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
|
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
218 218 '1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)M' non-polymer 38 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_218
#
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
218 OM7 O OH1 0.000 0.000 0.000 0.000
218 HOM7 H H 0.000 0.628 -0.242 0.694
218 CM7 C CH2 0.000 -1.273 -0.582 0.288
218 HM71 H H 0.000 -1.632 -0.214 1.251
218 HM72 H H 0.000 -1.175 -1.669 0.329
218 CM6 C CH2 0.000 -2.269 -0.199 -0.810
218 HM61 H H 0.000 -1.909 -0.567 -1.773
218 HM62 H H 0.000 -2.365 0.888 -0.850
218 C5 C CR6 0.000 -3.611 -0.813 -0.506
218 C6 C CR16 0.000 -3.971 -2.028 -1.068
218 H6 H H 0.000 -3.295 -2.554 -1.731
218 C1 C CR16 0.000 -5.216 -2.555 -0.761
218 H1 H H 0.000 -5.530 -3.502 -1.182
218 C2 C CR16 0.000 -6.052 -1.856 0.089
218 H2 H H 0.000 -7.026 -2.261 0.334
218 C4 C CR6 0.000 -4.502 -0.168 0.332
218 CM4 C CH3 0.000 -4.123 1.154 0.947
218 HM43 H H 0.000 -4.526 1.218 1.924
218 HM42 H H 0.000 -3.068 1.232 0.995
218 HM41 H H 0.000 -4.508 1.943 0.354
218 N3 N NR6 1.000 -5.677 -0.702 0.605
218 C7A C CH2 0.000 -6.592 0.010 1.501
218 H7A1 H H 0.000 -6.017 0.517 2.279
218 H7A2 H H 0.000 -7.277 -0.704 1.963
218 C5A C CR6 0.000 -7.378 1.026 0.713
218 C6A C CR16 0.000 -6.962 2.340 0.639
218 H6A H H 0.000 -6.061 2.659 1.148
218 N1A N NRD6 0.000 -7.678 3.207 -0.063
218 C4A C CR6 0.000 -8.546 0.662 0.040
218 N4A N NH2 0.000 -9.005 -0.644 0.084
218 H4A2 H H 0.000 -9.855 -0.909 -0.405
218 H4A1 H H 0.000 -8.498 -1.352 0.606
218 N3A N NRD6 0.000 -9.213 1.590 -0.640
218 C2A C CR6 0.000 -8.777 2.832 -0.687
218 CM2 C CH3 0.000 -9.557 3.853 -1.473
218 HM23 H H 0.000 -10.584 3.593 -1.468
218 HM22 H H 0.000 -9.433 4.808 -1.032
218 HM21 H H 0.000 -9.204 3.877 -2.471
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
218 OM7 n/a CM7 START
218 HOM7 OM7 . .
218 CM7 OM7 CM6 .
218 HM71 CM7 . .
218 HM72 CM7 . .
218 CM6 CM7 C5 .
218 HM61 CM6 . .
218 HM62 CM6 . .
218 C5 CM6 C4 .
218 C6 C5 C1 .
218 H6 C6 . .
218 C1 C6 C2 .
218 H1 C1 . .
218 C2 C1 H2 .
218 H2 C2 . .
218 C4 C5 N3 .
218 CM4 C4 HM41 .
218 HM43 CM4 . .
218 HM42 CM4 . .
218 HM41 CM4 . .
218 N3 C4 C7A .
218 C7A N3 C5A .
218 H7A1 C7A . .
218 H7A2 C7A . .
218 C5A C7A C4A .
218 C6A C5A N1A .
218 H6A C6A . .
218 N1A C6A . .
218 C4A C5A N3A .
218 N4A C4A H4A1 .
218 H4A2 N4A . .
218 H4A1 N4A . .
218 N3A C4A C2A .
218 C2A N3A CM2 .
218 CM2 C2A HM21 .
218 HM23 CM2 . .
218 HM22 CM2 . .
218 HM21 CM2 . END
218 C2A N1A . ADD
218 N3 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
218 CM2 C2A single 1.506 0.020
218 HM21 CM2 single 1.059 0.020
218 HM22 CM2 single 1.059 0.020
218 HM23 CM2 single 1.059 0.020
218 C2A N1A single 1.350 0.020
218 C2A N3A double 1.350 0.020
218 N1A C6A double 1.337 0.020
218 C6A C5A single 1.390 0.020
218 H6A C6A single 1.083 0.020
218 C5A C7A single 1.511 0.020
218 C4A C5A double 1.487 0.020
218 C7A N3 single 1.465 0.020
218 H7A1 C7A single 1.092 0.020
218 H7A2 C7A single 1.092 0.020
218 N3 C2 single 1.337 0.020
218 N3 C4 double 1.337 0.020
218 C2 C1 double 1.390 0.020
218 H2 C2 single 1.083 0.020
218 C1 C6 single 1.390 0.020
218 H1 C1 single 1.083 0.020
218 C6 C5 double 1.390 0.020
218 H6 C6 single 1.083 0.020
218 C5 CM6 single 1.511 0.020
218 C4 C5 single 1.487 0.020
218 CM6 CM7 single 1.524 0.020
218 HM61 CM6 single 1.092 0.020
218 HM62 CM6 single 1.092 0.020
218 CM7 OM7 single 1.432 0.020
218 HM71 CM7 single 1.092 0.020
218 HM72 CM7 single 1.092 0.020
218 HOM7 OM7 single 0.967 0.020
218 CM4 C4 single 1.506 0.020
218 HM41 CM4 single 1.059 0.020
218 HM42 CM4 single 1.059 0.020
218 HM43 CM4 single 1.059 0.020
218 N4A C4A single 1.355 0.020
218 N3A C4A single 1.350 0.020
218 H4A1 N4A single 1.010 0.020
218 H4A2 N4A single 1.010 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
218 HOM7 OM7 CM7 109.470 3.000
218 OM7 CM7 HM71 109.470 3.000
218 OM7 CM7 HM72 109.470 3.000
218 OM7 CM7 CM6 109.470 3.000
218 HM71 CM7 HM72 107.900 3.000
218 HM71 CM7 CM6 109.470 3.000
218 HM72 CM7 CM6 109.470 3.000
218 CM7 CM6 HM61 109.470 3.000
218 CM7 CM6 HM62 109.470 3.000
218 CM7 CM6 C5 109.470 3.000
218 HM61 CM6 HM62 107.900 3.000
218 HM61 CM6 C5 109.470 3.000
218 HM62 CM6 C5 109.470 3.000
218 CM6 C5 C6 120.000 3.000
218 CM6 C5 C4 120.000 3.000
218 C6 C5 C4 120.000 3.000
218 C5 C6 H6 120.000 3.000
218 C5 C6 C1 120.000 3.000
218 H6 C6 C1 120.000 3.000
218 C6 C1 H1 120.000 3.000
218 C6 C1 C2 120.000 3.000
218 H1 C1 C2 120.000 3.000
218 C1 C2 H2 120.000 3.000
218 C1 C2 N3 120.000 3.000
218 H2 C2 N3 120.000 3.000
218 C5 C4 CM4 120.000 3.000
218 C5 C4 N3 120.000 3.000
218 CM4 C4 N3 120.000 3.000
218 C4 CM4 HM43 109.470 3.000
218 C4 CM4 HM42 109.470 3.000
218 C4 CM4 HM41 109.470 3.000
218 HM43 CM4 HM42 109.470 3.000
218 HM43 CM4 HM41 109.470 3.000
218 HM42 CM4 HM41 109.470 3.000
218 C4 N3 C7A 120.000 3.000
218 C4 N3 C2 120.000 3.000
218 C7A N3 C2 120.000 3.000
218 N3 C7A H7A1 109.470 3.000
218 N3 C7A H7A2 109.470 3.000
218 N3 C7A C5A 109.500 3.000
218 H7A1 C7A H7A2 107.900 3.000
218 H7A1 C7A C5A 109.470 3.000
218 H7A2 C7A C5A 109.470 3.000
218 C7A C5A C6A 120.000 3.000
218 C7A C5A C4A 120.000 3.000
218 C6A C5A C4A 120.000 3.000
218 C5A C6A H6A 120.000 3.000
218 C5A C6A N1A 120.000 3.000
218 H6A C6A N1A 120.000 3.000
218 C6A N1A C2A 120.000 3.000
218 C5A C4A N4A 120.000 3.000
218 C5A C4A N3A 120.000 3.000
218 N4A C4A N3A 120.000 3.000
218 C4A N4A H4A2 120.000 3.000
218 C4A N4A H4A1 120.000 3.000
218 H4A2 N4A H4A1 120.000 3.000
218 C4A N3A C2A 120.000 3.000
218 N3A C2A CM2 120.000 3.000
218 N3A C2A N1A 120.000 3.000
218 CM2 C2A N1A 120.000 3.000
218 C2A CM2 HM23 109.470 3.000
218 C2A CM2 HM22 109.470 3.000
218 C2A CM2 HM21 109.470 3.000
218 HM23 CM2 HM22 109.470 3.000
218 HM23 CM2 HM21 109.470 3.000
218 HM22 CM2 HM21 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
218 var_1 HOM7 OM7 CM7 CM6 179.946 20.000 1
218 var_2 OM7 CM7 CM6 C5 -179.996 20.000 3
218 var_3 CM7 CM6 C5 C4 85.302 20.000 2
218 CONST_1 CM6 C5 C6 C1 180.000 0.000 0
218 CONST_2 C5 C6 C1 C2 0.000 0.000 0
218 CONST_3 C6 C1 C2 N3 0.000 0.000 0
218 CONST_4 CM6 C5 C4 N3 180.000 0.000 0
218 var_4 C5 C4 CM4 HM41 95.460 20.000 1
218 CONST_5 C5 C4 N3 C7A 180.000 0.000 0
218 CONST_6 C4 N3 C2 C1 0.000 0.000 0
218 var_5 C4 N3 C7A C5A 84.550 20.000 1
218 var_6 N3 C7A C5A C4A 85.004 20.000 2
218 CONST_7 C7A C5A C6A N1A 180.000 0.000 0
218 CONST_8 C5A C6A N1A C2A 0.000 0.000 0
218 CONST_9 C7A C5A C4A N3A 180.000 0.000 0
218 CONST_10 C5A C4A N4A H4A1 -0.058 0.000 0
218 CONST_11 C5A C4A N3A C2A 0.000 0.000 0
218 CONST_12 C4A N3A C2A CM2 180.000 0.000 0
218 CONST_13 N3A C2A N1A C6A 0.000 0.000 0
218 var_7 N3A C2A CM2 HM21 -90.220 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
218 plan-1 C2A 0.020
218 plan-1 CM2 0.020
218 plan-1 N1A 0.020
218 plan-1 N3A 0.020
218 plan-1 C6A 0.020
218 plan-1 C5A 0.020
218 plan-1 C4A 0.020
218 plan-1 H6A 0.020
218 plan-1 C7A 0.020
218 plan-1 N4A 0.020
218 plan-1 H4A2 0.020
218 plan-1 H4A1 0.020
218 plan-2 N3 0.020
218 plan-2 C7A 0.020
218 plan-2 C2 0.020
218 plan-2 C4 0.020
218 plan-2 C1 0.020
218 plan-2 C6 0.020
218 plan-2 C5 0.020
218 plan-2 H2 0.020
218 plan-2 H1 0.020
218 plan-2 H6 0.020
218 plan-2 CM6 0.020
218 plan-2 CM4 0.020
218 plan-3 N4A 0.020
218 plan-3 C4A 0.020
218 plan-3 H4A1 0.020
218 plan-3 H4A2 0.020
# ------------------------------------------------------
|
