PDB Chemical Component 1DP
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 1DP
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O3P |
1.602 |
1.610 |
| O3P |
HO3P |
0.950 |
0.968 |
| O5' |
P |
1.593 |
1.610 |
| O1P |
P |
1.486 |
1.479 |
| P |
O2P |
1.486 |
1.610 |
| O2P |
HO2P |
0.950 |
0.967 |
| O5' |
C5' |
1.420 |
1.429 |
| C4' |
C5' |
1.509 |
1.530 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.101 |
1.090 |
| C3' |
C4' |
1.522 |
1.541 |
| C4' |
O4' |
1.449 |
1.437 |
| C4' |
H4' |
1.100 |
1.090 |
| C1' |
O4' |
1.417 |
1.444 |
| C2' |
C1' |
1.527 |
1.550 |
| N9 |
C1' |
1.459 |
1.464 |
| C1' |
H1' |
1.100 |
1.090 |
| C4 |
N9 |
1.370 |
1.378 |
| N9 |
C8 |
1.372 |
1.363 |
| N3 |
C4 |
1.342 |
1.325 |
| C4 |
C5 |
1.383 |
1.404 |
| C2 |
N3 |
1.327 |
1.318 |
| C1 |
C2 |
1.340 |
1.382 |
| C2 |
H2 |
1.079 |
1.080 |
| C1 |
C6 |
1.350 |
1.391 |
| C1 |
H1 |
1.080 |
1.080 |
| N6 |
C6 |
1.332 |
1.391 |
| C6 |
C5 |
1.392 |
1.405 |
| N6 |
HN6 |
1.000 |
0.970 |
| N6 |
HN6A |
1.000 |
0.970 |
| C5 |
N7 |
1.383 |
1.356 |
| N7 |
C8 |
1.309 |
1.301 |
| C8 |
H8 |
1.080 |
1.080 |
| O2' |
C2' |
1.410 |
1.429 |
| C2' |
C3' |
1.519 |
1.548 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.966 |
| O3' |
C3' |
1.418 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.968 |
Bond Angles for 1DP
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
O3P |
HO3P |
109.5 |
114.0 |
| O1P |
P |
O2P |
119.6 |
109.5 |
| P |
O2P |
HO2P |
109.5 |
114.0 |
| O5' |
C5' |
H5' |
109.5 |
109.4 |
| O5' |
C5' |
H5'A |
109.4 |
109.5 |
| C4' |
C5' |
H5' |
109.4 |
109.5 |
| C4' |
C5' |
H5'A |
109.4 |
109.5 |
| H5' |
C5' |
H5'A |
109.5 |
109.5 |
| C3' |
C4' |
H4' |
108.5 |
110.0 |
| O4' |
C4' |
H4' |
115.6 |
109.9 |
| C2' |
C1' |
H1' |
109.5 |
110.6 |
| N9 |
C1' |
H1' |
108.8 |
110.5 |
| C4 |
N9 |
C8 |
105.8 |
107.4 |
| N9 |
C8 |
N7 |
113.9 |
110.0 |
| N9 |
C8 |
H8 |
123.1 |
125.0 |
| N3 |
C4 |
C5 |
127.0 |
120.4 |
| C4 |
C5 |
C6 |
117.1 |
118.9 |
| C4 |
C5 |
N7 |
110.9 |
107.2 |
| C1 |
C2 |
H2 |
115.4 |
119.3 |
| C6 |
C1 |
H1 |
120.6 |
120.3 |
| C1 |
C6 |
C5 |
117.6 |
118.1 |
| N6 |
C6 |
C5 |
123.5 |
121.0 |
| C6 |
C5 |
N7 |
132.0 |
133.9 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| C5 |
N7 |
C8 |
103.7 |
109.5 |
| N7 |
C8 |
H8 |
123.1 |
125.0 |
| O2' |
C2' |
C3' |
111.4 |
110.9 |
| O2' |
C2' |
H2' |
105.8 |
110.8 |
| C3' |
C2' |
H2' |
113.6 |
110.9 |
| C2' |
C3' |
H3' |
114.7 |
110.4 |
| O3' |
C3' |
H3' |
105.4 |
110.5 |
Torsion Angles for 1DP
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
O3P |
HO3P |
327.5 |
180.0 |
| O5' |
P |
O2P |
HO2P |
244.2 |
300.0 |
| O1P |
P |
O3P |
HO3P |
82.1 |
300.0 |
| O1P |
P |
O2P |
HO2P |
118.6 |
180.0 |
| O2P |
P |
O3P |
HO3P |
212.0 |
60.0 |
| C4' |
C5' |
O5' |
H5' |
240.0 |
240.0 |
| C4' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
O5' |
H5'A |
239.9 |
240.0 |
| O5' |
C5' |
C4' |
H5' |
120.0 |
119.9 |
| O5' |
C5' |
C4' |
H5'A |
240.0 |
240.0 |
| H5' |
C5' |
C4' |
H5'A |
120.0 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
120.0 |
120.0 |
| C4' |
C5' |
H5' |
H5'A |
240.1 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
240.0 |
240.0 |
| C4' |
C5' |
H5'A |
H5' |
120.0 |
120.0 |
| C3' |
C4' |
C5' |
H5' |
292.2 |
64.3 |
| C3' |
C4' |
C5' |
H5'A |
172.2 |
304.3 |
| O4' |
C4' |
C3' |
H4' |
236.2 |
240.5 |
| O4' |
C4' |
C5' |
H5' |
175.0 |
306.5 |
| O4' |
C4' |
C5' |
H5'A |
55.0 |
186.5 |
| C3' |
C4' |
O4' |
H4' |
119.1 |
119.6 |
| H4' |
C4' |
C5' |
H5' |
51.2 |
185.5 |
| H4' |
C4' |
C5' |
H5'A |
291.2 |
65.5 |
| C1' |
O4' |
C4' |
H4' |
259.5 |
267.0 |
| N9 |
C1' |
C2' |
H1' |
239.8 |
237.1 |
| C2' |
C1' |
N9 |
H1' |
120.6 |
123.0 |
| C4 |
N9 |
C1' |
H1' |
313.4 |
326.7 |
| C4 |
N9 |
C8 |
N7 |
359.5 |
359.6 |
| C4 |
N9 |
C8 |
H8 |
179.5 |
179.7 |
| C8 |
N9 |
C1' |
H1' |
134.2 |
146.4 |
| C5 |
N7 |
C8 |
N9 |
0.3 |
0.4 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
179.9 |
| N3 |
C4 |
N9 |
C8 |
180.1 |
180.2 |
| N3 |
C4 |
C5 |
C6 |
0.0 |
360.0 |
| N3 |
C4 |
C5 |
N7 |
180.0 |
180.0 |
| C5 |
C4 |
N9 |
C8 |
0.5 |
0.2 |
| C1 |
C6 |
C5 |
C4 |
359.8 |
360.0 |
| N6 |
C6 |
C5 |
C4 |
179.8 |
180.0 |
| C6 |
C5 |
C4 |
N7 |
180.0 |
180.0 |
| C4 |
C5 |
N7 |
C8 |
0.1 |
359.8 |
| C2 |
N3 |
C4 |
C5 |
0.1 |
0.1 |
| C4 |
C5 |
C6 |
C1 |
359.8 |
360.0 |
| C6 |
C1 |
C2 |
H2 |
179.9 |
180.0 |
| N6 |
C6 |
C1 |
C5 |
180.0 |
179.9 |
| C1 |
C6 |
C5 |
N7 |
179.8 |
180.0 |
| H1 |
C1 |
C2 |
H2 |
359.9 |
360.0 |
| H1 |
C1 |
C6 |
C5 |
180.2 |
180.1 |
| C4 |
C5 |
C6 |
N6 |
179.8 |
180.0 |
| N6 |
C6 |
C1 |
H1 |
0.2 |
0.0 |
| C1 |
C6 |
N6 |
C5 |
180.0 |
180.1 |
| N6 |
C6 |
C5 |
N7 |
359.8 |
0.0 |
| C4 |
C5 |
C6 |
N7 |
180.0 |
180.0 |
| C5 |
C6 |
C1 |
H1 |
180.2 |
180.1 |
| C6 |
C5 |
N7 |
C8 |
180.1 |
179.8 |
| HN6 |
N6 |
C6 |
C5 |
321.3 |
180.0 |
| HN6A |
N6 |
C6 |
C5 |
81.4 |
360.0 |
| N9 |
C8 |
N7 |
C5 |
0.3 |
0.4 |
| C4 |
C5 |
N7 |
C6 |
180.0 |
180.0 |
| C5 |
N7 |
C8 |
H8 |
180.3 |
180.3 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.1 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
179.9 |
| O2' |
C2' |
C1' |
H1' |
327.0 |
36.7 |
| C3' |
C2' |
O2' |
H2' |
236.1 |
236.3 |
| O2' |
C2' |
C3' |
H3' |
159.3 |
102.2 |
| C2' |
C3' |
C4' |
H4' |
88.1 |
117.4 |
| C3' |
C2' |
C1' |
H1' |
209.3 |
278.5 |
| O2' |
C2' |
C3' |
H2' |
119.4 |
123.6 |
| O3' |
C3' |
C2' |
H3' |
241.3 |
237.4 |
| H2' |
C2' |
C1' |
H1' |
86.2 |
160.3 |
| O2' |
C2' |
H2' |
C3' |
237.5 |
236.4 |
| H2' |
C2' |
C3' |
H3' |
39.9 |
338.6 |
| HO2' |
O2' |
C2' |
C3' |
244.6 |
292.7 |
| HO2' |
O2' |
C2' |
H2' |
8.5 |
56.4 |
| O3' |
C3' |
C4' |
H4' |
330.6 |
358.7 |
| O3' |
C3' |
C2' |
H2' |
281.2 |
216.0 |
| C2' |
C3' |
O3' |
H3' |
124.2 |
122.6 |
| H3' |
C3' |
C4' |
H4' |
211.8 |
236.1 |
| H3' |
C3' |
C2' |
H2' |
39.9 |
338.6 |
| HO3' |
O3' |
C3' |
H3' |
304.2 |
298.9 |