PDB Chemical Component DP
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 DP
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3' |
C3' |
1.427 |
1.429 |
| C3' |
C2' |
1.521 |
1.548 |
| C3' |
C4' |
1.542 |
1.550 |
| C2' |
C1' |
1.524 |
1.541 |
| OP1 |
P |
1.485 |
1.480 |
| OP2 |
P |
1.484 |
1.610 |
| O5' |
C5' |
1.419 |
1.429 |
| O5' |
P |
1.597 |
1.610 |
| C4' |
C5' |
1.539 |
1.530 |
| C4' |
O4' |
1.425 |
1.444 |
| C1' |
O4' |
1.414 |
1.438 |
| C1' |
N9 |
1.478 |
1.464 |
| N9 |
C8 |
1.400 |
1.382 |
| N9 |
C4 |
1.389 |
1.361 |
| N3 |
C4 |
1.358 |
1.325 |
| N3 |
C2 |
1.314 |
1.332 |
| C8 |
C7 |
1.381 |
1.331 |
| C4 |
N5 |
1.395 |
1.363 |
| N2 |
C2 |
1.329 |
1.377 |
| C2 |
N1 |
1.373 |
1.330 |
| C7 |
N5 |
1.394 |
1.383 |
| N5 |
C6 |
1.390 |
1.348 |
| N1 |
C6 |
1.372 |
1.332 |
| C6 |
O6 |
1.230 |
1.220 |
| P |
OP3 |
1.616 |
1.609 |
| OP2 |
H1 |
0.950 |
0.967 |
| C5' |
H5'' |
1.100 |
1.090 |
| C5' |
H5' |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.090 |
| C1' |
H1' |
1.100 |
1.090 |
| C8 |
H8 |
1.080 |
1.080 |
| C7 |
H7 |
1.080 |
1.079 |
| N2 |
H22 |
1.000 |
0.970 |
| N2 |
H21 |
1.000 |
0.971 |
| C2' |
H2'' |
1.100 |
1.089 |
| C2' |
H2' |
1.100 |
1.090 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
H3 |
0.950 |
0.967 |
| OP3 |
H4 |
0.950 |
0.966 |
Bond Angles for DP
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
H3' |
111.5 |
110.9 |
| C3' |
C2' |
H2'' |
111.2 |
110.5 |
| C3' |
C2' |
H2' |
111.2 |
110.6 |
| C3' |
C4' |
H4' |
107.9 |
110.7 |
| C2' |
C1' |
H1' |
108.6 |
110.0 |
| OP1 |
P |
OP3 |
108.5 |
109.5 |
| OP2 |
P |
OP3 |
109.8 |
109.5 |
| O5' |
C5' |
H5'' |
108.6 |
109.4 |
| O5' |
C5' |
H5' |
108.6 |
109.5 |
| O5' |
P |
OP3 |
101.7 |
109.5 |
| C4' |
C5' |
H5'' |
108.6 |
109.4 |
| C4' |
C5' |
H5' |
108.7 |
109.5 |
| O4' |
C4' |
H4' |
109.4 |
110.6 |
| C1' |
N9 |
C8 |
123.3 |
126.1 |
| C1' |
N9 |
C4 |
128.8 |
126.0 |
| N9 |
C1' |
H1' |
109.2 |
109.9 |
| C8 |
N9 |
C4 |
107.2 |
107.9 |
| N9 |
C8 |
C7 |
109.1 |
108.4 |
| N9 |
C8 |
H8 |
125.5 |
125.8 |
| N9 |
C4 |
N3 |
125.6 |
132.6 |
| N9 |
C4 |
N5 |
108.0 |
107.6 |
| C8 |
C7 |
N5 |
107.3 |
108.2 |
| C7 |
C8 |
H8 |
125.5 |
125.8 |
| C8 |
C7 |
H7 |
126.3 |
125.9 |
| C7 |
N5 |
C6 |
134.8 |
132.7 |
| N5 |
C7 |
H7 |
126.3 |
125.9 |
| N5 |
C6 |
O6 |
122.7 |
120.2 |
| N1 |
C6 |
O6 |
118.5 |
120.2 |
| P |
OP3 |
H4 |
109.5 |
114.1 |
| H5'' |
C5' |
H5' |
109.5 |
109.5 |
| H22 |
N2 |
H21 |
120.0 |
120.0 |
| H2'' |
C2' |
H2' |
109.5 |
110.4 |
Torsion Angles for DP
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
C2' |
H2'' |
207.2 |
20.4 |
| O3' |
C3' |
C2' |
H2' |
329.6 |
257.7 |
| O3' |
C3' |
C4' |
H4' |
17.1 |
323.4 |
| C2' |
C3' |
C4' |
H4' |
135.9 |
81.5 |
| C3' |
C2' |
C1' |
H1' |
277.2 |
242.5 |
| H2'' |
C2' |
C3' |
H2' |
237.6 |
122.6 |
| C3' |
C4' |
C5' |
H5'' |
298.5 |
60.6 |
| C3' |
C4' |
C5' |
H5' |
179.5 |
300.6 |
| O4' |
C4' |
C3' |
H4' |
241.4 |
241.5 |
| N9 |
C1' |
C2' |
H1' |
239.9 |
238.8 |
| OP2 |
P |
OP1 |
OP3 |
126.4 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
250.1 |
239.9 |
| OP1 |
P |
OP3 |
H4 |
360.0 |
60.0 |
| OP1 |
P |
OP2 |
OP3 |
234.2 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
109.9 |
120.0 |
| OP2 |
P |
OP3 |
H4 |
228.4 |
300.0 |
| C5' |
O5' |
P |
OP3 |
290.7 |
185.1 |
| C4' |
C5' |
O5' |
H5'' |
239.5 |
240.1 |
| C4' |
C5' |
O5' |
H5' |
120.5 |
120.1 |
| H5'' |
C5' |
O5' |
H5' |
241.0 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
114.4 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
244.6 |
240.0 |
| O5' |
P |
OP3 |
H4 |
114.7 |
180.0 |
| O5' |
C5' |
C4' |
H5'' |
120.5 |
119.9 |
| O5' |
C5' |
C4' |
H5' |
239.5 |
239.9 |
| H5'' |
C5' |
C4' |
H5' |
119.0 |
120.0 |
| C3' |
C4' |
O4' |
H4' |
117.6 |
118.7 |
| O4' |
C4' |
C5' |
H5'' |
176.9 |
306.5 |
| O4' |
C4' |
C5' |
H5' |
57.9 |
186.5 |
| C1' |
O4' |
C4' |
H4' |
247.3 |
281.4 |
| C2' |
C1' |
N9 |
H1' |
119.8 |
121.2 |
| C8 |
N9 |
C1' |
C4 |
190.1 |
180.3 |
| C1' |
N9 |
C8 |
C7 |
173.4 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
353.4 |
0.0 |
| C1' |
N9 |
C4 |
N3 |
4.0 |
0.8 |
| C1' |
N9 |
C4 |
N5 |
186.4 |
179.8 |
| C1' |
N9 |
C8 |
C4 |
171.8 |
179.7 |
| C8 |
N9 |
C1' |
H1' |
177.4 |
174.6 |
| C8 |
N9 |
C4 |
N3 |
175.2 |
180.5 |
| C8 |
N9 |
C4 |
N5 |
357.6 |
359.6 |
| N9 |
C8 |
C7 |
N5 |
359.9 |
0.0 |
| C7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
C7 |
H7 |
179.9 |
180.0 |
| C1' |
N9 |
C4 |
C8 |
188.8 |
180.3 |
| C4 |
N9 |
C1' |
H1' |
347.3 |
354.3 |
| C4 |
N9 |
C8 |
C7 |
1.6 |
0.3 |
| C4 |
N9 |
C8 |
H8 |
181.6 |
180.3 |
| N9 |
C4 |
N3 |
N5 |
182.8 |
178.9 |
| N9 |
C4 |
N3 |
C2 |
183.5 |
179.6 |
| C7 |
C8 |
N9 |
C4 |
1.6 |
0.3 |
| N9 |
C8 |
C7 |
H8 |
180.0 |
180.0 |
| C8 |
C7 |
N5 |
C6 |
184.0 |
180.0 |
| N5 |
C7 |
C8 |
H7 |
180.0 |
180.0 |
| N9 |
C4 |
N5 |
N3 |
177.6 |
180.8 |
| C4 |
N5 |
C7 |
H7 |
178.6 |
179.7 |
| C4 |
N5 |
C6 |
O6 |
177.8 |
180.3 |
| C2 |
N1 |
C6 |
O6 |
182.1 |
180.0 |
| N9 |
C4 |
N5 |
C7 |
2.4 |
0.4 |
| N5 |
C7 |
C8 |
H8 |
179.9 |
180.0 |
| C8 |
C7 |
N5 |
H7 |
180.0 |
180.0 |
| C7 |
N5 |
C6 |
O6 |
352.0 |
359.9 |
| N9 |
C4 |
N5 |
C6 |
178.1 |
180.2 |
| C6 |
N5 |
C7 |
H7 |
4.1 |
0.1 |
| N1 |
C6 |
N5 |
O6 |
180.6 |
180.0 |
| N5 |
C6 |
N1 |
O6 |
179.4 |
180.0 |
| H1 |
OP2 |
P |
OP3 |
125.8 |
300.0 |
| O5' |
C5' |
H5'' |
H5' |
118.5 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
241.5 |
240.0 |
| O5' |
C5' |
H5' |
H5'' |
241.5 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
118.5 |
120.0 |
| H4' |
C4' |
C5' |
H5'' |
58.1 |
183.6 |
| H4' |
C4' |
C5' |
H5' |
299.1 |
63.6 |
| H1' |
C1' |
N9 |
C8 |
177.4 |
174.6 |
| H1' |
C1' |
N9 |
C4 |
347.3 |
354.3 |
| H8 |
C8 |
N9 |
C4 |
181.6 |
180.3 |
| N9 |
C8 |
H8 |
C7 |
180.0 |
180.0 |
| H8 |
C8 |
C7 |
N5 |
179.9 |
180.0 |
| H8 |
C8 |
C7 |
H7 |
359.9 |
0.0 |
| C8 |
C7 |
H7 |
N5 |
180.0 |
180.0 |
| H7 |
C7 |
C8 |
H8 |
359.9 |
0.0 |
| H7 |
C7 |
N5 |
C6 |
4.1 |
0.1 |
| C3' |
C2' |
H2'' |
H2' |
123.4 |
237.3 |
| H2'' |
C2' |
C1' |
H1' |
158.4 |
1.3 |
| C3' |
C2' |
H2' |
H2'' |
236.6 |
122.7 |
| H2' |
C2' |
C1' |
H1' |
36.0 |
123.8 |
| H3' |
C3' |
C2' |
H2'' |
331.5 |
144.0 |
| H3' |
C3' |
C2' |
H2' |
93.8 |
21.4 |
| H3' |
C3' |
C4' |
H4' |
252.7 |
199.7 |
| H3 |
O3' |
C3' |
H3' |
56.6 |
297.8 |