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
|
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
SDF SDF '[(R)-(2,4-dichlorophenyl)(sulfanyl)m' non-polymer 21 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SDF
#
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
SDF O12 O O 0.000 0.000 0.000 0.000
SDF P1 P P 0.000 -1.088 -0.978 -0.227
SDF O11 O OH1 0.000 -0.668 -1.983 -1.412
SDF HO11 H H 0.000 0.124 -2.531 -1.323
SDF O13 O OH1 0.000 -1.345 -1.817 1.122
SDF HO13 H H 0.000 -1.977 -2.549 1.123
SDF C7 C CH1 0.000 -2.612 -0.093 -0.693
SDF H7 H H 0.000 -3.424 -0.817 -0.845
SDF S1 S SH1 0.000 -2.330 0.830 -2.229
SDF H61 H H 0.000 -1.346 1.710 -2.051
SDF C1 C CR6 0.000 -2.993 0.865 0.407
SDF C6 C CR16 0.000 -2.179 1.945 0.694
SDF H6 H H 0.000 -1.266 2.100 0.133
SDF C5 C CR16 0.000 -2.529 2.828 1.699
SDF H5 H H 0.000 -1.896 3.678 1.918
SDF C4 C CR6 0.000 -3.691 2.624 2.424
SDF CL2 CL CL 0.000 -4.128 3.729 3.690
SDF C3 C CR16 0.000 -4.501 1.540 2.141
SDF H3 H H 0.000 -5.409 1.380 2.709
SDF C2 C CR6 0.000 -4.153 0.661 1.132
SDF CL1 CL CL 0.000 -5.170 -0.700 0.775
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
SDF O12 n/a P1 START
SDF P1 O12 C7 .
SDF O11 P1 HO11 .
SDF HO11 O11 . .
SDF O13 P1 HO13 .
SDF HO13 O13 . .
SDF C7 P1 C1 .
SDF H7 C7 . .
SDF S1 C7 H61 .
SDF H61 S1 . .
SDF C1 C7 C6 .
SDF C6 C1 C5 .
SDF H6 C6 . .
SDF C5 C6 C4 .
SDF H5 C5 . .
SDF C4 C5 C3 .
SDF CL2 C4 . .
SDF C3 C4 C2 .
SDF H3 C3 . .
SDF C2 C3 CL1 .
SDF CL1 C2 . END
SDF 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
SDF C1 C7 single 1.480 0.020
SDF C6 C1 single 1.390 0.020
SDF O11 P1 single 1.610 0.020
SDF O13 P1 single 1.610 0.020
SDF S1 C7 single 1.790 0.020
SDF CL1 C2 single 1.795 0.020
SDF C1 C2 double 1.487 0.020
SDF CL2 C4 single 1.795 0.020
SDF C2 C3 single 1.390 0.020
SDF C3 C4 double 1.390 0.020
SDF H3 C3 single 1.083 0.020
SDF C4 C5 single 1.390 0.020
SDF C5 C6 double 1.390 0.020
SDF H5 C5 single 1.083 0.020
SDF H6 C6 single 1.083 0.020
SDF C7 P1 single 1.815 0.020
SDF HO11 O11 single 0.967 0.020
SDF P1 O12 double 1.480 0.020
SDF HO13 O13 single 0.967 0.020
SDF H61 S1 single 1.330 0.020
SDF H7 C7 single 1.099 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
SDF O12 P1 O11 109.500 3.000
SDF O12 P1 O13 109.500 3.000
SDF O12 P1 C7 109.500 3.000
SDF O11 P1 O13 109.500 3.000
SDF O11 P1 C7 109.500 3.000
SDF O13 P1 C7 109.500 3.000
SDF P1 O11 HO11 120.000 3.000
SDF P1 O13 HO13 120.000 3.000
SDF P1 C7 H7 109.500 3.000
SDF P1 C7 S1 109.500 3.000
SDF P1 C7 C1 109.500 3.000
SDF H7 C7 S1 109.500 3.000
SDF H7 C7 C1 109.470 3.000
SDF S1 C7 C1 109.500 3.000
SDF C7 S1 H61 109.500 3.000
SDF C7 C1 C6 120.000 3.000
SDF C7 C1 C2 120.000 3.000
SDF C6 C1 C2 120.000 3.000
SDF C1 C6 H6 120.000 3.000
SDF C1 C6 C5 120.000 3.000
SDF H6 C6 C5 120.000 3.000
SDF C6 C5 H5 120.000 3.000
SDF C6 C5 C4 120.000 3.000
SDF H5 C5 C4 120.000 3.000
SDF C5 C4 CL2 120.000 3.000
SDF C5 C4 C3 120.000 3.000
SDF CL2 C4 C3 120.000 3.000
SDF C4 C3 H3 120.000 3.000
SDF C4 C3 C2 120.000 3.000
SDF H3 C3 C2 120.000 3.000
SDF C3 C2 CL1 120.000 3.000
SDF C3 C2 C1 120.000 3.000
SDF CL1 C2 C1 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
SDF var_1 O12 P1 O11 HO11 60.005 20.000 1
SDF var_2 O12 P1 O13 HO13 -175.039 20.000 1
SDF var_3 O12 P1 C7 C1 -59.074 20.000 1
SDF var_4 P1 C7 S1 H61 -60.012 20.000 1
SDF var_5 P1 C7 C1 C6 65.955 20.000 1
SDF CONST_1 C7 C1 C2 C3 180.000 0.000 0
SDF CONST_2 C7 C1 C6 C5 180.000 0.000 0
SDF CONST_3 C1 C6 C5 C4 0.000 0.000 0
SDF CONST_4 C6 C5 C4 C3 0.000 0.000 0
SDF CONST_5 C5 C4 C3 C2 0.000 0.000 0
SDF CONST_6 C4 C3 C2 CL1 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
SDF chir_01 C7 C1 P1 S1 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
SDF plan-1 C1 0.020
SDF plan-1 C2 0.020
SDF plan-1 C6 0.020
SDF plan-1 C7 0.020
SDF plan-1 C3 0.020
SDF plan-1 C4 0.020
SDF plan-1 C5 0.020
SDF plan-1 CL1 0.020
SDF plan-1 H3 0.020
SDF plan-1 CL2 0.020
SDF plan-1 H5 0.020
SDF plan-1 H6 0.020
# ------------------------------------------------------
|
