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
|
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
252 252 '(1-HYDROXYNONANE-1,1-DIYL)BIS(PHOSPH' non-polymer 40 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_252
#
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
252 OAH O O 0.000 0.000 0.000 0.000
252 P1R P P 0.000 -1.301 -0.700 -0.087
252 OAG O OH1 0.000 -1.106 -2.104 -0.851
252 HOAG H H 0.000 -1.847 -2.720 -0.927
252 OAC O OH1 0.000 -1.865 -0.970 1.396
252 HOAC H H 0.000 -1.353 -1.506 2.018
252 CAP C CT 0.000 -2.487 0.334 -1.009
252 OAD O OH1 0.000 -1.923 0.695 -2.271
252 HOAD H H 0.000 -2.552 1.243 -2.760
252 P1P P P 0.000 -2.849 1.842 -0.052
252 OAB O O 0.000 -3.320 1.467 1.300
252 OAF O OH1 0.000 -3.994 2.691 -0.801
252 HOAF H H 0.000 -3.845 3.014 -1.700
252 OAE O OH1 0.000 -1.514 2.733 0.073
252 HOAE H H 0.000 -1.536 3.572 0.554
252 CAO C CH2 0.000 -3.780 -0.451 -1.234
252 HAO1 H H 0.000 -3.547 -1.406 -1.709
252 HAO2 H H 0.000 -4.446 0.124 -1.881
252 CAN C CH2 0.000 -4.465 -0.702 0.111
252 HAN1 H H 0.000 -4.782 0.251 0.541
252 HAN2 H H 0.000 -3.764 -1.190 0.791
252 CAM C CH2 0.000 -5.686 -1.600 -0.098
252 HAM1 H H 0.000 -5.367 -2.552 -0.529
252 HAM2 H H 0.000 -6.385 -1.110 -0.779
252 CAL C CH2 0.000 -6.371 -1.851 1.247
252 HAL1 H H 0.000 -6.688 -0.898 1.676
252 HAL2 H H 0.000 -5.669 -2.339 1.926
252 CAK C CH2 0.000 -7.592 -2.750 1.039
252 HAK1 H H 0.000 -7.273 -3.702 0.609
252 HAK2 H H 0.000 -8.291 -2.260 0.358
252 CAJ C CH2 0.000 -8.277 -2.999 2.383
252 HAJ1 H H 0.000 -8.594 -2.046 2.812
252 HAJ2 H H 0.000 -7.576 -3.487 3.064
252 CAI C CH2 0.000 -9.497 -3.899 2.174
252 HAI1 H H 0.000 -9.178 -4.851 1.745
252 HAI2 H H 0.000 -10.197 -3.410 1.493
252 CAA C CH3 0.000 -10.182 -4.148 3.519
252 HAA3 H H 0.000 -9.505 -4.623 4.182
252 HAA2 H H 0.000 -10.493 -3.225 3.938
252 HAA1 H H 0.000 -11.029 -4.771 3.378
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
252 OAH n/a P1R START
252 P1R OAH CAP .
252 OAG P1R HOAG .
252 HOAG OAG . .
252 OAC P1R HOAC .
252 HOAC OAC . .
252 CAP P1R CAO .
252 OAD CAP HOAD .
252 HOAD OAD . .
252 P1P CAP OAE .
252 OAB P1P . .
252 OAF P1P HOAF .
252 HOAF OAF . .
252 OAE P1P HOAE .
252 HOAE OAE . .
252 CAO CAP CAN .
252 HAO1 CAO . .
252 HAO2 CAO . .
252 CAN CAO CAM .
252 HAN1 CAN . .
252 HAN2 CAN . .
252 CAM CAN CAL .
252 HAM1 CAM . .
252 HAM2 CAM . .
252 CAL CAM CAK .
252 HAL1 CAL . .
252 HAL2 CAL . .
252 CAK CAL CAJ .
252 HAK1 CAK . .
252 HAK2 CAK . .
252 CAJ CAK CAI .
252 HAJ1 CAJ . .
252 HAJ2 CAJ . .
252 CAI CAJ CAA .
252 HAI1 CAI . .
252 HAI2 CAI . .
252 CAA CAI HAA1 .
252 HAA3 CAA . .
252 HAA2 CAA . .
252 HAA1 CAA . END
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
252 CAA CAI single 1.513 0.020
252 HAA1 CAA single 1.059 0.020
252 HAA2 CAA single 1.059 0.020
252 HAA3 CAA single 1.059 0.020
252 CAI CAJ single 1.524 0.020
252 HAI1 CAI single 1.092 0.020
252 HAI2 CAI single 1.092 0.020
252 CAJ CAK single 1.524 0.020
252 HAJ1 CAJ single 1.092 0.020
252 HAJ2 CAJ single 1.092 0.020
252 CAK CAL single 1.524 0.020
252 HAK1 CAK single 1.092 0.020
252 HAK2 CAK single 1.092 0.020
252 CAL CAM single 1.524 0.020
252 HAL1 CAL single 1.092 0.020
252 HAL2 CAL single 1.092 0.020
252 CAM CAN single 1.524 0.020
252 HAM1 CAM single 1.092 0.020
252 HAM2 CAM single 1.092 0.020
252 CAN CAO single 1.524 0.020
252 HAN1 CAN single 1.092 0.020
252 HAN2 CAN single 1.092 0.020
252 CAO CAP single 1.524 0.020
252 HAO1 CAO single 1.092 0.020
252 HAO2 CAO single 1.092 0.020
252 P1P CAP single 1.812 0.020
252 OAD CAP single 1.432 0.020
252 CAP P1R single 1.812 0.020
252 OAB P1P double 1.480 0.020
252 OAE P1P single 1.610 0.020
252 OAF P1P single 1.610 0.020
252 HOAE OAE single 0.967 0.020
252 HOAF OAF single 0.967 0.020
252 P1R OAH double 1.480 0.020
252 OAC P1R single 1.610 0.020
252 OAG P1R single 1.610 0.020
252 HOAG OAG single 0.967 0.020
252 HOAC OAC single 0.967 0.020
252 HOAD OAD single 0.967 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
252 OAH P1R OAG 109.500 3.000
252 OAH P1R OAC 109.500 3.000
252 OAH P1R CAP 109.500 3.000
252 OAG P1R OAC 109.500 3.000
252 OAG P1R CAP 109.500 3.000
252 OAC P1R CAP 109.500 3.000
252 P1R OAG HOAG 120.000 3.000
252 P1R OAC HOAC 120.000 3.000
252 P1R CAP P1P 109.500 3.000
252 P1R CAP OAD 109.500 3.000
252 P1R CAP CAO 109.500 3.000
252 P1P CAP OAD 109.500 3.000
252 P1P CAP CAO 109.500 3.000
252 OAD CAP CAO 109.470 3.000
252 CAP P1P OAB 109.500 3.000
252 CAP P1P OAF 109.500 3.000
252 CAP P1P OAE 109.500 3.000
252 OAB P1P OAF 109.500 3.000
252 OAB P1P OAE 109.500 3.000
252 OAF P1P OAE 109.500 3.000
252 P1P OAF HOAF 120.000 3.000
252 P1P OAE HOAE 120.000 3.000
252 CAP OAD HOAD 109.470 3.000
252 CAP CAO HAO1 109.470 3.000
252 CAP CAO HAO2 109.470 3.000
252 CAP CAO CAN 111.000 3.000
252 HAO1 CAO HAO2 107.900 3.000
252 HAO1 CAO CAN 109.470 3.000
252 HAO2 CAO CAN 109.470 3.000
252 CAO CAN HAN1 109.470 3.000
252 CAO CAN HAN2 109.470 3.000
252 CAO CAN CAM 111.000 3.000
252 HAN1 CAN HAN2 107.900 3.000
252 HAN1 CAN CAM 109.470 3.000
252 HAN2 CAN CAM 109.470 3.000
252 CAN CAM HAM1 109.470 3.000
252 CAN CAM HAM2 109.470 3.000
252 CAN CAM CAL 111.000 3.000
252 HAM1 CAM HAM2 107.900 3.000
252 HAM1 CAM CAL 109.470 3.000
252 HAM2 CAM CAL 109.470 3.000
252 CAM CAL HAL1 109.470 3.000
252 CAM CAL HAL2 109.470 3.000
252 CAM CAL CAK 111.000 3.000
252 HAL1 CAL HAL2 107.900 3.000
252 HAL1 CAL CAK 109.470 3.000
252 HAL2 CAL CAK 109.470 3.000
252 CAL CAK HAK1 109.470 3.000
252 CAL CAK HAK2 109.470 3.000
252 CAL CAK CAJ 111.000 3.000
252 HAK1 CAK HAK2 107.900 3.000
252 HAK1 CAK CAJ 109.470 3.000
252 HAK2 CAK CAJ 109.470 3.000
252 CAK CAJ HAJ1 109.470 3.000
252 CAK CAJ HAJ2 109.470 3.000
252 CAK CAJ CAI 111.000 3.000
252 HAJ1 CAJ HAJ2 107.900 3.000
252 HAJ1 CAJ CAI 109.470 3.000
252 HAJ2 CAJ CAI 109.470 3.000
252 CAJ CAI HAI1 109.470 3.000
252 CAJ CAI HAI2 109.470 3.000
252 CAJ CAI CAA 111.000 3.000
252 HAI1 CAI HAI2 107.900 3.000
252 HAI1 CAI CAA 109.470 3.000
252 HAI2 CAI CAA 109.470 3.000
252 CAI CAA HAA3 109.470 3.000
252 CAI CAA HAA2 109.470 3.000
252 CAI CAA HAA1 109.470 3.000
252 HAA3 CAA HAA2 109.470 3.000
252 HAA3 CAA HAA1 109.470 3.000
252 HAA2 CAA HAA1 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
252 var_1 OAH P1R OAG HOAG 174.845 20.000 1
252 var_2 OAH P1R OAC HOAC -60.062 20.000 1
252 var_3 OAH P1R CAP CAO 173.784 20.000 1
252 var_4 P1R CAP P1P OAE 64.994 20.000 1
252 var_5 CAP P1P OAF HOAF -59.964 20.000 1
252 var_6 CAP P1P OAE HOAE 179.932 20.000 1
252 var_7 P1R CAP OAD HOAD 179.980 20.000 1
252 var_8 P1R CAP CAO CAN 66.286 20.000 1
252 var_9 CAP CAO CAN CAM -174.597 20.000 3
252 var_10 CAO CAN CAM CAL 180.000 20.000 3
252 var_11 CAN CAM CAL CAK -179.995 20.000 3
252 var_12 CAM CAL CAK CAJ -179.962 20.000 3
252 var_13 CAL CAK CAJ CAI -179.967 20.000 3
252 var_14 CAK CAJ CAI CAA 180.000 20.000 3
252 var_15 CAJ CAI CAA HAA1 179.968 20.000 3
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
252 chir_01 CAP CAO P1P P1R negativ
# ------------------------------------------------------
|
