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
|
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
DXX DXX 'METHYLMALONIC ACID ' non-polymer 12 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DXX
#
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
DXX O2 O OC -0.500 0.000 0.000 0.000
DXX C C C 0.000 -1.246 -0.034 -0.111
DXX O O OC -0.500 -1.953 -0.332 0.877
DXX CA C CH1 0.000 -1.894 0.284 -1.433
DXX HA H H 0.000 -1.629 1.307 -1.734
DXX CB C CH3 0.000 -1.402 -0.703 -2.492
DXX HB3 H H 0.000 -1.857 -0.481 -3.423
DXX HB2 H H 0.000 -0.350 -0.625 -2.588
DXX HB1 H H 0.000 -1.657 -1.690 -2.203
DXX C1 C C 0.000 -3.390 0.171 -1.299
DXX O1 O OC -0.500 -4.126 0.395 -2.285
DXX OXT O OC -0.500 -3.897 -0.145 -0.200
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
DXX O2 n/a C START
DXX C O2 CA .
DXX O C . .
DXX CA C C1 .
DXX HA CA . .
DXX CB CA HB1 .
DXX HB3 CB . .
DXX HB2 CB . .
DXX HB1 CB . .
DXX C1 CA OXT .
DXX O1 C1 . .
DXX OXT C1 . 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
DXX O1 C1 deloc 1.250 0.020
DXX OXT C1 deloc 1.250 0.020
DXX C1 CA single 1.500 0.020
DXX CB CA single 1.524 0.020
DXX CA C single 1.500 0.020
DXX HA CA single 1.099 0.020
DXX HB1 CB single 1.059 0.020
DXX HB2 CB single 1.059 0.020
DXX HB3 CB single 1.059 0.020
DXX O C deloc 1.250 0.020
DXX C O2 deloc 1.250 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
DXX O2 C O 123.000 3.000
DXX O2 C CA 118.500 3.000
DXX O C CA 118.500 3.000
DXX C CA HA 108.810 3.000
DXX C CA CB 109.470 3.000
DXX C CA C1 111.000 3.000
DXX HA CA CB 108.340 3.000
DXX HA CA C1 108.810 3.000
DXX CB CA C1 109.470 3.000
DXX CA CB HB3 109.470 3.000
DXX CA CB HB2 109.470 3.000
DXX CA CB HB1 109.470 3.000
DXX HB3 CB HB2 109.470 3.000
DXX HB3 CB HB1 109.470 3.000
DXX HB2 CB HB1 109.470 3.000
DXX CA C1 O1 118.500 3.000
DXX CA C1 OXT 118.500 3.000
DXX O1 C1 OXT 123.000 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
DXX var_1 O2 C CA C1 179.976 20.000 3
DXX var_2 C CA CB HB1 60.000 20.000 3
DXX var_3 C CA C1 OXT 0.112 20.000 3
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
DXX chir_01 CA C1 CB C 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
DXX plan-1 C1 0.020
DXX plan-1 O1 0.020
DXX plan-1 OXT 0.020
DXX plan-1 CA 0.020
DXX plan-2 C 0.020
DXX plan-2 CA 0.020
DXX plan-2 O 0.020
DXX plan-2 O2 0.020
# ------------------------------------------------------
|
