PDB Chemical Component VD9
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 VD9
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C14 |
C13 |
1.517 |
1.530 |
| O4 |
S2 |
1.470 |
1.421 |
| C13 |
C12 |
1.510 |
1.530 |
| S2 |
O1 |
1.499 |
1.422 |
| S2 |
C5 |
1.742 |
1.762 |
| S2 |
N3 |
1.596 |
1.655 |
| C10 |
C5 |
1.387 |
1.382 |
| C10 |
C9 |
1.409 |
1.382 |
| C5 |
C6 |
1.383 |
1.383 |
| C12 |
S11 |
1.839 |
1.814 |
| C9 |
C8 |
1.393 |
1.389 |
| C6 |
C7 |
1.410 |
1.381 |
| C8 |
C7 |
1.400 |
1.390 |
| C8 |
S11 |
1.791 |
1.762 |
| N3 |
H1 |
1.000 |
0.970 |
| N3 |
H2 |
1.000 |
0.970 |
| C10 |
H3 |
1.080 |
1.080 |
| C9 |
H4 |
1.080 |
1.080 |
| C7 |
H5 |
1.079 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| C12 |
H7 |
1.100 |
1.090 |
| C12 |
H8 |
1.100 |
1.090 |
| C13 |
H9 |
1.100 |
1.090 |
| C13 |
H10 |
1.100 |
1.090 |
| C14 |
H11 |
1.100 |
1.090 |
| C14 |
H12 |
1.100 |
1.090 |
| C14 |
H13 |
1.100 |
1.090 |
Bond Angles for VD9
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C14 |
C13 |
H9 |
109.4 |
109.5 |
| C14 |
C13 |
H10 |
109.4 |
109.5 |
| O4 |
S2 |
O1 |
114.1 |
123.2 |
| O4 |
S2 |
C5 |
105.0 |
106.4 |
| O4 |
S2 |
N3 |
111.1 |
106.4 |
| C13 |
C12 |
H7 |
108.9 |
109.5 |
| C13 |
C12 |
H8 |
108.9 |
109.5 |
| O1 |
S2 |
C5 |
105.8 |
106.4 |
| O1 |
S2 |
N3 |
110.1 |
106.4 |
| N3 |
S2 |
C5 |
110.5 |
107.2 |
| S2 |
C5 |
C6 |
120.8 |
119.9 |
| S2 |
N3 |
H1 |
109.5 |
120.0 |
| S2 |
N3 |
H2 |
109.5 |
120.0 |
| C10 |
C5 |
C6 |
118.6 |
120.2 |
| C10 |
C9 |
C8 |
116.3 |
119.9 |
| C9 |
C10 |
H3 |
119.2 |
119.9 |
| C10 |
C9 |
H4 |
121.9 |
120.0 |
| C5 |
C6 |
C7 |
123.3 |
120.1 |
| C5 |
C6 |
H6 |
118.3 |
120.0 |
| C9 |
C8 |
C7 |
125.3 |
119.9 |
| C9 |
C8 |
S11 |
121.7 |
120.0 |
| C8 |
C9 |
H4 |
121.9 |
120.1 |
| C6 |
C7 |
H5 |
122.8 |
120.1 |
| C7 |
C8 |
S11 |
112.9 |
120.1 |
| C8 |
C7 |
H5 |
122.8 |
120.0 |
| H1 |
N3 |
H2 |
109.5 |
120.0 |
| H7 |
C12 |
H8 |
109.5 |
109.5 |
| H9 |
C13 |
H10 |
109.5 |
109.4 |
| H11 |
C14 |
H12 |
109.5 |
109.5 |
| H11 |
C14 |
H13 |
109.5 |
109.5 |
| H12 |
C14 |
H13 |
109.5 |
109.5 |
Torsion Angles for VD9
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C14 |
C13 |
C12 |
H7 |
302.6 |
59.9 |
| C14 |
C13 |
C12 |
H8 |
61.9 |
300.0 |
| H9 |
C13 |
C14 |
H10 |
240.0 |
119.9 |
| O1 |
S2 |
O4 |
C5 |
244.6 |
122.9 |
| O1 |
S2 |
O4 |
N3 |
125.1 |
237.0 |
| N3 |
S2 |
O4 |
C5 |
119.5 |
245.9 |
| O4 |
S2 |
C5 |
C6 |
75.8 |
336.4 |
| O4 |
S2 |
N3 |
H1 |
180.0 |
353.5 |
| O4 |
S2 |
N3 |
H2 |
300.0 |
173.6 |
| H7 |
C12 |
C13 |
H8 |
240.7 |
120.0 |
| O4 |
S2 |
O1 |
C5 |
114.9 |
237.1 |
| O4 |
S2 |
O1 |
N3 |
234.4 |
123.0 |
| N3 |
S2 |
O1 |
C5 |
240.6 |
114.1 |
| O1 |
S2 |
C5 |
C6 |
196.8 |
203.5 |
| O1 |
S2 |
N3 |
H1 |
52.7 |
126.4 |
| O1 |
S2 |
N3 |
H2 |
172.7 |
306.5 |
| O4 |
S2 |
C5 |
O1 |
239.0 |
132.9 |
| O4 |
S2 |
C5 |
N3 |
119.9 |
246.4 |
| O1 |
S2 |
C5 |
N3 |
240.9 |
113.5 |
| C5 |
S2 |
N3 |
H1 |
296.2 |
240.0 |
| C5 |
S2 |
N3 |
H2 |
56.2 |
60.0 |
| C10 |
C5 |
S2 |
C6 |
175.0 |
180.3 |
| S2 |
C5 |
C6 |
C7 |
183.8 |
179.7 |
| S2 |
C5 |
C6 |
H6 |
3.8 |
0.0 |
| O4 |
S2 |
N3 |
O1 |
127.3 |
227.1 |
| O4 |
S2 |
N3 |
C5 |
243.8 |
113.6 |
| O1 |
S2 |
N3 |
C5 |
116.5 |
246.5 |
| N3 |
S2 |
C5 |
C6 |
315.9 |
90.0 |
| H1 |
N3 |
S2 |
H2 |
240.0 |
179.9 |
| S2 |
C5 |
C10 |
C6 |
184.9 |
179.7 |
| C10 |
C5 |
C6 |
C7 |
8.7 |
359.4 |
| C10 |
C5 |
C6 |
H6 |
188.7 |
179.7 |
| C9 |
C10 |
C5 |
C6 |
352.9 |
0.3 |
| C10 |
C9 |
C8 |
C7 |
357.5 |
360.0 |
| C10 |
C9 |
C8 |
S11 |
181.8 |
180.0 |
| C8 |
C9 |
C10 |
H4 |
180.0 |
180.0 |
| C5 |
C6 |
C7 |
H5 |
173.1 |
180.3 |
| C8 |
C9 |
C10 |
H3 |
184.0 |
180.1 |
| C10 |
C9 |
C8 |
H4 |
180.0 |
180.0 |
| C7 |
C8 |
C9 |
S11 |
175.7 |
180.0 |
| C9 |
C8 |
C7 |
H5 |
183.8 |
180.0 |
| C5 |
C6 |
C7 |
H6 |
180.0 |
180.3 |
| C6 |
C7 |
C8 |
S11 |
179.8 |
179.7 |
| C8 |
C7 |
C6 |
H5 |
180.0 |
180.3 |
| C5 |
C6 |
C7 |
C8 |
353.1 |
0.6 |
| C9 |
C8 |
C7 |
S11 |
183.9 |
180.0 |
| C7 |
C8 |
C9 |
H4 |
177.6 |
180.0 |
| C6 |
C7 |
C8 |
H5 |
180.0 |
179.7 |
| C9 |
C8 |
S11 |
C7 |
176.2 |
180.0 |
| S11 |
C8 |
C9 |
H4 |
1.8 |
0.0 |
| S11 |
C8 |
C7 |
H5 |
359.8 |
360.0 |
| H1 |
N3 |
S2 |
C5 |
296.2 |
240.0 |
| S2 |
N3 |
H1 |
H2 |
120.0 |
180.1 |
| H2 |
N3 |
S2 |
C5 |
56.2 |
60.0 |
| S2 |
N3 |
H2 |
H1 |
240.0 |
179.9 |
| H3 |
C10 |
C5 |
C6 |
173.0 |
180.2 |
| H3 |
C10 |
C9 |
C8 |
184.0 |
180.1 |
| H3 |
C10 |
C9 |
H4 |
4.0 |
0.1 |
| C10 |
C9 |
H4 |
C8 |
180.0 |
180.0 |
| H4 |
C9 |
C10 |
H3 |
4.0 |
0.1 |
| H4 |
C9 |
C8 |
C7 |
177.6 |
180.0 |
| H4 |
C9 |
C8 |
S11 |
1.8 |
0.0 |
| H5 |
C7 |
C8 |
S11 |
359.8 |
360.0 |
| C5 |
C6 |
H6 |
C7 |
180.0 |
179.7 |
| H6 |
C6 |
C7 |
H5 |
353.1 |
360.0 |
| C13 |
C12 |
H7 |
H8 |
119.0 |
240.0 |
| C13 |
C12 |
H8 |
H7 |
241.0 |
120.0 |
| C14 |
C13 |
H9 |
H10 |
119.9 |
240.0 |
| H9 |
C13 |
C12 |
H7 |
182.6 |
180.0 |
| H9 |
C13 |
C12 |
H8 |
301.9 |
60.0 |
| C14 |
C13 |
H10 |
H9 |
240.1 |
120.0 |
| H10 |
C13 |
C12 |
H7 |
62.6 |
299.9 |
| H10 |
C13 |
C12 |
H8 |
181.9 |
180.0 |
| H11 |
C14 |
C13 |
H9 |
300.0 |
59.9 |
| H11 |
C14 |
C13 |
H10 |
60.0 |
300.0 |
| H12 |
C14 |
H11 |
H13 |
120.0 |
120.0 |
| H12 |
C14 |
C13 |
H9 |
60.0 |
180.0 |
| H12 |
C14 |
C13 |
H10 |
180.0 |
60.0 |
| H11 |
C14 |
H12 |
H13 |
240.0 |
240.0 |
| H13 |
C14 |
C13 |
H9 |
180.0 |
300.0 |
| H13 |
C14 |
C13 |
H10 |
300.0 |
180.0 |
| H11 |
C14 |
H13 |
H12 |
120.0 |
120.0 |