PDB Chemical Component VT8
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 VT8
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2 |
C2 |
1.193 |
1.216 |
| C2 |
N3 |
1.343 |
1.347 |
| C2 |
N1 |
1.339 |
1.345 |
| N3 |
C4 |
1.354 |
1.348 |
| C2' |
C1' |
1.526 |
1.545 |
| C2' |
C3' |
1.318 |
1.545 |
| C1' |
N1 |
1.350 |
1.465 |
| C1' |
O4' |
1.556 |
1.444 |
| N1 |
C6 |
1.352 |
1.368 |
| O3' |
C3' |
1.472 |
1.428 |
| C3' |
C4' |
1.616 |
1.545 |
| C4 |
O4 |
1.214 |
1.218 |
| C4 |
C5 |
1.418 |
1.416 |
| O4' |
C4' |
1.260 |
1.444 |
| C4' |
C5' |
1.574 |
1.530 |
| C6 |
C5 |
1.411 |
1.350 |
| C5 |
C7 |
1.526 |
1.507 |
| O2B |
PB |
1.541 |
1.480 |
| C5' |
O5' |
1.437 |
1.428 |
| O5' |
PA |
1.622 |
1.611 |
| O3A |
PB |
1.570 |
1.609 |
| O3A |
PA |
1.594 |
1.610 |
| PB |
O1B |
1.503 |
1.610 |
| PB |
C3B |
1.847 |
1.824 |
| CL1 |
C3B |
1.755 |
1.803 |
| PA |
O2A |
1.525 |
1.480 |
| PA |
O1A |
1.532 |
1.610 |
| C3B |
CL2 |
1.717 |
1.803 |
| C3B |
PG |
1.796 |
1.823 |
| O3G |
PG |
1.518 |
1.480 |
| PG |
O1G |
1.481 |
1.609 |
| PG |
O2G |
1.511 |
1.610 |
| N3 |
H1 |
1.000 |
0.970 |
| C7 |
H2 |
1.100 |
1.090 |
| C7 |
H3 |
1.100 |
1.090 |
| C7 |
H4 |
1.100 |
1.090 |
| C6 |
H5 |
1.080 |
1.080 |
| C1' |
H6 |
1.100 |
1.090 |
| O1A |
H7 |
0.950 |
0.967 |
| O1G |
H8 |
0.950 |
0.967 |
| C2' |
H9 |
1.100 |
1.090 |
| C2' |
H10 |
1.100 |
1.090 |
| O1B |
H11 |
0.950 |
0.967 |
| O2G |
H12 |
0.950 |
0.967 |
| C3' |
H13 |
1.100 |
1.090 |
| O3' |
H14 |
0.951 |
0.967 |
| C4' |
H15 |
1.100 |
1.090 |
| C5' |
H16 |
1.100 |
1.090 |
| C5' |
H17 |
1.100 |
1.090 |
Bond Angles for VT8
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2 |
C2 |
N3 |
118.3 |
119.5 |
| C2 |
N3 |
C4 |
120.9 |
120.3 |
| C2 |
N3 |
H1 |
119.5 |
119.8 |
| C2 |
N1 |
C6 |
119.1 |
120.6 |
| N3 |
C4 |
O4 |
120.4 |
120.3 |
| N3 |
C4 |
C5 |
119.6 |
119.4 |
| C4 |
N3 |
H1 |
119.6 |
119.9 |
| C2' |
C1' |
O4' |
102.4 |
104.8 |
| C2' |
C1' |
H6 |
109.1 |
110.4 |
| C2' |
C3' |
C4' |
102.7 |
104.1 |
| C3' |
C2' |
H9 |
110.7 |
110.5 |
| C3' |
C2' |
H10 |
110.7 |
110.5 |
| C2' |
C3' |
H13 |
110.3 |
110.5 |
| C1' |
O4' |
C4' |
108.3 |
105.3 |
| O4' |
C1' |
H6 |
108.7 |
110.4 |
| N1 |
C6 |
C5 |
121.6 |
119.7 |
| N1 |
C6 |
H5 |
119.2 |
120.2 |
| O3' |
C3' |
C4' |
111.9 |
110.5 |
| O3' |
C3' |
H13 |
108.1 |
110.6 |
| C3' |
C4' |
C5' |
110.7 |
110.4 |
| C4' |
C3' |
H13 |
106.5 |
110.5 |
| C3' |
C4' |
H15 |
108.1 |
110.4 |
| O4 |
C4 |
C5 |
120.0 |
120.4 |
| C4 |
C5 |
C7 |
123.5 |
120.4 |
| O4' |
C4' |
C5' |
111.3 |
110.4 |
| O4' |
C4' |
H15 |
113.5 |
110.5 |
| C4' |
C5' |
O5' |
107.9 |
109.5 |
| C5' |
C4' |
H15 |
108.7 |
110.3 |
| C4' |
C5' |
H16 |
109.8 |
109.5 |
| C4' |
C5' |
H17 |
109.8 |
109.5 |
| C5 |
C7 |
H2 |
109.5 |
109.5 |
| C5 |
C7 |
H3 |
109.5 |
109.5 |
| C5 |
C7 |
H4 |
109.5 |
109.5 |
| O2B |
PB |
O1B |
108.4 |
109.5 |
| O2B |
PB |
C3B |
109.5 |
109.4 |
| O5' |
C5' |
H16 |
109.9 |
109.5 |
| O5' |
C5' |
H17 |
109.9 |
109.5 |
| O3A |
PB |
C3B |
107.2 |
109.5 |
| O1B |
PB |
C3B |
113.4 |
109.5 |
| PB |
O1B |
H11 |
109.5 |
114.0 |
| PB |
C3B |
CL1 |
113.6 |
109.5 |
| PB |
C3B |
CL2 |
111.8 |
109.5 |
| PB |
C3B |
PG |
107.4 |
109.5 |
| CL1 |
C3B |
CL2 |
105.9 |
109.5 |
| O1A |
PA |
O2A |
112.2 |
109.5 |
| PA |
O1A |
H7 |
109.5 |
114.0 |
| O1G |
PG |
O2G |
107.9 |
109.5 |
| PG |
O1G |
H8 |
109.5 |
114.0 |
| PG |
O2G |
H12 |
109.5 |
114.0 |
| H2 |
C7 |
H3 |
109.5 |
109.5 |
| H2 |
C7 |
H4 |
109.5 |
109.5 |
| H3 |
C7 |
H4 |
109.5 |
109.5 |
| H9 |
C2' |
H10 |
109.5 |
110.5 |
| H16 |
C5' |
H17 |
109.5 |
109.4 |
Torsion Angles for VT8
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2 |
C2 |
N3 |
C4 |
180.4 |
180.0 |
| O2 |
C2 |
N3 |
H1 |
0.5 |
0.0 |
| O2 |
C2 |
N1 |
C6 |
179.6 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
1.3 |
360.0 |
| C2 |
N3 |
C4 |
O4 |
180.8 |
180.1 |
| C2 |
N3 |
C4 |
C5 |
1.0 |
0.0 |
| C4 |
N3 |
C2 |
H1 |
180.0 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
358.9 |
0.0 |
| C2 |
N1 |
C6 |
H5 |
178.9 |
179.9 |
| C2 |
N3 |
C4 |
H1 |
180.0 |
180.0 |
| O4 |
C4 |
N3 |
C5 |
179.7 |
180.1 |
| N3 |
C4 |
C5 |
C7 |
179.6 |
180.0 |
| C2' |
C1' |
O4' |
C4' |
356.4 |
319.5 |
| O4' |
C1' |
C2' |
H6 |
115.1 |
118.8 |
| C3' |
C2' |
C1' |
O4' |
335.1 |
24.0 |
| C3' |
C2' |
C1' |
H6 |
220.0 |
265.1 |
| O3' |
C3' |
C2' |
C4' |
122.9 |
118.6 |
| O3' |
C3' |
C2' |
H13 |
236.0 |
237.3 |
| C2' |
C3' |
C4' |
C5' |
197.2 |
217.2 |
| C4' |
C3' |
C2' |
H13 |
113.2 |
118.6 |
| C2' |
C3' |
C4' |
H15 |
78.3 |
95.0 |
| H9 |
C2' |
C3' |
H10 |
121.6 |
122.7 |
| C1' |
N1 |
C6 |
H5 |
357.6 |
0.2 |
| C2' |
C1' |
O4' |
H6 |
244.6 |
241.1 |
| C1' |
O4' |
C4' |
C5' |
144.7 |
159.3 |
| C1' |
O4' |
C4' |
H15 |
267.7 |
281.6 |
| C2' |
C3' |
O3' |
C4' |
242.0 |
245.4 |
| O3' |
C3' |
C2' |
H9 |
42.0 |
0.0 |
| O3' |
C3' |
C2' |
H10 |
280.4 |
237.3 |
| C2' |
C3' |
O3' |
H13 |
125.1 |
122.7 |
| O3' |
C3' |
C4' |
C5' |
71.1 |
98.6 |
| C4' |
C3' |
O3' |
H13 |
243.0 |
237.3 |
| O3' |
C3' |
C4' |
H15 |
312.2 |
336.4 |
| C4' |
C3' |
C2' |
H9 |
279.2 |
241.4 |
| C4' |
C3' |
C2' |
H10 |
157.6 |
118.7 |
| C2' |
C3' |
C4' |
H13 |
244.1 |
241.4 |
| C1' |
O4' |
C4' |
C3' |
25.2 |
40.5 |
| O3' |
C3' |
C4' |
H13 |
118.0 |
122.8 |
| O4' |
C4' |
C3' |
C5' |
119.9 |
118.9 |
| O4' |
C4' |
C3' |
H15 |
238.8 |
241.0 |
| C3' |
C4' |
C5' |
O5' |
62.5 |
185.0 |
| C5' |
C4' |
C3' |
H15 |
118.9 |
122.2 |
| C3' |
C4' |
C5' |
H16 |
182.2 |
305.0 |
| C3' |
C4' |
C5' |
H17 |
302.7 |
65.0 |
| N3 |
C4 |
O4 |
C5 |
180.3 |
179.9 |
| O4 |
C4 |
N3 |
H1 |
0.8 |
0.1 |
| O4 |
C4 |
C5 |
C7 |
359.8 |
359.9 |
| N3 |
C4 |
C5 |
O4 |
179.8 |
180.1 |
| C5 |
C4 |
N3 |
H1 |
181.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.9 |
360.0 |
| C4 |
C5 |
C7 |
H2 |
180.0 |
0.0 |
| C4 |
C5 |
C7 |
H3 |
300.0 |
120.0 |
| C4 |
C5 |
C7 |
H4 |
60.0 |
240.0 |
| C4' |
O4' |
C1' |
H6 |
111.8 |
78.4 |
| C3' |
C4' |
O4' |
C5' |
240.5 |
241.2 |
| O4' |
C4' |
C3' |
H13 |
73.0 |
94.7 |
| C3' |
C4' |
O4' |
H15 |
117.5 |
118.9 |
| O4' |
C4' |
C5' |
O5' |
306.8 |
69.6 |
| C5' |
C4' |
O4' |
H15 |
237.0 |
237.7 |
| O4' |
C4' |
C5' |
H16 |
66.5 |
189.6 |
| O4' |
C4' |
C5' |
H17 |
187.0 |
309.6 |
| C5' |
C4' |
C3' |
H13 |
313.1 |
335.8 |
| C3' |
C4' |
C5' |
H15 |
241.4 |
237.8 |
| O4' |
C4' |
C5' |
H15 |
125.7 |
122.4 |
| O5' |
C5' |
C4' |
H16 |
240.2 |
240.0 |
| O5' |
C5' |
C4' |
H17 |
119.8 |
120.0 |
| H16 |
C5' |
C4' |
H17 |
239.5 |
240.0 |
| N1 |
C6 |
C5 |
H5 |
180.0 |
179.9 |
| C6 |
C5 |
C7 |
H2 |
0.5 |
180.0 |
| C6 |
C5 |
C7 |
H3 |
120.5 |
300.0 |
| C6 |
C5 |
C7 |
H4 |
240.5 |
60.0 |
| N1 |
C6 |
C5 |
C7 |
180.5 |
180.0 |
| H2 |
C7 |
C5 |
H3 |
240.0 |
240.0 |
| H2 |
C7 |
C5 |
H4 |
120.0 |
120.0 |
| H3 |
C7 |
C5 |
H4 |
240.0 |
240.0 |
| O3A |
PB |
O2B |
C3B |
115.0 |
120.0 |
| O1B |
PB |
O2B |
C3B |
235.9 |
240.0 |
| O2B |
PB |
O1B |
H11 |
0.0 |
179.9 |
| O2B |
PB |
C3B |
CL1 |
337.1 |
60.0 |
| O2B |
PB |
C3B |
CL2 |
96.8 |
180.0 |
| O2B |
PB |
C3B |
PG |
215.2 |
300.0 |
| O5' |
C5' |
C4' |
H15 |
181.1 |
307.2 |
| C4' |
C5' |
O5' |
H16 |
119.7 |
120.0 |
| C4' |
C5' |
O5' |
H17 |
240.3 |
240.0 |
| H16 |
C5' |
O5' |
H17 |
120.5 |
119.9 |
| O5' |
PA |
O1A |
H7 |
238.4 |
60.0 |
| O2B |
PB |
O3A |
C3B |
243.5 |
240.0 |
| O1B |
PB |
O3A |
C3B |
125.5 |
120.0 |
| O3A |
PB |
O1B |
H11 |
116.2 |
300.0 |
| O3A |
PB |
C3B |
CL1 |
223.3 |
300.0 |
| O3A |
PB |
C3B |
CL2 |
343.0 |
60.0 |
| O3A |
PB |
C3B |
PG |
101.4 |
180.0 |
| O3A |
PA |
O1A |
H7 |
120.7 |
300.0 |
| O2B |
PB |
O1B |
C3B |
121.8 |
120.0 |
| O3A |
PB |
O1B |
C3B |
237.9 |
240.0 |
| O1B |
PB |
C3B |
CL1 |
98.2 |
180.0 |
| O1B |
PB |
C3B |
CL2 |
218.0 |
300.0 |
| O1B |
PB |
C3B |
PG |
336.3 |
60.0 |
| O2B |
PB |
C3B |
O1B |
238.9 |
240.0 |
| C3B |
PB |
O1B |
H11 |
238.3 |
60.0 |
| CL1 |
C3B |
PB |
CL2 |
240.3 |
240.0 |
| PB |
C3B |
CL1 |
CL2 |
123.0 |
120.0 |
| PB |
C3B |
CL1 |
PG |
239.5 |
240.0 |
| O2A |
PA |
O1A |
H7 |
0.0 |
180.0 |
| PB |
C3B |
CL2 |
CL1 |
235.8 |
240.0 |
| PB |
C3B |
CL2 |
PG |
118.0 |
120.0 |
| PB |
C3B |
PG |
CL1 |
124.1 |
120.0 |
| PB |
C3B |
PG |
CL2 |
239.3 |
240.0 |
| C3B |
PG |
O1G |
H8 |
116.6 |
60.0 |
| C3B |
PG |
O2G |
H12 |
240.7 |
180.0 |
| O3G |
PG |
O1G |
H8 |
0.0 |
180.0 |
| O3G |
PG |
O2G |
H12 |
360.0 |
60.0 |
| PB |
C3B |
PG |
O1G |
318.6 |
60.0 |
| O1G |
PG |
O2G |
H12 |
124.5 |
300.0 |
| PB |
C3B |
PG |
O2G |
201.5 |
180.0 |
| O2G |
PG |
O1G |
H8 |
235.7 |
300.0 |
| C2 |
N3 |
H1 |
C4 |
180.0 |
180.0 |
| H1 |
N3 |
C4 |
O4 |
0.8 |
0.1 |
| H1 |
N3 |
C4 |
C5 |
181.0 |
180.0 |
| C5 |
C7 |
H2 |
H3 |
120.0 |
120.0 |
| C5 |
C7 |
H2 |
H4 |
240.0 |
240.0 |
| H3 |
C7 |
H2 |
H4 |
120.0 |
120.1 |
| C5 |
C7 |
H3 |
H2 |
240.0 |
240.0 |
| C5 |
C7 |
H3 |
H4 |
120.0 |
120.0 |
| H2 |
C7 |
H3 |
H4 |
240.0 |
240.0 |
| C5 |
C7 |
H4 |
H2 |
120.0 |
120.0 |
| C5 |
C7 |
H4 |
H3 |
240.0 |
240.0 |
| H2 |
C7 |
H4 |
H3 |
120.0 |
120.0 |
| N1 |
C6 |
H5 |
C5 |
180.0 |
180.1 |
| C2' |
C1' |
H6 |
O4' |
111.0 |
115.4 |
| H6 |
C1' |
O4' |
C4' |
111.8 |
78.4 |
| H7 |
O1A |
PA |
O2A |
0.0 |
180.0 |
| H8 |
O1G |
PG |
O2G |
235.7 |
300.0 |
| H9 |
C2' |
C1' |
O4' |
94.3 |
142.6 |
| H9 |
C2' |
C1' |
H6 |
339.2 |
23.8 |
| H9 |
C2' |
C3' |
C4' |
279.2 |
241.4 |
| C3' |
C2' |
H9 |
H10 |
237.7 |
237.3 |
| H9 |
C2' |
C3' |
H13 |
166.0 |
122.7 |
| H10 |
C2' |
C1' |
O4' |
215.9 |
265.3 |
| H10 |
C2' |
C1' |
H6 |
100.8 |
146.5 |
| H10 |
C2' |
C3' |
C4' |
157.6 |
118.7 |
| C3' |
C2' |
H10 |
H9 |
122.3 |
122.7 |
| H10 |
C2' |
C3' |
H13 |
44.4 |
0.0 |
| H11 |
O1B |
PB |
C3B |
238.3 |
60.0 |
| C2' |
C3' |
H13 |
C4' |
110.7 |
114.6 |
| H13 |
C3' |
C2' |
H9 |
166.0 |
122.7 |
| H13 |
C3' |
C2' |
H10 |
44.4 |
0.0 |
| O3' |
C3' |
H13 |
C4' |
239.6 |
237.3 |
| H13 |
C3' |
C4' |
C5' |
313.1 |
335.8 |
| H13 |
C3' |
C4' |
H15 |
194.2 |
213.6 |
| H14 |
O3' |
C3' |
C4' |
259.0 |
176.1 |
| H14 |
O3' |
C3' |
H13 |
15.9 |
298.8 |
| C3' |
C4' |
H15 |
C5' |
120.2 |
122.2 |
| H15 |
C4' |
C3' |
H13 |
194.2 |
213.6 |
| O4' |
C4' |
H15 |
C5' |
235.5 |
237.6 |
| H15 |
C4' |
C5' |
O5' |
181.1 |
307.2 |
| H15 |
C4' |
C5' |
H16 |
300.8 |
67.2 |
| H15 |
C4' |
C5' |
H17 |
61.3 |
187.2 |
| C4' |
C5' |
H16 |
O5' |
241.4 |
240.0 |
| H16 |
C5' |
C4' |
H15 |
300.8 |
67.2 |
| C4' |
C5' |
H16 |
H17 |
120.7 |
120.0 |
| O5' |
C5' |
H16 |
H17 |
239.2 |
240.0 |
| C4' |
C5' |
H17 |
O5' |
118.6 |
120.0 |
| H17 |
C5' |
C4' |
H15 |
61.3 |
187.2 |
| C4' |
C5' |
H17 |
H16 |
239.3 |
240.0 |
| O5' |
C5' |
H17 |
H16 |
120.7 |
120.0 |