PDB Chemical Component 0DA
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 0DA
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
C8A |
N9A |
1.364 |
1.363 |
C8A |
N7A |
1.307 |
1.301 |
N9A |
C4A |
1.373 |
1.372 |
N9A |
C1' |
1.469 |
1.465 |
C4A |
C5A |
1.367 |
1.405 |
C4A |
N3A |
1.360 |
1.329 |
C5A |
N7A |
1.401 |
1.355 |
C5A |
C6A |
1.412 |
1.405 |
N3A |
C2A |
1.333 |
1.316 |
C2A |
N1A |
1.333 |
1.321 |
N1A |
C6A |
1.343 |
1.329 |
C6A |
N6A |
1.321 |
1.384 |
C4' |
O4' |
1.404 |
1.445 |
C4' |
C3' |
1.532 |
1.545 |
O4' |
C1' |
1.403 |
1.444 |
C3' |
C2' |
1.521 |
1.545 |
C2' |
C1' |
1.527 |
1.546 |
C3' |
O3' |
1.430 |
1.429 |
C4' |
C5' |
1.540 |
1.531 |
C5' |
O5' |
1.430 |
1.429 |
O5' |
P |
1.719 |
1.610 |
P |
OP2 |
1.721 |
1.610 |
P |
OP3 |
1.720 |
1.610 |
P |
OP1 |
1.721 |
1.481 |
C8A |
H8A |
1.080 |
1.080 |
C2A |
H2A |
1.080 |
1.080 |
N6A |
HN61 |
1.000 |
0.971 |
N6A |
HN62 |
1.000 |
0.970 |
C4' |
H4' |
1.100 |
1.090 |
C3' |
H3' |
1.100 |
1.089 |
C2' |
H2' |
1.100 |
1.090 |
C2' |
H2'' |
1.100 |
1.090 |
C1' |
H1' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.967 |
C5' |
H5' |
1.100 |
1.090 |
C5' |
H5'' |
1.100 |
1.090 |
OP2 |
H2P |
0.950 |
0.967 |
OP3 |
HOP3 |
0.949 |
0.966 |
Bond Angles for 0DA
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
N9A |
C8A |
N7A |
114.2 |
110.0 |
C8A |
N9A |
C4A |
105.9 |
107.4 |
C8A |
N9A |
C1' |
126.8 |
126.3 |
N9A |
C8A |
H8A |
122.9 |
125.0 |
C8A |
N7A |
C5A |
103.0 |
109.4 |
N7A |
C8A |
H8A |
122.9 |
125.0 |
C4A |
N9A |
C1' |
126.1 |
126.3 |
N9A |
C4A |
C5A |
105.8 |
106.0 |
N9A |
C4A |
N3A |
127.1 |
134.9 |
N9A |
C1' |
O4' |
107.0 |
110.4 |
N9A |
C1' |
C2' |
116.4 |
110.3 |
N9A |
C1' |
H1' |
106.3 |
110.3 |
C5A |
C4A |
N3A |
127.2 |
119.1 |
C4A |
C5A |
N7A |
111.0 |
107.2 |
C4A |
C5A |
C6A |
114.5 |
118.1 |
C4A |
N3A |
C2A |
111.6 |
120.6 |
N7A |
C5A |
C6A |
134.5 |
134.7 |
C5A |
C6A |
N1A |
121.0 |
118.5 |
C5A |
C6A |
N6A |
122.6 |
120.8 |
N3A |
C2A |
N1A |
128.4 |
122.5 |
N3A |
C2A |
H2A |
115.8 |
118.7 |
C2A |
N1A |
C6A |
117.3 |
121.1 |
N1A |
C2A |
H2A |
115.8 |
118.8 |
N1A |
C6A |
N6A |
116.4 |
120.7 |
C6A |
N6A |
HN61 |
109.5 |
120.0 |
C6A |
N6A |
HN62 |
109.5 |
120.1 |
O4' |
C4' |
C3' |
109.3 |
104.8 |
C4' |
O4' |
C1' |
109.6 |
105.2 |
O4' |
C4' |
C5' |
111.9 |
110.4 |
O4' |
C4' |
H4' |
109.6 |
110.4 |
C4' |
C3' |
C2' |
102.5 |
104.1 |
C4' |
C3' |
O3' |
86.0 |
110.5 |
C3' |
C4' |
C5' |
114.1 |
110.4 |
C3' |
C4' |
H4' |
107.2 |
110.4 |
C4' |
C3' |
H3' |
122.8 |
110.5 |
O4' |
C1' |
C2' |
108.8 |
104.8 |
O4' |
C1' |
H1' |
114.2 |
110.4 |
C3' |
C2' |
C1' |
103.3 |
104.0 |
C2' |
C3' |
O3' |
96.2 |
110.5 |
C2' |
C3' |
H3' |
115.4 |
110.5 |
C3' |
C2' |
H2' |
111.6 |
110.5 |
C3' |
C2' |
H2'' |
111.6 |
110.5 |
C1' |
C2' |
H2' |
111.6 |
110.5 |
C1' |
C2' |
H2'' |
111.6 |
110.5 |
C2' |
C1' |
H1' |
104.4 |
110.4 |
O3' |
C3' |
H3' |
127.5 |
110.6 |
C3' |
O3' |
HO3' |
109.5 |
114.0 |
C4' |
C5' |
O5' |
104.8 |
109.5 |
C5' |
C4' |
H4' |
104.4 |
110.4 |
C4' |
C5' |
H5' |
111.1 |
109.4 |
C4' |
C5' |
H5'' |
111.1 |
109.5 |
C5' |
O5' |
P |
120.0 |
123.0 |
O5' |
C5' |
H5' |
111.0 |
109.4 |
O5' |
C5' |
H5'' |
111.0 |
109.5 |
O5' |
P |
OP2 |
115.1 |
109.5 |
O5' |
P |
OP3 |
129.6 |
109.5 |
O5' |
P |
OP1 |
107.1 |
109.4 |
OP2 |
P |
OP3 |
75.5 |
109.5 |
OP2 |
P |
OP1 |
111.6 |
109.5 |
P |
OP2 |
H2P |
109.5 |
114.0 |
OP3 |
P |
OP1 |
114.0 |
109.4 |
P |
OP3 |
HOP3 |
109.5 |
114.1 |
HN61 |
N6A |
HN62 |
109.4 |
120.0 |
H2' |
C2' |
H2'' |
107.3 |
110.6 |
H5' |
C5' |
H5'' |
107.8 |
109.5 |
Torsion Angles for 0DA
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
N9A |
C8A |
N7A |
C5A |
2.6 |
360.0 |
N7A |
C8A |
N9A |
H8A |
180.0 |
180.3 |
C4A |
N9A |
C8A |
C1' |
191.9 |
180.1 |
C8A |
N9A |
C4A |
C5A |
3.0 |
360.0 |
C8A |
N9A |
C4A |
N3A |
183.3 |
180.0 |
C8A |
N9A |
C1' |
O4' |
321.3 |
336.5 |
C8A |
N9A |
C1' |
C2' |
83.2 |
91.9 |
C8A |
N9A |
C1' |
H1' |
198.9 |
214.2 |
N7A |
C8A |
N9A |
C4A |
356.3 |
0.0 |
N7A |
C8A |
N9A |
C1' |
164.5 |
180.0 |
N9A |
C8A |
N7A |
H8A |
180.0 |
179.7 |
C4A |
C5A |
N7A |
C8A |
359.4 |
0.0 |
C8A |
N7A |
C5A |
C6A |
178.0 |
179.9 |
C4A |
N9A |
C8A |
N7A |
356.3 |
0.0 |
C8A |
N9A |
C4A |
C1' |
168.3 |
179.9 |
C4A |
N9A |
C8A |
H8A |
176.3 |
179.7 |
C4A |
N9A |
C1' |
O4' |
127.1 |
156.5 |
C4A |
N9A |
C1' |
C2' |
249.0 |
271.8 |
C4A |
N9A |
C1' |
H1' |
4.7 |
34.2 |
C5A |
C4A |
N9A |
N3A |
179.7 |
180.0 |
N9A |
C4A |
C5A |
N7A |
358.4 |
360.0 |
N9A |
C4A |
C5A |
C6A |
179.6 |
180.1 |
N9A |
C4A |
N3A |
C2A |
178.8 |
179.9 |
C1' |
N9A |
C8A |
N7A |
164.5 |
180.0 |
C8A |
N9A |
C1' |
C4A |
194.1 |
180.1 |
C1' |
N9A |
C8A |
H8A |
344.5 |
359.7 |
C1' |
N9A |
C4A |
C5A |
194.7 |
180.1 |
C1' |
N9A |
C4A |
N3A |
15.1 |
0.1 |
C4' |
O4' |
C1' |
N9A |
116.8 |
159.3 |
O4' |
C1' |
N9A |
C2' |
238.1 |
244.6 |
O4' |
C1' |
N9A |
H1' |
122.4 |
122.3 |
C3' |
C2' |
C1' |
N9A |
261.3 |
217.2 |
N9A |
C1' |
C2' |
H2' |
141.3 |
98.6 |
N9A |
C1' |
C2' |
H2'' |
21.3 |
335.8 |
C2' |
C1' |
N9A |
H1' |
244.3 |
237.7 |
C8A |
N7A |
C5A |
C4A |
359.4 |
0.0 |
C5A |
C4A |
N9A |
C1' |
194.7 |
180.1 |
N9A |
C4A |
C5A |
N3A |
180.3 |
180.0 |
C5A |
C4A |
N3A |
C2A |
359.2 |
360.0 |
N7A |
C5A |
C4A |
C6A |
178.9 |
179.9 |
C4A |
C5A |
C6A |
N1A |
1.8 |
359.9 |
C4A |
C5A |
C6A |
N6A |
180.3 |
180.0 |
N3A |
C4A |
N9A |
C1' |
15.1 |
0.1 |
N9A |
C4A |
N3A |
C5A |
179.6 |
180.0 |
N3A |
C4A |
C5A |
N7A |
178.1 |
180.0 |
N3A |
C4A |
C5A |
C6A |
359.2 |
0.0 |
C4A |
N3A |
C2A |
N1A |
1.7 |
0.1 |
C4A |
N3A |
C2A |
H2A |
181.7 |
180.0 |
C5A |
N7A |
C8A |
H8A |
182.6 |
180.3 |
N7A |
C5A |
C4A |
N3A |
178.1 |
180.0 |
C4A |
C5A |
N7A |
C6A |
181.4 |
180.1 |
N7A |
C5A |
C6A |
N1A |
183.2 |
180.0 |
N7A |
C5A |
C6A |
N6A |
1.8 |
0.1 |
C6A |
C5A |
C4A |
N3A |
359.2 |
0.0 |
C4A |
C5A |
C6A |
N7A |
178.5 |
179.9 |
C2A |
N1A |
C6A |
C5A |
358.9 |
0.1 |
N1A |
C6A |
C5A |
N6A |
181.4 |
179.9 |
C5A |
C6A |
N6A |
HN61 |
181.4 |
359.9 |
C5A |
C6A |
N6A |
HN62 |
301.4 |
180.0 |
N3A |
C2A |
N1A |
C6A |
359.2 |
359.9 |
N1A |
C2A |
N3A |
H2A |
180.0 |
180.1 |
C5A |
C6A |
N1A |
C2A |
358.9 |
0.1 |
N3A |
C2A |
N1A |
H2A |
180.0 |
179.9 |
C2A |
N1A |
C6A |
N6A |
180.2 |
180.0 |
C5A |
C6A |
N1A |
N6A |
178.6 |
180.1 |
C6A |
N1A |
C2A |
H2A |
179.3 |
180.0 |
N1A |
C6A |
N6A |
HN61 |
0.0 |
180.0 |
N1A |
C6A |
N6A |
HN62 |
120.0 |
0.0 |
C5A |
C6A |
N6A |
N1A |
181.4 |
179.9 |
HN61 |
N6A |
C6A |
HN62 |
240.0 |
180.0 |
N9A |
C1' |
O4' |
C4' |
116.8 |
159.3 |
O4' |
C4' |
C3' |
C2' |
20.6 |
24.0 |
O4' |
C4' |
C3' |
O3' |
116.1 |
142.6 |
C3' |
C4' |
O4' |
C5' |
127.5 |
118.8 |
C3' |
C4' |
O4' |
H4' |
242.8 |
241.1 |
O4' |
C4' |
C3' |
H3' |
249.0 |
265.3 |
C4' |
O4' |
C1' |
C2' |
350.3 |
40.5 |
C4' |
O4' |
C1' |
H1' |
234.1 |
281.6 |
O4' |
C4' |
C5' |
O5' |
228.9 |
293.6 |
C5' |
C4' |
O4' |
H4' |
115.3 |
122.3 |
O4' |
C4' |
C5' |
H5' |
348.9 |
53.6 |
O4' |
C4' |
C5' |
H5'' |
108.9 |
173.6 |
C3' |
C4' |
O4' |
C1' |
352.9 |
319.5 |
O4' |
C4' |
C3' |
C5' |
233.8 |
241.2 |
O4' |
C4' |
C3' |
H4' |
118.8 |
118.9 |
C4' |
C3' |
C2' |
C1' |
335.3 |
0.0 |
C2' |
C3' |
C4' |
O3' |
264.5 |
241.4 |
C2' |
C3' |
C4' |
H3' |
131.6 |
118.6 |
C4' |
C3' |
C2' |
H2' |
95.2 |
118.6 |
C4' |
C3' |
C2' |
H2'' |
215.3 |
241.4 |
O3' |
C3' |
C4' |
H3' |
227.1 |
237.3 |
C4' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
C3' |
C4' |
C5' |
O5' |
104.0 |
178.2 |
C5' |
C4' |
C3' |
H4' |
245.0 |
237.7 |
C3' |
C4' |
C5' |
H5' |
224.0 |
298.2 |
C3' |
C4' |
C5' |
H5'' |
344.0 |
58.2 |
N9A |
C1' |
O4' |
C2' |
126.5 |
118.8 |
N9A |
C1' |
O4' |
H1' |
242.7 |
237.7 |
C1' |
O4' |
C4' |
C3' |
352.9 |
319.5 |
C1' |
O4' |
C4' |
C5' |
225.4 |
200.6 |
C1' |
O4' |
C4' |
H4' |
110.1 |
78.4 |
C3' |
C2' |
C1' |
O4' |
22.3 |
336.0 |
O4' |
C1' |
C2' |
H2' |
262.3 |
217.4 |
O4' |
C1' |
C2' |
H2'' |
142.3 |
94.6 |
C2' |
C1' |
O4' |
H1' |
116.2 |
118.9 |
N9A |
C1' |
C2' |
C3' |
261.3 |
217.2 |
C4' |
C3' |
C2' |
O3' |
87.3 |
118.6 |
C2' |
C3' |
C4' |
C5' |
146.8 |
142.8 |
C2' |
C3' |
C4' |
H4' |
261.8 |
265.1 |
C4' |
C3' |
C2' |
H3' |
224.1 |
241.4 |
O4' |
C1' |
C2' |
C3' |
22.3 |
336.0 |
C1' |
C2' |
C3' |
H2' |
240.0 |
241.4 |
C1' |
C2' |
C3' |
H2'' |
120.0 |
118.6 |
C3' |
C2' |
C1' |
H1' |
144.6 |
94.9 |
O3' |
C3' |
C2' |
H3' |
136.8 |
122.7 |
C2' |
C3' |
O3' |
HO3' |
282.1 |
294.6 |
H2' |
C2' |
C3' |
H2'' |
240.0 |
237.2 |
N9A |
C1' |
C2' |
O4' |
239.1 |
241.2 |
N9A |
C1' |
C2' |
H1' |
116.8 |
122.3 |
O4' |
C1' |
C2' |
H1' |
237.7 |
241.1 |
C1' |
C2' |
C3' |
O3' |
248.0 |
241.4 |
C1' |
C2' |
C3' |
H3' |
111.2 |
118.7 |
C3' |
C2' |
C1' |
H2' |
120.0 |
118.6 |
C3' |
C2' |
C1' |
H2'' |
240.0 |
241.4 |
H2' |
C2' |
C1' |
H2'' |
120.0 |
122.8 |
C4' |
C3' |
O3' |
C2' |
257.9 |
245.4 |
O3' |
C3' |
C4' |
C5' |
242.3 |
261.5 |
O3' |
C3' |
C4' |
H4' |
357.4 |
23.8 |
C4' |
C3' |
O3' |
H3' |
129.1 |
122.7 |
O3' |
C3' |
C2' |
C1' |
248.0 |
241.4 |
C2' |
C3' |
O3' |
H3' |
231.2 |
237.3 |
O3' |
C3' |
C2' |
H2' |
7.9 |
359.9 |
O3' |
C3' |
C2' |
H2'' |
127.9 |
122.7 |
O4' |
C4' |
C5' |
C3' |
124.8 |
115.4 |
C5' |
C4' |
O4' |
C1' |
225.4 |
200.6 |
O4' |
C4' |
C5' |
H4' |
241.5 |
237.7 |
C5' |
C4' |
C3' |
C2' |
146.8 |
142.8 |
C5' |
C4' |
C3' |
O3' |
242.3 |
261.5 |
C3' |
C4' |
C5' |
H4' |
116.7 |
122.3 |
C5' |
C4' |
C3' |
H3' |
15.2 |
24.2 |
C4' |
C5' |
O5' |
P |
181.7 |
180.0 |
O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
O5' |
C5' |
C4' |
H5'' |
120.0 |
120.1 |
H5' |
C5' |
C4' |
H5'' |
240.0 |
240.0 |
O5' |
C5' |
C4' |
H4' |
347.4 |
55.9 |
C4' |
C5' |
O5' |
H5' |
120.0 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
240.0 |
240.0 |
C5' |
O5' |
P |
OP2 |
8.2 |
64.9 |
C5' |
O5' |
P |
OP3 |
99.8 |
185.0 |
C5' |
O5' |
P |
OP1 |
243.6 |
304.9 |
H5' |
C5' |
O5' |
H5'' |
120.0 |
120.0 |
P |
O5' |
C5' |
H5' |
61.7 |
60.1 |
P |
O5' |
C5' |
H5'' |
301.7 |
300.1 |
OP2 |
P |
O5' |
OP3 |
268.4 |
240.0 |
OP2 |
P |
O5' |
OP1 |
124.6 |
120.0 |
O5' |
P |
OP2 |
H2P |
237.8 |
60.0 |
OP3 |
P |
O5' |
OP1 |
216.2 |
240.1 |
O5' |
P |
OP3 |
HOP3 |
141.8 |
180.0 |
O5' |
P |
OP2 |
OP3 |
127.3 |
120.0 |
O5' |
P |
OP2 |
OP1 |
237.7 |
240.0 |
OP3 |
P |
OP2 |
OP1 |
110.5 |
120.0 |
OP2 |
P |
OP3 |
HOP3 |
252.5 |
300.0 |
O5' |
P |
OP3 |
OP2 |
249.3 |
240.0 |
O5' |
P |
OP3 |
OP1 |
141.8 |
119.9 |
OP2 |
P |
OP3 |
OP1 |
252.5 |
240.0 |
OP3 |
P |
OP2 |
H2P |
110.5 |
299.9 |
O5' |
P |
OP1 |
OP2 |
126.7 |
120.0 |
O5' |
P |
OP1 |
OP3 |
209.9 |
240.0 |
OP2 |
P |
OP1 |
OP3 |
83.2 |
120.0 |
OP1 |
P |
OP2 |
H2P |
0.0 |
179.9 |
OP1 |
P |
OP3 |
HOP3 |
360.0 |
60.0 |
N9A |
C8A |
H8A |
N7A |
180.0 |
180.3 |
H8A |
C8A |
N9A |
C4A |
176.3 |
179.7 |
H8A |
C8A |
N9A |
C1' |
344.5 |
359.7 |
H8A |
C8A |
N7A |
C5A |
182.6 |
180.3 |
N3A |
C2A |
H2A |
N1A |
180.0 |
180.1 |
H2A |
C2A |
N1A |
C6A |
179.3 |
180.0 |
C6A |
N6A |
HN61 |
HN62 |
120.0 |
180.0 |
C6A |
N6A |
HN62 |
HN61 |
240.0 |
180.0 |
O4' |
C4' |
H4' |
C3' |
241.4 |
244.6 |
H4' |
C4' |
O4' |
C1' |
110.1 |
78.4 |
O4' |
C4' |
H4' |
C5' |
120.0 |
122.3 |
H4' |
C4' |
C3' |
C2' |
261.8 |
265.1 |
H4' |
C4' |
C3' |
O3' |
357.4 |
23.8 |
C3' |
C4' |
H4' |
C5' |
238.6 |
237.7 |
H4' |
C4' |
C3' |
H3' |
130.2 |
146.5 |
H4' |
C4' |
C5' |
O5' |
347.4 |
55.9 |
H4' |
C4' |
C5' |
H5' |
107.4 |
175.8 |
H4' |
C4' |
C5' |
H5'' |
227.4 |
295.8 |
C4' |
C3' |
H3' |
C2' |
126.1 |
114.6 |
C4' |
C3' |
H3' |
O3' |
247.1 |
237.3 |
H3' |
C3' |
C4' |
C5' |
15.2 |
24.2 |
H3' |
C3' |
C4' |
H4' |
130.2 |
146.5 |
H3' |
C3' |
C2' |
C1' |
111.2 |
118.7 |
C2' |
C3' |
H3' |
O3' |
121.0 |
122.7 |
H3' |
C3' |
C2' |
H2' |
231.1 |
237.2 |
H3' |
C3' |
C2' |
H2'' |
351.1 |
0.0 |
H3' |
C3' |
O3' |
HO3' |
50.9 |
57.3 |
C3' |
C2' |
H2' |
C1' |
245.0 |
245.4 |
H2' |
C2' |
C3' |
O3' |
7.9 |
359.9 |
H2' |
C2' |
C3' |
H3' |
231.1 |
237.2 |
C3' |
C2' |
H2' |
H2'' |
122.5 |
122.7 |
C1' |
C2' |
H2' |
H2'' |
237.5 |
237.3 |
H2' |
C2' |
C1' |
H1' |
24.6 |
336.3 |
C3' |
C2' |
H2'' |
C1' |
115.0 |
114.6 |
H2'' |
C2' |
C3' |
O3' |
127.9 |
122.7 |
H2'' |
C2' |
C3' |
H3' |
351.1 |
0.0 |
C3' |
C2' |
H2'' |
H2' |
237.5 |
237.3 |
C1' |
C2' |
H2'' |
H2' |
122.5 |
122.7 |
H2'' |
C2' |
C1' |
H1' |
264.6 |
213.5 |
N9A |
C1' |
H1' |
O4' |
117.8 |
122.3 |
N9A |
C1' |
H1' |
C2' |
236.5 |
237.7 |
O4' |
C1' |
H1' |
C2' |
118.7 |
115.5 |
H1' |
C1' |
C2' |
H2' |
24.6 |
336.3 |
H1' |
C1' |
C2' |
H2'' |
264.6 |
213.5 |
HO3' |
O3' |
C3' |
H3' |
50.9 |
57.3 |
C4' |
C5' |
H5' |
O5' |
243.8 |
240.0 |
H5' |
C5' |
C4' |
H4' |
107.4 |
175.8 |
C4' |
C5' |
H5' |
H5'' |
121.9 |
120.0 |
H5' |
C5' |
O5' |
P |
61.7 |
60.1 |
O5' |
C5' |
H5' |
H5'' |
238.1 |
240.0 |
C4' |
C5' |
H5'' |
O5' |
116.3 |
120.1 |
H5'' |
C5' |
C4' |
H4' |
227.4 |
295.8 |
C4' |
C5' |
H5'' |
H5' |
238.1 |
240.0 |
H5'' |
C5' |
O5' |
P |
301.7 |
300.1 |
O5' |
C5' |
H5'' |
H5' |
121.9 |
120.0 |
H2P |
OP2 |
P |
OP3 |
110.5 |
299.9 |
H2P |
OP2 |
P |
OP1 |
0.0 |
179.9 |
HOP3 |
OP3 |
P |
OP1 |
360.0 |
60.0 |