PDB Chemical Component AD3
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 AD3
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.436 |
1.429 |
| O5' |
HO5' |
0.950 |
0.967 |
| C5' |
C4' |
1.543 |
1.529 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.089 |
| C4' |
O4' |
1.448 |
1.444 |
| C4' |
C3' |
1.534 |
1.543 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.408 |
1.444 |
| C3' |
O3' |
1.432 |
1.429 |
| C3' |
C2' |
1.545 |
1.547 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C2' |
O2' |
1.422 |
1.429 |
| C2' |
C1' |
1.554 |
1.544 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
HO2' |
0.950 |
0.966 |
| C1' |
N9 |
1.507 |
1.464 |
| C1' |
H1' |
1.115 |
1.090 |
| N9 |
C8 |
1.410 |
1.362 |
| N9 |
C4 |
1.420 |
1.373 |
| C8 |
N7 |
1.322 |
1.301 |
| C8 |
H8 |
1.103 |
1.079 |
| N7 |
C5 |
1.416 |
1.355 |
| C5 |
C6 |
1.478 |
1.403 |
| C5 |
C4 |
1.414 |
1.405 |
| C6 |
N6 |
1.329 |
1.389 |
| C6 |
N1 |
1.392 |
1.321 |
| N6 |
HN61 |
1.020 |
0.970 |
| N6 |
HN62 |
1.020 |
0.970 |
| N1 |
C2 |
1.359 |
1.323 |
| C2 |
C3 |
1.369 |
1.367 |
| C2 |
H2 |
1.103 |
1.080 |
| C3 |
C4 |
1.426 |
1.394 |
| C3 |
H3 |
1.103 |
1.079 |
Bond Angles for AD3
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
HO5' |
116.1 |
106.8 |
| O5' |
C5' |
C4' |
116.1 |
109.5 |
| O5' |
C5' |
H5'1 |
109.8 |
109.4 |
| O5' |
C5' |
H5'2 |
109.8 |
109.4 |
| C4' |
C5' |
H5'1 |
109.8 |
109.5 |
| C4' |
C5' |
H5'2 |
109.8 |
109.5 |
| C5' |
C4' |
O4' |
91.7 |
110.4 |
| C5' |
C4' |
C3' |
102.2 |
110.5 |
| C5' |
C4' |
H4' |
121.9 |
110.3 |
| H5'1 |
C5' |
H5'2 |
100.4 |
109.5 |
| O4' |
C4' |
C3' |
103.2 |
104.8 |
| O4' |
C4' |
H4' |
121.1 |
110.3 |
| C4' |
O4' |
C1' |
116.1 |
105.3 |
| C3' |
C4' |
H4' |
113.0 |
110.4 |
| C4' |
C3' |
O3' |
110.8 |
110.5 |
| C4' |
C3' |
C2' |
107.6 |
104.1 |
| C4' |
C3' |
H3' |
110.7 |
110.5 |
| O4' |
C1' |
C2' |
104.2 |
104.9 |
| O4' |
C1' |
N9 |
109.4 |
110.4 |
| O4' |
C1' |
H1' |
118.3 |
110.3 |
| O3' |
C3' |
C2' |
111.8 |
110.6 |
| O3' |
C3' |
H3' |
106.4 |
110.5 |
| C3' |
O3' |
HO3' |
110.7 |
106.8 |
| C2' |
C3' |
H3' |
109.6 |
110.6 |
| C3' |
C2' |
O2' |
118.3 |
110.5 |
| C3' |
C2' |
C1' |
105.3 |
104.0 |
| C3' |
C2' |
H2' |
107.6 |
110.5 |
| O2' |
C2' |
C1' |
112.6 |
110.8 |
| O2' |
C2' |
H2' |
99.3 |
110.5 |
| C2' |
O2' |
HO2' |
118.3 |
106.8 |
| C1' |
C2' |
H2' |
113.8 |
110.4 |
| C2' |
C1' |
N9 |
121.6 |
110.4 |
| C2' |
C1' |
H1' |
105.0 |
110.3 |
| N9 |
C1' |
H1' |
99.3 |
110.4 |
| C1' |
N9 |
C8 |
125.8 |
126.4 |
| C1' |
N9 |
C4 |
129.9 |
126.3 |
| C8 |
N9 |
C4 |
104.4 |
107.3 |
| N9 |
C8 |
N7 |
115.0 |
110.0 |
| N9 |
C8 |
H8 |
125.4 |
125.0 |
| N9 |
C4 |
C5 |
105.9 |
106.2 |
| N9 |
C4 |
C3 |
128.0 |
135.2 |
| N7 |
C8 |
H8 |
119.6 |
125.0 |
| C8 |
N7 |
C5 |
103.9 |
109.6 |
| N7 |
C5 |
C6 |
133.5 |
134.5 |
| N7 |
C5 |
C4 |
110.8 |
106.9 |
| C6 |
C5 |
C4 |
115.7 |
118.5 |
| C5 |
C6 |
N6 |
123.2 |
120.0 |
| C5 |
C6 |
N1 |
118.0 |
120.0 |
| C5 |
C4 |
C3 |
126.1 |
118.6 |
| N6 |
C6 |
N1 |
118.8 |
120.0 |
| C6 |
N6 |
HN61 |
123.2 |
120.0 |
| C6 |
N6 |
HN62 |
107.4 |
120.0 |
| C6 |
N1 |
C2 |
120.4 |
122.2 |
| HN61 |
N6 |
HN62 |
107.3 |
120.0 |
| N1 |
C2 |
C3 |
127.6 |
121.5 |
| N1 |
C2 |
H2 |
115.7 |
119.3 |
| C3 |
C2 |
H2 |
116.7 |
119.2 |
| C2 |
C3 |
C4 |
112.1 |
119.0 |
| C2 |
C3 |
H3 |
122.2 |
120.5 |
| C4 |
C3 |
H3 |
125.7 |
120.5 |
Torsion Angles for AD3
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
234.8 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
69.0 |
61.4 |
| O5' |
C5' |
C4' |
C3' |
172.8 |
176.9 |
| O5' |
C5' |
C4' |
H4' |
300.1 |
299.2 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.5 |
120.0 |
| HO5' |
O5' |
C5' |
C4' |
180.1 |
180.0 |
| HO5' |
O5' |
C5' |
H5'1 |
305.3 |
60.0 |
| HO5' |
O5' |
C5' |
H5'2 |
54.8 |
300.0 |
| C4' |
C5' |
O5' |
HO5' |
180.1 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
119.9 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
239.9 |
| O4' |
C4' |
C5' |
C3' |
256.2 |
244.5 |
| O4' |
C4' |
C5' |
H4' |
128.9 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
121.1 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
232.7 |
237.7 |
| C5' |
C4' |
C3' |
O3' |
135.4 |
98.3 |
| C5' |
C4' |
C3' |
C2' |
257.9 |
217.0 |
| C5' |
C4' |
C3' |
H3' |
17.6 |
335.8 |
| H5'1 |
C5' |
O5' |
HO5' |
305.3 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
231.2 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
115.6 |
240.1 |
| C4' |
C5' |
H5'1 |
H5'2 |
244.4 |
120.1 |
| H5'1 |
C5' |
C4' |
O4' |
303.8 |
181.4 |
| H5'1 |
C5' |
C4' |
C3' |
47.6 |
296.8 |
| H5'1 |
C5' |
C4' |
H4' |
174.9 |
59.2 |
| H5'2 |
C5' |
O5' |
HO5' |
54.8 |
300.0 |
| O5' |
C5' |
H5'2 |
C4' |
128.8 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
244.4 |
119.9 |
| C4' |
C5' |
H5'2 |
H5'1 |
115.6 |
239.9 |
| H5'2 |
C5' |
C4' |
O4' |
194.3 |
301.5 |
| H5'2 |
C5' |
C4' |
C3' |
298.1 |
56.9 |
| H5'2 |
C5' |
C4' |
H4' |
65.4 |
179.3 |
| O4' |
C4' |
C5' |
H5'1 |
303.8 |
181.4 |
| O4' |
C4' |
C5' |
H5'2 |
194.3 |
301.5 |
| C5' |
C4' |
O4' |
C3' |
102.9 |
119.0 |
| C5' |
C4' |
O4' |
H4' |
230.5 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
127.6 |
118.8 |
| O4' |
C4' |
C3' |
O3' |
230.1 |
217.3 |
| O4' |
C4' |
C3' |
C2' |
352.5 |
336.0 |
| O4' |
C4' |
C3' |
H3' |
112.3 |
94.7 |
| C4' |
O4' |
C1' |
C2' |
339.5 |
319.6 |
| C4' |
O4' |
C1' |
N9 |
208.0 |
200.7 |
| C4' |
O4' |
C1' |
H1' |
95.5 |
78.4 |
| C3' |
C4' |
C5' |
H5'1 |
47.6 |
296.8 |
| C3' |
C4' |
C5' |
H5'2 |
298.1 |
56.9 |
| C5' |
C4' |
C3' |
O4' |
265.3 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
132.8 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
227.5 |
241.2 |
| C3' |
C4' |
O4' |
C1' |
18.2 |
40.5 |
| O3' |
C3' |
C4' |
C2' |
237.5 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
117.8 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
179.9 |
298.6 |
| C2' |
C3' |
C4' |
H3' |
240.3 |
241.3 |
| C4' |
C3' |
C2' |
O2' |
229.5 |
241.2 |
| C4' |
C3' |
C2' |
C1' |
356.5 |
0.1 |
| C4' |
C3' |
C2' |
H2' |
118.2 |
118.6 |
| H4' |
C4' |
C5' |
H5'1 |
174.9 |
59.2 |
| H4' |
C4' |
C5' |
H5'2 |
65.4 |
179.3 |
| C5' |
C4' |
H4' |
O4' |
114.6 |
122.2 |
| C5' |
C4' |
H4' |
C3' |
237.7 |
237.6 |
| O4' |
C4' |
H4' |
C3' |
123.1 |
115.3 |
| H4' |
C4' |
O4' |
C1' |
250.5 |
281.7 |
| H4' |
C4' |
C3' |
O3' |
2.6 |
336.0 |
| H4' |
C4' |
C3' |
C2' |
125.0 |
94.7 |
| H4' |
C4' |
C3' |
H3' |
244.8 |
213.4 |
| C1' |
O4' |
C4' |
C3' |
18.2 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
250.5 |
281.7 |
| C3' |
C2' |
C1' |
O4' |
13.5 |
23.8 |
| O2' |
C2' |
C1' |
O4' |
143.9 |
142.5 |
| O4' |
C1' |
C2' |
H2' |
256.0 |
265.3 |
| C2' |
C1' |
O4' |
N9 |
131.5 |
118.9 |
| C2' |
C1' |
O4' |
H1' |
244.0 |
241.2 |
| N9 |
C1' |
O4' |
H1' |
112.5 |
122.3 |
| O4' |
C1' |
N9 |
C8 |
178.6 |
27.0 |
| O4' |
C1' |
N9 |
C4 |
359.3 |
207.1 |
| O3' |
C3' |
C4' |
H4' |
2.6 |
336.0 |
| C4' |
C3' |
O3' |
C2' |
120.0 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
239.6 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
119.6 |
122.7 |
| O3' |
C3' |
C2' |
O2' |
351.3 |
359.9 |
| O3' |
C3' |
C2' |
C1' |
118.3 |
118.8 |
| O3' |
C3' |
C2' |
H2' |
240.0 |
237.3 |
| C2' |
C3' |
C4' |
H4' |
125.0 |
94.7 |
| C4' |
C3' |
C2' |
O3' |
238.2 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
120.4 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
13.5 |
23.8 |
| O3' |
C3' |
C2' |
H3' |
242.2 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
59.9 |
183.9 |
| O2' |
C2' |
C3' |
C1' |
233.0 |
241.1 |
| O2' |
C2' |
C3' |
H2' |
111.3 |
122.6 |
| C3' |
C2' |
O2' |
HO2' |
179.9 |
298.5 |
| C1' |
C2' |
C3' |
H2' |
238.3 |
241.5 |
| C3' |
C2' |
C1' |
N9 |
137.4 |
142.7 |
| C3' |
C2' |
C1' |
H1' |
248.6 |
265.0 |
| H3' |
C3' |
C4' |
H4' |
244.8 |
213.4 |
| C4' |
C3' |
H3' |
O3' |
120.4 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
241.5 |
245.3 |
| O3' |
C3' |
H3' |
C2' |
121.0 |
122.7 |
| H3' |
C3' |
O3' |
HO3' |
300.3 |
61.2 |
| H3' |
C3' |
C2' |
O2' |
109.1 |
122.5 |
| H3' |
C3' |
C2' |
C1' |
236.0 |
241.5 |
| H3' |
C3' |
C2' |
H2' |
357.8 |
360.0 |
| HO3' |
O3' |
C3' |
C2' |
59.9 |
183.9 |
| HO3' |
O3' |
C3' |
H3' |
300.3 |
61.2 |
| O4' |
C1' |
C2' |
O2' |
143.9 |
142.5 |
| O2' |
C2' |
C3' |
H3' |
109.1 |
122.5 |
| C3' |
C2' |
O2' |
C1' |
123.4 |
114.7 |
| C3' |
C2' |
O2' |
H2' |
244.2 |
237.4 |
| C1' |
C2' |
O2' |
H2' |
120.8 |
122.7 |
| O2' |
C2' |
C1' |
N9 |
267.8 |
261.5 |
| O2' |
C2' |
C1' |
H1' |
18.9 |
23.7 |
| O4' |
C1' |
C2' |
N9 |
236.1 |
241.1 |
| O4' |
C1' |
C2' |
H1' |
125.0 |
118.8 |
| C1' |
C2' |
C3' |
H3' |
236.0 |
241.5 |
| C3' |
C2' |
C1' |
O2' |
229.7 |
241.3 |
| C3' |
C2' |
C1' |
H2' |
117.6 |
118.5 |
| O2' |
C2' |
C1' |
H2' |
247.9 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
56.6 |
183.8 |
| N9 |
C1' |
C2' |
H1' |
248.9 |
237.8 |
| C2' |
C1' |
N9 |
C8 |
57.1 |
271.5 |
| C2' |
C1' |
N9 |
C4 |
237.8 |
91.6 |
| H2' |
C2' |
C3' |
H3' |
357.8 |
360.0 |
| C3' |
C2' |
H2' |
O2' |
123.8 |
122.6 |
| C3' |
C2' |
H2' |
C1' |
243.7 |
245.5 |
| O2' |
C2' |
H2' |
C1' |
119.9 |
122.9 |
| H2' |
C2' |
O2' |
HO2' |
295.8 |
61.1 |
| H2' |
C2' |
C1' |
N9 |
19.9 |
24.2 |
| H2' |
C2' |
C1' |
H1' |
131.0 |
146.4 |
| HO2' |
O2' |
C2' |
C1' |
56.6 |
183.8 |
| HO2' |
O2' |
C2' |
H2' |
295.8 |
61.1 |
| O4' |
C1' |
N9 |
C2' |
121.5 |
115.5 |
| O4' |
C1' |
N9 |
H1' |
235.5 |
237.7 |
| N9 |
C1' |
C2' |
H2' |
19.9 |
24.2 |
| C2' |
C1' |
N9 |
H1' |
114.1 |
122.2 |
| C8 |
N9 |
C1' |
C4 |
179.3 |
179.9 |
| C1' |
N9 |
C8 |
N7 |
180.5 |
180.1 |
| C1' |
N9 |
C8 |
H8 |
0.5 |
360.0 |
| C1' |
N9 |
C4 |
C5 |
179.4 |
180.2 |
| C1' |
N9 |
C4 |
C3 |
359.7 |
359.9 |
| O4' |
C1' |
H1' |
C2' |
244.4 |
244.6 |
| O4' |
C1' |
H1' |
N9 |
118.0 |
122.3 |
| H1' |
C1' |
C2' |
H2' |
131.0 |
146.4 |
| C2' |
C1' |
H1' |
N9 |
233.6 |
237.8 |
| H1' |
C1' |
N9 |
C8 |
303.1 |
149.3 |
| H1' |
C1' |
N9 |
C4 |
123.8 |
329.3 |
| C8 |
N9 |
C1' |
H1' |
303.1 |
149.3 |
| C1' |
N9 |
C8 |
C4 |
180.6 |
180.1 |
| C8 |
N9 |
C4 |
C5 |
360.0 |
0.3 |
| C8 |
N9 |
C4 |
C3 |
180.3 |
180.0 |
| N7 |
C8 |
N9 |
H8 |
179.9 |
180.1 |
| N9 |
C8 |
N7 |
C5 |
0.2 |
359.7 |
| C4 |
N9 |
C1' |
H1' |
123.8 |
329.3 |
| C1' |
N9 |
C4 |
C8 |
179.4 |
179.9 |
| C4 |
N9 |
C8 |
N7 |
359.9 |
0.0 |
| C4 |
N9 |
C8 |
H8 |
180.0 |
179.9 |
| N7 |
C5 |
C4 |
N9 |
0.1 |
359.6 |
| C6 |
C5 |
C4 |
N9 |
180.3 |
180.3 |
| C5 |
C4 |
N9 |
C3 |
179.7 |
180.2 |
| C2 |
C3 |
C4 |
N9 |
179.6 |
180.0 |
| N9 |
C4 |
C3 |
H3 |
359.6 |
0.0 |
| N7 |
C8 |
N9 |
C4 |
359.9 |
0.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
179.9 |
| C8 |
N7 |
C5 |
C6 |
179.6 |
179.5 |
| C8 |
N7 |
C5 |
C4 |
359.8 |
0.4 |
| H8 |
C8 |
N9 |
C4 |
180.0 |
179.9 |
| N9 |
C8 |
H8 |
N7 |
179.9 |
180.1 |
| H8 |
C8 |
N7 |
C5 |
180.1 |
179.8 |
| N9 |
C4 |
C5 |
N7 |
0.1 |
359.6 |
| C5 |
N7 |
C8 |
H8 |
180.1 |
179.8 |
| C6 |
C5 |
N7 |
C4 |
179.8 |
179.1 |
| N7 |
C5 |
C6 |
N6 |
0.0 |
0.7 |
| N7 |
C5 |
C6 |
N1 |
180.2 |
180.5 |
| N7 |
C5 |
C4 |
C3 |
179.8 |
179.8 |
| N9 |
C4 |
C5 |
C6 |
180.3 |
180.3 |
| N7 |
C5 |
C6 |
C4 |
180.2 |
181.0 |
| C6 |
C5 |
C4 |
C3 |
360.0 |
0.5 |
| N6 |
C6 |
C5 |
N1 |
179.8 |
180.3 |
| C5 |
C6 |
N6 |
HN61 |
180.0 |
179.7 |
| C5 |
C6 |
N6 |
HN62 |
54.8 |
359.4 |
| C5 |
C6 |
N1 |
C2 |
360.0 |
0.3 |
| N9 |
C4 |
C5 |
C3 |
180.3 |
179.8 |
| N7 |
C5 |
C4 |
C6 |
179.9 |
179.2 |
| C4 |
C5 |
C6 |
N6 |
179.8 |
179.7 |
| C4 |
C5 |
C6 |
N1 |
0.0 |
359.5 |
| C2 |
C3 |
C4 |
C5 |
360.0 |
359.7 |
| C5 |
C4 |
C3 |
H3 |
179.9 |
179.8 |
| N6 |
C6 |
C5 |
C4 |
179.8 |
179.7 |
| C5 |
C6 |
N6 |
N1 |
180.2 |
179.7 |
| N6 |
C6 |
N1 |
C2 |
180.2 |
180.0 |
| HN61 |
N6 |
C6 |
HN62 |
125.2 |
180.3 |
| N1 |
C6 |
C5 |
C4 |
0.0 |
359.5 |
| C5 |
C6 |
N1 |
N6 |
179.8 |
180.3 |
| N1 |
C6 |
N6 |
HN61 |
359.7 |
360.0 |
| N1 |
C6 |
N6 |
HN62 |
234.6 |
179.7 |
| C6 |
N1 |
C2 |
C3 |
360.0 |
0.0 |
| C6 |
N1 |
C2 |
H2 |
180.0 |
180.0 |
| HN61 |
N6 |
C6 |
N1 |
359.7 |
360.0 |
| C6 |
N6 |
HN61 |
HN62 |
234.8 |
179.7 |
| HN62 |
N6 |
C6 |
N1 |
234.6 |
179.7 |
| C6 |
N6 |
HN62 |
HN61 |
134.3 |
180.3 |
| C3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
C3 |
C4 |
0.1 |
360.0 |
| N1 |
C2 |
C3 |
H3 |
180.1 |
180.0 |
| N9 |
C4 |
C3 |
C2 |
179.6 |
180.0 |
| C5 |
C4 |
C3 |
C2 |
360.0 |
359.7 |
| N1 |
C2 |
C3 |
H2 |
180.0 |
180.0 |
| C4 |
C3 |
C2 |
H3 |
180.0 |
180.0 |
| N1 |
C2 |
H2 |
C3 |
180.0 |
180.0 |
| H2 |
C2 |
C3 |
C4 |
180.0 |
180.0 |
| H2 |
C2 |
C3 |
H3 |
0.1 |
360.0 |
| N9 |
C4 |
C3 |
C5 |
179.6 |
180.3 |
| C4 |
C3 |
C2 |
H2 |
180.0 |
180.0 |
| C2 |
C3 |
C4 |
H3 |
180.0 |
180.0 |
| H3 |
C3 |
C2 |
H2 |
0.1 |
360.0 |
| C2 |
C3 |
H3 |
C4 |
180.0 |
180.0 |