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
|
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
AAP AAP 'ALPHA-(2,6-DICHLOROPHENYL)-ALPHA-(2-' non-polymer 39 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AAP
#
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
AAP "O'" O O 0.000 0.000 0.000 0.000
AAP "C'" C C 0.000 0.029 0.227 1.191
AAP "CM'" C CH3 0.000 1.329 0.594 1.858
AAP "HM'3" H H 0.000 1.243 1.554 2.298
AAP "HM'2" H H 0.000 1.556 -0.118 2.608
AAP "HM'1" H H 0.000 2.106 0.606 1.137
AAP "C2'" C CR6 0.000 -1.204 0.144 1.983
AAP "C3'" C CR16 0.000 -1.158 0.287 3.376
AAP "H3'" H H 0.000 -0.211 0.459 3.872
AAP "C4'" C CR16 0.000 -2.317 0.208 4.112
AAP "H4'" H H 0.000 -2.280 0.318 5.189
AAP "C5'" C CR6 0.000 -3.534 -0.013 3.482
AAP CM5 C CH3 0.000 -4.795 -0.095 4.303
AAP HM53 H H 0.000 -5.487 -0.739 3.824
AAP HM52 H H 0.000 -4.567 -0.476 5.265
AAP HM51 H H 0.000 -5.219 0.871 4.398
AAP "C6'" C CR16 0.000 -3.598 -0.155 2.112
AAP "H6'" H H 0.000 -4.552 -0.329 1.630
AAP "C1'" C CR6 0.000 -2.439 -0.074 1.349
AAP "N'" N NH1 0.000 -2.501 -0.216 -0.029
AAP "HN'" H H 0.000 -1.650 -0.243 -0.573
AAP CA C CH1 0.000 -3.799 -0.328 -0.696
AAP HA H H 0.000 -4.533 0.307 -0.180
AAP C C C 0.000 -4.262 -1.762 -0.659
AAP N N NH2 0.000 -3.398 -2.740 -0.320
AAP HN2 H H 0.000 -2.438 -2.516 -0.089
AAP HN1 H H 0.000 -3.705 -3.705 -0.293
AAP O O O 0.000 -5.410 -2.037 -0.934
AAP C1 C CR6 0.000 -3.668 0.118 -2.129
AAP C6 C CR6 0.000 -4.580 1.012 -2.662
AAP CL6 CL CL 0.000 -5.872 1.623 -1.677
AAP C5 C CR16 0.000 -4.456 1.427 -3.976
AAP H5 H H 0.000 -5.165 2.133 -4.390
AAP C4 C CR16 0.000 -3.428 0.941 -4.759
AAP H4 H H 0.000 -3.334 1.262 -5.789
AAP C3 C CR16 0.000 -2.519 0.043 -4.230
AAP H3 H H 0.000 -1.714 -0.339 -4.845
AAP C2 C CR6 0.000 -2.639 -0.366 -2.914
AAP CL2 CL CL 0.000 -1.497 -1.494 -2.249
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
AAP "O'" n/a "C'" START
AAP "C'" "O'" "C2'" .
AAP "CM'" "C'" "HM'1" .
AAP "HM'3" "CM'" . .
AAP "HM'2" "CM'" . .
AAP "HM'1" "CM'" . .
AAP "C2'" "C'" "C3'" .
AAP "C3'" "C2'" "C4'" .
AAP "H3'" "C3'" . .
AAP "C4'" "C3'" "C5'" .
AAP "H4'" "C4'" . .
AAP "C5'" "C4'" "C6'" .
AAP CM5 "C5'" HM51 .
AAP HM53 CM5 . .
AAP HM52 CM5 . .
AAP HM51 CM5 . .
AAP "C6'" "C5'" "C1'" .
AAP "H6'" "C6'" . .
AAP "C1'" "C6'" "N'" .
AAP "N'" "C1'" CA .
AAP "HN'" "N'" . .
AAP CA "N'" C1 .
AAP HA CA . .
AAP C CA O .
AAP N C HN1 .
AAP HN2 N . .
AAP HN1 N . .
AAP O C . .
AAP C1 CA C6 .
AAP C6 C1 C5 .
AAP CL6 C6 . .
AAP C5 C6 C4 .
AAP H5 C5 . .
AAP C4 C5 C3 .
AAP H4 C4 . .
AAP C3 C4 C2 .
AAP H3 C3 . .
AAP C2 C3 CL2 .
AAP CL2 C2 . END
AAP C1 C2 . ADD
AAP "C1'" "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
AAP C CA single 1.500 0.020
AAP O C double 1.220 0.020
AAP N C single 1.332 0.020
AAP C1 CA single 1.480 0.020
AAP CA "N'" single 1.450 0.020
AAP HA CA single 1.099 0.020
AAP HN1 N single 1.010 0.020
AAP HN2 N single 1.010 0.020
AAP C1 C2 double 1.487 0.020
AAP C6 C1 single 1.487 0.020
AAP C2 C3 single 1.390 0.020
AAP CL2 C2 single 1.795 0.020
AAP C3 C4 double 1.390 0.020
AAP H3 C3 single 1.083 0.020
AAP C4 C5 single 1.390 0.020
AAP H4 C4 single 1.083 0.020
AAP C5 C6 double 1.390 0.020
AAP H5 C5 single 1.083 0.020
AAP CL6 C6 single 1.795 0.020
AAP "N'" "C1'" single 1.350 0.020
AAP "HN'" "N'" single 1.010 0.020
AAP "C1'" "C2'" double 1.487 0.020
AAP "C1'" "C6'" single 1.390 0.020
AAP "C3'" "C2'" single 1.390 0.020
AAP "C2'" "C'" single 1.500 0.020
AAP "C4'" "C3'" double 1.390 0.020
AAP "H3'" "C3'" single 1.083 0.020
AAP "C5'" "C4'" single 1.390 0.020
AAP "H4'" "C4'" single 1.083 0.020
AAP "C6'" "C5'" double 1.390 0.020
AAP CM5 "C5'" single 1.506 0.020
AAP "H6'" "C6'" single 1.083 0.020
AAP "C'" "O'" double 1.220 0.020
AAP "CM'" "C'" single 1.500 0.020
AAP "HM'1" "CM'" single 1.059 0.020
AAP "HM'2" "CM'" single 1.059 0.020
AAP "HM'3" "CM'" single 1.059 0.020
AAP HM51 CM5 single 1.059 0.020
AAP HM52 CM5 single 1.059 0.020
AAP HM53 CM5 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
AAP "O'" "C'" "CM'" 123.000 3.000
AAP "O'" "C'" "C2'" 120.500 3.000
AAP "CM'" "C'" "C2'" 120.000 3.000
AAP "C'" "CM'" "HM'3" 109.470 3.000
AAP "C'" "CM'" "HM'2" 109.470 3.000
AAP "C'" "CM'" "HM'1" 109.470 3.000
AAP "HM'3" "CM'" "HM'2" 109.470 3.000
AAP "HM'3" "CM'" "HM'1" 109.470 3.000
AAP "HM'2" "CM'" "HM'1" 109.470 3.000
AAP "C'" "C2'" "C3'" 120.000 3.000
AAP "C'" "C2'" "C1'" 120.000 3.000
AAP "C3'" "C2'" "C1'" 120.000 3.000
AAP "C2'" "C3'" "H3'" 120.000 3.000
AAP "C2'" "C3'" "C4'" 120.000 3.000
AAP "H3'" "C3'" "C4'" 120.000 3.000
AAP "C3'" "C4'" "H4'" 120.000 3.000
AAP "C3'" "C4'" "C5'" 120.000 3.000
AAP "H4'" "C4'" "C5'" 120.000 3.000
AAP "C4'" "C5'" CM5 120.000 3.000
AAP "C4'" "C5'" "C6'" 120.000 3.000
AAP CM5 "C5'" "C6'" 120.000 3.000
AAP "C5'" CM5 HM53 109.470 3.000
AAP "C5'" CM5 HM52 109.470 3.000
AAP "C5'" CM5 HM51 109.470 3.000
AAP HM53 CM5 HM52 109.470 3.000
AAP HM53 CM5 HM51 109.470 3.000
AAP HM52 CM5 HM51 109.470 3.000
AAP "C5'" "C6'" "H6'" 120.000 3.000
AAP "C5'" "C6'" "C1'" 120.000 3.000
AAP "H6'" "C6'" "C1'" 120.000 3.000
AAP "C6'" "C1'" "N'" 120.000 3.000
AAP "C6'" "C1'" "C2'" 120.000 3.000
AAP "N'" "C1'" "C2'" 120.000 3.000
AAP "C1'" "N'" "HN'" 120.000 3.000
AAP "C1'" "N'" CA 120.000 3.000
AAP "HN'" "N'" CA 118.500 3.000
AAP "N'" CA HA 108.550 3.000
AAP "N'" CA C 111.600 3.000
AAP "N'" CA C1 109.470 3.000
AAP HA CA C 108.810 3.000
AAP HA CA C1 109.470 3.000
AAP C CA C1 109.500 3.000
AAP CA C N 120.000 3.000
AAP CA C O 120.500 3.000
AAP N C O 123.000 3.000
AAP C N HN2 120.000 3.000
AAP C N HN1 120.000 3.000
AAP HN2 N HN1 120.000 3.000
AAP CA C1 C6 120.000 3.000
AAP CA C1 C2 120.000 3.000
AAP C6 C1 C2 120.000 3.000
AAP C1 C6 CL6 120.000 3.000
AAP C1 C6 C5 120.000 3.000
AAP CL6 C6 C5 120.000 3.000
AAP C6 C5 H5 120.000 3.000
AAP C6 C5 C4 120.000 3.000
AAP H5 C5 C4 120.000 3.000
AAP C5 C4 H4 120.000 3.000
AAP C5 C4 C3 120.000 3.000
AAP H4 C4 C3 120.000 3.000
AAP C4 C3 H3 120.000 3.000
AAP C4 C3 C2 120.000 3.000
AAP H3 C3 C2 120.000 3.000
AAP C3 C2 CL2 120.000 3.000
AAP C3 C2 C1 120.000 3.000
AAP CL2 C2 C1 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
AAP var_1 "O'" "C'" "CM'" "HM'1" 0.055 20.000 1
AAP var_2 "O'" "C'" "C2'" "C3'" 174.269 20.000 1
AAP CONST_1 "C'" "C2'" "C3'" "C4'" 180.000 0.000 0
AAP CONST_2 "C2'" "C3'" "C4'" "C5'" 0.000 0.000 0
AAP CONST_3 "C3'" "C4'" "C5'" "C6'" 0.000 0.000 0
AAP var_3 "C4'" "C5'" CM5 HM51 90.009 20.000 1
AAP CONST_4 "C4'" "C5'" "C6'" "C1'" 0.000 0.000 0
AAP CONST_5 "C5'" "C6'" "C1'" "N'" 180.000 0.000 0
AAP CONST_6 "C6'" "C1'" "C2'" "C'" 180.000 0.000 0
AAP var_4 "C6'" "C1'" "N'" CA 5.620 20.000 1
AAP var_5 "C1'" "N'" CA C1 155.723 20.000 3
AAP var_6 "N'" CA C O 166.557 20.000 3
AAP CONST_7 CA C N HN1 180.000 0.000 0
AAP var_7 "N'" CA C1 C6 -131.794 20.000 1
AAP CONST_8 CA C1 C2 C3 180.000 0.000 0
AAP CONST_9 CA C1 C6 C5 180.000 0.000 0
AAP CONST_10 C1 C6 C5 C4 0.000 0.000 0
AAP CONST_11 C6 C5 C4 C3 0.000 0.000 0
AAP CONST_12 C5 C4 C3 C2 0.000 0.000 0
AAP CONST_13 C4 C3 C2 CL2 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
AAP chir_01 CA C C1 "N'" 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
AAP plan-1 C 0.020
AAP plan-1 CA 0.020
AAP plan-1 O 0.020
AAP plan-1 N 0.020
AAP plan-1 HN2 0.020
AAP plan-1 HN1 0.020
AAP plan-2 N 0.020
AAP plan-2 C 0.020
AAP plan-2 HN1 0.020
AAP plan-2 HN2 0.020
AAP plan-3 C1 0.020
AAP plan-3 CA 0.020
AAP plan-3 C2 0.020
AAP plan-3 C6 0.020
AAP plan-3 C3 0.020
AAP plan-3 C4 0.020
AAP plan-3 C5 0.020
AAP plan-3 CL2 0.020
AAP plan-3 H3 0.020
AAP plan-3 H4 0.020
AAP plan-3 H5 0.020
AAP plan-3 CL6 0.020
AAP plan-4 "N'" 0.020
AAP plan-4 CA 0.020
AAP plan-4 "C1'" 0.020
AAP plan-4 "HN'" 0.020
AAP plan-5 "C1'" 0.020
AAP plan-5 "N'" 0.020
AAP plan-5 "C2'" 0.020
AAP plan-5 "C6'" 0.020
AAP plan-5 "C3'" 0.020
AAP plan-5 "C4'" 0.020
AAP plan-5 "C5'" 0.020
AAP plan-5 "C'" 0.020
AAP plan-5 "H3'" 0.020
AAP plan-5 "H4'" 0.020
AAP plan-5 CM5 0.020
AAP plan-5 "H6'" 0.020
AAP plan-5 "HN'" 0.020
AAP plan-6 "C'" 0.020
AAP plan-6 "C2'" 0.020
AAP plan-6 "O'" 0.020
AAP plan-6 "CM'" 0.020
# ------------------------------------------------------
|
