PDB Chemical Component PDU
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 PDU
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C5M |
C5B |
1.458 |
1.472 |
| OP1 |
P |
1.480 |
1.479 |
| C5B |
C5A |
1.190 |
1.174 |
| C5A |
C5 |
1.432 |
1.432 |
| C2' |
C3' |
1.491 |
1.548 |
| C2' |
C1' |
1.515 |
1.541 |
| C3' |
O3' |
1.436 |
1.430 |
| C3' |
C4' |
1.510 |
1.551 |
| C5 |
C6 |
1.351 |
1.365 |
| C5 |
C4 |
1.447 |
1.470 |
| P |
O5' |
1.647 |
1.611 |
| P |
OP2 |
1.483 |
1.611 |
| O5' |
C5' |
1.432 |
1.429 |
| O4 |
C4 |
1.230 |
1.217 |
| C6 |
N1 |
1.368 |
1.365 |
| C4 |
N3 |
1.381 |
1.351 |
| C5' |
C4' |
1.522 |
1.530 |
| N1 |
C1' |
1.501 |
1.465 |
| N1 |
C2 |
1.411 |
1.343 |
| C4' |
O4' |
1.459 |
1.444 |
| N3 |
C2 |
1.406 |
1.344 |
| C1' |
O4' |
1.437 |
1.437 |
| C2 |
O2 |
1.229 |
1.216 |
| P |
OP3 |
1.651 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| C5' |
H5' |
1.100 |
1.091 |
| C5' |
H5'' |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.089 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
H2 |
0.950 |
0.968 |
| C2' |
H2'' |
1.100 |
1.089 |
| C2' |
H2' |
1.100 |
1.090 |
| C1' |
H1' |
1.100 |
1.090 |
| N3 |
H3 |
1.000 |
0.970 |
| C5M |
H71 |
1.100 |
1.090 |
| C5M |
H72 |
1.100 |
1.091 |
| C5M |
H73 |
1.100 |
1.089 |
| C6 |
H6 |
1.080 |
1.080 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for PDU
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
O5' |
107.5 |
109.5 |
| OP1 |
P |
OP3 |
107.3 |
109.5 |
| C5A |
C5 |
C6 |
120.4 |
120.9 |
| C2' |
C3' |
H3' |
111.4 |
111.0 |
| C1' |
C2' |
H2'' |
109.7 |
110.5 |
| C1' |
C2' |
H2' |
109.6 |
110.5 |
| C2' |
C1' |
H1' |
111.3 |
109.8 |
| O3' |
C3' |
H3' |
112.3 |
110.8 |
| C3' |
O3' |
H2 |
109.5 |
114.0 |
| C3' |
C4' |
H4' |
109.1 |
110.8 |
| C5 |
C6 |
H6 |
119.3 |
120.3 |
| OP2 |
P |
O5' |
106.6 |
109.4 |
| P |
O5' |
C5' |
119.7 |
123.0 |
| O5' |
P |
OP3 |
109.9 |
109.5 |
| OP2 |
P |
OP3 |
106.9 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
113.9 |
| O5' |
C5' |
C4' |
122.9 |
109.4 |
| O5' |
C5' |
H5' |
106.0 |
109.4 |
| O5' |
C5' |
H5'' |
106.0 |
109.5 |
| C4 |
N3 |
H3 |
117.5 |
119.8 |
| C5' |
C4' |
O4' |
106.4 |
110.7 |
| C4' |
C5' |
H5' |
106.0 |
109.5 |
| C4' |
C5' |
H5'' |
106.0 |
109.5 |
| C5' |
C4' |
H4' |
108.9 |
110.6 |
| N1 |
C1' |
H1' |
111.5 |
110.0 |
| N1 |
C2 |
O2 |
122.7 |
119.1 |
| O4' |
C4' |
H4' |
109.8 |
110.7 |
| P |
OP3 |
HOP3 |
109.5 |
113.9 |
| H5' |
C5' |
H5'' |
109.5 |
109.5 |
| H2'' |
C2' |
H2' |
109.5 |
110.6 |
| H71 |
C5M |
H72 |
109.5 |
109.4 |
| H71 |
C5M |
H73 |
109.5 |
109.5 |
| H72 |
C5M |
H73 |
109.4 |
109.5 |
Torsion Angles for PDU
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP1 |
O5' |
120.8 |
120.0 |
| OP1 |
P |
O5' |
C5' |
256.3 |
55.0 |
| O5' |
P |
OP1 |
OP3 |
118.2 |
120.0 |
| OP2 |
P |
OP1 |
OP3 |
239.0 |
240.0 |
| OP1 |
P |
OP2 |
HOP2 |
360.0 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
360.0 |
300.0 |
| C5B |
C5A |
C5 |
C6 |
213.2 |
37.2 |
| C5A |
C5 |
C6 |
H6 |
0.8 |
359.5 |
| O3' |
C3' |
C2' |
H3' |
234.6 |
236.4 |
| C2' |
C3' |
O3' |
H2 |
180.0 |
67.3 |
| C2' |
C3' |
C4' |
H4' |
136.7 |
81.6 |
| C1' |
C2' |
C3' |
H3' |
208.4 |
262.6 |
| N1 |
C1' |
C2' |
H1' |
238.7 |
238.9 |
| H2'' |
C2' |
C1' |
H2' |
120.2 |
122.7 |
| C2' |
C3' |
O3' |
H3' |
125.0 |
123.7 |
| O3' |
C3' |
C4' |
H4' |
20.4 |
323.3 |
| C3' |
C4' |
C5' |
H5' |
171.2 |
60.6 |
| C3' |
C4' |
C5' |
H5'' |
54.9 |
300.5 |
| C5' |
C4' |
C3' |
H4' |
122.3 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
240.7 |
241.4 |
| C5 |
C4 |
N3 |
H3 |
179.9 |
180.0 |
| OP1 |
P |
O5' |
OP3 |
243.5 |
240.0 |
| OP2 |
P |
O5' |
OP3 |
115.5 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
121.2 |
300.0 |
| P |
O5' |
C5' |
C4' |
190.9 |
180.0 |
| P |
O5' |
C5' |
H5' |
312.8 |
300.0 |
| P |
O5' |
C5' |
H5'' |
69.1 |
60.0 |
| O5' |
P |
OP3 |
HOP3 |
243.3 |
180.0 |
| OP1 |
P |
OP2 |
O5' |
238.8 |
240.0 |
| OP1 |
P |
OP2 |
OP3 |
121.2 |
120.0 |
| OP2 |
P |
O5' |
C5' |
128.3 |
295.0 |
| O5' |
P |
OP2 |
OP3 |
242.5 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
128.0 |
60.1 |
| C5' |
O5' |
P |
OP3 |
12.8 |
175.0 |
| O5' |
C5' |
C4' |
O4' |
173.7 |
66.5 |
| C4' |
C5' |
O5' |
H5' |
238.1 |
240.0 |
| C4' |
C5' |
O5' |
H5'' |
121.8 |
120.0 |
| O5' |
C5' |
C4' |
H4' |
55.4 |
303.5 |
| H5' |
C5' |
O5' |
H5'' |
243.7 |
240.0 |
| O4 |
C4 |
N3 |
H3 |
359.8 |
0.0 |
| C6 |
N1 |
C1' |
H1' |
180.8 |
353.6 |
| C3' |
C4' |
C5' |
H4' |
237.7 |
237.0 |
| O5' |
C5' |
C4' |
H5' |
121.8 |
119.9 |
| O5' |
C5' |
C4' |
H5'' |
238.2 |
240.0 |
| O4' |
C4' |
C5' |
H4' |
118.3 |
123.0 |
| H5' |
C5' |
C4' |
H5'' |
116.3 |
120.1 |
| N1 |
C1' |
C2' |
H2'' |
38.4 |
2.8 |
| N1 |
C1' |
C2' |
H2' |
278.2 |
240.1 |
| C2' |
C1' |
N1 |
H1' |
121.2 |
121.1 |
| C2 |
N1 |
C1' |
H1' |
0.3 |
174.0 |
| C3' |
C4' |
O4' |
H4' |
118.9 |
118.6 |
| O4' |
C4' |
C5' |
H5' |
51.9 |
306.5 |
| O4' |
C4' |
C5' |
H5'' |
295.5 |
186.5 |
| C5' |
C4' |
O4' |
H4' |
242.2 |
237.1 |
| C1' |
O4' |
C4' |
H4' |
246.9 |
281.4 |
| OP1 |
P |
OP3 |
O5' |
116.6 |
120.0 |
| OP2 |
P |
OP3 |
O5' |
244.7 |
240.0 |
| OP3 |
P |
O5' |
C5' |
12.8 |
175.0 |
| OP3 |
P |
OP2 |
HOP2 |
238.7 |
60.0 |
| HOP2 |
OP2 |
P |
O5' |
121.2 |
300.0 |
| HOP2 |
OP2 |
P |
OP3 |
238.7 |
60.0 |
| O5' |
C5' |
H5' |
C4' |
227.9 |
240.1 |
| O5' |
C5' |
H5' |
H5'' |
113.9 |
120.0 |
| H5' |
C5' |
C4' |
O4' |
51.9 |
306.5 |
| C4' |
C5' |
H5' |
H5'' |
246.0 |
239.9 |
| H5' |
C5' |
C4' |
H4' |
293.5 |
183.6 |
| O5' |
C5' |
H5'' |
C4' |
132.1 |
120.0 |
| O5' |
C5' |
H5'' |
H5' |
246.1 |
240.0 |
| H5'' |
C5' |
C4' |
O4' |
295.5 |
186.5 |
| C4' |
C5' |
H5'' |
H5' |
114.0 |
120.1 |
| H5'' |
C5' |
C4' |
H4' |
177.2 |
63.5 |
| C5' |
C4' |
H4' |
O4' |
116.2 |
123.0 |
| H4' |
C4' |
C5' |
H5' |
293.5 |
183.6 |
| H4' |
C4' |
C5' |
H5'' |
177.2 |
63.5 |
| H3' |
C3' |
O3' |
H2 |
55.1 |
303.6 |
| H3' |
C3' |
C4' |
H4' |
254.0 |
199.8 |
| H2 |
O3' |
C3' |
H3' |
55.1 |
303.6 |
| H2'' |
C2' |
C3' |
H3' |
328.4 |
21.3 |
| C1' |
C2' |
H2'' |
H2' |
239.7 |
237.4 |
| H2'' |
C2' |
C1' |
H1' |
159.7 |
124.0 |
| H2' |
C2' |
C3' |
H3' |
88.5 |
144.0 |
| C1' |
C2' |
H2' |
H2'' |
120.3 |
122.7 |
| H2' |
C2' |
C1' |
H1' |
39.5 |
1.2 |
| H1' |
C1' |
C2' |
H2'' |
159.7 |
124.0 |
| H1' |
C1' |
C2' |
H2' |
39.5 |
1.2 |
| H72 |
C5M |
H71 |
H73 |
120.0 |
120.0 |
| H71 |
C5M |
H72 |
H73 |
240.0 |
240.0 |
| H71 |
C5M |
H73 |
H72 |
120.0 |
120.0 |