PDB Chemical Component VOD
The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.
Bond Distances for VOD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2 |
C3 |
1.321 |
1.326 |
| C3 |
C4 |
1.483 |
1.478 |
| C4 |
C5 |
1.349 |
1.396 |
| C4 |
C9 |
1.402 |
1.395 |
| C5 |
C6 |
1.379 |
1.379 |
| C6 |
C7 |
1.387 |
1.383 |
| C7 |
C8 |
1.403 |
1.383 |
| C7 |
C10 |
1.514 |
1.508 |
| C8 |
C9 |
1.394 |
1.380 |
| C10 |
S11 |
1.677 |
1.814 |
| S11 |
O12 |
1.470 |
1.421 |
| S11 |
O13 |
1.475 |
1.421 |
| S11 |
O11 |
1.648 |
1.522 |
| C2 |
H21C |
1.080 |
1.080 |
| C2 |
H22C |
1.080 |
1.080 |
| C3 |
H3 |
1.080 |
1.080 |
| C5 |
H5 |
1.080 |
1.080 |
| C9 |
H9 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| C8 |
H8 |
1.080 |
1.080 |
| C10 |
H101 |
1.100 |
1.089 |
| C10 |
H102 |
1.100 |
1.090 |
| O11 |
H11 |
0.950 |
0.968 |
Bond Angles for VOD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C3 |
C4 |
122.9 |
120.0 |
| C3 |
C2 |
H21C |
120.0 |
120.0 |
| C3 |
C2 |
H22C |
120.0 |
120.0 |
| C2 |
C3 |
H3 |
118.6 |
120.0 |
| C3 |
C4 |
C5 |
119.1 |
120.1 |
| C3 |
C4 |
C9 |
124.3 |
120.1 |
| C4 |
C3 |
H3 |
118.5 |
120.0 |
| C5 |
C4 |
C9 |
116.5 |
119.8 |
| C4 |
C5 |
C6 |
125.5 |
119.8 |
| C4 |
C5 |
H5 |
117.2 |
120.1 |
| C4 |
C9 |
C8 |
119.6 |
119.8 |
| C4 |
C9 |
H9 |
120.3 |
120.1 |
| C5 |
C6 |
C7 |
118.9 |
120.1 |
| C6 |
C5 |
H5 |
117.2 |
120.1 |
| C5 |
C6 |
H6 |
120.6 |
120.0 |
| C6 |
C7 |
C8 |
117.1 |
120.3 |
| C6 |
C7 |
C10 |
126.1 |
119.9 |
| C7 |
C6 |
H6 |
120.5 |
119.9 |
| C8 |
C7 |
C10 |
116.8 |
119.8 |
| C7 |
C8 |
C9 |
122.4 |
120.1 |
| C7 |
C8 |
H8 |
118.8 |
120.0 |
| C7 |
C10 |
S11 |
116.3 |
109.5 |
| C7 |
C10 |
H101 |
107.7 |
109.5 |
| C7 |
C10 |
H102 |
107.7 |
109.4 |
| C8 |
C9 |
H9 |
120.2 |
120.1 |
| C9 |
C8 |
H8 |
118.9 |
119.9 |
| C10 |
S11 |
O12 |
105.5 |
110.6 |
| C10 |
S11 |
O13 |
125.6 |
110.5 |
| C10 |
S11 |
O11 |
99.9 |
104.4 |
| S11 |
C10 |
H101 |
107.7 |
109.5 |
| S11 |
C10 |
H102 |
107.7 |
109.5 |
| O12 |
S11 |
O13 |
111.4 |
121.0 |
| O12 |
S11 |
O11 |
107.7 |
104.3 |
| O13 |
S11 |
O11 |
105.1 |
104.3 |
| S11 |
O11 |
H11 |
109.5 |
114.0 |
| H21C |
C2 |
H22C |
120.0 |
120.0 |
| H101 |
C10 |
H102 |
109.5 |
109.5 |
Torsion Angles for VOD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C3 |
C4 |
C5 |
359.4 |
180.0 |
| C2 |
C3 |
C4 |
C9 |
174.6 |
359.7 |
| C4 |
C3 |
C2 |
H3 |
180.0 |
180.0 |
| H21C |
C2 |
C3 |
H22C |
180.0 |
180.3 |
| C4 |
C3 |
C2 |
H21C |
0.0 |
180.0 |
| C4 |
C3 |
C2 |
H22C |
180.0 |
359.7 |
| C2 |
C3 |
C4 |
H3 |
180.0 |
180.0 |
| C5 |
C4 |
C3 |
C9 |
184.8 |
180.3 |
| C3 |
C4 |
C5 |
C6 |
180.0 |
180.0 |
| C3 |
C4 |
C5 |
H5 |
0.0 |
0.0 |
| C3 |
C4 |
C9 |
C8 |
181.4 |
179.7 |
| C3 |
C4 |
C9 |
H9 |
1.3 |
0.0 |
| C3 |
C4 |
C5 |
C9 |
175.5 |
179.7 |
| C5 |
C4 |
C3 |
H3 |
179.4 |
360.0 |
| C5 |
C4 |
C9 |
C8 |
356.6 |
359.4 |
| C5 |
C4 |
C9 |
H9 |
176.6 |
179.8 |
| C4 |
C5 |
C6 |
C7 |
357.3 |
0.1 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
177.3 |
180.0 |
| C3 |
C4 |
C9 |
C5 |
184.7 |
180.3 |
| C9 |
C4 |
C3 |
H3 |
354.6 |
179.7 |
| C9 |
C4 |
C5 |
C6 |
4.5 |
0.3 |
| C9 |
C4 |
C5 |
H5 |
184.5 |
180.3 |
| C7 |
C8 |
C9 |
C4 |
0.7 |
0.6 |
| C8 |
C9 |
C4 |
H9 |
180.0 |
179.6 |
| C4 |
C9 |
C8 |
H8 |
180.7 |
180.3 |
| C6 |
C5 |
C4 |
C9 |
4.5 |
0.3 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| C5 |
C6 |
C7 |
C8 |
359.7 |
360.0 |
| C5 |
C6 |
C7 |
C10 |
179.8 |
180.0 |
| C7 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C7 |
C6 |
C5 |
H5 |
177.3 |
180.0 |
| C5 |
C6 |
C7 |
H6 |
180.0 |
180.0 |
| C8 |
C7 |
C6 |
C10 |
180.0 |
180.0 |
| C6 |
C7 |
C8 |
C9 |
1.1 |
359.7 |
| C6 |
C7 |
C8 |
H8 |
181.1 |
180.0 |
| C6 |
C7 |
C10 |
S11 |
323.5 |
90.0 |
| C6 |
C7 |
C10 |
H101 |
84.5 |
210.0 |
| C6 |
C7 |
C10 |
H102 |
202.5 |
330.0 |
| C4 |
C9 |
C8 |
C7 |
0.7 |
0.6 |
| C6 |
C7 |
C8 |
C10 |
180.0 |
180.0 |
| C8 |
C7 |
C6 |
H6 |
179.7 |
180.0 |
| C8 |
C7 |
C10 |
S11 |
143.5 |
270.0 |
| C8 |
C7 |
C10 |
H101 |
264.5 |
30.0 |
| C8 |
C7 |
C10 |
H102 |
22.5 |
150.0 |
| C7 |
C8 |
C9 |
H9 |
180.7 |
180.2 |
| C9 |
C8 |
C7 |
H8 |
180.0 |
179.7 |
| C6 |
C7 |
C10 |
C8 |
180.0 |
180.0 |
| C10 |
C7 |
C6 |
H6 |
359.8 |
360.0 |
| C10 |
C7 |
C8 |
C9 |
181.1 |
179.7 |
| C10 |
C7 |
C8 |
H8 |
1.1 |
360.0 |
| C7 |
C10 |
S11 |
O12 |
181.8 |
291.6 |
| C7 |
C10 |
S11 |
O13 |
313.5 |
68.4 |
| C7 |
C10 |
S11 |
O11 |
70.2 |
180.0 |
| S11 |
C10 |
C7 |
H101 |
239.0 |
240.0 |
| S11 |
C10 |
C7 |
H102 |
121.0 |
120.0 |
| H101 |
C10 |
C7 |
H102 |
242.0 |
240.0 |
| C4 |
C9 |
C8 |
H9 |
180.0 |
180.4 |
| C9 |
C8 |
C7 |
C10 |
181.1 |
179.7 |
| C7 |
C8 |
C9 |
H8 |
180.0 |
180.3 |
| C7 |
C10 |
S11 |
H101 |
121.0 |
120.0 |
| C7 |
C10 |
S11 |
H102 |
239.0 |
240.1 |
| O12 |
S11 |
C10 |
O13 |
228.4 |
223.2 |
| O12 |
S11 |
C10 |
O11 |
111.6 |
111.6 |
| O13 |
S11 |
C10 |
O11 |
243.2 |
248.4 |
| C10 |
S11 |
O11 |
H11 |
228.8 |
180.0 |
| H101 |
C10 |
S11 |
H102 |
118.0 |
120.1 |
| C10 |
S11 |
O12 |
O13 |
139.2 |
131.5 |
| C10 |
S11 |
O12 |
O11 |
254.0 |
248.3 |
| O12 |
S11 |
C10 |
H101 |
60.9 |
171.6 |
| O12 |
S11 |
C10 |
H102 |
302.8 |
51.6 |
| O13 |
S11 |
O12 |
O11 |
114.8 |
116.8 |
| O12 |
S11 |
O11 |
H11 |
118.9 |
63.9 |
| C10 |
S11 |
O13 |
O12 |
230.7 |
228.5 |
| C10 |
S11 |
O13 |
O11 |
114.3 |
111.7 |
| O13 |
S11 |
C10 |
H101 |
192.5 |
308.4 |
| O13 |
S11 |
C10 |
H102 |
74.5 |
188.3 |
| O12 |
S11 |
O13 |
O11 |
243.6 |
243.2 |
| O13 |
S11 |
O11 |
H11 |
360.0 |
296.1 |
| C10 |
S11 |
O11 |
O12 |
109.9 |
116.1 |
| C10 |
S11 |
O11 |
O13 |
228.8 |
243.9 |
| O11 |
S11 |
C10 |
H101 |
309.3 |
60.0 |
| O11 |
S11 |
C10 |
H102 |
191.2 |
300.0 |
| O12 |
S11 |
O11 |
O13 |
118.9 |
127.9 |
| H21C |
C2 |
C3 |
C4 |
0.0 |
180.0 |
| C3 |
C2 |
H21C |
H22C |
180.0 |
179.7 |
| H21C |
C2 |
C3 |
H3 |
180.0 |
0.0 |
| H22C |
C2 |
C3 |
C4 |
180.0 |
359.7 |
| C3 |
C2 |
H22C |
H21C |
180.0 |
180.3 |
| H22C |
C2 |
C3 |
H3 |
0.0 |
179.7 |
| C2 |
C3 |
H3 |
C4 |
180.0 |
180.0 |
| H3 |
C3 |
C2 |
H21C |
180.0 |
0.0 |
| H3 |
C3 |
C2 |
H22C |
0.0 |
179.7 |
| H3 |
C3 |
C4 |
C5 |
179.4 |
360.0 |
| H3 |
C3 |
C4 |
C9 |
354.6 |
179.7 |
| H5 |
C5 |
C4 |
C9 |
184.5 |
180.3 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
| H5 |
C5 |
C6 |
C7 |
177.3 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
357.3 |
360.0 |
| C4 |
C9 |
H9 |
C8 |
180.0 |
179.6 |
| H9 |
C9 |
C8 |
H8 |
0.7 |
360.0 |
| C5 |
C6 |
H6 |
C7 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
357.3 |
360.0 |
| H6 |
C6 |
C7 |
C8 |
179.7 |
180.0 |
| H6 |
C6 |
C7 |
C10 |
359.8 |
360.0 |
| H8 |
C8 |
C7 |
C10 |
1.1 |
360.0 |
| C7 |
C8 |
H8 |
C9 |
180.0 |
179.7 |
| H8 |
C8 |
C9 |
H9 |
0.7 |
360.0 |
| C7 |
C10 |
H101 |
S11 |
233.8 |
240.0 |
| C7 |
C10 |
H101 |
H102 |
116.9 |
120.0 |
| H101 |
C10 |
S11 |
O12 |
60.9 |
171.6 |
| H101 |
C10 |
S11 |
O13 |
192.5 |
308.4 |
| H101 |
C10 |
S11 |
O11 |
309.3 |
60.0 |
| S11 |
C10 |
H101 |
H102 |
243.1 |
239.9 |
| C7 |
C10 |
H102 |
S11 |
126.2 |
120.0 |
| C7 |
C10 |
H102 |
H101 |
243.1 |
240.0 |
| H102 |
C10 |
S11 |
O12 |
302.8 |
51.6 |
| H102 |
C10 |
S11 |
O13 |
74.5 |
188.3 |
| H102 |
C10 |
S11 |
O11 |
191.2 |
300.0 |
| S11 |
C10 |
H102 |
H101 |
116.9 |
120.0 |