PDB Chemical Component 5V6
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 5V6
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| S |
C7 |
1.719 |
1.758 |
| S |
C6 |
1.732 |
1.758 |
| C7 |
C8 |
1.390 |
1.331 |
| C6 |
C5 |
1.401 |
1.346 |
| C8 |
C5 |
1.412 |
1.395 |
| C5 |
C4 |
1.497 |
1.483 |
| C4 |
C3 |
1.406 |
1.392 |
| C4 |
C9 |
1.487 |
1.399 |
| O2 |
C9 |
1.376 |
1.359 |
| O2 |
C10 |
1.431 |
1.429 |
| C3 |
C2 |
1.404 |
1.381 |
| C9 |
C11 |
1.416 |
1.385 |
| C2 |
C1 |
1.522 |
1.507 |
| C2 |
C12 |
1.403 |
1.384 |
| C11 |
C12 |
1.397 |
1.382 |
| C1 |
C |
1.505 |
1.506 |
| O1 |
C |
1.249 |
1.209 |
| C |
O |
1.241 |
1.342 |
| C1 |
H1 |
1.100 |
1.090 |
| C1 |
H2 |
1.100 |
1.090 |
| C3 |
H3 |
1.080 |
1.080 |
| C11 |
H4 |
1.080 |
1.080 |
| C12 |
H5 |
1.079 |
1.080 |
| O |
H6 |
0.950 |
0.967 |
| C10 |
H7 |
1.100 |
1.090 |
| C10 |
H8 |
1.100 |
1.090 |
| C10 |
H9 |
1.100 |
1.090 |
| C6 |
H10 |
1.080 |
1.079 |
| C7 |
H11 |
1.080 |
1.080 |
| C8 |
H12 |
1.080 |
1.080 |
Bond Angles for 5V6
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| S |
C7 |
C8 |
104.9 |
109.9 |
| S |
C7 |
H11 |
127.6 |
125.1 |
| S |
C6 |
H10 |
126.8 |
125.2 |
| C8 |
C7 |
H11 |
127.5 |
125.0 |
| C7 |
C8 |
H12 |
121.3 |
122.6 |
| C4 |
C3 |
H3 |
119.5 |
120.0 |
| O2 |
C9 |
C4 |
119.5 |
120.1 |
| C9 |
O2 |
C10 |
121.4 |
117.0 |
| O2 |
C9 |
C11 |
121.3 |
120.2 |
| O2 |
C10 |
H7 |
109.5 |
109.5 |
| O2 |
C10 |
H8 |
109.5 |
109.5 |
| O2 |
C10 |
H9 |
109.5 |
109.5 |
| C3 |
C2 |
C12 |
120.7 |
120.2 |
| C9 |
C11 |
H4 |
119.9 |
120.0 |
| C2 |
C1 |
C |
112.4 |
109.5 |
| C2 |
C1 |
H1 |
108.7 |
109.5 |
| C2 |
C1 |
H2 |
108.8 |
109.4 |
| C2 |
C12 |
C11 |
120.9 |
120.3 |
| C2 |
C12 |
H5 |
119.5 |
119.8 |
| C12 |
C11 |
H4 |
119.9 |
120.0 |
| C11 |
C12 |
H5 |
119.5 |
119.9 |
| C1 |
C |
O1 |
119.1 |
120.0 |
| C1 |
C |
O |
118.5 |
120.0 |
| C |
C1 |
H1 |
108.7 |
109.5 |
| C |
C1 |
H2 |
108.7 |
109.5 |
| O1 |
C |
O |
122.4 |
120.0 |
| C |
O |
H6 |
109.5 |
117.0 |
| H1 |
C1 |
H2 |
109.5 |
109.4 |
| H7 |
C10 |
H8 |
109.5 |
109.5 |
| H7 |
C10 |
H9 |
109.4 |
109.5 |
| H8 |
C10 |
H9 |
109.5 |
109.5 |
Torsion Angles for 5V6
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C7 |
S |
C6 |
H10 |
181.9 |
180.0 |
| C8 |
C7 |
S |
H11 |
180.0 |
179.8 |
| S |
C7 |
C8 |
H12 |
181.4 |
180.0 |
| S |
C7 |
C8 |
H11 |
180.0 |
180.2 |
| C5 |
C4 |
C3 |
H3 |
358.5 |
0.0 |
| C9 |
C4 |
C3 |
H3 |
181.2 |
180.0 |
| C4 |
C9 |
O2 |
C10 |
186.3 |
180.0 |
| O2 |
C9 |
C4 |
C11 |
179.1 |
180.3 |
| C4 |
C9 |
C11 |
H4 |
180.7 |
180.2 |
| C9 |
O2 |
C10 |
H7 |
180.0 |
60.0 |
| C9 |
O2 |
C10 |
H8 |
300.0 |
180.0 |
| C9 |
O2 |
C10 |
H9 |
60.0 |
300.0 |
| O2 |
C9 |
C11 |
H4 |
1.7 |
360.0 |
| C10 |
O2 |
C9 |
C4 |
186.3 |
180.0 |
| C10 |
O2 |
C9 |
C11 |
5.3 |
0.2 |
| H7 |
C10 |
O2 |
H8 |
240.0 |
240.0 |
| H7 |
C10 |
O2 |
H9 |
120.0 |
120.0 |
| H8 |
C10 |
O2 |
H9 |
240.0 |
240.0 |
| C3 |
C2 |
C1 |
C |
285.1 |
270.3 |
| C3 |
C2 |
C1 |
H1 |
45.5 |
30.4 |
| C3 |
C2 |
C1 |
H2 |
164.7 |
150.3 |
| C3 |
C2 |
C12 |
C11 |
1.8 |
359.8 |
| C3 |
C2 |
C12 |
H5 |
181.8 |
179.7 |
| O2 |
C9 |
C11 |
C4 |
180.9 |
179.7 |
| C11 |
C9 |
O2 |
C10 |
5.3 |
0.2 |
| C12 |
C11 |
C9 |
H4 |
180.0 |
180.1 |
| C9 |
C11 |
C12 |
H5 |
178.7 |
180.0 |
| C2 |
C1 |
C |
O1 |
151.7 |
0.0 |
| C2 |
C1 |
C |
O |
330.9 |
180.0 |
| C |
C1 |
C2 |
H1 |
239.6 |
239.9 |
| C |
C1 |
C2 |
H2 |
120.4 |
120.0 |
| H1 |
C1 |
C2 |
H2 |
240.8 |
240.1 |
| C12 |
C2 |
C1 |
C |
108.6 |
90.0 |
| C12 |
C2 |
C1 |
H1 |
229.0 |
210.0 |
| C12 |
C2 |
C1 |
H2 |
348.2 |
330.0 |
| C2 |
C12 |
C11 |
H4 |
178.7 |
180.0 |
| C11 |
C12 |
C2 |
H5 |
180.0 |
180.1 |
| O2 |
C9 |
C11 |
C12 |
181.7 |
180.0 |
| C9 |
C11 |
C12 |
H4 |
180.0 |
179.9 |
| C2 |
C12 |
C11 |
H5 |
180.0 |
179.9 |
| C2 |
C1 |
C |
H1 |
120.4 |
120.0 |
| C2 |
C1 |
C |
H2 |
239.6 |
240.0 |
| O1 |
C |
C1 |
O |
180.8 |
180.0 |
| C1 |
C |
O |
H6 |
180.8 |
180.0 |
| H1 |
C1 |
C |
H2 |
119.1 |
120.0 |
| C1 |
C |
O1 |
O |
179.2 |
180.0 |
| O1 |
C |
C1 |
H1 |
31.3 |
240.0 |
| O1 |
C |
C1 |
H2 |
272.1 |
120.0 |
| O1 |
C |
O |
H6 |
360.0 |
360.0 |
| C1 |
C |
O |
O1 |
180.8 |
180.0 |
| O |
C |
C1 |
H1 |
210.5 |
60.0 |
| O |
C |
C1 |
H2 |
91.3 |
300.0 |
| C2 |
C1 |
H1 |
C |
237.4 |
240.0 |
| C2 |
C1 |
H1 |
H2 |
118.7 |
119.9 |
| H1 |
C1 |
C |
O1 |
31.3 |
240.0 |
| H1 |
C1 |
C |
O |
210.5 |
60.0 |
| C |
C1 |
H1 |
H2 |
241.3 |
240.0 |
| C2 |
C1 |
H2 |
C |
122.6 |
120.0 |
| C2 |
C1 |
H2 |
H1 |
241.3 |
240.1 |
| H2 |
C1 |
C |
O1 |
272.1 |
120.0 |
| H2 |
C1 |
C |
O |
91.3 |
300.0 |
| C |
C1 |
H2 |
H1 |
118.7 |
120.0 |
| H3 |
C3 |
C2 |
C12 |
178.2 |
180.2 |
| H4 |
C11 |
C12 |
H5 |
358.7 |
0.1 |
| C2 |
C12 |
H5 |
C11 |
180.0 |
180.1 |
| H5 |
C12 |
C11 |
H4 |
358.7 |
0.1 |
| O2 |
C10 |
H7 |
H8 |
120.0 |
120.0 |
| O2 |
C10 |
H7 |
H9 |
240.0 |
240.0 |
| H8 |
C10 |
H7 |
H9 |
120.0 |
120.0 |
| O2 |
C10 |
H8 |
H7 |
240.0 |
240.0 |
| O2 |
C10 |
H8 |
H9 |
120.0 |
120.0 |
| H7 |
C10 |
H8 |
H9 |
240.0 |
240.0 |
| O2 |
C10 |
H9 |
H7 |
120.0 |
120.0 |
| O2 |
C10 |
H9 |
H8 |
240.0 |
240.0 |
| H7 |
C10 |
H9 |
H8 |
120.0 |
120.0 |
| S |
C7 |
H11 |
C8 |
180.0 |
179.8 |
| H11 |
C7 |
C8 |
H12 |
1.4 |
359.8 |
| H12 |
C8 |
C7 |
H11 |
1.4 |
359.8 |