PDB Chemical Component B8K
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 B8K
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N2 |
C2 |
1.343 |
1.372 |
| C2 |
N3 |
1.340 |
1.315 |
| C2 |
N1 |
1.346 |
1.361 |
| N3 |
C4 |
1.341 |
1.343 |
| N1 |
C6 |
1.336 |
1.349 |
| O3' |
C3' |
1.422 |
1.430 |
| C4 |
N9 |
1.315 |
1.384 |
| C4 |
C5 |
1.464 |
1.387 |
| C1' |
O4' |
1.406 |
1.445 |
| C1' |
N9 |
1.457 |
1.465 |
| C1' |
C2' |
1.509 |
1.544 |
| O4' |
C4' |
1.450 |
1.444 |
| C6 |
C5 |
1.458 |
1.403 |
| C6 |
O6 |
1.233 |
1.221 |
| N9 |
C8 |
1.450 |
1.467 |
| C4' |
C3' |
1.521 |
1.545 |
| C4' |
C5' |
1.505 |
1.530 |
| O2' |
C2' |
1.404 |
1.429 |
| C3' |
C2' |
1.515 |
1.544 |
| C5 |
N7 |
1.330 |
1.409 |
| C5' |
O5' |
1.423 |
1.430 |
| N7 |
C8 |
1.441 |
1.469 |
| N7 |
C71 |
1.382 |
1.347 |
| P |
OP1 |
1.500 |
1.480 |
| P |
O5' |
1.591 |
1.610 |
| P |
OP3 |
1.496 |
1.610 |
| C71 |
C72 |
1.498 |
1.507 |
| C71 |
O71 |
1.215 |
1.213 |
| N2 |
H1 |
1.000 |
0.971 |
| N2 |
H2 |
1.001 |
0.969 |
| C8 |
H3 |
1.100 |
1.090 |
| N1 |
H4 |
1.000 |
0.970 |
| C1' |
H5 |
1.099 |
1.090 |
| C2' |
H6 |
1.100 |
1.091 |
| C3' |
H7 |
1.101 |
1.090 |
| C4' |
H8 |
1.100 |
1.090 |
| C5' |
H9 |
1.100 |
1.090 |
| C5' |
H10 |
1.100 |
1.090 |
| O2' |
H11 |
0.950 |
0.966 |
| O3' |
H12 |
0.950 |
0.967 |
| OP3 |
H14 |
0.950 |
0.967 |
| C72 |
H15 |
1.100 |
1.089 |
| C72 |
H16 |
1.100 |
1.090 |
| C72 |
H17 |
1.100 |
1.091 |
| C8 |
H18 |
1.100 |
1.090 |
| P |
OP2 |
|
1.610 |
| OP2 |
H13 |
|
0.967 |
Bond Angles for B8K
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N2 |
C2 |
N3 |
116.5 |
119.2 |
| N2 |
C2 |
N1 |
119.8 |
119.2 |
| C2 |
N2 |
H1 |
120.0 |
119.9 |
| C2 |
N2 |
H2 |
120.0 |
120.0 |
| N1 |
C2 |
N3 |
123.7 |
121.6 |
| C2 |
N3 |
C4 |
119.0 |
121.3 |
| C2 |
N1 |
C6 |
123.3 |
120.0 |
| C2 |
N1 |
H4 |
118.4 |
119.9 |
| N3 |
C4 |
N9 |
136.4 |
130.6 |
| N1 |
C6 |
C5 |
116.0 |
118.8 |
| N1 |
C6 |
O6 |
121.5 |
120.6 |
| C6 |
N1 |
H4 |
118.4 |
120.0 |
| O3' |
C3' |
H7 |
113.3 |
110.5 |
| C4 |
N9 |
C1' |
127.5 |
126.1 |
| C4 |
C5 |
N7 |
105.3 |
109.8 |
| N9 |
C1' |
O4' |
109.7 |
110.4 |
| C2' |
C1' |
O4' |
105.0 |
104.8 |
| C1' |
O4' |
C4' |
109.2 |
105.3 |
| O4' |
C1' |
H5 |
110.3 |
110.3 |
| C2' |
C1' |
N9 |
113.4 |
110.4 |
| N9 |
C1' |
H5 |
109.5 |
110.3 |
| C2' |
C1' |
H5 |
108.8 |
110.5 |
| C1' |
C2' |
H6 |
109.3 |
110.5 |
| O4' |
C4' |
H8 |
109.1 |
110.5 |
| C5 |
C6 |
O6 |
122.5 |
120.6 |
| C6 |
C5 |
N7 |
136.4 |
131.2 |
| N9 |
C8 |
H3 |
113.0 |
110.2 |
| N9 |
C8 |
H18 |
113.0 |
110.3 |
| C4' |
C3' |
H7 |
111.7 |
110.5 |
| C4' |
C5' |
O5' |
112.1 |
109.4 |
| C5' |
C4' |
H8 |
108.4 |
110.3 |
| C4' |
C5' |
H9 |
108.8 |
109.5 |
| C4' |
C5' |
H10 |
108.8 |
109.5 |
| O2' |
C2' |
H6 |
110.8 |
110.4 |
| C3' |
C2' |
H6 |
109.3 |
110.5 |
| C5 |
N7 |
C71 |
126.3 |
126.7 |
| O5' |
C5' |
H9 |
108.8 |
109.4 |
| O5' |
C5' |
H10 |
108.8 |
109.4 |
| N7 |
C8 |
H3 |
113.0 |
110.2 |
| N7 |
C8 |
H18 |
113.0 |
110.2 |
| N7 |
C71 |
C72 |
122.7 |
120.0 |
| N7 |
C71 |
O71 |
119.2 |
120.0 |
| P |
OP3 |
H14 |
109.5 |
114.0 |
| C72 |
C71 |
O71 |
118.1 |
120.0 |
| C71 |
C72 |
H15 |
109.5 |
109.5 |
| C71 |
C72 |
H16 |
109.5 |
109.5 |
| C71 |
C72 |
H17 |
109.5 |
109.5 |
| H1 |
N2 |
H2 |
120.0 |
120.0 |
| H3 |
C8 |
H18 |
109.5 |
110.1 |
| H9 |
C5' |
H10 |
109.5 |
109.5 |
| H15 |
C72 |
H16 |
109.5 |
109.5 |
| H15 |
C72 |
H17 |
109.5 |
109.4 |
| H16 |
C72 |
H17 |
109.5 |
109.4 |
| P |
OP2 |
H13 |
|
114.0 |
Torsion Angles for B8K
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N1 |
C2 |
N2 |
N3 |
178.9 |
180.3 |
| N2 |
C2 |
N3 |
C4 |
179.8 |
179.8 |
| N2 |
C2 |
N1 |
C6 |
180.5 |
180.0 |
| N2 |
C2 |
N1 |
H4 |
0.5 |
0.0 |
| H1 |
N2 |
C2 |
H2 |
180.0 |
180.2 |
| N2 |
C2 |
N3 |
N1 |
178.8 |
180.3 |
| N3 |
C2 |
N2 |
H1 |
360.0 |
359.9 |
| N3 |
C2 |
N2 |
H2 |
180.0 |
179.7 |
| N3 |
C2 |
N1 |
C6 |
359.3 |
0.3 |
| N3 |
C2 |
N1 |
H4 |
179.3 |
180.3 |
| C2 |
N3 |
C4 |
N9 |
180.0 |
180.3 |
| N2 |
C2 |
N1 |
N3 |
181.2 |
179.7 |
| N1 |
C2 |
N2 |
H1 |
178.9 |
180.2 |
| N1 |
C2 |
N2 |
H2 |
358.8 |
360.0 |
| N1 |
C2 |
N3 |
C4 |
1.0 |
359.5 |
| C2 |
N1 |
C6 |
C5 |
0.2 |
0.0 |
| C2 |
N1 |
C6 |
O6 |
180.4 |
180.0 |
| C6 |
N1 |
C2 |
H4 |
180.0 |
180.0 |
| N3 |
C4 |
N9 |
C1' |
0.9 |
0.2 |
| N3 |
C4 |
C5 |
N7 |
180.4 |
179.8 |
| C6 |
N1 |
C2 |
N3 |
359.3 |
0.3 |
| C2 |
N1 |
C6 |
H4 |
180.0 |
180.0 |
| C5 |
C6 |
N1 |
O6 |
179.8 |
180.0 |
| N1 |
C6 |
C5 |
N7 |
180.0 |
180.0 |
| C4' |
C3' |
O3' |
H7 |
235.2 |
237.3 |
| O3' |
C3' |
C2' |
H6 |
192.2 |
237.5 |
| N9 |
C4 |
C5 |
N7 |
359.8 |
360.0 |
| C4 |
N9 |
C1' |
O4' |
236.7 |
53.6 |
| C2' |
C1' |
N9 |
C4 |
119.7 |
298.2 |
| C4 |
N9 |
C1' |
H5 |
357.9 |
175.8 |
| C4 |
N9 |
C8 |
H3 |
118.2 |
240.9 |
| C4 |
N9 |
C8 |
H18 |
243.2 |
119.1 |
| C2 |
N3 |
C4 |
C5 |
359.2 |
0.5 |
| C4 |
C5 |
C6 |
O6 |
179.7 |
180.0 |
| C6 |
C5 |
C4 |
N7 |
180.1 |
180.0 |
| C4 |
C5 |
N7 |
C71 |
180.0 |
180.0 |
| C2' |
C1' |
O4' |
N9 |
122.2 |
118.9 |
| N9 |
C1' |
O4' |
H5 |
120.7 |
122.2 |
| C2' |
C1' |
O4' |
H5 |
242.9 |
241.1 |
| O4' |
C1' |
C2' |
H6 |
284.7 |
265.3 |
| C1' |
O4' |
C4' |
H8 |
245.2 |
281.6 |
| C2' |
C1' |
N9 |
O4' |
242.9 |
244.6 |
| N9 |
C1' |
O4' |
C4' |
211.8 |
200.6 |
| O4' |
C1' |
N9 |
H5 |
238.8 |
237.8 |
| C2' |
C1' |
N9 |
H5 |
121.8 |
122.4 |
| N9 |
C1' |
C2' |
H6 |
44.5 |
24.1 |
| C1' |
N9 |
C8 |
H3 |
296.5 |
61.0 |
| C1' |
N9 |
C8 |
H18 |
61.5 |
299.2 |
| C4 |
N9 |
C1' |
C2' |
119.7 |
298.2 |
| N9 |
C1' |
C2' |
O4' |
119.8 |
118.9 |
| C2' |
C1' |
O4' |
C4' |
334.0 |
319.5 |
| O4' |
C1' |
C2' |
H5 |
118.1 |
118.8 |
| N9 |
C1' |
C2' |
H5 |
237.8 |
237.7 |
| O2' |
C2' |
C1' |
H6 |
237.1 |
237.5 |
| C3' |
C2' |
C1' |
H6 |
115.0 |
118.7 |
| C4' |
O4' |
C1' |
H5 |
91.1 |
78.4 |
| O4' |
C4' |
C3' |
H7 |
143.1 |
94.6 |
| O4' |
C4' |
C5' |
O5' |
345.6 |
69.6 |
| C5' |
C4' |
O4' |
H8 |
241.7 |
237.7 |
| O4' |
C4' |
C5' |
H9 |
106.0 |
189.6 |
| O4' |
C4' |
C5' |
H10 |
225.2 |
309.7 |
| N1 |
C6 |
C5 |
O6 |
180.2 |
180.0 |
| C5 |
C6 |
N1 |
H4 |
180.2 |
180.0 |
| C4 |
C5 |
C6 |
N7 |
179.9 |
180.0 |
| C6 |
C5 |
N7 |
C71 |
359.9 |
360.0 |
| N1 |
C6 |
O6 |
C5 |
179.8 |
180.0 |
| O6 |
C6 |
N1 |
H4 |
0.4 |
359.9 |
| O6 |
C6 |
C5 |
N7 |
359.8 |
0.1 |
| N7 |
C8 |
N9 |
H3 |
242.5 |
119.1 |
| N7 |
C8 |
N9 |
H18 |
117.5 |
240.9 |
| H3 |
C8 |
N9 |
H18 |
235.0 |
121.8 |
| O3' |
C3' |
C4' |
H7 |
125.7 |
122.7 |
| C1' |
O4' |
C4' |
C3' |
1.4 |
40.5 |
| C4' |
C3' |
C2' |
H6 |
77.5 |
118.6 |
| C1' |
O4' |
C4' |
C5' |
126.9 |
159.3 |
| O4' |
C4' |
C5' |
H8 |
118.8 |
122.4 |
| C5' |
C4' |
C3' |
H7 |
21.8 |
335.8 |
| O5' |
C5' |
C4' |
H9 |
239.6 |
240.1 |
| O5' |
C5' |
C4' |
H10 |
120.4 |
119.9 |
| H9 |
C5' |
C4' |
H10 |
240.8 |
239.9 |
| O2' |
C2' |
C1' |
O4' |
161.8 |
142.8 |
| O2' |
C2' |
C1' |
H5 |
43.8 |
23.9 |
| C1' |
C2' |
O2' |
H6 |
122.0 |
122.5 |
| C3' |
C2' |
O2' |
H6 |
235.8 |
237.3 |
| C3' |
C2' |
C1' |
O4' |
39.8 |
24.0 |
| C3' |
C2' |
C1' |
N9 |
159.5 |
142.8 |
| C3' |
C2' |
C1' |
H5 |
281.7 |
265.1 |
| C1' |
C2' |
C3' |
H6 |
244.9 |
241.3 |
| O2' |
C2' |
C3' |
H6 |
125.0 |
122.6 |
| N7 |
C5 |
C6 |
O6 |
359.8 |
0.1 |
| C5 |
N7 |
C8 |
H3 |
241.6 |
119.0 |
| C5 |
N7 |
C8 |
H18 |
116.7 |
240.8 |
| C5 |
N7 |
C71 |
C72 |
66.1 |
174.9 |
| C5 |
N7 |
C71 |
O71 |
243.5 |
354.9 |
| O5' |
C5' |
C4' |
H8 |
226.8 |
307.2 |
| C4' |
C5' |
O5' |
H9 |
120.4 |
120.0 |
| C4' |
C5' |
O5' |
H10 |
239.6 |
240.0 |
| H9 |
C5' |
O5' |
H10 |
119.2 |
120.0 |
| N9 |
C8 |
N7 |
H3 |
117.5 |
241.0 |
| N9 |
C8 |
N7 |
H18 |
242.5 |
119.2 |
| H3 |
C8 |
N7 |
H18 |
125.0 |
238.2 |
| C71 |
N7 |
C8 |
H3 |
62.3 |
299.1 |
| C71 |
N7 |
C8 |
H18 |
297.4 |
60.8 |
| C72 |
C71 |
N7 |
O71 |
182.6 |
180.0 |
| N7 |
C71 |
C72 |
H15 |
177.4 |
5.0 |
| N7 |
C71 |
C72 |
H16 |
297.5 |
125.1 |
| N7 |
C71 |
C72 |
H17 |
57.4 |
245.0 |
| P |
O5' |
C5' |
H9 |
344.6 |
60.0 |
| P |
O5' |
C5' |
H10 |
225.4 |
300.0 |
| N7 |
C71 |
C72 |
O71 |
177.4 |
180.0 |
| H15 |
C72 |
C71 |
H16 |
240.0 |
239.9 |
| H15 |
C72 |
C71 |
H17 |
120.0 |
120.0 |
| H16 |
C72 |
C71 |
H17 |
240.0 |
240.1 |
| N7 |
C71 |
O71 |
C72 |
182.5 |
180.0 |
| O71 |
C71 |
C72 |
H15 |
0.0 |
185.0 |
| O71 |
C71 |
C72 |
H16 |
120.0 |
305.0 |
| O71 |
C71 |
C72 |
H17 |
240.0 |
65.0 |
| H1 |
N2 |
C2 |
N3 |
360.0 |
359.9 |
| H1 |
N2 |
C2 |
N1 |
178.9 |
180.2 |
| C2 |
N2 |
H1 |
H2 |
180.0 |
179.8 |
| H2 |
N2 |
C2 |
N3 |
180.0 |
179.7 |
| H2 |
N2 |
C2 |
N1 |
358.8 |
360.0 |
| C2 |
N2 |
H2 |
H1 |
180.0 |
180.2 |
| N9 |
C8 |
H3 |
H18 |
126.8 |
238.1 |
| N7 |
C8 |
H3 |
H18 |
233.2 |
121.9 |
| H4 |
N1 |
C2 |
N3 |
179.3 |
180.3 |
| C2 |
N1 |
H4 |
C6 |
180.0 |
180.0 |
| H4 |
N1 |
C6 |
C5 |
180.2 |
180.0 |
| H4 |
N1 |
C6 |
O6 |
0.4 |
359.9 |
| N9 |
C1' |
H5 |
O4' |
239.2 |
237.8 |
| C2' |
C1' |
H5 |
O4' |
114.7 |
115.4 |
| H5 |
C1' |
O4' |
C4' |
91.1 |
78.4 |
| C2' |
C1' |
H5 |
N9 |
235.5 |
237.6 |
| H5 |
C1' |
C2' |
H6 |
166.6 |
146.4 |
| H6 |
C2' |
C1' |
O4' |
284.7 |
265.3 |
| H6 |
C2' |
C1' |
N9 |
44.5 |
24.1 |
| H6 |
C2' |
C1' |
H5 |
166.6 |
146.4 |
| H7 |
C3' |
C2' |
H6 |
317.9 |
0.0 |
| H8 |
C4' |
C3' |
H7 |
259.9 |
213.6 |
| H8 |
C4' |
C5' |
O5' |
226.8 |
307.2 |
| H8 |
C4' |
C5' |
H9 |
347.2 |
67.2 |
| H8 |
C4' |
C5' |
H10 |
106.4 |
187.3 |
| C4' |
C5' |
H9 |
O5' |
237.6 |
240.0 |
| H9 |
C5' |
C4' |
H8 |
347.2 |
67.2 |
| C4' |
C5' |
H9 |
H10 |
118.8 |
120.1 |
| O5' |
C5' |
H9 |
H10 |
241.2 |
240.0 |
| C4' |
C5' |
H10 |
O5' |
122.4 |
119.9 |
| H10 |
C5' |
C4' |
H8 |
106.4 |
187.3 |
| C4' |
C5' |
H10 |
H9 |
241.2 |
239.9 |
| O5' |
C5' |
H10 |
H9 |
118.8 |
120.0 |
| H11 |
O2' |
C2' |
H6 |
58.0 |
57.4 |
| H12 |
O3' |
C3' |
H7 |
304.8 |
298.8 |
| H15 |
C72 |
C71 |
O71 |
0.0 |
185.0 |
| C71 |
C72 |
H15 |
H16 |
120.0 |
120.0 |
| C71 |
C72 |
H15 |
H17 |
240.0 |
240.0 |
| H16 |
C72 |
H15 |
H17 |
120.0 |
119.9 |
| H16 |
C72 |
C71 |
O71 |
120.0 |
305.0 |
| C71 |
C72 |
H16 |
H15 |
239.9 |
239.9 |
| C71 |
C72 |
H16 |
H17 |
120.0 |
120.0 |
| H15 |
C72 |
H16 |
H17 |
240.0 |
240.0 |
| H17 |
C72 |
C71 |
O71 |
240.0 |
65.0 |
| C71 |
C72 |
H17 |
H15 |
120.0 |
120.0 |
| C71 |
C72 |
H17 |
H16 |
240.0 |
240.0 |
| H15 |
C72 |
H17 |
H16 |
120.0 |
120.0 |
| N9 |
C8 |
H18 |
H3 |
233.2 |
121.9 |
| N7 |
C8 |
H18 |
H3 |
126.8 |
238.1 |
| OP2 |
P |
OP3 |
H14 |
|
299.9 |