PDB Chemical Component C5P
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 C5P
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3P |
P |
1.584 |
1.610 |
| O3P |
HOP3 |
0.950 |
0.966 |
| P |
O1P |
1.445 |
1.480 |
| P |
O2P |
1.563 |
1.610 |
| P |
O5' |
1.614 |
1.610 |
| O2P |
HOP2 |
0.950 |
0.967 |
| O5' |
C5' |
1.392 |
1.429 |
| C5' |
C4' |
1.447 |
1.530 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C4' |
O4' |
1.428 |
1.445 |
| C4' |
C3' |
1.556 |
1.544 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.408 |
1.444 |
| C3' |
O3' |
1.450 |
1.429 |
| C3' |
C2' |
1.510 |
1.546 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C2' |
O2' |
1.412 |
1.429 |
| C2' |
C1' |
1.476 |
1.545 |
| C2' |
H2'1 |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| C1' |
N1 |
1.567 |
1.466 |
| C1' |
H1' |
1.100 |
1.090 |
| N1 |
C2 |
1.437 |
1.345 |
| N1 |
C6 |
1.432 |
1.362 |
| C2 |
N3 |
1.359 |
1.331 |
| C2 |
O2 |
1.251 |
1.220 |
| N3 |
C4 |
1.422 |
1.327 |
| C4 |
C5 |
1.429 |
1.410 |
| C4 |
N4 |
1.359 |
1.375 |
| C5 |
C6 |
1.394 |
1.355 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| N4 |
HN41 |
1.000 |
0.970 |
| N4 |
HN42 |
1.000 |
0.970 |
Bond Angles for C5P
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
O3P |
HOP3 |
109.5 |
106.8 |
| O3P |
P |
O1P |
112.7 |
109.5 |
| O3P |
P |
O2P |
115.3 |
109.5 |
| O3P |
P |
O5' |
104.5 |
109.5 |
| O1P |
P |
O2P |
117.1 |
109.5 |
| O1P |
P |
O5' |
105.9 |
109.4 |
| O2P |
P |
O5' |
99.0 |
109.4 |
| P |
O2P |
HOP2 |
109.5 |
106.8 |
| P |
O5' |
C5' |
122.0 |
106.8 |
| O5' |
C5' |
C4' |
105.7 |
109.5 |
| O5' |
C5' |
H5'1 |
110.7 |
109.5 |
| O5' |
C5' |
H5'2 |
111.5 |
109.5 |
| C4' |
C5' |
H5'1 |
110.8 |
109.4 |
| C4' |
C5' |
H5'2 |
111.6 |
109.4 |
| C5' |
C4' |
O4' |
125.5 |
110.4 |
| C5' |
C4' |
C3' |
117.3 |
110.5 |
| C5' |
C4' |
H4' |
86.2 |
110.3 |
| H5'1 |
C5' |
H5'2 |
106.6 |
109.5 |
| O4' |
C4' |
C3' |
106.6 |
104.8 |
| O4' |
C4' |
H4' |
103.1 |
110.4 |
| C4' |
O4' |
C1' |
109.2 |
105.3 |
| C3' |
C4' |
H4' |
115.6 |
110.4 |
| C4' |
C3' |
O3' |
120.7 |
110.5 |
| C4' |
C3' |
C2' |
103.7 |
104.1 |
| C4' |
C3' |
H3' |
113.0 |
110.5 |
| O4' |
C1' |
C2' |
109.3 |
104.9 |
| O4' |
C1' |
N1 |
90.4 |
110.4 |
| O4' |
C1' |
H1' |
121.4 |
110.4 |
| O3' |
C3' |
C2' |
122.9 |
110.5 |
| O3' |
C3' |
H3' |
85.1 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
106.8 |
| C2' |
C3' |
H3' |
109.9 |
110.6 |
| C3' |
C2' |
O2' |
97.3 |
110.5 |
| C3' |
C2' |
C1' |
106.9 |
104.0 |
| C3' |
C2' |
H2'1 |
113.1 |
110.5 |
| O2' |
C2' |
C1' |
89.1 |
110.7 |
| O2' |
C2' |
H2'1 |
126.9 |
110.5 |
| C2' |
O2' |
HO2' |
109.5 |
106.8 |
| C1' |
C2' |
H2'1 |
119.3 |
110.4 |
| C2' |
C1' |
N1 |
110.9 |
110.4 |
| C2' |
C1' |
H1' |
104.3 |
110.4 |
| N1 |
C1' |
H1' |
120.1 |
110.3 |
| C1' |
N1 |
C2 |
118.9 |
119.8 |
| C1' |
N1 |
C6 |
126.5 |
119.8 |
| C2 |
N1 |
C6 |
114.6 |
120.4 |
| N1 |
C2 |
N3 |
123.8 |
121.1 |
| N1 |
C2 |
O2 |
120.2 |
119.5 |
| N1 |
C6 |
C5 |
124.7 |
119.2 |
| N1 |
C6 |
H6 |
117.6 |
120.4 |
| N3 |
C2 |
O2 |
116.0 |
119.4 |
| C2 |
N3 |
C4 |
118.9 |
120.7 |
| N3 |
C4 |
C5 |
121.6 |
119.6 |
| N3 |
C4 |
N4 |
119.5 |
120.2 |
| C5 |
C4 |
N4 |
118.9 |
120.2 |
| C4 |
C5 |
C6 |
116.4 |
119.0 |
| C4 |
C5 |
H5 |
121.8 |
120.5 |
| C4 |
N4 |
HN41 |
108.4 |
120.1 |
| C4 |
N4 |
HN42 |
125.8 |
120.0 |
| C6 |
C5 |
H5 |
121.8 |
120.5 |
| C5 |
C6 |
H6 |
117.7 |
120.4 |
| HN41 |
N4 |
HN42 |
125.8 |
119.9 |
Torsion Angles for C5P
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O3P |
O2P |
138.0 |
240.0 |
| O1P |
P |
O3P |
O5' |
245.5 |
120.0 |
| O2P |
P |
O3P |
O5' |
107.5 |
240.0 |
| O3P |
P |
O2P |
HOP2 |
157.4 |
59.9 |
| O3P |
P |
O5' |
C5' |
182.5 |
175.0 |
| HOP3 |
O3P |
P |
O1P |
135.0 |
300.0 |
| HOP3 |
O3P |
P |
O2P |
357.0 |
60.1 |
| HOP3 |
O3P |
P |
O5' |
249.5 |
180.0 |
| O1P |
P |
O3P |
HOP3 |
135.0 |
300.0 |
| O3P |
P |
O1P |
O2P |
222.8 |
120.0 |
| O3P |
P |
O1P |
O5' |
113.7 |
240.0 |
| O2P |
P |
O1P |
O5' |
250.9 |
119.9 |
| O1P |
P |
O2P |
HOP2 |
21.3 |
180.0 |
| O1P |
P |
O5' |
C5' |
301.7 |
55.0 |
| O2P |
P |
O3P |
HOP3 |
357.0 |
60.1 |
| O3P |
P |
O2P |
O1P |
136.1 |
239.9 |
| O3P |
P |
O2P |
O5' |
249.2 |
120.0 |
| O1P |
P |
O2P |
O5' |
113.1 |
240.1 |
| O2P |
P |
O5' |
C5' |
63.4 |
295.0 |
| O5' |
P |
O3P |
HOP3 |
249.5 |
180.0 |
| O3P |
P |
O5' |
O1P |
240.8 |
120.0 |
| O3P |
P |
O5' |
O2P |
119.1 |
240.0 |
| O1P |
P |
O5' |
O2P |
238.4 |
120.0 |
| O5' |
P |
O2P |
HOP2 |
268.2 |
300.0 |
| P |
O5' |
C5' |
C4' |
178.5 |
180.0 |
| P |
O5' |
C5' |
H5'1 |
298.5 |
60.0 |
| P |
O5' |
C5' |
H5'2 |
57.0 |
300.0 |
| HOP2 |
O2P |
P |
O5' |
268.2 |
300.0 |
| C4' |
C5' |
O5' |
H5'1 |
240.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
121.4 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
288.6 |
66.4 |
| O5' |
C5' |
C4' |
C3' |
68.3 |
181.9 |
| O5' |
C5' |
C4' |
H4' |
185.2 |
304.2 |
| H5'1 |
C5' |
O5' |
H5'2 |
241.4 |
120.0 |
| O5' |
C5' |
C4' |
H5'1 |
120.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
238.6 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
118.6 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
220.2 |
244.6 |
| O4' |
C4' |
C5' |
H4' |
103.3 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
164.5 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
243.1 |
237.7 |
| C5' |
C4' |
C3' |
O3' |
55.4 |
98.3 |
| C5' |
C4' |
C3' |
C2' |
198.2 |
217.1 |
| C5' |
C4' |
C3' |
H3' |
317.1 |
335.8 |
| O5' |
C5' |
H5'1 |
C4' |
243.1 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
121.5 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
238.4 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
168.6 |
186.5 |
| H5'1 |
C5' |
C4' |
C3' |
308.3 |
301.9 |
| H5'1 |
C5' |
C4' |
H4' |
65.3 |
64.2 |
| O5' |
C5' |
H5'2 |
C4' |
118.0 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
239.0 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
121.0 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
50.0 |
306.4 |
| H5'2 |
C5' |
C4' |
C3' |
189.7 |
61.9 |
| H5'2 |
C5' |
C4' |
H4' |
306.6 |
184.2 |
| O4' |
C4' |
C5' |
H5'1 |
168.6 |
186.5 |
| O4' |
C4' |
C5' |
H5'2 |
50.0 |
306.4 |
| C5' |
C4' |
O4' |
C3' |
143.2 |
119.0 |
| C5' |
C4' |
O4' |
H4' |
265.3 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
122.1 |
118.8 |
| O4' |
C4' |
C3' |
O3' |
202.1 |
217.2 |
| O4' |
C4' |
C3' |
C2' |
344.9 |
335.9 |
| O4' |
C4' |
C3' |
H3' |
103.8 |
94.7 |
| C4' |
O4' |
C1' |
C2' |
340.9 |
319.5 |
| C4' |
O4' |
C1' |
N1 |
228.6 |
200.6 |
| C4' |
O4' |
C1' |
H1' |
102.3 |
78.4 |
| C3' |
C4' |
C5' |
H5'1 |
308.3 |
301.9 |
| C3' |
C4' |
C5' |
H5'2 |
189.7 |
61.9 |
| C5' |
C4' |
C3' |
O4' |
213.3 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
99.4 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
246.1 |
241.2 |
| C3' |
C4' |
O4' |
C1' |
21.3 |
40.5 |
| O3' |
C3' |
C4' |
C2' |
217.2 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
98.3 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
25.4 |
180.0 |
| C2' |
C3' |
C4' |
H3' |
241.1 |
241.3 |
| C4' |
C3' |
C2' |
O2' |
272.8 |
241.2 |
| C4' |
C3' |
C2' |
C1' |
4.1 |
0.1 |
| C4' |
C3' |
C2' |
H2'1 |
137.4 |
118.6 |
| H4' |
C4' |
C5' |
H5'1 |
65.3 |
64.2 |
| H4' |
C4' |
C5' |
H5'2 |
306.6 |
184.2 |
| C5' |
C4' |
H4' |
O4' |
125.6 |
122.2 |
| C5' |
C4' |
H4' |
C3' |
241.5 |
237.6 |
| O4' |
C4' |
H4' |
C3' |
115.9 |
115.4 |
| H4' |
C4' |
O4' |
C1' |
259.1 |
281.7 |
| H4' |
C4' |
C3' |
O3' |
316.0 |
336.1 |
| H4' |
C4' |
C3' |
C2' |
98.7 |
94.8 |
| H4' |
C4' |
C3' |
H3' |
217.6 |
213.5 |
| C1' |
O4' |
C4' |
C3' |
21.3 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
259.1 |
281.7 |
| C3' |
C2' |
C1' |
O4' |
8.6 |
23.9 |
| O2' |
C2' |
C1' |
O4' |
105.9 |
142.6 |
| O4' |
C1' |
C2' |
H2'1 |
238.7 |
265.3 |
| C2' |
C1' |
O4' |
N1 |
112.4 |
118.9 |
| C2' |
C1' |
O4' |
H1' |
238.6 |
241.1 |
| N1 |
C1' |
O4' |
H1' |
126.3 |
122.2 |
| O4' |
C1' |
N1 |
C2 |
228.9 |
52.0 |
| O4' |
C1' |
N1 |
C6 |
49.6 |
232.0 |
| O3' |
C3' |
C4' |
H4' |
316.0 |
336.1 |
| C4' |
C3' |
O3' |
C2' |
135.5 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
246.1 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
110.6 |
122.7 |
| O3' |
C3' |
C2' |
O2' |
54.5 |
359.9 |
| O3' |
C3' |
C2' |
C1' |
145.8 |
118.8 |
| O3' |
C3' |
C2' |
H2'1 |
279.1 |
237.3 |
| C2' |
C3' |
C4' |
H4' |
98.7 |
94.8 |
| C4' |
C3' |
C2' |
O3' |
218.3 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
121.0 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
8.6 |
23.9 |
| O3' |
C3' |
C2' |
H3' |
262.7 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
249.8 |
65.3 |
| O2' |
C2' |
C3' |
C1' |
268.8 |
241.1 |
| O2' |
C2' |
C3' |
H2'1 |
135.4 |
122.6 |
| C3' |
C2' |
O2' |
HO2' |
100.9 |
298.5 |
| C1' |
C2' |
C3' |
H2'1 |
226.7 |
241.5 |
| C3' |
C2' |
C1' |
N1 |
106.8 |
142.8 |
| C3' |
C2' |
C1' |
H1' |
237.3 |
265.0 |
| H3' |
C3' |
C4' |
H4' |
217.6 |
213.5 |
| C4' |
C3' |
H3' |
O3' |
121.4 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
244.7 |
245.3 |
| O3' |
C3' |
H3' |
C2' |
123.3 |
122.7 |
| H3' |
C3' |
O3' |
HO3' |
139.3 |
302.6 |
| H3' |
C3' |
C2' |
O2' |
151.8 |
122.6 |
| H3' |
C3' |
C2' |
C1' |
243.1 |
241.5 |
| H3' |
C3' |
C2' |
H2'1 |
16.4 |
360.0 |
| HO3' |
O3' |
C3' |
C2' |
249.8 |
65.3 |
| HO3' |
O3' |
C3' |
H3' |
139.3 |
302.6 |
| O4' |
C1' |
C2' |
O2' |
105.9 |
142.6 |
| O2' |
C2' |
C3' |
H3' |
151.8 |
122.6 |
| C3' |
C2' |
O2' |
C1' |
106.9 |
114.7 |
| C3' |
C2' |
O2' |
H2'1 |
233.8 |
237.4 |
| C1' |
C2' |
O2' |
H2'1 |
126.8 |
122.7 |
| O2' |
C2' |
C1' |
N1 |
204.1 |
261.5 |
| O2' |
C2' |
C1' |
H1' |
334.7 |
23.7 |
| O4' |
C1' |
C2' |
N1 |
261.9 |
241.1 |
| O4' |
C1' |
C2' |
H1' |
131.3 |
118.9 |
| C1' |
C2' |
C3' |
H3' |
243.1 |
241.5 |
| C3' |
C2' |
C1' |
O2' |
262.7 |
241.3 |
| C3' |
C2' |
C1' |
H2'1 |
129.9 |
118.6 |
| O2' |
C2' |
C1' |
H2'1 |
227.2 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
353.9 |
183.8 |
| N1 |
C1' |
C2' |
H1' |
229.4 |
237.8 |
| C2' |
C1' |
N1 |
C2 |
117.9 |
296.6 |
| C2' |
C1' |
N1 |
C6 |
298.6 |
116.5 |
| H2'1 |
C2' |
C3' |
H3' |
16.4 |
360.0 |
| C3' |
C2' |
H2'1 |
O2' |
119.5 |
122.7 |
| C3' |
C2' |
H2'1 |
C1' |
232.9 |
245.5 |
| O2' |
C2' |
H2'1 |
C1' |
113.4 |
122.8 |
| H2'1 |
C2' |
O2' |
HO2' |
227.1 |
61.2 |
| H2'1 |
C2' |
C1' |
N1 |
336.8 |
24.2 |
| H2'1 |
C2' |
C1' |
H1' |
107.4 |
146.4 |
| HO2' |
O2' |
C2' |
C1' |
353.9 |
183.8 |
| HO2' |
O2' |
C2' |
H2'1 |
227.1 |
61.2 |
| O4' |
C1' |
N1 |
C2' |
110.9 |
115.5 |
| O4' |
C1' |
N1 |
H1' |
232.7 |
237.7 |
| N1 |
C1' |
C2' |
H2'1 |
336.8 |
24.2 |
| C2' |
C1' |
N1 |
H1' |
121.7 |
122.2 |
| C2 |
N1 |
C1' |
C6 |
179.3 |
180.0 |
| C1' |
N1 |
C2 |
N3 |
180.2 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
359.6 |
359.9 |
| C1' |
N1 |
C6 |
C5 |
180.0 |
179.7 |
| C1' |
N1 |
C6 |
H6 |
0.0 |
360.0 |
| O4' |
C1' |
H1' |
C2' |
236.2 |
244.5 |
| O4' |
C1' |
H1' |
N1 |
111.3 |
122.3 |
| H1' |
C1' |
C2' |
H2'1 |
107.4 |
146.4 |
| C2' |
C1' |
H1' |
N1 |
235.1 |
237.8 |
| H1' |
C1' |
N1 |
C2 |
356.2 |
174.3 |
| H1' |
C1' |
N1 |
C6 |
176.9 |
354.3 |
| C2 |
N1 |
C1' |
H1' |
356.2 |
174.3 |
| C1' |
N1 |
C2 |
C6 |
180.6 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
0.7 |
359.7 |
| C2 |
N1 |
C6 |
H6 |
180.7 |
180.0 |
| N3 |
C2 |
N1 |
O2 |
180.6 |
180.1 |
| N1 |
C2 |
N3 |
C4 |
359.8 |
360.0 |
| C6 |
N1 |
C1' |
H1' |
176.9 |
354.3 |
| C1' |
N1 |
C6 |
C2 |
179.3 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
359.5 |
0.0 |
| C6 |
N1 |
C2 |
O2 |
178.9 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
359.8 |
0.5 |
| N1 |
C6 |
C5 |
H5 |
179.8 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.7 |
| N3 |
C2 |
N1 |
C6 |
359.5 |
0.0 |
| N1 |
C2 |
N3 |
O2 |
179.4 |
179.9 |
| C2 |
N3 |
C4 |
C5 |
0.7 |
0.2 |
| C2 |
N3 |
C4 |
N4 |
180.6 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
178.9 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
180.6 |
180.1 |
| O2 |
C2 |
N3 |
C4 |
180.4 |
180.1 |
| C4 |
N3 |
C2 |
O2 |
180.4 |
180.1 |
| C5 |
C4 |
N3 |
N4 |
180.2 |
180.3 |
| N3 |
C4 |
C5 |
C6 |
359.5 |
359.5 |
| N3 |
C4 |
C5 |
H5 |
179.5 |
180.0 |
| N3 |
C4 |
N4 |
HN41 |
0.1 |
360.0 |
| N3 |
C4 |
N4 |
HN42 |
180.1 |
179.7 |
| N1 |
C6 |
C5 |
C4 |
359.8 |
0.5 |
| N3 |
C4 |
C5 |
N4 |
179.8 |
179.7 |
| C5 |
C4 |
N4 |
HN41 |
179.9 |
179.7 |
| C5 |
C4 |
N4 |
HN42 |
359.9 |
359.5 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.5 |
| C4 |
C5 |
C6 |
H6 |
179.8 |
180.3 |
| N3 |
C4 |
N4 |
C5 |
180.2 |
180.3 |
| N4 |
C4 |
C5 |
C6 |
179.6 |
179.7 |
| N4 |
C4 |
C5 |
H5 |
359.6 |
0.2 |
| HN41 |
N4 |
C4 |
HN42 |
180.0 |
180.2 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.3 |
| C6 |
C5 |
C4 |
N4 |
179.6 |
179.7 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.5 |
| H5 |
C5 |
C4 |
N4 |
359.6 |
0.2 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.5 |
| H5 |
C5 |
C6 |
H6 |
359.8 |
359.8 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.7 |
| H6 |
C6 |
C5 |
H5 |
359.8 |
359.8 |
| C4 |
N4 |
HN41 |
HN42 |
180.0 |
179.8 |
| C4 |
N4 |
HN42 |
HN41 |
180.0 |
180.2 |