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
|
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
DEP DEP 'DIETHYL PHOSPHONATE ' non-polymer 19 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DEP
#
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
DEP O3 O O 0.000 0.000 0.000 0.000
DEP P P P 0.000 -0.619 0.052 1.373
DEP HP1 H H 0.000 -0.542 -1.184 1.991
DEP O2 O O2 0.000 0.075 1.200 2.293
DEP C3 C CH2 0.000 -0.572 1.579 3.495
DEP H31 H H 0.000 -0.661 0.712 4.153
DEP H32 H H 0.000 -1.567 1.968 3.270
DEP C4 C CH3 0.000 0.249 2.652 4.179
DEP H43 H H 0.000 1.213 2.274 4.397
DEP H42 H H 0.000 0.335 3.492 3.539
DEP H41 H H 0.000 -0.229 2.942 5.079
DEP O1 O O2 0.000 -2.160 0.573 1.320
DEP C1 C CH2 0.000 -3.136 -0.326 0.824
DEP H11 H H 0.000 -3.160 -1.223 1.445
DEP H12 H H 0.000 -2.893 -0.602 -0.204
DEP C2 C CH3 0.000 -4.490 0.350 0.859
DEP H23 H H 0.000 -4.726 0.617 1.856
DEP H22 H H 0.000 -4.466 1.220 0.256
DEP H21 H H 0.000 -5.226 -0.316 0.488
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
DEP O3 n/a P START
DEP P O3 O1 .
DEP HP1 P . .
DEP O2 P C3 .
DEP C3 O2 C4 .
DEP H31 C3 . .
DEP H32 C3 . .
DEP C4 C3 H41 .
DEP H43 C4 . .
DEP H42 C4 . .
DEP H41 C4 . .
DEP O1 P C1 .
DEP C1 O1 C2 .
DEP H11 C1 . .
DEP H12 C1 . .
DEP C2 C1 H21 .
DEP H23 C2 . .
DEP H22 C2 . .
DEP H21 C2 . END
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
DEP C2 C1 single 1.513 0.020
DEP C1 O1 single 1.426 0.020
DEP H11 C1 single 1.092 0.020
DEP H12 C1 single 1.092 0.020
DEP H21 C2 single 1.059 0.020
DEP H22 C2 single 1.059 0.020
DEP H23 C2 single 1.059 0.020
DEP C4 C3 single 1.513 0.020
DEP C3 O2 single 1.426 0.020
DEP H31 C3 single 1.092 0.020
DEP H32 C3 single 1.092 0.020
DEP H41 C4 single 1.059 0.020
DEP H42 C4 single 1.059 0.020
DEP H43 C4 single 1.059 0.020
DEP O1 P single 1.610 0.020
DEP O2 P single 1.610 0.020
DEP P O3 double 1.480 0.020
DEP HP1 P single 1.383 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
DEP O3 P HP1 109.500 3.000
DEP O3 P O2 109.500 3.000
DEP O3 P O1 109.500 3.000
DEP HP1 P O2 109.500 3.000
DEP HP1 P O1 109.500 3.000
DEP O2 P O1 102.600 3.000
DEP P O2 C3 120.500 3.000
DEP O2 C3 H31 109.470 3.000
DEP O2 C3 H32 109.470 3.000
DEP O2 C3 C4 109.470 3.000
DEP H31 C3 H32 107.900 3.000
DEP H31 C3 C4 109.470 3.000
DEP H32 C3 C4 109.470 3.000
DEP C3 C4 H43 109.470 3.000
DEP C3 C4 H42 109.470 3.000
DEP C3 C4 H41 109.470 3.000
DEP H43 C4 H42 109.470 3.000
DEP H43 C4 H41 109.470 3.000
DEP H42 C4 H41 109.470 3.000
DEP P O1 C1 120.500 3.000
DEP O1 C1 H11 109.470 3.000
DEP O1 C1 H12 109.470 3.000
DEP O1 C1 C2 109.470 3.000
DEP H11 C1 H12 107.900 3.000
DEP H11 C1 C2 109.470 3.000
DEP H12 C1 C2 109.470 3.000
DEP C1 C2 H23 109.470 3.000
DEP C1 C2 H22 109.470 3.000
DEP C1 C2 H21 109.470 3.000
DEP H23 C2 H22 109.470 3.000
DEP H23 C2 H21 109.470 3.000
DEP H22 C2 H21 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
DEP var_1 O3 P O2 C3 166.445 20.000 1
DEP var_2 P O2 C3 C4 179.994 20.000 1
DEP var_3 O2 C3 C4 H41 179.958 20.000 3
DEP var_4 O3 P O1 C1 73.911 20.000 1
DEP var_5 P O1 C1 C2 -179.973 20.000 1
DEP var_6 O1 C1 C2 H21 179.959 20.000 3
# ------------------------------------------------------
|
