PDB Chemical Component A1P
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 A1P
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O1P |
1.486 |
1.506 |
| P |
O2P |
1.486 |
1.625 |
| P |
O5' |
1.590 |
1.626 |
| O2P |
H2P |
0.950 |
0.981 |
| O5' |
C5' |
1.425 |
1.417 |
| N9 |
C4 |
1.379 |
1.368 |
| N9 |
C8 |
1.373 |
1.371 |
| N9 |
C1' |
1.463 |
1.459 |
| C4 |
N3 |
1.351 |
1.341 |
| C4 |
C5 |
1.379 |
1.386 |
| N3 |
C2 |
1.324 |
1.350 |
| C2 |
N2 |
1.342 |
1.414 |
| C2 |
N1 |
1.374 |
1.355 |
| N2 |
H2N1 |
1.020 |
0.998 |
| N2 |
H2N2 |
1.020 |
0.998 |
| N1 |
C6 |
1.393 |
1.355 |
| C6 |
C5 |
1.424 |
1.392 |
| C6 |
H6 |
1.103 |
1.083 |
| C5 |
N7 |
1.388 |
1.372 |
| N7 |
C8 |
1.307 |
1.317 |
| C8 |
H8 |
1.103 |
1.082 |
| C2' |
C1' |
1.522 |
1.522 |
| C2' |
C3' |
1.521 |
1.512 |
| C2' |
H2'1 |
1.115 |
1.097 |
| C2' |
H2'2 |
1.115 |
1.094 |
| C5' |
C4' |
1.511 |
1.523 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.091 |
| C4' |
O4' |
1.448 |
1.443 |
| C4' |
C3' |
1.530 |
1.525 |
| C4' |
H4' |
1.115 |
1.095 |
| O4' |
C1' |
1.417 |
1.439 |
| C1' |
H1' |
1.114 |
1.095 |
| C3' |
O3' |
1.431 |
1.425 |
| C3' |
H3' |
1.115 |
1.093 |
| O3' |
HA |
0.950 |
0.969 |
| HP1 |
P |
1.420 |
1.412 |
Bond Angles for A1P
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O2P |
119.9 |
111.5 |
| O1P |
P |
O5' |
109.5 |
111.9 |
| O2P |
P |
O5' |
106.4 |
101.5 |
| P |
O2P |
H2P |
119.9 |
118.7 |
| P |
O5' |
C5' |
121.3 |
118.3 |
| O5' |
C5' |
C4' |
109.7 |
108.7 |
| O5' |
C5' |
H5'1 |
112.1 |
109.2 |
| O5' |
C5' |
H5'2 |
112.1 |
109.2 |
| C4 |
N9 |
C8 |
106.3 |
106.9 |
| C4 |
N9 |
C1' |
126.5 |
126.9 |
| N9 |
C4 |
N3 |
126.1 |
127.5 |
| N9 |
C4 |
C5 |
105.3 |
105.3 |
| C8 |
N9 |
C1' |
127.2 |
126.2 |
| N9 |
C8 |
N7 |
113.1 |
112.3 |
| N9 |
C8 |
H8 |
123.4 |
122.2 |
| N9 |
C1' |
C2' |
114.8 |
114.3 |
| N9 |
C1' |
O4' |
107.8 |
110.0 |
| N9 |
C1' |
H1' |
109.5 |
105.9 |
| N3 |
C4 |
C5 |
128.6 |
127.2 |
| C4 |
N3 |
C2 |
112.1 |
110.5 |
| C4 |
C5 |
C6 |
118.7 |
116.9 |
| C4 |
C5 |
N7 |
110.8 |
110.7 |
| N3 |
C2 |
N2 |
119.6 |
115.6 |
| N3 |
C2 |
N1 |
123.9 |
128.9 |
| N2 |
C2 |
N1 |
116.5 |
115.5 |
| C2 |
N2 |
H2N1 |
119.5 |
119.0 |
| C2 |
N2 |
H2N2 |
116.5 |
119.0 |
| C2 |
N1 |
C6 |
125.0 |
117.5 |
| H2N1 |
N2 |
H2N2 |
123.9 |
121.6 |
| N1 |
C6 |
C5 |
111.6 |
119.1 |
| N1 |
C6 |
H6 |
124.2 |
117.0 |
| C5 |
C6 |
H6 |
124.2 |
123.9 |
| C6 |
C5 |
N7 |
130.5 |
132.4 |
| C5 |
N7 |
C8 |
104.4 |
104.8 |
| N7 |
C8 |
H8 |
123.4 |
125.6 |
| C1' |
C2' |
C3' |
102.3 |
101.6 |
| C1' |
C2' |
H2'1 |
114.9 |
110.5 |
| C1' |
C2' |
H2'2 |
115.0 |
111.7 |
| C2' |
C1' |
O4' |
105.7 |
106.7 |
| C2' |
C1' |
H1' |
109.5 |
111.7 |
| C3' |
C2' |
H2'1 |
115.0 |
110.0 |
| C3' |
C2' |
H2'2 |
114.9 |
114.2 |
| C2' |
C3' |
C4' |
102.8 |
103.2 |
| C2' |
C3' |
O3' |
109.4 |
108.4 |
| C2' |
C3' |
H3' |
111.5 |
113.7 |
| H2'1 |
C2' |
H2'2 |
95.5 |
108.7 |
| C4' |
C5' |
H5'1 |
112.1 |
110.1 |
| C4' |
C5' |
H5'2 |
112.1 |
110.1 |
| C5' |
C4' |
O4' |
108.2 |
108.0 |
| C5' |
C4' |
C3' |
114.3 |
112.7 |
| C5' |
C4' |
H4' |
109.5 |
109.4 |
| H5'1 |
C5' |
H5'2 |
98.2 |
109.6 |
| O4' |
C4' |
C3' |
105.9 |
106.8 |
| O4' |
C4' |
H4' |
109.4 |
107.7 |
| C4' |
O4' |
C1' |
110.5 |
108.7 |
| C3' |
C4' |
H4' |
109.4 |
112.0 |
| C4' |
C3' |
O3' |
109.8 |
109.6 |
| C4' |
C3' |
H3' |
111.5 |
114.0 |
| O4' |
C1' |
H1' |
109.5 |
108.1 |
| O3' |
C3' |
H3' |
111.5 |
107.8 |
| C3' |
O3' |
HA |
109.4 |
106.6 |
Torsion Angles for A1P
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2P |
P |
O1P |
O5' |
236.8 |
247.0 |
| O1P |
P |
O2P |
H2P |
180.0 |
45.8 |
| O1P |
P |
O5' |
C5' |
56.8 |
193.6 |
| O1P |
P |
O2P |
O5' |
124.8 |
119.3 |
| O2P |
P |
O5' |
C5' |
187.7 |
312.7 |
| O1P |
P |
O5' |
O2P |
229.1 |
240.9 |
| O5' |
P |
O2P |
H2P |
55.2 |
286.5 |
| P |
O5' |
C5' |
C4' |
175.3 |
210.0 |
| P |
O5' |
C5' |
H5'1 |
50.0 |
330.1 |
| P |
O5' |
C5' |
H5'2 |
300.5 |
89.9 |
| H2P |
O2P |
P |
O5' |
55.2 |
286.5 |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
239.9 |
| C4' |
C5' |
O5' |
H5'2 |
234.7 |
120.1 |
| O5' |
C5' |
C4' |
O4' |
298.3 |
61.8 |
| O5' |
C5' |
C4' |
C3' |
56.0 |
179.5 |
| O5' |
C5' |
C4' |
H4' |
179.1 |
304.8 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.4 |
240.2 |
| C8 |
N9 |
C4 |
C1' |
179.5 |
180.0 |
| C4 |
N9 |
C8 |
N7 |
359.5 |
360.0 |
| C4 |
N9 |
C8 |
H8 |
179.5 |
179.9 |
| C4 |
N9 |
C1' |
C2' |
132.1 |
93.5 |
| C4 |
N9 |
C1' |
O4' |
249.6 |
213.5 |
| C4 |
N9 |
C1' |
H1' |
8.5 |
330.0 |
| N3 |
C4 |
N9 |
C5 |
179.4 |
179.9 |
| N9 |
C4 |
N3 |
C2 |
180.9 |
180.1 |
| N9 |
C4 |
C5 |
C6 |
178.7 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
358.9 |
359.9 |
| C4 |
N9 |
C8 |
C1' |
180.5 |
180.0 |
| C8 |
N9 |
C4 |
N3 |
180.4 |
179.9 |
| C8 |
N9 |
C4 |
C5 |
1.0 |
0.1 |
| C8 |
N9 |
C1' |
C2' |
312.6 |
273.4 |
| C8 |
N9 |
C1' |
O4' |
70.1 |
33.5 |
| C8 |
N9 |
C1' |
H1' |
189.1 |
150.0 |
| C5 |
N7 |
C8 |
N9 |
359.9 |
360.0 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| C4 |
N9 |
C1' |
C8 |
179.4 |
180.0 |
| C1' |
N9 |
C4 |
N3 |
0.8 |
359.9 |
| C1' |
N9 |
C4 |
C5 |
181.4 |
180.1 |
| C1' |
N9 |
C8 |
N7 |
179.0 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
359.0 |
360.0 |
| N9 |
C1' |
C2' |
C3' |
151.9 |
154.5 |
| N9 |
C1' |
C2' |
H2'1 |
26.7 |
37.8 |
| N9 |
C1' |
C2' |
H2'2 |
277.2 |
276.7 |
| C2' |
C1' |
N9 |
O4' |
242.5 |
240.0 |
| C2' |
C1' |
N9 |
H1' |
123.5 |
123.5 |
| C4' |
O4' |
C1' |
N9 |
218.0 |
218.2 |
| O4' |
C1' |
N9 |
H1' |
241.0 |
243.5 |
| N3 |
C4 |
N9 |
C8 |
180.4 |
179.9 |
| N3 |
C4 |
N9 |
C1' |
0.8 |
359.9 |
| N9 |
C4 |
N3 |
C5 |
180.7 |
180.2 |
| N3 |
C4 |
C5 |
C6 |
359.4 |
0.1 |
| N3 |
C4 |
C5 |
N7 |
179.5 |
180.1 |
| C4 |
N3 |
C2 |
N2 |
180.8 |
180.0 |
| C4 |
N3 |
C2 |
N1 |
0.6 |
0.0 |
| C5 |
C4 |
N9 |
C8 |
1.0 |
0.1 |
| C5 |
C4 |
N9 |
C1' |
181.4 |
180.1 |
| N9 |
C4 |
C5 |
N3 |
179.4 |
179.9 |
| C5 |
C4 |
N3 |
C2 |
0.1 |
359.9 |
| N1 |
C6 |
C5 |
C4 |
0.4 |
359.9 |
| C4 |
C5 |
C6 |
H6 |
180.4 |
180.0 |
| C6 |
C5 |
C4 |
N7 |
179.8 |
180.1 |
| C4 |
C5 |
N7 |
C8 |
0.8 |
0.1 |
| C2 |
N3 |
C4 |
C5 |
0.1 |
359.9 |
| N2 |
C2 |
N3 |
N1 |
180.2 |
180.0 |
| N3 |
C2 |
N2 |
H2N1 |
180.0 |
16.9 |
| N3 |
C2 |
N2 |
H2N2 |
359.8 |
203.3 |
| N3 |
C2 |
N1 |
C6 |
359.2 |
0.0 |
| N3 |
C2 |
N2 |
N1 |
179.8 |
180.0 |
| N2 |
C2 |
N1 |
C6 |
179.1 |
180.0 |
| H2N1 |
N2 |
C2 |
H2N2 |
180.2 |
173.6 |
| N3 |
C2 |
N1 |
N2 |
180.2 |
180.0 |
| N1 |
C2 |
N2 |
H2N1 |
0.2 |
197.0 |
| N1 |
C2 |
N2 |
H2N2 |
180.0 |
23.3 |
| C2 |
N1 |
C6 |
C5 |
0.2 |
0.0 |
| C2 |
N1 |
C6 |
H6 |
180.2 |
180.0 |
| H2N1 |
N2 |
C2 |
N1 |
0.2 |
197.0 |
| C2 |
N2 |
H2N1 |
H2N2 |
179.8 |
186.5 |
| H2N2 |
N2 |
C2 |
N1 |
180.0 |
23.3 |
| C2 |
N2 |
H2N2 |
H2N1 |
180.2 |
173.5 |
| C4 |
C5 |
C6 |
N1 |
0.4 |
359.9 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
N7 |
180.2 |
180.0 |
| C4 |
C5 |
C6 |
N7 |
180.2 |
179.9 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
N7 |
C8 |
181.0 |
180.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
N7 |
0.2 |
0.0 |
| N9 |
C8 |
N7 |
C5 |
359.9 |
360.0 |
| C4 |
C5 |
N7 |
C6 |
179.8 |
180.1 |
| N7 |
C5 |
C6 |
H6 |
0.2 |
0.0 |
| C5 |
N7 |
C8 |
H8 |
179.9 |
180.0 |
| N7 |
C8 |
N9 |
C1' |
179.0 |
180.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| H8 |
C8 |
N9 |
C1' |
359.0 |
360.0 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| N9 |
C1' |
C2' |
O4' |
118.7 |
121.8 |
| N9 |
C1' |
C2' |
H1' |
236.5 |
239.7 |
| C3' |
C2' |
C1' |
H2'1 |
125.3 |
116.7 |
| C3' |
C2' |
C1' |
H2'2 |
234.7 |
237.8 |
| C1' |
C2' |
C3' |
C4' |
325.7 |
325.2 |
| C1' |
C2' |
C3' |
O3' |
82.3 |
81.3 |
| C1' |
C2' |
C3' |
H3' |
206.1 |
201.2 |
| H2'1 |
C2' |
C1' |
H2'2 |
109.5 |
121.1 |
| C4' |
O4' |
C1' |
C2' |
341.1 |
342.7 |
| O4' |
C1' |
C2' |
H1' |
117.8 |
117.9 |
| C1' |
C2' |
C3' |
H2'1 |
234.8 |
243.0 |
| C1' |
C2' |
C3' |
H2'2 |
125.3 |
120.4 |
| C3' |
C2' |
C1' |
O4' |
33.3 |
32.7 |
| C3' |
C2' |
C1' |
H1' |
275.5 |
274.8 |
| H2'1 |
C2' |
C3' |
H2'2 |
250.5 |
237.5 |
| C5' |
C4' |
C3' |
C2' |
265.1 |
267.4 |
| O4' |
C4' |
C3' |
C2' |
24.1 |
25.9 |
| C2' |
C3' |
C4' |
H4' |
142.0 |
143.6 |
| C4' |
C3' |
C2' |
O3' |
243.4 |
243.8 |
| C4' |
C3' |
C2' |
H3' |
119.6 |
123.9 |
| O3' |
C3' |
C2' |
H3' |
236.2 |
240.1 |
| C2' |
C3' |
O3' |
HA |
180.0 |
294.7 |
| C1' |
C2' |
H2'1 |
C3' |
118.4 |
111.4 |
| C1' |
C2' |
H2'1 |
H2'2 |
239.2 |
237.1 |
| H2'1 |
C2' |
C1' |
O4' |
268.0 |
276.0 |
| H2'1 |
C2' |
C1' |
H1' |
150.2 |
158.1 |
| C3' |
C2' |
H2'1 |
H2'2 |
120.8 |
125.7 |
| H2'1 |
C2' |
C3' |
C4' |
90.9 |
82.2 |
| H2'1 |
C2' |
C3' |
O3' |
207.5 |
198.4 |
| H2'1 |
C2' |
C3' |
H3' |
331.3 |
318.3 |
| C1' |
C2' |
H2'2 |
C3' |
241.6 |
245.4 |
| C1' |
C2' |
H2'2 |
H2'1 |
120.8 |
122.1 |
| H2'2 |
C2' |
C1' |
O4' |
158.6 |
154.9 |
| H2'2 |
C2' |
C1' |
H1' |
40.8 |
37.0 |
| C3' |
C2' |
H2'2 |
H2'1 |
239.2 |
236.7 |
| H2'2 |
C2' |
C3' |
C4' |
200.4 |
204.8 |
| H2'2 |
C2' |
C3' |
O3' |
317.0 |
320.9 |
| H2'2 |
C2' |
C3' |
H3' |
80.8 |
80.8 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
119.6 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
240.5 |
| C2' |
C3' |
C4' |
C5' |
265.1 |
267.4 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.6 |
120.9 |
| O4' |
C4' |
C5' |
C3' |
242.3 |
242.3 |
| O4' |
C4' |
C5' |
H4' |
119.2 |
117.0 |
| C5' |
C4' |
O4' |
C1' |
119.5 |
116.0 |
| C3' |
C4' |
C5' |
H4' |
236.9 |
234.7 |
| C5' |
C4' |
C3' |
O3' |
148.8 |
152.1 |
| C5' |
C4' |
C3' |
H3' |
24.7 |
31.2 |
| O5' |
C5' |
H5'1 |
C4' |
123.9 |
240.8 |
| O5' |
C5' |
H5'1 |
H5'2 |
242.0 |
119.6 |
| C4' |
C5' |
H5'1 |
H5'2 |
118.0 |
238.8 |
| H5'1 |
C5' |
C4' |
O4' |
63.6 |
302.2 |
| H5'1 |
C5' |
C4' |
C3' |
181.3 |
60.0 |
| H5'1 |
C5' |
C4' |
H4' |
304.4 |
185.3 |
| O5' |
C5' |
H5'2 |
C4' |
236.1 |
119.2 |
| O5' |
C5' |
H5'2 |
H5'1 |
118.0 |
240.4 |
| C4' |
C5' |
H5'2 |
H5'1 |
242.0 |
121.2 |
| H5'2 |
C5' |
C4' |
O4' |
173.0 |
181.3 |
| H5'2 |
C5' |
C4' |
C3' |
290.7 |
299.1 |
| H5'2 |
C5' |
C4' |
H4' |
53.8 |
64.3 |
| N9 |
C1' |
O4' |
C4' |
218.0 |
218.2 |
| C2' |
C1' |
O4' |
C4' |
341.1 |
342.7 |
| C2' |
C3' |
C4' |
O4' |
24.1 |
25.9 |
| O4' |
C4' |
C5' |
H5'1 |
63.6 |
302.2 |
| O4' |
C4' |
C5' |
H5'2 |
173.0 |
181.3 |
| C5' |
C4' |
O4' |
C3' |
123.0 |
121.5 |
| C5' |
C4' |
O4' |
H4' |
240.8 |
242.0 |
| C3' |
C4' |
O4' |
H4' |
117.8 |
120.5 |
| O4' |
C4' |
C3' |
O3' |
267.8 |
270.6 |
| O4' |
C4' |
C3' |
H3' |
143.7 |
149.7 |
| C4' |
O4' |
C1' |
H1' |
99.0 |
103.1 |
| C4' |
C3' |
C2' |
H2'1 |
90.9 |
82.2 |
| C4' |
C3' |
C2' |
H2'2 |
200.4 |
204.8 |
| C2' |
C3' |
C4' |
O3' |
116.3 |
115.3 |
| C2' |
C3' |
C4' |
H3' |
240.4 |
236.3 |
| C3' |
C4' |
C5' |
H5'1 |
181.3 |
60.0 |
| C3' |
C4' |
C5' |
H5'2 |
290.7 |
299.1 |
| C5' |
C4' |
C3' |
O4' |
241.0 |
241.5 |
| C5' |
C4' |
C3' |
H4' |
123.1 |
123.8 |
| O4' |
C4' |
C3' |
H4' |
242.2 |
242.3 |
| C3' |
C4' |
O4' |
C1' |
356.5 |
354.5 |
| O3' |
C3' |
C4' |
H3' |
124.1 |
120.9 |
| C4' |
C3' |
O3' |
HA |
292.1 |
46.6 |
| H4' |
C4' |
C5' |
H5'1 |
304.4 |
185.3 |
| H4' |
C4' |
C5' |
H5'2 |
53.8 |
64.3 |
| C5' |
C4' |
H4' |
O4' |
118.4 |
117.2 |
| C5' |
C4' |
H4' |
C3' |
234.0 |
234.3 |
| O4' |
C4' |
H4' |
C3' |
115.6 |
117.2 |
| H4' |
C4' |
O4' |
C1' |
238.7 |
234.0 |
| H4' |
C4' |
C3' |
O3' |
25.6 |
28.3 |
| H4' |
C4' |
C3' |
H3' |
261.5 |
267.4 |
| N9 |
C1' |
O4' |
C2' |
236.8 |
235.5 |
| N9 |
C1' |
O4' |
H1' |
119.0 |
115.2 |
| O4' |
C1' |
C2' |
C3' |
33.3 |
32.7 |
| O4' |
C1' |
C2' |
H2'1 |
268.0 |
276.0 |
| O4' |
C1' |
C2' |
H2'2 |
158.6 |
154.9 |
| C2' |
C1' |
O4' |
H1' |
242.2 |
239.7 |
| C1' |
O4' |
C4' |
C3' |
356.5 |
354.5 |
| C1' |
O4' |
C4' |
H4' |
238.7 |
234.0 |
| N9 |
C1' |
H1' |
C2' |
126.6 |
125.1 |
| N9 |
C1' |
H1' |
O4' |
242.1 |
242.2 |
| H1' |
C1' |
C2' |
C3' |
275.5 |
274.8 |
| H1' |
C1' |
C2' |
H2'1 |
150.2 |
158.1 |
| H1' |
C1' |
C2' |
H2'2 |
40.8 |
37.0 |
| C2' |
C1' |
H1' |
O4' |
115.4 |
117.1 |
| O3' |
C3' |
C2' |
H2'1 |
207.5 |
198.4 |
| O3' |
C3' |
C2' |
H2'2 |
317.0 |
320.9 |
| C2' |
C3' |
O3' |
C4' |
247.9 |
248.1 |
| C2' |
C3' |
O3' |
H3' |
123.8 |
123.5 |
| O3' |
C3' |
C4' |
H4' |
25.6 |
28.3 |
| C4' |
C3' |
O3' |
H3' |
235.9 |
235.4 |
| H3' |
C3' |
C2' |
H2'1 |
331.3 |
318.3 |
| H3' |
C3' |
C2' |
H2'2 |
80.8 |
80.8 |
| C2' |
C3' |
H3' |
C4' |
114.3 |
117.9 |
| C2' |
C3' |
H3' |
O3' |
237.4 |
239.8 |
| H3' |
C3' |
C4' |
H4' |
261.5 |
267.4 |
| C4' |
C3' |
H3' |
O3' |
123.1 |
121.9 |
| H3' |
C3' |
O3' |
HA |
56.2 |
171.2 |
| HA |
O3' |
C3' |
H3' |
56.2 |
171.2 |