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
|
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
STH STH '2-AMINO-4H-1,3-BENZOXATHIIN-4-OL ' non-polymer 21 12 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_STH
#
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
STH O8 O OH1 0.000 0.000 0.000 0.000
STH HO8 H H 0.000 0.854 0.031 -0.452
STH C8 C CH1 0.000 -1.035 -0.243 -0.955
STH H8 H H 0.000 -0.850 -1.202 -1.460
STH S7 S S2 0.000 -1.053 1.094 -2.183
STH C7 C CH1 0.000 -1.911 2.339 -1.169
STH H7 H H 0.000 -1.390 2.458 -0.209
STH N7 N NH2 0.000 -1.939 3.624 -1.881
STH HN72 H H 0.000 -1.509 3.713 -2.794
STH HN71 H H 0.000 -2.389 4.430 -1.463
STH O2 O O2 0.000 -3.233 1.890 -0.943
STH C2 C CR6 0.000 -3.300 0.722 -0.269
STH C3 C CR16 0.000 -4.477 0.565 0.482
STH H3 H H 0.000 -5.212 1.361 0.489
STH C4 C CR16 0.000 -4.715 -0.577 1.207
STH H4 H H 0.000 -5.629 -0.675 1.780
STH C5 C CR16 0.000 -3.785 -1.600 1.203
STH H5 H H 0.000 -3.968 -2.508 1.765
STH C6 C CR16 0.000 -2.624 -1.454 0.476
STH H6 H H 0.000 -1.894 -2.254 0.470
STH C1 C CR6 0.000 -2.372 -0.293 -0.250
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
STH O8 n/a C8 START
STH HO8 O8 . .
STH C8 O8 S7 .
STH H8 C8 . .
STH S7 C8 C7 .
STH C7 S7 O2 .
STH H7 C7 . .
STH N7 C7 HN71 .
STH HN72 N7 . .
STH HN71 N7 . .
STH O2 C7 C2 .
STH C2 O2 C3 .
STH C3 C2 C4 .
STH H3 C3 . .
STH C4 C3 C5 .
STH H4 C4 . .
STH C5 C4 C6 .
STH H5 C5 . .
STH C6 C5 C1 .
STH H6 C6 . .
STH C1 C6 . END
STH C8 C1 . ADD
STH 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
STH C8 O8 single 1.432 0.020
STH C8 C1 single 1.480 0.020
STH S7 C8 single 1.765 0.020
STH H8 C8 single 1.099 0.020
STH HO8 O8 single 0.967 0.020
STH C1 C2 double 1.487 0.020
STH C1 C6 single 1.390 0.020
STH C3 C2 single 1.390 0.020
STH C2 O2 single 1.370 0.020
STH C4 C3 double 1.390 0.020
STH H3 C3 single 1.083 0.020
STH C5 C4 single 1.390 0.020
STH H4 C4 single 1.083 0.020
STH C6 C5 double 1.390 0.020
STH H5 C5 single 1.083 0.020
STH H6 C6 single 1.083 0.020
STH O2 C7 single 1.426 0.020
STH N7 C7 single 1.450 0.020
STH C7 S7 single 1.765 0.020
STH H7 C7 single 1.099 0.020
STH HN71 N7 single 1.010 0.020
STH HN72 N7 single 1.010 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
STH HO8 O8 C8 109.470 3.000
STH O8 C8 H8 109.470 3.000
STH O8 C8 S7 109.500 3.000
STH O8 C8 C1 109.470 3.000
STH H8 C8 S7 109.500 3.000
STH H8 C8 C1 109.470 3.000
STH S7 C8 C1 109.500 3.000
STH C8 S7 C7 97.573 3.000
STH S7 C7 H7 109.500 3.000
STH S7 C7 N7 109.500 3.000
STH S7 C7 O2 109.500 3.000
STH H7 C7 N7 109.470 3.000
STH H7 C7 O2 109.470 3.000
STH N7 C7 O2 109.500 3.000
STH C7 N7 HN72 120.000 3.000
STH C7 N7 HN71 120.000 3.000
STH HN72 N7 HN71 120.000 3.000
STH C7 O2 C2 120.000 3.000
STH O2 C2 C3 120.000 3.000
STH O2 C2 C1 120.000 3.000
STH C3 C2 C1 120.000 3.000
STH C2 C3 H3 120.000 3.000
STH C2 C3 C4 120.000 3.000
STH H3 C3 C4 120.000 3.000
STH C3 C4 H4 120.000 3.000
STH C3 C4 C5 120.000 3.000
STH H4 C4 C5 120.000 3.000
STH C4 C5 H5 120.000 3.000
STH C4 C5 C6 120.000 3.000
STH H5 C5 C6 120.000 3.000
STH C5 C6 H6 120.000 3.000
STH C5 C6 C1 120.000 3.000
STH H6 C6 C1 120.000 3.000
STH C6 C1 C8 120.000 3.000
STH C6 C1 C2 120.000 3.000
STH C8 C1 C2 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
STH var_1 HO8 O8 C8 S7 -60.167 20.000 1
STH var_2 O8 C8 C1 C6 -90.000 20.000 1
STH var_3 O8 C8 S7 C7 -90.000 20.000 1
STH var_4 C8 S7 C7 O2 -60.000 20.000 1
STH var_5 S7 C7 N7 HN71 179.359 20.000 1
STH var_6 S7 C7 O2 C2 60.000 20.000 1
STH var_7 C7 O2 C2 C3 150.000 20.000 1
STH CONST_1 O2 C2 C3 C4 180.000 0.000 0
STH CONST_2 C2 C3 C4 C5 0.000 0.000 0
STH CONST_3 C3 C4 C5 C6 0.000 0.000 0
STH CONST_4 C4 C5 C6 C1 0.000 0.000 0
STH CONST_5 C5 C6 C1 C8 180.000 0.000 0
STH CONST_6 C6 C1 C2 O2 180.000 0.000 0
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
STH chir_01 C8 O8 C1 S7 negativ
STH chir_02 C7 O2 N7 S7 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
STH plan-1 C1 0.020
STH plan-1 C8 0.020
STH plan-1 C2 0.020
STH plan-1 C6 0.020
STH plan-1 C3 0.020
STH plan-1 C4 0.020
STH plan-1 C5 0.020
STH plan-1 O2 0.020
STH plan-1 H3 0.020
STH plan-1 H4 0.020
STH plan-1 H5 0.020
STH plan-1 H6 0.020
STH plan-2 N7 0.020
STH plan-2 C7 0.020
STH plan-2 HN71 0.020
STH plan-2 HN72 0.020
# ------------------------------------------------------
|
