PDB Chemical Component B9B
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 B9B
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2' |
C2' |
1.411 |
1.429 |
| C61 |
C62 |
1.517 |
1.530 |
| C61 |
O6 |
1.419 |
1.429 |
| N2 |
C2 |
1.348 |
1.385 |
| C2 |
N1 |
1.348 |
1.327 |
| C2 |
N3 |
1.342 |
1.324 |
| N1 |
C6 |
1.342 |
1.327 |
| C62 |
C63 |
1.506 |
1.530 |
| N3 |
C4 |
1.338 |
1.329 |
| C6 |
O6 |
1.361 |
1.354 |
| C6 |
C5 |
1.461 |
1.403 |
| C2' |
C1' |
1.516 |
1.545 |
| C2' |
C3' |
1.519 |
1.545 |
| O3' |
C3' |
1.419 |
1.429 |
| C4 |
C5 |
1.453 |
1.405 |
| C4 |
N9 |
1.308 |
1.372 |
| C5 |
N7 |
1.335 |
1.356 |
| N9 |
C1' |
1.454 |
1.465 |
| N9 |
C8 |
1.334 |
1.364 |
| C1' |
O4' |
1.403 |
1.444 |
| N7 |
C8 |
1.344 |
1.301 |
| C3' |
C4' |
1.528 |
1.545 |
| O4' |
C4' |
1.445 |
1.444 |
| C4' |
C5' |
1.504 |
1.531 |
| O5' |
C5' |
1.420 |
1.429 |
| O5' |
P |
1.582 |
1.610 |
| OP1 |
P |
1.499 |
1.480 |
| P |
OP2 |
1.502 |
1.610 |
| C8 |
H1 |
1.080 |
1.080 |
| C1' |
H2 |
1.100 |
1.090 |
| C2' |
H3 |
1.100 |
1.090 |
| C3' |
H4 |
1.100 |
1.090 |
| C4' |
H5 |
1.100 |
1.090 |
| C5' |
H6 |
1.100 |
1.091 |
| C5' |
H7 |
1.100 |
1.089 |
| N2 |
H8 |
1.000 |
0.970 |
| N2 |
H9 |
1.000 |
0.970 |
| O2' |
H10 |
0.950 |
0.967 |
| O3' |
H11 |
0.950 |
0.966 |
| OP2 |
H13 |
0.950 |
0.967 |
| C61 |
H14 |
1.101 |
1.090 |
| C61 |
H15 |
1.100 |
1.090 |
| C62 |
H16 |
1.100 |
1.090 |
| C62 |
H17 |
1.100 |
1.090 |
| C63 |
H18 |
1.100 |
1.090 |
| C63 |
H19 |
1.100 |
1.090 |
| C63 |
H20 |
1.100 |
1.090 |
| P |
OP3 |
1.599 |
1.610 |
| OP3 |
H12 |
0.951 |
0.967 |
Bond Angles for B9B
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2' |
C2' |
H3 |
110.6 |
110.6 |
| C61 |
C62 |
C63 |
109.6 |
109.5 |
| C62 |
C61 |
H14 |
109.7 |
109.5 |
| C62 |
C61 |
H15 |
109.7 |
109.5 |
| C61 |
C62 |
H16 |
109.4 |
109.5 |
| C61 |
C62 |
H17 |
109.4 |
109.5 |
| N2 |
C2 |
N3 |
118.4 |
118.8 |
| N1 |
C2 |
N3 |
122.6 |
122.2 |
| C2 |
N1 |
C6 |
122.5 |
121.2 |
| C2 |
N3 |
C4 |
120.0 |
120.5 |
| N1 |
C6 |
O6 |
122.1 |
120.7 |
| C63 |
C62 |
H16 |
109.4 |
109.5 |
| C63 |
C62 |
H17 |
109.4 |
109.4 |
| C62 |
C63 |
H18 |
109.5 |
109.5 |
| C62 |
C63 |
H19 |
109.4 |
109.4 |
| C62 |
C63 |
H20 |
109.5 |
109.5 |
| N3 |
C4 |
N9 |
133.7 |
134.9 |
| C6 |
C5 |
N7 |
135.9 |
134.5 |
| C2' |
C1' |
O4' |
106.1 |
104.8 |
| C2' |
C1' |
H2 |
109.2 |
110.4 |
| C2' |
C3' |
C4' |
103.5 |
104.1 |
| C3' |
C2' |
H3 |
109.0 |
110.5 |
| C2' |
C3' |
H4 |
110.8 |
110.5 |
| O3' |
C3' |
H4 |
112.3 |
110.5 |
| C4 |
C5 |
N7 |
107.4 |
107.1 |
| C5 |
N7 |
C8 |
106.6 |
109.5 |
| N9 |
C1' |
O4' |
109.1 |
110.3 |
| N9 |
C1' |
H2 |
110.0 |
110.4 |
| N9 |
C8 |
H1 |
124.5 |
125.0 |
| C1' |
O4' |
C4' |
109.7 |
105.2 |
| O4' |
C1' |
H2 |
110.8 |
110.4 |
| N7 |
C8 |
H1 |
124.5 |
125.0 |
| C3' |
C4' |
C5' |
114.6 |
110.4 |
| C4' |
C3' |
H4 |
110.7 |
110.5 |
| C3' |
C4' |
H5 |
108.6 |
110.3 |
| O4' |
C4' |
H5 |
109.7 |
110.5 |
| C5' |
C4' |
H5 |
108.9 |
110.3 |
| C4' |
C5' |
H6 |
109.0 |
109.4 |
| C4' |
C5' |
H7 |
109.0 |
109.4 |
| O5' |
C5' |
H6 |
109.0 |
109.5 |
| O5' |
C5' |
H7 |
109.0 |
109.5 |
| O5' |
P |
OP1 |
108.6 |
109.5 |
| O5' |
P |
OP2 |
106.1 |
109.5 |
| O5' |
P |
OP3 |
103.7 |
109.5 |
| OP1 |
P |
OP2 |
121.0 |
109.5 |
| OP1 |
P |
OP3 |
109.4 |
109.5 |
| P |
OP2 |
H13 |
109.5 |
114.0 |
| H6 |
C5' |
H7 |
109.5 |
109.5 |
| H8 |
N2 |
H9 |
109.5 |
120.0 |
| H14 |
C61 |
H15 |
109.5 |
109.5 |
| H16 |
C62 |
H17 |
109.5 |
109.5 |
| H18 |
C63 |
H19 |
109.5 |
109.4 |
| H18 |
C63 |
H20 |
109.4 |
109.5 |
| H19 |
C63 |
H20 |
109.4 |
109.5 |
| P |
OP3 |
H12 |
109.5 |
114.0 |
Torsion Angles for B9B
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2' |
C2' |
C1' |
O4' |
157.7 |
142.6 |
| O2' |
C2' |
C1' |
H2 |
38.2 |
23.8 |
| C3' |
C2' |
O2' |
H3 |
236.3 |
237.3 |
| O2' |
C2' |
C3' |
H4 |
90.3 |
122.7 |
| C63 |
C62 |
C61 |
H16 |
240.0 |
240.0 |
| C63 |
C62 |
C61 |
H17 |
120.0 |
119.9 |
| C61 |
C62 |
C63 |
H18 |
180.0 |
300.1 |
| C61 |
C62 |
C63 |
H19 |
300.0 |
60.0 |
| C61 |
C62 |
C63 |
H20 |
60.0 |
180.0 |
| H14 |
C61 |
C62 |
H15 |
239.7 |
120.0 |
| H16 |
C62 |
C61 |
H17 |
240.1 |
240.0 |
| N1 |
C2 |
N2 |
N3 |
176.1 |
179.8 |
| N2 |
C2 |
N3 |
C4 |
178.9 |
179.7 |
| N2 |
C2 |
N1 |
N3 |
184.0 |
180.3 |
| N1 |
C2 |
N3 |
C4 |
3.0 |
360.0 |
| C2 |
N1 |
C6 |
O6 |
182.3 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
356.4 |
0.0 |
| C2 |
N3 |
C4 |
N9 |
178.1 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
356.4 |
0.0 |
| N1 |
C6 |
C5 |
N7 |
179.6 |
180.0 |
| C63 |
C62 |
C61 |
H14 |
189.4 |
60.0 |
| C63 |
C62 |
C61 |
H15 |
309.7 |
300.0 |
| C61 |
C62 |
C63 |
H16 |
120.0 |
120.1 |
| C61 |
C62 |
C63 |
H17 |
240.0 |
240.0 |
| H16 |
C62 |
C63 |
H17 |
120.0 |
120.0 |
| H18 |
C63 |
C62 |
H19 |
240.0 |
240.1 |
| H18 |
C63 |
C62 |
H20 |
120.0 |
120.1 |
| H19 |
C63 |
C62 |
H20 |
240.0 |
240.0 |
| N3 |
C4 |
C5 |
N7 |
179.8 |
180.0 |
| O6 |
C6 |
C5 |
N7 |
359.4 |
360.0 |
| C2 |
N1 |
C6 |
C5 |
2.0 |
359.9 |
| C4 |
C5 |
C6 |
N7 |
180.2 |
180.0 |
| C6 |
C5 |
N7 |
C8 |
180.6 |
180.0 |
| N9 |
C1' |
C2' |
O4' |
118.7 |
118.8 |
| N9 |
C1' |
C2' |
H2 |
238.2 |
237.7 |
| C2' |
C1' |
O4' |
C4' |
334.6 |
319.5 |
| O4' |
C1' |
C2' |
H2 |
119.5 |
118.9 |
| O2' |
C2' |
C3' |
H3 |
124.6 |
122.7 |
| C3' |
C2' |
C1' |
O4' |
35.1 |
24.0 |
| C3' |
C2' |
C1' |
H2 |
275.7 |
265.2 |
| O3' |
C3' |
C2' |
H4 |
235.9 |
237.3 |
| C2' |
C3' |
C4' |
C5' |
257.2 |
217.2 |
| C4' |
C3' |
C2' |
H4 |
118.7 |
118.6 |
| C2' |
C3' |
C4' |
H5 |
135.2 |
95.0 |
| O3' |
C3' |
C2' |
H3 |
201.7 |
237.3 |
| C2' |
C3' |
O3' |
H4 |
123.2 |
122.6 |
| C4' |
C3' |
O3' |
H4 |
236.2 |
237.3 |
| O3' |
C3' |
C4' |
H5 |
18.6 |
336.3 |
| C2 |
N3 |
C4 |
C5 |
359.0 |
0.0 |
| C6 |
C5 |
C4 |
N7 |
179.8 |
180.0 |
| C4 |
C5 |
N7 |
C8 |
0.4 |
360.0 |
| N9 |
C4 |
C5 |
N7 |
0.5 |
0.0 |
| C4 |
N9 |
C1' |
O4' |
250.8 |
203.5 |
| C4 |
N9 |
C1' |
H2 |
12.6 |
325.8 |
| C4 |
N9 |
C8 |
H1 |
181.6 |
180.0 |
| C5 |
N7 |
C8 |
H1 |
178.8 |
180.0 |
| C2' |
C1' |
N9 |
O4' |
243.1 |
244.6 |
| C2' |
C1' |
N9 |
H2 |
121.4 |
122.4 |
| C1' |
N9 |
C8 |
H1 |
357.8 |
0.1 |
| N9 |
C1' |
O4' |
C4' |
214.3 |
200.6 |
| O4' |
C1' |
N9 |
H2 |
238.2 |
237.8 |
| N7 |
C8 |
N9 |
H1 |
180.0 |
180.0 |
| C2' |
C1' |
O4' |
H2 |
241.6 |
241.1 |
| N9 |
C1' |
O4' |
H2 |
121.3 |
122.2 |
| C1' |
O4' |
C4' |
H5 |
247.7 |
281.7 |
| N9 |
C8 |
N7 |
H1 |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
H3 |
84.4 |
118.6 |
| C2' |
C3' |
C4' |
H4 |
241.3 |
241.4 |
| O3' |
C3' |
C4' |
H4 |
124.7 |
122.7 |
| C1' |
O4' |
C4' |
C3' |
5.0 |
40.5 |
| O4' |
C4' |
C3' |
H5 |
241.9 |
241.1 |
| C5' |
C4' |
C3' |
H5 |
122.0 |
122.2 |
| C3' |
C4' |
C5' |
H6 |
183.5 |
305.0 |
| C3' |
C4' |
C5' |
H7 |
302.9 |
65.0 |
| C4' |
O4' |
C1' |
H2 |
93.0 |
78.3 |
| O4' |
C4' |
C3' |
H4 |
135.8 |
94.6 |
| C3' |
C4' |
O4' |
H5 |
117.3 |
118.9 |
| C5' |
C4' |
O4' |
H5 |
241.1 |
237.7 |
| O4' |
C4' |
C5' |
H6 |
64.7 |
189.6 |
| O4' |
C4' |
C5' |
H7 |
184.2 |
309.6 |
| C1' |
O4' |
C4' |
C5' |
128.9 |
159.4 |
| C5' |
C4' |
C3' |
H4 |
15.9 |
335.8 |
| C3' |
C4' |
C5' |
H5 |
238.1 |
237.8 |
| O4' |
C4' |
C5' |
H5 |
119.4 |
122.4 |
| O5' |
C5' |
C4' |
H6 |
239.7 |
240.1 |
| O5' |
C5' |
C4' |
H7 |
120.2 |
120.1 |
| H6 |
C5' |
C4' |
H7 |
240.5 |
240.0 |
| O5' |
C5' |
C4' |
H5 |
185.0 |
307.3 |
| C4' |
C5' |
O5' |
H6 |
120.3 |
119.9 |
| C4' |
C5' |
O5' |
H7 |
239.8 |
240.0 |
| H6 |
C5' |
O5' |
H7 |
119.5 |
120.1 |
| P |
O5' |
C5' |
H6 |
26.0 |
60.1 |
| P |
O5' |
C5' |
H7 |
266.5 |
300.0 |
| OP1 |
P |
O5' |
OP2 |
131.6 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
243.7 |
120.0 |
| O5' |
P |
OP2 |
H13 |
124.1 |
60.0 |
| O5' |
P |
OP3 |
H12 |
244.3 |
180.1 |
| O5' |
P |
OP1 |
OP2 |
237.1 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
112.5 |
240.0 |
| OP1 |
P |
OP2 |
H13 |
360.0 |
180.0 |
| OP1 |
P |
OP3 |
H12 |
360.0 |
60.0 |
| O5' |
P |
OP2 |
OP1 |
124.1 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
249.9 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
125.8 |
239.9 |
| C2' |
C1' |
H2 |
O4' |
116.5 |
115.4 |
| N9 |
C1' |
H2 |
O4' |
239.2 |
237.8 |
| H2 |
C1' |
O4' |
C4' |
93.0 |
78.3 |
| H3 |
C2' |
C1' |
O4' |
279.9 |
265.4 |
| H3 |
C2' |
C1' |
H2 |
160.4 |
146.5 |
| H3 |
C2' |
C3' |
C4' |
84.4 |
118.6 |
| H3 |
C2' |
C3' |
H4 |
325.8 |
360.0 |
| C2' |
C3' |
H4 |
C4' |
114.2 |
114.6 |
| H4 |
C3' |
C2' |
H3 |
325.8 |
360.0 |
| H4 |
C3' |
C4' |
C5' |
15.9 |
335.8 |
| H4 |
C3' |
C4' |
H5 |
253.9 |
213.6 |
| C3' |
C4' |
H5 |
C5' |
125.5 |
122.3 |
| H5 |
C4' |
C3' |
H4 |
253.9 |
213.6 |
| H5 |
C4' |
C5' |
H6 |
305.3 |
67.2 |
| H5 |
C4' |
C5' |
H7 |
64.8 |
187.2 |
| H6 |
C5' |
C4' |
H5 |
305.3 |
67.2 |
| C4' |
C5' |
H6 |
H7 |
119.2 |
120.0 |
| O5' |
C5' |
H6 |
H7 |
240.8 |
239.9 |
| H7 |
C5' |
C4' |
H5 |
64.8 |
187.2 |
| C4' |
C5' |
H7 |
H6 |
240.8 |
240.1 |
| O5' |
C5' |
H7 |
H6 |
119.2 |
120.0 |
| H8 |
N2 |
C2 |
N3 |
183.9 |
180.3 |
| H9 |
N2 |
C2 |
N3 |
303.9 |
0.2 |
| H10 |
O2' |
C2' |
H3 |
58.7 |
57.3 |
| H11 |
O3' |
C3' |
H4 |
56.8 |
298.7 |
| H14 |
C61 |
C62 |
C63 |
189.4 |
60.0 |
| C62 |
C61 |
H14 |
H15 |
120.4 |
239.9 |
| H14 |
C61 |
C62 |
H16 |
309.5 |
180.0 |
| H14 |
C61 |
C62 |
H17 |
69.4 |
300.1 |
| H15 |
C61 |
C62 |
C63 |
309.7 |
300.0 |
| C62 |
C61 |
H15 |
H14 |
239.6 |
120.0 |
| H15 |
C61 |
C62 |
H16 |
69.8 |
60.0 |
| H15 |
C61 |
C62 |
H17 |
189.7 |
180.0 |
| C61 |
C62 |
H16 |
C63 |
239.8 |
240.0 |
| H16 |
C62 |
C61 |
H14 |
309.5 |
180.0 |
| H16 |
C62 |
C61 |
H15 |
69.8 |
60.0 |
| C61 |
C62 |
H16 |
H17 |
119.9 |
120.0 |
| C63 |
C62 |
H16 |
H17 |
240.1 |
240.1 |
| H16 |
C62 |
C63 |
H18 |
60.0 |
180.0 |
| H16 |
C62 |
C63 |
H19 |
180.0 |
299.9 |
| H16 |
C62 |
C63 |
H20 |
300.0 |
59.9 |
| C61 |
C62 |
H17 |
C63 |
120.2 |
120.0 |
| H17 |
C62 |
C61 |
H14 |
69.4 |
300.1 |
| H17 |
C62 |
C61 |
H15 |
189.7 |
180.0 |
| C61 |
C62 |
H17 |
H16 |
240.1 |
240.0 |
| C63 |
C62 |
H17 |
H16 |
119.9 |
120.0 |
| H17 |
C62 |
C63 |
H18 |
300.0 |
60.0 |
| H17 |
C62 |
C63 |
H19 |
60.0 |
179.9 |
| H17 |
C62 |
C63 |
H20 |
180.0 |
300.0 |
| H18 |
C63 |
C62 |
H16 |
60.0 |
180.0 |
| H18 |
C63 |
C62 |
H17 |
300.0 |
60.0 |
| C62 |
C63 |
H18 |
H19 |
120.0 |
119.9 |
| C62 |
C63 |
H18 |
H20 |
240.0 |
240.0 |
| H19 |
C63 |
H18 |
H20 |
120.0 |
120.0 |
| H19 |
C63 |
C62 |
H16 |
180.0 |
299.9 |
| H19 |
C63 |
C62 |
H17 |
60.0 |
179.9 |
| C62 |
C63 |
H19 |
H18 |
240.0 |
240.0 |
| C62 |
C63 |
H19 |
H20 |
120.0 |
120.0 |
| H18 |
C63 |
H19 |
H20 |
240.0 |
240.0 |
| H20 |
C63 |
C62 |
H16 |
300.0 |
59.9 |
| H20 |
C63 |
C62 |
H17 |
180.0 |
300.0 |
| C62 |
C63 |
H20 |
H18 |
120.0 |
120.0 |
| C62 |
C63 |
H20 |
H19 |
240.0 |
240.0 |
| H18 |
C63 |
H20 |
H19 |
120.0 |
120.0 |
| O5' |
P |
OP3 |
OP1 |
244.3 |
120.0 |
| O5' |
P |
OP3 |
OP2 |
111.7 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
227.5 |
120.0 |
| OP3 |
P |
OP2 |
H13 |
234.2 |
300.0 |