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
|
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
DDZ DDZ '3,3-DIHYDROXY L-ALANINE ' peptide 14 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DDZ
#
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
DDZ N N NH2 0.000 0.000 0.000 0.000
DDZ HN1 H H 0.000 0.769 -0.338 -0.568
DDZ HN2 H H 0.000 0.102 0.872 0.506
DDZ CA C CH1 0.000 -1.250 -0.767 0.088
DDZ HA H H 0.000 -1.389 -1.124 1.119
DDZ CB C CH1 0.000 -2.427 0.130 -0.303
DDZ HB H H 0.000 -2.335 0.414 -1.360
DDZ OG2 O OH1 0.000 -2.421 1.305 0.508
DDZ HG2 H H 0.000 -3.164 1.872 0.260
DDZ OG1 O OH1 0.000 -3.651 -0.579 -0.106
DDZ HG1 H H 0.000 -3.732 -0.828 0.825
DDZ C C C 0.000 -1.184 -1.946 -0.847
DDZ O O OC -0.500 -0.368 -1.948 -1.795
DDZ OXT O OC -0.500 -1.945 -2.924 -0.676
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
DDZ N n/a CA START
DDZ HN1 N . .
DDZ HN2 N . .
DDZ CA N C .
DDZ HA CA . .
DDZ CB CA OG1 .
DDZ HB CB . .
DDZ OG2 CB HG2 .
DDZ HG2 OG2 . .
DDZ OG1 CB HG1 .
DDZ HG1 OG1 . .
DDZ C CA . END
DDZ O C . .
DDZ OXT C . .
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
DDZ CA N single 1.450 0.020
DDZ C CA single 1.500 0.020
DDZ CB CA single 1.524 0.020
DDZ O C deloc 1.250 0.020
DDZ OXT C deloc 1.250 0.020
DDZ OG1 CB single 1.432 0.020
DDZ OG2 CB single 1.432 0.020
DDZ HA CA single 1.099 0.020
DDZ HB CB single 1.099 0.020
DDZ HG1 OG1 single 0.967 0.020
DDZ HG2 OG2 single 0.967 0.020
DDZ HN1 N single 1.010 0.020
DDZ HN2 N single 1.010 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
DDZ HN1 N HN2 120.000 3.000
DDZ HN1 N CA 120.000 3.000
DDZ HN2 N CA 120.000 3.000
DDZ N CA HA 109.470 3.000
DDZ N CA CB 109.470 3.000
DDZ N CA C 109.470 3.000
DDZ HA CA CB 108.340 3.000
DDZ HA CA C 108.810 3.000
DDZ CB CA C 109.470 3.000
DDZ CA CB HB 108.340 3.000
DDZ CA CB OG2 109.470 3.000
DDZ CA CB OG1 109.470 3.000
DDZ HB CB OG2 109.470 3.000
DDZ HB CB OG1 109.470 3.000
DDZ OG2 CB OG1 109.500 3.000
DDZ CB OG2 HG2 109.470 3.000
DDZ CB OG1 HG1 109.470 3.000
DDZ CA C O 118.500 3.000
DDZ CA C OXT 118.500 3.000
DDZ O C 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
DDZ var_1 HN2 N CA C 175.000 20.000 1
DDZ var_2 N CA CB OG1 -175.008 20.000 3
DDZ var_3 CA CB OG2 HG2 179.934 20.000 1
DDZ var_4 CA CB OG1 HG1 60.102 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
DDZ chir_01 CA N C CB positiv
DDZ chir_02 CB CA OG1 OG2 negativ
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
DDZ plan-1 N 0.020
DDZ plan-1 CA 0.020
DDZ plan-1 HN1 0.020
DDZ plan-1 HN2 0.020
DDZ plan-2 C 0.020
DDZ plan-2 CA 0.020
DDZ plan-2 O 0.020
DDZ plan-2 OXT 0.020
# ------------------------------------------------------
|
