PDB Chemical Component AF2
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 AF2
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| F |
C2' |
1.390 |
1.399 |
| P |
OP1 |
1.485 |
1.480 |
| P |
OP2 |
1.488 |
1.610 |
| N1 |
C6 |
1.335 |
1.329 |
| C2 |
N1 |
1.327 |
1.320 |
| C2 |
N3 |
1.328 |
1.317 |
| N3 |
C4 |
1.363 |
1.329 |
| C4 |
N9 |
1.375 |
1.371 |
| C4 |
C5 |
1.370 |
1.405 |
| C5 |
N7 |
1.405 |
1.355 |
| C6 |
C5 |
1.419 |
1.405 |
| C6 |
N6 |
1.319 |
1.384 |
| N6 |
HN6A |
1.000 |
0.970 |
| C8 |
N7 |
1.310 |
1.301 |
| C8 |
H8 |
1.080 |
1.080 |
| N9 |
C8 |
1.376 |
1.363 |
| C1' |
N9 |
1.485 |
1.465 |
| C1' |
C2' |
1.531 |
1.540 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| C2' |
H2' |
1.101 |
1.090 |
| C2' |
C3' |
1.535 |
1.548 |
| C3' |
H3' |
1.099 |
1.090 |
| C3' |
O3' |
1.420 |
1.429 |
| O3' |
HO3' |
0.950 |
0.967 |
| C4' |
C3' |
1.535 |
1.550 |
| C4' |
C5' |
1.536 |
1.530 |
| O4' |
C1' |
1.423 |
1.437 |
| O4' |
C4' |
1.427 |
1.444 |
| C5' |
O5' |
1.422 |
1.429 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
P |
1.616 |
1.610 |
| H2 |
C2 |
1.080 |
1.080 |
| H5' |
C5' |
1.100 |
1.090 |
| H1' |
C1' |
1.100 |
1.090 |
| H4' |
C4' |
1.100 |
1.091 |
| HN6 |
N6 |
1.000 |
0.970 |
| P |
OP3 |
1.720 |
1.611 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for AF2
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| F |
C2' |
C1' |
108.2 |
110.5 |
| F |
C2' |
H2' |
106.2 |
110.4 |
| F |
C2' |
C3' |
112.5 |
110.5 |
| OP2 |
P |
OP1 |
118.4 |
109.5 |
| OP1 |
P |
OP3 |
101.9 |
109.4 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| OP2 |
P |
OP3 |
101.2 |
109.5 |
| C2 |
N1 |
C6 |
117.9 |
121.2 |
| N1 |
C6 |
C5 |
121.1 |
118.5 |
| N1 |
C6 |
N6 |
113.8 |
120.8 |
| C2 |
N3 |
C4 |
112.2 |
120.6 |
| N3 |
C4 |
N9 |
126.7 |
134.9 |
| N3 |
C4 |
C5 |
126.9 |
119.1 |
| C5 |
C4 |
N9 |
106.3 |
106.0 |
| C4 |
N9 |
C8 |
105.4 |
107.5 |
| C4 |
C5 |
N7 |
110.9 |
107.1 |
| C6 |
C5 |
N7 |
135.2 |
134.7 |
| C6 |
N6 |
HN6A |
109.5 |
120.0 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| N9 |
C8 |
H8 |
122.8 |
125.0 |
| C1' |
C2' |
H2' |
116.0 |
110.5 |
| C1' |
C2' |
C3' |
102.1 |
104.2 |
| C3' |
C2' |
H2' |
111.9 |
110.5 |
| C2' |
C3' |
H3' |
114.9 |
110.9 |
| C2' |
C3' |
O3' |
113.7 |
110.9 |
| O3' |
C3' |
H3' |
101.4 |
110.8 |
| C4' |
C3' |
H3' |
115.7 |
110.9 |
| C3' |
O3' |
HO3' |
109.5 |
113.9 |
| O4' |
C4' |
C5' |
111.9 |
110.6 |
| C4' |
C5' |
O5' |
112.7 |
109.5 |
| C4' |
C5' |
H5'A |
108.4 |
109.5 |
| O5' |
C5' |
H5'A |
108.4 |
109.5 |
| H5' |
C5' |
H5'A |
110.5 |
109.4 |
| O5' |
P |
OP3 |
119.7 |
109.4 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
Torsion Angles for AF2
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C1' |
C2' |
F |
H2' |
125.2 |
122.6 |
| C1' |
C2' |
F |
C3' |
247.9 |
245.2 |
| C3' |
C2' |
F |
H2' |
237.2 |
237.4 |
| F |
C2' |
C3' |
H3' |
159.3 |
144.0 |
| F |
C2' |
C3' |
O3' |
43.0 |
20.4 |
| OP1 |
P |
OP2 |
HOP2 |
0.0 |
180.0 |
| OP2 |
P |
OP1 |
OP3 |
250.2 |
240.0 |
| O5' |
P |
OP1 |
OP3 |
126.8 |
120.0 |
| OP1 |
P |
OP3 |
HOP3 |
360.0 |
300.0 |
| OP1 |
P |
OP2 |
OP3 |
110.2 |
119.9 |
| O5' |
P |
OP2 |
OP3 |
233.2 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
122.4 |
59.9 |
| N1 |
C6 |
C5 |
N7 |
179.6 |
180.0 |
| N1 |
C6 |
N6 |
HN6A |
360.0 |
0.0 |
| C2 |
N1 |
C6 |
C5 |
0.6 |
360.0 |
| C2 |
N1 |
C6 |
N6 |
180.6 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
359.9 |
0.0 |
| C2 |
N3 |
C4 |
N9 |
179.7 |
179.9 |
| C2 |
N3 |
C4 |
C5 |
359.8 |
359.9 |
| C5 |
C4 |
N3 |
N9 |
180.1 |
180.0 |
| N3 |
C4 |
N9 |
C8 |
179.4 |
180.0 |
| N3 |
C4 |
C5 |
N7 |
180.3 |
180.0 |
| N3 |
C4 |
N9 |
C5 |
180.1 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
0.4 |
0.0 |
| C4 |
N9 |
C8 |
H8 |
180.9 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
359.3 |
360.0 |
| N3 |
C4 |
C5 |
N9 |
179.9 |
180.0 |
| C5 |
C4 |
N9 |
C8 |
359.3 |
0.0 |
| C6 |
C5 |
C4 |
N7 |
180.3 |
180.1 |
| N7 |
C5 |
C4 |
N9 |
0.4 |
0.0 |
| N1 |
C6 |
C5 |
N6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
N9 |
180.7 |
180.1 |
| C4 |
C5 |
C6 |
N7 |
179.7 |
179.9 |
| N1 |
C6 |
N6 |
C5 |
180.0 |
180.0 |
| N6 |
C6 |
C5 |
N7 |
359.6 |
0.1 |
| HN6 |
N6 |
C6 |
HN6A |
120.0 |
180.0 |
| C4 |
N9 |
C8 |
N7 |
0.9 |
360.0 |
| F |
C2' |
C1' |
N9 |
209.3 |
240.1 |
| C1' |
N9 |
C8 |
H8 |
3.2 |
360.0 |
| F |
C2' |
C1' |
H2' |
240.8 |
237.4 |
| F |
C2' |
C1' |
C3' |
118.9 |
118.7 |
| C3' |
C2' |
C1' |
H2' |
121.9 |
118.8 |
| C1' |
C2' |
C3' |
H3' |
275.1 |
262.7 |
| C1' |
C2' |
C3' |
O3' |
158.8 |
139.1 |
| HOP2 |
OP2 |
P |
OP1 |
0.0 |
180.0 |
| HOP2 |
OP2 |
P |
OP3 |
249.8 |
60.1 |
| F |
C2' |
H2' |
C1' |
120.2 |
122.6 |
| F |
C2' |
H2' |
C3' |
236.8 |
237.5 |
| C1' |
C2' |
H2' |
C3' |
116.6 |
114.8 |
| H2' |
C2' |
C3' |
H3' |
39.8 |
21.4 |
| H2' |
C2' |
C3' |
O3' |
283.5 |
257.9 |
| F |
C2' |
C3' |
C1' |
244.2 |
241.3 |
| F |
C2' |
C3' |
H2' |
119.5 |
122.5 |
| C1' |
C2' |
C3' |
H2' |
235.3 |
241.2 |
| O3' |
C3' |
C2' |
H3' |
243.7 |
236.4 |
| C4' |
C3' |
C2' |
H3' |
123.8 |
118.2 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.5 |
| H3' |
C3' |
C2' |
H2' |
39.8 |
21.4 |
| C2' |
C3' |
H3' |
O3' |
236.9 |
236.3 |
| H3' |
C3' |
O3' |
HO3' |
56.1 |
297.8 |
| O3' |
C3' |
C2' |
H2' |
283.5 |
257.9 |
| C2' |
C3' |
O3' |
H3' |
123.9 |
123.7 |
| C4' |
C3' |
O3' |
H3' |
235.6 |
236.4 |
| HO3' |
O3' |
C3' |
H3' |
56.1 |
297.8 |
| C4' |
C3' |
C2' |
H2' |
163.5 |
139.7 |
| C2' |
C3' |
C4' |
H3' |
236.7 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
116.2 |
123.5 |
| C4' |
C3' |
O3' |
HO3' |
291.7 |
174.2 |
| C5' |
C4' |
C3' |
H3' |
322.6 |
322.7 |
| O5' |
C5' |
C4' |
H5'A |
240.0 |
120.0 |
| H5' |
C5' |
C4' |
H5'A |
120.0 |
240.1 |
| O4' |
C1' |
C2' |
H2' |
208.3 |
243.3 |
| O4' |
C4' |
C3' |
H3' |
86.7 |
81.2 |
| O4' |
C4' |
C5' |
O5' |
301.1 |
71.0 |
| O4' |
C4' |
C5' |
H5'A |
61.1 |
310.9 |
| C4' |
C5' |
O5' |
H5'A |
120.0 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
240.0 |
120.0 |
| C5' |
O5' |
P |
OP3 |
288.4 |
175.0 |
| C4' |
C5' |
H5'A |
O5' |
237.4 |
120.0 |
| OP1 |
P |
O5' |
OP3 |
244.4 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
122.9 |
300.1 |
| OP2 |
P |
O5' |
OP3 |
115.2 |
120.0 |
| O5' |
P |
OP3 |
HOP3 |
241.4 |
180.0 |
| C4' |
C5' |
H5' |
H5'A |
241.3 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
118.7 |
240.0 |
| H1' |
C1' |
C2' |
H2' |
86.9 |
123.7 |
| C6 |
N6 |
HN6 |
HN6A |
240.0 |
180.0 |
| OP2 |
P |
OP3 |
OP1 |
122.4 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
249.8 |
60.1 |