PDB Chemical Component P4U
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 P4U
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.496 |
1.610 |
| O3' |
C3' |
1.406 |
1.429 |
| C5' |
O5' |
1.406 |
1.429 |
| C5' |
C4' |
1.498 |
1.530 |
| O5' |
P |
1.585 |
1.610 |
| C4' |
C3' |
1.506 |
1.540 |
| C4' |
O4' |
1.448 |
1.439 |
| P |
OP1 |
1.495 |
1.481 |
| C3' |
C2' |
1.515 |
1.549 |
| O2' |
C2' |
1.417 |
1.429 |
| O4' |
C1' |
1.412 |
1.444 |
| C2' |
C1' |
1.530 |
1.550 |
| C1' |
N1 |
1.475 |
1.465 |
| N1 |
C6 |
1.327 |
1.362 |
| N1 |
C2 |
1.399 |
1.345 |
| C6 |
C5 |
1.368 |
1.356 |
| C5 |
C4 |
1.364 |
1.408 |
| C2 |
O2 |
1.243 |
1.220 |
| C2 |
N3 |
1.338 |
1.333 |
| C4 |
N3 |
1.337 |
1.324 |
| C4 |
O4 |
1.369 |
1.351 |
| C41 |
O4 |
1.429 |
1.428 |
| C41 |
C42 |
1.517 |
1.530 |
| C42 |
C43 |
1.505 |
1.530 |
| C1' |
H1 |
1.100 |
1.090 |
| C2' |
H2 |
1.100 |
1.089 |
| C3' |
H3 |
1.100 |
1.090 |
| C4' |
H4 |
1.100 |
1.090 |
| C5 |
H5 |
1.080 |
1.080 |
| C5' |
H6 |
1.101 |
1.090 |
| C5' |
H7 |
1.100 |
1.090 |
| C6 |
H8 |
1.080 |
1.080 |
| O2' |
H9 |
0.950 |
0.966 |
| O3' |
H10 |
0.950 |
0.966 |
| OP2 |
H12 |
0.950 |
0.967 |
| C41 |
H13 |
1.100 |
1.090 |
| C41 |
H14 |
1.100 |
1.090 |
| C42 |
H15 |
1.100 |
1.090 |
| C42 |
H16 |
1.100 |
1.090 |
| C43 |
H17 |
1.100 |
1.090 |
| C43 |
H18 |
1.101 |
1.090 |
| C43 |
H19 |
1.100 |
1.090 |
| P |
OP3 |
1.596 |
1.610 |
| OP3 |
H11 |
0.950 |
0.967 |
Bond Angles for P4U
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP2 |
108.7 |
109.5 |
| P |
OP2 |
H12 |
109.5 |
113.9 |
| OP2 |
P |
OP3 |
108.8 |
109.5 |
| O3' |
C3' |
H3 |
109.6 |
110.4 |
| C5' |
O5' |
P |
121.5 |
123.0 |
| O5' |
C5' |
H6 |
109.0 |
109.5 |
| O5' |
C5' |
H7 |
109.0 |
109.5 |
| C5' |
C4' |
O4' |
110.3 |
110.0 |
| C5' |
C4' |
H4 |
109.4 |
109.9 |
| O5' |
P |
OP1 |
110.7 |
109.4 |
| O5' |
P |
OP3 |
102.5 |
109.5 |
| C4' |
C3' |
H3 |
108.2 |
110.5 |
| O4' |
C4' |
H4 |
110.0 |
109.7 |
| C3' |
C2' |
H2 |
111.4 |
110.9 |
| O2' |
C2' |
H2 |
113.0 |
110.8 |
| O4' |
C1' |
H1 |
110.8 |
110.6 |
| C2' |
C1' |
N1 |
111.0 |
110.6 |
| C2' |
C1' |
H1 |
109.2 |
110.6 |
| C1' |
N1 |
C6 |
120.1 |
119.8 |
| C1' |
N1 |
C2 |
121.3 |
119.9 |
| N1 |
C1' |
H1 |
109.9 |
110.6 |
| N1 |
C6 |
H8 |
119.3 |
120.4 |
| N1 |
C2 |
O2 |
122.2 |
119.5 |
| N1 |
C2 |
N3 |
119.7 |
121.0 |
| C6 |
C5 |
H5 |
120.3 |
120.5 |
| C5 |
C4 |
N3 |
119.7 |
119.6 |
| C5 |
C4 |
O4 |
119.1 |
120.2 |
| N3 |
C2 |
O2 |
118.1 |
119.5 |
| C2 |
N3 |
C4 |
121.3 |
120.8 |
| N3 |
C4 |
O4 |
121.2 |
120.2 |
| C41 |
C42 |
C43 |
110.6 |
109.5 |
| C42 |
C41 |
H13 |
109.1 |
109.4 |
| C42 |
C41 |
H14 |
109.1 |
109.4 |
| C41 |
C42 |
H15 |
109.2 |
109.4 |
| C41 |
C42 |
H16 |
109.2 |
109.5 |
| C43 |
C42 |
H15 |
109.2 |
109.5 |
| C43 |
C42 |
H16 |
109.2 |
109.5 |
| C42 |
C43 |
H17 |
109.5 |
109.5 |
| C42 |
C43 |
H18 |
109.5 |
109.5 |
| C42 |
C43 |
H19 |
109.4 |
109.5 |
| H6 |
C5' |
H7 |
109.5 |
109.5 |
| H13 |
C41 |
H14 |
109.5 |
109.5 |
| H15 |
C42 |
H16 |
109.5 |
109.4 |
| H17 |
C43 |
H18 |
109.5 |
109.5 |
| H17 |
C43 |
H19 |
109.5 |
109.5 |
| H18 |
C43 |
H19 |
109.5 |
109.4 |
| P |
OP3 |
H11 |
109.5 |
114.0 |
Torsion Angles for P4U
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
P |
OP2 |
299.1 |
64.9 |
| O5' |
P |
OP2 |
OP1 |
127.6 |
240.1 |
| O5' |
P |
OP2 |
OP3 |
249.1 |
120.1 |
| OP2 |
P |
OP3 |
H11 |
128.9 |
300.0 |
| C4' |
C3' |
O3' |
H3 |
238.8 |
237.3 |
| O3' |
C3' |
C2' |
H2 |
280.7 |
216.1 |
| O5' |
C5' |
C4' |
O4' |
17.5 |
67.0 |
| O5' |
C5' |
C4' |
H4 |
256.4 |
306.1 |
| C5' |
O5' |
P |
OP1 |
71.2 |
305.0 |
| C5' |
O5' |
P |
OP3 |
184.0 |
185.0 |
| H6 |
C5' |
O5' |
H7 |
240.6 |
120.1 |
| C5' |
C4' |
C3' |
H3 |
313.4 |
357.2 |
| O4' |
C4' |
C5' |
H4 |
121.1 |
120.9 |
| O5' |
P |
OP2 |
H12 |
127.7 |
60.0 |
| OP2 |
P |
O5' |
OP3 |
115.1 |
239.9 |
| P |
O5' |
C5' |
H6 |
342.4 |
60.1 |
| P |
O5' |
C5' |
H7 |
101.8 |
300.0 |
| O5' |
P |
OP3 |
H11 |
243.9 |
179.9 |
| O3' |
C3' |
C4' |
H3 |
122.0 |
122.6 |
| C4' |
C3' |
C2' |
H2 |
157.2 |
97.3 |
| C5' |
C4' |
O4' |
H4 |
239.3 |
239.0 |
| O4' |
C4' |
C3' |
H3 |
73.2 |
116.8 |
| C4' |
O4' |
C1' |
H1 |
118.5 |
78.8 |
| O5' |
P |
OP1 |
OP2 |
233.3 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
110.5 |
240.0 |
| O2' |
C2' |
C3' |
H2 |
127.1 |
123.7 |
| C3' |
C2' |
C1' |
N1 |
94.1 |
155.5 |
| C3' |
C2' |
C1' |
H1 |
215.4 |
278.4 |
| C3' |
C2' |
O2' |
H2 |
233.8 |
236.3 |
| O2' |
C2' |
C1' |
H1 |
332.3 |
36.6 |
| C2' |
C1' |
O4' |
H1 |
241.0 |
241.4 |
| N1 |
C1' |
O4' |
H1 |
121.0 |
122.8 |
| O4' |
C1' |
C2' |
H1 |
120.1 |
118.5 |
| C2' |
C1' |
N1 |
C6 |
254.2 |
117.2 |
| C2' |
C1' |
N1 |
C2 |
72.4 |
297.2 |
| N1 |
C1' |
C2' |
H1 |
238.7 |
237.1 |
| O4' |
C1' |
N1 |
H1 |
238.4 |
237.2 |
| C2' |
C1' |
N1 |
H1 |
120.8 |
122.9 |
| C1' |
N1 |
C6 |
H8 |
358.2 |
359.8 |
| C1' |
N1 |
C2 |
O2 |
2.1 |
0.0 |
| C1' |
N1 |
C2 |
N3 |
181.1 |
180.3 |
| C1' |
N1 |
C6 |
C2 |
178.3 |
180.0 |
| C6 |
N1 |
C1' |
H1 |
133.3 |
354.3 |
| C6 |
N1 |
C2 |
O2 |
180.4 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
359.4 |
0.3 |
| N1 |
C6 |
C5 |
H5 |
180.4 |
180.0 |
| C1' |
N1 |
C2 |
C6 |
181.7 |
180.0 |
| C2 |
N1 |
C1' |
H1 |
311.6 |
174.3 |
| N3 |
C2 |
N1 |
O2 |
179.0 |
180.2 |
| N1 |
C2 |
N3 |
C4 |
1.0 |
359.8 |
| C1' |
N1 |
C6 |
C5 |
178.2 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
0.0 |
0.2 |
| C6 |
C5 |
C4 |
O4 |
179.0 |
180.2 |
| C2 |
N3 |
C4 |
C5 |
359.3 |
0.0 |
| N3 |
C4 |
C5 |
O4 |
181.0 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
179.0 |
180.2 |
| O2 |
C2 |
N3 |
C4 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
181.0 |
179.8 |
| C5 |
C4 |
N3 |
C2 |
359.3 |
0.0 |
| C2 |
N3 |
C4 |
O4 |
180.3 |
180.0 |
| C5 |
C4 |
N3 |
O4 |
179.0 |
180.0 |
| C4 |
N3 |
C2 |
O2 |
180.0 |
180.0 |
| C5 |
C4 |
O4 |
N3 |
181.0 |
180.0 |
| C43 |
C42 |
C41 |
H15 |
239.9 |
240.0 |
| C43 |
C42 |
C41 |
H16 |
120.2 |
120.0 |
| C41 |
C42 |
C43 |
H17 |
180.0 |
300.0 |
| C41 |
C42 |
C43 |
H18 |
300.0 |
60.0 |
| C41 |
C42 |
C43 |
H19 |
60.0 |
179.9 |
| H13 |
C41 |
C42 |
H14 |
119.6 |
120.0 |
| H15 |
C42 |
C41 |
H16 |
240.3 |
240.0 |
| C43 |
C42 |
C41 |
H13 |
287.4 |
60.0 |
| C43 |
C42 |
C41 |
H14 |
167.8 |
300.0 |
| C41 |
C42 |
C43 |
H15 |
120.1 |
120.0 |
| C41 |
C42 |
C43 |
H16 |
239.8 |
240.0 |
| H15 |
C42 |
C43 |
H16 |
119.7 |
120.0 |
| H17 |
C43 |
C42 |
H18 |
240.0 |
239.9 |
| H17 |
C43 |
C42 |
H19 |
120.0 |
120.0 |
| H18 |
C43 |
C42 |
H19 |
240.0 |
240.1 |
| C2' |
C1' |
H1 |
N1 |
238.1 |
237.1 |
| H1 |
C1' |
N1 |
C6 |
133.3 |
354.3 |
| H1 |
C1' |
N1 |
C2 |
311.6 |
174.3 |
| H2 |
C2' |
C1' |
N1 |
335.9 |
37.4 |
| H2 |
C2' |
C1' |
H1 |
97.2 |
160.2 |
| H3 |
C3' |
C2' |
H2 |
43.4 |
338.5 |
| C5' |
C4' |
H4 |
O4' |
121.3 |
121.0 |
| H4 |
C4' |
C3' |
H3 |
190.2 |
236.1 |
| H5 |
C5 |
C4 |
N3 |
180.0 |
180.0 |
| H5 |
C5 |
C4 |
O4 |
359.0 |
0.0 |
| H6 |
C5' |
O5' |
P |
342.4 |
60.1 |
| O5' |
C5' |
H6 |
H7 |
119.1 |
239.9 |
| H6 |
C5' |
C4' |
O4' |
257.2 |
187.0 |
| H6 |
C5' |
C4' |
H4 |
136.1 |
66.1 |
| H7 |
C5' |
O5' |
P |
101.8 |
300.0 |
| O5' |
C5' |
H7 |
H6 |
240.9 |
120.1 |
| H7 |
C5' |
C4' |
O4' |
137.8 |
307.0 |
| H7 |
C5' |
C4' |
H4 |
16.7 |
186.0 |
| H8 |
C6 |
C5 |
H5 |
0.4 |
0.1 |
| H9 |
O2' |
C2' |
H2 |
306.3 |
56.4 |
| H10 |
O3' |
C3' |
H3 |
301.2 |
299.0 |
| H12 |
OP2 |
P |
OP3 |
238.6 |
300.0 |
| H13 |
C41 |
C42 |
C43 |
287.4 |
60.0 |
| C42 |
C41 |
H13 |
H14 |
240.7 |
240.0 |
| H13 |
C41 |
C42 |
H15 |
47.5 |
180.0 |
| H13 |
C41 |
C42 |
H16 |
167.2 |
300.0 |
| H14 |
C41 |
C42 |
C43 |
167.8 |
300.0 |
| C42 |
C41 |
H14 |
H13 |
119.3 |
120.0 |
| H14 |
C41 |
C42 |
H15 |
287.9 |
60.0 |
| H14 |
C41 |
C42 |
H16 |
47.6 |
180.0 |
| C41 |
C42 |
H15 |
C43 |
239.0 |
240.0 |
| H15 |
C42 |
C41 |
H13 |
47.5 |
180.0 |
| H15 |
C42 |
C41 |
H14 |
287.9 |
60.0 |
| C41 |
C42 |
H15 |
H16 |
119.5 |
120.0 |
| C43 |
C42 |
H15 |
H16 |
240.5 |
240.0 |
| H15 |
C42 |
C43 |
H17 |
59.8 |
180.0 |
| H15 |
C42 |
C43 |
H18 |
179.9 |
300.1 |
| H15 |
C42 |
C43 |
H19 |
299.8 |
60.0 |
| C41 |
C42 |
H16 |
C43 |
121.0 |
120.0 |
| H16 |
C42 |
C41 |
H13 |
167.2 |
300.0 |
| H16 |
C42 |
C41 |
H14 |
47.6 |
180.0 |
| C41 |
C42 |
H16 |
H15 |
240.5 |
240.0 |
| C43 |
C42 |
H16 |
H15 |
119.5 |
120.0 |
| H16 |
C42 |
C43 |
H17 |
300.2 |
60.0 |
| H16 |
C42 |
C43 |
H18 |
60.2 |
180.1 |
| H16 |
C42 |
C43 |
H19 |
180.2 |
300.0 |
| H17 |
C43 |
C42 |
H15 |
59.8 |
180.0 |
| H17 |
C43 |
C42 |
H16 |
300.2 |
60.0 |
| C42 |
C43 |
H17 |
H18 |
120.0 |
120.0 |
| C42 |
C43 |
H17 |
H19 |
240.0 |
240.0 |
| H18 |
C43 |
H17 |
H19 |
120.0 |
120.0 |
| H18 |
C43 |
C42 |
H15 |
179.9 |
300.1 |
| H18 |
C43 |
C42 |
H16 |
60.2 |
180.1 |
| C42 |
C43 |
H18 |
H17 |
239.9 |
240.0 |
| C42 |
C43 |
H18 |
H19 |
120.0 |
119.9 |
| H17 |
C43 |
H18 |
H19 |
240.0 |
240.0 |
| H19 |
C43 |
C42 |
H15 |
299.8 |
60.0 |
| H19 |
C43 |
C42 |
H16 |
180.2 |
300.0 |
| C42 |
C43 |
H19 |
H17 |
120.1 |
120.0 |
| C42 |
C43 |
H19 |
H18 |
240.0 |
240.1 |
| H17 |
C43 |
H19 |
H18 |
120.0 |
120.0 |
| O5' |
P |
OP3 |
OP2 |
115.0 |
239.9 |
| OP3 |
P |
OP2 |
H12 |
238.6 |
300.0 |
| O5' |
P |
OP3 |
OP1 |
243.9 |
120.0 |