PDB Chemical Component P2P
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 P2P
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
O1P |
1.489 |
1.479 |
P |
O2P |
1.496 |
1.610 |
P |
O3P |
1.486 |
1.610 |
P |
O6' |
1.602 |
1.610 |
O2P |
HOP2 |
0.950 |
0.967 |
O3P |
HOP3 |
0.950 |
0.967 |
O6' |
C5' |
1.452 |
1.428 |
C5' |
C4' |
1.515 |
1.529 |
C5' |
H5'1 |
1.116 |
1.090 |
C5' |
H5'2 |
1.115 |
1.088 |
C4' |
O5' |
1.468 |
1.446 |
C4' |
C3' |
1.515 |
1.544 |
C4' |
H4' |
1.114 |
1.090 |
O5' |
C1' |
1.456 |
1.443 |
C3' |
O3' |
1.442 |
1.429 |
C3' |
C2' |
1.530 |
1.544 |
C3' |
H3' |
1.116 |
1.089 |
O3' |
HO3' |
0.950 |
0.967 |
C2' |
O2' |
1.440 |
1.429 |
C2' |
C1' |
1.529 |
1.545 |
C2' |
H2' |
1.116 |
1.091 |
O2' |
HO2' |
0.950 |
0.966 |
C1' |
N7 |
1.514 |
1.465 |
C1' |
H1' |
1.115 |
1.089 |
C8 |
N9 |
1.362 |
1.303 |
C8 |
N7 |
1.353 |
1.351 |
C8 |
H8 |
1.103 |
1.080 |
N9 |
C4 |
1.382 |
1.346 |
C4 |
C5 |
1.391 |
1.408 |
C4 |
N3 |
1.351 |
1.334 |
C5 |
N7 |
1.381 |
1.380 |
C5 |
C6 |
1.414 |
1.386 |
N3 |
C2 |
1.354 |
1.321 |
C2 |
N1 |
1.382 |
1.324 |
C2 |
O11 |
1.368 |
1.355 |
N1 |
C6 |
1.362 |
1.325 |
C6 |
H6 |
1.103 |
1.080 |
O11 |
HO11 |
0.950 |
0.966 |
Bond Angles for P2P
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O1P |
P |
O2P |
109.9 |
109.4 |
O1P |
P |
O3P |
109.5 |
109.5 |
O1P |
P |
O6' |
109.3 |
109.5 |
O2P |
P |
O3P |
108.7 |
109.5 |
O2P |
P |
O6' |
111.2 |
109.5 |
P |
O2P |
HOP2 |
109.9 |
106.8 |
O3P |
P |
O6' |
108.1 |
109.5 |
P |
O3P |
HOP3 |
109.5 |
106.8 |
P |
O6' |
C5' |
120.3 |
106.8 |
O6' |
C5' |
C4' |
108.5 |
109.5 |
O6' |
C5' |
H5'1 |
112.6 |
109.4 |
O6' |
C5' |
H5'2 |
112.5 |
109.5 |
C4' |
C5' |
H5'1 |
112.6 |
109.5 |
C4' |
C5' |
H5'2 |
112.6 |
109.5 |
C5' |
C4' |
O5' |
109.3 |
110.4 |
C5' |
C4' |
C3' |
116.2 |
110.7 |
C5' |
C4' |
H4' |
103.7 |
110.3 |
H5'1 |
C5' |
H5'2 |
97.8 |
109.4 |
O5' |
C4' |
C3' |
105.3 |
104.7 |
O5' |
C4' |
H4' |
115.0 |
110.4 |
C4' |
O5' |
C1' |
110.8 |
105.4 |
C3' |
C4' |
H4' |
107.8 |
110.3 |
C4' |
C3' |
O3' |
113.8 |
110.5 |
C4' |
C3' |
C2' |
98.9 |
104.2 |
C4' |
C3' |
H3' |
114.3 |
110.5 |
O5' |
C1' |
C2' |
102.2 |
104.8 |
O5' |
C1' |
N7 |
116.2 |
110.4 |
O5' |
C1' |
H1' |
111.6 |
110.4 |
O3' |
C3' |
C2' |
111.5 |
110.5 |
O3' |
C3' |
H3' |
102.4 |
110.4 |
C3' |
O3' |
HO3' |
113.7 |
106.8 |
C2' |
C3' |
H3' |
116.6 |
110.5 |
C3' |
C2' |
O2' |
107.7 |
110.6 |
C3' |
C2' |
C1' |
105.1 |
104.1 |
C3' |
C2' |
H2' |
114.3 |
110.5 |
O2' |
C2' |
C1' |
112.0 |
110.6 |
O2' |
C2' |
H2' |
107.7 |
110.4 |
C2' |
O2' |
HO2' |
107.7 |
106.8 |
C1' |
C2' |
H2' |
110.2 |
110.5 |
C2' |
C1' |
N7 |
113.7 |
110.3 |
C2' |
C1' |
H1' |
114.1 |
110.4 |
N7 |
C1' |
H1' |
99.6 |
110.3 |
C1' |
N7 |
C8 |
128.0 |
126.4 |
C1' |
N7 |
C5 |
129.1 |
126.4 |
N9 |
C8 |
N7 |
114.1 |
110.2 |
N9 |
C8 |
H8 |
123.2 |
124.9 |
C8 |
N9 |
C4 |
105.5 |
109.8 |
N7 |
C8 |
H8 |
122.6 |
124.9 |
C8 |
N7 |
C5 |
102.9 |
107.2 |
N9 |
C4 |
C5 |
106.4 |
106.8 |
N9 |
C4 |
N3 |
126.5 |
134.5 |
C5 |
C4 |
N3 |
127.1 |
118.7 |
C4 |
C5 |
N7 |
111.1 |
106.0 |
C4 |
C5 |
C6 |
118.4 |
118.7 |
C4 |
N3 |
C2 |
111.1 |
120.3 |
N7 |
C5 |
C6 |
130.6 |
135.2 |
C5 |
C6 |
N1 |
116.3 |
118.7 |
C5 |
C6 |
H6 |
123.5 |
120.7 |
N3 |
C2 |
N1 |
127.1 |
122.3 |
N3 |
C2 |
O11 |
116.4 |
118.9 |
N1 |
C2 |
O11 |
116.5 |
118.9 |
C2 |
N1 |
C6 |
120.0 |
121.2 |
C2 |
O11 |
HO11 |
116.4 |
106.7 |
N1 |
C6 |
H6 |
120.2 |
120.6 |
Torsion Angles for P2P
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O2P |
P |
O1P |
O3P |
119.4 |
119.9 |
O2P |
P |
O1P |
O6' |
237.7 |
240.0 |
O1P |
P |
O2P |
HOP2 |
180.0 |
300.0 |
O3P |
P |
O1P |
O6' |
118.3 |
120.0 |
O1P |
P |
O3P |
HOP3 |
180.0 |
180.0 |
O1P |
P |
O6' |
C5' |
54.3 |
60.0 |
O1P |
P |
O2P |
O3P |
240.1 |
240.0 |
O1P |
P |
O2P |
O6' |
121.2 |
120.1 |
O3P |
P |
O2P |
O6' |
241.1 |
240.0 |
O2P |
P |
O3P |
HOP3 |
59.9 |
60.0 |
O2P |
P |
O6' |
C5' |
175.9 |
179.9 |
O1P |
P |
O3P |
O2P |
120.1 |
119.9 |
O1P |
P |
O3P |
O6' |
240.9 |
239.9 |
O2P |
P |
O3P |
O6' |
120.8 |
120.0 |
O3P |
P |
O2P |
HOP2 |
299.9 |
60.0 |
O3P |
P |
O6' |
C5' |
295.1 |
299.9 |
O1P |
P |
O6' |
O2P |
238.4 |
240.0 |
O1P |
P |
O6' |
O3P |
119.2 |
120.0 |
O2P |
P |
O6' |
O3P |
240.8 |
240.0 |
O6' |
P |
O2P |
HOP2 |
58.8 |
180.0 |
O6' |
P |
O3P |
HOP3 |
299.1 |
300.0 |
P |
O6' |
C5' |
C4' |
99.0 |
180.0 |
P |
O6' |
C5' |
H5'1 |
224.3 |
60.0 |
P |
O6' |
C5' |
H5'2 |
333.6 |
300.1 |
HOP2 |
O2P |
P |
O3P |
299.9 |
60.0 |
HOP2 |
O2P |
P |
O6' |
58.8 |
180.0 |
HOP3 |
O3P |
P |
O6' |
299.1 |
300.0 |
C4' |
C5' |
O6' |
H5'1 |
234.7 |
120.0 |
C4' |
C5' |
O6' |
H5'2 |
125.3 |
239.9 |
O6' |
C5' |
C4' |
O5' |
55.0 |
61.5 |
O6' |
C5' |
C4' |
C3' |
173.9 |
176.9 |
O6' |
C5' |
C4' |
H4' |
291.9 |
299.2 |
H5'1 |
C5' |
O6' |
H5'2 |
250.6 |
119.9 |
O6' |
C5' |
C4' |
H5'1 |
125.3 |
240.1 |
O6' |
C5' |
C4' |
H5'2 |
234.7 |
120.1 |
H5'1 |
C5' |
C4' |
H5'2 |
109.4 |
240.0 |
O5' |
C4' |
C5' |
C3' |
241.1 |
244.6 |
O5' |
C4' |
C5' |
H4' |
123.1 |
122.3 |
C5' |
C4' |
O5' |
C1' |
106.9 |
159.4 |
C3' |
C4' |
C5' |
H4' |
241.9 |
237.7 |
C5' |
C4' |
C3' |
O3' |
157.0 |
98.6 |
C5' |
C4' |
C3' |
C2' |
275.2 |
217.3 |
C5' |
C4' |
C3' |
H3' |
39.8 |
336.0 |
O6' |
C5' |
H5'1 |
C4' |
236.9 |
120.0 |
O6' |
C5' |
H5'1 |
H5'2 |
118.4 |
240.0 |
C4' |
C5' |
H5'1 |
H5'2 |
241.5 |
120.1 |
H5'1 |
C5' |
C4' |
O5' |
289.7 |
181.4 |
H5'1 |
C5' |
C4' |
C3' |
48.6 |
296.8 |
H5'1 |
C5' |
C4' |
H4' |
166.6 |
59.2 |
O6' |
C5' |
H5'2 |
C4' |
123.0 |
239.9 |
O6' |
C5' |
H5'2 |
H5'1 |
241.6 |
119.9 |
C4' |
C5' |
H5'2 |
H5'1 |
118.5 |
240.0 |
H5'2 |
C5' |
C4' |
O5' |
180.3 |
301.4 |
H5'2 |
C5' |
C4' |
C3' |
299.1 |
56.8 |
H5'2 |
C5' |
C4' |
H4' |
57.2 |
179.2 |
O5' |
C4' |
C5' |
H5'1 |
289.7 |
181.4 |
O5' |
C4' |
C5' |
H5'2 |
180.3 |
301.4 |
C5' |
C4' |
O5' |
C3' |
125.5 |
119.1 |
C5' |
C4' |
O5' |
H4' |
244.0 |
237.8 |
C3' |
C4' |
O5' |
H4' |
118.5 |
118.6 |
O5' |
C4' |
C3' |
O3' |
278.0 |
217.5 |
O5' |
C4' |
C3' |
C2' |
36.3 |
336.2 |
O5' |
C4' |
C3' |
H3' |
160.8 |
95.0 |
C4' |
O5' |
C1' |
C2' |
352.1 |
319.6 |
C4' |
O5' |
C1' |
N7 |
116.5 |
78.4 |
C4' |
O5' |
C1' |
H1' |
229.7 |
200.7 |
C3' |
C4' |
C5' |
H5'1 |
48.6 |
296.8 |
C3' |
C4' |
C5' |
H5'2 |
299.1 |
56.8 |
C5' |
C4' |
C3' |
O5' |
239.0 |
241.1 |
C5' |
C4' |
C3' |
H4' |
115.8 |
122.4 |
O5' |
C4' |
C3' |
H4' |
236.8 |
241.3 |
C3' |
C4' |
O5' |
C1' |
341.4 |
40.3 |
O3' |
C3' |
C4' |
C2' |
241.7 |
241.3 |
O3' |
C3' |
C4' |
H3' |
117.2 |
122.5 |
C4' |
C3' |
O3' |
HO3' |
180.0 |
178.1 |
C2' |
C3' |
C4' |
H3' |
235.5 |
241.2 |
C4' |
C3' |
C2' |
O2' |
198.8 |
241.1 |
C4' |
C3' |
C2' |
C1' |
318.3 |
360.0 |
C4' |
C3' |
C2' |
H2' |
79.2 |
118.6 |
H4' |
C4' |
C5' |
H5'1 |
166.6 |
59.2 |
H4' |
C4' |
C5' |
H5'2 |
57.2 |
179.2 |
C5' |
C4' |
H4' |
O5' |
119.2 |
122.3 |
C5' |
C4' |
H4' |
C3' |
236.3 |
237.5 |
O5' |
C4' |
H4' |
C3' |
117.1 |
115.2 |
H4' |
C4' |
O5' |
C1' |
222.9 |
281.7 |
H4' |
C4' |
C3' |
O3' |
41.2 |
336.2 |
H4' |
C4' |
C3' |
C2' |
159.5 |
94.9 |
H4' |
C4' |
C3' |
H3' |
284.0 |
213.7 |
C1' |
O5' |
C4' |
C3' |
341.4 |
40.3 |
C1' |
O5' |
C4' |
H4' |
222.9 |
281.7 |
C3' |
C2' |
C1' |
O5' |
31.4 |
23.9 |
O2' |
C2' |
C1' |
O5' |
148.0 |
142.7 |
O5' |
C1' |
C2' |
H2' |
267.9 |
265.3 |
C2' |
C1' |
O5' |
N7 |
235.6 |
241.2 |
C2' |
C1' |
O5' |
H1' |
122.3 |
118.9 |
N7 |
C1' |
O5' |
H1' |
246.8 |
237.7 |
O5' |
C1' |
N7 |
C8 |
192.4 |
344.1 |
O5' |
C1' |
N7 |
C5 |
13.1 |
163.8 |
O3' |
C3' |
C4' |
H4' |
41.2 |
336.2 |
C4' |
C3' |
O3' |
C2' |
110.8 |
114.8 |
C4' |
C3' |
O3' |
H3' |
236.1 |
237.4 |
C2' |
C3' |
O3' |
H3' |
125.3 |
122.6 |
O3' |
C3' |
C2' |
O2' |
318.8 |
359.8 |
O3' |
C3' |
C2' |
C1' |
78.3 |
118.7 |
O3' |
C3' |
C2' |
H2' |
199.2 |
237.3 |
C2' |
C3' |
C4' |
H4' |
159.5 |
94.9 |
C4' |
C3' |
C2' |
O3' |
240.0 |
241.3 |
C4' |
C3' |
C2' |
H3' |
123.0 |
118.8 |
O5' |
C1' |
C2' |
C3' |
31.4 |
23.9 |
O3' |
C3' |
C2' |
H3' |
243.0 |
237.5 |
C2' |
C3' |
O3' |
HO3' |
69.3 |
63.3 |
O2' |
C2' |
C3' |
C1' |
240.5 |
241.2 |
O2' |
C2' |
C3' |
H2' |
119.6 |
122.6 |
C3' |
C2' |
O2' |
HO2' |
180.0 |
298.5 |
C1' |
C2' |
C3' |
H2' |
239.1 |
241.4 |
C3' |
C2' |
C1' |
N7 |
265.4 |
265.0 |
C3' |
C2' |
C1' |
H1' |
152.0 |
142.9 |
H3' |
C3' |
C4' |
H4' |
284.0 |
213.7 |
C4' |
C3' |
H3' |
O3' |
123.6 |
122.6 |
C4' |
C3' |
H3' |
C2' |
245.5 |
245.2 |
O3' |
C3' |
H3' |
C2' |
121.9 |
122.6 |
H3' |
C3' |
O3' |
HO3' |
303.9 |
300.7 |
H3' |
C3' |
C2' |
O2' |
75.8 |
122.4 |
H3' |
C3' |
C2' |
C1' |
195.3 |
241.2 |
H3' |
C3' |
C2' |
H2' |
316.3 |
359.8 |
HO3' |
O3' |
C3' |
C2' |
69.3 |
63.3 |
HO3' |
O3' |
C3' |
H3' |
303.9 |
300.7 |
O5' |
C1' |
C2' |
O2' |
148.0 |
142.7 |
O2' |
C2' |
C3' |
H3' |
75.8 |
122.4 |
C3' |
C2' |
O2' |
C1' |
115.0 |
114.7 |
C3' |
C2' |
O2' |
H2' |
236.3 |
237.4 |
C1' |
C2' |
O2' |
H2' |
121.3 |
122.6 |
O2' |
C2' |
C1' |
N7 |
22.0 |
23.8 |
O2' |
C2' |
C1' |
H1' |
268.6 |
261.6 |
O5' |
C1' |
C2' |
N7 |
126.0 |
118.9 |
O5' |
C1' |
C2' |
H1' |
239.4 |
241.1 |
C1' |
C2' |
C3' |
H3' |
195.3 |
241.2 |
C3' |
C2' |
C1' |
O2' |
243.4 |
241.2 |
C3' |
C2' |
C1' |
H2' |
123.6 |
118.6 |
O2' |
C2' |
C1' |
H2' |
240.2 |
237.4 |
C1' |
C2' |
O2' |
HO2' |
65.0 |
183.8 |
N7 |
C1' |
C2' |
H1' |
113.4 |
122.2 |
C2' |
C1' |
N7 |
C8 |
310.7 |
99.6 |
C2' |
C1' |
N7 |
C5 |
131.4 |
279.2 |
H2' |
C2' |
C3' |
H3' |
316.3 |
359.8 |
C3' |
C2' |
H2' |
O2' |
119.6 |
122.7 |
C3' |
C2' |
H2' |
C1' |
242.0 |
245.4 |
O2' |
C2' |
H2' |
C1' |
122.4 |
122.7 |
H2' |
C2' |
O2' |
HO2' |
303.7 |
61.2 |
H2' |
C2' |
C1' |
N7 |
141.8 |
146.4 |
H2' |
C2' |
C1' |
H1' |
28.5 |
24.2 |
HO2' |
O2' |
C2' |
C1' |
65.0 |
183.8 |
HO2' |
O2' |
C2' |
H2' |
303.7 |
61.2 |
O5' |
C1' |
N7 |
C2' |
241.7 |
244.6 |
O5' |
C1' |
N7 |
H1' |
119.9 |
122.4 |
N7 |
C1' |
C2' |
H2' |
141.8 |
146.4 |
C2' |
C1' |
N7 |
H1' |
238.2 |
237.8 |
N9 |
C8 |
N7 |
C1' |
181.6 |
179.9 |
C1' |
N7 |
C8 |
H8 |
1.6 |
359.9 |
C8 |
N7 |
C1' |
C5 |
179.3 |
180.4 |
C4 |
C5 |
N7 |
C1' |
177.2 |
179.9 |
C1' |
N7 |
C5 |
C6 |
357.9 |
0.8 |
O5' |
C1' |
H1' |
C2' |
115.3 |
115.5 |
O5' |
C1' |
H1' |
N7 |
236.8 |
237.6 |
H1' |
C1' |
C2' |
H2' |
28.5 |
24.2 |
C2' |
C1' |
H1' |
N7 |
121.5 |
122.2 |
H1' |
C1' |
N7 |
C8 |
72.5 |
221.8 |
H1' |
C1' |
N7 |
C5 |
253.2 |
41.4 |
C1' |
N7 |
C8 |
N9 |
181.6 |
179.9 |
N7 |
C8 |
N9 |
H8 |
180.0 |
179.9 |
N9 |
C8 |
N7 |
C5 |
1.0 |
0.3 |
C8 |
N9 |
C4 |
C5 |
358.2 |
359.7 |
C8 |
N9 |
C4 |
N3 |
178.8 |
180.0 |
C8 |
N7 |
C1' |
H1' |
72.5 |
221.8 |
C1' |
N7 |
C8 |
C5 |
180.6 |
179.7 |
N9 |
C8 |
N7 |
H8 |
180.0 |
180.1 |
N7 |
C8 |
N9 |
C4 |
0.5 |
0.0 |
C4 |
C5 |
N7 |
C8 |
357.8 |
359.6 |
C8 |
N7 |
C5 |
C6 |
178.5 |
180.4 |
N9 |
C8 |
H8 |
N7 |
180.0 |
179.9 |
H8 |
C8 |
N9 |
C4 |
180.5 |
180.1 |
H8 |
C8 |
N7 |
C5 |
181.0 |
180.2 |
C4 |
N9 |
C8 |
N7 |
0.5 |
0.0 |
C4 |
N9 |
C8 |
H8 |
180.5 |
180.1 |
C5 |
C4 |
N9 |
N3 |
179.4 |
179.7 |
N9 |
C4 |
C5 |
N7 |
2.5 |
0.4 |
N9 |
C4 |
C5 |
C6 |
181.9 |
179.7 |
N9 |
C4 |
N3 |
C2 |
178.2 |
179.9 |
C1' |
N7 |
C5 |
C4 |
177.2 |
179.9 |
C8 |
N7 |
C5 |
C4 |
357.8 |
359.6 |
N9 |
C4 |
C5 |
N3 |
180.6 |
180.2 |
C5 |
C4 |
N3 |
C2 |
359.0 |
0.2 |
N7 |
C5 |
C4 |
C6 |
180.6 |
180.7 |
C4 |
C5 |
C6 |
N1 |
358.9 |
0.5 |
C4 |
C5 |
C6 |
H6 |
178.9 |
180.3 |
N9 |
C4 |
N3 |
C5 |
179.2 |
179.7 |
N3 |
C4 |
C5 |
N7 |
181.9 |
180.2 |
N3 |
C4 |
C5 |
C6 |
1.3 |
359.5 |
C4 |
N3 |
C2 |
N1 |
0.7 |
0.1 |
C4 |
N3 |
C2 |
O11 |
179.5 |
180.0 |
C5 |
N7 |
C1' |
H1' |
253.2 |
41.4 |
C1' |
N7 |
C5 |
C8 |
179.4 |
180.3 |
C5 |
N7 |
C8 |
H8 |
181.0 |
180.2 |
N7 |
C5 |
C4 |
N3 |
181.9 |
180.2 |
C4 |
C5 |
N7 |
C6 |
179.3 |
179.2 |
N7 |
C5 |
C6 |
N1 |
178.1 |
179.6 |
N7 |
C5 |
C6 |
H6 |
358.1 |
359.3 |
C6 |
C5 |
C4 |
N3 |
1.3 |
359.5 |
C4 |
C5 |
C6 |
N7 |
180.7 |
180.9 |
C2 |
N1 |
C6 |
C5 |
0.9 |
359.8 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
N1 |
C2 |
N3 |
O11 |
181.2 |
180.1 |
N3 |
C2 |
N1 |
C6 |
359.3 |
359.9 |
N3 |
C2 |
O11 |
HO11 |
180.0 |
90.0 |
C5 |
C6 |
N1 |
C2 |
0.9 |
359.8 |
N3 |
C2 |
N1 |
O11 |
178.8 |
179.9 |
N1 |
C2 |
O11 |
HO11 |
358.9 |
270.0 |
C2 |
N1 |
C6 |
H6 |
180.9 |
180.0 |
N3 |
C2 |
O11 |
N1 |
181.1 |
180.1 |
O11 |
C2 |
N1 |
C6 |
180.5 |
180.0 |
C5 |
C6 |
N1 |
H6 |
180.0 |
179.8 |
C6 |
N1 |
C2 |
O11 |
180.5 |
180.0 |
C5 |
C6 |
H6 |
N1 |
180.0 |
180.2 |