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
358
359
360
361
362
363
364
365
366
367
|
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
SCX SCX 'N-((2-aminopyrimidin-5-yl)methyl)-5-' non-polymer 45 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SCX
#
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
SCX F28 F F 0.000 0.000 0.000 0.000
SCX C23 C CR6 0.000 -0.084 -0.654 1.180
SCX C22 C CR16 0.000 0.940 -1.488 1.585
SCX H22 H H 0.000 1.814 -1.615 0.958
SCX C21 C CR16 0.000 0.853 -2.161 2.790
SCX H21 H H 0.000 1.658 -2.816 3.101
SCX C20 C CR16 0.000 -0.257 -2.002 3.600
SCX H20 H H 0.000 -0.318 -2.534 4.541
SCX C19 C CR6 0.000 -1.287 -1.168 3.211
SCX F27 F F 0.000 -2.370 -1.013 4.004
SCX C11 C CR6 0.000 -1.206 -0.484 1.996
SCX C07 C CR6 0.000 -2.306 0.412 1.570
SCX N06 N NRD6 0.000 -2.285 1.691 1.911
SCX C02 C CR56 0.000 -3.270 2.518 1.536
SCX C08 C CR16 0.000 -3.371 -0.099 0.807
SCX H08 H H 0.000 -3.393 -1.145 0.527
SCX C09 C CR6 0.000 -4.378 0.739 0.421
SCX N03 N NR56 0.000 -4.326 2.059 0.791
SCX N04 N NRD5 0.000 -5.183 3.140 0.558
SCX C05 C CR15 0.000 -4.685 4.209 1.135
SCX H05 H H 0.000 -5.135 5.194 1.129
SCX C01 C CR5 0.000 -3.489 3.873 1.753
SCX C24 C CH2 0.000 -2.592 4.807 2.525
SCX H241 H H 0.000 -2.140 4.269 3.360
SCX H242 H H 0.000 -3.181 5.643 2.907
SCX C26 C CH3 0.000 -1.492 5.336 1.602
SCX H263 H H 0.000 -0.919 4.526 1.229
SCX H262 H H 0.000 -1.929 5.859 0.789
SCX H261 H H 0.000 -0.860 5.994 2.141
SCX N10 N NH1 0.000 -5.435 0.265 -0.327
SCX HN10 H H 0.000 -6.177 0.891 -0.606
SCX C12 C CH2 0.000 -5.481 -1.147 -0.717
SCX H121 H H 0.000 -5.490 -1.771 0.179
SCX H122 H H 0.000 -4.602 -1.388 -1.317
SCX C13 C CR6 0.000 -6.728 -1.405 -1.523
SCX C18 C CR16 0.000 -7.906 -1.788 -0.902
SCX H18 H H 0.000 -7.944 -1.911 0.174
SCX N17 N NRD6 0.000 -8.985 -2.001 -1.638
SCX C16 C CR6 0.000 -8.943 -1.863 -2.955
SCX N25 N NH2 0.000 -10.088 -2.099 -3.696
SCX H252 H H 0.000 -10.952 -2.374 -3.238
SCX H251 H H 0.000 -10.079 -1.999 -4.707
SCX N15 N NRD6 0.000 -7.831 -1.503 -3.580
SCX C14 C CR16 0.000 -6.719 -1.270 -2.903
SCX H14 H H 0.000 -5.814 -0.977 -3.419
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
SCX F28 n/a C23 START
SCX C23 F28 C11 .
SCX C22 C23 C21 .
SCX H22 C22 . .
SCX C21 C22 C20 .
SCX H21 C21 . .
SCX C20 C21 C19 .
SCX H20 C20 . .
SCX C19 C20 F27 .
SCX F27 C19 . .
SCX C11 C23 C07 .
SCX C07 C11 C08 .
SCX N06 C07 C02 .
SCX C02 N06 . .
SCX C08 C07 C09 .
SCX H08 C08 . .
SCX C09 C08 N10 .
SCX N03 C09 N04 .
SCX N04 N03 C05 .
SCX C05 N04 C01 .
SCX H05 C05 . .
SCX C01 C05 C24 .
SCX C24 C01 C26 .
SCX H241 C24 . .
SCX H242 C24 . .
SCX C26 C24 H261 .
SCX H263 C26 . .
SCX H262 C26 . .
SCX H261 C26 . .
SCX N10 C09 C12 .
SCX HN10 N10 . .
SCX C12 N10 C13 .
SCX H121 C12 . .
SCX H122 C12 . .
SCX C13 C12 C18 .
SCX C18 C13 N17 .
SCX H18 C18 . .
SCX N17 C18 C16 .
SCX C16 N17 N15 .
SCX N25 C16 H251 .
SCX H252 N25 . .
SCX H251 N25 . .
SCX N15 C16 C14 .
SCX C14 N15 H14 .
SCX H14 C14 . END
SCX C01 C02 . ADD
SCX C02 N03 . ADD
SCX C11 C19 . ADD
SCX C13 C14 . 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
SCX N25 C16 single 1.355 0.020
SCX C16 N17 double 1.350 0.020
SCX N17 C18 single 1.337 0.020
SCX N15 C16 single 1.350 0.020
SCX C18 C13 double 1.390 0.020
SCX C14 N15 double 1.337 0.020
SCX C13 C14 single 1.390 0.020
SCX C13 C12 single 1.511 0.020
SCX C05 N04 double 1.350 0.020
SCX N04 N03 single 1.402 0.020
SCX C01 C05 single 1.387 0.020
SCX C12 N10 single 1.450 0.020
SCX N10 C09 single 1.350 0.020
SCX N03 C09 single 1.337 0.020
SCX C02 N03 single 1.337 0.020
SCX C09 C08 double 1.390 0.020
SCX C01 C02 double 1.490 0.020
SCX C24 C01 single 1.510 0.020
SCX C26 C24 single 1.513 0.020
SCX C02 N06 single 1.355 0.020
SCX C23 F28 single 1.345 0.020
SCX C08 C07 single 1.390 0.020
SCX N06 C07 double 1.350 0.020
SCX C07 C11 single 1.487 0.020
SCX C11 C23 double 1.487 0.020
SCX C22 C23 single 1.390 0.020
SCX C11 C19 single 1.487 0.020
SCX C21 C22 double 1.390 0.020
SCX F27 C19 single 1.345 0.020
SCX C19 C20 double 1.390 0.020
SCX C20 C21 single 1.390 0.020
SCX H05 C05 single 1.083 0.020
SCX H08 C08 single 1.083 0.020
SCX HN10 N10 single 1.010 0.020
SCX H121 C12 single 1.092 0.020
SCX H122 C12 single 1.092 0.020
SCX H14 C14 single 1.083 0.020
SCX H18 C18 single 1.083 0.020
SCX H20 C20 single 1.083 0.020
SCX H21 C21 single 1.083 0.020
SCX H22 C22 single 1.083 0.020
SCX H241 C24 single 1.092 0.020
SCX H242 C24 single 1.092 0.020
SCX H251 N25 single 1.010 0.020
SCX H252 N25 single 1.010 0.020
SCX H261 C26 single 1.059 0.020
SCX H262 C26 single 1.059 0.020
SCX H263 C26 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
SCX F28 C23 C22 120.000 3.000
SCX F28 C23 C11 120.000 3.000
SCX C22 C23 C11 120.000 3.000
SCX C23 C22 H22 120.000 3.000
SCX C23 C22 C21 120.000 3.000
SCX H22 C22 C21 120.000 3.000
SCX C22 C21 H21 120.000 3.000
SCX C22 C21 C20 120.000 3.000
SCX H21 C21 C20 120.000 3.000
SCX C21 C20 H20 120.000 3.000
SCX C21 C20 C19 120.000 3.000
SCX H20 C20 C19 120.000 3.000
SCX C20 C19 F27 120.000 3.000
SCX C20 C19 C11 120.000 3.000
SCX F27 C19 C11 120.000 3.000
SCX C23 C11 C07 120.000 3.000
SCX C23 C11 C19 120.000 3.000
SCX C07 C11 C19 120.000 3.000
SCX C11 C07 N06 120.000 3.000
SCX C11 C07 C08 120.000 3.000
SCX N06 C07 C08 120.000 3.000
SCX C07 N06 C02 120.000 3.000
SCX N06 C02 C01 120.000 3.000
SCX N06 C02 N03 120.000 3.000
SCX C01 C02 N03 108.000 3.000
SCX C07 C08 H08 120.000 3.000
SCX C07 C08 C09 120.000 3.000
SCX H08 C08 C09 120.000 3.000
SCX C08 C09 N03 120.000 3.000
SCX C08 C09 N10 120.000 3.000
SCX N03 C09 N10 120.000 3.000
SCX C09 N03 N04 120.000 3.000
SCX C09 N03 C02 120.000 3.000
SCX N04 N03 C02 120.000 3.000
SCX N03 N04 C05 108.000 3.000
SCX N04 C05 H05 126.000 3.000
SCX N04 C05 C01 108.000 3.000
SCX H05 C05 C01 126.000 3.000
SCX C05 C01 C24 126.000 3.000
SCX C05 C01 C02 108.000 3.000
SCX C24 C01 C02 126.000 3.000
SCX C01 C24 H241 109.470 3.000
SCX C01 C24 H242 109.470 3.000
SCX C01 C24 C26 109.470 3.000
SCX H241 C24 H242 107.900 3.000
SCX H241 C24 C26 109.470 3.000
SCX H242 C24 C26 109.470 3.000
SCX C24 C26 H263 109.470 3.000
SCX C24 C26 H262 109.470 3.000
SCX C24 C26 H261 109.470 3.000
SCX H263 C26 H262 109.470 3.000
SCX H263 C26 H261 109.470 3.000
SCX H262 C26 H261 109.470 3.000
SCX C09 N10 HN10 120.000 3.000
SCX C09 N10 C12 120.000 3.000
SCX HN10 N10 C12 118.500 3.000
SCX N10 C12 H121 109.470 3.000
SCX N10 C12 H122 109.470 3.000
SCX N10 C12 C13 109.500 3.000
SCX H121 C12 H122 107.900 3.000
SCX H121 C12 C13 109.470 3.000
SCX H122 C12 C13 109.470 3.000
SCX C12 C13 C18 120.000 3.000
SCX C12 C13 C14 120.000 3.000
SCX C18 C13 C14 120.000 3.000
SCX C13 C18 H18 120.000 3.000
SCX C13 C18 N17 120.000 3.000
SCX H18 C18 N17 120.000 3.000
SCX C18 N17 C16 120.000 3.000
SCX N17 C16 N25 120.000 3.000
SCX N17 C16 N15 120.000 3.000
SCX N25 C16 N15 120.000 3.000
SCX C16 N25 H252 120.000 3.000
SCX C16 N25 H251 120.000 3.000
SCX H252 N25 H251 120.000 3.000
SCX C16 N15 C14 120.000 3.000
SCX N15 C14 H14 120.000 3.000
SCX N15 C14 C13 120.000 3.000
SCX H14 C14 C13 120.000 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
SCX CONST_1 F28 C23 C22 C21 180.000 0.000 0
SCX CONST_2 C23 C22 C21 C20 0.000 0.000 0
SCX CONST_3 C22 C21 C20 C19 0.000 0.000 0
SCX CONST_4 C21 C20 C19 F27 180.000 0.000 0
SCX CONST_5 F28 C23 C11 C07 0.000 0.000 0
SCX CONST_6 C23 C11 C19 C20 0.000 0.000 0
SCX CONST_7 C23 C11 C07 C08 0.000 0.000 0
SCX CONST_8 C11 C07 N06 C02 180.000 0.000 0
SCX CONST_9 C07 N06 C02 C01 180.000 0.000 0
SCX CONST_10 N06 C02 N03 C09 0.000 0.000 0
SCX CONST_11 C11 C07 C08 C09 180.000 0.000 0
SCX CONST_12 C07 C08 C09 N10 180.000 0.000 0
SCX CONST_13 C08 C09 N03 N04 180.000 0.000 0
SCX CONST_14 C09 N03 N04 C05 180.000 0.000 0
SCX CONST_15 N03 N04 C05 C01 0.000 0.000 0
SCX CONST_16 N04 C05 C01 C24 180.000 0.000 0
SCX CONST_17 C05 C01 C02 N06 180.000 0.000 0
SCX var_1 C05 C01 C24 C26 -95.301 20.000 2
SCX var_2 C01 C24 C26 H261 179.984 20.000 3
SCX var_3 C08 C09 N10 C12 -0.105 20.000 1
SCX var_4 C09 N10 C12 C13 -179.981 20.000 3
SCX var_5 N10 C12 C13 C18 -90.244 20.000 2
SCX CONST_18 C12 C13 C14 N15 180.000 0.000 0
SCX CONST_19 C12 C13 C18 N17 180.000 0.000 0
SCX CONST_20 C13 C18 N17 C16 0.000 0.000 0
SCX CONST_21 C18 N17 C16 N15 0.000 0.000 0
SCX CONST_22 N17 C16 N25 H251 -179.982 0.000 0
SCX CONST_23 N17 C16 N15 C14 0.000 0.000 0
SCX CONST_24 C16 N15 C14 C13 0.000 0.000 0
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
SCX plan-1 C01 0.020
SCX plan-1 C02 0.020
SCX plan-1 C05 0.020
SCX plan-1 C24 0.020
SCX plan-1 N04 0.020
SCX plan-1 N03 0.020
SCX plan-1 N06 0.020
SCX plan-1 C07 0.020
SCX plan-1 C08 0.020
SCX plan-1 C09 0.020
SCX plan-1 H05 0.020
SCX plan-1 C11 0.020
SCX plan-1 H08 0.020
SCX plan-1 N10 0.020
SCX plan-1 HN10 0.020
SCX plan-2 N10 0.020
SCX plan-2 C09 0.020
SCX plan-2 C12 0.020
SCX plan-2 HN10 0.020
SCX plan-3 C11 0.020
SCX plan-3 C07 0.020
SCX plan-3 C19 0.020
SCX plan-3 C23 0.020
SCX plan-3 C20 0.020
SCX plan-3 C21 0.020
SCX plan-3 C22 0.020
SCX plan-3 F27 0.020
SCX plan-3 H20 0.020
SCX plan-3 H21 0.020
SCX plan-3 H22 0.020
SCX plan-3 F28 0.020
SCX plan-4 C13 0.020
SCX plan-4 C12 0.020
SCX plan-4 C14 0.020
SCX plan-4 C18 0.020
SCX plan-4 N15 0.020
SCX plan-4 C16 0.020
SCX plan-4 N17 0.020
SCX plan-4 H14 0.020
SCX plan-4 N25 0.020
SCX plan-4 H18 0.020
SCX plan-4 H252 0.020
SCX plan-4 H251 0.020
SCX plan-5 N25 0.020
SCX plan-5 C16 0.020
SCX plan-5 H251 0.020
SCX plan-5 H252 0.020
# ------------------------------------------------------
|
