PDB Chemical Component P2U
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 P2U
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.393 |
1.345 |
| N1 |
C6 |
1.330 |
1.367 |
| N1 |
HN1 |
1.019 |
0.970 |
| C2 |
N3 |
1.396 |
1.346 |
| C2 |
O2 |
1.227 |
1.216 |
| N3 |
C4 |
1.374 |
1.348 |
| N3 |
HN3 |
1.021 |
0.970 |
| C4 |
C5 |
1.393 |
1.415 |
| C4 |
O4 |
1.219 |
1.217 |
| C5 |
C6 |
1.373 |
1.351 |
| C5 |
C1' |
1.551 |
1.507 |
| C6 |
H6 |
1.103 |
1.080 |
| C1' |
C2' |
1.551 |
1.544 |
| C1' |
O4' |
1.423 |
1.445 |
| C1' |
H1' |
1.115 |
1.090 |
| C2' |
C3' |
1.524 |
1.544 |
| C2' |
H2' |
1.116 |
1.091 |
| C2' |
H2'' |
1.116 |
1.091 |
| C3' |
C4' |
1.514 |
1.544 |
| C3' |
O3' |
1.429 |
1.429 |
| C3' |
H3' |
1.116 |
1.089 |
| C4' |
O4' |
1.449 |
1.446 |
| C4' |
C5' |
1.478 |
1.530 |
| C4' |
H4' |
1.114 |
1.090 |
| O3' |
HO3' |
0.949 |
0.967 |
| C5' |
O5' |
1.278 |
1.427 |
| C5' |
H5' |
1.116 |
1.090 |
| C5' |
H5'' |
1.115 |
1.090 |
| O5' |
P |
1.580 |
1.610 |
| P |
OP1 |
1.482 |
1.480 |
| P |
OP2 |
1.477 |
1.610 |
| P |
OP3 |
1.600 |
1.609 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.966 |
Bond Angles for P2U
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
120.2 |
120.6 |
| C2 |
N1 |
HN1 |
108.3 |
119.7 |
| N1 |
C2 |
N3 |
115.6 |
120.9 |
| N1 |
C2 |
O2 |
125.3 |
119.5 |
| C6 |
N1 |
HN1 |
108.4 |
119.7 |
| N1 |
C6 |
C5 |
122.9 |
119.7 |
| N1 |
C6 |
H6 |
116.9 |
120.2 |
| N3 |
C2 |
O2 |
119.2 |
119.5 |
| C2 |
N3 |
C4 |
126.0 |
120.3 |
| C2 |
N3 |
HN3 |
117.9 |
119.9 |
| C4 |
N3 |
HN3 |
116.1 |
119.9 |
| N3 |
C4 |
C5 |
114.6 |
119.4 |
| N3 |
C4 |
O4 |
121.8 |
120.3 |
| C5 |
C4 |
O4 |
123.6 |
120.3 |
| C4 |
C5 |
C6 |
120.7 |
119.1 |
| C4 |
C5 |
C1' |
116.7 |
120.4 |
| C6 |
C5 |
C1' |
107.5 |
120.4 |
| C5 |
C6 |
H6 |
120.2 |
120.1 |
| C5 |
C1' |
C2' |
111.2 |
110.4 |
| C5 |
C1' |
O4' |
108.1 |
110.4 |
| C5 |
C1' |
H1' |
108.0 |
110.3 |
| C2' |
C1' |
O4' |
105.8 |
104.8 |
| C2' |
C1' |
H1' |
110.3 |
110.4 |
| C1' |
C2' |
C3' |
107.8 |
104.1 |
| C1' |
C2' |
H2' |
112.9 |
110.5 |
| C1' |
C2' |
H2'' |
112.9 |
110.5 |
| O4' |
C1' |
H1' |
113.4 |
110.4 |
| C1' |
O4' |
C4' |
112.5 |
105.3 |
| C3' |
C2' |
H2' |
112.9 |
110.5 |
| C3' |
C2' |
H2'' |
112.8 |
110.5 |
| C2' |
C3' |
C4' |
104.6 |
104.2 |
| C2' |
C3' |
O3' |
111.0 |
110.5 |
| C2' |
C3' |
H3' |
113.8 |
110.5 |
| H2' |
C2' |
H2'' |
97.5 |
110.5 |
| C4' |
C3' |
O3' |
115.2 |
110.5 |
| C4' |
C3' |
H3' |
109.5 |
110.5 |
| C3' |
C4' |
O4' |
108.6 |
104.7 |
| C3' |
C4' |
C5' |
105.1 |
110.7 |
| C3' |
C4' |
H4' |
115.1 |
110.3 |
| O3' |
C3' |
H3' |
103.0 |
110.5 |
| C3' |
O3' |
HO3' |
111.0 |
106.8 |
| O4' |
C4' |
C5' |
115.4 |
110.3 |
| O4' |
C4' |
H4' |
104.8 |
110.4 |
| C5' |
C4' |
H4' |
108.3 |
110.3 |
| C4' |
C5' |
O5' |
105.0 |
109.5 |
| C4' |
C5' |
H5' |
113.9 |
109.5 |
| C4' |
C5' |
H5'' |
113.9 |
109.4 |
| O5' |
C5' |
H5' |
113.9 |
109.5 |
| O5' |
C5' |
H5'' |
113.9 |
109.5 |
| C5' |
O5' |
P |
120.7 |
106.8 |
| H5' |
C5' |
H5'' |
96.5 |
109.5 |
| O5' |
P |
OP1 |
105.1 |
109.4 |
| O5' |
P |
OP2 |
110.4 |
109.5 |
| O5' |
P |
OP3 |
103.7 |
109.5 |
| OP1 |
P |
OP2 |
119.9 |
109.4 |
| OP1 |
P |
OP3 |
109.3 |
109.5 |
| OP2 |
P |
OP3 |
107.3 |
109.5 |
| P |
OP2 |
HOP2 |
110.4 |
106.8 |
| P |
OP3 |
HOP3 |
103.7 |
106.8 |
Torsion Angles for P2U
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
HN1 |
125.3 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
1.2 |
360.0 |
| C2 |
N1 |
C6 |
H6 |
181.2 |
180.1 |
| N3 |
C2 |
N1 |
O2 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
359.4 |
359.8 |
| N1 |
C2 |
N3 |
HN3 |
179.4 |
180.0 |
| C2 |
N1 |
C6 |
HN1 |
234.8 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
359.5 |
0.0 |
| C6 |
N1 |
C2 |
O2 |
179.6 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
359.0 |
0.2 |
| N1 |
C6 |
C5 |
C1' |
221.7 |
180.1 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.9 |
| C2 |
N1 |
HN1 |
C6 |
131.9 |
180.0 |
| HN1 |
N1 |
C2 |
N3 |
234.3 |
180.0 |
| HN1 |
N1 |
C2 |
O2 |
54.3 |
0.0 |
| HN1 |
N1 |
C6 |
C5 |
126.4 |
180.0 |
| HN1 |
N1 |
C6 |
H6 |
306.4 |
0.1 |
| N3 |
C2 |
N1 |
C6 |
359.5 |
0.0 |
| N3 |
C2 |
N1 |
HN1 |
234.3 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
180.0 |
180.0 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
179.8 |
| C2 |
N3 |
C4 |
C5 |
0.8 |
0.5 |
| C2 |
N3 |
C4 |
O4 |
179.5 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
179.6 |
180.0 |
| O2 |
C2 |
N1 |
HN1 |
54.3 |
0.0 |
| N1 |
C2 |
O2 |
N3 |
180.0 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
179.4 |
179.7 |
| O2 |
C2 |
N3 |
HN3 |
359.4 |
360.0 |
| C4 |
N3 |
C2 |
O2 |
179.4 |
179.7 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
180.2 |
| C5 |
C4 |
N3 |
O4 |
181.3 |
180.5 |
| N3 |
C4 |
C5 |
C6 |
359.9 |
359.5 |
| N3 |
C4 |
C5 |
C1' |
133.6 |
179.7 |
| HN3 |
N3 |
C2 |
O2 |
359.4 |
360.0 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
179.8 |
| HN3 |
N3 |
C4 |
C5 |
180.8 |
180.3 |
| HN3 |
N3 |
C4 |
O4 |
359.5 |
359.8 |
| N1 |
C6 |
C5 |
C4 |
359.0 |
0.2 |
| C5 |
C4 |
N3 |
HN3 |
180.8 |
180.3 |
| N3 |
C4 |
C5 |
O4 |
178.7 |
179.5 |
| C6 |
C5 |
C4 |
C1' |
226.3 |
179.8 |
| C4 |
C5 |
C6 |
H6 |
179.1 |
180.2 |
| C4 |
C5 |
C1' |
C2' |
71.5 |
299.8 |
| C4 |
C5 |
C1' |
O4' |
187.2 |
55.2 |
| C4 |
C5 |
C1' |
H1' |
310.3 |
177.5 |
| O4 |
C4 |
N3 |
HN3 |
359.5 |
359.8 |
| N3 |
C4 |
O4 |
C5 |
181.4 |
180.5 |
| O4 |
C4 |
C5 |
C6 |
181.3 |
180.0 |
| O4 |
C4 |
C5 |
C1' |
315.0 |
0.2 |
| C5 |
C6 |
N1 |
HN1 |
126.4 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.1 |
| C6 |
C5 |
C4 |
O4 |
181.3 |
180.0 |
| C4 |
C5 |
C6 |
C1' |
137.3 |
180.2 |
| C6 |
C5 |
C1' |
C2' |
210.8 |
120.0 |
| C6 |
C5 |
C1' |
O4' |
326.5 |
235.4 |
| C6 |
C5 |
C1' |
H1' |
89.6 |
357.7 |
| C1' |
C5 |
C4 |
O4 |
315.0 |
0.2 |
| C4 |
C5 |
C1' |
C6 |
220.7 |
179.8 |
| C1' |
C5 |
C6 |
H6 |
41.7 |
360.0 |
| C2' |
C1' |
C5 |
O4' |
244.2 |
244.5 |
| C2' |
C1' |
C5 |
H1' |
121.2 |
122.3 |
| C5 |
C1' |
C2' |
C3' |
121.1 |
142.9 |
| C5 |
C1' |
C2' |
H2' |
246.4 |
24.3 |
| C5 |
C1' |
C2' |
H2'' |
355.9 |
261.6 |
| O4' |
C1' |
C5 |
H1' |
237.0 |
237.7 |
| C5 |
C1' |
O4' |
C4' |
242.3 |
200.7 |
| H6 |
C6 |
N1 |
HN1 |
306.4 |
0.1 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.9 |
| H6 |
C6 |
C5 |
C1' |
41.7 |
360.0 |
| C5 |
C1' |
C2' |
O4' |
117.2 |
118.9 |
| C5 |
C1' |
C2' |
H1' |
240.1 |
237.8 |
| O4' |
C1' |
C2' |
H1' |
123.0 |
118.9 |
| C2' |
C1' |
O4' |
C4' |
1.6 |
319.6 |
| C3' |
C2' |
C1' |
H2' |
234.7 |
118.6 |
| C3' |
C2' |
C1' |
H2'' |
125.3 |
241.3 |
| C1' |
C2' |
C3' |
C4' |
352.4 |
359.9 |
| C1' |
C2' |
C3' |
O3' |
117.3 |
118.6 |
| C1' |
C2' |
C3' |
H3' |
232.9 |
241.3 |
| H2' |
C2' |
C1' |
H2'' |
250.6 |
122.7 |
| C5 |
C1' |
O4' |
C2' |
240.7 |
241.1 |
| C5 |
C1' |
O4' |
H1' |
119.7 |
122.2 |
| C2' |
C1' |
O4' |
H1' |
239.0 |
241.1 |
| O4' |
C1' |
C2' |
C3' |
3.9 |
24.0 |
| O4' |
C1' |
C2' |
H2' |
129.3 |
265.3 |
| O4' |
C1' |
C2' |
H2'' |
238.7 |
142.7 |
| C3' |
C4' |
O4' |
C1' |
353.4 |
40.3 |
| C1' |
O4' |
C4' |
C5' |
111.0 |
159.5 |
| C1' |
O4' |
C4' |
H4' |
229.9 |
281.6 |
| C5 |
C1' |
H1' |
C2' |
121.8 |
122.3 |
| C5 |
C1' |
H1' |
O4' |
240.2 |
237.7 |
| C2' |
C1' |
H1' |
O4' |
118.4 |
115.4 |
| H1' |
C1' |
C2' |
C3' |
241.0 |
265.1 |
| H1' |
C1' |
C2' |
H2' |
6.3 |
146.5 |
| H1' |
C1' |
C2' |
H2'' |
115.7 |
23.8 |
| H1' |
C1' |
O4' |
C4' |
122.6 |
78.5 |
| C3' |
C2' |
C1' |
O4' |
3.9 |
24.0 |
| C3' |
C2' |
C1' |
H1' |
241.0 |
265.1 |
| C1' |
C2' |
C3' |
H2' |
125.3 |
241.4 |
| C1' |
C2' |
C3' |
H2'' |
234.7 |
118.7 |
| H2' |
C2' |
C3' |
H2'' |
109.4 |
237.3 |
| C4' |
C3' |
C2' |
O3' |
235.1 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
119.5 |
118.7 |
| C2' |
C3' |
C4' |
O4' |
8.6 |
336.2 |
| C2' |
C3' |
C4' |
C5' |
244.6 |
217.2 |
| C2' |
C3' |
C4' |
H4' |
125.6 |
94.9 |
| O3' |
C3' |
C2' |
H3' |
244.4 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
63.4 |
| H2' |
C2' |
C1' |
O4' |
129.3 |
265.3 |
| H2' |
C2' |
C1' |
H1' |
6.3 |
146.5 |
| C1' |
C2' |
H2' |
C3' |
237.5 |
114.7 |
| C1' |
C2' |
H2' |
H2'' |
118.8 |
237.3 |
| C3' |
C2' |
H2' |
H2'' |
241.3 |
122.7 |
| H2' |
C2' |
C3' |
C4' |
227.1 |
118.6 |
| H2' |
C2' |
C3' |
O3' |
352.0 |
237.3 |
| H2' |
C2' |
C3' |
H3' |
107.6 |
359.9 |
| H2'' |
C2' |
C1' |
O4' |
238.7 |
142.7 |
| H2'' |
C2' |
C1' |
H1' |
115.7 |
23.8 |
| C1' |
C2' |
H2'' |
C3' |
122.5 |
245.3 |
| C1' |
C2' |
H2'' |
H2' |
241.2 |
122.7 |
| C3' |
C2' |
H2'' |
H2' |
118.8 |
237.4 |
| H2'' |
C2' |
C3' |
C4' |
117.7 |
241.2 |
| H2'' |
C2' |
C3' |
O3' |
242.6 |
359.9 |
| H2'' |
C2' |
C3' |
H3' |
358.2 |
122.6 |
| C1' |
O4' |
C4' |
C3' |
353.4 |
40.3 |
| C4' |
C3' |
C2' |
H2' |
227.1 |
118.6 |
| C4' |
C3' |
C2' |
H2'' |
117.7 |
241.2 |
| C2' |
C3' |
C4' |
O3' |
122.1 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
237.6 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
115.5 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
298.7 |
178.2 |
| O4' |
C4' |
C3' |
C5' |
124.0 |
118.9 |
| O4' |
C4' |
C3' |
H4' |
243.0 |
241.3 |
| C5' |
C4' |
C3' |
H4' |
119.0 |
122.3 |
| C3' |
C4' |
C5' |
O5' |
198.2 |
176.9 |
| C3' |
C4' |
C5' |
H5' |
323.5 |
297.0 |
| C3' |
C4' |
C5' |
H5'' |
72.9 |
56.9 |
| O3' |
C3' |
C2' |
H2' |
352.0 |
237.3 |
| O3' |
C3' |
C2' |
H2'' |
242.6 |
359.9 |
| C2' |
C3' |
O3' |
C4' |
241.3 |
245.2 |
| C2' |
C3' |
O3' |
H3' |
122.2 |
122.7 |
| C4' |
C3' |
O3' |
H3' |
240.8 |
237.4 |
| O3' |
C3' |
C4' |
O4' |
246.5 |
217.5 |
| O3' |
C3' |
C4' |
C5' |
122.4 |
98.5 |
| O3' |
C3' |
C4' |
H4' |
3.5 |
336.2 |
| H3' |
C3' |
C2' |
H2' |
107.6 |
359.9 |
| H3' |
C3' |
C2' |
H2'' |
358.2 |
122.6 |
| C2' |
C3' |
H3' |
C4' |
116.7 |
114.8 |
| C2' |
C3' |
H3' |
O3' |
239.8 |
237.4 |
| C4' |
C3' |
H3' |
O3' |
123.1 |
122.6 |
| H3' |
C3' |
C4' |
O4' |
131.0 |
94.9 |
| H3' |
C3' |
C4' |
C5' |
7.0 |
336.0 |
| H3' |
C3' |
C4' |
H4' |
248.0 |
213.6 |
| H3' |
C3' |
O3' |
HO3' |
57.8 |
300.7 |
| C4' |
O4' |
C1' |
H1' |
122.6 |
78.5 |
| O4' |
C4' |
C3' |
O3' |
246.5 |
217.5 |
| O4' |
C4' |
C3' |
H3' |
131.0 |
94.9 |
| C3' |
C4' |
O4' |
C5' |
242.4 |
240.8 |
| C3' |
C4' |
O4' |
H4' |
123.5 |
118.7 |
| C5' |
C4' |
O4' |
H4' |
241.1 |
237.9 |
| O4' |
C4' |
C5' |
O5' |
78.6 |
61.4 |
| O4' |
C4' |
C5' |
H5' |
203.9 |
181.5 |
| O4' |
C4' |
C5' |
H5'' |
313.4 |
301.4 |
| C5' |
C4' |
C3' |
O3' |
122.4 |
98.5 |
| C5' |
C4' |
C3' |
H3' |
7.0 |
336.0 |
| C3' |
C4' |
C5' |
O4' |
119.6 |
115.5 |
| C3' |
C4' |
C5' |
H4' |
236.5 |
237.7 |
| O4' |
C4' |
C5' |
H4' |
117.0 |
122.2 |
| O5' |
C5' |
C4' |
H5' |
234.7 |
239.9 |
| O5' |
C5' |
C4' |
H5'' |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
P |
185.4 |
180.0 |
| H5' |
C5' |
C4' |
H5'' |
250.6 |
240.1 |
| H4' |
C4' |
C3' |
O3' |
3.5 |
336.2 |
| H4' |
C4' |
C3' |
H3' |
248.0 |
213.6 |
| C3' |
C4' |
H4' |
O4' |
240.8 |
244.8 |
| C3' |
C4' |
H4' |
C5' |
117.2 |
122.6 |
| O4' |
C4' |
H4' |
C5' |
236.4 |
237.9 |
| H4' |
C4' |
C5' |
O5' |
321.7 |
299.2 |
| H4' |
C4' |
C5' |
H5' |
87.0 |
59.3 |
| H4' |
C4' |
C5' |
H5'' |
196.4 |
179.2 |
| HO3' |
O3' |
C3' |
H3' |
57.8 |
300.7 |
| O5' |
C5' |
C4' |
H4' |
321.7 |
299.2 |
| C4' |
C5' |
O5' |
H5' |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
234.7 |
240.0 |
| H5' |
C5' |
O5' |
H5'' |
109.4 |
120.0 |
| C5' |
O5' |
P |
OP1 |
166.0 |
60.0 |
| C5' |
O5' |
P |
OP2 |
35.4 |
180.0 |
| C5' |
O5' |
P |
OP3 |
280.7 |
300.0 |
| H5' |
C5' |
C4' |
H4' |
87.0 |
59.3 |
| C4' |
C5' |
H5' |
O5' |
239.6 |
239.9 |
| C4' |
C5' |
H5' |
H5'' |
119.8 |
119.9 |
| O5' |
C5' |
H5' |
H5'' |
240.2 |
240.0 |
| H5' |
C5' |
O5' |
P |
60.1 |
60.0 |
| H5'' |
C5' |
C4' |
H4' |
196.4 |
179.2 |
| C4' |
C5' |
H5'' |
O5' |
120.4 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
240.2 |
240.1 |
| O5' |
C5' |
H5'' |
H5' |
119.8 |
120.0 |
| H5'' |
C5' |
O5' |
P |
310.6 |
300.0 |
| P |
O5' |
C5' |
H5' |
60.1 |
60.0 |
| P |
O5' |
C5' |
H5'' |
310.6 |
300.0 |
| OP1 |
P |
O5' |
OP2 |
130.6 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
245.3 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
114.6 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
180.0 |
180.0 |
| O5' |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
| O5' |
P |
OP1 |
OP2 |
235.2 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
110.7 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
235.6 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
57.7 |
300.0 |
| OP1 |
P |
OP3 |
HOP3 |
291.6 |
180.0 |
| O5' |
P |
OP2 |
OP1 |
122.3 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
247.7 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
125.4 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
63.2 |
60.0 |
| O5' |
P |
OP3 |
OP1 |
248.3 |
120.0 |
| O5' |
P |
OP3 |
OP2 |
116.8 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
228.5 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
292.3 |
60.0 |
| HOP2 |
OP2 |
P |
OP3 |
292.3 |
60.0 |