0.389
7MG N3 N NRD6 0.000 -6.764 1.030 2.105
7MG C2 C CR6 0.000 -7.016 1.616 3.254
7MG N2 N NH2 0.000 -6.169 2.594 3.709
7MG HN22 H H 0.000 -6.350 3.059 4.591
7MG HN21 H H 0.000 -5.355 2.859 3.166
7MG N1 N NR16 0.000 -8.103 1.278 4.001
7MG HN1 H H 0.000 -8.283 1.759 4.905
7MG C6 C CR6 0.000 -8.946 0.318 3.570
7MG O6 O O 0.000 -9.925 0.007 4.232
7MG "O3'" O OH1 0.000 -4.625 1.413 -2.730
7MG "HO3'" H H 0.000 -5.076 2.240 -2.950
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
7MG OP3 n/a P START
7MG P OP3 "O5'" .
7MG OP1 P . .
7MG OP2 P . .
7MG "O5'" P "C5'" .
7MG "C5'" "O5'" "C4'" .
7MG "H5'" "C5'" . .
7MG "H5''" "C5'" . .
7MG "C4'" "C5'" "C3'" .
7MG "H4'" "C4'" . .
7MG "C3'" "C4'" "O3'" .
7MG "H3'" "C3'" . .
7MG "C2'" "C3'" "C1'" .
7MG "H2'" "C2'" . .
7MG "O2'" "C2'" "HO2'" .
7MG "HO2'" "O2'" . .
7MG "C1'" "C2'" N9 .
7MG "H1'" "C1'" . .
7MG "O4'" "C1'" . .
7MG N9 "C1'" C4 .
7MG C4 N9 N3 .
7MG C5 C4 N7 .
7MG N7 C5 C8 .
7MG CM7 N7 HM71 .
7MG HM73 CM7 . .
7MG HM72 CM7 . .
7MG HM71 CM7 . .
7MG C8 N7 H81 .
7MG H82 C8 . .
7MG H81 C8 . .
7MG N3 C4 C2 .
7MG C2 N3 N1 .
7MG N2 C2 HN21 .
7MG HN22 N2 . .
7MG HN21 N2 . .
7MG N1 C2 C6 .
7MG HN1 N1 . .
7MG C6 N1 O6 .
7MG O6 C6 . .
7MG "O3'" "C3'" . END
7MG "HO3'" "O3'" . .
7MG "C4'" "O4'" . ADD
7MG N9 C8 . ADD
7MG C5 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
7MG OP1 P deloc 1.510 0.020
7MG OP2 P deloc 1.510 0.020
7MG P OP3 deloc 1.510 0.020
7MG "O5'" P single 1.610 0.020
7MG "C5'" "O5'" single 1.426 0.020
7MG "C4'" "C5'" single 1.524 0.020
7MG "H5'" "C5'" single 1.092 0.020
7MG "H5''" "C5'" single 1.092 0.020
7MG "C4'" "O4'" single 1.426 0.020
7MG "C3'" "C4'" single 1.524 0.020
7MG "H4'" "C4'" single 1.099 0.020
7MG "O4'" "C1'" single 1.426 0.020
7MG "O3'" "C3'" single 1.432 0.020
7MG "C2'" "C3'" single 1.524 0.020
7MG "H3'" "C3'" single 1.099 0.020
7MG "HO3'" "O3'" single 0.967 0.020
7MG "O2'" "C2'" single 1.432 0.020
7MG "C1'" "C2'" single 1.524 0.020
7MG "H2'" "C2'" single 1.099 0.020
7MG "HO2'" "O2'" single 0.967 0.020
7MG N9 "C1'" single 1.485 0.020
7MG "H1'" "C1'" single 1.099 0.020
7MG N9 C8 single 1.462 0.020
7MG C4 N9 single 1.337 0.020
7MG C8 N7 single 1.462 0.020
7MG H81 C8 single 1.092 0.020
7MG H82 C8 single 1.092 0.020
7MG N7 C5 single 1.337 0.020
7MG CM7 N7 single 1.485 0.020
7MG C5 C6 single 1.490 0.020
7MG C5 C4 double 1.490 0.020
7MG O6 C6 double 1.250 0.020
7MG C6 N1 single 1.337 0.020
7MG N1 C2 single 1.337 0.020
7MG HN1 N1 single 1.040 0.020
7MG N2 C2 single 1.355 0.020
7MG C2 N3 double 1.350 0.020
7MG HN21 N2 single 1.010 0.020
7MG HN22 N2 single 1.010 0.020
7MG N3 C4 single 1.355 0.020
7MG HM71 CM7 single 1.059 0.020
7MG HM72 CM7 single 1.059 0.020
7MG HM73 CM7 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
7MG OP3 P OP1 119.900 3.000
7MG OP3 P OP2 119.900 3.000
7MG OP3 P "O5'" 108.200 3.000
7MG OP1 P OP2 119.900 3.000
7MG OP1 P "O5'" 108.200 3.000
7MG OP2 P "O5'" 108.200 3.000
7MG P "O5'" "C5'" 120.500 3.000
7MG "O5'" "C5'" "H5'" 109.470 3.000
7MG "O5'" "C5'" "H5''" 109.470 3.000
7MG "O5'" "C5'" "C4'" 109.470 3.000
7MG "H5'" "C5'" "H5''" 107.900 3.000
7MG "H5'" "C5'" "C4'" 109.470 3.000
7MG "H5''" "C5'" "C4'" 109.470 3.000
7MG "C5'" "C4'" "H4'" 108.340 3.000
7MG "C5'" "C4'" "C3'" 111.000 3.000
7MG "C5'" "C4'" "O4'" 109.470 3.000
7MG "H4'" "C4'" "C3'" 108.340 3.000
7MG "H4'" "C4'" "O4'" 109.470 3.000
7MG "C3'" "C4'" "O4'" 109.470 3.000
7MG "C4'" "C3'" "H3'" 108.340 3.000
7MG "C4'" "C3'" "C2'" 111.000 3.000
7MG "C4'" "C3'" "O3'" 109.470 3.000
7MG "H3'" "C3'" "C2'" 108.340 3.000
7MG "H3'" "C3'" "O3'" 109.470 3.000
7MG "C2'" "C3'" "O3'" 109.470 3.000
7MG "C3'" "C2'" "H2'" 108.340 3.000
7MG "C3'" "C2'" "O2'" 109.470 3.000
7MG "C3'" "C2'" "C1'" 111.000 3.000
7MG "H2'" "C2'" "O2'" 109.470 3.000
7MG "H2'" "C2'" "C1'" 108.340 3.000
7MG "O2'" "C2'" "C1'" 109.470 3.000
7MG "C2'" "O2'" "HO2'" 109.470 3.000
7MG "C2'" "C1'" "H1'" 108.340 3.000
7MG "C2'" "C1'" "O4'" 109.470 3.000
7MG "C2'" "C1'" N9 109.470 3.000
7MG "H1'" "C1'" "O4'" 109.470 3.000
7MG "H1'" "C1'" N9 109.470 3.000
7MG "O4'" "C1'" N9 109.470 3.000
7MG "C1'" "O4'" "C4'" 111.800 3.000
7MG "C1'" N9 C4 126.000 3.000
7MG "C1'" N9 C8 108.000 3.000
7MG C4 N9 C8 126.000 3.000
7MG N9 C4 C5 108.000 3.000
7MG N9 C4 N3 132.000 3.000
7MG C5 C4 N3 120.000 3.000
7MG C4 C5 N7 108.000 3.000
7MG C4 C5 C6 120.000 3.000
7MG N7 C5 C6 120.000 3.000
7MG C5 N7 CM7 126.000 3.000
7MG C5 N7 C8 126.000 3.000
7MG CM7 N7 C8 108.000 3.000
7MG N7 CM7 HM73 109.470 3.000
7MG N7 CM7 HM72 109.470 3.000
7MG N7 CM7 HM71 109.470 3.000
7MG HM73 CM7 HM72 109.470 3.000
7MG HM73 CM7 HM71 109.470 3.000
7MG HM72 CM7 HM71 109.470 3.000
7MG N7 C8 H82 109.500 3.000
7MG N7 C8 H81 109.500 3.000
7MG N7 C8 N9 109.500 3.000
7MG H82 C8 H81 107.900 3.000
7MG H82 C8 N9 109.500 3.000
7MG H81 C8 N9 109.500 3.000
7MG C4 N3 C2 120.000 3.000
7MG N3 C2 N2 120.000 3.000
7MG N3 C2 N1 120.000 3.000
7MG N2 C2 N1 120.000 3.000
7MG C2 N2 HN22 120.000 3.000
7MG C2 N2 HN21 120.000 3.000
7MG HN22 N2 HN21 120.000 3.000
7MG C2 N1 HN1 120.000 3.000
7MG C2 N1 C6 120.000 3.000
7MG HN1 N1 C6 120.000 3.000
7MG N1 C6 O6 120.000 3.000
7MG N1 C6 C5 120.000 3.000
7MG O6 C6 C5 120.000 3.000
7MG "C3'" "O3'" "HO3'" 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
7MG var_1 OP3 P "O5'" "C5'" -60.105 20.000 1
7MG var_2 P "O5'" "C5'" "C4'" -179.972 20.000 1
7MG var_3 "O5'" "C5'" "C4'" "C3'" 176.943 20.000 3
7MG var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
7MG var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
7MG var_6 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
7MG var_7 "C3'" "C2'" "O2'" "HO2'" -61.398 20.000 1
7MG var_8 "C3'" "C2'" "C1'" N9 150.000 20.000 3
7MG var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
7MG var_10 "C2'" "C1'" N9 C4 -58.442 20.000 1
7MG CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
7MG CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
7MG CONST_3 N9 C4 C5 N7 0.000 0.000 0
7MG CONST_4 C4 C5 C6 N1 0.000 0.000 0
7MG CONST_5 C4 C5 N7 C8 0.000 0.000 0
7MG var_11 C5 N7 CM7 HM71 -0.293 20.000 1
7MG CONST_6 C5 N7 C8 N9 0.000 0.000 0
7MG CONST_7 N9 C4 N3 C2 180.000 0.000 0
7MG CONST_8 C4 N3 C2 N1 0.000 0.000 0
7MG CONST_9 N3 C2 N2 HN21 -0.246 0.000 0
7MG CONST_10 N3 C2 N1 C6 0.000 0.000 0
7MG CONST_11 C2 N1 C6 O6 180.000 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
7MG chir_01 "C4'" "C5'" "O4'" "C3'" negativ
7MG chir_02 "C3'" "C4'" "O3'" "C2'" negativ
7MG chir_03 "C2'" "C3'" "O2'" "C1'" negativ
7MG chir_04 "C1'" "O4'" "C2'" N9 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
7MG plan-1 N9 0.020
7MG plan-1 "C1'" 0.020
7MG plan-1 C8 0.020
7MG plan-1 C4 0.020
7MG plan-1 N7 0.020
7MG plan-1 C5 0.020
7MG plan-1 CM7 0.020
7MG plan-1 C6 0.020
7MG plan-1 N1 0.020
7MG plan-1 C2 0.020
7MG plan-1 N3 0.020
7MG plan-1 O6 0.020
7MG plan-1 HN1 0.020
7MG plan-1 N2 0.020
7MG plan-1 HN22 0.020
7MG plan-1 HN21 0.020
7MG plan-2 N2 0.020
7MG plan-2 C2 0.020
7MG plan-2 HN21 0.020
7MG plan-2 HN22 0.020
# ------------------------------------------------------
|
