PDB Chemical Component ADN
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 ADN
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.425 |
1.429 |
| O5' |
HO5' |
0.950 |
0.967 |
| C5' |
C4' |
1.522 |
1.530 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.114 |
1.089 |
| C4' |
O4' |
1.463 |
1.444 |
| C4' |
C3' |
1.532 |
1.544 |
| C4' |
H4' |
1.114 |
1.089 |
| O4' |
C1' |
1.420 |
1.443 |
| C3' |
O3' |
1.434 |
1.429 |
| C3' |
C2' |
1.544 |
1.547 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
HO3' |
0.951 |
0.967 |
| C2' |
O2' |
1.432 |
1.429 |
| C2' |
C1' |
1.540 |
1.544 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
HO2' |
0.951 |
0.967 |
| C1' |
N9 |
1.478 |
1.463 |
| C1' |
H1' |
1.116 |
1.090 |
| N9 |
C8 |
1.403 |
1.363 |
| N9 |
C4 |
1.385 |
1.372 |
| C8 |
N7 |
1.313 |
1.302 |
| C8 |
H8 |
1.103 |
1.079 |
| N7 |
C5 |
1.405 |
1.355 |
| C5 |
C6 |
1.443 |
1.406 |
| C5 |
C4 |
1.395 |
1.404 |
| C6 |
N6 |
1.336 |
1.383 |
| C6 |
N1 |
1.353 |
1.328 |
| N6 |
HN61 |
1.020 |
0.970 |
| N6 |
HN62 |
1.020 |
0.970 |
| N1 |
C2 |
1.340 |
1.321 |
| C2 |
N3 |
1.344 |
1.317 |
| C2 |
H2 |
1.103 |
1.080 |
| N3 |
C4 |
1.348 |
1.329 |
Bond Angles for ADN
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
HO5' |
103.1 |
106.8 |
| O5' |
C5' |
C4' |
103.1 |
109.5 |
| O5' |
C5' |
H5'1 |
114.7 |
109.5 |
| O5' |
C5' |
H5'2 |
114.7 |
109.5 |
| C4' |
C5' |
H5'1 |
114.6 |
109.4 |
| C4' |
C5' |
H5'2 |
114.6 |
109.5 |
| C5' |
C4' |
O4' |
111.1 |
110.4 |
| C5' |
C4' |
C3' |
110.9 |
110.5 |
| C5' |
C4' |
H4' |
105.5 |
110.3 |
| H5'1 |
C5' |
H5'2 |
95.9 |
109.5 |
| O4' |
C4' |
C3' |
102.6 |
104.8 |
| O4' |
C4' |
H4' |
113.4 |
110.4 |
| C4' |
O4' |
C1' |
104.2 |
105.3 |
| C3' |
C4' |
H4' |
113.5 |
110.4 |
| C4' |
C3' |
O3' |
106.3 |
110.5 |
| C4' |
C3' |
C2' |
105.9 |
104.1 |
| C4' |
C3' |
H3' |
114.2 |
110.5 |
| O4' |
C1' |
C2' |
104.3 |
104.9 |
| O4' |
C1' |
N9 |
116.4 |
110.4 |
| O4' |
C1' |
H1' |
110.9 |
110.4 |
| O3' |
C3' |
C2' |
110.7 |
110.5 |
| O3' |
C3' |
H3' |
109.6 |
110.4 |
| C3' |
O3' |
HO3' |
106.3 |
106.8 |
| C2' |
C3' |
H3' |
110.0 |
110.6 |
| C3' |
C2' |
O2' |
113.8 |
110.5 |
| C3' |
C2' |
C1' |
101.5 |
104.0 |
| C3' |
C2' |
H2' |
114.5 |
110.5 |
| O2' |
C2' |
C1' |
116.1 |
110.8 |
| O2' |
C2' |
H2' |
99.4 |
110.4 |
| C2' |
O2' |
HO2' |
113.8 |
106.9 |
| C1' |
C2' |
H2' |
112.2 |
110.4 |
| C2' |
C1' |
N9 |
115.7 |
110.4 |
| C2' |
C1' |
H1' |
111.6 |
110.4 |
| N9 |
C1' |
H1' |
98.0 |
110.3 |
| C1' |
N9 |
C8 |
126.9 |
126.3 |
| C1' |
N9 |
C4 |
128.3 |
126.3 |
| C8 |
N9 |
C4 |
104.8 |
107.4 |
| N9 |
C8 |
N7 |
114.5 |
110.0 |
| N9 |
C8 |
H8 |
125.7 |
125.0 |
| N9 |
C4 |
C5 |
106.4 |
106.0 |
| N9 |
C4 |
N3 |
126.4 |
134.9 |
| N7 |
C8 |
H8 |
119.8 |
125.0 |
| C8 |
N7 |
C5 |
103.5 |
109.4 |
| N7 |
C5 |
C6 |
133.0 |
134.6 |
| N7 |
C5 |
C4 |
110.8 |
107.2 |
| C6 |
C5 |
C4 |
116.2 |
118.2 |
| C5 |
C6 |
N6 |
123.6 |
120.8 |
| C5 |
C6 |
N1 |
117.1 |
118.4 |
| C5 |
C4 |
N3 |
127.2 |
119.1 |
| N6 |
C6 |
N1 |
119.3 |
120.8 |
| C6 |
N6 |
HN61 |
123.6 |
120.0 |
| C6 |
N6 |
HN62 |
107.2 |
120.0 |
| C6 |
N1 |
C2 |
119.8 |
121.2 |
| HN61 |
N6 |
HN62 |
107.1 |
119.9 |
| N1 |
C2 |
N3 |
128.7 |
122.5 |
| N1 |
C2 |
H2 |
115.5 |
118.7 |
| N3 |
C2 |
H2 |
115.9 |
118.8 |
| C2 |
N3 |
C4 |
111.1 |
120.6 |
Torsion Angles for ADN
| 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 |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
56.8 |
61.5 |
| O5' |
C5' |
C4' |
C3' |
170.2 |
176.9 |
| O5' |
C5' |
C4' |
H4' |
293.6 |
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 |
305.3 |
60.0 |
| HO5' |
O5' |
C5' |
H5'2 |
54.8 |
299.9 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.4 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
246.5 |
244.6 |
| O4' |
C4' |
C5' |
H4' |
123.2 |
122.3 |
| C5' |
C4' |
O4' |
C1' |
161.1 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
236.7 |
237.7 |
| C5' |
C4' |
C3' |
O3' |
102.2 |
98.4 |
| C5' |
C4' |
C3' |
C2' |
220.0 |
217.1 |
| C5' |
C4' |
C3' |
H3' |
341.2 |
335.8 |
| H5'1 |
C5' |
O5' |
HO5' |
305.3 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
241.0 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
120.6 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
239.5 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
291.5 |
181.5 |
| H5'1 |
C5' |
C4' |
C3' |
45.0 |
296.9 |
| H5'1 |
C5' |
C4' |
H4' |
168.3 |
59.2 |
| H5'2 |
C5' |
O5' |
HO5' |
54.8 |
299.9 |
| O5' |
C5' |
H5'2 |
C4' |
119.0 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
239.4 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
120.5 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
182.0 |
301.5 |
| H5'2 |
C5' |
C4' |
C3' |
295.5 |
56.9 |
| H5'2 |
C5' |
C4' |
H4' |
58.8 |
179.2 |
| O4' |
C4' |
C5' |
H5'1 |
291.5 |
181.5 |
| O4' |
C4' |
C5' |
H5'2 |
182.0 |
301.5 |
| C5' |
C4' |
O4' |
C3' |
118.6 |
118.9 |
| C5' |
C4' |
O4' |
H4' |
241.4 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
122.9 |
118.8 |
| O4' |
C4' |
C3' |
O3' |
221.0 |
217.2 |
| O4' |
C4' |
C3' |
C2' |
338.7 |
335.9 |
| O4' |
C4' |
C3' |
H3' |
99.9 |
94.7 |
| C4' |
O4' |
C1' |
C2' |
312.7 |
319.5 |
| C4' |
O4' |
C1' |
N9 |
183.9 |
200.7 |
| C4' |
O4' |
C1' |
H1' |
73.0 |
78.4 |
| C3' |
C4' |
C5' |
H5'1 |
45.0 |
296.9 |
| C3' |
C4' |
C5' |
H5'2 |
295.5 |
56.9 |
| C5' |
C4' |
C3' |
O4' |
241.3 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
118.5 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
237.3 |
241.2 |
| C3' |
C4' |
O4' |
C1' |
42.5 |
40.5 |
| O3' |
C3' |
C4' |
C2' |
242.2 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
121.0 |
122.5 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
298.6 |
| C2' |
C3' |
C4' |
H3' |
238.8 |
241.2 |
| C4' |
C3' |
C2' |
O2' |
228.9 |
241.2 |
| C4' |
C3' |
C2' |
C1' |
354.4 |
0.1 |
| C4' |
C3' |
C2' |
H2' |
115.5 |
118.6 |
| H4' |
C4' |
C5' |
H5'1 |
168.3 |
59.2 |
| H4' |
C4' |
C5' |
H5'2 |
58.8 |
179.2 |
| C5' |
C4' |
H4' |
O4' |
121.8 |
122.3 |
| C5' |
C4' |
H4' |
C3' |
238.4 |
237.6 |
| O4' |
C4' |
H4' |
C3' |
116.6 |
115.3 |
| H4' |
C4' |
O4' |
C1' |
279.7 |
281.7 |
| H4' |
C4' |
C3' |
O3' |
343.7 |
336.1 |
| H4' |
C4' |
C3' |
C2' |
101.5 |
94.8 |
| H4' |
C4' |
C3' |
H3' |
222.7 |
213.5 |
| C1' |
O4' |
C4' |
C3' |
42.5 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
279.7 |
281.7 |
| C3' |
C2' |
C1' |
O4' |
31.7 |
23.8 |
| O2' |
C2' |
C1' |
O4' |
155.7 |
142.6 |
| O4' |
C1' |
C2' |
H2' |
269.0 |
265.3 |
| C2' |
C1' |
O4' |
N9 |
128.8 |
118.9 |
| C2' |
C1' |
O4' |
H1' |
239.7 |
241.1 |
| N9 |
C1' |
O4' |
H1' |
110.9 |
122.2 |
| O4' |
C1' |
N9 |
C8 |
57.3 |
27.0 |
| O4' |
C1' |
N9 |
C4 |
236.2 |
207.1 |
| O3' |
C3' |
C4' |
H4' |
343.7 |
336.1 |
| C4' |
C3' |
O3' |
C2' |
114.6 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
236.1 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
121.5 |
122.7 |
| O3' |
C3' |
C2' |
O2' |
343.7 |
359.9 |
| O3' |
C3' |
C2' |
C1' |
109.2 |
118.8 |
| O3' |
C3' |
C2' |
H2' |
230.3 |
237.4 |
| C2' |
C3' |
C4' |
H4' |
101.5 |
94.8 |
| C4' |
C3' |
C2' |
O3' |
245.2 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
123.9 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
31.7 |
23.8 |
| O3' |
C3' |
C2' |
H3' |
238.7 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
65.4 |
183.9 |
| O2' |
C2' |
C3' |
C1' |
234.5 |
241.1 |
| O2' |
C2' |
C3' |
H2' |
113.4 |
122.5 |
| C3' |
C2' |
O2' |
HO2' |
180.0 |
298.5 |
| C1' |
C2' |
C3' |
H2' |
238.9 |
241.5 |
| C3' |
C2' |
C1' |
N9 |
160.9 |
142.8 |
| C3' |
C2' |
C1' |
H1' |
271.9 |
265.0 |
| H3' |
C3' |
C4' |
H4' |
222.7 |
213.5 |
| C4' |
C3' |
H3' |
O3' |
119.2 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
241.1 |
245.3 |
| O3' |
C3' |
H3' |
C2' |
121.9 |
122.7 |
| H3' |
C3' |
O3' |
HO3' |
303.9 |
61.2 |
| H3' |
C3' |
C2' |
O2' |
105.1 |
122.5 |
| H3' |
C3' |
C2' |
C1' |
230.5 |
241.4 |
| H3' |
C3' |
C2' |
H2' |
351.7 |
359.9 |
| HO3' |
O3' |
C3' |
C2' |
65.4 |
183.9 |
| HO3' |
O3' |
C3' |
H3' |
303.9 |
61.2 |
| O4' |
C1' |
C2' |
O2' |
155.7 |
142.6 |
| O2' |
C2' |
C3' |
H3' |
105.1 |
122.5 |
| C3' |
C2' |
O2' |
C1' |
117.3 |
114.7 |
| C3' |
C2' |
O2' |
H2' |
237.8 |
237.4 |
| C1' |
C2' |
O2' |
H2' |
120.5 |
122.7 |
| O2' |
C2' |
C1' |
N9 |
284.9 |
261.5 |
| O2' |
C2' |
C1' |
H1' |
35.8 |
23.7 |
| O4' |
C1' |
C2' |
N9 |
230.8 |
241.1 |
| O4' |
C1' |
C2' |
H1' |
119.8 |
118.9 |
| C1' |
C2' |
C3' |
H3' |
230.5 |
241.4 |
| C3' |
C2' |
C1' |
O2' |
236.0 |
241.3 |
| C3' |
C2' |
C1' |
H2' |
122.7 |
118.6 |
| O2' |
C2' |
C1' |
H2' |
246.7 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
62.7 |
183.8 |
| N9 |
C1' |
C2' |
H1' |
249.0 |
237.8 |
| C2' |
C1' |
N9 |
C8 |
294.3 |
271.5 |
| C2' |
C1' |
N9 |
C4 |
113.2 |
91.6 |
| H2' |
C2' |
C3' |
H3' |
351.7 |
359.9 |
| C3' |
C2' |
H2' |
O2' |
121.7 |
122.6 |
| C3' |
C2' |
H2' |
C1' |
245.0 |
245.5 |
| O2' |
C2' |
H2' |
C1' |
123.3 |
122.9 |
| H2' |
C2' |
O2' |
HO2' |
302.2 |
61.1 |
| H2' |
C2' |
C1' |
N9 |
38.2 |
24.2 |
| H2' |
C2' |
C1' |
H1' |
149.1 |
146.4 |
| HO2' |
O2' |
C2' |
C1' |
62.7 |
183.8 |
| HO2' |
O2' |
C2' |
H2' |
302.2 |
61.1 |
| O4' |
C1' |
N9 |
C2' |
123.0 |
115.5 |
| O4' |
C1' |
N9 |
H1' |
241.8 |
237.7 |
| N9 |
C1' |
C2' |
H2' |
38.2 |
24.2 |
| C2' |
C1' |
N9 |
H1' |
118.8 |
122.3 |
| C8 |
N9 |
C1' |
C4 |
181.2 |
179.9 |
| C1' |
N9 |
C8 |
N7 |
178.7 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
358.8 |
0.1 |
| C1' |
N9 |
C4 |
C5 |
181.5 |
180.2 |
| C1' |
N9 |
C4 |
N3 |
0.9 |
360.0 |
| O4' |
C1' |
H1' |
C2' |
244.2 |
244.5 |
| O4' |
C1' |
H1' |
N9 |
122.3 |
122.3 |
| H1' |
C1' |
C2' |
H2' |
149.1 |
146.4 |
| C2' |
C1' |
H1' |
N9 |
238.2 |
237.8 |
| H1' |
C1' |
N9 |
C8 |
175.6 |
149.2 |
| H1' |
C1' |
N9 |
C4 |
354.4 |
329.3 |
| C8 |
N9 |
C1' |
H1' |
175.6 |
149.2 |
| C1' |
N9 |
C8 |
C4 |
179.1 |
180.1 |
| C8 |
N9 |
C4 |
C5 |
0.5 |
0.3 |
| C8 |
N9 |
C4 |
N3 |
180.0 |
180.0 |
| N7 |
C8 |
N9 |
H8 |
179.9 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
360.0 |
359.8 |
| C4 |
N9 |
C1' |
H1' |
354.4 |
329.3 |
| C1' |
N9 |
C4 |
C8 |
181.0 |
179.9 |
| C4 |
N9 |
C8 |
N7 |
359.7 |
359.9 |
| C4 |
N9 |
C8 |
H8 |
179.7 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
359.4 |
359.6 |
| C6 |
C5 |
C4 |
N9 |
179.2 |
180.4 |
| C5 |
C4 |
N9 |
N3 |
180.6 |
180.3 |
| C2 |
N3 |
C4 |
N9 |
180.8 |
180.0 |
| N7 |
C8 |
N9 |
C4 |
359.7 |
359.9 |
| N9 |
C8 |
N7 |
H8 |
180.1 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
180.7 |
179.4 |
| C8 |
N7 |
C5 |
C4 |
0.4 |
0.4 |
| H8 |
C8 |
N9 |
C4 |
179.7 |
180.0 |
| N9 |
C8 |
H8 |
N7 |
179.9 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
179.9 |
179.8 |
| N9 |
C4 |
C5 |
N7 |
359.4 |
359.6 |
| C5 |
N7 |
C8 |
H8 |
179.9 |
179.8 |
| C6 |
C5 |
N7 |
C4 |
180.3 |
179.0 |
| N7 |
C5 |
C6 |
N6 |
359.8 |
0.8 |
| N7 |
C5 |
C6 |
N1 |
179.7 |
180.4 |
| N7 |
C5 |
C4 |
N3 |
180.0 |
179.8 |
| N9 |
C4 |
C5 |
C6 |
179.2 |
180.4 |
| N7 |
C5 |
C6 |
C4 |
179.7 |
181.0 |
| C6 |
C5 |
C4 |
N3 |
359.7 |
0.6 |
| N6 |
C6 |
C5 |
N1 |
180.1 |
180.4 |
| C5 |
C6 |
N6 |
HN61 |
179.9 |
179.7 |
| C5 |
C6 |
N6 |
HN62 |
54.8 |
359.4 |
| C5 |
C6 |
N1 |
C2 |
0.3 |
0.3 |
| N9 |
C4 |
C5 |
N3 |
179.4 |
179.8 |
| N7 |
C5 |
C4 |
C6 |
180.2 |
179.2 |
| C4 |
C5 |
C6 |
N6 |
180.2 |
179.8 |
| C4 |
C5 |
C6 |
N1 |
0.0 |
359.4 |
| C2 |
N3 |
C4 |
C5 |
0.1 |
359.8 |
| N6 |
C6 |
C5 |
C4 |
180.2 |
179.8 |
| C5 |
C6 |
N6 |
N1 |
179.9 |
179.6 |
| N6 |
C6 |
N1 |
C2 |
180.2 |
180.0 |
| HN61 |
N6 |
C6 |
HN62 |
125.2 |
180.3 |
| N1 |
C6 |
C5 |
C4 |
0.0 |
359.4 |
| C5 |
C6 |
N1 |
N6 |
180.1 |
180.4 |
| N1 |
C6 |
N6 |
HN61 |
0.1 |
0.1 |
| N1 |
C6 |
N6 |
HN62 |
234.9 |
179.8 |
| C6 |
N1 |
C2 |
N3 |
359.5 |
0.0 |
| C6 |
N1 |
C2 |
H2 |
179.5 |
179.9 |
| HN61 |
N6 |
C6 |
N1 |
0.1 |
0.1 |
| C6 |
N6 |
HN61 |
HN62 |
234.8 |
179.7 |
| HN62 |
N6 |
C6 |
N1 |
234.9 |
179.8 |
| C6 |
N6 |
HN62 |
HN61 |
134.6 |
180.3 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
| N1 |
C2 |
N3 |
C4 |
0.3 |
359.9 |
| N9 |
C4 |
N3 |
C2 |
180.8 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
0.1 |
359.8 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.1 |
| H2 |
C2 |
N3 |
C4 |
180.2 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
180.7 |
180.3 |
| C4 |
N3 |
C2 |
H2 |
180.2 |
180.0 |