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
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
|
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
DX5 DX5 'D-XYLITOL-5-PHOSPHATE ' non-polymer 25 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DX5
#
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
DX5 O3P O OP -0.666 0.000 0.000 0.000
DX5 P P P 0.000 -0.941 -1.007 0.625
DX5 O1P O OP -0.666 -1.208 -0.622 2.063
DX5 O2P O OP -0.666 -0.310 -2.382 0.580
DX5 O5 O O2 0.000 -2.328 -1.025 -0.192
DX5 C5 C CH2 0.000 -2.813 0.319 -0.214
DX5 H51 H H 0.000 -2.080 0.961 -0.707
DX5 H52 H H 0.000 -2.969 0.665 0.810
DX5 C4 C CH1 0.000 -4.136 0.371 -0.979
DX5 H4 H H 0.000 -3.997 -0.061 -1.980
DX5 O4 O OH1 0.000 -5.126 -0.376 -0.271
DX5 HO4 H H 0.000 -5.248 0.004 0.609
DX5 C3 C CH1 0.000 -4.592 1.826 -1.110
DX5 H3 H H 0.000 -3.874 2.381 -1.731
DX5 O3 O OH1 0.000 -4.660 2.423 0.187
DX5 HO3 H H 0.000 -5.291 1.934 0.732
DX5 C2 C CH1 0.000 -5.974 1.871 -1.765
DX5 H2 H H 0.000 -5.903 1.495 -2.796
DX5 O2 O OH1 0.000 -6.880 1.054 -1.021
DX5 HO2 H H 0.000 -6.941 1.386 -0.115
DX5 C1 C CH2 0.000 -6.483 3.314 -1.783
DX5 H11 H H 0.000 -5.747 3.954 -2.274
DX5 H12 H H 0.000 -6.637 3.658 -0.758
DX5 O1 O OH1 0.000 -7.719 3.372 -2.498
DX5 HO1 H H 0.000 -8.042 4.284 -2.509
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
DX5 O3P n/a P START
DX5 P O3P O5 .
DX5 O1P P . .
DX5 O2P P . .
DX5 O5 P C5 .
DX5 C5 O5 C4 .
DX5 H51 C5 . .
DX5 H52 C5 . .
DX5 C4 C5 C3 .
DX5 H4 C4 . .
DX5 O4 C4 HO4 .
DX5 HO4 O4 . .
DX5 C3 C4 C2 .
DX5 H3 C3 . .
DX5 O3 C3 HO3 .
DX5 HO3 O3 . .
DX5 C2 C3 C1 .
DX5 H2 C2 . .
DX5 O2 C2 HO2 .
DX5 HO2 O2 . .
DX5 C1 C2 O1 .
DX5 H11 C1 . .
DX5 H12 C1 . .
DX5 O1 C1 HO1 .
DX5 HO1 O1 . 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
DX5 C1 C2 single 1.524 0.020
DX5 O1 C1 single 1.432 0.020
DX5 H11 C1 single 1.092 0.020
DX5 H12 C1 single 1.092 0.020
DX5 C2 C3 single 1.524 0.020
DX5 O2 C2 single 1.432 0.020
DX5 H2 C2 single 1.099 0.020
DX5 C3 C4 single 1.524 0.020
DX5 O3 C3 single 1.432 0.020
DX5 H3 C3 single 1.099 0.020
DX5 C4 C5 single 1.524 0.020
DX5 O4 C4 single 1.432 0.020
DX5 H4 C4 single 1.099 0.020
DX5 C5 O5 single 1.426 0.020
DX5 H51 C5 single 1.092 0.020
DX5 H52 C5 single 1.092 0.020
DX5 HO1 O1 single 0.967 0.020
DX5 HO2 O2 single 0.967 0.020
DX5 HO3 O3 single 0.967 0.020
DX5 HO4 O4 single 0.967 0.020
DX5 O5 P single 1.610 0.020
DX5 O1P P deloc 1.510 0.020
DX5 O2P P deloc 1.510 0.020
DX5 P O3P deloc 1.510 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
DX5 O3P P O1P 119.900 3.000
DX5 O3P P O2P 119.900 3.000
DX5 O3P P O5 108.200 3.000
DX5 O1P P O2P 119.900 3.000
DX5 O1P P O5 108.200 3.000
DX5 O2P P O5 108.200 3.000
DX5 P O5 C5 120.500 3.000
DX5 O5 C5 H51 109.470 3.000
DX5 O5 C5 H52 109.470 3.000
DX5 O5 C5 C4 109.470 3.000
DX5 H51 C5 H52 107.900 3.000
DX5 H51 C5 C4 109.470 3.000
DX5 H52 C5 C4 109.470 3.000
DX5 C5 C4 H4 108.340 3.000
DX5 C5 C4 O4 109.470 3.000
DX5 C5 C4 C3 111.000 3.000
DX5 H4 C4 O4 109.470 3.000
DX5 H4 C4 C3 108.340 3.000
DX5 O4 C4 C3 109.470 3.000
DX5 C4 O4 HO4 109.470 3.000
DX5 C4 C3 H3 108.340 3.000
DX5 C4 C3 O3 109.470 3.000
DX5 C4 C3 C2 111.000 3.000
DX5 H3 C3 O3 109.470 3.000
DX5 H3 C3 C2 108.340 3.000
DX5 O3 C3 C2 109.470 3.000
DX5 C3 O3 HO3 109.470 3.000
DX5 C3 C2 H2 108.340 3.000
DX5 C3 C2 O2 109.470 3.000
DX5 C3 C2 C1 111.000 3.000
DX5 H2 C2 O2 109.470 3.000
DX5 H2 C2 C1 108.340 3.000
DX5 O2 C2 C1 109.470 3.000
DX5 C2 O2 HO2 109.470 3.000
DX5 C2 C1 H11 109.470 3.000
DX5 C2 C1 H12 109.470 3.000
DX5 C2 C1 O1 109.470 3.000
DX5 H11 C1 H12 107.900 3.000
DX5 H11 C1 O1 109.470 3.000
DX5 H12 C1 O1 109.470 3.000
DX5 C1 O1 HO1 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
DX5 var_1 O3P P O5 C5 -54.948 20.000 1
DX5 var_2 P O5 C5 C4 179.994 20.000 1
DX5 var_3 O5 C5 C4 C3 -175.007 20.000 3
DX5 var_4 C5 C4 O4 HO4 60.025 20.000 1
DX5 var_5 C5 C4 C3 C2 -175.026 20.000 3
DX5 var_6 C4 C3 O3 HO3 -59.968 20.000 1
DX5 var_7 C4 C3 C2 C1 174.988 20.000 3
DX5 var_8 C3 C2 O2 HO2 59.992 20.000 1
DX5 var_9 C3 C2 C1 O1 174.994 20.000 3
DX5 var_10 C2 C1 O1 HO1 179.985 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
DX5 chir_01 C2 C1 C3 O2 negativ
DX5 chir_02 C3 C2 C4 O3 positiv
DX5 chir_03 C4 C3 C5 O4 negativ
# ------------------------------------------------------
|
