PDB Chemical Component VA6
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 VA6
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3' |
C3' |
1.486 |
1.429 |
| C4' |
C5' |
1.409 |
1.530 |
| C4' |
O4' |
1.599 |
1.434 |
| C4' |
C3' |
1.533 |
1.543 |
| C5' |
O5' |
1.449 |
1.429 |
| O1B |
PB |
1.519 |
1.480 |
| O4' |
C1' |
1.290 |
1.437 |
| C3' |
C2' |
1.342 |
1.554 |
| C2' |
C1' |
1.611 |
1.549 |
| O2B |
PB |
1.517 |
1.610 |
| O3G |
PG |
1.559 |
1.480 |
| C1' |
N9 |
1.376 |
1.465 |
| PB |
O3A |
1.639 |
1.610 |
| PB |
C3B |
1.807 |
1.823 |
| O1A |
PA |
1.537 |
1.480 |
| O5' |
PA |
1.556 |
1.610 |
| O1G |
PG |
1.507 |
1.611 |
| N3 |
C2 |
1.344 |
1.316 |
| N3 |
C4 |
1.412 |
1.330 |
| O3A |
PA |
1.512 |
1.610 |
| PA |
O2A |
1.607 |
1.610 |
| PG |
C3B |
1.824 |
1.823 |
| PG |
O2G |
1.462 |
1.611 |
| F1B |
C3B |
1.327 |
1.399 |
| N9 |
C4 |
1.350 |
1.371 |
| N9 |
C8 |
1.345 |
1.364 |
| C3B |
F2B |
1.409 |
1.400 |
| C2 |
N1 |
1.333 |
1.321 |
| C4 |
C5 |
1.421 |
1.405 |
| C8 |
N7 |
1.324 |
1.301 |
| N1 |
C6 |
1.400 |
1.329 |
| C5 |
N7 |
1.358 |
1.354 |
| C5 |
C6 |
1.433 |
1.406 |
| C6 |
N6 |
1.380 |
1.383 |
| C2 |
H1 |
1.080 |
1.079 |
| N6 |
H2 |
1.000 |
0.970 |
| N6 |
H3 |
1.000 |
0.970 |
| C8 |
H4 |
1.080 |
1.080 |
| C1' |
H5 |
1.100 |
1.089 |
| O2B |
H6 |
0.950 |
0.966 |
| O1G |
H7 |
0.949 |
0.968 |
| C2' |
H8 |
1.100 |
1.090 |
| C2' |
H9 |
1.100 |
1.090 |
| O2A |
H10 |
0.950 |
0.967 |
| O2G |
H11 |
0.950 |
0.967 |
| C3' |
H12 |
1.100 |
1.091 |
| O3' |
H13 |
0.950 |
0.966 |
| C4' |
H14 |
1.100 |
1.089 |
| C5' |
H15 |
1.100 |
1.090 |
| C5' |
H16 |
1.100 |
1.090 |
Bond Angles for VA6
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
H12 |
108.5 |
110.7 |
| O4' |
C4' |
C5' |
110.8 |
109.8 |
| C4' |
C5' |
O5' |
113.0 |
109.4 |
| C5' |
C4' |
H14 |
111.0 |
109.8 |
| C4' |
C5' |
H15 |
108.6 |
109.5 |
| C4' |
C5' |
H16 |
108.6 |
109.5 |
| O4' |
C4' |
H14 |
108.4 |
109.9 |
| C4' |
C3' |
H12 |
107.9 |
110.9 |
| O5' |
C5' |
H15 |
108.6 |
109.5 |
| O5' |
C5' |
H16 |
108.6 |
109.5 |
| O1B |
PB |
O3A |
111.9 |
109.5 |
| O1B |
PB |
C3B |
108.2 |
109.5 |
| O4' |
C1' |
H5 |
101.8 |
110.3 |
| C3' |
C2' |
H8 |
114.1 |
111.1 |
| C3' |
C2' |
H9 |
114.1 |
111.2 |
| C2' |
C1' |
H5 |
99.4 |
110.3 |
| O2B |
PB |
O3A |
109.0 |
109.5 |
| O2B |
PB |
C3B |
109.9 |
109.5 |
| O3A |
PB |
C3B |
109.9 |
109.5 |
| PB |
C3B |
PG |
112.2 |
109.5 |
| PB |
C3B |
F2B |
109.9 |
109.5 |
| O1A |
PA |
O2A |
108.0 |
109.5 |
| O1G |
PG |
C3B |
112.0 |
109.4 |
| O1G |
PG |
O2G |
107.6 |
109.4 |
| N3 |
C2 |
H1 |
118.4 |
118.8 |
| N3 |
C4 |
C5 |
118.1 |
119.1 |
| PA |
O2A |
H10 |
109.5 |
114.0 |
| O2G |
PG |
C3B |
108.0 |
109.5 |
| PG |
C3B |
F2B |
108.7 |
109.5 |
| PG |
O2G |
H11 |
109.5 |
114.0 |
| F1B |
C3B |
F2B |
110.2 |
109.5 |
| N9 |
C8 |
H4 |
124.9 |
125.0 |
| C2 |
N1 |
C6 |
120.3 |
121.2 |
| C4 |
C5 |
N7 |
107.3 |
107.2 |
| C4 |
C5 |
C6 |
118.9 |
118.2 |
| N1 |
C6 |
C5 |
118.9 |
118.4 |
| N1 |
C6 |
N6 |
122.2 |
120.8 |
| C6 |
C5 |
N7 |
133.8 |
134.7 |
| C5 |
C6 |
N6 |
119.0 |
120.8 |
| C6 |
N6 |
H2 |
109.5 |
120.0 |
| C6 |
N6 |
H3 |
109.4 |
120.0 |
| H2 |
N6 |
H3 |
109.5 |
120.0 |
| H8 |
C2' |
H9 |
109.4 |
111.0 |
| H15 |
C5' |
H16 |
109.4 |
109.5 |
Torsion Angles for VA6
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C3' |
O3' |
H12 |
237.8 |
236.4 |
| O3' |
C3' |
C2' |
H8 |
290.4 |
34.7 |
| O3' |
C3' |
C2' |
H9 |
57.2 |
270.5 |
| O4' |
C4' |
C5' |
H14 |
120.5 |
120.9 |
| C5' |
C4' |
C3' |
H12 |
331.1 |
337.3 |
| O5' |
C5' |
C4' |
H15 |
239.5 |
240.0 |
| O5' |
C5' |
C4' |
H16 |
120.5 |
120.0 |
| H15 |
C5' |
C4' |
H16 |
241.1 |
239.9 |
| O4' |
C4' |
C5' |
O5' |
301.4 |
66.5 |
| C5' |
C4' |
O4' |
H14 |
237.9 |
239.1 |
| O4' |
C4' |
C5' |
H15 |
62.0 |
186.4 |
| O4' |
C4' |
C5' |
H16 |
180.9 |
306.5 |
| O4' |
C4' |
C3' |
H12 |
91.3 |
96.7 |
| C4' |
O4' |
C1' |
H5 |
308.7 |
265.3 |
| O3' |
C3' |
C4' |
H12 |
122.5 |
123.6 |
| C4' |
C3' |
C2' |
H8 |
165.3 |
276.2 |
| C4' |
C3' |
C2' |
H9 |
292.2 |
152.1 |
| O5' |
C5' |
C4' |
H14 |
180.9 |
305.6 |
| C4' |
C5' |
O5' |
H15 |
120.5 |
120.0 |
| C4' |
C5' |
O5' |
H16 |
239.5 |
240.0 |
| H15 |
C5' |
O5' |
H16 |
118.9 |
120.0 |
| O2B |
PB |
O1B |
O3A |
240.1 |
240.0 |
| O2B |
PB |
O1B |
C3B |
118.9 |
120.0 |
| O3A |
PB |
O1B |
C3B |
238.8 |
240.0 |
| O1B |
PB |
C3B |
PG |
344.3 |
60.0 |
| O1B |
PB |
C3B |
F2B |
223.2 |
300.0 |
| C2' |
C1' |
O4' |
H5 |
103.0 |
119.0 |
| C3' |
C2' |
C1' |
H5 |
32.0 |
82.6 |
| H8 |
C2' |
C3' |
H9 |
233.2 |
124.2 |
| O4' |
C1' |
C2' |
H5 |
255.2 |
241.0 |
| O1B |
PB |
O2B |
O3A |
121.7 |
120.0 |
| O1B |
PB |
O2B |
C3B |
242.2 |
240.0 |
| O3A |
PB |
O2B |
C3B |
120.5 |
120.0 |
| O2B |
PB |
C3B |
PG |
226.6 |
300.0 |
| O2B |
PB |
C3B |
F2B |
105.5 |
180.0 |
| O3G |
PG |
O2G |
H11 |
0.0 |
180.0 |
| C1' |
N9 |
C8 |
H4 |
357.1 |
359.9 |
| O1B |
PB |
O3A |
C3B |
120.2 |
120.0 |
| O2B |
PB |
O3A |
C3B |
239.5 |
240.0 |
| O3A |
PB |
C3B |
PG |
106.7 |
180.0 |
| O3A |
PB |
C3B |
F2B |
345.6 |
60.0 |
| O1B |
PB |
C3B |
O3A |
237.6 |
240.0 |
| O2B |
PB |
C3B |
O3A |
119.9 |
120.0 |
| O1G |
PG |
C3B |
PB |
325.2 |
180.0 |
| O2G |
PG |
C3B |
PB |
206.8 |
300.0 |
| PG |
C3B |
PB |
F2B |
121.1 |
120.0 |
| F1B |
C3B |
PB |
F2B |
237.8 |
240.0 |
| O1A |
PA |
O2A |
H10 |
360.0 |
180.1 |
| O5' |
PA |
O2A |
H10 |
115.7 |
300.1 |
| PB |
C3B |
PG |
O1G |
325.2 |
180.0 |
| O2G |
PG |
O1G |
C3B |
118.5 |
240.0 |
| O1G |
PG |
C3B |
F2B |
87.0 |
300.0 |
| O1G |
PG |
O2G |
H11 |
122.5 |
60.0 |
| N3 |
C2 |
N1 |
C6 |
0.4 |
0.1 |
| C4 |
N3 |
C2 |
H1 |
179.9 |
180.0 |
| N3 |
C4 |
C5 |
N7 |
179.8 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.0 |
0.0 |
| O3A |
PA |
O2A |
H10 |
235.8 |
60.1 |
| PB |
C3B |
PG |
F2B |
238.2 |
240.0 |
| O1G |
PG |
C3B |
O2G |
118.3 |
240.0 |
| C3B |
PG |
O2G |
H11 |
243.6 |
300.1 |
| F1B |
C3B |
PG |
F2B |
117.7 |
120.0 |
| PB |
C3B |
PG |
O2G |
206.8 |
300.0 |
| O1G |
PG |
O2G |
C3B |
238.9 |
120.0 |
| O2G |
PG |
C3B |
F2B |
328.6 |
59.9 |
| PB |
C3B |
F1B |
F2B |
122.0 |
120.0 |
| PG |
C3B |
F1B |
F2B |
243.3 |
240.0 |
| PB |
C3B |
F2B |
PG |
123.2 |
120.0 |
| C2 |
N1 |
C6 |
C5 |
359.4 |
359.9 |
| C2 |
N1 |
C6 |
N6 |
179.4 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.3 |
0.0 |
| C6 |
C5 |
C4 |
N7 |
180.3 |
180.0 |
| C4 |
C5 |
C6 |
N6 |
180.4 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
0.3 |
0.0 |
| N1 |
C6 |
C5 |
N7 |
180.7 |
180.1 |
| C5 |
C6 |
N1 |
N6 |
180.1 |
180.0 |
| N1 |
C6 |
N6 |
H2 |
360.0 |
360.0 |
| N1 |
C6 |
N6 |
H3 |
120.0 |
180.0 |
| C4 |
C5 |
N7 |
C6 |
180.3 |
180.1 |
| N7 |
C5 |
C6 |
N6 |
0.8 |
0.1 |
| C4 |
C5 |
C6 |
N7 |
179.6 |
179.9 |
| N1 |
C6 |
C5 |
N6 |
179.9 |
180.0 |
| C5 |
C6 |
N6 |
H2 |
179.9 |
180.0 |
| C5 |
C6 |
N6 |
H3 |
299.9 |
360.0 |
| N1 |
C6 |
N6 |
C5 |
180.1 |
180.0 |
| N6 |
C6 |
C5 |
N7 |
0.8 |
0.1 |
| H2 |
N6 |
C6 |
H3 |
240.0 |
180.0 |
| H1 |
C2 |
N1 |
C6 |
180.4 |
180.1 |
| C6 |
N6 |
H2 |
H3 |
120.0 |
180.0 |
| C6 |
N6 |
H3 |
H2 |
240.0 |
180.0 |
| H6 |
O2B |
PB |
O3A |
238.3 |
60.0 |
| H6 |
O2B |
PB |
C3B |
117.8 |
300.0 |
| H7 |
O1G |
PG |
C3B |
122.9 |
180.0 |
| H7 |
O1G |
PG |
O2G |
241.4 |
60.0 |
| C3' |
C2' |
H8 |
H9 |
129.2 |
235.7 |
| H8 |
C2' |
C1' |
H5 |
275.4 |
200.5 |
| C3' |
C2' |
H9 |
H8 |
230.8 |
124.2 |
| H9 |
C2' |
C1' |
H5 |
148.6 |
324.7 |
| H11 |
O2G |
PG |
C3B |
243.6 |
300.1 |
| H12 |
C3' |
C2' |
H8 |
50.8 |
158.0 |
| H12 |
C3' |
C2' |
H9 |
177.6 |
33.9 |
| H13 |
O3' |
C3' |
H12 |
302.2 |
298.0 |
| O4' |
C4' |
H14 |
C5' |
238.1 |
239.1 |
| H14 |
C4' |
C5' |
O5' |
180.9 |
305.6 |
| H14 |
C4' |
C5' |
H15 |
301.5 |
65.5 |
| H14 |
C4' |
C5' |
H16 |
60.4 |
185.6 |
| H14 |
C4' |
C3' |
H12 |
206.8 |
216.4 |
| C4' |
C5' |
H15 |
O5' |
236.8 |
240.0 |
| H15 |
C5' |
C4' |
H14 |
301.5 |
65.5 |
| C4' |
C5' |
H15 |
H16 |
118.4 |
120.0 |
| O5' |
C5' |
H15 |
H16 |
241.6 |
240.0 |
| C4' |
C5' |
H16 |
O5' |
123.2 |
119.9 |
| H16 |
C5' |
C4' |
H14 |
60.4 |
185.6 |
| C4' |
C5' |
H16 |
H15 |
241.6 |
239.9 |
| O5' |
C5' |
H16 |
H15 |
118.4 |
120.0 |