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
ARA ARA 'ALPHA-L-ARABINOSE ' pyranose 20 10 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_ARA
#
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
ARA C1 C CH1 0.000 0.000 0.000 0.000
ARA H1 H H 0.000 0.195 -1.070 0.156
ARA O1 O OH1 0.000 0.740 0.761 0.957
ARA HO1 H H 0.000 1.684 0.585 0.848
ARA O5 O O2 0.000 0.407 0.368 -1.316
ARA C5 C CH2 0.000 -0.217 -0.532 -2.228
ARA H51 H H 0.000 -0.006 -1.558 -1.923
ARA H52 H H 0.000 0.181 -0.362 -3.231
ARA C4 C CH1 0.000 -1.729 -0.300 -2.233
ARA H4 H H 0.000 -2.203 -0.982 -2.954
ARA C3 C CH1 0.000 -2.282 -0.572 -0.831
ARA H3 H H 0.000 -2.165 -1.637 -0.588
ARA O3 O OH1 0.000 -3.666 -0.217 -0.777
ARA HO3 H H 0.000 -4.160 -0.752 -1.413
ARA C2 C CH1 0.000 -1.494 0.274 0.177
ARA H2 H H 0.000 -1.695 1.340 -0.001
ARA O2 O OH1 0.000 -1.889 -0.071 1.507
ARA HO2 H H 0.000 -1.387 0.459 2.140
ARA O4 O OH1 0.000 -2.005 1.052 -2.602
ARA HO4 H H 0.000 -1.639 1.181 -3.487
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
ARA C1 n/a O5 START
ARA H1 C1 . .
ARA O1 C1 HO1 .
ARA HO1 O1 . .
ARA O5 C1 . END
ARA C5 O5 C4 .
ARA H51 C5 . .
ARA H52 C5 . .
ARA C4 C5 O4 .
ARA H4 C4 . .
ARA C3 C4 C2 .
ARA H3 C3 . .
ARA O3 C3 HO3 .
ARA HO3 O3 . .
ARA C2 C3 O2 .
ARA H2 C2 . .
ARA O2 C2 HO2 .
ARA HO2 O2 . .
ARA O4 C4 . .
ARA HO4 O4 . .
ARA C1 C2 . 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
ARA C1 C2 single 1.524 0.020
ARA O1 C1 single 1.432 0.020
ARA O5 C1 single 1.426 0.020
ARA H1 C1 single 1.099 0.020
ARA C2 C3 single 1.524 0.020
ARA O2 C2 single 1.432 0.020
ARA H2 C2 single 1.099 0.020
ARA C3 C4 single 1.524 0.020
ARA O3 C3 single 1.432 0.020
ARA H3 C3 single 1.099 0.020
ARA C4 C5 single 1.524 0.020
ARA O4 C4 single 1.432 0.020
ARA H4 C4 single 1.099 0.020
ARA C5 O5 single 1.426 0.020
ARA H51 C5 single 1.092 0.020
ARA H52 C5 single 1.092 0.020
ARA HO1 O1 single 0.967 0.020
ARA HO2 O2 single 0.967 0.020
ARA HO3 O3 single 0.967 0.020
ARA HO4 O4 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
ARA H1 C1 O1 109.470 3.000
ARA H1 C1 O5 109.470 3.000
ARA O1 C1 O5 109.470 3.000
ARA H1 C1 C2 108.340 3.000
ARA O1 C1 C2 109.470 3.000
ARA O5 C1 C2 109.470 3.000
ARA C1 O1 HO1 109.470 3.000
ARA C1 O5 C5 111.800 3.000
ARA O5 C5 H51 109.470 3.000
ARA O5 C5 H52 109.470 3.000
ARA O5 C5 C4 109.470 3.000
ARA H51 C5 H52 107.900 3.000
ARA H51 C5 C4 109.470 3.000
ARA H52 C5 C4 109.470 3.000
ARA C5 C4 H4 108.340 3.000
ARA C5 C4 C3 111.000 3.000
ARA C5 C4 O4 109.470 3.000
ARA H4 C4 C3 108.340 3.000
ARA H4 C4 O4 109.470 3.000
ARA C3 C4 O4 109.470 3.000
ARA C4 C3 H3 108.340 3.000
ARA C4 C3 O3 109.470 3.000
ARA C4 C3 C2 111.000 3.000
ARA H3 C3 O3 109.470 3.000
ARA H3 C3 C2 108.340 3.000
ARA O3 C3 C2 109.470 3.000
ARA C3 O3 HO3 109.470 3.000
ARA C3 C2 H2 108.340 3.000
ARA C3 C2 O2 109.470 3.000
ARA C3 C2 C1 111.000 3.000
ARA H2 C2 O2 109.470 3.000
ARA H2 C2 C1 108.340 3.000
ARA O2 C2 C1 109.470 3.000
ARA C2 O2 HO2 109.470 3.000
ARA C4 O4 HO4 109.470 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
ARA var_1 O5 C1 O1 HO1 -59.850 20.000 1
ARA var_2 C1 O5 C5 C4 60.000 20.000 1
ARA var_3 O5 C5 C4 O4 60.000 20.000 3
ARA var_4 C5 C4 C3 C2 60.000 20.000 3
ARA var_5 C4 C3 O3 HO3 60.759 20.000 1
ARA var_6 C4 C3 C2 O2 180.000 20.000 3
ARA var_7 C3 C2 C1 O5 60.000 20.000 3
ARA var_8 C3 C2 O2 HO2 179.612 20.000 1
ARA var_1 C5 O5 C1 C2 0.000 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
ARA chir_01 C1 C2 O1 O5 positiv
ARA chir_02 C2 C1 C3 O2 negativ
ARA chir_03 C3 C2 C4 O3 positiv
ARA chir_04 C4 C3 C5 O4 positiv
# ------------------------------------------------------
|
