PDB Chemical Component TBN
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 TBN
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.440 |
1.429 |
| O5' |
H5' |
0.950 |
0.966 |
| C5' |
C4' |
1.550 |
1.530 |
| C5' |
H5'1 |
1.115 |
1.089 |
| C5' |
H5'2 |
1.115 |
1.090 |
| C4' |
O4' |
1.433 |
1.444 |
| C4' |
C3' |
1.532 |
1.544 |
| C4' |
H4' |
1.115 |
1.089 |
| O4' |
C1' |
1.437 |
1.445 |
| C1' |
N9 |
1.498 |
1.465 |
| C1' |
C2' |
1.541 |
1.545 |
| C1' |
H1' |
1.115 |
1.090 |
| N9 |
C8 |
1.396 |
1.370 |
| N9 |
C4 |
1.415 |
1.367 |
| C8 |
C7 |
1.366 |
1.342 |
| C8 |
H8 |
1.103 |
1.081 |
| C7 |
C5 |
1.361 |
1.462 |
| C7 |
H7 |
1.103 |
1.080 |
| C5 |
C6 |
1.422 |
1.404 |
| C5 |
C4 |
1.381 |
1.407 |
| C6 |
N1 |
1.381 |
1.330 |
| C6 |
N6 |
1.343 |
1.383 |
| N1 |
C2 |
1.362 |
1.321 |
| C2 |
N3 |
1.360 |
1.315 |
| C2 |
H2 |
1.103 |
1.080 |
| N3 |
C4 |
1.381 |
1.332 |
| N6 |
HN61 |
1.020 |
0.969 |
| N6 |
HN62 |
1.020 |
0.970 |
| C2' |
O2' |
1.429 |
1.429 |
| C2' |
C3' |
1.525 |
1.547 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
H1 |
0.950 |
0.967 |
| C3' |
O3' |
1.437 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
H3 |
0.950 |
0.968 |
Bond Angles for TBN
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
H5' |
111.7 |
106.8 |
| O5' |
C5' |
C4' |
111.7 |
109.5 |
| O5' |
C5' |
H5'1 |
111.4 |
109.5 |
| O5' |
C5' |
H5'2 |
111.4 |
109.4 |
| C4' |
C5' |
H5'1 |
111.4 |
109.5 |
| C4' |
C5' |
H5'2 |
111.4 |
109.5 |
| C5' |
C4' |
O4' |
112.5 |
110.3 |
| C5' |
C4' |
C3' |
109.7 |
110.4 |
| C5' |
C4' |
H4' |
106.8 |
110.3 |
| H5'1 |
C5' |
H5'2 |
99.0 |
109.5 |
| O4' |
C4' |
C3' |
108.0 |
104.8 |
| O4' |
C4' |
H4' |
108.5 |
110.4 |
| C4' |
O4' |
C1' |
109.8 |
105.2 |
| C3' |
C4' |
H4' |
111.4 |
110.4 |
| C4' |
C3' |
C2' |
105.7 |
104.1 |
| C4' |
C3' |
O3' |
113.8 |
110.5 |
| C4' |
C3' |
H3' |
110.7 |
110.6 |
| O4' |
C1' |
N9 |
106.5 |
110.4 |
| O4' |
C1' |
C2' |
108.2 |
104.9 |
| O4' |
C1' |
H1' |
117.4 |
110.4 |
| N9 |
C1' |
C2' |
121.2 |
110.4 |
| N9 |
C1' |
H1' |
103.0 |
110.3 |
| C1' |
N9 |
C8 |
126.0 |
125.0 |
| C1' |
N9 |
C4 |
128.5 |
125.0 |
| C2' |
C1' |
H1' |
101.1 |
110.3 |
| C1' |
C2' |
O2' |
107.2 |
110.8 |
| C1' |
C2' |
C3' |
105.3 |
104.0 |
| C1' |
C2' |
H2' |
114.8 |
110.4 |
| C8 |
N9 |
C4 |
105.5 |
110.0 |
| N9 |
C8 |
C7 |
110.8 |
109.8 |
| N9 |
C8 |
H8 |
125.5 |
125.1 |
| N9 |
C4 |
C5 |
106.4 |
107.1 |
| N9 |
C4 |
N3 |
129.2 |
134.3 |
| C7 |
C8 |
H8 |
123.7 |
125.1 |
| C8 |
C7 |
C5 |
106.1 |
106.8 |
| C8 |
C7 |
H7 |
127.1 |
126.6 |
| C5 |
C7 |
H7 |
126.8 |
126.6 |
| C7 |
C5 |
C6 |
127.1 |
135.1 |
| C7 |
C5 |
C4 |
111.2 |
106.2 |
| C6 |
C5 |
C4 |
121.8 |
118.7 |
| C5 |
C6 |
N1 |
114.0 |
118.3 |
| C5 |
C6 |
N6 |
124.5 |
120.8 |
| C5 |
C4 |
N3 |
124.4 |
118.5 |
| N1 |
C6 |
N6 |
121.5 |
120.8 |
| C6 |
N1 |
C2 |
120.3 |
121.0 |
| C6 |
N6 |
HN61 |
106.9 |
120.0 |
| C6 |
N6 |
HN62 |
124.5 |
120.0 |
| N1 |
C2 |
N3 |
128.6 |
122.7 |
| N1 |
C2 |
H2 |
115.8 |
118.7 |
| N3 |
C2 |
H2 |
115.6 |
118.6 |
| C2 |
N3 |
C4 |
110.9 |
120.7 |
| HN61 |
N6 |
HN62 |
106.9 |
120.0 |
| O2' |
C2' |
C3' |
112.7 |
110.5 |
| O2' |
C2' |
H2' |
107.6 |
110.5 |
| C2' |
O2' |
H1 |
107.1 |
106.8 |
| C3' |
C2' |
H2' |
109.3 |
110.5 |
| C2' |
C3' |
O3' |
113.5 |
110.5 |
| C2' |
C3' |
H3' |
111.0 |
110.5 |
| O3' |
C3' |
H3' |
102.3 |
110.5 |
| C3' |
O3' |
H3 |
113.8 |
106.7 |
Torsion Angles for TBN
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.7 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
34.0 |
66.4 |
| O5' |
C5' |
C4' |
C3' |
154.3 |
181.8 |
| O5' |
C5' |
C4' |
H4' |
275.1 |
304.1 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
120.0 |
| H5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| H5' |
O5' |
C5' |
H5'1 |
54.7 |
60.0 |
| H5' |
O5' |
C5' |
H5'2 |
305.3 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
239.9 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
119.9 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
239.8 |
244.6 |
| O4' |
C4' |
C5' |
H4' |
118.9 |
122.3 |
| C5' |
C4' |
O4' |
C1' |
103.1 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
239.2 |
237.7 |
| C5' |
C4' |
C3' |
C2' |
250.3 |
217.0 |
| C5' |
C4' |
C3' |
O3' |
125.1 |
98.4 |
| C5' |
C4' |
C3' |
H3' |
10.6 |
335.7 |
| H5'1 |
C5' |
O5' |
H5' |
54.7 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
125.4 |
120.1 |
| O5' |
C5' |
H5'1 |
H5'2 |
242.7 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
117.3 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
159.3 |
186.5 |
| H5'1 |
C5' |
C4' |
C3' |
279.5 |
301.9 |
| H5'1 |
C5' |
C4' |
H4' |
40.4 |
64.2 |
| H5'2 |
C5' |
O5' |
H5' |
305.3 |
300.0 |
| O5' |
C5' |
H5'2 |
C4' |
234.6 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
117.3 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
242.7 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
268.7 |
306.5 |
| H5'2 |
C5' |
C4' |
C3' |
29.0 |
61.9 |
| H5'2 |
C5' |
C4' |
H4' |
149.8 |
184.2 |
| O4' |
C4' |
C5' |
H5'1 |
159.3 |
186.5 |
| O4' |
C4' |
C5' |
H5'2 |
268.7 |
306.5 |
| C5' |
C4' |
O4' |
C3' |
121.2 |
118.9 |
| C5' |
C4' |
O4' |
H4' |
242.1 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
120.9 |
118.9 |
| O4' |
C4' |
C3' |
C2' |
13.2 |
335.8 |
| O4' |
C4' |
C3' |
O3' |
248.0 |
217.2 |
| O4' |
C4' |
C3' |
H3' |
133.5 |
94.6 |
| C4' |
O4' |
C1' |
N9 |
243.8 |
200.6 |
| C4' |
O4' |
C1' |
C2' |
15.6 |
319.5 |
| C4' |
O4' |
C1' |
H1' |
129.1 |
78.4 |
| C3' |
C4' |
C5' |
H5'1 |
279.5 |
301.9 |
| C3' |
C4' |
C5' |
H5'2 |
29.0 |
61.9 |
| C5' |
C4' |
C3' |
O4' |
237.1 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
118.0 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
240.9 |
241.1 |
| C3' |
C4' |
O4' |
C1' |
341.9 |
40.6 |
| C1' |
C2' |
C3' |
C4' |
356.1 |
0.2 |
| O2' |
C2' |
C3' |
C4' |
239.6 |
241.2 |
| C4' |
C3' |
C2' |
H2' |
119.9 |
118.7 |
| C2' |
C3' |
C4' |
O3' |
125.2 |
118.6 |
| C2' |
C3' |
C4' |
H3' |
239.7 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
114.5 |
122.7 |
| C4' |
C3' |
O3' |
H3 |
180.0 |
298.5 |
| H4' |
C4' |
C5' |
H5'1 |
40.4 |
64.2 |
| H4' |
C4' |
C5' |
H5'2 |
149.8 |
184.2 |
| C5' |
C4' |
H4' |
O4' |
121.5 |
122.2 |
| C5' |
C4' |
H4' |
C3' |
240.3 |
237.7 |
| O4' |
C4' |
H4' |
C3' |
118.8 |
115.4 |
| H4' |
C4' |
O4' |
C1' |
221.0 |
281.7 |
| H4' |
C4' |
C3' |
C2' |
132.3 |
94.7 |
| H4' |
C4' |
C3' |
O3' |
7.1 |
336.1 |
| H4' |
C4' |
C3' |
H3' |
252.5 |
213.5 |
| C1' |
O4' |
C4' |
C3' |
341.9 |
40.6 |
| C1' |
O4' |
C4' |
H4' |
221.0 |
281.7 |
| N9 |
C1' |
O4' |
C2' |
228.2 |
241.1 |
| N9 |
C1' |
O4' |
H1' |
114.7 |
122.3 |
| O4' |
C1' |
N9 |
C8 |
279.7 |
22.0 |
| O4' |
C1' |
N9 |
C4 |
99.3 |
202.0 |
| C2' |
C1' |
O4' |
H1' |
246.5 |
241.2 |
| O4' |
C1' |
C2' |
O2' |
113.6 |
142.6 |
| O4' |
C1' |
C2' |
C3' |
353.3 |
23.8 |
| O4' |
C1' |
C2' |
H2' |
233.0 |
265.3 |
| O4' |
C1' |
N9 |
C2' |
124.0 |
115.5 |
| O4' |
C1' |
N9 |
H1' |
235.8 |
237.7 |
| C2' |
C1' |
N9 |
H1' |
111.8 |
122.2 |
| N9 |
C1' |
C2' |
O2' |
236.8 |
261.5 |
| N9 |
C1' |
C2' |
C3' |
116.6 |
142.7 |
| N9 |
C1' |
C2' |
H2' |
356.3 |
24.2 |
| C8 |
N9 |
C1' |
C4 |
180.3 |
180.0 |
| C1' |
N9 |
C8 |
C7 |
179.7 |
180.1 |
| C1' |
N9 |
C8 |
H8 |
359.7 |
360.0 |
| C1' |
N9 |
C4 |
C5 |
180.4 |
180.2 |
| C1' |
N9 |
C4 |
N3 |
0.3 |
360.0 |
| C4' |
C3' |
C2' |
C1' |
356.1 |
0.2 |
| O4' |
C1' |
C2' |
N9 |
236.7 |
241.1 |
| O4' |
C1' |
C2' |
H1' |
123.9 |
118.9 |
| N9 |
C1' |
C2' |
H1' |
247.2 |
237.8 |
| C2' |
C1' |
N9 |
C8 |
155.6 |
266.5 |
| C2' |
C1' |
N9 |
C4 |
335.3 |
86.5 |
| O2' |
C2' |
C1' |
C3' |
120.3 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
240.6 |
237.2 |
| C1' |
C2' |
O2' |
H1 |
180.0 |
183.8 |
| C3' |
C2' |
C1' |
H2' |
120.3 |
118.5 |
| C1' |
C2' |
C3' |
O3' |
121.6 |
118.9 |
| C1' |
C2' |
C3' |
H3' |
236.1 |
241.4 |
| O4' |
C1' |
H1' |
N9 |
116.6 |
122.3 |
| O4' |
C1' |
H1' |
C2' |
242.6 |
244.5 |
| N9 |
C1' |
H1' |
C2' |
126.0 |
122.2 |
| H1' |
C1' |
N9 |
C8 |
43.8 |
144.3 |
| H1' |
C1' |
N9 |
C4 |
223.5 |
324.3 |
| H1' |
C1' |
C2' |
O2' |
349.6 |
23.7 |
| H1' |
C1' |
C2' |
C3' |
229.4 |
264.9 |
| H1' |
C1' |
C2' |
H2' |
109.1 |
146.4 |
| C8 |
N9 |
C1' |
C2' |
155.6 |
266.5 |
| C8 |
N9 |
C1' |
H1' |
43.8 |
144.3 |
| C1' |
N9 |
C8 |
C4 |
179.7 |
180.0 |
| C8 |
N9 |
C4 |
C5 |
0.2 |
0.2 |
| C8 |
N9 |
C4 |
N3 |
180.0 |
180.0 |
| C7 |
C8 |
N9 |
H8 |
180.0 |
180.1 |
| N9 |
C8 |
C7 |
C5 |
360.0 |
359.7 |
| N9 |
C8 |
C7 |
H7 |
180.0 |
180.0 |
| C4 |
N9 |
C1' |
C2' |
335.3 |
86.5 |
| C4 |
N9 |
C1' |
H1' |
223.5 |
324.3 |
| C1' |
N9 |
C4 |
C8 |
180.3 |
180.0 |
| C4 |
N9 |
C8 |
C7 |
359.9 |
0.0 |
| C4 |
N9 |
C8 |
H8 |
179.9 |
179.9 |
| C7 |
C5 |
C4 |
N9 |
359.8 |
359.6 |
| C6 |
C5 |
C4 |
N9 |
179.7 |
180.4 |
| C5 |
C4 |
N9 |
N3 |
180.2 |
180.2 |
| C2 |
N3 |
C4 |
N9 |
180.2 |
180.0 |
| C7 |
C8 |
N9 |
C4 |
359.9 |
0.0 |
| N9 |
C8 |
C7 |
H8 |
180.0 |
179.9 |
| C5 |
C7 |
C8 |
H7 |
180.0 |
179.7 |
| C8 |
C7 |
C5 |
C6 |
180.3 |
179.5 |
| C8 |
C7 |
C5 |
C4 |
0.1 |
0.4 |
| H8 |
C8 |
N9 |
C4 |
179.9 |
179.9 |
| N9 |
C8 |
H8 |
C7 |
180.0 |
180.1 |
| H8 |
C8 |
C7 |
C5 |
180.0 |
179.8 |
| H8 |
C8 |
C7 |
H7 |
360.0 |
0.1 |
| N9 |
C4 |
C5 |
C7 |
359.8 |
359.6 |
| C5 |
C7 |
C8 |
H8 |
180.0 |
179.8 |
| C8 |
C7 |
C5 |
H7 |
180.0 |
180.3 |
| C6 |
C5 |
C7 |
C4 |
180.1 |
179.1 |
| C7 |
C5 |
C6 |
N1 |
180.0 |
180.5 |
| C7 |
C5 |
C6 |
N6 |
0.1 |
0.7 |
| C7 |
C5 |
C4 |
N3 |
180.0 |
179.8 |
| H7 |
C7 |
C8 |
H8 |
360.0 |
0.1 |
| C8 |
C7 |
H7 |
C5 |
180.0 |
179.6 |
| H7 |
C7 |
C5 |
C6 |
0.3 |
359.2 |
| H7 |
C7 |
C5 |
C4 |
180.1 |
180.1 |
| N9 |
C4 |
C5 |
C6 |
179.7 |
180.4 |
| C6 |
C5 |
C7 |
H7 |
0.3 |
359.2 |
| C7 |
C5 |
C6 |
C4 |
179.8 |
181.0 |
| C6 |
C5 |
C4 |
N3 |
359.8 |
0.5 |
| N1 |
C6 |
C5 |
N6 |
179.9 |
179.8 |
| C5 |
C6 |
N1 |
C2 |
0.0 |
0.2 |
| C5 |
C6 |
N6 |
HN61 |
54.7 |
179.7 |
| C5 |
C6 |
N6 |
HN62 |
180.0 |
359.4 |
| N9 |
C4 |
C5 |
N3 |
179.8 |
179.8 |
| C4 |
C5 |
C7 |
H7 |
180.1 |
180.1 |
| C7 |
C5 |
C4 |
C6 |
180.1 |
179.3 |
| C4 |
C5 |
C6 |
N1 |
0.1 |
359.5 |
| C4 |
C5 |
C6 |
N6 |
180.2 |
179.7 |
| C2 |
N3 |
C4 |
C5 |
0.0 |
359.7 |
| N1 |
C6 |
C5 |
C4 |
0.1 |
359.5 |
| C5 |
C6 |
N1 |
N6 |
180.1 |
180.2 |
| N1 |
C6 |
N6 |
HN61 |
234.9 |
359.9 |
| N1 |
C6 |
N6 |
HN62 |
0.1 |
179.7 |
| C6 |
N1 |
C2 |
N3 |
359.8 |
0.1 |
| C6 |
N1 |
C2 |
H2 |
179.8 |
180.1 |
| N6 |
C6 |
C5 |
C4 |
180.2 |
179.7 |
| C5 |
C6 |
N6 |
N1 |
179.9 |
179.8 |
| N6 |
C6 |
N1 |
C2 |
179.9 |
180.0 |
| HN61 |
N6 |
C6 |
HN62 |
234.8 |
180.2 |
| C2 |
N1 |
C6 |
N6 |
179.9 |
180.0 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.1 |
360.0 |
| N9 |
C4 |
N3 |
C2 |
180.2 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
0.0 |
359.7 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
| H2 |
C2 |
N3 |
C4 |
180.1 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
180.2 |
180.3 |
| C4 |
N3 |
C2 |
H2 |
180.1 |
180.0 |
| C6 |
N6 |
HN61 |
HN62 |
135.3 |
179.8 |
| C6 |
N6 |
HN62 |
HN61 |
234.8 |
180.2 |
| C4' |
C3' |
C2' |
O2' |
239.6 |
241.2 |
| O2' |
C2' |
C1' |
H1' |
349.6 |
23.7 |
| C1' |
C2' |
O2' |
C3' |
244.6 |
245.3 |
| C1' |
C2' |
O2' |
H2' |
123.9 |
122.7 |
| C3' |
C2' |
O2' |
H2' |
239.4 |
237.4 |
| O2' |
C2' |
C3' |
O3' |
5.0 |
359.9 |
| O2' |
C2' |
C3' |
H3' |
119.6 |
122.5 |
| C2' |
C3' |
C4' |
H4' |
132.3 |
94.7 |
| C4' |
C3' |
C2' |
O3' |
234.6 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
120.0 |
118.8 |
| C3' |
C2' |
C1' |
H1' |
229.4 |
264.9 |
| C1' |
C2' |
C3' |
O2' |
116.5 |
118.9 |
| C1' |
C2' |
C3' |
H2' |
236.2 |
241.5 |
| O2' |
C2' |
C3' |
H2' |
119.7 |
122.6 |
| C3' |
C2' |
O2' |
H1 |
295.4 |
298.5 |
| O3' |
C3' |
C2' |
H3' |
245.4 |
237.4 |
| C2' |
C3' |
O3' |
H3 |
59.0 |
183.9 |
| H2' |
C2' |
C1' |
H1' |
109.1 |
146.4 |
| C1' |
C2' |
H2' |
O2' |
240.8 |
237.0 |
| C1' |
C2' |
H2' |
C3' |
118.0 |
114.4 |
| O2' |
C2' |
H2' |
C3' |
237.2 |
237.4 |
| H2' |
C2' |
O2' |
H1 |
56.1 |
61.1 |
| H2' |
C2' |
C3' |
O3' |
245.4 |
237.3 |
| H2' |
C2' |
C3' |
H3' |
359.9 |
359.9 |
| H1 |
O2' |
C2' |
C3' |
295.4 |
298.5 |
| H1 |
O2' |
C2' |
H2' |
56.1 |
61.1 |
| O3' |
C3' |
C4' |
H4' |
7.1 |
336.1 |
| C4' |
C3' |
O3' |
C2' |
120.9 |
114.6 |
| C4' |
C3' |
O3' |
H3' |
240.6 |
237.3 |
| O3' |
C3' |
C2' |
H2' |
245.4 |
237.3 |
| C2' |
C3' |
O3' |
H3' |
119.7 |
122.6 |
| H3' |
C3' |
C4' |
H4' |
252.5 |
213.5 |
| C4' |
C3' |
H3' |
C2' |
243.0 |
245.3 |
| C4' |
C3' |
H3' |
O3' |
121.6 |
122.7 |
| H3' |
C3' |
C2' |
H2' |
359.9 |
359.9 |
| C2' |
C3' |
H3' |
O3' |
238.6 |
237.4 |
| H3' |
C3' |
O3' |
H3 |
299.4 |
61.3 |
| H3 |
O3' |
C3' |
H3' |
299.4 |
61.3 |