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
183
|
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
RIB RIB 'RIBOSE ' furanose 20 10 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_RIB
#
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
RIB "O1'" O OH1 0.000 0.000 0.000 0.000
RIB "HO1'" H H 0.000 0.105 0.002 -0.961
RIB "C1'" C CH1 0.000 -1.274 0.550 0.340
RIB "H1'" H H 0.000 -1.349 1.586 -0.019
RIB "O4'" O O2 0.000 -2.328 -0.248 -0.218
RIB "C2'" C CH1 0.000 -1.493 0.495 1.872
RIB "H2'" H H 0.000 -1.071 1.383 2.363
RIB "O2'" O OH1 0.000 -0.953 -0.705 2.428
RIB "HO2'" H H 0.000 0.001 -0.731 2.269
RIB "C3'" C CH1 0.000 -3.045 0.499 1.949
RIB "H3'" H H 0.000 -3.436 1.525 1.899
RIB "O3'" O OH1 0.000 -3.497 -0.159 3.135
RIB "HO3'" H H 0.000 -3.164 0.312 3.911
RIB "C4'" C CH1 0.000 -3.434 -0.298 0.687
RIB "H4'" H H 0.000 -3.647 -1.342 0.956
RIB "C5'" C CH2 0.000 -4.668 0.331 0.035
RIB "H5'1" H H 0.000 -4.445 1.364 -0.241
RIB "H5'2" H H 0.000 -5.499 0.315 0.742
RIB "O5'" O OH1 0.000 -5.020 -0.410 -1.134
RIB "HO5'" H H 0.000 -5.799 -0.011 -1.544
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
RIB "O1'" n/a "C1'" START
RIB "HO1'" "O1'" . .
RIB "C1'" "O1'" "C2'" .
RIB "H1'" "C1'" . .
RIB "O4'" "C1'" . .
RIB "C2'" "C1'" "C3'" .
RIB "H2'" "C2'" . .
RIB "O2'" "C2'" "HO2'" .
RIB "HO2'" "O2'" . .
RIB "C3'" "C2'" "C4'" .
RIB "H3'" "C3'" . .
RIB "O3'" "C3'" "HO3'" .
RIB "HO3'" "O3'" . .
RIB "C4'" "C3'" "C5'" .
RIB "H4'" "C4'" . .
RIB "C5'" "C4'" "O5'" .
RIB "H5'1" "C5'" . .
RIB "H5'2" "C5'" . .
RIB "O5'" "C5'" "HO5'" .
RIB "HO5'" "O5'" . END
RIB "C4'" "O4'" . 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
RIB "O5'" "C5'" single 1.432 0.020
RIB "HO5'" "O5'" single 0.967 0.020
RIB "C5'" "C4'" single 1.524 0.020
RIB "H5'1" "C5'" single 1.092 0.020
RIB "H5'2" "C5'" single 1.092 0.020
RIB "C4'" "O4'" single 1.426 0.020
RIB "C4'" "C3'" single 1.524 0.020
RIB "H4'" "C4'" single 1.099 0.020
RIB "O4'" "C1'" single 1.426 0.020
RIB "O3'" "C3'" single 1.432 0.020
RIB "C3'" "C2'" single 1.524 0.020
RIB "H3'" "C3'" single 1.099 0.020
RIB "HO3'" "O3'" single 0.967 0.020
RIB "O2'" "C2'" single 1.432 0.020
RIB "C2'" "C1'" single 1.524 0.020
RIB "H2'" "C2'" single 1.099 0.020
RIB "HO2'" "O2'" single 0.967 0.020
RIB "C1'" "O1'" single 1.432 0.020
RIB "H1'" "C1'" single 1.099 0.020
RIB "HO1'" "O1'" 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
RIB "HO1'" "O1'" "C1'" 109.470 3.000
RIB "O1'" "C1'" "H1'" 109.470 3.000
RIB "O1'" "C1'" "O4'" 109.470 3.000
RIB "O1'" "C1'" "C2'" 109.470 3.000
RIB "H1'" "C1'" "O4'" 109.470 3.000
RIB "H1'" "C1'" "C2'" 108.340 3.000
RIB "O4'" "C1'" "C2'" 109.470 3.000
RIB "C1'" "O4'" "C4'" 111.800 3.000
RIB "C1'" "C2'" "H2'" 108.340 3.000
RIB "C1'" "C2'" "O2'" 109.470 3.000
RIB "C1'" "C2'" "C3'" 111.000 3.000
RIB "H2'" "C2'" "O2'" 109.470 3.000
RIB "H2'" "C2'" "C3'" 108.340 3.000
RIB "O2'" "C2'" "C3'" 109.470 3.000
RIB "C2'" "O2'" "HO2'" 109.470 3.000
RIB "C2'" "C3'" "H3'" 108.340 3.000
RIB "C2'" "C3'" "O3'" 109.470 3.000
RIB "C2'" "C3'" "C4'" 111.000 3.000
RIB "H3'" "C3'" "O3'" 109.470 3.000
RIB "H3'" "C3'" "C4'" 108.340 3.000
RIB "O3'" "C3'" "C4'" 109.470 3.000
RIB "C3'" "O3'" "HO3'" 109.470 3.000
RIB "C3'" "C4'" "H4'" 108.340 3.000
RIB "C3'" "C4'" "C5'" 111.000 3.000
RIB "C3'" "C4'" "O4'" 109.470 3.000
RIB "H4'" "C4'" "C5'" 108.340 3.000
RIB "H4'" "C4'" "O4'" 109.470 3.000
RIB "C5'" "C4'" "O4'" 109.470 3.000
RIB "C4'" "C5'" "H5'1" 109.470 3.000
RIB "C4'" "C5'" "H5'2" 109.470 3.000
RIB "C4'" "C5'" "O5'" 109.470 3.000
RIB "H5'1" "C5'" "H5'2" 107.900 3.000
RIB "H5'1" "C5'" "O5'" 109.470 3.000
RIB "H5'2" "C5'" "O5'" 109.470 3.000
RIB "C5'" "O5'" "HO5'" 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
RIB var_1 "HO1'" "O1'" "C1'" "C2'" 177.268 20.000 1
RIB var_2 "O1'" "C1'" "O4'" "C4'" 150.000 20.000 1
RIB var_3 "O1'" "C1'" "C2'" "C3'" -150.000 20.000 3
RIB var_4 "C1'" "C2'" "O2'" "HO2'" 61.428 20.000 1
RIB var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
RIB var_6 "C2'" "C3'" "O3'" "HO3'" 61.459 20.000 1
RIB var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
RIB var_8 "C3'" "C4'" "O4'" "C1'" 0.000 20.000 1
RIB var_9 "C3'" "C4'" "C5'" "O5'" 179.891 20.000 3
RIB var_10 "C4'" "C5'" "O5'" "HO5'" -179.946 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
RIB chir_01 "C4'" "C5'" "O4'" "C3'" negativ
RIB chir_02 "C3'" "C4'" "O3'" "C2'" negativ
RIB chir_03 "C2'" "C3'" "O2'" "C1'" negativ
RIB chir_04 "C1'" "O4'" "C2'" "O1'" negativ
# ------------------------------------------------------
|
