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
|
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
PLA PLA '"2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOO' non-polymer 40 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PLA
#
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
PLA OXT O OC -0.500 0.000 0.000 0.000
PLA C C C 0.000 -0.782 -0.327 -0.920
PLA O O OC -0.500 -0.456 -1.225 -1.728
PLA CA C CT 0.000 -2.117 0.359 -1.053
PLA CB2 C CH3 0.000 -3.130 -0.609 -1.665
PLA HB23 H H 0.000 -2.794 -0.916 -2.621
PLA HB22 H H 0.000 -3.233 -1.457 -1.038
PLA HB21 H H 0.000 -4.068 -0.126 -1.759
PLA CB1 C CH2 0.000 -1.971 1.583 -1.960
PLA HB11 H H 0.000 -1.248 2.275 -1.523
PLA HB12 H H 0.000 -2.938 2.081 -2.056
PLA CG C C 0.000 -1.492 1.147 -3.320
PLA OD2 O OC -0.500 -1.305 1.996 -4.220
PLA OD1 O OC -0.500 -1.279 -0.064 -3.550
PLA N N NH1 0.000 -2.585 0.784 0.272
PLA HN H H 0.000 -2.786 1.730 0.565
PLA C4A C CH2 0.000 -2.703 -0.431 1.088
PLA H4A1 H H 0.000 -1.729 -0.919 1.156
PLA H4A2 H H 0.000 -3.419 -1.112 0.623
PLA C4 C CR6 0.000 -3.180 -0.064 2.468
PLA C3 C CR6 0.000 -2.275 0.244 3.478
PLA O3 O OH1 0.000 -0.938 0.215 3.237
PLA HO3 H H 0.000 -0.647 1.086 2.934
PLA C2 C CR6 0.000 -2.755 0.570 4.737
PLA C2A C CH3 0.000 -1.784 0.901 5.843
PLA H2A3 H H 0.000 -0.909 1.329 5.428
PLA H2A2 H H 0.000 -2.231 1.590 6.511
PLA H2A1 H H 0.000 -1.531 0.016 6.367
PLA C5 C CR6 0.000 -4.533 -0.022 2.763
PLA C6 C CR16 0.000 -4.936 0.318 4.041
PLA H6 H H 0.000 -5.992 0.354 4.277
PLA N1 N NRD6 0.000 -4.050 0.599 4.977
PLA C5A C CH2 0.000 -5.554 -0.340 1.702
PLA H5A1 H H 0.000 -5.397 -1.359 1.341
PLA H5A2 H H 0.000 -5.445 0.360 0.872
PLA O4P O O2 0.000 -6.868 -0.226 2.255
PLA P P P 0.000 -7.903 -0.578 1.073
PLA O1P O OP -0.666 -7.647 -1.987 0.584
PLA O2P O OP -0.666 -9.319 -0.474 1.596
PLA O3P O OP -0.666 -7.713 0.394 -0.070
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
PLA OXT n/a C START
PLA C OXT CA .
PLA O C . .
PLA CA C N .
PLA CB2 CA HB21 .
PLA HB23 CB2 . .
PLA HB22 CB2 . .
PLA HB21 CB2 . .
PLA CB1 CA CG .
PLA HB11 CB1 . .
PLA HB12 CB1 . .
PLA CG CB1 OD1 .
PLA OD2 CG . .
PLA OD1 CG . .
PLA N CA C4A .
PLA HN N . .
PLA C4A N C4 .
PLA H4A1 C4A . .
PLA H4A2 C4A . .
PLA C4 C4A C5 .
PLA C3 C4 C2 .
PLA O3 C3 HO3 .
PLA HO3 O3 . .
PLA C2 C3 C2A .
PLA C2A C2 H2A1 .
PLA H2A3 C2A . .
PLA H2A2 C2A . .
PLA H2A1 C2A . .
PLA C5 C4 C5A .
PLA C6 C5 N1 .
PLA H6 C6 . .
PLA N1 C6 . .
PLA C5A C5 O4P .
PLA H5A1 C5A . .
PLA H5A2 C5A . .
PLA O4P C5A P .
PLA P O4P O3P .
PLA O1P P . .
PLA O2P P . .
PLA O3P P . END
PLA N1 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
PLA N1 C2 double 1.350 0.020
PLA N1 C6 single 1.337 0.020
PLA C2A C2 single 1.506 0.020
PLA C2 C3 single 1.487 0.020
PLA H2A1 C2A single 1.059 0.020
PLA H2A2 C2A single 1.059 0.020
PLA H2A3 C2A single 1.059 0.020
PLA O3 C3 single 1.362 0.020
PLA C3 C4 double 1.487 0.020
PLA HO3 O3 single 0.967 0.020
PLA C4 C4A single 1.511 0.020
PLA C5 C4 single 1.487 0.020
PLA C4A N single 1.450 0.020
PLA H4A1 C4A single 1.092 0.020
PLA H4A2 C4A single 1.092 0.020
PLA C6 C5 double 1.390 0.020
PLA C5A C5 single 1.511 0.020
PLA H6 C6 single 1.083 0.020
PLA O4P C5A single 1.426 0.020
PLA H5A1 C5A single 1.092 0.020
PLA H5A2 C5A single 1.092 0.020
PLA P O4P single 1.610 0.020
PLA O1P P deloc 1.510 0.020
PLA O2P P deloc 1.510 0.020
PLA O3P P deloc 1.510 0.020
PLA N CA single 1.450 0.020
PLA HN N single 1.010 0.020
PLA CB1 CA single 1.524 0.020
PLA CB2 CA single 1.524 0.020
PLA CA C single 1.507 0.020
PLA CG CB1 single 1.510 0.020
PLA HB11 CB1 single 1.092 0.020
PLA HB12 CB1 single 1.092 0.020
PLA HB21 CB2 single 1.059 0.020
PLA HB22 CB2 single 1.059 0.020
PLA HB23 CB2 single 1.059 0.020
PLA OD1 CG deloc 1.250 0.020
PLA OD2 CG deloc 1.250 0.020
PLA O C deloc 1.250 0.020
PLA C OXT 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
PLA OXT C O 123.000 3.000
PLA OXT C CA 118.500 3.000
PLA O C CA 118.500 3.000
PLA C CA CB2 109.470 3.000
PLA C CA CB1 109.470 3.000
PLA C CA N 111.600 3.000
PLA CB2 CA CB1 111.000 3.000
PLA CB2 CA N 110.000 3.000
PLA CB1 CA N 110.000 3.000
PLA CA CB2 HB23 109.470 3.000
PLA CA CB2 HB22 109.470 3.000
PLA CA CB2 HB21 109.470 3.000
PLA HB23 CB2 HB22 109.470 3.000
PLA HB23 CB2 HB21 109.470 3.000
PLA HB22 CB2 HB21 109.470 3.000
PLA CA CB1 HB11 109.470 3.000
PLA CA CB1 HB12 109.470 3.000
PLA CA CB1 CG 109.470 3.000
PLA HB11 CB1 HB12 107.900 3.000
PLA HB11 CB1 CG 109.470 3.000
PLA HB12 CB1 CG 109.470 3.000
PLA CB1 CG OD2 118.500 3.000
PLA CB1 CG OD1 118.500 3.000
PLA OD2 CG OD1 123.000 3.000
PLA CA N HN 118.500 3.000
PLA CA N C4A 120.000 3.000
PLA HN N C4A 118.500 3.000
PLA N C4A H4A1 109.470 3.000
PLA N C4A H4A2 109.470 3.000
PLA N C4A C4 109.500 3.000
PLA H4A1 C4A H4A2 107.900 3.000
PLA H4A1 C4A C4 109.470 3.000
PLA H4A2 C4A C4 109.470 3.000
PLA C4A C4 C3 120.000 3.000
PLA C4A C4 C5 120.000 3.000
PLA C3 C4 C5 120.000 3.000
PLA C4 C3 O3 120.000 3.000
PLA C4 C3 C2 120.000 3.000
PLA O3 C3 C2 120.000 3.000
PLA C3 O3 HO3 109.470 3.000
PLA C3 C2 C2A 120.000 3.000
PLA C3 C2 N1 120.000 3.000
PLA C2A C2 N1 120.000 3.000
PLA C2 C2A H2A3 109.470 3.000
PLA C2 C2A H2A2 109.470 3.000
PLA C2 C2A H2A1 109.470 3.000
PLA H2A3 C2A H2A2 109.470 3.000
PLA H2A3 C2A H2A1 109.470 3.000
PLA H2A2 C2A H2A1 109.470 3.000
PLA C4 C5 C6 120.000 3.000
PLA C4 C5 C5A 120.000 3.000
PLA C6 C5 C5A 120.000 3.000
PLA C5 C6 H6 120.000 3.000
PLA C5 C6 N1 120.000 3.000
PLA H6 C6 N1 120.000 3.000
PLA C6 N1 C2 120.000 3.000
PLA C5 C5A H5A1 109.470 3.000
PLA C5 C5A H5A2 109.470 3.000
PLA C5 C5A O4P 109.470 3.000
PLA H5A1 C5A H5A2 107.900 3.000
PLA H5A1 C5A O4P 109.470 3.000
PLA H5A2 C5A O4P 109.470 3.000
PLA C5A O4P P 120.500 3.000
PLA O4P P O1P 108.200 3.000
PLA O4P P O2P 108.200 3.000
PLA O4P P O3P 108.200 3.000
PLA O1P P O2P 119.900 3.000
PLA O1P P O3P 119.900 3.000
PLA O2P P O3P 119.900 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
PLA var_1 OXT C CA N -29.923 20.000 1
PLA var_2 C CA CB2 HB21 -179.925 20.000 1
PLA var_3 C CA CB1 CG 60.005 20.000 1
PLA var_4 CA CB1 CG OD1 -0.048 20.000 3
PLA var_5 C CA N C4A -60.058 20.000 1
PLA var_6 CA N C4A C4 179.929 20.000 3
PLA var_7 N C4A C4 C5 90.105 20.000 2
PLA CONST_1 C4A C4 C3 C2 180.000 0.000 0
PLA var_8 C4 C3 O3 HO3 89.945 20.000 1
PLA CONST_2 C4 C3 C2 C2A 180.000 0.000 0
PLA var_9 C3 C2 C2A H2A1 -90.327 20.000 1
PLA CONST_3 C4A C4 C5 C5A 0.000 0.000 0
PLA CONST_4 C4 C5 C6 N1 0.000 0.000 0
PLA CONST_5 C5 C6 N1 C2 0.000 0.000 0
PLA CONST_6 C6 N1 C2 C3 0.000 0.000 0
PLA var_10 C4 C5 C5A O4P -179.937 20.000 2
PLA var_11 C5 C5A O4P P -179.974 20.000 1
PLA var_12 C5A O4P P O3P -59.900 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
PLA chir_01 CA N CB1 CB2 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
PLA plan-1 N1 0.020
PLA plan-1 C2 0.020
PLA plan-1 C6 0.020
PLA plan-1 C3 0.020
PLA plan-1 C4 0.020
PLA plan-1 C5 0.020
PLA plan-1 C2A 0.020
PLA plan-1 O3 0.020
PLA plan-1 C4A 0.020
PLA plan-1 C5A 0.020
PLA plan-1 H6 0.020
PLA plan-2 N 0.020
PLA plan-2 C4A 0.020
PLA plan-2 CA 0.020
PLA plan-2 HN 0.020
PLA plan-3 CG 0.020
PLA plan-3 CB1 0.020
PLA plan-3 OD1 0.020
PLA plan-3 OD2 0.020
PLA plan-4 C 0.020
PLA plan-4 CA 0.020
PLA plan-4 O 0.020
PLA plan-4 OXT 0.020
# ------------------------------------------------------
|
