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
|
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
JCL JCL '4-(6-CHLORO-2,4-DIOXO-1,2,3,4-TETRAH' non-polymer 28 18 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_JCL
#
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
JCL O3P O OP -0.666 0.000 0.000 0.000
JCL P P P 0.000 -0.207 -0.863 -1.225
JCL O1P O OP -0.666 0.953 -0.674 -2.177
JCL O2P O OP -0.666 -0.289 -2.316 -0.810
JCL O27 O O2 0.000 -1.577 -0.436 -1.957
JCL C10 C CH2 0.000 -2.613 -0.522 -0.976
JCL H101 H H 0.000 -2.388 0.154 -0.149
JCL H102 H H 0.000 -2.676 -1.546 -0.601
JCL C9 C CH2 0.000 -3.949 -0.127 -1.610
JCL H9C1 H H 0.000 -4.172 -0.803 -2.438
JCL H9C2 H H 0.000 -3.885 0.897 -1.985
JCL C8 C CH2 0.000 -5.058 -0.220 -0.560
JCL H8C1 H H 0.000 -4.833 0.456 0.267
JCL H8C2 H H 0.000 -5.120 -1.244 -0.186
JCL C7 C CH2 0.000 -6.394 0.175 -1.195
JCL H7C1 H H 0.000 -6.617 -0.501 -2.023
JCL H7C2 H H 0.000 -6.330 1.199 -1.569
JCL C5 C CR6 0.000 -7.487 0.084 -0.161
JCL C4 C CR6 0.000 -8.135 -1.147 0.089
JCL O2 O O 0.000 -7.812 -2.147 -0.526
JCL N3 N NR16 0.000 -9.106 -1.205 1.022
JCL H3 H H 0.000 -9.582 -2.109 1.217
JCL C6 C CR6 0.000 -7.864 1.181 0.536
JCL CL CL CL 0.000 -7.092 2.708 0.246
JCL N1 N NR16 0.000 -8.860 1.079 1.471
JCL H1 H H 0.000 -9.151 1.921 2.008
JCL C2 C CR6 0.000 -9.463 -0.101 1.702
JCL O1 O O 0.000 -10.346 -0.170 2.536
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
JCL O3P n/a P START
JCL P O3P O27 .
JCL O1P P . .
JCL O2P P . .
JCL O27 P C10 .
JCL C10 O27 C9 .
JCL H101 C10 . .
JCL H102 C10 . .
JCL C9 C10 C8 .
JCL H9C1 C9 . .
JCL H9C2 C9 . .
JCL C8 C9 C7 .
JCL H8C1 C8 . .
JCL H8C2 C8 . .
JCL C7 C8 C5 .
JCL H7C1 C7 . .
JCL H7C2 C7 . .
JCL C5 C7 C6 .
JCL C4 C5 N3 .
JCL O2 C4 . .
JCL N3 C4 H3 .
JCL H3 N3 . .
JCL C6 C5 N1 .
JCL CL C6 . .
JCL N1 C6 C2 .
JCL H1 N1 . .
JCL C2 N1 O1 .
JCL O1 C2 . END
JCL N3 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
JCL N3 C2 single 1.337 0.020
JCL N3 C4 single 1.337 0.020
JCL H3 N3 single 1.040 0.020
JCL N1 C6 single 1.337 0.020
JCL C2 N1 single 1.337 0.020
JCL H1 N1 single 1.040 0.020
JCL CL C6 single 1.795 0.020
JCL C6 C5 double 1.487 0.020
JCL C5 C7 single 1.511 0.020
JCL C4 C5 single 1.487 0.020
JCL C7 C8 single 1.524 0.020
JCL H7C1 C7 single 1.092 0.020
JCL H7C2 C7 single 1.092 0.020
JCL O1 C2 double 1.250 0.020
JCL O2 C4 double 1.250 0.020
JCL C8 C9 single 1.524 0.020
JCL H8C1 C8 single 1.092 0.020
JCL H8C2 C8 single 1.092 0.020
JCL C9 C10 single 1.524 0.020
JCL H9C1 C9 single 1.092 0.020
JCL H9C2 C9 single 1.092 0.020
JCL C10 O27 single 1.426 0.020
JCL H101 C10 single 1.092 0.020
JCL H102 C10 single 1.092 0.020
JCL O27 P single 1.610 0.020
JCL O1P P deloc 1.510 0.020
JCL O2P P deloc 1.510 0.020
JCL P O3P deloc 1.510 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
JCL O3P P O1P 119.900 3.000
JCL O3P P O2P 119.900 3.000
JCL O3P P O27 108.200 3.000
JCL O1P P O2P 119.900 3.000
JCL O1P P O27 108.200 3.000
JCL O2P P O27 108.200 3.000
JCL P O27 C10 120.500 3.000
JCL O27 C10 H101 109.470 3.000
JCL O27 C10 H102 109.470 3.000
JCL O27 C10 C9 109.470 3.000
JCL H101 C10 H102 107.900 3.000
JCL H101 C10 C9 109.470 3.000
JCL H102 C10 C9 109.470 3.000
JCL C10 C9 H9C1 109.470 3.000
JCL C10 C9 H9C2 109.470 3.000
JCL C10 C9 C8 111.000 3.000
JCL H9C1 C9 H9C2 107.900 3.000
JCL H9C1 C9 C8 109.470 3.000
JCL H9C2 C9 C8 109.470 3.000
JCL C9 C8 H8C1 109.470 3.000
JCL C9 C8 H8C2 109.470 3.000
JCL C9 C8 C7 111.000 3.000
JCL H8C1 C8 H8C2 107.900 3.000
JCL H8C1 C8 C7 109.470 3.000
JCL H8C2 C8 C7 109.470 3.000
JCL C8 C7 H7C1 109.470 3.000
JCL C8 C7 H7C2 109.470 3.000
JCL C8 C7 C5 109.470 3.000
JCL H7C1 C7 H7C2 107.900 3.000
JCL H7C1 C7 C5 109.470 3.000
JCL H7C2 C7 C5 109.470 3.000
JCL C7 C5 C4 120.000 3.000
JCL C7 C5 C6 120.000 3.000
JCL C4 C5 C6 120.000 3.000
JCL C5 C4 O2 120.000 3.000
JCL C5 C4 N3 120.000 3.000
JCL O2 C4 N3 120.000 3.000
JCL C4 N3 H3 120.000 3.000
JCL C4 N3 C2 120.000 3.000
JCL H3 N3 C2 120.000 3.000
JCL C5 C6 CL 120.000 3.000
JCL C5 C6 N1 120.000 3.000
JCL CL C6 N1 120.000 3.000
JCL C6 N1 H1 120.000 3.000
JCL C6 N1 C2 120.000 3.000
JCL H1 N1 C2 120.000 3.000
JCL N1 C2 O1 120.000 3.000
JCL N1 C2 N3 120.000 3.000
JCL O1 C2 N3 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
JCL var_1 O3P P O27 C10 -54.933 20.000 1
JCL var_2 P O27 C10 C9 -179.990 20.000 1
JCL var_3 O27 C10 C9 C8 179.959 20.000 3
JCL var_4 C10 C9 C8 C7 180.000 20.000 3
JCL var_5 C9 C8 C7 C5 -179.987 20.000 3
JCL var_6 C8 C7 C5 C6 95.006 20.000 2
JCL CONST_1 C7 C5 C4 N3 180.000 0.000 0
JCL CONST_2 C5 C4 N3 C2 0.000 0.000 0
JCL CONST_3 C4 N3 C2 N1 0.000 0.000 0
JCL CONST_4 C7 C5 C6 N1 180.000 0.000 0
JCL CONST_5 C5 C6 N1 C2 0.000 0.000 0
JCL CONST_6 C6 N1 C2 O1 180.000 0.000 0
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
JCL plan-1 N3 0.020
JCL plan-1 C2 0.020
JCL plan-1 C4 0.020
JCL plan-1 H3 0.020
JCL plan-1 N1 0.020
JCL plan-1 C6 0.020
JCL plan-1 C5 0.020
JCL plan-1 H1 0.020
JCL plan-1 CL 0.020
JCL plan-1 C7 0.020
JCL plan-1 O1 0.020
JCL plan-1 O2 0.020
# ------------------------------------------------------
|
