PDB Chemical Component C3P
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 C3P
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O1P |
1.490 |
1.480 |
| P |
O2P |
1.508 |
1.609 |
| P |
O3P |
1.490 |
1.610 |
| P |
O3' |
1.609 |
1.609 |
| O2P |
HOP2 |
0.950 |
0.966 |
| O3P |
HOP3 |
0.950 |
0.967 |
| O5' |
C5' |
1.419 |
1.429 |
| O5' |
HO5' |
0.950 |
0.965 |
| C5' |
C4' |
1.550 |
1.530 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.090 |
| C4' |
O4' |
1.468 |
1.443 |
| C4' |
C3' |
1.499 |
1.544 |
| C4' |
H4' |
1.115 |
1.089 |
| O4' |
C1' |
1.416 |
1.444 |
| C3' |
O3' |
1.387 |
1.428 |
| C3' |
C2' |
1.526 |
1.546 |
| C3' |
H3' |
1.115 |
1.089 |
| C2' |
O2' |
1.443 |
1.430 |
| C2' |
C1' |
1.496 |
1.544 |
| C2' |
H2'1 |
1.115 |
1.089 |
| O2' |
HO2' |
0.951 |
0.966 |
| C1' |
N1 |
1.435 |
1.466 |
| C1' |
H1' |
1.115 |
1.090 |
| N1 |
C2 |
1.337 |
1.345 |
| N1 |
C6 |
1.363 |
1.362 |
| C2 |
N3 |
1.343 |
1.332 |
| C2 |
O2 |
1.210 |
1.219 |
| N3 |
C4 |
1.331 |
1.327 |
| C4 |
C5 |
1.395 |
1.409 |
| C4 |
N4 |
1.325 |
1.376 |
| C5 |
C6 |
1.312 |
1.355 |
| C5 |
H5 |
1.102 |
1.080 |
| C6 |
H6 |
1.102 |
1.079 |
| N4 |
HN41 |
1.019 |
0.970 |
| N4 |
HN42 |
1.020 |
0.970 |
Bond Angles for C3P
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O2P |
108.2 |
109.5 |
| O1P |
P |
O3P |
117.3 |
109.4 |
| O1P |
P |
O3' |
108.2 |
109.5 |
| O2P |
P |
O3P |
111.5 |
109.5 |
| O2P |
P |
O3' |
106.8 |
109.6 |
| P |
O2P |
HOP2 |
108.2 |
106.8 |
| O3P |
P |
O3' |
104.3 |
109.5 |
| P |
O3P |
HOP3 |
117.3 |
106.7 |
| P |
O3' |
C3' |
123.0 |
106.9 |
| C5' |
O5' |
HO5' |
108.6 |
106.9 |
| O5' |
C5' |
C4' |
108.7 |
109.6 |
| O5' |
C5' |
H5'1 |
112.5 |
109.5 |
| O5' |
C5' |
H5'2 |
112.5 |
109.4 |
| C4' |
C5' |
H5'1 |
112.5 |
109.5 |
| C4' |
C5' |
H5'2 |
112.5 |
109.4 |
| C5' |
C4' |
O4' |
120.8 |
110.3 |
| C5' |
C4' |
C3' |
114.4 |
110.5 |
| C5' |
C4' |
H4' |
95.4 |
110.3 |
| H5'1 |
C5' |
H5'2 |
97.9 |
109.5 |
| O4' |
C4' |
C3' |
104.8 |
104.8 |
| O4' |
C4' |
H4' |
106.9 |
110.4 |
| C4' |
O4' |
C1' |
112.0 |
105.2 |
| C3' |
C4' |
H4' |
114.5 |
110.4 |
| C4' |
C3' |
O3' |
115.5 |
110.5 |
| C4' |
C3' |
C2' |
105.4 |
104.1 |
| C4' |
C3' |
H3' |
110.0 |
110.5 |
| O4' |
C1' |
C2' |
105.4 |
104.9 |
| O4' |
C1' |
N1 |
108.3 |
110.3 |
| O4' |
C1' |
H1' |
116.4 |
110.4 |
| O3' |
C3' |
C2' |
114.1 |
110.6 |
| O3' |
C3' |
H3' |
100.4 |
110.4 |
| C2' |
C3' |
H3' |
111.4 |
110.6 |
| C3' |
C2' |
O2' |
112.5 |
110.5 |
| C3' |
C2' |
C1' |
104.3 |
104.0 |
| C3' |
C2' |
H2'1 |
124.8 |
110.5 |
| O2' |
C2' |
C1' |
131.3 |
110.7 |
| O2' |
C2' |
H2'1 |
86.2 |
110.4 |
| C2' |
O2' |
HO2' |
112.6 |
106.8 |
| C1' |
C2' |
H2'1 |
98.3 |
110.5 |
| C2' |
C1' |
N1 |
118.3 |
110.4 |
| C2' |
C1' |
H1' |
106.0 |
110.4 |
| N1 |
C1' |
H1' |
102.9 |
110.3 |
| C1' |
N1 |
C2 |
117.8 |
119.8 |
| C1' |
N1 |
C6 |
120.8 |
119.8 |
| C2 |
N1 |
C6 |
121.3 |
120.4 |
| N1 |
C2 |
N3 |
118.5 |
121.0 |
| N1 |
C2 |
O2 |
117.7 |
119.5 |
| N1 |
C6 |
C5 |
120.4 |
119.3 |
| N1 |
C6 |
H6 |
121.8 |
120.4 |
| N3 |
C2 |
O2 |
123.8 |
119.5 |
| C2 |
N3 |
C4 |
121.2 |
120.7 |
| N3 |
C4 |
C5 |
119.8 |
119.6 |
| N3 |
C4 |
N4 |
124.5 |
120.2 |
| C5 |
C4 |
N4 |
115.7 |
120.2 |
| C4 |
C5 |
C6 |
118.7 |
119.0 |
| C4 |
C5 |
H5 |
123.6 |
120.5 |
| C4 |
N4 |
HN41 |
124.5 |
120.0 |
| C4 |
N4 |
HN42 |
106.9 |
120.0 |
| C6 |
C5 |
H5 |
117.7 |
120.5 |
| C5 |
C6 |
H6 |
117.9 |
120.3 |
| HN41 |
N4 |
HN42 |
107.0 |
120.0 |
Torsion Angles for C3P
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2P |
P |
O1P |
O3P |
232.8 |
119.9 |
| O2P |
P |
O1P |
O3' |
115.3 |
239.9 |
| O1P |
P |
O2P |
HOP2 |
180.0 |
300.1 |
| O3P |
P |
O1P |
O3' |
242.5 |
120.0 |
| O1P |
P |
O3P |
HOP3 |
180.0 |
180.0 |
| O1P |
P |
O3' |
C3' |
49.2 |
60.0 |
| O1P |
P |
O2P |
O3P |
130.4 |
240.1 |
| O1P |
P |
O2P |
O3' |
243.8 |
120.0 |
| O3P |
P |
O2P |
O3' |
113.4 |
240.0 |
| O2P |
P |
O3P |
HOP3 |
305.6 |
60.0 |
| O2P |
P |
O3' |
C3' |
292.9 |
180.0 |
| O1P |
P |
O3P |
O2P |
234.5 |
120.0 |
| O1P |
P |
O3P |
O3' |
119.6 |
240.0 |
| O2P |
P |
O3P |
O3' |
245.1 |
120.1 |
| O3P |
P |
O2P |
HOP2 |
49.6 |
60.0 |
| O3P |
P |
O3' |
C3' |
174.7 |
300.1 |
| O1P |
P |
O3' |
O2P |
116.3 |
240.0 |
| O1P |
P |
O3' |
O3P |
234.4 |
119.9 |
| O2P |
P |
O3' |
O3P |
118.2 |
240.0 |
| O3' |
P |
O2P |
HOP2 |
296.2 |
180.0 |
| O3' |
P |
O3P |
HOP3 |
60.4 |
299.9 |
| C4' |
C3' |
O3' |
P |
195.3 |
238.5 |
| P |
O3' |
C3' |
C2' |
72.9 |
123.9 |
| P |
O3' |
C3' |
H3' |
313.6 |
1.1 |
| HOP2 |
O2P |
P |
O3P |
49.6 |
60.0 |
| HOP2 |
O2P |
P |
O3' |
296.2 |
180.0 |
| HOP3 |
O3P |
P |
O3' |
60.4 |
299.9 |
| C4' |
C5' |
O5' |
H5'1 |
234.7 |
120.1 |
| C4' |
C5' |
O5' |
H5'2 |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
84.6 |
61.4 |
| O5' |
C5' |
C4' |
C3' |
211.3 |
176.8 |
| O5' |
C5' |
C4' |
H4' |
331.3 |
299.2 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.5 |
120.0 |
| HO5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| HO5' |
O5' |
C5' |
H5'1 |
305.2 |
59.9 |
| HO5' |
O5' |
C5' |
H5'2 |
54.7 |
300.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.3 |
239.9 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.4 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
233.3 |
244.5 |
| O4' |
C4' |
C5' |
H4' |
113.3 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
129.6 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
240.0 |
237.7 |
| C5' |
C4' |
C3' |
O3' |
82.5 |
98.3 |
| C5' |
C4' |
C3' |
C2' |
209.4 |
217.1 |
| C5' |
C4' |
C3' |
H3' |
329.7 |
335.8 |
| H5'1 |
C5' |
O5' |
HO5' |
305.2 |
59.9 |
| O5' |
C5' |
H5'1 |
C4' |
236.9 |
120.1 |
| O5' |
C5' |
H5'1 |
H5'2 |
118.5 |
240.1 |
| C4' |
C5' |
H5'1 |
H5'2 |
241.6 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
319.3 |
181.5 |
| H5'1 |
C5' |
C4' |
C3' |
86.1 |
296.9 |
| H5'1 |
C5' |
C4' |
H4' |
206.0 |
59.3 |
| H5'2 |
C5' |
O5' |
HO5' |
54.7 |
300.0 |
| O5' |
C5' |
H5'2 |
C4' |
123.1 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
241.5 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
118.4 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
209.9 |
301.4 |
| H5'2 |
C5' |
C4' |
C3' |
336.6 |
56.9 |
| H5'2 |
C5' |
C4' |
H4' |
96.6 |
179.2 |
| O4' |
C4' |
C5' |
H5'1 |
319.3 |
181.5 |
| O4' |
C4' |
C5' |
H5'2 |
209.9 |
301.4 |
| C5' |
C4' |
O4' |
C3' |
131.0 |
119.0 |
| C5' |
C4' |
O4' |
H4' |
252.8 |
237.9 |
| C3' |
C4' |
O4' |
H4' |
121.9 |
118.9 |
| O4' |
C4' |
C3' |
O3' |
217.0 |
217.2 |
| O4' |
C4' |
C3' |
C2' |
344.0 |
335.9 |
| O4' |
C4' |
C3' |
H3' |
104.3 |
94.6 |
| C4' |
O4' |
C1' |
C2' |
18.5 |
319.5 |
| C4' |
O4' |
C1' |
N1 |
250.9 |
200.6 |
| C4' |
O4' |
C1' |
H1' |
135.6 |
78.5 |
| P |
O3' |
C3' |
C4' |
195.3 |
238.5 |
| C3' |
C4' |
C5' |
H5'1 |
86.1 |
296.9 |
| C3' |
C4' |
C5' |
H5'2 |
336.6 |
56.9 |
| C5' |
C4' |
C3' |
O4' |
225.4 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
108.6 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
243.2 |
241.1 |
| C3' |
C4' |
O4' |
C1' |
358.7 |
40.5 |
| O3' |
C3' |
C4' |
C2' |
233.0 |
241.2 |
| O3' |
C3' |
C4' |
H3' |
112.8 |
122.5 |
| C2' |
C3' |
C4' |
H3' |
239.7 |
241.3 |
| C4' |
C3' |
C2' |
O2' |
239.4 |
241.2 |
| C4' |
C3' |
C2' |
C1' |
26.8 |
0.1 |
| C4' |
C3' |
C2' |
H2'1 |
137.8 |
118.7 |
| H4' |
C4' |
C5' |
H5'1 |
206.0 |
59.3 |
| H4' |
C4' |
C5' |
H5'2 |
96.6 |
179.2 |
| C5' |
C4' |
H4' |
O4' |
124.5 |
122.2 |
| C5' |
C4' |
H4' |
C3' |
240.1 |
237.6 |
| O4' |
C4' |
H4' |
C3' |
115.6 |
115.4 |
| H4' |
C4' |
O4' |
C1' |
236.8 |
281.7 |
| H4' |
C4' |
C3' |
O3' |
333.8 |
336.0 |
| H4' |
C4' |
C3' |
C2' |
100.8 |
94.8 |
| H4' |
C4' |
C3' |
H3' |
221.0 |
213.5 |
| C1' |
O4' |
C4' |
C3' |
358.7 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
236.8 |
281.7 |
| C3' |
C2' |
C1' |
O4' |
332.5 |
23.9 |
| O2' |
C2' |
C1' |
O4' |
111.1 |
142.6 |
| O4' |
C1' |
C2' |
H2'1 |
203.3 |
265.3 |
| C2' |
C1' |
O4' |
N1 |
127.5 |
118.9 |
| C2' |
C1' |
O4' |
H1' |
242.9 |
241.0 |
| N1 |
C1' |
O4' |
H1' |
115.3 |
122.2 |
| O4' |
C1' |
N1 |
C2 |
193.9 |
57.1 |
| O4' |
C1' |
N1 |
C6 |
9.8 |
237.0 |
| O3' |
C3' |
C4' |
H4' |
333.8 |
336.0 |
| C4' |
C3' |
O3' |
C2' |
122.4 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
241.7 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
119.3 |
122.7 |
| O3' |
C3' |
C2' |
O2' |
7.2 |
359.9 |
| O3' |
C3' |
C2' |
C1' |
154.6 |
118.7 |
| O3' |
C3' |
C2' |
H2'1 |
265.6 |
237.4 |
| C2' |
C3' |
C4' |
H4' |
100.8 |
94.8 |
| C4' |
C3' |
C2' |
O3' |
232.2 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
119.3 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
332.5 |
23.9 |
| O3' |
C3' |
C2' |
H3' |
247.1 |
237.3 |
| O2' |
C2' |
C3' |
C1' |
212.5 |
241.1 |
| O2' |
C2' |
C3' |
H2'1 |
101.5 |
122.5 |
| C3' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| C1' |
C2' |
C3' |
H2'1 |
249.0 |
241.4 |
| C3' |
C2' |
C1' |
N1 |
93.7 |
142.7 |
| C3' |
C2' |
C1' |
H1' |
208.5 |
265.0 |
| H3' |
C3' |
C4' |
H4' |
221.0 |
213.5 |
| C4' |
C3' |
H3' |
O3' |
122.2 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
243.4 |
245.3 |
| O3' |
C3' |
H3' |
C2' |
121.2 |
122.8 |
| H3' |
C3' |
C2' |
O2' |
120.0 |
122.5 |
| H3' |
C3' |
C2' |
C1' |
267.5 |
241.4 |
| H3' |
C3' |
C2' |
H2'1 |
18.5 |
0.0 |
| O4' |
C1' |
C2' |
O2' |
111.1 |
142.6 |
| O2' |
C2' |
C3' |
H3' |
120.0 |
122.5 |
| C3' |
C2' |
O2' |
C1' |
136.1 |
114.7 |
| C3' |
C2' |
O2' |
H2'1 |
233.8 |
237.4 |
| C1' |
C2' |
O2' |
H2'1 |
97.6 |
122.7 |
| O2' |
C2' |
C1' |
N1 |
232.3 |
261.4 |
| O2' |
C2' |
C1' |
H1' |
347.1 |
23.7 |
| O4' |
C1' |
C2' |
N1 |
238.8 |
241.2 |
| O4' |
C1' |
C2' |
H1' |
124.0 |
119.0 |
| C1' |
C2' |
C3' |
H3' |
267.5 |
241.4 |
| C3' |
C2' |
C1' |
O2' |
221.4 |
241.3 |
| C3' |
C2' |
C1' |
H2'1 |
129.2 |
118.6 |
| O2' |
C2' |
C1' |
H2'1 |
267.8 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
43.9 |
65.3 |
| N1 |
C1' |
C2' |
H1' |
245.2 |
237.8 |
| C2' |
C1' |
N1 |
C2 |
74.1 |
301.7 |
| C2' |
C1' |
N1 |
C6 |
250.0 |
121.5 |
| H2'1 |
C2' |
C3' |
H3' |
18.5 |
0.0 |
| C3' |
C2' |
H2'1 |
O2' |
114.9 |
122.6 |
| C3' |
C2' |
H2'1 |
C1' |
246.1 |
245.4 |
| O2' |
C2' |
H2'1 |
C1' |
131.2 |
122.9 |
| H2'1 |
C2' |
O2' |
HO2' |
306.2 |
302.6 |
| H2'1 |
C2' |
C1' |
N1 |
324.5 |
24.1 |
| H2'1 |
C2' |
C1' |
H1' |
79.3 |
146.3 |
| HO2' |
O2' |
C2' |
C1' |
43.9 |
65.3 |
| HO2' |
O2' |
C2' |
H2'1 |
306.2 |
302.6 |
| O4' |
C1' |
N1 |
C2' |
119.7 |
115.4 |
| O4' |
C1' |
N1 |
H1' |
236.2 |
237.7 |
| N1 |
C1' |
C2' |
H2'1 |
324.5 |
24.1 |
| C2' |
C1' |
N1 |
H1' |
116.4 |
122.3 |
| C2 |
N1 |
C1' |
C6 |
184.1 |
180.2 |
| C1' |
N1 |
C2 |
N3 |
174.8 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
356.1 |
359.8 |
| C1' |
N1 |
C6 |
C5 |
181.9 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
1.9 |
0.0 |
| O4' |
C1' |
H1' |
C2' |
243.2 |
244.5 |
| O4' |
C1' |
H1' |
N1 |
118.3 |
122.2 |
| H1' |
C1' |
C2' |
H2'1 |
79.3 |
146.3 |
| C2' |
C1' |
H1' |
N1 |
235.1 |
237.7 |
| H1' |
C1' |
N1 |
C2 |
317.7 |
179.4 |
| H1' |
C1' |
N1 |
C6 |
133.6 |
359.2 |
| C2 |
N1 |
C1' |
H1' |
317.7 |
179.4 |
| C1' |
N1 |
C2 |
C6 |
175.9 |
179.8 |
| C2 |
N1 |
C6 |
C5 |
357.7 |
359.6 |
| C2 |
N1 |
C6 |
H6 |
177.7 |
179.9 |
| N3 |
C2 |
N1 |
O2 |
178.7 |
180.2 |
| N1 |
C2 |
N3 |
C4 |
2.9 |
359.9 |
| C6 |
N1 |
C1' |
H1' |
133.6 |
359.2 |
| C1' |
N1 |
C6 |
C2 |
184.2 |
180.2 |
| C6 |
N1 |
C2 |
N3 |
358.9 |
0.2 |
| C6 |
N1 |
C2 |
O2 |
180.2 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
3.8 |
0.5 |
| N1 |
C6 |
C5 |
H5 |
183.8 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.7 |
| N3 |
C2 |
N1 |
C6 |
358.9 |
0.2 |
| N1 |
C2 |
N3 |
O2 |
181.4 |
179.8 |
| C2 |
N3 |
C4 |
C5 |
358.6 |
0.3 |
| C2 |
N3 |
C4 |
N4 |
180.0 |
180.1 |
| O2 |
C2 |
N1 |
C6 |
180.2 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
178.7 |
180.2 |
| O2 |
C2 |
N3 |
C4 |
181.5 |
180.0 |
| C4 |
N3 |
C2 |
O2 |
181.5 |
180.0 |
| C5 |
C4 |
N3 |
N4 |
178.6 |
180.2 |
| N3 |
C4 |
C5 |
C6 |
358.0 |
359.5 |
| N3 |
C4 |
C5 |
H5 |
178.0 |
180.0 |
| N3 |
C4 |
N4 |
HN41 |
180.0 |
360.0 |
| N3 |
C4 |
N4 |
HN42 |
54.7 |
179.7 |
| N1 |
C6 |
C5 |
C4 |
3.8 |
0.5 |
| N3 |
C4 |
C5 |
N4 |
181.3 |
179.8 |
| C5 |
C4 |
N4 |
HN41 |
1.4 |
179.8 |
| C5 |
C4 |
N4 |
HN42 |
236.1 |
359.5 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.5 |
| C4 |
C5 |
C6 |
H6 |
183.8 |
180.3 |
| N3 |
C4 |
N4 |
C5 |
178.6 |
180.2 |
| N4 |
C4 |
C5 |
C6 |
176.7 |
179.7 |
| N4 |
C4 |
C5 |
H5 |
356.7 |
0.3 |
| HN41 |
N4 |
C4 |
HN42 |
125.3 |
180.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.3 |
| C6 |
C5 |
C4 |
N4 |
176.7 |
179.7 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.5 |
| H5 |
C5 |
C4 |
N4 |
356.7 |
0.3 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.5 |
| H5 |
C5 |
C6 |
H6 |
3.8 |
359.7 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.7 |
| H6 |
C6 |
C5 |
H5 |
3.8 |
359.7 |
| C4 |
N4 |
HN41 |
HN42 |
234.7 |
179.7 |
| C4 |
N4 |
HN42 |
HN41 |
135.3 |
180.3 |