PDB Chemical Component GRB
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 GRB
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.491 |
1.480 |
| OP1 |
P |
1.476 |
1.611 |
| P |
OP3 |
1.586 |
1.610 |
| P |
O5' |
1.594 |
1.609 |
| C8 |
BR |
1.893 |
1.891 |
| C2 |
N1 |
1.382 |
1.363 |
| N1 |
C6 |
1.393 |
1.351 |
| N1 |
HN1 |
1.000 |
0.970 |
| N2 |
C2 |
1.353 |
1.373 |
| C2 |
N3 |
1.329 |
1.315 |
| N2 |
HN2 |
0.999 |
0.970 |
| N2 |
HN2A |
1.000 |
0.970 |
| N3 |
C4 |
1.357 |
1.337 |
| C4 |
C5 |
1.378 |
1.399 |
| C4 |
N9 |
1.377 |
1.369 |
| C6 |
C5 |
1.408 |
1.415 |
| C5 |
N7 |
1.378 |
1.355 |
| C6 |
O6 |
1.240 |
1.220 |
| N7 |
C8 |
1.299 |
1.302 |
| N9 |
C8 |
1.374 |
1.365 |
| C1' |
N9 |
1.466 |
1.465 |
| O4' |
C1' |
1.412 |
1.444 |
| C1' |
C2' |
1.513 |
1.550 |
| C1' |
H1' |
1.100 |
1.090 |
| C3' |
C2' |
1.516 |
1.549 |
| C2' |
O2' |
1.422 |
1.429 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.951 |
0.967 |
| C4' |
C3' |
1.513 |
1.540 |
| O3' |
C3' |
1.405 |
1.429 |
| C3' |
H3' |
1.099 |
1.089 |
| O3' |
HO3' |
0.950 |
0.967 |
| C5' |
C4' |
1.513 |
1.530 |
| C4' |
O4' |
1.441 |
1.438 |
| C4' |
H4' |
1.100 |
1.090 |
| O5' |
C5' |
1.414 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| OP1 |
HOP1 |
0.950 |
0.966 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for GRB
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP3 |
107.1 |
109.5 |
| OP1 |
P |
OP3 |
108.9 |
109.4 |
| O5' |
P |
OP3 |
99.6 |
109.5 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| P |
O5' |
C5' |
121.1 |
123.1 |
| C2 |
N1 |
C6 |
124.5 |
120.3 |
| C2 |
N1 |
HN1 |
117.8 |
119.8 |
| C6 |
N1 |
HN1 |
117.8 |
119.8 |
| N1 |
C6 |
C5 |
111.6 |
118.4 |
| N1 |
C6 |
O6 |
121.5 |
120.8 |
| N2 |
C2 |
N3 |
119.4 |
119.1 |
| C2 |
N3 |
C4 |
112.0 |
121.1 |
| HN2 |
N2 |
HN2A |
120.0 |
120.1 |
| N3 |
C4 |
C5 |
127.6 |
119.7 |
| N3 |
C4 |
N9 |
127.5 |
134.2 |
| C5 |
C4 |
N9 |
104.9 |
106.1 |
| C4 |
C5 |
N7 |
111.5 |
107.3 |
| C4 |
N9 |
C8 |
105.9 |
107.5 |
| C6 |
C5 |
N7 |
128.3 |
134.2 |
| C5 |
N7 |
C8 |
103.9 |
109.4 |
| O4' |
C1' |
H1' |
112.3 |
110.7 |
| C2' |
C1' |
H1' |
107.3 |
110.7 |
| C1' |
C2' |
O2' |
109.3 |
110.9 |
| C1' |
C2' |
H2' |
118.0 |
110.9 |
| C3' |
C2' |
H2' |
112.4 |
110.9 |
| O2' |
C2' |
H2' |
103.1 |
110.8 |
| C2' |
O2' |
HO2' |
109.5 |
114.0 |
| C4' |
C3' |
H3' |
115.0 |
110.5 |
| O3' |
C3' |
H3' |
106.0 |
110.4 |
| C5' |
C4' |
H4' |
104.6 |
110.0 |
| O4' |
C4' |
H4' |
114.2 |
109.8 |
| O5' |
C5' |
H5' |
109.6 |
109.4 |
| O5' |
C5' |
H5'A |
109.6 |
109.4 |
| H5' |
C5' |
H5'A |
109.3 |
109.5 |
Torsion Angles for GRB
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
OP3 |
123.8 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
253.8 |
120.1 |
| OP2 |
P |
OP3 |
HOP3 |
360.0 |
300.1 |
| OP2 |
P |
OP1 |
OP3 |
237.1 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
109.8 |
240.0 |
| OP1 |
P |
OP3 |
HOP3 |
230.3 |
60.1 |
| OP3 |
P |
O5' |
C5' |
157.6 |
175.0 |
| OP2 |
P |
O5' |
OP3 |
111.4 |
239.9 |
| OP1 |
P |
O5' |
OP3 |
244.5 |
120.0 |
| O5' |
P |
OP3 |
HOP3 |
111.6 |
180.0 |
| P |
O5' |
C5' |
H5' |
72.2 |
60.0 |
| P |
O5' |
C5' |
H5'A |
312.2 |
300.0 |
| C6 |
N1 |
C2 |
HN1 |
180.0 |
180.3 |
| C2 |
N1 |
C6 |
C5 |
0.7 |
359.9 |
| C2 |
N1 |
C6 |
O6 |
178.4 |
179.8 |
| C2 |
N1 |
C6 |
HN1 |
180.0 |
179.7 |
| N1 |
C6 |
C5 |
N7 |
179.8 |
180.0 |
| C2 |
N1 |
HN1 |
C6 |
180.0 |
180.3 |
| HN1 |
N1 |
C6 |
C5 |
180.7 |
180.3 |
| HN1 |
N1 |
C6 |
O6 |
358.5 |
0.1 |
| N2 |
C2 |
N1 |
C6 |
179.5 |
180.0 |
| N2 |
C2 |
N1 |
HN1 |
359.4 |
359.7 |
| N2 |
C2 |
N3 |
C4 |
179.8 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
0.6 |
0.0 |
| N3 |
C2 |
N1 |
HN1 |
180.6 |
179.7 |
| C2 |
N3 |
C4 |
C5 |
0.9 |
0.0 |
| C2 |
N3 |
C4 |
N9 |
180.2 |
180.0 |
| HN2 |
N2 |
C2 |
N3 |
360.0 |
180.0 |
| HN2A |
N2 |
C2 |
N3 |
180.0 |
360.0 |
| C5 |
C4 |
N3 |
N9 |
180.7 |
180.0 |
| N3 |
C4 |
C5 |
N7 |
179.6 |
180.0 |
| N3 |
C4 |
N9 |
C8 |
180.2 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
358.9 |
0.1 |
| N3 |
C4 |
C5 |
N9 |
179.4 |
180.0 |
| C5 |
C4 |
N9 |
C8 |
359.6 |
360.0 |
| C6 |
C5 |
C4 |
N7 |
180.8 |
179.9 |
| C4 |
C5 |
N7 |
C8 |
0.1 |
360.0 |
| N3 |
C4 |
N9 |
C5 |
180.6 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
0.2 |
0.0 |
| C5 |
C6 |
N1 |
HN1 |
180.7 |
180.3 |
| N1 |
C6 |
C5 |
O6 |
177.6 |
179.8 |
| C6 |
C5 |
C4 |
N9 |
180.9 |
180.0 |
| C4 |
C5 |
C6 |
N7 |
179.1 |
180.1 |
| C6 |
C5 |
N7 |
C8 |
179.3 |
180.1 |
| N7 |
C5 |
C4 |
N9 |
0.2 |
0.0 |
| O6 |
C6 |
N1 |
HN1 |
358.5 |
0.1 |
| N1 |
C6 |
O6 |
C5 |
182.6 |
180.2 |
| O6 |
C6 |
C5 |
N7 |
2.2 |
0.2 |
| C4 |
N9 |
C8 |
N7 |
0.4 |
360.0 |
| C2' |
C1' |
O4' |
H1' |
241.9 |
241.4 |
| O4' |
C1' |
C2' |
H2' |
207.9 |
278.8 |
| O4' |
C1' |
C2' |
H1' |
121.3 |
118.6 |
| C3' |
C2' |
C1' |
H2' |
121.8 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
242.7 |
236.4 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| H1' |
C1' |
C2' |
O2' |
329.3 |
36.6 |
| H1' |
C1' |
C2' |
H2' |
86.6 |
160.2 |
| C3' |
C2' |
C1' |
H1' |
208.3 |
278.4 |
| C1' |
C2' |
C3' |
H2' |
234.3 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
117.7 |
123.6 |
| C3' |
C2' |
O2' |
HO2' |
290.8 |
292.7 |
| O2' |
C2' |
C1' |
H1' |
329.3 |
36.6 |
| C1' |
C2' |
O2' |
H2' |
126.3 |
123.6 |
| C3' |
C2' |
O2' |
H2' |
237.2 |
236.3 |
| H2' |
C2' |
C1' |
H1' |
86.6 |
160.2 |
| C1' |
C2' |
H2' |
O2' |
239.5 |
236.4 |
| H2' |
C2' |
O2' |
HO2' |
53.6 |
56.4 |
| HO2' |
O2' |
C2' |
H2' |
53.6 |
56.4 |
| C4' |
C3' |
C2' |
H2' |
166.5 |
97.3 |
| O3' |
C3' |
C4' |
H3' |
119.2 |
122.6 |
| O3' |
C3' |
C2' |
H2' |
283.2 |
216.1 |
| C4' |
C3' |
O3' |
H3' |
235.4 |
237.3 |
| H3' |
C3' |
C2' |
H2' |
42.5 |
338.6 |
| HO3' |
O3' |
C3' |
H3' |
56.4 |
299.0 |
| P |
O5' |
C5' |
C4' |
192.2 |
180.0 |
| C5' |
C4' |
C3' |
H3' |
324.8 |
357.2 |
| O4' |
C4' |
C5' |
H4' |
123.1 |
121.0 |
| C4' |
O4' |
C1' |
H1' |
125.2 |
78.6 |
| O4' |
C4' |
C3' |
H3' |
84.4 |
116.6 |
| C5' |
C4' |
O4' |
H4' |
242.7 |
238.9 |
| H4' |
C4' |
C3' |
H3' |
207.4 |
236.1 |
| C5' |
O5' |
P |
OP3 |
157.6 |
175.0 |
| O5' |
C5' |
C4' |
H4' |
295.8 |
306.1 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
55.8 |
66.1 |
| O5' |
C5' |
H5' |
H5'A |
239.8 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
175.8 |
186.1 |
| O5' |
C5' |
H5'A |
H5' |
120.2 |
119.9 |
| HOP1 |
OP1 |
P |
OP3 |
122.9 |
60.0 |