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
|
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
XDL XDL 'XYLOSE-DERIVED ISOFAGOMINE LACTAM ' non-polymer 17 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_XDL
#
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
XDL O2 O O 0.000 0.000 0.000 0.000
XDL C2 C C 0.000 -1.150 0.067 -0.379
XDL C3 C CH1 0.000 -1.402 0.339 -1.832
XDL H3 H H 0.000 -1.246 1.408 -2.036
XDL O3 O OH1 0.000 -0.497 -0.431 -2.624
XDL HA H H 0.000 0.412 -0.190 -2.400
XDL C4 C CH2 0.000 -2.841 -0.040 -2.191
XDL H4C1 H H 0.000 -2.954 -1.126 -2.178
XDL H4C2 H H 0.000 -3.090 0.339 -3.184
XDL C5 C CH2 0.000 -3.780 0.585 -1.152
XDL H5C1 H H 0.000 -4.818 0.438 -1.456
XDL H5C2 H H 0.000 -3.575 1.654 -1.064
XDL C6 C CH2 0.000 -3.541 -0.094 0.195
XDL H6C1 H H 0.000 -3.909 -1.121 0.144
XDL H6C2 H H 0.000 -4.088 0.450 0.968
XDL N1 N NH1 0.000 -2.120 -0.102 0.518
XDL H1 H H 0.000 -1.854 -0.244 1.482
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
XDL O2 n/a C2 START
XDL C2 O2 C3 .
XDL C3 C2 C4 .
XDL H3 C3 . .
XDL O3 C3 HA .
XDL HA O3 . .
XDL C4 C3 C5 .
XDL H4C1 C4 . .
XDL H4C2 C4 . .
XDL C5 C4 C6 .
XDL H5C1 C5 . .
XDL H5C2 C5 . .
XDL C6 C5 N1 .
XDL H6C1 C6 . .
XDL H6C2 C6 . .
XDL N1 C6 H1 .
XDL H1 N1 . END
XDL N1 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
XDL N1 C2 single 1.330 0.020
XDL N1 C6 single 1.450 0.020
XDL H1 N1 single 1.010 0.020
XDL C3 C2 single 1.500 0.020
XDL C2 O2 double 1.220 0.020
XDL O3 C3 single 1.432 0.020
XDL C4 C3 single 1.524 0.020
XDL H3 C3 single 1.099 0.020
XDL HA O3 single 0.967 0.020
XDL C5 C4 single 1.524 0.020
XDL H4C1 C4 single 1.092 0.020
XDL H4C2 C4 single 1.092 0.020
XDL C6 C5 single 1.524 0.020
XDL H5C1 C5 single 1.092 0.020
XDL H5C2 C5 single 1.092 0.020
XDL H6C1 C6 single 1.092 0.020
XDL H6C2 C6 single 1.092 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
XDL O2 C2 C3 120.500 3.000
XDL O2 C2 N1 123.000 3.000
XDL C3 C2 N1 116.500 3.000
XDL C2 C3 H3 108.810 3.000
XDL C2 C3 O3 109.470 3.000
XDL C2 C3 C4 109.470 3.000
XDL H3 C3 O3 109.470 3.000
XDL H3 C3 C4 108.340 3.000
XDL O3 C3 C4 109.470 3.000
XDL C3 O3 HA 109.470 3.000
XDL C3 C4 H4C1 109.470 3.000
XDL C3 C4 H4C2 109.470 3.000
XDL C3 C4 C5 111.000 3.000
XDL H4C1 C4 H4C2 107.900 3.000
XDL H4C1 C4 C5 109.470 3.000
XDL H4C2 C4 C5 109.470 3.000
XDL C4 C5 H5C1 109.470 3.000
XDL C4 C5 H5C2 109.470 3.000
XDL C4 C5 C6 111.000 3.000
XDL H5C1 C5 H5C2 107.900 3.000
XDL H5C1 C5 C6 109.470 3.000
XDL H5C2 C5 C6 109.470 3.000
XDL C5 C6 H6C1 109.470 3.000
XDL C5 C6 H6C2 109.470 3.000
XDL C5 C6 N1 112.000 3.000
XDL H6C1 C6 H6C2 107.900 3.000
XDL H6C1 C6 N1 109.470 3.000
XDL H6C2 C6 N1 109.470 3.000
XDL C6 N1 H1 118.500 3.000
XDL C6 N1 C2 121.500 3.000
XDL H1 N1 C2 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
XDL var_1 O2 C2 C3 C4 150.000 20.000 3
XDL var_2 C2 C3 O3 HA -59.760 20.000 1
XDL var_3 C2 C3 C4 C5 60.000 20.000 3
XDL var_4 C3 C4 C5 C6 -60.000 20.000 3
XDL var_5 C4 C5 C6 N1 60.000 20.000 3
XDL var_6 C5 C6 N1 C2 -30.000 20.000 3
XDL CONST_1 C6 N1 C2 O2 180.000 0.000 0
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
XDL chir_01 C3 C2 O3 C4 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
XDL plan-1 N1 0.020
XDL plan-1 C2 0.020
XDL plan-1 C6 0.020
XDL plan-1 H1 0.020
XDL plan-2 C2 0.020
XDL plan-2 N1 0.020
XDL plan-2 C3 0.020
XDL plan-2 O2 0.020
XDL plan-2 H1 0.020
# ------------------------------------------------------
|
