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
|
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
MA MA 'METHYL L-ALANINATE ' non-polymer 16 7 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MA
#
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
MA O O O -0.500 0.000 0.000 0.000
MA C C C 0.000 -1.073 -0.294 -0.571
MA OXT O O2 -0.500 -2.165 0.057 -0.071
MA CH3 C CH3 0.000 -2.189 0.830 1.210
MA HH3B H H 0.000 -1.675 1.756 1.093
MA HH3A H H 0.000 -3.193 1.034 1.500
MA HH3 H H 0.000 -1.717 0.275 1.986
MA CA C CH1 0.000 -1.052 -1.073 -1.861
MA HA H H 0.000 -1.813 -0.671 -2.544
MA CB C CH3 0.000 -1.352 -2.546 -1.573
MA HBB H H 0.000 -2.308 -2.631 -1.125
MA HBA H H 0.000 -1.337 -3.094 -2.480
MA HB H H 0.000 -0.619 -2.934 -0.915
MA N N NH2 0.000 0.274 -0.955 -2.482
MA HNA H H 0.000 0.859 -1.774 -2.599
MA HN H H 0.000 0.613 -0.054 -2.796
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
MA O n/a C START
MA C O CA .
MA OXT C CH3 .
MA CH3 OXT HH3 .
MA HH3B CH3 . .
MA HH3A CH3 . .
MA HH3 CH3 . .
MA CA C N .
MA HA CA . .
MA CB CA HB .
MA HBB CB . .
MA HBA CB . .
MA HB CB . .
MA N CA HN .
MA HNA N . .
MA HN N . 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
MA N CA single 1.450 0.020
MA CA C single 1.500 0.020
MA CB CA single 1.524 0.020
MA C O deloc 1.220 0.020
MA OXT C deloc 1.454 0.020
MA CH3 OXT single 1.426 0.020
MA HN N single 1.010 0.020
MA HNA N single 1.010 0.020
MA HA CA single 1.099 0.020
MA HB CB single 1.059 0.020
MA HBA CB single 1.059 0.020
MA HBB CB single 1.059 0.020
MA HH3 CH3 single 1.059 0.020
MA HH3A CH3 single 1.059 0.020
MA HH3B CH3 single 1.059 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
MA O C OXT 119.000 3.000
MA O C CA 120.500 3.000
MA OXT C CA 120.000 3.000
MA C OXT CH3 120.000 3.000
MA OXT CH3 HH3B 109.470 3.000
MA OXT CH3 HH3A 109.470 3.000
MA OXT CH3 HH3 109.470 3.000
MA HH3B CH3 HH3A 109.470 3.000
MA HH3B CH3 HH3 109.470 3.000
MA HH3A CH3 HH3 109.470 3.000
MA C CA HA 108.810 3.000
MA C CA CB 109.470 3.000
MA C CA N 109.470 3.000
MA HA CA CB 108.340 3.000
MA HA CA N 109.470 3.000
MA CB CA N 109.470 3.000
MA CA CB HBB 109.470 3.000
MA CA CB HBA 109.470 3.000
MA CA CB HB 109.470 3.000
MA HBB CB HBA 109.470 3.000
MA HBB CB HB 109.470 3.000
MA HBA CB HB 109.470 3.000
MA CA N HNA 120.000 3.000
MA CA N HN 120.000 3.000
MA HNA N HN 120.000 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
MA var_1 O C OXT CH3 0.059 20.000 1
MA var_2 C OXT CH3 HH3 -59.154 20.000 1
MA var_3 O C CA N -20.044 20.000 3
MA var_4 C CA CB HB -60.004 20.000 3
MA var_5 C CA N HN -63.945 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
MA chir_01 CA N C CB 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
MA plan-1 N 0.020
MA plan-1 CA 0.020
MA plan-1 HN 0.020
MA plan-1 HNA 0.020
MA plan-2 C 0.020
MA plan-2 CA 0.020
MA plan-2 O 0.020
MA plan-2 OXT 0.020
# ------------------------------------------------------
|
