PDB Chemical Component VC9
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 VC9
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2 |
C2 |
1.252 |
1.220 |
| C2 |
N3 |
1.315 |
1.332 |
| C2 |
N1 |
1.325 |
1.346 |
| C2' |
C1' |
1.585 |
1.545 |
| C2' |
C3' |
1.311 |
1.546 |
| N3 |
C4 |
1.332 |
1.327 |
| C1' |
N1 |
1.348 |
1.465 |
| C1' |
O4' |
1.542 |
1.444 |
| N1 |
C6 |
1.306 |
1.363 |
| O3' |
C3' |
1.488 |
1.428 |
| C3' |
C4' |
1.630 |
1.545 |
| C4 |
N4 |
1.481 |
1.376 |
| C4 |
C5 |
1.363 |
1.410 |
| O4' |
C4' |
1.295 |
1.444 |
| C4' |
C5' |
1.558 |
1.530 |
| C6 |
C5 |
1.406 |
1.354 |
| O2B |
PB |
1.553 |
1.480 |
| C5' |
O5' |
1.381 |
1.428 |
| O5' |
PA |
1.647 |
1.610 |
| O3A |
PB |
1.694 |
1.610 |
| O3A |
PA |
1.590 |
1.610 |
| PB |
O1B |
1.497 |
1.610 |
| PB |
C3B |
1.830 |
1.823 |
| BR2 |
C3B |
1.932 |
1.967 |
| PA |
O2A |
1.492 |
1.480 |
| PA |
O1A |
1.469 |
1.610 |
| C3B |
BR1 |
1.921 |
1.966 |
| C3B |
PG |
1.852 |
1.823 |
| O3G |
PG |
1.471 |
1.480 |
| PG |
O2G |
1.533 |
1.610 |
| PG |
O1G |
1.535 |
1.610 |
| N4 |
H1 |
1.000 |
0.970 |
| N4 |
H2 |
1.000 |
0.970 |
| C5 |
H3 |
1.080 |
1.080 |
| C6 |
H4 |
1.080 |
1.080 |
| C1' |
H5 |
1.100 |
1.090 |
| C2' |
H6 |
1.100 |
1.089 |
| C2' |
H7 |
1.100 |
1.090 |
| C3' |
H8 |
1.100 |
1.090 |
| O3' |
H9 |
0.950 |
0.967 |
| C4' |
H10 |
1.100 |
1.090 |
| C5' |
H11 |
1.100 |
1.091 |
| C5' |
H12 |
1.100 |
1.090 |
| O1A |
H13 |
0.950 |
0.967 |
| O1B |
H14 |
0.949 |
0.967 |
| O2G |
H15 |
0.950 |
0.967 |
| O1G |
H16 |
0.950 |
0.967 |
Bond Angles for VC9
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2 |
C2 |
N1 |
118.2 |
119.4 |
| C2' |
C1' |
O4' |
102.3 |
104.8 |
| C2' |
C1' |
H5 |
108.4 |
110.4 |
| C2' |
C3' |
C4' |
103.5 |
104.0 |
| C3' |
C2' |
H6 |
111.1 |
110.5 |
| C3' |
C2' |
H7 |
111.1 |
110.5 |
| C2' |
C3' |
H8 |
111.6 |
110.5 |
| C1' |
O4' |
C4' |
108.7 |
105.3 |
| O4' |
C1' |
H5 |
109.0 |
110.4 |
| N1 |
C6 |
H4 |
119.4 |
120.4 |
| O3' |
C3' |
C4' |
108.6 |
110.5 |
| O3' |
C3' |
H8 |
108.9 |
110.6 |
| C3' |
C4' |
O4' |
103.7 |
104.8 |
| C3' |
C4' |
C5' |
109.9 |
110.4 |
| C4' |
C3' |
H8 |
107.3 |
110.5 |
| C3' |
C4' |
H10 |
108.5 |
110.4 |
| N4 |
C4 |
C5 |
118.8 |
120.2 |
| C4 |
N4 |
H1 |
120.0 |
120.0 |
| C4 |
N4 |
H2 |
120.0 |
120.0 |
| C4 |
C5 |
H3 |
121.9 |
120.5 |
| O4' |
C4' |
C5' |
111.8 |
110.3 |
| O4' |
C4' |
H10 |
113.5 |
110.3 |
| C4' |
C5' |
O5' |
110.4 |
109.5 |
| C5' |
C4' |
H10 |
109.3 |
110.4 |
| C4' |
C5' |
H11 |
109.2 |
109.4 |
| C4' |
C5' |
H12 |
109.2 |
109.4 |
| C6 |
C5 |
H3 |
121.9 |
120.5 |
| O2B |
PB |
C3B |
111.8 |
109.5 |
| C5' |
O5' |
PA |
120.6 |
123.0 |
| O5' |
C5' |
H11 |
109.2 |
109.5 |
| O5' |
C5' |
H12 |
109.2 |
109.5 |
| O5' |
PA |
O2A |
110.7 |
109.5 |
| O5' |
PA |
O1A |
110.3 |
109.5 |
| O3A |
PB |
O1B |
112.5 |
109.5 |
| O3A |
PB |
C3B |
105.2 |
109.5 |
| O1B |
PB |
C3B |
112.4 |
109.5 |
| PB |
O1B |
H14 |
109.5 |
114.0 |
| PB |
C3B |
BR1 |
113.2 |
109.5 |
| PB |
C3B |
PG |
112.4 |
109.5 |
| BR2 |
C3B |
PG |
109.5 |
109.4 |
| O1A |
PA |
O2A |
112.3 |
109.4 |
| PA |
O1A |
H13 |
109.5 |
114.0 |
| BR1 |
C3B |
PG |
107.1 |
109.5 |
| C3B |
PG |
O2G |
106.9 |
109.5 |
| C3B |
PG |
O1G |
107.3 |
109.5 |
| O2G |
PG |
O1G |
108.3 |
109.5 |
| PG |
O2G |
H15 |
109.5 |
114.0 |
| PG |
O1G |
H16 |
109.5 |
114.0 |
| H1 |
N4 |
H2 |
120.0 |
120.0 |
| H6 |
C2' |
H7 |
109.5 |
110.6 |
| H11 |
C5' |
H12 |
109.5 |
109.5 |
Torsion Angles for VC9
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
H4 |
179.9 |
179.7 |
| C2' |
C1' |
O4' |
C4' |
358.1 |
319.5 |
| O4' |
C1' |
C2' |
H5 |
115.1 |
118.9 |
| C3' |
C2' |
C1' |
O4' |
333.0 |
24.0 |
| C3' |
C2' |
C1' |
H5 |
217.9 |
265.1 |
| O3' |
C3' |
C2' |
C4' |
119.1 |
118.7 |
| O3' |
C3' |
C2' |
H8 |
234.2 |
237.3 |
| C2' |
C3' |
C4' |
O4' |
316.0 |
336.0 |
| C2' |
C3' |
C4' |
C5' |
196.4 |
217.2 |
| C4' |
C3' |
C2' |
H8 |
115.1 |
118.6 |
| C2' |
C3' |
C4' |
H10 |
76.9 |
94.8 |
| H6 |
C2' |
C3' |
H7 |
122.1 |
122.7 |
| N3 |
C4 |
N4 |
H1 |
360.0 |
179.7 |
| N3 |
C4 |
N4 |
H2 |
180.0 |
359.8 |
| N3 |
C4 |
C5 |
H3 |
180.7 |
180.3 |
| C1' |
N1 |
C6 |
H4 |
359.1 |
359.9 |
| C2' |
C1' |
O4' |
H5 |
245.3 |
241.1 |
| C3' |
C4' |
O4' |
C1' |
24.1 |
40.5 |
| C1' |
O4' |
C4' |
C5' |
142.5 |
159.4 |
| C1' |
O4' |
C4' |
H10 |
266.7 |
281.7 |
| N1 |
C6 |
C5 |
H3 |
179.7 |
180.0 |
| C2' |
C3' |
O3' |
C4' |
243.7 |
245.4 |
| O3' |
C3' |
C2' |
H6 |
40.3 |
360.0 |
| O3' |
C3' |
C2' |
H7 |
278.2 |
237.3 |
| C2' |
C3' |
O3' |
H8 |
127.2 |
122.7 |
| O3' |
C3' |
C4' |
O4' |
191.8 |
217.4 |
| O3' |
C3' |
C4' |
C5' |
72.1 |
98.5 |
| C4' |
C3' |
O3' |
H8 |
243.4 |
237.3 |
| O3' |
C3' |
C4' |
H10 |
312.7 |
336.2 |
| C4' |
C3' |
C2' |
H6 |
281.2 |
241.3 |
| C4' |
C3' |
C2' |
H7 |
159.1 |
118.6 |
| C2' |
C3' |
C4' |
H8 |
241.9 |
241.4 |
| C1' |
O4' |
C4' |
C3' |
24.1 |
40.5 |
| O3' |
C3' |
C4' |
H8 |
117.6 |
122.7 |
| O4' |
C4' |
C3' |
C5' |
119.7 |
118.8 |
| O4' |
C4' |
C3' |
H10 |
239.1 |
241.2 |
| C3' |
C4' |
C5' |
O5' |
65.3 |
185.1 |
| C5' |
C4' |
C3' |
H10 |
119.4 |
122.4 |
| C3' |
C4' |
C5' |
H11 |
185.4 |
305.0 |
| C3' |
C4' |
C5' |
H12 |
305.1 |
65.0 |
| N4 |
C4 |
C5 |
H3 |
1.4 |
0.1 |
| H1 |
N4 |
C4 |
H2 |
180.0 |
179.9 |
| C5 |
C4 |
N4 |
H1 |
179.3 |
359.9 |
| C5 |
C4 |
N4 |
H2 |
359.3 |
180.0 |
| C6 |
C5 |
C4 |
H3 |
180.0 |
179.9 |
| C4' |
O4' |
C1' |
H5 |
112.8 |
78.4 |
| C3' |
C4' |
O4' |
C5' |
241.7 |
241.1 |
| O4' |
C4' |
C3' |
H8 |
74.2 |
94.7 |
| C3' |
C4' |
O4' |
H10 |
117.5 |
118.8 |
| O4' |
C4' |
C5' |
O5' |
310.7 |
69.6 |
| C5' |
C4' |
O4' |
H10 |
235.8 |
237.7 |
| O4' |
C4' |
C5' |
H11 |
70.8 |
189.6 |
| O4' |
C4' |
C5' |
H12 |
190.5 |
309.6 |
| C3' |
C4' |
C5' |
O4' |
114.6 |
115.4 |
| C5' |
C4' |
C3' |
H8 |
314.5 |
335.8 |
| C3' |
C4' |
C5' |
H10 |
241.1 |
237.7 |
| O4' |
C4' |
C5' |
H10 |
126.5 |
122.2 |
| C4' |
C5' |
O5' |
PA |
225.1 |
180.0 |
| O5' |
C5' |
C4' |
H11 |
239.9 |
240.0 |
| O5' |
C5' |
C4' |
H12 |
120.1 |
120.1 |
| H11 |
C5' |
C4' |
H12 |
240.3 |
240.0 |
| C4 |
C5 |
C6 |
H3 |
180.0 |
180.1 |
| O3A |
PB |
O2B |
C3B |
113.5 |
120.0 |
| O1B |
PB |
O2B |
C3B |
234.7 |
240.0 |
| O2B |
PB |
O1B |
H14 |
360.0 |
180.0 |
| O2B |
PB |
C3B |
BR1 |
98.2 |
60.0 |
| O2B |
PB |
C3B |
PG |
219.7 |
300.0 |
| O5' |
C5' |
C4' |
H10 |
184.2 |
307.4 |
| C4' |
C5' |
O5' |
H11 |
120.1 |
119.9 |
| C4' |
C5' |
O5' |
H12 |
239.9 |
240.0 |
| C5' |
O5' |
PA |
O2A |
177.8 |
304.9 |
| C5' |
O5' |
PA |
O1A |
302.7 |
64.9 |
| H11 |
C5' |
O5' |
H12 |
119.7 |
120.1 |
| PA |
O5' |
C5' |
H11 |
104.9 |
60.1 |
| PA |
O5' |
C5' |
H12 |
345.2 |
300.0 |
| O1A |
PA |
O5' |
O2A |
124.9 |
120.0 |
| O5' |
PA |
O1A |
H13 |
236.0 |
60.0 |
| O2B |
PB |
O3A |
C3B |
241.9 |
240.0 |
| O1B |
PB |
O3A |
C3B |
122.6 |
120.0 |
| O3A |
PB |
O1B |
H14 |
116.5 |
300.0 |
| O3A |
PB |
C3B |
BR1 |
344.7 |
300.0 |
| O3A |
PB |
C3B |
PG |
106.2 |
180.0 |
| O3A |
PA |
O1A |
H13 |
118.2 |
299.9 |
| O2B |
PB |
O1B |
C3B |
125.0 |
120.0 |
| O3A |
PB |
O1B |
C3B |
241.5 |
240.0 |
| O1B |
PB |
C3B |
BR1 |
222.0 |
180.0 |
| O1B |
PB |
C3B |
PG |
343.5 |
60.0 |
| O3A |
PB |
C3B |
O1B |
122.7 |
120.0 |
| C3B |
PB |
O1B |
H14 |
235.0 |
60.0 |
| BR2 |
C3B |
PB |
PG |
125.7 |
240.0 |
| BR1 |
C3B |
PB |
PG |
238.5 |
120.0 |
| PB |
C3B |
PG |
O2G |
311.6 |
60.0 |
| PB |
C3B |
PG |
O1G |
195.6 |
180.0 |
| PB |
C3B |
BR2 |
PG |
232.8 |
120.0 |
| BR1 |
C3B |
BR2 |
PG |
112.0 |
240.0 |
| BR2 |
C3B |
PG |
O2G |
183.3 |
180.0 |
| BR2 |
C3B |
PG |
O1G |
67.4 |
300.0 |
| O5' |
PA |
O2A |
O1A |
123.7 |
120.0 |
| O2A |
PA |
O1A |
H13 |
360.0 |
180.0 |
| O5' |
PA |
O1A |
O2A |
236.1 |
240.0 |
| PB |
C3B |
BR1 |
PG |
124.4 |
240.0 |
| BR2 |
C3B |
BR1 |
PG |
246.1 |
120.0 |
| BR1 |
C3B |
PG |
O2G |
76.5 |
300.0 |
| BR1 |
C3B |
PG |
O1G |
320.5 |
60.0 |
| PB |
C3B |
PG |
BR1 |
235.1 |
120.0 |
| O2G |
PG |
C3B |
O1G |
116.0 |
240.0 |
| C3B |
PG |
O2G |
H15 |
123.1 |
60.1 |
| C3B |
PG |
O1G |
H16 |
240.0 |
180.0 |
| O3G |
PG |
O2G |
H15 |
360.0 |
180.0 |
| O3G |
PG |
O1G |
H16 |
0.0 |
60.0 |
| C3B |
PG |
O2G |
O1G |
244.7 |
120.0 |
| O2G |
PG |
O1G |
H16 |
125.0 |
300.0 |
| C3B |
PG |
O1G |
O2G |
115.0 |
240.0 |
| O1G |
PG |
O2G |
H15 |
238.5 |
300.0 |
| H1 |
N4 |
C4 |
C5 |
179.3 |
359.9 |
| C4 |
N4 |
H1 |
H2 |
180.0 |
180.1 |
| H2 |
N4 |
C4 |
C5 |
359.3 |
180.0 |
| C4 |
N4 |
H2 |
H1 |
180.0 |
179.9 |
| H4 |
C6 |
C5 |
H3 |
359.6 |
0.0 |
| C2' |
C1' |
H5 |
O4' |
110.7 |
115.5 |
| H5 |
C1' |
O4' |
C4' |
112.8 |
78.4 |
| H6 |
C2' |
C1' |
O4' |
92.0 |
142.6 |
| H6 |
C2' |
C1' |
H5 |
336.9 |
23.7 |
| H6 |
C2' |
C3' |
C4' |
281.2 |
241.3 |
| C3' |
C2' |
H6 |
H7 |
236.9 |
237.4 |
| H6 |
C2' |
C3' |
H8 |
166.1 |
122.7 |
| H7 |
C2' |
C1' |
O4' |
214.1 |
265.4 |
| H7 |
C2' |
C1' |
H5 |
99.0 |
146.5 |
| H7 |
C2' |
C3' |
C4' |
159.1 |
118.6 |
| C3' |
C2' |
H7 |
H6 |
123.1 |
122.6 |
| H7 |
C2' |
C3' |
H8 |
44.0 |
0.0 |
| C2' |
C3' |
H8 |
C4' |
112.8 |
114.6 |
| H8 |
C3' |
C2' |
H6 |
166.1 |
122.7 |
| H8 |
C3' |
C2' |
H7 |
44.0 |
0.0 |
| O3' |
C3' |
H8 |
C4' |
242.6 |
237.3 |
| H8 |
C3' |
C4' |
O4' |
74.2 |
94.7 |
| H8 |
C3' |
C4' |
C5' |
314.5 |
335.8 |
| H8 |
C3' |
C4' |
H10 |
195.0 |
213.5 |
| H9 |
O3' |
C3' |
C4' |
257.1 |
176.1 |
| H9 |
O3' |
C3' |
H8 |
13.7 |
298.7 |
| C3' |
C4' |
H10 |
O4' |
245.3 |
244.6 |
| C3' |
C4' |
H10 |
C5' |
119.8 |
122.4 |
| H10 |
C4' |
C3' |
H8 |
195.0 |
213.5 |
| O4' |
C4' |
H10 |
C5' |
234.5 |
237.8 |
| H10 |
C4' |
C5' |
O5' |
184.2 |
307.4 |
| H10 |
C4' |
C5' |
H11 |
304.3 |
67.4 |
| H10 |
C4' |
C5' |
H12 |
64.0 |
187.3 |
| C4' |
C5' |
H11 |
O5' |
239.1 |
240.0 |
| H11 |
C5' |
C4' |
H10 |
304.3 |
67.4 |
| C4' |
C5' |
H11 |
H12 |
119.6 |
119.9 |
| H11 |
C5' |
O5' |
PA |
104.9 |
60.1 |
| O5' |
C5' |
H11 |
H12 |
240.4 |
239.9 |
| C4' |
C5' |
H12 |
O5' |
120.9 |
120.0 |
| H12 |
C5' |
C4' |
H10 |
64.0 |
187.3 |
| C4' |
C5' |
H12 |
H11 |
240.5 |
240.1 |
| H12 |
C5' |
O5' |
PA |
345.2 |
300.0 |
| O5' |
C5' |
H12 |
H11 |
119.6 |
120.1 |
| H13 |
O1A |
PA |
O2A |
360.0 |
180.0 |
| H14 |
O1B |
PB |
C3B |
235.0 |
60.0 |
| H15 |
O2G |
PG |
O1G |
238.5 |
300.0 |