PDB Chemical Component C6B
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 C6B
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O1P |
P |
1.665 |
1.610 |
| P |
O2P |
1.677 |
1.610 |
| P |
O3P |
1.519 |
1.480 |
| P |
O3' |
1.670 |
1.611 |
| O3' |
C3' |
1.432 |
1.429 |
| C3' |
C2' |
1.534 |
1.549 |
| C3' |
C4' |
1.577 |
1.550 |
| C2' |
O2' |
1.440 |
1.429 |
| C2' |
C1' |
1.528 |
1.540 |
| C4' |
C5' |
1.553 |
1.530 |
| C4' |
O4' |
1.472 |
1.444 |
| C5' |
O5' |
1.438 |
1.428 |
| O4' |
C1' |
1.478 |
1.437 |
| C1' |
N1 |
1.481 |
1.465 |
| N1 |
C6 |
1.402 |
1.363 |
| N1 |
C2 |
1.401 |
1.346 |
| C6 |
C5 |
1.382 |
1.354 |
| C5 |
C4 |
1.383 |
1.410 |
| C4 |
N4 |
1.326 |
1.376 |
| C4 |
N3 |
1.358 |
1.327 |
| N3 |
C2 |
1.353 |
1.331 |
| C2 |
O2 |
1.239 |
1.221 |
| O1P |
HO1P |
0.950 |
0.967 |
| O2P |
HO2P |
0.950 |
0.967 |
| C3' |
H3' |
1.100 |
1.089 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.949 |
0.968 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
HO5' |
0.950 |
0.967 |
| C1' |
H1' |
1.100 |
1.090 |
| C6 |
H6 |
1.080 |
1.080 |
| C5 |
H5 |
1.080 |
1.080 |
| N4 |
HN4 |
1.000 |
0.970 |
| N4 |
HN4A |
1.000 |
0.970 |
Bond Angles for C6B
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O2P |
105.8 |
109.5 |
| O1P |
P |
O3P |
113.4 |
109.5 |
| O1P |
P |
O3' |
104.8 |
109.4 |
| P |
O1P |
HO1P |
109.5 |
114.0 |
| O2P |
P |
O3P |
113.9 |
109.5 |
| O2P |
P |
O3' |
103.9 |
109.4 |
| P |
O2P |
HO2P |
109.5 |
114.0 |
| O3P |
P |
O3' |
114.0 |
109.5 |
| P |
O3' |
C3' |
114.7 |
123.0 |
| O3' |
C3' |
C2' |
112.6 |
110.9 |
| O3' |
C3' |
C4' |
117.1 |
110.9 |
| O3' |
C3' |
H3' |
100.4 |
110.8 |
| C2' |
C3' |
C4' |
105.3 |
102.1 |
| C3' |
C2' |
O2' |
113.2 |
110.5 |
| C3' |
C2' |
C1' |
88.9 |
104.2 |
| C2' |
C3' |
H3' |
113.3 |
110.9 |
| C3' |
C2' |
H2' |
121.6 |
110.5 |
| C3' |
C4' |
C5' |
119.5 |
110.6 |
| C3' |
C4' |
O4' |
102.0 |
103.5 |
| C4' |
C3' |
H3' |
108.3 |
110.9 |
| C3' |
C4' |
H4' |
107.0 |
110.6 |
| O2' |
C2' |
C1' |
114.3 |
110.5 |
| O2' |
C2' |
H2' |
99.4 |
110.5 |
| C2' |
O2' |
HO2' |
109.5 |
113.9 |
| C2' |
C1' |
O4' |
102.5 |
107.3 |
| C2' |
C1' |
N1 |
125.6 |
109.9 |
| C1' |
C2' |
H2' |
120.6 |
110.6 |
| C2' |
C1' |
H1' |
107.3 |
109.9 |
| C5' |
C4' |
O4' |
106.2 |
110.6 |
| C4' |
C5' |
O5' |
110.4 |
109.5 |
| C5' |
C4' |
H4' |
103.0 |
110.6 |
| C4' |
C5' |
H5' |
109.2 |
109.5 |
| C4' |
C5' |
H5'A |
109.0 |
109.5 |
| C4' |
O4' |
C1' |
101.2 |
107.0 |
| O4' |
C4' |
H4' |
120.2 |
110.7 |
| O5' |
C5' |
H5' |
109.2 |
109.5 |
| O5' |
C5' |
H5'A |
109.0 |
109.5 |
| C5' |
O5' |
HO5' |
109.5 |
114.0 |
| O4' |
C1' |
N1 |
118.2 |
109.9 |
| O4' |
C1' |
H1' |
117.4 |
109.8 |
| C1' |
N1 |
C6 |
114.7 |
119.8 |
| C1' |
N1 |
C2 |
124.3 |
119.9 |
| N1 |
C1' |
H1' |
85.4 |
109.9 |
| C6 |
N1 |
C2 |
121.0 |
120.3 |
| N1 |
C6 |
C5 |
119.5 |
119.3 |
| N1 |
C6 |
H6 |
120.2 |
120.4 |
| N1 |
C2 |
N3 |
117.1 |
121.1 |
| N1 |
C2 |
O2 |
121.1 |
119.4 |
| C6 |
C5 |
C4 |
118.5 |
119.0 |
| C5 |
C6 |
H6 |
120.2 |
120.3 |
| C6 |
C5 |
H5 |
120.8 |
120.5 |
| C5 |
C4 |
N4 |
117.2 |
120.2 |
| C5 |
C4 |
N3 |
120.9 |
119.6 |
| C4 |
C5 |
H5 |
120.8 |
120.5 |
| N4 |
C4 |
N3 |
121.9 |
120.2 |
| C4 |
N4 |
HN4 |
109.5 |
120.0 |
| C4 |
N4 |
HN4A |
125.3 |
119.9 |
| C4 |
N3 |
C2 |
123.0 |
120.7 |
| N3 |
C2 |
O2 |
121.8 |
119.5 |
| H5' |
C5' |
H5'A |
110.2 |
109.4 |
| HN4 |
N4 |
HN4A |
125.2 |
120.0 |
Torsion Angles for C6B
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2P |
P |
O1P |
O3P |
125.5 |
240.0 |
| O2P |
P |
O1P |
O3' |
250.5 |
120.0 |
| O1P |
P |
O2P |
HO2P |
80.1 |
60.0 |
| O3P |
P |
O1P |
O3' |
125.0 |
240.0 |
| O1P |
P |
O3' |
C3' |
72.0 |
295.0 |
| O1P |
P |
O2P |
O3P |
234.7 |
120.0 |
| O1P |
P |
O2P |
O3' |
110.1 |
240.0 |
| O2P |
P |
O1P |
HO1P |
122.8 |
59.9 |
| O3P |
P |
O2P |
O3' |
235.3 |
120.0 |
| O2P |
P |
O3' |
C3' |
182.8 |
175.0 |
| O1P |
P |
O3P |
O2P |
121.1 |
240.0 |
| O1P |
P |
O3P |
O3' |
240.2 |
120.0 |
| O3P |
P |
O1P |
HO1P |
357.3 |
180.0 |
| O2P |
P |
O3P |
O3' |
119.0 |
240.0 |
| O3P |
P |
O2P |
HO2P |
205.3 |
300.0 |
| O3P |
P |
O3' |
C3' |
307.4 |
55.0 |
| O1P |
P |
O3' |
O2P |
249.2 |
120.0 |
| O1P |
P |
O3' |
O3P |
124.6 |
240.0 |
| O3' |
P |
O1P |
HO1P |
232.3 |
300.0 |
| O2P |
P |
O3' |
O3P |
235.4 |
120.0 |
| O3' |
P |
O2P |
HO2P |
330.0 |
180.0 |
| P |
O3' |
C3' |
C2' |
117.5 |
120.0 |
| P |
O3' |
C3' |
C4' |
239.8 |
232.7 |
| P |
O3' |
C3' |
H3' |
356.8 |
356.4 |
| C2' |
C3' |
O3' |
C4' |
237.7 |
247.3 |
| O3' |
C3' |
C2' |
O2' |
60.1 |
338.6 |
| O3' |
C3' |
C2' |
C1' |
176.2 |
97.3 |
| C2' |
C3' |
O3' |
H3' |
120.8 |
123.6 |
| O3' |
C3' |
C2' |
H2' |
302.0 |
216.1 |
| O3' |
C3' |
C4' |
C5' |
330.5 |
37.4 |
| O3' |
C3' |
C4' |
O4' |
213.9 |
278.9 |
| C4' |
C3' |
O3' |
H3' |
243.1 |
236.3 |
| O3' |
C3' |
C4' |
H4' |
86.8 |
160.2 |
| O3' |
C3' |
C2' |
C4' |
128.7 |
118.2 |
| O3' |
C3' |
C2' |
H3' |
246.9 |
236.4 |
| C2' |
C3' |
C4' |
C5' |
96.5 |
155.5 |
| C2' |
C3' |
C4' |
O4' |
339.9 |
37.0 |
| C4' |
C3' |
C2' |
H3' |
118.2 |
118.2 |
| C2' |
C3' |
C4' |
H4' |
212.8 |
278.4 |
| O2' |
C2' |
C3' |
C1' |
243.9 |
241.3 |
| O2' |
C2' |
C3' |
H2' |
118.1 |
122.5 |
| C3' |
C2' |
O2' |
HO2' |
17.9 |
186.4 |
| C3' |
C2' |
C1' |
O4' |
298.6 |
358.0 |
| C3' |
C2' |
C1' |
N1 |
159.7 |
238.5 |
| C1' |
C2' |
C3' |
H2' |
234.2 |
241.2 |
| C3' |
C2' |
C1' |
H1' |
62.8 |
117.4 |
| O3' |
C3' |
C4' |
C2' |
234.0 |
241.9 |
| O3' |
C3' |
C4' |
H3' |
112.5 |
123.6 |
| C4' |
C3' |
C2' |
O2' |
291.4 |
220.5 |
| C4' |
C3' |
C2' |
C1' |
47.5 |
339.1 |
| C2' |
C3' |
C4' |
H3' |
238.5 |
241.8 |
| C4' |
C3' |
C2' |
H2' |
173.3 |
98.0 |
| C5' |
C4' |
C3' |
O4' |
116.6 |
118.5 |
| C3' |
C4' |
C5' |
O5' |
133.6 |
175.0 |
| C5' |
C4' |
C3' |
H4' |
243.7 |
237.2 |
| C3' |
C4' |
C5' |
H5' |
253.6 |
295.0 |
| C3' |
C4' |
C5' |
H5'A |
14.0 |
55.0 |
| C3' |
C4' |
O4' |
C1' |
341.3 |
320.0 |
| O4' |
C4' |
C3' |
H4' |
127.1 |
118.7 |
| O2' |
C2' |
C3' |
C4' |
291.4 |
220.5 |
| C3' |
C2' |
O2' |
C1' |
99.8 |
114.7 |
| O2' |
C2' |
C3' |
H3' |
173.2 |
102.2 |
| C3' |
C2' |
O2' |
H2' |
229.6 |
237.5 |
| O2' |
C2' |
C1' |
O4' |
53.6 |
116.6 |
| O2' |
C2' |
C1' |
N1 |
274.8 |
357.1 |
| C1' |
C2' |
O2' |
H2' |
129.8 |
122.8 |
| O2' |
C2' |
C1' |
H1' |
177.9 |
236.0 |
| C1' |
C2' |
C3' |
C4' |
47.5 |
339.1 |
| C3' |
C2' |
C1' |
O2' |
245.0 |
241.4 |
| C1' |
C2' |
C3' |
H3' |
289.3 |
220.9 |
| C3' |
C2' |
C1' |
H2' |
126.7 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
241.7 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
278.1 |
71.7 |
| C4' |
O4' |
C1' |
C2' |
53.3 |
26.5 |
| O4' |
C1' |
C2' |
N1 |
138.9 |
119.5 |
| O4' |
C1' |
C2' |
H1' |
235.8 |
240.6 |
| C2' |
C1' |
N1 |
C6 |
268.6 |
94.4 |
| C2' |
C1' |
N1 |
C2 |
90.9 |
274.2 |
| N1 |
C1' |
C2' |
H1' |
96.9 |
121.1 |
| C3' |
C4' |
C5' |
O4' |
245.6 |
245.9 |
| C5' |
C4' |
C3' |
H3' |
218.0 |
273.7 |
| C3' |
C4' |
C5' |
H4' |
118.4 |
122.9 |
| C5' |
C4' |
O4' |
C1' |
215.4 |
201.4 |
| O4' |
C4' |
C5' |
H4' |
232.8 |
237.0 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
119.6 |
120.0 |
| C4' |
C5' |
O5' |
HO5' |
351.0 |
180.1 |
| H5' |
C5' |
C4' |
H5'A |
239.7 |
240.0 |
| C3' |
C4' |
O4' |
C5' |
125.9 |
118.5 |
| O4' |
C4' |
C3' |
H3' |
101.4 |
155.2 |
| C3' |
C4' |
O4' |
H4' |
241.9 |
241.5 |
| C2' |
C1' |
O4' |
C4' |
53.3 |
26.5 |
| O4' |
C4' |
C5' |
O5' |
248.0 |
289.1 |
| C5' |
C4' |
O4' |
H4' |
116.1 |
122.9 |
| O4' |
C4' |
C5' |
H5' |
8.0 |
49.1 |
| O4' |
C4' |
C5' |
H5'A |
128.4 |
169.1 |
| C4' |
O4' |
C1' |
N1 |
195.9 |
146.0 |
| C4' |
O4' |
C1' |
H1' |
296.0 |
267.0 |
| O5' |
C5' |
C4' |
O4' |
248.0 |
289.1 |
| O5' |
C5' |
C4' |
H4' |
15.2 |
52.1 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
240.4 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.4 |
120.0 |
| C2' |
C1' |
O4' |
N1 |
217.3 |
240.5 |
| O4' |
C1' |
C2' |
H2' |
171.9 |
239.3 |
| C2' |
C1' |
O4' |
H1' |
117.3 |
119.5 |
| C1' |
O4' |
C4' |
H4' |
99.3 |
78.5 |
| O4' |
C1' |
N1 |
C6 |
135.3 |
336.5 |
| O4' |
C1' |
N1 |
C2 |
317.7 |
156.3 |
| N1 |
C1' |
O4' |
H1' |
259.9 |
238.9 |
| C2' |
C1' |
N1 |
O4' |
133.2 |
117.9 |
| N1 |
C1' |
C2' |
H2' |
33.1 |
119.8 |
| C2' |
C1' |
N1 |
H1' |
251.9 |
238.9 |
| O4' |
C1' |
N1 |
H1' |
118.7 |
121.0 |
| C6 |
N1 |
C1' |
C2 |
177.7 |
180.2 |
| C1' |
N1 |
C6 |
C5 |
181.2 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
1.2 |
0.1 |
| C1' |
N1 |
C2 |
N3 |
178.6 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
358.1 |
360.0 |
| C1' |
N1 |
C6 |
C2 |
182.3 |
179.8 |
| C6 |
N1 |
C1' |
H1' |
16.6 |
215.5 |
| C6 |
N1 |
C2 |
N3 |
1.0 |
359.5 |
| C6 |
N1 |
C2 |
O2 |
180.5 |
179.7 |
| N1 |
C6 |
C5 |
C4 |
0.6 |
0.1 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
H5 |
180.7 |
180.0 |
| C1' |
N1 |
C2 |
C6 |
177.5 |
180.2 |
| C2 |
N1 |
C1' |
H1' |
199.0 |
35.3 |
| C2 |
N1 |
C6 |
C5 |
359.0 |
0.2 |
| C2 |
N1 |
C6 |
H6 |
178.9 |
180.3 |
| C4 |
N3 |
C2 |
N1 |
359.3 |
0.5 |
| N3 |
C2 |
N1 |
O2 |
180.5 |
179.7 |
| C5 |
C6 |
N1 |
C2 |
359.0 |
0.2 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
N4 |
179.7 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
359.7 |
359.9 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| C4 |
C5 |
C6 |
H6 |
180.7 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| N4 |
C4 |
C5 |
N3 |
180.1 |
180.1 |
| C5 |
C4 |
N4 |
HN4 |
180.0 |
359.9 |
| C5 |
C4 |
N4 |
HN4A |
0.0 |
179.9 |
| C5 |
C4 |
N3 |
C2 |
0.4 |
359.8 |
| C5 |
C4 |
N4 |
N3 |
179.9 |
179.9 |
| N4 |
C4 |
C5 |
H5 |
359.7 |
0.1 |
| N4 |
C4 |
N3 |
C2 |
180.3 |
179.7 |
| HN4 |
N4 |
C4 |
HN4A |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
359.3 |
0.5 |
| C5 |
C4 |
N3 |
N4 |
180.1 |
180.1 |
| N3 |
C4 |
C5 |
H5 |
179.7 |
180.0 |
| N3 |
C4 |
N4 |
HN4 |
0.1 |
180.1 |
| N3 |
C4 |
N4 |
HN4A |
180.1 |
0.1 |
| C4 |
N3 |
C2 |
O2 |
179.8 |
180.3 |
| N1 |
C2 |
N3 |
O2 |
179.5 |
180.3 |
| N1 |
C2 |
O2 |
N3 |
180.5 |
179.7 |
| HO1P |
O1P |
P |
O2P |
122.8 |
59.9 |
| HO1P |
O1P |
P |
O3P |
357.3 |
180.0 |
| HO1P |
O1P |
P |
O3' |
232.3 |
300.0 |
| HO2P |
O2P |
P |
O3P |
205.3 |
300.0 |
| HO2P |
O2P |
P |
O3' |
330.0 |
180.0 |
| O3' |
C3' |
H3' |
C2' |
120.3 |
123.6 |
| O3' |
C3' |
H3' |
C4' |
236.7 |
236.3 |
| C2' |
C3' |
H3' |
C4' |
116.5 |
112.7 |
| H3' |
C3' |
C2' |
O2' |
173.2 |
102.2 |
| H3' |
C3' |
C2' |
C1' |
289.3 |
220.9 |
| H3' |
C3' |
C2' |
H2' |
55.1 |
339.7 |
| H3' |
C3' |
C4' |
C5' |
218.0 |
273.7 |
| H3' |
C3' |
C4' |
O4' |
101.4 |
155.2 |
| H3' |
C3' |
C4' |
H4' |
334.3 |
36.6 |
| H2' |
C2' |
C3' |
C4' |
173.3 |
98.0 |
| C3' |
C2' |
H2' |
O2' |
124.7 |
122.5 |
| C3' |
C2' |
H2' |
C1' |
250.3 |
245.2 |
| H2' |
C2' |
C3' |
H3' |
55.1 |
339.7 |
| O2' |
C2' |
H2' |
C1' |
125.6 |
122.7 |
| H2' |
C2' |
O2' |
HO2' |
148.3 |
308.9 |
| H2' |
C2' |
C1' |
O4' |
171.9 |
239.3 |
| H2' |
C2' |
C1' |
N1 |
33.1 |
119.8 |
| H2' |
C2' |
C1' |
H1' |
296.2 |
358.7 |
| HO2' |
O2' |
C2' |
C1' |
278.1 |
71.7 |
| HO2' |
O2' |
C2' |
H2' |
148.3 |
308.9 |
| C3' |
C4' |
H4' |
C5' |
233.2 |
237.1 |
| C3' |
C4' |
H4' |
O4' |
115.5 |
114.2 |
| H4' |
C4' |
C3' |
H3' |
334.3 |
36.6 |
| C5' |
C4' |
H4' |
O4' |
242.3 |
237.0 |
| H4' |
C4' |
C5' |
O5' |
15.2 |
52.1 |
| H4' |
C4' |
C5' |
H5' |
135.2 |
172.2 |
| H4' |
C4' |
C5' |
H5'A |
255.5 |
292.1 |
| H4' |
C4' |
O4' |
C1' |
99.3 |
78.5 |
| H5' |
C5' |
C4' |
O4' |
8.0 |
49.1 |
| C4' |
C5' |
H5' |
O5' |
239.3 |
240.0 |
| H5' |
C5' |
C4' |
H4' |
135.2 |
172.2 |
| C4' |
C5' |
H5' |
H5'A |
119.6 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
240.4 |
240.0 |
| H5' |
C5' |
O5' |
HO5' |
231.0 |
60.1 |
| H5'A |
C5' |
C4' |
O4' |
128.4 |
169.1 |
| C4' |
C5' |
H5'A |
O5' |
120.5 |
120.1 |
| H5'A |
C5' |
C4' |
H4' |
255.5 |
292.1 |
| C4' |
C5' |
H5'A |
H5' |
240.3 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
119.8 |
120.0 |
| H5'A |
C5' |
O5' |
HO5' |
110.6 |
300.1 |
| HO5' |
O5' |
C5' |
H5' |
231.0 |
60.1 |
| HO5' |
O5' |
C5' |
H5'A |
110.6 |
300.1 |
| C2' |
C1' |
H1' |
O4' |
245.4 |
242.1 |
| C2' |
C1' |
H1' |
N1 |
125.9 |
121.1 |
| H1' |
C1' |
C2' |
H2' |
296.2 |
358.7 |
| O4' |
C1' |
H1' |
N1 |
240.5 |
239.0 |
| H1' |
C1' |
N1 |
C6 |
16.6 |
215.5 |
| H1' |
C1' |
N1 |
C2 |
199.0 |
35.3 |
| H6 |
C6 |
N1 |
C2 |
178.9 |
180.3 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.9 |
| H6 |
C6 |
C5 |
C4 |
180.7 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
0.7 |
359.9 |
| C6 |
C5 |
H5 |
C4 |
180.0 |
180.1 |
| H5 |
C5 |
C6 |
H6 |
0.7 |
359.9 |
| H5 |
C5 |
C4 |
N4 |
359.7 |
0.1 |
| H5 |
C5 |
C4 |
N3 |
179.7 |
180.0 |
| HN4 |
N4 |
C4 |
N3 |
0.1 |
180.1 |
| C4 |
N4 |
HN4 |
HN4A |
180.0 |
180.0 |
| HN4A |
N4 |
C4 |
N3 |
180.1 |
0.1 |
| C4 |
N4 |
HN4A |
HN4 |
180.0 |
180.0 |