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
|
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
PCV PCV '5-AMINO-3-HYDROXY-2-(2-OXO-AZETIDIN-' non-polymer 27 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PCV
#
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
PCV O4 O OC -0.500 0.000 0.000 0.000
PCV C3 C C 0.000 -1.212 0.290 -0.113
PCV O2 O OC -0.500 -1.611 0.929 -1.111
PCV C1 C CH1 0.000 -2.190 -0.133 0.953
PCV HC1 H H 0.000 -1.900 0.313 1.914
PCV C2 C CH1 0.000 -2.184 -1.657 1.076
PCV H22 H H 0.000 -1.200 -1.992 1.435
PCV O3 O OH1 0.000 -2.448 -2.239 -0.202
PCV HO3 H H 0.000 -3.313 -1.944 -0.517
PCV C4 C CH2 0.000 -3.265 -2.093 2.068
PCV HC41 H H 0.000 -4.248 -1.838 1.668
PCV HC42 H H 0.000 -3.114 -1.578 3.018
PCV C5 C CH2 0.000 -3.177 -3.604 2.286
PCV HC51 H H 0.000 -2.193 -3.857 2.684
PCV HC52 H H 0.000 -3.326 -4.118 1.334
PCV N2 N NH2 0.000 -4.214 -4.024 3.237
PCV HN22 H H 0.000 -3.956 -4.387 4.147
PCV HN21 H H 0.000 -5.194 -3.952 2.990
PCV N1 N N 0.000 -3.535 0.323 0.590
PCV C7 C CH2 0.000 -4.523 1.206 1.209
PCV HC71 H H 0.000 -4.286 2.269 1.279
PCV HC72 H H 0.000 -4.991 0.876 2.139
PCV C9 C CH2 0.000 -5.484 0.972 0.043
PCV HC91 H H 0.000 -5.682 1.763 -0.684
PCV HC92 H H 0.000 -6.383 0.365 0.173
PCV C8 C C 0.000 -4.357 0.104 -0.452
PCV O1 O O 0.000 -4.235 -0.570 -1.453
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
PCV O4 n/a C3 START
PCV C3 O4 C1 .
PCV O2 C3 . .
PCV C1 C3 N1 .
PCV HC1 C1 . .
PCV C2 C1 C4 .
PCV H22 C2 . .
PCV O3 C2 HO3 .
PCV HO3 O3 . .
PCV C4 C2 C5 .
PCV HC41 C4 . .
PCV HC42 C4 . .
PCV C5 C4 N2 .
PCV HC51 C5 . .
PCV HC52 C5 . .
PCV N2 C5 HN21 .
PCV HN22 N2 . .
PCV HN21 N2 . .
PCV N1 C1 C7 .
PCV C7 N1 C9 .
PCV HC71 C7 . .
PCV HC72 C7 . .
PCV C9 C7 C8 .
PCV HC91 C9 . .
PCV HC92 C9 . .
PCV C8 C9 O1 .
PCV O1 C8 . END
PCV N1 C8 . 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
PCV N1 C8 single 1.330 0.020
PCV C7 N1 single 1.455 0.020
PCV N1 C1 single 1.455 0.020
PCV O1 C8 double 1.220 0.020
PCV C8 C9 single 1.510 0.020
PCV C9 C7 single 1.524 0.020
PCV HC91 C9 single 1.092 0.020
PCV HC92 C9 single 1.092 0.020
PCV HC71 C7 single 1.092 0.020
PCV HC72 C7 single 1.092 0.020
PCV C2 C1 single 1.524 0.020
PCV C1 C3 single 1.500 0.020
PCV HC1 C1 single 1.099 0.020
PCV C4 C2 single 1.524 0.020
PCV O3 C2 single 1.432 0.020
PCV H22 C2 single 1.099 0.020
PCV C5 C4 single 1.524 0.020
PCV HC41 C4 single 1.092 0.020
PCV HC42 C4 single 1.092 0.020
PCV N2 C5 single 1.450 0.020
PCV HC51 C5 single 1.092 0.020
PCV HC52 C5 single 1.092 0.020
PCV HN21 N2 single 1.010 0.020
PCV HN22 N2 single 1.010 0.020
PCV HO3 O3 single 0.967 0.020
PCV O2 C3 deloc 1.250 0.020
PCV C3 O4 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
PCV O4 C3 O2 123.000 3.000
PCV O4 C3 C1 118.500 3.000
PCV O2 C3 C1 118.500 3.000
PCV C3 C1 HC1 108.810 3.000
PCV C3 C1 C2 109.470 3.000
PCV C3 C1 N1 111.600 3.000
PCV HC1 C1 C2 108.340 3.000
PCV HC1 C1 N1 109.470 3.000
PCV C2 C1 N1 105.000 3.000
PCV C1 C2 H22 108.340 3.000
PCV C1 C2 O3 109.470 3.000
PCV C1 C2 C4 111.000 3.000
PCV H22 C2 O3 109.470 3.000
PCV H22 C2 C4 108.340 3.000
PCV O3 C2 C4 109.470 3.000
PCV C2 O3 HO3 109.470 3.000
PCV C2 C4 HC41 109.470 3.000
PCV C2 C4 HC42 109.470 3.000
PCV C2 C4 C5 111.000 3.000
PCV HC41 C4 HC42 107.900 3.000
PCV HC41 C4 C5 109.470 3.000
PCV HC42 C4 C5 109.470 3.000
PCV C4 C5 HC51 109.470 3.000
PCV C4 C5 HC52 109.470 3.000
PCV C4 C5 N2 109.470 3.000
PCV HC51 C5 HC52 107.900 3.000
PCV HC51 C5 N2 109.470 3.000
PCV HC52 C5 N2 109.470 3.000
PCV C5 N2 HN22 120.000 3.000
PCV C5 N2 HN21 120.000 3.000
PCV HN22 N2 HN21 120.000 3.000
PCV C1 N1 C7 112.000 3.000
PCV C1 N1 C8 121.000 3.000
PCV C7 N1 C8 127.000 3.000
PCV N1 C7 HC71 109.470 3.000
PCV N1 C7 HC72 109.470 3.000
PCV N1 C7 C9 105.000 3.000
PCV HC71 C7 HC72 107.900 3.000
PCV HC71 C7 C9 109.470 3.000
PCV HC72 C7 C9 109.470 3.000
PCV C7 C9 HC91 109.470 3.000
PCV C7 C9 HC92 109.470 3.000
PCV C7 C9 C8 109.470 3.000
PCV HC91 C9 HC92 107.900 3.000
PCV HC91 C9 C8 109.470 3.000
PCV HC92 C9 C8 109.470 3.000
PCV C9 C8 O1 120.500 3.000
PCV C9 C8 N1 116.500 3.000
PCV O1 C8 N1 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
PCV var_1 O4 C3 C1 N1 -179.971 20.000 3
PCV var_2 C3 C1 C2 C4 -174.996 20.000 3
PCV var_3 C1 C2 O3 HO3 -59.939 20.000 1
PCV var_4 C1 C2 C4 C5 -175.011 20.000 3
PCV var_5 C2 C4 C5 N2 179.997 20.000 3
PCV var_6 C4 C5 N2 HN21 66.181 20.000 1
PCV var_7 C3 C1 N1 C7 -119.936 20.000 3
PCV CONST_1 C1 N1 C8 C9 180.000 0.000 0
PCV var_8 C1 N1 C7 C9 179.962 20.000 1
PCV var_9 N1 C7 C9 C8 -0.236 20.000 3
PCV var_10 C7 C9 C8 O1 -179.932 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
PCV chir_01 C1 N1 C2 C3 negativ
PCV chir_02 C2 C1 C4 O3 negativ
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
PCV plan-1 N1 0.020
PCV plan-1 C8 0.020
PCV plan-1 C7 0.020
PCV plan-1 C1 0.020
PCV plan-2 C8 0.020
PCV plan-2 N1 0.020
PCV plan-2 O1 0.020
PCV plan-2 C9 0.020
PCV plan-3 N2 0.020
PCV plan-3 C5 0.020
PCV plan-3 HN21 0.020
PCV plan-3 HN22 0.020
PCV plan-4 C3 0.020
PCV plan-4 C1 0.020
PCV plan-4 O2 0.020
PCV plan-4 O4 0.020
# ------------------------------------------------------
|
