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
|
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
RMB RMB 'N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METH' non-polymer 38 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_RMB
#
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
RMB O3P O OP -0.666 0.000 0.000 0.000
RMB P P P 0.000 -1.116 -0.470 -0.907
RMB O1P O OP -0.666 -1.163 -1.982 -0.906
RMB O2P O OP -0.666 -0.865 0.025 -2.315
RMB "O5'" O O2 0.000 -2.521 0.110 -0.377
RMB "C5'" C CH2 0.000 -2.701 -0.389 0.949
RMB "H5'1" H H 0.000 -1.877 -0.049 1.580
RMB "H5'2" H H 0.000 -2.714 -1.481 0.927
RMB "C4'" C CH1 0.000 -4.025 0.127 1.514
RMB "H4'" H H 0.000 -4.019 1.225 1.553
RMB "C3'" C CH1 0.000 -4.274 -0.458 2.926
RMB "H3'" H H 0.000 -3.935 -1.502 2.986
RMB "O3'" O OH1 0.000 -3.653 0.341 3.934
RMB "HO3'" H H 0.000 -3.824 -0.047 4.803
RMB "C2'" C CH1 0.000 -5.823 -0.370 3.014
RMB "H2'" H H 0.000 -6.222 -1.147 3.681
RMB "O2'" O OH1 0.000 -6.234 0.929 3.444
RMB "HO2'" H H 0.000 -5.880 1.103 4.326
RMB "C1'" C CH1 0.000 -6.247 -0.629 1.553
RMB "H1'" H H 0.000 -6.539 -1.681 1.431
RMB "O4'" O O2 0.000 -5.123 -0.336 0.716
RMB N1 N NR5 0.000 -7.371 0.242 1.201
RMB C2 C CR15 0.000 -7.284 1.491 0.669
RMB H21 H H 0.000 -6.359 2.005 0.437
RMB C7A C CR56 0.000 -8.711 -0.051 1.345
RMB C7 C CR16 0.000 -9.415 -1.148 1.821
RMB H71 H H 0.000 -8.883 -2.020 2.183
RMB C6 C CR16 0.000 -10.794 -1.123 1.832
RMB H61 H H 0.000 -11.344 -1.979 2.203
RMB C5 C CR6 0.000 -11.481 -0.010 1.371
RMB C8 C CH3 0.000 -12.987 -0.003 1.390
RMB H83 H H 0.000 -13.347 0.600 0.598
RMB H82 H H 0.000 -13.347 -0.992 1.272
RMB H81 H H 0.000 -13.327 0.388 2.314
RMB C4 C CR16 0.000 -10.805 1.076 0.893
RMB H41 H H 0.000 -11.351 1.936 0.526
RMB C3A C CR56 0.000 -9.408 1.076 0.878
RMB N3 N NRD5 0.000 -8.476 1.980 0.480
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
RMB O3P n/a P START
RMB P O3P "O5'" .
RMB O1P P . .
RMB O2P P . .
RMB "O5'" P "C5'" .
RMB "C5'" "O5'" "C4'" .
RMB "H5'1" "C5'" . .
RMB "H5'2" "C5'" . .
RMB "C4'" "C5'" "C3'" .
RMB "H4'" "C4'" . .
RMB "C3'" "C4'" "C2'" .
RMB "H3'" "C3'" . .
RMB "O3'" "C3'" "HO3'" .
RMB "HO3'" "O3'" . .
RMB "C2'" "C3'" "C1'" .
RMB "H2'" "C2'" . .
RMB "O2'" "C2'" "HO2'" .
RMB "HO2'" "O2'" . .
RMB "C1'" "C2'" N1 .
RMB "H1'" "C1'" . .
RMB "O4'" "C1'" . .
RMB N1 "C1'" C7A .
RMB C2 N1 H21 .
RMB H21 C2 . .
RMB C7A N1 C7 .
RMB C7 C7A C6 .
RMB H71 C7 . .
RMB C6 C7 C5 .
RMB H61 C6 . .
RMB C5 C6 C4 .
RMB C8 C5 H81 .
RMB H83 C8 . .
RMB H82 C8 . .
RMB H81 C8 . .
RMB C4 C5 C3A .
RMB H41 C4 . .
RMB C3A C4 N3 .
RMB N3 C3A . END
RMB N3 C2 . ADD
RMB C7A C3A . ADD
RMB "C4'" "O4'" . 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
RMB N3 C2 double 1.350 0.020
RMB N3 C3A single 1.350 0.020
RMB C2 N1 single 1.337 0.020
RMB C7A N1 single 1.337 0.020
RMB N1 "C1'" single 1.485 0.020
RMB H21 C2 single 1.083 0.020
RMB C7A C3A double 1.490 0.020
RMB C7 C7A single 1.390 0.020
RMB C3A C4 single 1.390 0.020
RMB C4 C5 double 1.390 0.020
RMB H41 C4 single 1.083 0.020
RMB C5 C6 single 1.390 0.020
RMB C8 C5 single 1.506 0.020
RMB C6 C7 double 1.390 0.020
RMB H61 C6 single 1.083 0.020
RMB H71 C7 single 1.083 0.020
RMB H81 C8 single 1.059 0.020
RMB H82 C8 single 1.059 0.020
RMB H83 C8 single 1.059 0.020
RMB O1P P deloc 1.510 0.020
RMB O2P P deloc 1.510 0.020
RMB P O3P deloc 1.510 0.020
RMB "O5'" P single 1.610 0.020
RMB "C5'" "O5'" single 1.426 0.020
RMB "C4'" "C5'" single 1.524 0.020
RMB "H5'1" "C5'" single 1.092 0.020
RMB "H5'2" "C5'" single 1.092 0.020
RMB "C4'" "O4'" single 1.426 0.020
RMB "C3'" "C4'" single 1.524 0.020
RMB "H4'" "C4'" single 1.099 0.020
RMB "O4'" "C1'" single 1.426 0.020
RMB "O3'" "C3'" single 1.432 0.020
RMB "C2'" "C3'" single 1.524 0.020
RMB "H3'" "C3'" single 1.099 0.020
RMB "HO3'" "O3'" single 0.967 0.020
RMB "O2'" "C2'" single 1.432 0.020
RMB "C1'" "C2'" single 1.524 0.020
RMB "H2'" "C2'" single 1.099 0.020
RMB "HO2'" "O2'" single 0.967 0.020
RMB "H1'" "C1'" single 1.099 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
RMB O3P P O1P 119.900 3.000
RMB O3P P O2P 119.900 3.000
RMB O3P P "O5'" 108.200 3.000
RMB O1P P O2P 119.900 3.000
RMB O1P P "O5'" 108.200 3.000
RMB O2P P "O5'" 108.200 3.000
RMB P "O5'" "C5'" 120.500 3.000
RMB "O5'" "C5'" "H5'1" 109.470 3.000
RMB "O5'" "C5'" "H5'2" 109.470 3.000
RMB "O5'" "C5'" "C4'" 109.470 3.000
RMB "H5'1" "C5'" "H5'2" 107.900 3.000
RMB "H5'1" "C5'" "C4'" 109.470 3.000
RMB "H5'2" "C5'" "C4'" 109.470 3.000
RMB "C5'" "C4'" "H4'" 108.340 3.000
RMB "C5'" "C4'" "C3'" 111.000 3.000
RMB "C5'" "C4'" "O4'" 109.470 3.000
RMB "H4'" "C4'" "C3'" 108.340 3.000
RMB "H4'" "C4'" "O4'" 109.470 3.000
RMB "C3'" "C4'" "O4'" 109.470 3.000
RMB "C4'" "C3'" "H3'" 108.340 3.000
RMB "C4'" "C3'" "O3'" 109.470 3.000
RMB "C4'" "C3'" "C2'" 111.000 3.000
RMB "H3'" "C3'" "O3'" 109.470 3.000
RMB "H3'" "C3'" "C2'" 108.340 3.000
RMB "O3'" "C3'" "C2'" 109.470 3.000
RMB "C3'" "O3'" "HO3'" 109.470 3.000
RMB "C3'" "C2'" "H2'" 108.340 3.000
RMB "C3'" "C2'" "O2'" 109.470 3.000
RMB "C3'" "C2'" "C1'" 111.000 3.000
RMB "H2'" "C2'" "O2'" 109.470 3.000
RMB "H2'" "C2'" "C1'" 108.340 3.000
RMB "O2'" "C2'" "C1'" 109.470 3.000
RMB "C2'" "O2'" "HO2'" 109.470 3.000
RMB "C2'" "C1'" "H1'" 108.340 3.000
RMB "C2'" "C1'" "O4'" 109.470 3.000
RMB "C2'" "C1'" N1 109.470 3.000
RMB "H1'" "C1'" "O4'" 109.470 3.000
RMB "H1'" "C1'" N1 109.470 3.000
RMB "O4'" "C1'" N1 109.470 3.000
RMB "C1'" "O4'" "C4'" 111.800 3.000
RMB "C1'" N1 C2 126.000 3.000
RMB "C1'" N1 C7A 126.000 3.000
RMB C2 N1 C7A 108.000 3.000
RMB N1 C2 H21 126.000 3.000
RMB N1 C2 N3 108.000 3.000
RMB H21 C2 N3 126.000 3.000
RMB N1 C7A C7 132.000 3.000
RMB N1 C7A C3A 108.000 3.000
RMB C7 C7A C3A 120.000 3.000
RMB C7A C7 H71 120.000 3.000
RMB C7A C7 C6 120.000 3.000
RMB H71 C7 C6 120.000 3.000
RMB C7 C6 H61 120.000 3.000
RMB C7 C6 C5 120.000 3.000
RMB H61 C6 C5 120.000 3.000
RMB C6 C5 C8 120.000 3.000
RMB C6 C5 C4 120.000 3.000
RMB C8 C5 C4 120.000 3.000
RMB C5 C8 H83 109.470 3.000
RMB C5 C8 H82 109.470 3.000
RMB C5 C8 H81 109.470 3.000
RMB H83 C8 H82 109.470 3.000
RMB H83 C8 H81 109.470 3.000
RMB H82 C8 H81 109.470 3.000
RMB C5 C4 H41 120.000 3.000
RMB C5 C4 C3A 120.000 3.000
RMB H41 C4 C3A 120.000 3.000
RMB C4 C3A N3 132.000 3.000
RMB C4 C3A C7A 120.000 3.000
RMB N3 C3A C7A 108.000 3.000
RMB C3A N3 C2 108.000 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
RMB var_1 O3P P "O5'" "C5'" -59.927 20.000 1
RMB var_2 P "O5'" "C5'" "C4'" -179.989 20.000 1
RMB var_3 "O5'" "C5'" "C4'" "C3'" 177.244 20.000 3
RMB var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
RMB var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
RMB var_6 "C4'" "C3'" "O3'" "HO3'" -179.961 20.000 1
RMB var_7 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
RMB var_8 "C3'" "C2'" "O2'" "HO2'" -61.448 20.000 1
RMB var_9 "C3'" "C2'" "C1'" N1 -150.000 20.000 3
RMB var_10 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
RMB var_11 "C2'" "C1'" N1 C7A -90.168 20.000 1
RMB CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
RMB CONST_2 "C1'" N1 C7A C7 0.000 0.000 0
RMB CONST_3 N1 C7A C3A C4 180.000 0.000 0
RMB CONST_4 N1 C7A C7 C6 180.000 0.000 0
RMB CONST_5 C7A C7 C6 C5 0.000 0.000 0
RMB CONST_6 C7 C6 C5 C4 0.000 0.000 0
RMB var_12 C6 C5 C8 H81 90.015 20.000 1
RMB CONST_7 C6 C5 C4 C3A 0.000 0.000 0
RMB CONST_8 C5 C4 C3A N3 180.000 0.000 0
RMB CONST_9 C4 C3A N3 C2 180.000 0.000 0
RMB CONST_10 C3A N3 C2 N1 0.000 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
RMB chir_01 "C4'" "C5'" "O4'" "C3'" negativ
RMB chir_02 "C3'" "C4'" "O3'" "C2'" negativ
RMB chir_03 "C2'" "C3'" "O2'" "C1'" negativ
RMB chir_04 "C1'" N1 "O4'" "C2'" negativ
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
RMB plan-1 N3 0.020
RMB plan-1 C2 0.020
RMB plan-1 C3A 0.020
RMB plan-1 N1 0.020
RMB plan-1 C7A 0.020
RMB plan-1 "C1'" 0.020
RMB plan-1 H21 0.020
RMB plan-1 C7 0.020
RMB plan-1 C4 0.020
RMB plan-1 C5 0.020
RMB plan-1 C6 0.020
RMB plan-1 H41 0.020
RMB plan-1 C8 0.020
RMB plan-1 H61 0.020
RMB plan-1 H71 0.020
# ------------------------------------------------------
|
