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
|
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
PGG PGG 'PARA-NITROPHENYLPHOSPHONOBUTANOYL-GL' non-polymer 37 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PGG
#
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
PGG O5 O O -1.000 0.000 0.000 0.000
PGG N1 N N 1.000 -0.687 -0.964 0.283
PGG O4 O O 0.000 -0.294 -2.088 0.023
PGG C4 C CR6 0.000 -1.875 -0.790 0.878
PGG C3 C CR16 0.000 -2.332 0.507 1.178
PGG H31 H H 0.000 -1.725 1.368 0.929
PGG C2 C CR16 0.000 -3.541 0.676 1.784
PGG H21 H H 0.000 -3.894 1.673 2.016
PGG C5 C CR16 0.000 -2.672 -1.904 1.205
PGG H51 H H 0.000 -2.328 -2.904 0.974
PGG C6 C CR16 0.000 -3.877 -1.718 1.815
PGG H61 H H 0.000 -4.488 -2.574 2.075
PGG C1 C CR6 0.000 -4.325 -0.431 2.105
PGG O1 O O2 0.000 -5.526 -0.255 2.708
PGG P1 P P 0.000 -6.619 -0.113 1.533
PGG O3 O O 0.000 -6.620 -1.343 0.711
PGG O2 O OH1 0.000 -6.253 1.151 0.609
PGG HO21 H H 0.000 -6.209 2.036 0.996
PGG C8 C CH2 0.000 -8.270 0.127 2.266
PGG H81 H H 0.000 -8.269 1.032 2.876
PGG H82 H H 0.000 -8.518 -0.733 2.893
PGG C9 C CH2 0.000 -9.308 0.262 1.151
PGG H91 H H 0.000 -9.308 -0.644 0.542
PGG H92 H H 0.000 -9.058 1.121 0.524
PGG C10 C CH2 0.000 -10.695 0.465 1.767
PGG H101 H H 0.000 -10.693 1.371 2.376
PGG H102 H H 0.000 -10.942 -0.394 2.395
PGG C11 C C 0.000 -11.717 0.597 0.669
PGG O6 O O 0.000 -11.371 0.535 -0.492
PGG N2 N NH1 0.000 -13.016 0.784 0.975
PGG HN21 H H 0.000 -13.304 0.835 1.942
PGG C12 C CH2 0.000 -14.010 0.912 -0.092
PGG H121 H H 0.000 -14.010 0.006 -0.700
PGG H122 H H 0.000 -13.761 1.770 -0.719
PGG C13 C C 0.000 -15.376 1.112 0.514
PGG O7 O OC -0.500 -16.376 1.245 -0.226
PGG O8 O OC -0.500 -15.510 1.144 1.758
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
PGG O5 n/a N1 START
PGG N1 O5 C4 .
PGG O4 N1 . .
PGG C4 N1 C5 .
PGG C3 C4 C2 .
PGG H31 C3 . .
PGG C2 C3 H21 .
PGG H21 C2 . .
PGG C5 C4 C6 .
PGG H51 C5 . .
PGG C6 C5 C1 .
PGG H61 C6 . .
PGG C1 C6 O1 .
PGG O1 C1 P1 .
PGG P1 O1 C8 .
PGG O3 P1 . .
PGG O2 P1 HO21 .
PGG HO21 O2 . .
PGG C8 P1 C9 .
PGG H81 C8 . .
PGG H82 C8 . .
PGG C9 C8 C10 .
PGG H91 C9 . .
PGG H92 C9 . .
PGG C10 C9 C11 .
PGG H101 C10 . .
PGG H102 C10 . .
PGG C11 C10 N2 .
PGG O6 C11 . .
PGG N2 C11 C12 .
PGG HN21 N2 . .
PGG C12 N2 C13 .
PGG H121 C12 . .
PGG H122 C12 . .
PGG C13 C12 O8 .
PGG O7 C13 . .
PGG O8 C13 . END
PGG 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
PGG C1 C2 double 1.390 0.020
PGG C1 C6 single 1.390 0.020
PGG O1 C1 single 1.370 0.020
PGG C2 C3 single 1.390 0.020
PGG H21 C2 single 1.083 0.020
PGG C3 C4 double 1.390 0.020
PGG H31 C3 single 1.083 0.020
PGG C5 C4 single 1.390 0.020
PGG C4 N1 single 1.400 0.020
PGG C6 C5 double 1.390 0.020
PGG H51 C5 single 1.083 0.020
PGG H61 C6 single 1.083 0.020
PGG P1 O1 single 1.610 0.020
PGG O2 P1 single 1.610 0.020
PGG O3 P1 double 1.480 0.020
PGG C8 P1 single 1.812 0.020
PGG HO21 O2 single 0.967 0.020
PGG C9 C8 single 1.524 0.020
PGG H81 C8 single 1.092 0.020
PGG H82 C8 single 1.092 0.020
PGG C10 C9 single 1.524 0.020
PGG H91 C9 single 1.092 0.020
PGG H92 C9 single 1.092 0.020
PGG C11 C10 single 1.510 0.020
PGG H101 C10 single 1.092 0.020
PGG H102 C10 single 1.092 0.020
PGG N2 C11 single 1.330 0.020
PGG O6 C11 double 1.220 0.020
PGG C12 N2 single 1.450 0.020
PGG HN21 N2 single 1.010 0.020
PGG C13 C12 single 1.510 0.020
PGG H121 C12 single 1.092 0.020
PGG H122 C12 single 1.092 0.020
PGG O7 C13 deloc 1.250 0.020
PGG O8 C13 deloc 1.250 0.020
PGG O4 N1 double 1.220 0.020
PGG N1 O5 single 1.400 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
PGG O5 N1 O4 120.000 3.000
PGG O5 N1 C4 120.000 3.000
PGG O4 N1 C4 120.000 3.000
PGG N1 C4 C3 120.000 3.000
PGG N1 C4 C5 120.000 3.000
PGG C3 C4 C5 120.000 3.000
PGG C4 C3 H31 120.000 3.000
PGG C4 C3 C2 120.000 3.000
PGG H31 C3 C2 120.000 3.000
PGG C3 C2 H21 120.000 3.000
PGG C3 C2 C1 120.000 3.000
PGG H21 C2 C1 120.000 3.000
PGG C4 C5 H51 120.000 3.000
PGG C4 C5 C6 120.000 3.000
PGG H51 C5 C6 120.000 3.000
PGG C5 C6 H61 120.000 3.000
PGG C5 C6 C1 120.000 3.000
PGG H61 C6 C1 120.000 3.000
PGG C6 C1 O1 120.000 3.000
PGG C6 C1 C2 120.000 3.000
PGG O1 C1 C2 120.000 3.000
PGG C1 O1 P1 120.000 3.000
PGG O1 P1 O3 109.500 3.000
PGG O1 P1 O2 109.500 3.000
PGG O1 P1 C8 109.500 3.000
PGG O3 P1 O2 109.500 3.000
PGG O3 P1 C8 109.500 3.000
PGG O2 P1 C8 109.500 3.000
PGG P1 O2 HO21 120.000 3.000
PGG P1 C8 H81 109.500 3.000
PGG P1 C8 H82 109.500 3.000
PGG P1 C8 C9 109.500 3.000
PGG H81 C8 H82 107.900 3.000
PGG H81 C8 C9 109.470 3.000
PGG H82 C8 C9 109.470 3.000
PGG C8 C9 H91 109.470 3.000
PGG C8 C9 H92 109.470 3.000
PGG C8 C9 C10 111.000 3.000
PGG H91 C9 H92 107.900 3.000
PGG H91 C9 C10 109.470 3.000
PGG H92 C9 C10 109.470 3.000
PGG C9 C10 H101 109.470 3.000
PGG C9 C10 H102 109.470 3.000
PGG C9 C10 C11 109.470 3.000
PGG H101 C10 H102 107.900 3.000
PGG H101 C10 C11 109.470 3.000
PGG H102 C10 C11 109.470 3.000
PGG C10 C11 O6 120.500 3.000
PGG C10 C11 N2 116.500 3.000
PGG O6 C11 N2 123.000 3.000
PGG C11 N2 HN21 120.000 3.000
PGG C11 N2 C12 121.500 3.000
PGG HN21 N2 C12 118.500 3.000
PGG N2 C12 H121 109.470 3.000
PGG N2 C12 H122 109.470 3.000
PGG N2 C12 C13 111.600 3.000
PGG H121 C12 H122 107.900 3.000
PGG H121 C12 C13 109.470 3.000
PGG H122 C12 C13 109.470 3.000
PGG C12 C13 O7 118.500 3.000
PGG C12 C13 O8 118.500 3.000
PGG O7 C13 O8 123.000 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
PGG var_1 O5 N1 C4 C5 179.984 20.000 1
PGG CONST_1 N1 C4 C3 C2 180.000 0.000 0
PGG CONST_2 C4 C3 C2 C1 0.000 0.000 0
PGG CONST_3 N1 C4 C5 C6 180.000 0.000 0
PGG CONST_4 C4 C5 C6 C1 0.000 0.000 0
PGG CONST_5 C5 C6 C1 O1 180.000 0.000 0
PGG CONST_6 C6 C1 C2 C3 0.000 0.000 0
PGG var_2 C6 C1 O1 P1 -90.325 20.000 1
PGG var_3 C1 O1 P1 C8 179.957 20.000 1
PGG var_4 O1 P1 O2 HO21 -60.000 20.000 1
PGG var_5 O1 P1 C8 C9 179.984 20.000 1
PGG var_6 P1 C8 C9 C10 -179.962 20.000 3
PGG var_7 C8 C9 C10 C11 -179.953 20.000 3
PGG var_8 C9 C10 C11 N2 -179.988 20.000 3
PGG CONST_7 C10 C11 N2 C12 180.000 0.000 0
PGG var_9 C11 N2 C12 C13 179.989 20.000 3
PGG var_10 N2 C12 C13 O8 0.003 20.000 3
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
PGG plan-1 C1 0.020
PGG plan-1 C2 0.020
PGG plan-1 C6 0.020
PGG plan-1 O1 0.020
PGG plan-1 C3 0.020
PGG plan-1 C4 0.020
PGG plan-1 C5 0.020
PGG plan-1 H21 0.020
PGG plan-1 H31 0.020
PGG plan-1 N1 0.020
PGG plan-1 H51 0.020
PGG plan-1 H61 0.020
PGG plan-2 C11 0.020
PGG plan-2 C10 0.020
PGG plan-2 N2 0.020
PGG plan-2 O6 0.020
PGG plan-2 HN21 0.020
PGG plan-3 N2 0.020
PGG plan-3 C11 0.020
PGG plan-3 C12 0.020
PGG plan-3 HN21 0.020
PGG plan-4 C13 0.020
PGG plan-4 C12 0.020
PGG plan-4 O7 0.020
PGG plan-4 O8 0.020
PGG plan-5 N1 0.020
PGG plan-5 C4 0.020
PGG plan-5 O4 0.020
PGG plan-5 O5 0.020
# ------------------------------------------------------
|
