PDB Chemical Component B8W
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 B8W
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2' |
C2' |
1.418 |
1.429 |
| C4' |
O4' |
1.446 |
1.438 |
| C4' |
C5' |
1.508 |
1.530 |
| C4' |
C3' |
1.521 |
1.540 |
| O4' |
C1' |
1.406 |
1.444 |
| C5' |
O5' |
1.419 |
1.429 |
| O3' |
C3' |
1.417 |
1.429 |
| C1' |
C2' |
1.519 |
1.550 |
| C1' |
N9 |
1.471 |
1.465 |
| C2' |
C3' |
1.524 |
1.548 |
| OP2 |
P |
1.506 |
1.610 |
| O5' |
P |
1.593 |
1.610 |
| N9 |
C4 |
1.322 |
1.372 |
| N9 |
C8 |
1.336 |
1.364 |
| P |
OP1 |
1.504 |
1.480 |
| N3 |
C4 |
1.344 |
1.329 |
| N3 |
C2 |
1.348 |
1.322 |
| C4 |
C5 |
1.462 |
1.406 |
| N2 |
C2 |
1.341 |
1.386 |
| C8 |
N7 |
1.350 |
1.301 |
| C2 |
N1 |
1.345 |
1.327 |
| C5 |
N7 |
1.335 |
1.356 |
| C5 |
C6 |
1.473 |
1.404 |
| N1 |
C6 |
1.340 |
1.327 |
| C6 |
O6 |
1.364 |
1.354 |
| O6 |
C61 |
1.422 |
1.429 |
| N2 |
H1 |
1.000 |
0.970 |
| N2 |
H2 |
1.000 |
0.970 |
| C8 |
H3 |
1.080 |
1.080 |
| C1' |
H4 |
1.100 |
1.090 |
| C2' |
H5 |
1.100 |
1.090 |
| C3' |
H6 |
1.100 |
1.090 |
| C4' |
H7 |
1.100 |
1.090 |
| C5' |
H8 |
1.100 |
1.090 |
| C5' |
H9 |
1.100 |
1.089 |
| C61 |
H10 |
1.100 |
1.089 |
| C61 |
H11 |
1.100 |
1.090 |
| C61 |
H12 |
1.100 |
1.090 |
| O2' |
H13 |
0.950 |
0.967 |
| O3' |
H14 |
0.950 |
0.968 |
| OP2 |
H16 |
0.950 |
0.967 |
| P |
OP3 |
1.603 |
1.610 |
| OP3 |
H15 |
0.950 |
0.967 |
Bond Angles for B8W
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2' |
C2' |
H5 |
113.1 |
110.8 |
| C5' |
C4' |
O4' |
109.1 |
109.9 |
| O4' |
C4' |
H7 |
109.5 |
109.8 |
| C4' |
C5' |
O5' |
111.5 |
109.4 |
| C5' |
C4' |
H7 |
108.7 |
109.9 |
| C4' |
C5' |
H8 |
109.0 |
109.5 |
| C4' |
C5' |
H9 |
109.0 |
109.5 |
| C4' |
C3' |
H6 |
108.8 |
110.5 |
| O4' |
C1' |
H4 |
109.7 |
110.8 |
| C5' |
O5' |
P |
121.1 |
123.0 |
| O5' |
C5' |
H8 |
109.0 |
109.4 |
| O5' |
C5' |
H9 |
109.0 |
109.5 |
| O3' |
C3' |
H6 |
110.2 |
110.4 |
| C2' |
C1' |
N9 |
113.8 |
110.6 |
| C1' |
C2' |
C3' |
102.0 |
102.1 |
| C2' |
C1' |
H4 |
108.2 |
110.6 |
| C1' |
C2' |
H5 |
111.5 |
111.0 |
| N9 |
C1' |
H4 |
108.8 |
110.6 |
| C3' |
C2' |
H5 |
111.4 |
110.9 |
| C2' |
C3' |
H6 |
108.7 |
110.5 |
| O5' |
P |
OP2 |
106.7 |
109.5 |
| P |
OP2 |
H16 |
109.5 |
114.0 |
| OP2 |
P |
OP3 |
109.0 |
109.4 |
| O5' |
P |
OP1 |
110.5 |
109.5 |
| O5' |
P |
OP3 |
104.2 |
109.5 |
| N9 |
C8 |
H3 |
124.2 |
125.0 |
| N3 |
C2 |
N1 |
123.4 |
122.3 |
| C4 |
C5 |
N7 |
106.7 |
107.1 |
| C4 |
C5 |
C6 |
117.5 |
118.3 |
| N2 |
C2 |
N1 |
118.9 |
118.9 |
| C5 |
N7 |
C8 |
107.0 |
109.4 |
| N7 |
C8 |
H3 |
124.2 |
125.0 |
| C2 |
N1 |
C6 |
121.6 |
121.2 |
| C6 |
C5 |
N7 |
135.8 |
134.6 |
| C5 |
C6 |
O6 |
121.8 |
120.7 |
| C6 |
O6 |
C61 |
118.6 |
117.0 |
| O6 |
C61 |
H10 |
109.5 |
109.5 |
| O6 |
C61 |
H11 |
109.5 |
109.5 |
| O6 |
C61 |
H12 |
109.5 |
109.5 |
| H1 |
N2 |
H2 |
109.4 |
120.0 |
| H8 |
C5' |
H9 |
109.5 |
109.5 |
| H10 |
C61 |
H11 |
109.5 |
109.5 |
| H10 |
C61 |
H12 |
109.5 |
109.5 |
| H11 |
C61 |
H12 |
109.5 |
109.5 |
| P |
OP3 |
H15 |
109.5 |
114.0 |
Torsion Angles for B8W
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2' |
C2' |
C1' |
H4 |
333.8 |
36.6 |
| C1' |
C2' |
O2' |
H5 |
123.6 |
123.7 |
| C3' |
C2' |
O2' |
H5 |
234.3 |
236.4 |
| O2' |
C2' |
C3' |
H6 |
162.6 |
102.2 |
| O4' |
C4' |
C5' |
O5' |
307.7 |
66.5 |
| C5' |
C4' |
O4' |
H7 |
241.2 |
239.0 |
| O4' |
C4' |
C5' |
H8 |
68.0 |
186.4 |
| O4' |
C4' |
C5' |
H9 |
187.4 |
306.5 |
| O4' |
C4' |
C3' |
H6 |
85.3 |
116.7 |
| C4' |
O4' |
C1' |
H4 |
123.1 |
78.5 |
| O4' |
C4' |
C5' |
H7 |
119.3 |
120.9 |
| C5' |
C4' |
C3' |
H6 |
324.9 |
357.3 |
| C4' |
C5' |
O5' |
P |
153.5 |
180.0 |
| O5' |
C5' |
C4' |
H8 |
239.7 |
240.1 |
| O5' |
C5' |
C4' |
H9 |
120.3 |
120.0 |
| H8 |
C5' |
C4' |
H9 |
240.6 |
239.9 |
| O3' |
C3' |
C4' |
H6 |
122.2 |
122.5 |
| C4' |
C3' |
C2' |
H5 |
151.4 |
97.4 |
| C2' |
C3' |
C4' |
H6 |
244.5 |
241.3 |
| C2' |
C1' |
O4' |
H4 |
242.3 |
241.5 |
| O4' |
C1' |
C2' |
H5 |
217.1 |
278.8 |
| N9 |
C1' |
O4' |
H4 |
118.5 |
123.0 |
| O5' |
C5' |
C4' |
O4' |
307.7 |
66.5 |
| O5' |
C5' |
C4' |
H7 |
188.4 |
305.5 |
| C4' |
C5' |
O5' |
H8 |
120.3 |
119.9 |
| C4' |
C5' |
O5' |
H9 |
239.7 |
240.0 |
| C5' |
O5' |
P |
OP2 |
48.6 |
65.0 |
| C5' |
O5' |
P |
OP1 |
179.6 |
305.0 |
| C5' |
O5' |
P |
OP3 |
293.4 |
185.0 |
| H8 |
C5' |
O5' |
H9 |
119.4 |
120.0 |
| C4' |
C3' |
O3' |
H6 |
238.6 |
237.4 |
| O3' |
C3' |
C2' |
H5 |
273.1 |
216.2 |
| C2' |
C3' |
O3' |
H6 |
121.9 |
122.6 |
| O2' |
C2' |
C1' |
H5 |
235.4 |
236.4 |
| O4' |
C1' |
C2' |
H4 |
118.7 |
118.7 |
| N9 |
C1' |
C2' |
H4 |
239.0 |
237.2 |
| C3' |
C2' |
C1' |
H5 |
119.0 |
118.2 |
| C1' |
C2' |
C3' |
H6 |
276.9 |
220.4 |
| O4' |
C1' |
N9 |
H4 |
240.9 |
236.9 |
| N9 |
C1' |
C2' |
C3' |
96.3 |
155.5 |
| C2' |
C1' |
N9 |
H4 |
120.7 |
122.9 |
| N9 |
C1' |
C2' |
H5 |
337.4 |
37.3 |
| C1' |
N9 |
C8 |
H3 |
1.7 |
0.0 |
| O2' |
C2' |
C3' |
H5 |
126.7 |
123.5 |
| C4' |
C3' |
C2' |
H6 |
115.5 |
118.7 |
| O3' |
C3' |
C2' |
H6 |
237.2 |
237.5 |
| C3' |
C2' |
C1' |
N9 |
96.3 |
155.5 |
| C3' |
C2' |
C1' |
H4 |
217.4 |
278.4 |
| C1' |
C2' |
C3' |
H5 |
241.0 |
241.8 |
| O5' |
P |
OP2 |
OP1 |
126.0 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
248.0 |
120.0 |
| OP2 |
P |
OP3 |
H15 |
129.6 |
299.9 |
| P |
O5' |
C5' |
H8 |
33.2 |
60.0 |
| P |
O5' |
C5' |
H9 |
273.8 |
300.0 |
| O5' |
P |
OP2 |
H16 |
126.0 |
60.0 |
| OP2 |
P |
O5' |
OP3 |
115.2 |
240.0 |
| O5' |
P |
OP3 |
H15 |
243.2 |
180.0 |
| N7 |
C8 |
N9 |
H3 |
180.0 |
180.0 |
| O5' |
P |
OP1 |
OP2 |
235.9 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
112.5 |
240.0 |
| C4 |
N3 |
C2 |
N1 |
359.9 |
360.0 |
| N3 |
C4 |
C5 |
N7 |
179.9 |
180.0 |
| N2 |
C2 |
N3 |
N1 |
180.5 |
180.3 |
| N3 |
C2 |
N1 |
C6 |
360.0 |
0.0 |
| C4 |
C5 |
N7 |
C8 |
0.0 |
360.0 |
| C6 |
C5 |
C4 |
N7 |
180.2 |
179.9 |
| C4 |
C5 |
C6 |
O6 |
179.8 |
180.1 |
| N3 |
C2 |
N2 |
N1 |
179.5 |
179.7 |
| N2 |
C2 |
N1 |
C6 |
179.5 |
179.7 |
| N9 |
C8 |
N7 |
H3 |
180.0 |
180.0 |
| C6 |
C5 |
N7 |
C8 |
179.8 |
180.0 |
| C4 |
C5 |
N7 |
C6 |
180.2 |
179.9 |
| C5 |
N7 |
C8 |
H3 |
180.7 |
180.0 |
| N7 |
C5 |
C6 |
O6 |
0.1 |
0.0 |
| C4 |
C5 |
C6 |
N7 |
179.8 |
180.1 |
| C2 |
N1 |
C6 |
C5 |
0.2 |
360.0 |
| C5 |
C6 |
O6 |
C61 |
214.8 |
180.0 |
| N1 |
C6 |
C5 |
N7 |
180.0 |
180.0 |
| N1 |
C6 |
O6 |
C61 |
34.9 |
0.0 |
| C2 |
N1 |
C6 |
O6 |
180.1 |
179.9 |
| O6 |
C6 |
C5 |
N7 |
0.1 |
0.0 |
| C6 |
O6 |
C61 |
H10 |
180.0 |
300.0 |
| C6 |
O6 |
C61 |
H11 |
300.0 |
60.0 |
| C6 |
O6 |
C61 |
H12 |
60.0 |
180.0 |
| H10 |
C61 |
O6 |
H11 |
240.0 |
240.0 |
| H10 |
C61 |
O6 |
H12 |
120.0 |
120.0 |
| H11 |
C61 |
O6 |
H12 |
240.0 |
240.0 |
| H1 |
N2 |
C2 |
N1 |
180.5 |
0.0 |
| H2 |
N2 |
C2 |
N1 |
300.5 |
180.0 |
| C2' |
C1' |
H4 |
N9 |
235.9 |
237.1 |
| H4 |
C1' |
C2' |
C3' |
217.4 |
278.4 |
| H4 |
C1' |
C2' |
H5 |
98.4 |
160.2 |
| H5 |
C2' |
C1' |
N9 |
337.4 |
37.3 |
| C1' |
C2' |
H5 |
C3' |
113.2 |
112.7 |
| H5 |
C2' |
C1' |
H4 |
98.4 |
160.2 |
| H5 |
C2' |
C3' |
H6 |
35.9 |
338.7 |
| H6 |
C3' |
C2' |
H5 |
35.9 |
338.7 |
| C5' |
C4' |
H7 |
O4' |
119.1 |
121.0 |
| H7 |
C4' |
C5' |
O5' |
188.4 |
305.5 |
| H7 |
C4' |
C5' |
H8 |
308.7 |
65.5 |
| H7 |
C4' |
C5' |
H9 |
68.1 |
185.5 |
| H7 |
C4' |
C3' |
H6 |
202.2 |
236.1 |
| H8 |
C5' |
C4' |
O4' |
68.0 |
186.4 |
| C4' |
C5' |
H8 |
O5' |
238.1 |
240.1 |
| H8 |
C5' |
C4' |
H7 |
308.7 |
65.5 |
| C4' |
C5' |
H8 |
H9 |
119.1 |
120.1 |
| H8 |
C5' |
O5' |
P |
33.2 |
60.0 |
| O5' |
C5' |
H8 |
H9 |
240.9 |
240.0 |
| H9 |
C5' |
C4' |
O4' |
187.4 |
306.5 |
| C4' |
C5' |
H9 |
O5' |
121.9 |
120.0 |
| H9 |
C5' |
C4' |
H7 |
68.1 |
185.5 |
| C4' |
C5' |
H9 |
H8 |
240.9 |
240.0 |
| H9 |
C5' |
O5' |
P |
273.8 |
300.0 |
| O5' |
C5' |
H9 |
H8 |
119.1 |
120.0 |
| O6 |
C61 |
H10 |
H11 |
120.0 |
120.0 |
| O6 |
C61 |
H10 |
H12 |
240.0 |
240.0 |
| H11 |
C61 |
H10 |
H12 |
120.0 |
120.0 |
| O6 |
C61 |
H11 |
H10 |
240.0 |
240.0 |
| O6 |
C61 |
H11 |
H12 |
120.0 |
120.0 |
| H10 |
C61 |
H11 |
H12 |
240.0 |
240.0 |
| O6 |
C61 |
H12 |
H10 |
120.0 |
120.0 |
| O6 |
C61 |
H12 |
H11 |
240.0 |
240.0 |
| H10 |
C61 |
H12 |
H11 |
120.0 |
120.0 |
| H13 |
O2' |
C2' |
H5 |
56.4 |
56.3 |
| H14 |
O3' |
C3' |
H6 |
301.4 |
298.9 |
| H16 |
OP2 |
P |
OP3 |
238.0 |
300.0 |
| O5' |
P |
OP3 |
OP2 |
113.6 |
240.0 |
| OP3 |
P |
OP2 |
H16 |
238.0 |
300.0 |
| O5' |
P |
OP3 |
OP1 |
243.2 |
120.0 |