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
|
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
PAV PAV '(2R,4S)-2-METHYL-2,3,3,4-TETRAHYDROX' non-polymer 20 10 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PAV
#
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
PAV O13 O OH1 0.000 0.000 0.000 0.000
PAV H13 H H 0.000 0.559 0.383 -0.689
PAV C8 C CT 0.000 -1.134 0.841 0.214
PAV O1 O OH1 0.000 -0.721 2.138 0.651
PAV HO1 H H 0.000 -0.170 2.546 -0.031
PAV C4 C CT 0.000 -2.094 0.210 1.239
PAV C11 C CH3 0.000 -2.254 1.138 2.445
PAV H113 H H 0.000 -1.311 1.288 2.903
PAV H112 H H 0.000 -2.643 2.070 2.125
PAV H111 H H 0.000 -2.919 0.699 3.143
PAV O3 O OH1 0.000 -1.585 -1.056 1.666
PAV HO3 H H 0.000 -2.194 -1.449 2.305
PAV C7 C CH1 0.000 -1.983 0.949 -1.079
PAV H7 H H 0.000 -2.409 1.957 -1.185
PAV O12 O OH1 0.000 -1.208 0.599 -2.228
PAV H12 H H 0.000 -1.778 0.583 -3.008
PAV C6 C CH2 0.000 -3.097 -0.098 -0.824
PAV H62 H H 0.000 -2.768 -1.116 -1.042
PAV H61 H H 0.000 -4.007 0.118 -1.388
PAV O5 O O2 0.000 -3.363 0.032 0.588
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
PAV O13 n/a C8 START
PAV H13 O13 . .
PAV C8 O13 C7 .
PAV O1 C8 HO1 .
PAV HO1 O1 . .
PAV C4 C8 O3 .
PAV C11 C4 H111 .
PAV H113 C11 . .
PAV H112 C11 . .
PAV H111 C11 . .
PAV O3 C4 HO3 .
PAV HO3 O3 . .
PAV C7 C8 C6 .
PAV H7 C7 . .
PAV O12 C7 H12 .
PAV H12 O12 . .
PAV C6 C7 O5 .
PAV H62 C6 . .
PAV H61 C6 . .
PAV O5 C6 . END
PAV C4 O5 . 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
PAV O3 C4 single 1.432 0.020
PAV HO3 O3 single 0.967 0.020
PAV C11 C4 single 1.524 0.020
PAV C4 O5 single 1.426 0.020
PAV C4 C8 single 1.524 0.020
PAV H111 C11 single 1.059 0.020
PAV H112 C11 single 1.059 0.020
PAV H113 C11 single 1.059 0.020
PAV O5 C6 single 1.426 0.020
PAV C6 C7 single 1.524 0.020
PAV H61 C6 single 1.092 0.020
PAV H62 C6 single 1.092 0.020
PAV O12 C7 single 1.432 0.020
PAV C7 C8 single 1.524 0.020
PAV H7 C7 single 1.099 0.020
PAV H12 O12 single 0.967 0.020
PAV O1 C8 single 1.432 0.020
PAV C8 O13 single 1.432 0.020
PAV HO1 O1 single 0.967 0.020
PAV H13 O13 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
PAV H13 O13 C8 109.470 3.000
PAV O13 C8 O1 109.470 3.000
PAV O13 C8 C4 109.470 3.000
PAV O13 C8 C7 109.470 3.000
PAV O1 C8 C4 109.470 3.000
PAV O1 C8 C7 109.470 3.000
PAV C4 C8 C7 111.000 3.000
PAV C8 O1 HO1 109.470 3.000
PAV C8 C4 C11 111.000 3.000
PAV C8 C4 O3 109.470 3.000
PAV C8 C4 O5 109.470 3.000
PAV C11 C4 O3 109.470 3.000
PAV C11 C4 O5 109.470 3.000
PAV O3 C4 O5 109.470 3.000
PAV C4 C11 H113 109.470 3.000
PAV C4 C11 H112 109.470 3.000
PAV C4 C11 H111 109.470 3.000
PAV H113 C11 H112 109.470 3.000
PAV H113 C11 H111 109.470 3.000
PAV H112 C11 H111 109.470 3.000
PAV C4 O3 HO3 109.470 3.000
PAV C8 C7 H7 108.340 3.000
PAV C8 C7 O12 109.470 3.000
PAV C8 C7 C6 111.000 3.000
PAV H7 C7 O12 109.470 3.000
PAV H7 C7 C6 108.340 3.000
PAV O12 C7 C6 109.470 3.000
PAV C7 O12 H12 109.470 3.000
PAV C7 C6 H62 109.470 3.000
PAV C7 C6 H61 109.470 3.000
PAV C7 C6 O5 109.470 3.000
PAV H62 C6 H61 107.900 3.000
PAV H62 C6 O5 109.470 3.000
PAV H61 C6 O5 109.470 3.000
PAV C6 O5 C4 111.800 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
PAV var_1 H13 O13 C8 C7 61.411 20.000 1
PAV var_2 O13 C8 O1 HO1 61.134 20.000 1
PAV var_3 O13 C8 C4 O3 0.000 20.000 1
PAV var_4 C8 C4 O5 C6 30.000 20.000 1
PAV var_5 C8 C4 C11 H111 179.730 20.000 1
PAV var_6 C8 C4 O3 HO3 -179.707 20.000 1
PAV var_7 O13 C8 C7 C6 90.000 20.000 1
PAV var_8 C8 C7 O12 H12 174.059 20.000 1
PAV var_9 C8 C7 C6 O5 30.000 20.000 3
PAV var_10 C7 C6 O5 C4 -30.000 20.000 1
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
PAV chir_01 C4 O3 C11 O5 positiv
PAV chir_02 C7 C6 O12 C8 positiv
PAV chir_03 C8 C4 C7 O1 negativ
# ------------------------------------------------------
|
