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
368
369
370
371
372
373
374
375
376
|
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
ABY ABY 'N-(4-AMINOBUTANOYL)-S-(4-METHOXYBENZ' non-polymer 50 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_ABY
#
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
ABY O32 O OC -0.500 0.000 0.000 0.000
ABY C3 C C 0.000 -1.216 0.093 0.278
ABY O31 O OC -0.500 -1.668 1.157 0.756
ABY CA3 C CH2 0.000 -2.135 -1.075 0.040
ABY HA31 H H 0.000 -1.793 -1.932 0.625
ABY HA32 H H 0.000 -2.125 -1.334 -1.021
ABY N3 N NH1 0.000 -3.497 -0.717 0.444
ABY HN3 H H 0.000 -3.688 0.202 0.816
ABY C2 C C 0.000 -4.495 -1.614 0.320
ABY O2 O O 0.000 -4.266 -2.718 -0.127
ABY CA2 C CH1 0.000 -5.896 -1.244 0.735
ABY HA2 H H 0.000 -6.427 -2.144 1.076
ABY N2 N NH1 0.000 -5.840 -0.268 1.825
ABY HN2 H H 0.000 -5.823 0.720 1.618
ABY CD1 C C 0.000 -5.813 -0.689 3.105
ABY CG1 C CH2 0.000 -5.756 0.315 4.227
ABY HG11 H H 0.000 -6.634 0.963 4.180
ABY HG12 H H 0.000 -4.852 0.921 4.127
ABY CB1 C CH2 0.000 -5.733 -0.420 5.569
ABY HB11 H H 0.000 -4.855 -1.068 5.613
ABY HB12 H H 0.000 -6.637 -1.026 5.666
ABY CA1 C CH2 0.000 -5.676 0.599 6.708
ABY HA11 H H 0.000 -6.554 1.247 6.661
ABY HA12 H H 0.000 -4.772 1.205 6.609
ABY N1 N NH2 0.000 -5.654 -0.106 7.996
ABY HN12 H H 0.000 -5.678 -1.119 8.025
ABY HN11 H H 0.000 -5.616 0.415 8.864
ABY OE1 O O 0.000 -5.834 -1.876 3.354
ABY CB2 C CH2 0.000 -6.639 -0.636 -0.457
ABY HB21 H H 0.000 -6.679 -1.365 -1.270
ABY HB22 H H 0.000 -6.111 0.257 -0.796
ABY SG2 S S2 0.000 -8.324 -0.192 0.044
ABY "C'" C CH2 0.000 -8.949 0.482 -1.518
ABY "H'1" H H 0.000 -8.902 -0.288 -2.291
ABY "H'2" H H 0.000 -8.334 1.334 -1.818
ABY "C1'" C CR6 0.000 -10.376 0.930 -1.338
ABY "C6'" C CR16 0.000 -10.649 2.224 -0.936
ABY "H6'" H H 0.000 -9.836 2.916 -0.750
ABY "C5'" C CR16 0.000 -11.956 2.637 -0.771
ABY "H5'" H H 0.000 -12.169 3.651 -0.457
ABY "C2'" C CR16 0.000 -11.412 0.045 -1.573
ABY "H2'" H H 0.000 -11.197 -0.967 -1.890
ABY "C3'" C CR16 0.000 -12.721 0.451 -1.402
ABY "H3'" H H 0.000 -13.532 -0.246 -1.578
ABY "C4'" C CR6 0.000 -12.997 1.751 -1.006
ABY "O4'" O O2 0.000 -14.285 2.154 -0.843
ABY "C7'" C CH3 0.000 -15.111 1.032 -1.157
ABY "H7'3" H H 0.000 -14.935 0.733 -2.158
ABY "H7'2" H H 0.000 -14.882 0.230 -0.504
ABY "H7'1" H H 0.000 -16.129 1.300 -1.043
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
ABY O32 n/a C3 START
ABY C3 O32 CA3 .
ABY O31 C3 . .
ABY CA3 C3 N3 .
ABY HA31 CA3 . .
ABY HA32 CA3 . .
ABY N3 CA3 C2 .
ABY HN3 N3 . .
ABY C2 N3 CA2 .
ABY O2 C2 . .
ABY CA2 C2 CB2 .
ABY HA2 CA2 . .
ABY N2 CA2 CD1 .
ABY HN2 N2 . .
ABY CD1 N2 OE1 .
ABY CG1 CD1 CB1 .
ABY HG11 CG1 . .
ABY HG12 CG1 . .
ABY CB1 CG1 CA1 .
ABY HB11 CB1 . .
ABY HB12 CB1 . .
ABY CA1 CB1 N1 .
ABY HA11 CA1 . .
ABY HA12 CA1 . .
ABY N1 CA1 HN11 .
ABY HN12 N1 . .
ABY HN11 N1 . .
ABY OE1 CD1 . .
ABY CB2 CA2 SG2 .
ABY HB21 CB2 . .
ABY HB22 CB2 . .
ABY SG2 CB2 "C'" .
ABY "C'" SG2 "C1'" .
ABY "H'1" "C'" . .
ABY "H'2" "C'" . .
ABY "C1'" "C'" "C2'" .
ABY "C6'" "C1'" "C5'" .
ABY "H6'" "C6'" . .
ABY "C5'" "C6'" "H5'" .
ABY "H5'" "C5'" . .
ABY "C2'" "C1'" "C3'" .
ABY "H2'" "C2'" . .
ABY "C3'" "C2'" "C4'" .
ABY "H3'" "C3'" . .
ABY "C4'" "C3'" "O4'" .
ABY "O4'" "C4'" "C7'" .
ABY "C7'" "O4'" "H7'1" .
ABY "H7'3" "C7'" . .
ABY "H7'2" "C7'" . .
ABY "H7'1" "C7'" . END
ABY "C4'" "C5'" . 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
ABY "C7'" "O4'" single 1.426 0.020
ABY "H7'1" "C7'" single 1.059 0.020
ABY "H7'2" "C7'" single 1.059 0.020
ABY "H7'3" "C7'" single 1.059 0.020
ABY "O4'" "C4'" single 1.370 0.020
ABY "C4'" "C5'" single 1.390 0.020
ABY "C4'" "C3'" double 1.390 0.020
ABY "C5'" "C6'" double 1.390 0.020
ABY "H5'" "C5'" single 1.083 0.020
ABY "C6'" "C1'" single 1.390 0.020
ABY "H6'" "C6'" single 1.083 0.020
ABY "C2'" "C1'" double 1.390 0.020
ABY "C1'" "C'" single 1.511 0.020
ABY "C3'" "C2'" single 1.390 0.020
ABY "H2'" "C2'" single 1.083 0.020
ABY "H3'" "C3'" single 1.083 0.020
ABY "C'" SG2 single 1.762 0.020
ABY "H'1" "C'" single 1.092 0.020
ABY "H'2" "C'" single 1.092 0.020
ABY SG2 CB2 single 1.762 0.020
ABY CB2 CA2 single 1.524 0.020
ABY HB21 CB2 single 1.092 0.020
ABY HB22 CB2 single 1.092 0.020
ABY N2 CA2 single 1.450 0.020
ABY CA2 C2 single 1.500 0.020
ABY HA2 CA2 single 1.099 0.020
ABY CD1 N2 single 1.330 0.020
ABY HN2 N2 single 1.010 0.020
ABY OE1 CD1 double 1.220 0.020
ABY CG1 CD1 single 1.510 0.020
ABY CB1 CG1 single 1.524 0.020
ABY HG11 CG1 single 1.092 0.020
ABY HG12 CG1 single 1.092 0.020
ABY CA1 CB1 single 1.524 0.020
ABY HB11 CB1 single 1.092 0.020
ABY HB12 CB1 single 1.092 0.020
ABY N1 CA1 single 1.450 0.020
ABY HA11 CA1 single 1.092 0.020
ABY HA12 CA1 single 1.092 0.020
ABY HN11 N1 single 1.010 0.020
ABY HN12 N1 single 1.010 0.020
ABY O2 C2 double 1.220 0.020
ABY C2 N3 single 1.330 0.020
ABY N3 CA3 single 1.450 0.020
ABY HN3 N3 single 1.010 0.020
ABY CA3 C3 single 1.510 0.020
ABY HA31 CA3 single 1.092 0.020
ABY HA32 CA3 single 1.092 0.020
ABY O31 C3 deloc 1.250 0.020
ABY C3 O32 deloc 1.250 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
ABY O32 C3 O31 123.000 3.000
ABY O32 C3 CA3 118.500 3.000
ABY O31 C3 CA3 118.500 3.000
ABY C3 CA3 HA31 109.470 3.000
ABY C3 CA3 HA32 109.470 3.000
ABY C3 CA3 N3 111.600 3.000
ABY HA31 CA3 HA32 107.900 3.000
ABY HA31 CA3 N3 109.470 3.000
ABY HA32 CA3 N3 109.470 3.000
ABY CA3 N3 HN3 118.500 3.000
ABY CA3 N3 C2 121.500 3.000
ABY HN3 N3 C2 120.000 3.000
ABY N3 C2 O2 123.000 3.000
ABY N3 C2 CA2 116.500 3.000
ABY O2 C2 CA2 120.500 3.000
ABY C2 CA2 HA2 108.810 3.000
ABY C2 CA2 N2 111.600 3.000
ABY C2 CA2 CB2 109.470 3.000
ABY HA2 CA2 N2 108.550 3.000
ABY HA2 CA2 CB2 108.340 3.000
ABY N2 CA2 CB2 110.000 3.000
ABY CA2 N2 HN2 118.500 3.000
ABY CA2 N2 CD1 121.500 3.000
ABY HN2 N2 CD1 120.000 3.000
ABY N2 CD1 CG1 116.500 3.000
ABY N2 CD1 OE1 123.000 3.000
ABY CG1 CD1 OE1 120.500 3.000
ABY CD1 CG1 HG11 109.470 3.000
ABY CD1 CG1 HG12 109.470 3.000
ABY CD1 CG1 CB1 109.470 3.000
ABY HG11 CG1 HG12 107.900 3.000
ABY HG11 CG1 CB1 109.470 3.000
ABY HG12 CG1 CB1 109.470 3.000
ABY CG1 CB1 HB11 109.470 3.000
ABY CG1 CB1 HB12 109.470 3.000
ABY CG1 CB1 CA1 111.000 3.000
ABY HB11 CB1 HB12 107.900 3.000
ABY HB11 CB1 CA1 109.470 3.000
ABY HB12 CB1 CA1 109.470 3.000
ABY CB1 CA1 HA11 109.470 3.000
ABY CB1 CA1 HA12 109.470 3.000
ABY CB1 CA1 N1 109.470 3.000
ABY HA11 CA1 HA12 107.900 3.000
ABY HA11 CA1 N1 109.470 3.000
ABY HA12 CA1 N1 109.470 3.000
ABY CA1 N1 HN12 120.000 3.000
ABY CA1 N1 HN11 120.000 3.000
ABY HN12 N1 HN11 120.000 3.000
ABY CA2 CB2 HB21 109.470 3.000
ABY CA2 CB2 HB22 109.470 3.000
ABY CA2 CB2 SG2 109.500 3.000
ABY HB21 CB2 HB22 107.900 3.000
ABY HB21 CB2 SG2 109.500 3.000
ABY HB22 CB2 SG2 109.500 3.000
ABY CB2 SG2 "C'" 100.001 3.000
ABY SG2 "C'" "H'1" 109.500 3.000
ABY SG2 "C'" "H'2" 109.500 3.000
ABY SG2 "C'" "C1'" 109.500 3.000
ABY "H'1" "C'" "H'2" 107.900 3.000
ABY "H'1" "C'" "C1'" 109.470 3.000
ABY "H'2" "C'" "C1'" 109.470 3.000
ABY "C'" "C1'" "C6'" 120.000 3.000
ABY "C'" "C1'" "C2'" 120.000 3.000
ABY "C6'" "C1'" "C2'" 120.000 3.000
ABY "C1'" "C6'" "H6'" 120.000 3.000
ABY "C1'" "C6'" "C5'" 120.000 3.000
ABY "H6'" "C6'" "C5'" 120.000 3.000
ABY "C6'" "C5'" "H5'" 120.000 3.000
ABY "C6'" "C5'" "C4'" 120.000 3.000
ABY "H5'" "C5'" "C4'" 120.000 3.000
ABY "C1'" "C2'" "H2'" 120.000 3.000
ABY "C1'" "C2'" "C3'" 120.000 3.000
ABY "H2'" "C2'" "C3'" 120.000 3.000
ABY "C2'" "C3'" "H3'" 120.000 3.000
ABY "C2'" "C3'" "C4'" 120.000 3.000
ABY "H3'" "C3'" "C4'" 120.000 3.000
ABY "C3'" "C4'" "O4'" 120.000 3.000
ABY "C3'" "C4'" "C5'" 120.000 3.000
ABY "O4'" "C4'" "C5'" 120.000 3.000
ABY "C4'" "O4'" "C7'" 120.000 3.000
ABY "O4'" "C7'" "H7'3" 109.470 3.000
ABY "O4'" "C7'" "H7'2" 109.470 3.000
ABY "O4'" "C7'" "H7'1" 109.470 3.000
ABY "H7'3" "C7'" "H7'2" 109.470 3.000
ABY "H7'3" "C7'" "H7'1" 109.470 3.000
ABY "H7'2" "C7'" "H7'1" 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
ABY var_1 O32 C3 CA3 N3 179.982 20.000 3
ABY var_2 C3 CA3 N3 C2 -180.000 20.000 3
ABY CONST_1 CA3 N3 C2 CA2 180.000 0.000 0
ABY var_3 N3 C2 CA2 CB2 89.990 20.000 3
ABY var_4 C2 CA2 N2 CD1 -89.954 20.000 3
ABY CONST_2 CA2 N2 CD1 OE1 0.000 0.000 0
ABY var_5 N2 CD1 CG1 CB1 -179.999 20.000 3
ABY var_6 CD1 CG1 CB1 CA1 -179.996 20.000 3
ABY var_7 CG1 CB1 CA1 N1 180.000 20.000 3
ABY var_8 CB1 CA1 N1 HN11 179.973 20.000 1
ABY var_9 C2 CA2 CB2 SG2 179.999 20.000 3
ABY var_10 CA2 CB2 SG2 "C'" -179.997 20.000 1
ABY var_11 CB2 SG2 "C'" "C1'" -179.984 20.000 1
ABY var_12 SG2 "C'" "C1'" "C2'" -89.976 20.000 2
ABY CONST_3 "C'" "C1'" "C6'" "C5'" 180.000 0.000 0
ABY CONST_4 "C1'" "C6'" "C5'" "C4'" 0.000 0.000 0
ABY CONST_5 "C'" "C1'" "C2'" "C3'" 180.000 0.000 0
ABY CONST_6 "C1'" "C2'" "C3'" "C4'" 0.000 0.000 0
ABY CONST_7 "C2'" "C3'" "C4'" "O4'" 180.000 0.000 0
ABY CONST_8 "C3'" "C4'" "C5'" "C6'" 0.000 0.000 0
ABY var_13 "C3'" "C4'" "O4'" "C7'" -0.365 20.000 1
ABY var_14 "C4'" "O4'" "C7'" "H7'1" -179.988 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
ABY chir_01 CA2 CB2 N2 C2 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
ABY plan-1 "C4'" 0.020
ABY plan-1 "O4'" 0.020
ABY plan-1 "C5'" 0.020
ABY plan-1 "C3'" 0.020
ABY plan-1 "C6'" 0.020
ABY plan-1 "C1'" 0.020
ABY plan-1 "C2'" 0.020
ABY plan-1 "H5'" 0.020
ABY plan-1 "H6'" 0.020
ABY plan-1 "C'" 0.020
ABY plan-1 "H2'" 0.020
ABY plan-1 "H3'" 0.020
ABY plan-2 N2 0.020
ABY plan-2 CA2 0.020
ABY plan-2 CD1 0.020
ABY plan-2 HN2 0.020
ABY plan-3 CD1 0.020
ABY plan-3 N2 0.020
ABY plan-3 OE1 0.020
ABY plan-3 CG1 0.020
ABY plan-3 HN2 0.020
ABY plan-4 N1 0.020
ABY plan-4 CA1 0.020
ABY plan-4 HN11 0.020
ABY plan-4 HN12 0.020
ABY plan-5 C2 0.020
ABY plan-5 CA2 0.020
ABY plan-5 O2 0.020
ABY plan-5 N3 0.020
ABY plan-5 HN3 0.020
ABY plan-6 N3 0.020
ABY plan-6 C2 0.020
ABY plan-6 CA3 0.020
ABY plan-6 HN3 0.020
ABY plan-7 C3 0.020
ABY plan-7 CA3 0.020
ABY plan-7 O31 0.020
ABY plan-7 O32 0.020
# ------------------------------------------------------
|
