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
|
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
DOB DOB '2,4-DIHYDROXYBENZOIC ACID ' non-polymer 16 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DOB
#
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
DOB "O2'" O OC -0.500 0.000 0.000 0.000
DOB "C1'" C C 0.000 -1.180 0.010 0.415
DOB "O1'" O OC -0.500 -1.410 0.018 1.645
DOB C1 C CR6 0.000 -2.297 0.012 -0.543
DOB C6 C CR16 0.000 -2.042 0.004 -1.917
DOB H6 H H 0.000 -1.021 -0.004 -2.278
DOB C5 C CR16 0.000 -3.079 0.006 -2.806
DOB H5 H H 0.000 -2.877 -0.002 -3.870
DOB C4 C CR6 0.000 -4.395 0.018 -2.351
DOB O4 O OH1 0.000 -5.418 0.020 -3.242
DOB HO4 H H 0.000 -5.667 -0.891 -3.448
DOB C3 C CR16 0.000 -4.664 0.027 -0.991
DOB H3 H H 0.000 -5.689 0.041 -0.642
DOB C2 C CR6 0.000 -3.621 0.018 -0.079
DOB O2 O OH1 0.000 -3.879 0.027 1.251
DOB HO2 H H 0.000 -3.950 -0.883 1.570
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
DOB "O2'" n/a "C1'" START
DOB "C1'" "O2'" C1 .
DOB "O1'" "C1'" . .
DOB C1 "C1'" C6 .
DOB C6 C1 C5 .
DOB H6 C6 . .
DOB C5 C6 C4 .
DOB H5 C5 . .
DOB C4 C5 C3 .
DOB O4 C4 HO4 .
DOB HO4 O4 . .
DOB C3 C4 C2 .
DOB H3 C3 . .
DOB C2 C3 O2 .
DOB O2 C2 HO2 .
DOB HO2 O2 . END
DOB 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
DOB "O1'" "C1'" deloc 1.250 0.020
DOB "C1'" "O2'" deloc 1.250 0.020
DOB C1 "C1'" single 1.500 0.020
DOB C1 C2 single 1.487 0.020
DOB C6 C1 double 1.390 0.020
DOB C2 C3 double 1.390 0.020
DOB O2 C2 single 1.362 0.020
DOB C3 C4 single 1.390 0.020
DOB H3 C3 single 1.083 0.020
DOB C4 C5 double 1.390 0.020
DOB O4 C4 single 1.362 0.020
DOB C5 C6 single 1.390 0.020
DOB H5 C5 single 1.083 0.020
DOB H6 C6 single 1.083 0.020
DOB HO2 O2 single 0.967 0.020
DOB HO4 O4 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
DOB "O2'" "C1'" "O1'" 123.000 3.000
DOB "O2'" "C1'" C1 120.000 3.000
DOB "O1'" "C1'" C1 120.000 3.000
DOB "C1'" C1 C6 120.000 3.000
DOB "C1'" C1 C2 120.000 3.000
DOB C6 C1 C2 120.000 3.000
DOB C1 C6 H6 120.000 3.000
DOB C1 C6 C5 120.000 3.000
DOB H6 C6 C5 120.000 3.000
DOB C6 C5 H5 120.000 3.000
DOB C6 C5 C4 120.000 3.000
DOB H5 C5 C4 120.000 3.000
DOB C5 C4 O4 120.000 3.000
DOB C5 C4 C3 120.000 3.000
DOB O4 C4 C3 120.000 3.000
DOB C4 O4 HO4 109.470 3.000
DOB C4 C3 H3 120.000 3.000
DOB C4 C3 C2 120.000 3.000
DOB H3 C3 C2 120.000 3.000
DOB C3 C2 O2 120.000 3.000
DOB C3 C2 C1 120.000 3.000
DOB O2 C2 C1 120.000 3.000
DOB C2 O2 HO2 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
DOB var_1 "O2'" "C1'" C1 C6 -0.086 20.000 1
DOB CONST_1 "C1'" C1 C2 C3 180.000 0.000 0
DOB CONST_2 "C1'" C1 C6 C5 180.000 0.000 0
DOB CONST_3 C1 C6 C5 C4 0.000 0.000 0
DOB CONST_4 C6 C5 C4 C3 0.000 0.000 0
DOB var_2 C5 C4 O4 HO4 90.043 20.000 1
DOB CONST_5 C5 C4 C3 C2 0.000 0.000 0
DOB CONST_6 C4 C3 C2 O2 180.000 0.000 0
DOB var_3 C3 C2 O2 HO2 90.113 20.000 1
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
DOB plan-1 "C1'" 0.020
DOB plan-1 "O1'" 0.020
DOB plan-1 "O2'" 0.020
DOB plan-1 C1 0.020
DOB plan-2 C1 0.020
DOB plan-2 "C1'" 0.020
DOB plan-2 C2 0.020
DOB plan-2 C6 0.020
DOB plan-2 C3 0.020
DOB plan-2 C4 0.020
DOB plan-2 C5 0.020
DOB plan-2 O2 0.020
DOB plan-2 H3 0.020
DOB plan-2 O4 0.020
DOB plan-2 H5 0.020
DOB plan-2 H6 0.020
# ------------------------------------------------------
|
