PDB Chemical Component VA4
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 VA4
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2 |
N1 |
1.311 |
1.320 |
| C2 |
N3 |
1.323 |
1.317 |
| N1 |
C6 |
1.329 |
1.329 |
| N3 |
C4 |
1.334 |
1.328 |
| C6 |
N6 |
1.484 |
1.384 |
| C6 |
C5 |
1.409 |
1.405 |
| C4 |
C5 |
1.408 |
1.406 |
| C4 |
N9 |
1.351 |
1.372 |
| C2' |
C1' |
1.300 |
1.546 |
| C2' |
C3' |
1.486 |
1.545 |
| C1' |
N9 |
1.468 |
1.465 |
| C1' |
O4' |
1.620 |
1.444 |
| C5 |
N7 |
1.393 |
1.355 |
| N9 |
C8 |
1.376 |
1.363 |
| O3' |
C3' |
1.384 |
1.428 |
| C3' |
C4' |
1.586 |
1.545 |
| O4' |
C4' |
1.229 |
1.444 |
| N7 |
C8 |
1.316 |
1.301 |
| C4' |
C5' |
1.524 |
1.530 |
| O2B |
PB |
1.560 |
1.480 |
| C5' |
O5' |
1.396 |
1.429 |
| O5' |
PA |
1.603 |
1.610 |
| PB |
O3A |
1.590 |
1.610 |
| PB |
O1B |
1.560 |
1.610 |
| PB |
C3B |
1.879 |
1.823 |
| O3A |
PA |
1.627 |
1.610 |
| CL1 |
C3B |
1.755 |
1.803 |
| PA |
O2A |
1.477 |
1.480 |
| PA |
O1A |
1.528 |
1.610 |
| C3B |
PG |
1.803 |
1.823 |
| PG |
O3G |
1.461 |
1.480 |
| PG |
O1G |
1.526 |
1.610 |
| PG |
O2G |
1.587 |
1.610 |
| C2 |
H1 |
1.080 |
1.081 |
| N6 |
H2 |
1.000 |
0.970 |
| N6 |
H3 |
1.000 |
0.970 |
| C8 |
H4 |
1.080 |
1.080 |
| C1' |
H5 |
1.100 |
1.090 |
| O1A |
H6 |
0.950 |
0.967 |
| O1G |
H7 |
0.950 |
0.967 |
| C2' |
H8 |
1.100 |
1.090 |
| C2' |
H9 |
1.100 |
1.089 |
| O1B |
H10 |
0.950 |
0.967 |
| O2G |
H11 |
0.950 |
0.967 |
| C3' |
H12 |
1.099 |
1.090 |
| O3' |
H13 |
0.950 |
0.967 |
| C3B |
H14 |
1.100 |
1.090 |
| C4' |
H15 |
1.100 |
1.089 |
| C5' |
H16 |
1.100 |
1.089 |
| C5' |
H17 |
1.100 |
1.091 |
Bond Angles for VA4
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
121.3 |
121.2 |
| C2 |
N3 |
C4 |
119.0 |
120.6 |
| N3 |
C2 |
H1 |
118.5 |
118.7 |
| N1 |
C6 |
N6 |
120.5 |
120.8 |
| N1 |
C6 |
C5 |
119.4 |
118.4 |
| N3 |
C4 |
C5 |
121.2 |
119.1 |
| N3 |
C4 |
N9 |
132.9 |
135.0 |
| C6 |
N6 |
H2 |
109.5 |
120.0 |
| C6 |
N6 |
H3 |
109.5 |
120.1 |
| C6 |
C5 |
N7 |
135.9 |
134.7 |
| C5 |
C4 |
N9 |
105.9 |
106.0 |
| C4 |
C5 |
N7 |
108.0 |
107.1 |
| C4 |
N9 |
C8 |
108.7 |
107.5 |
| C2' |
C1' |
O4' |
105.2 |
104.8 |
| C2' |
C1' |
H5 |
113.4 |
110.4 |
| C2' |
C3' |
C4' |
100.1 |
104.1 |
| C3' |
C2' |
H8 |
110.3 |
110.5 |
| C3' |
C2' |
H9 |
110.3 |
110.6 |
| C2' |
C3' |
H12 |
109.7 |
110.5 |
| C1' |
O4' |
C4' |
108.5 |
105.3 |
| O4' |
C1' |
H5 |
108.5 |
110.3 |
| C5 |
N7 |
C8 |
107.1 |
109.5 |
| N9 |
C8 |
H4 |
124.9 |
125.0 |
| O3' |
C3' |
C4' |
112.1 |
110.5 |
| O3' |
C3' |
H12 |
111.3 |
110.6 |
| C3' |
C4' |
C5' |
109.5 |
110.4 |
| C4' |
C3' |
H12 |
108.5 |
110.5 |
| C3' |
C4' |
H15 |
109.1 |
110.4 |
| O4' |
C4' |
C5' |
109.8 |
110.4 |
| O4' |
C4' |
H15 |
114.9 |
110.4 |
| N7 |
C8 |
H4 |
124.9 |
125.1 |
| C4' |
C5' |
O5' |
106.9 |
109.5 |
| C5' |
C4' |
H15 |
109.9 |
110.3 |
| C4' |
C5' |
H16 |
110.1 |
109.5 |
| C4' |
C5' |
H17 |
110.1 |
109.5 |
| O2B |
PB |
O3A |
107.1 |
109.4 |
| O2B |
PB |
O1B |
109.1 |
109.5 |
| O2B |
PB |
C3B |
109.5 |
109.5 |
| O5' |
C5' |
H16 |
110.1 |
109.5 |
| O5' |
C5' |
H17 |
110.1 |
109.4 |
| O1B |
PB |
O3A |
114.3 |
109.5 |
| O3A |
PB |
C3B |
104.6 |
109.5 |
| O1B |
PB |
C3B |
111.9 |
109.5 |
| PB |
O1B |
H10 |
109.5 |
114.0 |
| PB |
C3B |
PG |
111.9 |
109.5 |
| PB |
C3B |
H14 |
107.0 |
109.5 |
| CL1 |
C3B |
H14 |
108.2 |
109.4 |
| O1A |
PA |
O2A |
109.6 |
109.5 |
| PA |
O1A |
H6 |
109.5 |
114.0 |
| C3B |
PG |
O3G |
111.5 |
109.5 |
| O1G |
PG |
O3G |
111.7 |
109.5 |
| O2G |
PG |
O3G |
108.9 |
109.5 |
| O1G |
PG |
O2G |
107.8 |
109.5 |
| PG |
O1G |
H7 |
109.5 |
114.0 |
| PG |
O2G |
H11 |
109.5 |
114.0 |
| H2 |
N6 |
H3 |
109.5 |
120.0 |
| H8 |
C2' |
H9 |
109.4 |
110.6 |
| H16 |
C5' |
H17 |
109.5 |
109.4 |
Torsion Angles for VA4
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
N6 |
179.3 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
359.9 |
360.0 |
| N3 |
C2 |
N1 |
C6 |
358.7 |
0.0 |
| C2 |
N3 |
C4 |
C5 |
359.2 |
360.0 |
| C2 |
N3 |
C4 |
N9 |
179.0 |
179.9 |
| N1 |
C6 |
N6 |
H2 |
360.0 |
360.0 |
| N1 |
C6 |
N6 |
H3 |
120.0 |
180.0 |
| N1 |
C6 |
C5 |
N7 |
178.8 |
180.0 |
| C4 |
N3 |
C2 |
H1 |
181.7 |
180.0 |
| C5 |
C4 |
N3 |
N9 |
180.2 |
180.1 |
| N3 |
C4 |
C5 |
N7 |
181.1 |
180.0 |
| N3 |
C4 |
N9 |
C8 |
179.5 |
180.0 |
| N1 |
C6 |
N6 |
C5 |
180.6 |
179.9 |
| N6 |
C6 |
C5 |
N7 |
359.4 |
360.0 |
| H2 |
N6 |
C6 |
H3 |
240.0 |
180.0 |
| N1 |
C6 |
C5 |
N6 |
179.4 |
180.1 |
| C6 |
C5 |
C4 |
N9 |
179.7 |
180.1 |
| C4 |
C5 |
C6 |
N7 |
182.2 |
180.0 |
| C6 |
C5 |
N7 |
C8 |
180.7 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.9 |
0.0 |
| N3 |
C4 |
C5 |
N9 |
179.9 |
180.0 |
| C6 |
C5 |
C4 |
N7 |
178.4 |
180.0 |
| C5 |
C4 |
N9 |
C8 |
359.3 |
360.0 |
| C4 |
C5 |
N7 |
C8 |
358.6 |
360.0 |
| N3 |
C4 |
N9 |
C5 |
180.2 |
180.1 |
| N9 |
C4 |
C5 |
N7 |
1.3 |
0.1 |
| C4 |
N9 |
C8 |
H4 |
179.8 |
180.1 |
| C2' |
C1' |
O4' |
C4' |
355.9 |
319.5 |
| O4' |
C1' |
C2' |
H5 |
118.5 |
118.8 |
| C3' |
C2' |
C1' |
O4' |
337.3 |
24.0 |
| C3' |
C2' |
C1' |
H5 |
218.8 |
265.1 |
| O3' |
C3' |
C2' |
C4' |
120.1 |
118.6 |
| O3' |
C3' |
C2' |
H12 |
234.1 |
237.3 |
| C2' |
C3' |
C4' |
C5' |
203.3 |
217.2 |
| C4' |
C3' |
C2' |
H12 |
113.9 |
118.6 |
| C2' |
C3' |
C4' |
H15 |
83.0 |
95.0 |
| H8 |
C2' |
C3' |
H9 |
121.1 |
122.8 |
| C1' |
N9 |
C8 |
H4 |
357.9 |
0.0 |
| C2' |
C1' |
O4' |
H5 |
238.3 |
241.1 |
| C1' |
O4' |
C4' |
C5' |
143.5 |
159.3 |
| C1' |
O4' |
C4' |
H15 |
268.0 |
281.6 |
| N7 |
C5 |
C4 |
N9 |
1.3 |
0.1 |
| C5 |
N7 |
C8 |
H4 |
181.0 |
180.0 |
| N7 |
C8 |
N9 |
H4 |
180.0 |
180.0 |
| C2' |
C3' |
O3' |
C4' |
246.8 |
245.3 |
| O3' |
C3' |
C2' |
H8 |
37.9 |
0.1 |
| O3' |
C3' |
C2' |
H9 |
276.8 |
237.3 |
| C2' |
C3' |
O3' |
H12 |
125.1 |
122.7 |
| O3' |
C3' |
C4' |
C5' |
81.5 |
98.6 |
| C4' |
C3' |
O3' |
H12 |
238.3 |
237.3 |
| O3' |
C3' |
C4' |
H15 |
321.2 |
336.3 |
| C4' |
C3' |
C2' |
H8 |
277.8 |
241.4 |
| C4' |
C3' |
C2' |
H9 |
156.7 |
118.6 |
| C2' |
C3' |
C4' |
H12 |
245.1 |
241.4 |
| C1' |
O4' |
C4' |
C3' |
26.7 |
40.5 |
| O3' |
C3' |
C4' |
H12 |
123.3 |
122.7 |
| O4' |
C4' |
C3' |
C5' |
117.0 |
118.8 |
| O4' |
C4' |
C3' |
H15 |
237.3 |
241.1 |
| C3' |
C4' |
C5' |
O5' |
60.3 |
185.0 |
| C5' |
C4' |
C3' |
H15 |
120.3 |
122.3 |
| C3' |
C4' |
C5' |
H16 |
179.9 |
305.0 |
| C3' |
C4' |
C5' |
H17 |
300.7 |
65.0 |
| C4' |
O4' |
C1' |
H5 |
117.6 |
78.4 |
| C3' |
C4' |
O4' |
C5' |
243.2 |
241.2 |
| O4' |
C4' |
C3' |
H12 |
75.2 |
94.7 |
| C3' |
C4' |
O4' |
H15 |
118.7 |
118.9 |
| O4' |
C4' |
C5' |
O5' |
307.4 |
69.6 |
| C5' |
C4' |
O4' |
H15 |
235.5 |
237.7 |
| O4' |
C4' |
C5' |
H16 |
67.0 |
189.7 |
| O4' |
C4' |
C5' |
H17 |
187.8 |
309.6 |
| C4 |
N9 |
C8 |
N7 |
359.8 |
0.0 |
| N9 |
C8 |
N7 |
H4 |
180.0 |
180.0 |
| C5' |
C4' |
C3' |
H12 |
318.2 |
335.9 |
| C3' |
C4' |
C5' |
H15 |
240.2 |
237.7 |
| O4' |
C4' |
C5' |
H15 |
127.3 |
122.3 |
| O5' |
C5' |
C4' |
H16 |
240.4 |
239.9 |
| O5' |
C5' |
C4' |
H17 |
119.6 |
120.0 |
| H16 |
C5' |
C4' |
H17 |
239.2 |
240.0 |
| O1B |
PB |
O2B |
O3A |
124.3 |
120.0 |
| O3A |
PB |
O2B |
C3B |
112.9 |
120.0 |
| O1B |
PB |
O2B |
C3B |
237.1 |
240.0 |
| O2B |
PB |
O1B |
H10 |
360.0 |
180.0 |
| O2B |
PB |
C3B |
PG |
216.3 |
300.0 |
| O2B |
PB |
C3B |
H14 |
98.5 |
180.0 |
| O5' |
C5' |
C4' |
H15 |
180.1 |
307.3 |
| C4' |
C5' |
O5' |
H16 |
119.6 |
120.0 |
| C4' |
C5' |
O5' |
H17 |
240.4 |
240.0 |
| H16 |
C5' |
O5' |
H17 |
120.8 |
119.9 |
| O5' |
PA |
O1A |
H6 |
238.3 |
60.0 |
| O2B |
PB |
O3A |
O1B |
121.0 |
120.0 |
| O2B |
PB |
O3A |
C3B |
243.8 |
240.0 |
| O1B |
PB |
O3A |
C3B |
122.8 |
120.0 |
| O3A |
PB |
O1B |
H10 |
119.9 |
300.0 |
| O3A |
PB |
C3B |
PG |
101.8 |
180.0 |
| O3A |
PB |
C3B |
H14 |
344.0 |
60.0 |
| O2B |
PB |
O1B |
O3A |
240.1 |
240.0 |
| O2B |
PB |
O1B |
C3B |
121.4 |
120.0 |
| O3A |
PB |
O1B |
C3B |
241.3 |
240.0 |
| O1B |
PB |
C3B |
PG |
337.5 |
60.0 |
| O1B |
PB |
C3B |
H14 |
219.7 |
300.0 |
| O2B |
PB |
C3B |
O3A |
114.5 |
120.0 |
| O2B |
PB |
C3B |
O1B |
238.8 |
240.0 |
| O1B |
PB |
C3B |
O3A |
235.7 |
240.0 |
| C3B |
PB |
O1B |
H10 |
238.6 |
60.0 |
| CL1 |
C3B |
PB |
H14 |
241.2 |
240.0 |
| PB |
C3B |
PG |
O3G |
87.7 |
300.0 |
| O3A |
PA |
O1A |
H6 |
120.6 |
300.0 |
| PB |
C3B |
CL1 |
H14 |
118.1 |
120.0 |
| CL1 |
C3B |
PG |
O3G |
322.3 |
180.0 |
| O2A |
PA |
O1A |
H6 |
0.0 |
180.0 |
| PB |
C3B |
PG |
H14 |
242.7 |
240.0 |
| O1G |
PG |
C3B |
O3G |
236.9 |
120.0 |
| O2G |
PG |
C3B |
O3G |
120.1 |
240.0 |
| C3B |
PG |
O1G |
H7 |
123.0 |
60.1 |
| C3B |
PG |
O2G |
H11 |
238.2 |
180.0 |
| O1G |
PG |
O3G |
O2G |
241.0 |
120.0 |
| O3G |
PG |
O1G |
H7 |
360.0 |
180.0 |
| O3G |
PG |
O2G |
H11 |
360.0 |
60.0 |
| PB |
C3B |
PG |
O1G |
324.6 |
60.0 |
| C3B |
PG |
O1G |
O3G |
123.0 |
240.0 |
| O2G |
PG |
O1G |
O3G |
240.4 |
120.0 |
| O1G |
PG |
O2G |
H11 |
121.3 |
299.9 |
| PB |
C3B |
PG |
O2G |
207.8 |
180.0 |
| C3B |
PG |
O2G |
O3G |
238.3 |
120.0 |
| O1G |
PG |
O2G |
O3G |
121.4 |
240.0 |
| O2G |
PG |
O1G |
H7 |
240.4 |
300.1 |
| H1 |
C2 |
N1 |
C6 |
178.7 |
180.0 |
| H1 |
C2 |
N3 |
C4 |
181.7 |
180.0 |
| C6 |
N6 |
H2 |
H3 |
120.0 |
180.0 |
| C6 |
N6 |
H3 |
H2 |
240.0 |
180.0 |
| C2' |
C1' |
H5 |
O4' |
116.6 |
115.4 |
| H5 |
C1' |
O4' |
C4' |
117.6 |
78.4 |
| H6 |
O1A |
PA |
O2A |
0.0 |
180.0 |
| H7 |
O1G |
PG |
O3G |
360.0 |
180.0 |
| H7 |
O1G |
PG |
O2G |
240.4 |
300.1 |
| H8 |
C2' |
C1' |
O4' |
96.7 |
142.6 |
| H8 |
C2' |
C1' |
H5 |
338.2 |
23.8 |
| H8 |
C2' |
C3' |
C4' |
277.8 |
241.4 |
| C3' |
C2' |
H8 |
H9 |
238.4 |
237.2 |
| H8 |
C2' |
C3' |
H12 |
163.8 |
122.8 |
| H9 |
C2' |
C1' |
O4' |
217.8 |
265.3 |
| H9 |
C2' |
C1' |
H5 |
99.3 |
146.5 |
| H9 |
C2' |
C3' |
C4' |
156.7 |
118.6 |
| C3' |
C2' |
H9 |
H8 |
121.6 |
122.7 |
| H9 |
C2' |
C3' |
H12 |
42.8 |
0.0 |
| H10 |
O1B |
PB |
O3A |
119.9 |
300.0 |
| H10 |
O1B |
PB |
C3B |
238.6 |
60.0 |
| H11 |
O2G |
PG |
O3G |
360.0 |
60.0 |
| C2' |
C3' |
H12 |
C4' |
108.5 |
114.6 |
| H12 |
C3' |
C2' |
H8 |
163.8 |
122.8 |
| H12 |
C3' |
C2' |
H9 |
42.8 |
0.0 |
| O3' |
C3' |
H12 |
C4' |
236.2 |
237.3 |
| H12 |
C3' |
C4' |
C5' |
318.2 |
335.9 |
| H12 |
C3' |
C4' |
H15 |
197.9 |
213.6 |
| H13 |
O3' |
C3' |
C4' |
254.0 |
176.1 |
| H13 |
O3' |
C3' |
H12 |
15.7 |
298.8 |
| PB |
C3B |
H14 |
PG |
120.5 |
120.0 |
| H14 |
C3B |
PG |
O3G |
205.0 |
60.0 |
| C3' |
C4' |
H15 |
C5' |
120.1 |
122.3 |
| H15 |
C4' |
C3' |
H12 |
197.9 |
213.6 |
| O4' |
C4' |
H15 |
C5' |
235.6 |
237.7 |
| H15 |
C4' |
C5' |
O5' |
180.1 |
307.3 |
| H15 |
C4' |
C5' |
H16 |
299.7 |
67.3 |
| H15 |
C4' |
C5' |
H17 |
60.5 |
187.3 |
| C4' |
C5' |
H16 |
O5' |
242.4 |
240.0 |
| H16 |
C5' |
C4' |
H15 |
299.7 |
67.3 |
| C4' |
C5' |
H16 |
H17 |
121.2 |
120.0 |
| O5' |
C5' |
H16 |
H17 |
238.8 |
240.0 |
| C4' |
C5' |
H17 |
O5' |
117.6 |
120.0 |
| H17 |
C5' |
C4' |
H15 |
60.5 |
187.3 |
| C4' |
C5' |
H17 |
H16 |
238.8 |
240.0 |
| O5' |
C5' |
H17 |
H16 |
121.2 |
120.0 |