PDB Chemical Component VT7
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 VT7
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2 |
C2 |
1.204 |
1.215 |
| C2 |
N3 |
1.329 |
1.346 |
| C2 |
N1 |
1.329 |
1.345 |
| N3 |
C4 |
1.340 |
1.349 |
| C2' |
C1' |
1.293 |
1.545 |
| C2' |
C3' |
1.537 |
1.545 |
| C1' |
N1 |
1.455 |
1.465 |
| C1' |
O4' |
1.611 |
1.445 |
| N1 |
C6 |
1.319 |
1.369 |
| O3' |
C3' |
1.377 |
1.430 |
| C4 |
O4 |
1.425 |
1.217 |
| C4 |
C5 |
1.400 |
1.416 |
| C3' |
C4' |
1.543 |
1.545 |
| O4' |
C4' |
1.289 |
1.444 |
| C6 |
C5 |
1.404 |
1.350 |
| C4' |
C5' |
1.576 |
1.530 |
| C5 |
C5M |
1.511 |
1.507 |
| O2B |
PB |
1.517 |
1.479 |
| C5' |
O5' |
1.462 |
1.428 |
| O5' |
PA |
1.611 |
1.610 |
| PB |
O3A |
1.602 |
1.611 |
| PB |
O1B |
1.528 |
1.610 |
| PB |
C3B |
1.850 |
1.823 |
| O3A |
PA |
1.565 |
1.610 |
| F3B |
C3B |
1.348 |
1.399 |
| PA |
O2A |
1.516 |
1.480 |
| PA |
O1A |
1.514 |
1.610 |
| C3B |
F2B |
1.363 |
1.399 |
| C3B |
PG |
1.846 |
1.823 |
| O3G |
PG |
1.490 |
1.479 |
| PG |
O1G |
1.508 |
1.609 |
| PG |
O2G |
1.463 |
1.610 |
| C5M |
H1 |
1.100 |
1.090 |
| C5M |
H2 |
1.100 |
1.090 |
| C5M |
H3 |
1.100 |
1.090 |
| C6 |
H4 |
1.080 |
1.079 |
| N3 |
H5 |
1.000 |
0.971 |
| C1' |
H6 |
1.099 |
1.089 |
| C2' |
H7 |
1.100 |
1.091 |
| C2' |
H8 |
1.100 |
1.090 |
| C3' |
H9 |
1.100 |
1.090 |
| O3' |
H10 |
0.950 |
0.966 |
| C4' |
H11 |
1.100 |
1.089 |
| C5' |
H12 |
1.099 |
1.090 |
| C5' |
H13 |
1.100 |
1.090 |
| O1A |
H14 |
0.950 |
0.967 |
| O1B |
H15 |
0.950 |
0.967 |
| O2G |
H16 |
0.950 |
0.967 |
| O1G |
H17 |
0.949 |
0.967 |
Bond Angles for VT7
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2 |
C2 |
N1 |
118.4 |
119.5 |
| C2 |
N3 |
H5 |
120.2 |
119.8 |
| C2' |
C1' |
O4' |
106.3 |
104.8 |
| C2' |
C1' |
H6 |
113.0 |
110.5 |
| C2' |
C3' |
C4' |
101.3 |
104.1 |
| C3' |
C2' |
H7 |
110.2 |
110.5 |
| C3' |
C2' |
H8 |
110.2 |
110.6 |
| C2' |
C3' |
H9 |
107.9 |
110.5 |
| C1' |
O4' |
C4' |
108.2 |
105.3 |
| O4' |
C1' |
H6 |
108.2 |
110.4 |
| N1 |
C6 |
H4 |
119.6 |
120.2 |
| O3' |
C3' |
C4' |
113.2 |
110.5 |
| O3' |
C3' |
H9 |
110.1 |
110.5 |
| C4 |
C5 |
C5M |
122.7 |
120.4 |
| C3' |
C4' |
O4' |
103.4 |
104.8 |
| C3' |
C4' |
C5' |
109.9 |
110.4 |
| C4' |
C3' |
H9 |
107.9 |
110.5 |
| C3' |
C4' |
H11 |
109.4 |
110.4 |
| O4' |
C4' |
C5' |
111.8 |
110.3 |
| O4' |
C4' |
H11 |
113.4 |
110.4 |
| C4' |
C5' |
O5' |
108.8 |
109.5 |
| C5' |
C4' |
H11 |
108.9 |
110.4 |
| C4' |
C5' |
H12 |
109.6 |
109.4 |
| C4' |
C5' |
H13 |
109.6 |
109.5 |
| C5 |
C5M |
H1 |
109.5 |
109.5 |
| C5 |
C5M |
H2 |
109.5 |
109.5 |
| C5 |
C5M |
H3 |
109.5 |
109.5 |
| O2B |
PB |
O1B |
107.4 |
109.5 |
| O2B |
PB |
C3B |
107.7 |
109.5 |
| C5' |
O5' |
PA |
118.4 |
123.0 |
| O5' |
C5' |
H12 |
109.6 |
109.5 |
| O5' |
C5' |
H13 |
109.6 |
109.5 |
| O5' |
PA |
O2A |
109.4 |
109.5 |
| O5' |
PA |
O1A |
109.8 |
109.5 |
| O1B |
PB |
C3B |
114.9 |
109.5 |
| PB |
O1B |
H15 |
109.5 |
114.0 |
| PB |
C3B |
F2B |
110.1 |
109.5 |
| PB |
C3B |
PG |
107.3 |
109.4 |
| O1A |
PA |
O2A |
111.0 |
109.5 |
| PA |
O1A |
H14 |
109.5 |
114.1 |
| PG |
C3B |
F2B |
114.0 |
109.5 |
| C3B |
PG |
O1G |
105.5 |
109.5 |
| C3B |
PG |
O2G |
110.4 |
109.5 |
| O3G |
PG |
O1G |
109.5 |
109.5 |
| O3G |
PG |
O2G |
108.7 |
109.4 |
| O2G |
PG |
O1G |
113.7 |
109.4 |
| PG |
O1G |
H17 |
109.5 |
114.0 |
| PG |
O2G |
H16 |
109.5 |
114.0 |
| H1 |
C5M |
H2 |
109.4 |
109.5 |
| H1 |
C5M |
H3 |
109.5 |
109.5 |
| H2 |
C5M |
H3 |
109.5 |
109.4 |
| H7 |
C2' |
H8 |
109.5 |
110.6 |
| H12 |
C5' |
H13 |
109.5 |
109.5 |
Torsion Angles for VT7
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2 |
C2 |
N3 |
H5 |
1.2 |
359.9 |
| N1 |
C2 |
N3 |
H5 |
180.2 |
179.9 |
| C2 |
N1 |
C6 |
H4 |
180.8 |
179.8 |
| C2' |
C1' |
O4' |
C4' |
352.8 |
319.4 |
| O4' |
C1' |
C2' |
H6 |
118.5 |
118.9 |
| C3' |
C2' |
C1' |
O4' |
342.4 |
24.0 |
| C3' |
C2' |
C1' |
H6 |
223.8 |
265.1 |
| O3' |
C3' |
C2' |
C4' |
122.9 |
118.7 |
| O3' |
C3' |
C2' |
H9 |
236.0 |
237.3 |
| C2' |
C3' |
C4' |
O4' |
322.5 |
336.0 |
| C2' |
C3' |
C4' |
C5' |
203.1 |
217.2 |
| C4' |
C3' |
C2' |
H9 |
113.2 |
118.7 |
| C2' |
C3' |
C4' |
H11 |
83.6 |
94.9 |
| H7 |
C2' |
C3' |
H8 |
121.0 |
122.8 |
| C1' |
N1 |
C6 |
H4 |
357.3 |
0.1 |
| C2' |
C1' |
O4' |
H6 |
238.4 |
241.0 |
| C3' |
C4' |
O4' |
C1' |
27.8 |
40.6 |
| C1' |
O4' |
C4' |
C5' |
146.0 |
159.4 |
| C1' |
O4' |
C4' |
H11 |
269.5 |
281.7 |
| C2' |
C3' |
O3' |
C4' |
243.6 |
245.3 |
| O3' |
C3' |
C2' |
H7 |
36.9 |
0.0 |
| O3' |
C3' |
C2' |
H8 |
275.9 |
237.3 |
| C2' |
C3' |
O3' |
H9 |
122.8 |
122.6 |
| O3' |
C3' |
C4' |
O4' |
197.8 |
217.3 |
| O3' |
C3' |
C4' |
C5' |
78.4 |
98.6 |
| C4' |
C3' |
O3' |
H9 |
239.2 |
237.3 |
| O3' |
C3' |
C4' |
H11 |
318.8 |
336.2 |
| C4 |
C5 |
C5M |
H1 |
180.0 |
360.0 |
| C4 |
C5 |
C5M |
H2 |
300.0 |
120.0 |
| C4 |
C5 |
C5M |
H3 |
60.0 |
239.9 |
| C4' |
C3' |
C2' |
H7 |
274.0 |
241.4 |
| C4' |
C3' |
C2' |
H8 |
153.0 |
118.6 |
| C2' |
C3' |
C4' |
H9 |
246.8 |
241.3 |
| C1' |
O4' |
C4' |
C3' |
27.8 |
40.6 |
| O3' |
C3' |
C4' |
H9 |
122.0 |
122.7 |
| O4' |
C4' |
C3' |
C5' |
119.4 |
118.8 |
| O4' |
C4' |
C3' |
H11 |
239.0 |
241.1 |
| C3' |
C4' |
C5' |
O5' |
61.9 |
185.0 |
| C5' |
C4' |
C3' |
H11 |
119.5 |
122.4 |
| C3' |
C4' |
C5' |
H12 |
181.8 |
305.0 |
| C3' |
C4' |
C5' |
H13 |
302.0 |
65.0 |
| C4' |
O4' |
C1' |
H6 |
114.4 |
78.4 |
| C3' |
C4' |
O4' |
C5' |
241.9 |
241.2 |
| O4' |
C4' |
C3' |
H9 |
75.8 |
94.7 |
| C3' |
C4' |
O4' |
H11 |
118.3 |
118.8 |
| O4' |
C4' |
C5' |
O5' |
307.7 |
69.7 |
| C5' |
C4' |
O4' |
H11 |
236.4 |
237.6 |
| O4' |
C4' |
C5' |
H12 |
67.6 |
189.7 |
| O4' |
C4' |
C5' |
H13 |
187.8 |
309.6 |
| C6 |
C5 |
C5M |
H1 |
0.2 |
180.0 |
| C6 |
C5 |
C5M |
H2 |
120.2 |
300.1 |
| C6 |
C5 |
C5M |
H3 |
240.1 |
60.0 |
| C3' |
C4' |
C5' |
O4' |
114.2 |
115.3 |
| C5' |
C4' |
C3' |
H9 |
316.3 |
335.9 |
| C3' |
C4' |
C5' |
H11 |
240.2 |
237.7 |
| O4' |
C4' |
C5' |
H11 |
126.0 |
122.3 |
| C4' |
C5' |
O5' |
PA |
224.2 |
180.0 |
| O5' |
C5' |
C4' |
H12 |
240.1 |
240.0 |
| O5' |
C5' |
C4' |
H13 |
119.9 |
120.0 |
| H12 |
C5' |
C4' |
H13 |
239.8 |
240.0 |
| H1 |
C5M |
C5 |
H2 |
240.0 |
240.0 |
| H1 |
C5M |
C5 |
H3 |
120.0 |
120.0 |
| H2 |
C5M |
C5 |
H3 |
240.0 |
240.1 |
| O1B |
PB |
O2B |
C3B |
235.7 |
239.9 |
| O2B |
PB |
O1B |
H15 |
0.0 |
180.0 |
| O2B |
PB |
C3B |
F2B |
91.3 |
59.9 |
| O2B |
PB |
C3B |
PG |
215.8 |
300.0 |
| O5' |
C5' |
C4' |
H11 |
181.7 |
307.3 |
| C4' |
C5' |
O5' |
H12 |
119.9 |
120.0 |
| C4' |
C5' |
O5' |
H13 |
240.1 |
240.0 |
| C5' |
O5' |
PA |
O2A |
185.6 |
305.0 |
| C5' |
O5' |
PA |
O1A |
307.7 |
65.0 |
| H12 |
C5' |
O5' |
H13 |
120.3 |
120.0 |
| PA |
O5' |
C5' |
H12 |
104.3 |
60.0 |
| PA |
O5' |
C5' |
H13 |
344.0 |
300.0 |
| O1A |
PA |
O5' |
O2A |
122.0 |
120.0 |
| O5' |
PA |
O1A |
H14 |
238.9 |
60.0 |
| O2B |
PB |
O1B |
C3B |
119.9 |
120.1 |
| O1B |
PB |
C3B |
F2B |
211.0 |
180.0 |
| O1B |
PB |
C3B |
PG |
335.5 |
60.0 |
| O2B |
PB |
C3B |
O1B |
240.3 |
239.9 |
| C3B |
PB |
O1B |
H15 |
240.2 |
59.9 |
| PG |
C3B |
PB |
F2B |
124.6 |
240.0 |
| PB |
C3B |
PG |
O1G |
315.3 |
300.0 |
| PB |
C3B |
PG |
O2G |
192.1 |
180.0 |
| O3A |
PA |
O1A |
H14 |
117.5 |
300.0 |
| O5' |
PA |
O2A |
O1A |
121.3 |
120.0 |
| O2A |
PA |
O1A |
H14 |
360.0 |
180.0 |
| O5' |
PA |
O1A |
O2A |
239.0 |
240.0 |
| PB |
C3B |
F2B |
PG |
120.6 |
240.1 |
| F2B |
C3B |
PG |
O1G |
77.5 |
180.0 |
| F2B |
C3B |
PG |
O2G |
314.3 |
60.0 |
| PB |
C3B |
PG |
F2B |
237.8 |
119.9 |
| O3G |
PG |
C3B |
O1G |
117.6 |
120.0 |
| O3G |
PG |
C3B |
O2G |
240.7 |
240.0 |
| O2G |
PG |
C3B |
O1G |
236.8 |
240.0 |
| C3B |
PG |
O1G |
H17 |
117.2 |
300.0 |
| C3B |
PG |
O2G |
H16 |
240.5 |
180.0 |
| O3G |
PG |
C3B |
F2B |
195.0 |
300.1 |
| C3B |
PG |
O3G |
O1G |
245.0 |
240.0 |
| C3B |
PG |
O3G |
O2G |
120.3 |
120.0 |
| O2G |
PG |
O3G |
O1G |
124.7 |
119.9 |
| O3G |
PG |
O1G |
H17 |
360.0 |
180.0 |
| O3G |
PG |
O2G |
H16 |
360.0 |
300.0 |
| O1G |
PG |
C3B |
F2B |
77.5 |
180.0 |
| C3B |
PG |
O1G |
O2G |
238.9 |
240.0 |
| O3G |
PG |
O1G |
O2G |
121.8 |
120.0 |
| O1G |
PG |
O2G |
H16 |
122.2 |
60.0 |
| O2G |
PG |
C3B |
F2B |
314.3 |
60.0 |
| C3B |
PG |
O2G |
O1G |
118.3 |
120.0 |
| O3G |
PG |
O2G |
O1G |
237.8 |
240.0 |
| O2G |
PG |
O1G |
H17 |
238.2 |
60.0 |
| C5 |
C5M |
H1 |
H2 |
120.0 |
120.0 |
| C5 |
C5M |
H1 |
H3 |
240.0 |
240.0 |
| H2 |
C5M |
H1 |
H3 |
120.0 |
120.0 |
| C5 |
C5M |
H2 |
H1 |
240.0 |
240.0 |
| C5 |
C5M |
H2 |
H3 |
120.0 |
120.0 |
| H1 |
C5M |
H2 |
H3 |
240.0 |
240.0 |
| C5 |
C5M |
H3 |
H1 |
120.1 |
120.0 |
| C5 |
C5M |
H3 |
H2 |
240.0 |
240.0 |
| H1 |
C5M |
H3 |
H2 |
119.9 |
120.0 |
| C2' |
C1' |
H6 |
O4' |
117.4 |
115.4 |
| H6 |
C1' |
O4' |
C4' |
114.4 |
78.4 |
| H7 |
C2' |
C1' |
O4' |
101.9 |
142.7 |
| H7 |
C2' |
C1' |
H6 |
343.3 |
23.8 |
| H7 |
C2' |
C3' |
C4' |
274.0 |
241.4 |
| C3' |
C2' |
H7 |
H8 |
238.6 |
237.2 |
| H7 |
C2' |
C3' |
H9 |
160.9 |
122.7 |
| H8 |
C2' |
C1' |
O4' |
222.9 |
265.3 |
| H8 |
C2' |
C1' |
H6 |
104.3 |
146.4 |
| H8 |
C2' |
C3' |
C4' |
153.0 |
118.6 |
| C3' |
C2' |
H8 |
H7 |
121.4 |
122.7 |
| H8 |
C2' |
C3' |
H9 |
39.8 |
360.0 |
| C2' |
C3' |
H9 |
C4' |
108.7 |
114.7 |
| H9 |
C3' |
C2' |
H7 |
160.9 |
122.7 |
| H9 |
C3' |
C2' |
H8 |
39.8 |
360.0 |
| O3' |
C3' |
H9 |
C4' |
236.1 |
237.3 |
| H9 |
C3' |
C4' |
O4' |
75.8 |
94.7 |
| H9 |
C3' |
C4' |
C5' |
316.3 |
335.9 |
| H9 |
C3' |
C4' |
H11 |
196.8 |
213.5 |
| H10 |
O3' |
C3' |
C4' |
255.0 |
176.1 |
| H10 |
O3' |
C3' |
H9 |
15.8 |
298.8 |
| C3' |
C4' |
H11 |
O4' |
245.2 |
244.6 |
| C3' |
C4' |
H11 |
C5' |
120.1 |
122.3 |
| H11 |
C4' |
C3' |
H9 |
196.8 |
213.5 |
| O4' |
C4' |
H11 |
C5' |
234.9 |
237.7 |
| H11 |
C4' |
C5' |
O5' |
181.7 |
307.3 |
| H11 |
C4' |
C5' |
H12 |
301.6 |
67.3 |
| H11 |
C4' |
C5' |
H13 |
61.8 |
187.3 |
| C4' |
C5' |
H12 |
O5' |
240.6 |
240.0 |
| H12 |
C5' |
C4' |
H11 |
301.6 |
67.3 |
| C4' |
C5' |
H12 |
H13 |
120.3 |
120.0 |
| H12 |
C5' |
O5' |
PA |
104.3 |
60.0 |
| O5' |
C5' |
H12 |
H13 |
239.7 |
240.0 |
| C4' |
C5' |
H13 |
O5' |
119.4 |
120.0 |
| H13 |
C5' |
C4' |
H11 |
61.8 |
187.3 |
| C4' |
C5' |
H13 |
H12 |
239.7 |
240.0 |
| H13 |
C5' |
O5' |
PA |
344.0 |
300.0 |
| O5' |
C5' |
H13 |
H12 |
120.3 |
120.0 |
| H14 |
O1A |
PA |
O2A |
360.0 |
180.0 |
| H15 |
O1B |
PB |
C3B |
240.2 |
59.9 |
| H16 |
O2G |
PG |
O1G |
122.2 |
60.0 |