PDB Chemical Component 2AD
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 2AD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.437 |
1.429 |
| O5' |
H5' |
0.990 |
0.967 |
| C5' |
C4' |
1.512 |
1.529 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C4' |
O4' |
1.451 |
1.438 |
| C4' |
C3' |
1.520 |
1.540 |
| C4' |
H4' |
1.100 |
1.089 |
| O4' |
C1' |
1.417 |
1.444 |
| C3' |
O3' |
1.425 |
1.429 |
| C3' |
C2' |
1.525 |
1.548 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HA |
0.990 |
0.967 |
| C2' |
C1' |
1.526 |
1.549 |
| C2' |
N |
1.475 |
1.469 |
| C2' |
H2' |
1.101 |
1.090 |
| C1' |
N9 |
1.459 |
1.464 |
| C1' |
H1' |
1.100 |
1.091 |
| N9 |
C8 |
1.375 |
1.363 |
| N9 |
C4 |
1.373 |
1.371 |
| C8 |
N7 |
1.310 |
1.301 |
| C8 |
H8 |
1.062 |
1.080 |
| N7 |
C5 |
1.387 |
1.355 |
| C5 |
C6 |
1.403 |
1.405 |
| C5 |
C4 |
1.382 |
1.404 |
| C6 |
N6 |
1.335 |
1.384 |
| C6 |
N1 |
1.352 |
1.328 |
| N6 |
H6N1 |
0.995 |
0.971 |
| N6 |
H6N2 |
0.995 |
0.970 |
| N1 |
C2 |
1.340 |
1.320 |
| C2 |
N3 |
1.328 |
1.317 |
| C2 |
H2 |
1.062 |
1.080 |
| N3 |
C4 |
1.345 |
1.329 |
| N |
HN1 |
1.030 |
1.009 |
| N |
HN2 |
1.030 |
1.009 |
Bond Angles for 2AD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
H5' |
109.5 |
106.8 |
| O5' |
C5' |
C4' |
110.2 |
109.5 |
| O5' |
C5' |
H5'1 |
109.3 |
109.5 |
| O5' |
C5' |
H5'2 |
109.0 |
109.4 |
| C4' |
C5' |
H5'1 |
109.3 |
109.5 |
| C4' |
C5' |
H5'2 |
109.1 |
109.4 |
| C5' |
C4' |
O4' |
109.5 |
110.0 |
| C5' |
C4' |
C3' |
114.2 |
109.9 |
| C5' |
C4' |
H4' |
104.7 |
109.9 |
| H5'1 |
C5' |
H5'2 |
110.0 |
109.5 |
| O4' |
C4' |
C3' |
104.3 |
107.3 |
| O4' |
C4' |
H4' |
114.6 |
109.8 |
| C4' |
O4' |
C1' |
109.3 |
107.0 |
| C3' |
C4' |
H4' |
109.9 |
109.9 |
| C4' |
C3' |
O3' |
110.4 |
110.6 |
| C4' |
C3' |
C2' |
103.2 |
104.2 |
| C4' |
C3' |
H3' |
113.9 |
110.5 |
| O4' |
C1' |
C2' |
108.4 |
103.5 |
| O4' |
C1' |
N9 |
108.8 |
110.7 |
| O4' |
C1' |
H1' |
112.4 |
110.6 |
| O3' |
C3' |
C2' |
112.1 |
110.5 |
| O3' |
C3' |
H3' |
105.3 |
110.4 |
| C3' |
O3' |
HA |
109.5 |
106.8 |
| C2' |
C3' |
H3' |
112.2 |
110.5 |
| C3' |
C2' |
C1' |
102.9 |
102.1 |
| C3' |
C2' |
N |
119.5 |
110.9 |
| C3' |
C2' |
H2' |
108.0 |
110.9 |
| C1' |
C2' |
N |
111.0 |
110.9 |
| C1' |
C2' |
H2' |
116.9 |
110.9 |
| C2' |
C1' |
N9 |
114.2 |
110.8 |
| C2' |
C1' |
H1' |
106.8 |
110.6 |
| N |
C2' |
H2' |
99.3 |
110.8 |
| C2' |
N |
HN1 |
109.5 |
106.6 |
| C2' |
N |
HN2 |
109.5 |
106.7 |
| N9 |
C1' |
H1' |
106.3 |
110.5 |
| C1' |
N9 |
C8 |
128.6 |
126.3 |
| C1' |
N9 |
C4 |
125.6 |
126.4 |
| C8 |
N9 |
C4 |
105.9 |
107.4 |
| N9 |
C8 |
N7 |
113.7 |
110.0 |
| N9 |
C8 |
H8 |
123.1 |
125.1 |
| N9 |
C4 |
C5 |
105.7 |
106.1 |
| N9 |
C4 |
N3 |
127.3 |
134.9 |
| N7 |
C8 |
H8 |
123.2 |
125.0 |
| C8 |
N7 |
C5 |
103.9 |
109.5 |
| N7 |
C5 |
C6 |
132.2 |
134.7 |
| N7 |
C5 |
C4 |
110.8 |
107.1 |
| C6 |
C5 |
C4 |
117.0 |
118.2 |
| C5 |
C6 |
N6 |
123.6 |
120.8 |
| C5 |
C6 |
N1 |
117.7 |
118.5 |
| C5 |
C4 |
N3 |
126.9 |
119.1 |
| N6 |
C6 |
N1 |
118.7 |
120.7 |
| C6 |
N6 |
H6N1 |
120.0 |
120.1 |
| C6 |
N6 |
H6N2 |
120.0 |
120.0 |
| C6 |
N1 |
C2 |
118.5 |
121.2 |
| H6N1 |
N6 |
H6N2 |
120.0 |
119.9 |
| N1 |
C2 |
N3 |
129.3 |
122.5 |
| N1 |
C2 |
H2 |
115.4 |
118.8 |
| N3 |
C2 |
H2 |
115.4 |
118.8 |
| C2 |
N3 |
C4 |
110.6 |
120.6 |
| HN1 |
N |
HN2 |
109.5 |
106.7 |
Torsion Angles for 2AD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
239.9 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
119.7 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
60.2 |
62.1 |
| O5' |
C5' |
C4' |
C3' |
176.7 |
180.0 |
| O5' |
C5' |
C4' |
H4' |
296.9 |
301.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
239.8 |
120.0 |
| H5' |
O5' |
C5' |
C4' |
127.6 |
180.0 |
| H5' |
O5' |
C5' |
H5'1 |
247.7 |
60.0 |
| H5' |
O5' |
C5' |
H5'2 |
7.9 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
127.6 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
120.1 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
240.3 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
120.2 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
243.5 |
242.1 |
| O4' |
C4' |
C5' |
H4' |
123.3 |
121.0 |
| C5' |
C4' |
O4' |
C1' |
149.3 |
146.0 |
| C3' |
C4' |
C5' |
H4' |
239.8 |
239.0 |
| C5' |
C4' |
C3' |
O3' |
85.9 |
119.6 |
| C5' |
C4' |
C3' |
C2' |
205.8 |
238.4 |
| C5' |
C4' |
C3' |
H3' |
327.7 |
357.1 |
| H5'1 |
C5' |
O5' |
H5' |
247.7 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
239.3 |
120.1 |
| O5' |
C5' |
H5'1 |
H5'2 |
119.6 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
240.3 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
300.1 |
182.1 |
| H5'1 |
C5' |
C4' |
C3' |
56.6 |
300.0 |
| H5'1 |
C5' |
C4' |
H4' |
176.8 |
61.1 |
| H5'2 |
C5' |
O5' |
H5' |
7.9 |
300.0 |
| O5' |
C5' |
H5'2 |
C4' |
120.4 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
240.2 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
119.8 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
179.9 |
302.1 |
| H5'2 |
C5' |
C4' |
C3' |
296.3 |
60.0 |
| H5'2 |
C5' |
C4' |
H4' |
56.6 |
181.1 |
| O4' |
C4' |
C5' |
H5'1 |
300.1 |
182.1 |
| O4' |
C4' |
C5' |
H5'2 |
179.9 |
302.1 |
| C5' |
C4' |
O4' |
C3' |
122.6 |
119.5 |
| C5' |
C4' |
O4' |
H4' |
242.8 |
238.9 |
| C3' |
C4' |
O4' |
H4' |
120.2 |
119.4 |
| O4' |
C4' |
C3' |
O3' |
205.4 |
239.3 |
| O4' |
C4' |
C3' |
C2' |
325.3 |
358.0 |
| O4' |
C4' |
C3' |
H3' |
87.2 |
116.7 |
| C4' |
O4' |
C1' |
C2' |
352.4 |
320.0 |
| C4' |
O4' |
C1' |
N9 |
227.7 |
201.3 |
| C4' |
O4' |
C1' |
H1' |
110.2 |
78.5 |
| C3' |
C4' |
C5' |
H5'1 |
56.6 |
300.0 |
| C3' |
C4' |
C5' |
H5'2 |
296.3 |
60.0 |
| C5' |
C4' |
C3' |
O4' |
240.5 |
240.4 |
| C5' |
C4' |
C3' |
H4' |
117.3 |
121.0 |
| O4' |
C4' |
C3' |
H4' |
236.7 |
240.7 |
| C3' |
C4' |
O4' |
C1' |
26.7 |
26.4 |
| O3' |
C3' |
C4' |
C2' |
240.1 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
118.1 |
122.5 |
| C4' |
C3' |
O3' |
HA |
141.6 |
294.8 |
| C2' |
C3' |
C4' |
H3' |
238.1 |
241.3 |
| C4' |
C3' |
C2' |
C1' |
29.5 |
339.1 |
| C4' |
C3' |
C2' |
N |
266.0 |
220.9 |
| C4' |
C3' |
C2' |
H2' |
153.7 |
97.3 |
| H4' |
C4' |
C5' |
H5'1 |
176.8 |
61.1 |
| H4' |
C4' |
C5' |
H5'2 |
56.6 |
181.1 |
| C5' |
C4' |
H4' |
O4' |
120.0 |
121.2 |
| C5' |
C4' |
H4' |
C3' |
236.9 |
238.9 |
| O4' |
C4' |
H4' |
C3' |
117.0 |
117.8 |
| H4' |
C4' |
O4' |
C1' |
266.5 |
267.0 |
| H4' |
C4' |
C3' |
O3' |
328.6 |
358.6 |
| H4' |
C4' |
C3' |
C2' |
88.6 |
117.3 |
| H4' |
C4' |
C3' |
H3' |
210.5 |
236.1 |
| C1' |
O4' |
C4' |
C3' |
26.7 |
26.4 |
| C1' |
O4' |
C4' |
H4' |
266.5 |
267.0 |
| C3' |
C2' |
C1' |
O4' |
345.6 |
36.9 |
| O4' |
C1' |
C2' |
N |
114.6 |
155.2 |
| O4' |
C1' |
C2' |
H2' |
227.5 |
278.7 |
| C2' |
C1' |
O4' |
N9 |
124.7 |
118.7 |
| C2' |
C1' |
O4' |
H1' |
242.2 |
241.6 |
| N9 |
C1' |
O4' |
H1' |
117.5 |
122.8 |
| O4' |
C1' |
N9 |
C8 |
76.6 |
28.5 |
| O4' |
C1' |
N9 |
C4 |
257.5 |
208.3 |
| O3' |
C3' |
C4' |
H4' |
328.6 |
358.6 |
| C4' |
C3' |
O3' |
C2' |
114.4 |
114.9 |
| C4' |
C3' |
O3' |
H3' |
236.7 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
122.3 |
122.5 |
| O3' |
C3' |
C2' |
C1' |
148.3 |
98.0 |
| O3' |
C3' |
C2' |
N |
24.7 |
339.8 |
| O3' |
C3' |
C2' |
H2' |
272.5 |
216.2 |
| C2' |
C3' |
C4' |
H4' |
88.6 |
117.3 |
| C4' |
C3' |
C2' |
O3' |
241.2 |
241.2 |
| C4' |
C3' |
C2' |
H3' |
123.0 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
345.6 |
36.9 |
| O3' |
C3' |
C2' |
H3' |
241.8 |
237.6 |
| C2' |
C3' |
O3' |
HA |
27.2 |
180.0 |
| C1' |
C2' |
C3' |
N |
123.6 |
118.2 |
| C1' |
C2' |
C3' |
H2' |
235.8 |
241.8 |
| C3' |
C2' |
C1' |
N9 |
107.1 |
155.6 |
| C3' |
C2' |
C1' |
H1' |
224.3 |
278.5 |
| N |
C2' |
C3' |
H2' |
112.2 |
123.6 |
| C3' |
C2' |
N |
HN1 |
338.1 |
295.7 |
| C3' |
C2' |
N |
HN2 |
98.2 |
49.4 |
| H3' |
C3' |
C4' |
H4' |
210.5 |
236.1 |
| C4' |
C3' |
H3' |
O3' |
121.0 |
122.7 |
| C4' |
C3' |
H3' |
C2' |
243.2 |
245.2 |
| O3' |
C3' |
H3' |
C2' |
122.2 |
122.5 |
| H3' |
C3' |
O3' |
HA |
264.9 |
57.4 |
| H3' |
C3' |
C2' |
C1' |
266.5 |
220.4 |
| H3' |
C3' |
C2' |
N |
142.9 |
102.2 |
| H3' |
C3' |
C2' |
H2' |
30.7 |
338.6 |
| HA |
O3' |
C3' |
C2' |
27.2 |
180.0 |
| HA |
O3' |
C3' |
H3' |
264.9 |
57.4 |
| O4' |
C1' |
C2' |
N9 |
238.6 |
241.3 |
| O4' |
C1' |
C2' |
H1' |
121.3 |
118.4 |
| C1' |
C2' |
C3' |
H3' |
266.5 |
220.4 |
| C3' |
C2' |
C1' |
N |
231.0 |
241.8 |
| C3' |
C2' |
C1' |
H2' |
118.1 |
118.2 |
| N |
C2' |
C1' |
H2' |
247.1 |
236.5 |
| C1' |
C2' |
N |
HN1 |
218.6 |
182.9 |
| C1' |
C2' |
N |
HN2 |
338.6 |
296.7 |
| N9 |
C1' |
C2' |
H1' |
242.8 |
237.1 |
| C2' |
C1' |
N9 |
C8 |
315.4 |
274.3 |
| C2' |
C1' |
N9 |
C4 |
136.3 |
94.1 |
| N |
C2' |
C3' |
H3' |
142.9 |
102.2 |
| C3' |
C2' |
N |
C1' |
119.5 |
112.7 |
| C3' |
C2' |
N |
H2' |
243.2 |
236.3 |
| C1' |
C2' |
N |
H2' |
123.6 |
123.6 |
| N |
C2' |
C1' |
N9 |
236.1 |
273.8 |
| N |
C2' |
C1' |
H1' |
353.3 |
36.7 |
| HN1 |
N |
C2' |
HN2 |
240.0 |
246.2 |
| H2' |
C2' |
C3' |
H3' |
30.7 |
338.6 |
| C3' |
C2' |
H2' |
C1' |
244.6 |
247.3 |
| C3' |
C2' |
H2' |
N |
125.2 |
123.7 |
| C1' |
C2' |
H2' |
N |
240.6 |
236.4 |
| H2' |
C2' |
C1' |
N9 |
348.9 |
37.3 |
| H2' |
C2' |
C1' |
H1' |
106.2 |
160.2 |
| H2' |
C2' |
N |
HN1 |
95.0 |
59.3 |
| H2' |
C2' |
N |
HN2 |
215.0 |
173.1 |
| O4' |
C1' |
N9 |
C2' |
121.2 |
114.2 |
| O4' |
C1' |
N9 |
H1' |
238.7 |
237.1 |
| N9 |
C1' |
C2' |
N |
236.1 |
273.8 |
| N9 |
C1' |
C2' |
H2' |
348.9 |
37.3 |
| C2' |
C1' |
N9 |
H1' |
117.5 |
122.9 |
| C8 |
N9 |
C1' |
C4 |
179.1 |
180.2 |
| C1' |
N9 |
C8 |
N7 |
181.7 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
1.7 |
0.0 |
| C1' |
N9 |
C4 |
C5 |
178.2 |
179.8 |
| C1' |
N9 |
C4 |
N3 |
358.4 |
0.7 |
| O4' |
C1' |
H1' |
C2' |
241.3 |
246.0 |
| O4' |
C1' |
H1' |
N9 |
118.9 |
122.9 |
| H1' |
C1' |
C2' |
N |
353.3 |
36.7 |
| H1' |
C1' |
C2' |
H2' |
106.2 |
160.2 |
| C2' |
C1' |
H1' |
N9 |
237.7 |
236.9 |
| H1' |
C1' |
N9 |
C8 |
197.9 |
151.4 |
| H1' |
C1' |
N9 |
C4 |
18.8 |
331.2 |
| C8 |
N9 |
C1' |
H1' |
197.9 |
151.4 |
| C1' |
N9 |
C8 |
C4 |
180.7 |
179.8 |
| C8 |
N9 |
C4 |
C5 |
359.0 |
359.6 |
| C8 |
N9 |
C4 |
N3 |
179.1 |
180.5 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
359.6 |
0.0 |
| C4 |
N9 |
C1' |
H1' |
18.8 |
331.2 |
| C1' |
N9 |
C4 |
C8 |
179.3 |
180.2 |
| C4 |
N9 |
C8 |
N7 |
0.9 |
0.2 |
| C4 |
N9 |
C8 |
H8 |
180.9 |
180.2 |
| N7 |
C5 |
C4 |
N9 |
0.9 |
0.4 |
| C6 |
C5 |
C4 |
N9 |
180.8 |
180.1 |
| C5 |
C4 |
N9 |
N3 |
179.8 |
179.1 |
| C2 |
N3 |
C4 |
N9 |
179.5 |
179.6 |
| N7 |
C8 |
N9 |
C4 |
0.9 |
0.2 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
179.8 |
180.0 |
| C8 |
N7 |
C5 |
C4 |
359.7 |
359.8 |
| H8 |
C8 |
N9 |
C4 |
180.9 |
180.2 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
179.6 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
0.9 |
0.4 |
| C5 |
N7 |
C8 |
H8 |
179.6 |
180.0 |
| C6 |
C5 |
N7 |
C4 |
180.1 |
180.3 |
| N7 |
C5 |
C6 |
N6 |
359.4 |
0.0 |
| N7 |
C5 |
C6 |
N1 |
179.5 |
180.0 |
| N7 |
C5 |
C4 |
N3 |
180.7 |
179.6 |
| N9 |
C4 |
C5 |
C6 |
180.8 |
180.1 |
| N7 |
C5 |
C6 |
C4 |
179.8 |
179.7 |
| C6 |
C5 |
C4 |
N3 |
0.6 |
359.4 |
| N6 |
C6 |
C5 |
N1 |
180.0 |
180.0 |
| C5 |
C6 |
N6 |
H6N1 |
360.0 |
180.0 |
| C5 |
C6 |
N6 |
H6N2 |
180.0 |
360.0 |
| C5 |
C6 |
N1 |
C2 |
0.0 |
360.0 |
| N9 |
C4 |
C5 |
N3 |
180.2 |
180.7 |
| N7 |
C5 |
C4 |
C6 |
180.1 |
180.2 |
| C4 |
C5 |
C6 |
N6 |
179.6 |
180.3 |
| C4 |
C5 |
C6 |
N1 |
359.6 |
0.3 |
| C2 |
N3 |
C4 |
C5 |
359.7 |
0.6 |
| N6 |
C6 |
C5 |
C4 |
179.6 |
180.3 |
| C5 |
C6 |
N6 |
N1 |
180.0 |
180.0 |
| N6 |
C6 |
N1 |
C2 |
180.0 |
180.0 |
| H6N1 |
N6 |
C6 |
H6N2 |
180.0 |
180.1 |
| N1 |
C6 |
C5 |
C4 |
359.6 |
0.3 |
| C5 |
C6 |
N1 |
N6 |
180.0 |
180.0 |
| N1 |
C6 |
N6 |
H6N1 |
180.0 |
0.1 |
| N1 |
C6 |
N6 |
H6N2 |
360.0 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
0.3 |
0.0 |
| C6 |
N1 |
C2 |
H2 |
180.3 |
179.9 |
| H6N1 |
N6 |
C6 |
N1 |
180.0 |
0.1 |
| C6 |
N6 |
H6N1 |
H6N2 |
180.0 |
179.9 |
| H6N2 |
N6 |
C6 |
N1 |
360.0 |
180.0 |
| C6 |
N6 |
H6N2 |
H6N1 |
180.0 |
180.1 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
| N1 |
C2 |
N3 |
C4 |
359.8 |
359.7 |
| N9 |
C4 |
N3 |
C2 |
179.5 |
179.6 |
| C5 |
C4 |
N3 |
C2 |
359.7 |
0.6 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.1 |
| H2 |
C2 |
N3 |
C4 |
179.8 |
179.8 |
| N9 |
C4 |
N3 |
C5 |
179.8 |
179.0 |
| C4 |
N3 |
C2 |
H2 |
179.8 |
179.8 |
| HN1 |
N |
C2' |
H2' |
95.0 |
59.3 |
| C2' |
N |
HN1 |
HN2 |
120.0 |
113.8 |
| HN2 |
N |
C2' |
H2' |
215.0 |
173.1 |
| C2' |
N |
HN2 |
HN1 |
240.0 |
246.3 |