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
|
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
DX4 DX4 '2-amino-1,9-dihydro-6H-purine-6-thio' non-polymer 16 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DX4
#
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
DX4 S6 S S1 0.000 0.000 0.000 0.000
DX4 C6 C CR6 0.000 -1.496 0.832 -0.002
DX4 N1 N NR16 0.000 -1.538 2.182 -0.001
DX4 H5 H H 0.000 -0.651 2.726 0.001
DX4 C2 C CR6 0.000 -2.734 2.835 -0.002
DX4 N2 N NH2 0.000 -2.745 4.207 -0.002
DX4 HN2A H H 0.000 -3.623 4.711 -0.003
DX4 HN2 H H 0.000 -1.874 4.725 -0.002
DX4 N3 N NRD6 0.000 -3.878 2.187 -0.002
DX4 C4 C CR56 0.000 -3.915 0.850 -0.002
DX4 N9 N NR15 0.000 -4.923 -0.077 0.002
DX4 HN9 H H 0.000 -5.943 0.123 0.002
DX4 C8 C CR15 0.000 -4.343 -1.313 0.005
DX4 H8 H H 0.000 -4.881 -2.253 0.013
DX4 N7 N NRD5 0.000 -3.048 -1.193 -0.002
DX4 C5 C CR56 0.000 -2.719 0.122 -0.002
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
DX4 S6 n/a C6 START
DX4 C6 S6 N1 .
DX4 N1 C6 C2 .
DX4 H5 N1 . .
DX4 C2 N1 N3 .
DX4 N2 C2 HN2 .
DX4 HN2A N2 . .
DX4 HN2 N2 . .
DX4 N3 C2 C4 .
DX4 C4 N3 N9 .
DX4 N9 C4 C8 .
DX4 HN9 N9 . .
DX4 C8 N9 N7 .
DX4 H8 C8 . .
DX4 N7 C8 C5 .
DX4 C5 N7 . END
DX4 C4 C5 . ADD
DX4 C5 C6 . 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
DX4 C4 C5 double 1.490 0.020
DX4 C4 N3 single 1.355 0.020
DX4 N9 C4 single 1.340 0.020
DX4 C5 C6 single 1.490 0.020
DX4 C5 N7 single 1.350 0.020
DX4 N1 C6 single 1.337 0.020
DX4 C6 S6 double 1.595 0.020
DX4 C8 N9 single 1.350 0.020
DX4 N7 C8 double 1.350 0.020
DX4 H8 C8 single 1.083 0.020
DX4 C2 N1 single 1.337 0.020
DX4 H5 N1 single 1.040 0.020
DX4 N2 C2 single 1.355 0.020
DX4 HN2 N2 single 1.010 0.020
DX4 HN2A N2 single 1.010 0.020
DX4 N3 C2 double 1.350 0.020
DX4 HN9 N9 single 1.040 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
DX4 S6 C6 N1 120.000 3.000
DX4 S6 C6 C5 120.000 3.000
DX4 N1 C6 C5 120.000 3.000
DX4 C6 N1 H5 120.000 3.000
DX4 C6 N1 C2 120.000 3.000
DX4 H5 N1 C2 120.000 3.000
DX4 N1 C2 N2 120.000 3.000
DX4 N1 C2 N3 120.000 3.000
DX4 N2 C2 N3 120.000 3.000
DX4 C2 N2 HN2A 120.000 3.000
DX4 C2 N2 HN2 120.000 3.000
DX4 HN2A N2 HN2 120.000 3.000
DX4 C2 N3 C4 120.000 3.000
DX4 N3 C4 N9 132.000 3.000
DX4 N3 C4 C5 120.000 3.000
DX4 N9 C4 C5 108.000 3.000
DX4 C4 N9 HN9 126.000 3.000
DX4 C4 N9 C8 108.000 3.000
DX4 HN9 N9 C8 126.000 3.000
DX4 N9 C8 H8 126.000 3.000
DX4 N9 C8 N7 108.000 3.000
DX4 H8 C8 N7 126.000 3.000
DX4 C8 N7 C5 108.000 3.000
DX4 N7 C5 C4 108.000 3.000
DX4 N7 C5 C6 132.000 3.000
DX4 C4 C5 C6 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
DX4 CONST_1 S6 C6 N1 C2 180.000 0.000 0
DX4 CONST_2 C6 N1 C2 N3 0.000 0.000 0
DX4 CONST_3 N1 C2 N2 HN2 0.027 0.000 0
DX4 CONST_4 N1 C2 N3 C4 0.000 0.000 0
DX4 CONST_5 C2 N3 C4 N9 180.000 0.000 0
DX4 CONST_6 N3 C4 C5 N7 180.000 0.000 0
DX4 CONST_7 N3 C4 N9 C8 180.000 0.000 0
DX4 CONST_8 C4 N9 C8 N7 0.000 0.000 0
DX4 CONST_9 N9 C8 N7 C5 0.000 0.000 0
DX4 CONST_10 C8 N7 C5 C4 0.000 0.000 0
DX4 CONST_11 N7 C5 C6 S6 0.000 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
DX4 plan-1 C4 0.020
DX4 plan-1 C5 0.020
DX4 plan-1 N3 0.020
DX4 plan-1 N9 0.020
DX4 plan-1 C8 0.020
DX4 plan-1 N7 0.020
DX4 plan-1 C6 0.020
DX4 plan-1 N1 0.020
DX4 plan-1 S6 0.020
DX4 plan-1 C2 0.020
DX4 plan-1 H8 0.020
DX4 plan-1 H5 0.020
DX4 plan-1 N2 0.020
DX4 plan-1 HN9 0.020
DX4 plan-1 HN2A 0.020
DX4 plan-1 HN2 0.020
DX4 plan-2 N2 0.020
DX4 plan-2 C2 0.020
DX4 plan-2 HN2 0.020
DX4 plan-2 HN2A 0.020
# ------------------------------------------------------
|
