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
|
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
POP POP 'PYROPHOSPHATE 2- ' non-polymer 9 9 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_POP
#
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
POP O6 O OP -0.666 0.000 0.000 0.000
POP P2 P P 0.000 -1.483 0.030 0.297
POP O4 O OP -0.666 -1.995 -1.386 0.447
POP O5 O OP -0.666 -1.724 0.792 1.581
POP O O O2 0.000 -2.258 0.757 -0.913
POP P1 P P 0.000 -1.654 0.157 -2.279
POP O1 O OP -0.666 -2.285 -1.189 -2.562
POP O2 O OP -0.666 -1.954 1.104 -3.421
POP O3 O OP -0.666 -0.157 -0.007 -2.139
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
POP O6 n/a P2 START
POP P2 O6 O .
POP O4 P2 . .
POP O5 P2 . .
POP O P2 P1 .
POP P1 O O3 .
POP O1 P1 . .
POP O2 P1 . .
POP O3 P1 . 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
POP O1 P1 deloc 1.510 0.020
POP O2 P1 deloc 1.510 0.020
POP O3 P1 deloc 1.510 0.020
POP P1 O single 1.610 0.020
POP O P2 single 1.610 0.020
POP O4 P2 deloc 1.510 0.020
POP O5 P2 deloc 1.510 0.020
POP P2 O6 deloc 1.510 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
POP O6 P2 O4 119.900 3.000
POP O6 P2 O5 119.900 3.000
POP O6 P2 O 108.200 3.000
POP O4 P2 O5 119.900 3.000
POP O4 P2 O 108.200 3.000
POP O5 P2 O 108.200 3.000
POP P2 O P1 120.500 3.000
POP O P1 O1 108.200 3.000
POP O P1 O2 108.200 3.000
POP O P1 O3 108.200 3.000
POP O1 P1 O2 119.900 3.000
POP O1 P1 O3 119.900 3.000
POP O2 P1 O3 119.900 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
POP var_1 O6 P2 O P1 45.049 20.000 1
POP var_2 P2 O P1 O3 -40.054 20.000 1
# ------------------------------------------------------
|
