PDB Chemical Component 1DA
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 1DA
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.430 |
1.429 |
| O5' |
HO5' |
0.950 |
0.967 |
| C5' |
C4' |
1.525 |
1.530 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.114 |
1.090 |
| C4' |
O4' |
1.434 |
1.444 |
| C4' |
C3' |
1.531 |
1.544 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.431 |
1.443 |
| C3' |
O3' |
1.432 |
1.429 |
| C3' |
C2' |
1.518 |
1.546 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
HO3' |
0.951 |
0.967 |
| C2' |
O2' |
1.419 |
1.429 |
| C2' |
C1' |
1.529 |
1.544 |
| C2' |
H2' |
1.115 |
1.090 |
| O2' |
HO2' |
0.951 |
0.967 |
| C1' |
N9 |
1.406 |
1.464 |
| C1' |
H1' |
1.115 |
1.091 |
| N9 |
C8 |
1.345 |
1.363 |
| N9 |
C4 |
1.339 |
1.378 |
| C8 |
N7 |
1.341 |
1.300 |
| C8 |
H8 |
1.103 |
1.079 |
| N7 |
C5 |
1.359 |
1.356 |
| C5 |
C6 |
1.367 |
1.406 |
| C5 |
C4 |
1.353 |
1.402 |
| C6 |
N6 |
1.336 |
1.391 |
| C6 |
C1 |
1.377 |
1.390 |
| N6 |
HN61 |
1.019 |
0.969 |
| N6 |
HN62 |
1.021 |
0.970 |
| C1 |
C2 |
1.389 |
1.383 |
| C1 |
H1 |
1.103 |
1.080 |
| C2 |
N3 |
1.324 |
1.318 |
| C2 |
H2 |
1.102 |
1.079 |
| N3 |
C4 |
1.341 |
1.326 |
Bond Angles for 1DA
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
HO5' |
111.9 |
106.9 |
| O5' |
C5' |
C4' |
111.9 |
109.5 |
| O5' |
C5' |
H5'1 |
111.3 |
109.5 |
| O5' |
C5' |
H5'2 |
111.3 |
109.5 |
| C4' |
C5' |
H5'1 |
111.3 |
109.5 |
| C4' |
C5' |
H5'2 |
111.3 |
109.4 |
| C5' |
C4' |
O4' |
110.1 |
110.4 |
| C5' |
C4' |
C3' |
113.5 |
110.5 |
| C5' |
C4' |
H4' |
105.1 |
110.3 |
| H5'1 |
C5' |
H5'2 |
99.1 |
109.5 |
| O4' |
C4' |
C3' |
105.4 |
104.8 |
| O4' |
C4' |
H4' |
113.1 |
110.4 |
| C4' |
O4' |
C1' |
109.3 |
105.3 |
| C3' |
C4' |
H4' |
109.8 |
110.4 |
| C4' |
C3' |
O3' |
113.7 |
110.5 |
| C4' |
C3' |
C2' |
103.2 |
104.1 |
| C4' |
C3' |
H3' |
111.8 |
110.5 |
| O4' |
C1' |
C2' |
107.6 |
104.9 |
| O4' |
C1' |
N9 |
114.5 |
110.4 |
| O4' |
C1' |
H1' |
107.6 |
110.4 |
| O3' |
C3' |
C2' |
112.1 |
110.6 |
| O3' |
C3' |
H3' |
102.9 |
110.4 |
| C3' |
O3' |
HO3' |
113.7 |
106.8 |
| C2' |
C3' |
H3' |
113.5 |
110.6 |
| C3' |
C2' |
O2' |
104.3 |
110.5 |
| C3' |
C2' |
C1' |
104.8 |
104.0 |
| C3' |
C2' |
H2' |
113.9 |
110.5 |
| O2' |
C2' |
C1' |
104.2 |
110.8 |
| O2' |
C2' |
H2' |
114.4 |
110.5 |
| C2' |
O2' |
HO2' |
104.3 |
106.8 |
| C1' |
C2' |
H2' |
114.0 |
110.4 |
| C2' |
C1' |
N9 |
110.3 |
110.4 |
| C2' |
C1' |
H1' |
112.0 |
110.3 |
| N9 |
C1' |
H1' |
104.8 |
110.3 |
| C1' |
N9 |
C8 |
127.6 |
126.3 |
| C1' |
N9 |
C4 |
126.0 |
126.4 |
| C8 |
N9 |
C4 |
106.2 |
107.3 |
| N9 |
C8 |
N7 |
111.4 |
110.0 |
| N9 |
C8 |
H8 |
124.5 |
125.0 |
| N9 |
C4 |
C5 |
108.2 |
106.0 |
| N9 |
C4 |
N3 |
128.3 |
133.6 |
| N7 |
C8 |
H8 |
124.2 |
125.1 |
| C8 |
N7 |
C5 |
104.8 |
109.5 |
| N7 |
C5 |
C6 |
132.0 |
133.9 |
| N7 |
C5 |
C4 |
109.1 |
107.2 |
| C6 |
C5 |
C4 |
118.9 |
119.0 |
| C5 |
C6 |
N6 |
121.8 |
121.0 |
| C5 |
C6 |
C1 |
118.0 |
118.0 |
| C5 |
C4 |
N3 |
123.4 |
120.4 |
| N6 |
C6 |
C1 |
120.2 |
121.0 |
| C6 |
N6 |
HN61 |
121.8 |
120.0 |
| C6 |
N6 |
HN62 |
107.8 |
120.0 |
| C6 |
C1 |
C2 |
120.8 |
119.4 |
| C6 |
C1 |
H1 |
119.1 |
120.2 |
| HN61 |
N6 |
HN62 |
107.8 |
120.0 |
| C2 |
C1 |
H1 |
120.1 |
120.3 |
| C1 |
C2 |
N3 |
119.8 |
121.4 |
| C1 |
C2 |
H2 |
122.5 |
119.2 |
| N3 |
C2 |
H2 |
117.7 |
119.3 |
| C2 |
N3 |
C4 |
119.1 |
121.7 |
Torsion Angles for 1DA
| 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 |
240.1 |
| O5' |
C5' |
C4' |
O4' |
296.1 |
61.4 |
| O5' |
C5' |
C4' |
C3' |
54.0 |
176.9 |
| O5' |
C5' |
C4' |
H4' |
173.9 |
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 |
305.2 |
60.0 |
| HO5' |
O5' |
C5' |
H5'2 |
54.8 |
299.9 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
234.8 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
242.1 |
244.6 |
| O4' |
C4' |
C5' |
H4' |
122.2 |
122.3 |
| C5' |
C4' |
O4' |
C1' |
150.2 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
240.1 |
237.7 |
| C5' |
C4' |
C3' |
O3' |
86.5 |
98.3 |
| C5' |
C4' |
C3' |
C2' |
208.2 |
217.0 |
| C5' |
C4' |
C3' |
H3' |
330.5 |
335.8 |
| H5'1 |
C5' |
O5' |
HO5' |
305.2 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
234.4 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
117.2 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
242.8 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
170.8 |
181.4 |
| H5'1 |
C5' |
C4' |
C3' |
288.8 |
296.9 |
| H5'1 |
C5' |
C4' |
H4' |
48.7 |
59.2 |
| H5'2 |
C5' |
O5' |
HO5' |
54.8 |
299.9 |
| O5' |
C5' |
H5'2 |
C4' |
125.6 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
242.8 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
117.2 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
61.3 |
301.5 |
| H5'2 |
C5' |
C4' |
C3' |
179.2 |
56.9 |
| H5'2 |
C5' |
C4' |
H4' |
299.2 |
179.2 |
| O4' |
C4' |
C5' |
H5'1 |
170.8 |
181.4 |
| O4' |
C4' |
C5' |
H5'2 |
61.3 |
301.5 |
| C5' |
C4' |
O4' |
C3' |
122.8 |
119.0 |
| C5' |
C4' |
O4' |
H4' |
242.7 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
120.0 |
118.8 |
| O4' |
C4' |
C3' |
O3' |
207.1 |
217.2 |
| O4' |
C4' |
C3' |
C2' |
328.8 |
335.9 |
| O4' |
C4' |
C3' |
H3' |
91.1 |
94.7 |
| C4' |
O4' |
C1' |
C2' |
347.7 |
319.6 |
| C4' |
O4' |
C1' |
N9 |
224.7 |
200.6 |
| C4' |
O4' |
C1' |
H1' |
108.7 |
78.4 |
| C3' |
C4' |
C5' |
H5'1 |
288.8 |
296.9 |
| C3' |
C4' |
C5' |
H5'2 |
179.2 |
56.9 |
| C5' |
C4' |
C3' |
O4' |
239.4 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
117.2 |
122.2 |
| O4' |
C4' |
C3' |
H4' |
237.8 |
241.2 |
| C3' |
C4' |
O4' |
C1' |
27.4 |
40.5 |
| O3' |
C3' |
C4' |
C2' |
238.3 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
116.0 |
122.5 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
298.6 |
| C2' |
C3' |
C4' |
H3' |
237.7 |
241.3 |
| C4' |
C3' |
C2' |
O2' |
274.1 |
241.2 |
| C4' |
C3' |
C2' |
C1' |
23.4 |
0.2 |
| C4' |
C3' |
C2' |
H2' |
148.7 |
118.6 |
| H4' |
C4' |
C5' |
H5'1 |
48.7 |
59.2 |
| H4' |
C4' |
C5' |
H5'2 |
299.2 |
179.2 |
| C5' |
C4' |
H4' |
O4' |
120.2 |
122.3 |
| C5' |
C4' |
H4' |
C3' |
237.6 |
237.6 |
| O4' |
C4' |
H4' |
C3' |
117.5 |
115.4 |
| H4' |
C4' |
O4' |
C1' |
267.5 |
281.7 |
| H4' |
C4' |
C3' |
O3' |
329.3 |
336.1 |
| H4' |
C4' |
C3' |
C2' |
90.9 |
94.8 |
| H4' |
C4' |
C3' |
H3' |
213.3 |
213.5 |
| C1' |
O4' |
C4' |
C3' |
27.4 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
267.5 |
281.7 |
| C3' |
C2' |
C1' |
O4' |
352.1 |
23.8 |
| O2' |
C2' |
C1' |
O4' |
101.4 |
142.6 |
| O4' |
C1' |
C2' |
H2' |
226.8 |
265.3 |
| C2' |
C1' |
O4' |
N9 |
123.0 |
119.0 |
| C2' |
C1' |
O4' |
H1' |
239.1 |
241.1 |
| N9 |
C1' |
O4' |
H1' |
116.1 |
122.2 |
| O4' |
C1' |
N9 |
C8 |
78.1 |
27.0 |
| O4' |
C1' |
N9 |
C4 |
252.7 |
207.0 |
| O3' |
C3' |
C4' |
H4' |
329.3 |
336.1 |
| C4' |
C3' |
O3' |
C2' |
116.6 |
114.7 |
| C4' |
C3' |
O3' |
H3' |
238.9 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
122.2 |
122.7 |
| O3' |
C3' |
C2' |
O2' |
36.9 |
359.9 |
| O3' |
C3' |
C2' |
C1' |
146.2 |
118.9 |
| O3' |
C3' |
C2' |
H2' |
271.5 |
237.3 |
| C2' |
C3' |
C4' |
H4' |
90.9 |
94.8 |
| C4' |
C3' |
C2' |
O3' |
237.2 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
121.2 |
118.7 |
| O4' |
C1' |
C2' |
C3' |
352.1 |
23.8 |
| O3' |
C3' |
C2' |
H3' |
244.0 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
63.4 |
183.9 |
| O2' |
C2' |
C3' |
C1' |
250.8 |
241.0 |
| O2' |
C2' |
C3' |
H2' |
125.5 |
122.6 |
| C3' |
C2' |
O2' |
HO2' |
180.1 |
298.5 |
| C1' |
C2' |
C3' |
H2' |
234.7 |
241.6 |
| C3' |
C2' |
C1' |
N9 |
117.6 |
142.8 |
| C3' |
C2' |
C1' |
H1' |
233.9 |
264.9 |
| H3' |
C3' |
C4' |
H4' |
213.3 |
213.5 |
| C4' |
C3' |
H3' |
O3' |
122.4 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
243.7 |
245.3 |
| O3' |
C3' |
H3' |
C2' |
121.3 |
122.7 |
| H3' |
C3' |
O3' |
HO3' |
301.2 |
61.2 |
| H3' |
C3' |
C2' |
O2' |
152.9 |
122.5 |
| H3' |
C3' |
C2' |
C1' |
262.2 |
241.5 |
| H3' |
C3' |
C2' |
H2' |
27.5 |
359.9 |
| HO3' |
O3' |
C3' |
C2' |
63.4 |
183.9 |
| HO3' |
O3' |
C3' |
H3' |
301.2 |
61.2 |
| O4' |
C1' |
C2' |
O2' |
101.4 |
142.6 |
| O2' |
C2' |
C3' |
H3' |
152.9 |
122.5 |
| C3' |
C2' |
O2' |
C1' |
109.6 |
114.7 |
| C3' |
C2' |
O2' |
H2' |
234.8 |
237.4 |
| C1' |
C2' |
O2' |
H2' |
125.2 |
122.6 |
| O2' |
C2' |
C1' |
N9 |
226.9 |
261.5 |
| O2' |
C2' |
C1' |
H1' |
343.2 |
23.7 |
| O4' |
C1' |
C2' |
N9 |
234.5 |
241.0 |
| O4' |
C1' |
C2' |
H1' |
118.1 |
118.9 |
| C1' |
C2' |
C3' |
H3' |
262.2 |
241.5 |
| C3' |
C2' |
C1' |
O2' |
250.7 |
241.2 |
| C3' |
C2' |
C1' |
H2' |
125.3 |
118.5 |
| O2' |
C2' |
C1' |
H2' |
234.6 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
70.4 |
183.8 |
| N9 |
C1' |
C2' |
H1' |
243.7 |
237.8 |
| C2' |
C1' |
N9 |
C8 |
316.5 |
271.5 |
| C2' |
C1' |
N9 |
C4 |
131.1 |
91.5 |
| H2' |
C2' |
C3' |
H3' |
27.5 |
359.9 |
| C3' |
C2' |
H2' |
O2' |
119.9 |
122.6 |
| C3' |
C2' |
H2' |
C1' |
239.8 |
245.5 |
| O2' |
C2' |
H2' |
C1' |
119.9 |
122.9 |
| H2' |
C2' |
O2' |
HO2' |
305.2 |
61.2 |
| H2' |
C2' |
C1' |
N9 |
352.3 |
24.2 |
| H2' |
C2' |
C1' |
H1' |
108.7 |
146.4 |
| HO2' |
O2' |
C2' |
C1' |
70.4 |
183.8 |
| HO2' |
O2' |
C2' |
H2' |
305.2 |
61.2 |
| O4' |
C1' |
N9 |
C2' |
121.6 |
115.6 |
| O4' |
C1' |
N9 |
H1' |
242.3 |
237.8 |
| N9 |
C1' |
C2' |
H2' |
352.3 |
24.2 |
| C2' |
C1' |
N9 |
H1' |
120.8 |
122.2 |
| C8 |
N9 |
C1' |
C4 |
185.4 |
180.0 |
| C1' |
N9 |
C8 |
N7 |
176.7 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
356.7 |
0.1 |
| C1' |
N9 |
C4 |
C5 |
186.6 |
180.2 |
| C1' |
N9 |
C4 |
N3 |
4.7 |
0.0 |
| O4' |
C1' |
H1' |
C2' |
241.9 |
244.5 |
| O4' |
C1' |
H1' |
N9 |
122.3 |
122.3 |
| H1' |
C1' |
C2' |
H2' |
108.7 |
146.4 |
| C2' |
C1' |
H1' |
N9 |
240.4 |
237.8 |
| H1' |
C1' |
N9 |
C8 |
195.8 |
149.3 |
| H1' |
C1' |
N9 |
C4 |
10.4 |
329.3 |
| C8 |
N9 |
C1' |
H1' |
195.8 |
149.3 |
| C1' |
N9 |
C8 |
C4 |
175.5 |
180.0 |
| C8 |
N9 |
C4 |
C5 |
2.2 |
0.2 |
| C8 |
N9 |
C4 |
N3 |
180.3 |
180.0 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
356.0 |
359.8 |
| C4 |
N9 |
C1' |
H1' |
10.4 |
329.3 |
| C1' |
N9 |
C4 |
C8 |
184.5 |
180.0 |
| C4 |
N9 |
C8 |
N7 |
1.2 |
360.0 |
| C4 |
N9 |
C8 |
H8 |
181.2 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
355.3 |
359.6 |
| C6 |
C5 |
C4 |
N9 |
177.8 |
180.3 |
| C5 |
C4 |
N9 |
N3 |
181.9 |
180.2 |
| C2 |
N3 |
C4 |
N9 |
182.5 |
179.9 |
| N7 |
C8 |
N9 |
C4 |
1.2 |
360.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
182.3 |
179.5 |
| C8 |
N7 |
C5 |
C4 |
5.3 |
0.4 |
| H8 |
C8 |
N9 |
C4 |
181.2 |
180.0 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
176.0 |
179.7 |
| N9 |
C4 |
C5 |
N7 |
355.3 |
359.6 |
| C5 |
N7 |
C8 |
H8 |
176.0 |
179.7 |
| C6 |
C5 |
N7 |
C4 |
177.0 |
179.1 |
| N7 |
C5 |
C6 |
N6 |
3.7 |
0.7 |
| N7 |
C5 |
C6 |
C1 |
183.5 |
180.5 |
| N7 |
C5 |
C4 |
N3 |
177.0 |
179.8 |
| N9 |
C4 |
C5 |
C6 |
177.8 |
180.3 |
| N7 |
C5 |
C6 |
C4 |
183.2 |
181.0 |
| C6 |
C5 |
C4 |
N3 |
359.6 |
0.5 |
| N6 |
C6 |
C5 |
C1 |
180.2 |
180.3 |
| C5 |
C6 |
N6 |
HN61 |
180.0 |
179.8 |
| C5 |
C6 |
N6 |
HN62 |
54.7 |
359.4 |
| C5 |
C6 |
C1 |
C2 |
360.0 |
0.3 |
| C5 |
C6 |
C1 |
H1 |
180.0 |
180.2 |
| N9 |
C4 |
C5 |
N3 |
178.2 |
179.8 |
| N7 |
C5 |
C4 |
C6 |
177.5 |
179.3 |
| C4 |
C5 |
C6 |
N6 |
180.5 |
179.8 |
| C4 |
C5 |
C6 |
C1 |
0.2 |
359.5 |
| C2 |
N3 |
C4 |
C5 |
0.4 |
359.7 |
| N6 |
C6 |
C5 |
C4 |
180.5 |
179.8 |
| C5 |
C6 |
N6 |
C1 |
179.8 |
179.7 |
| N6 |
C6 |
C1 |
C2 |
179.7 |
180.0 |
| N6 |
C6 |
C1 |
H1 |
359.8 |
360.0 |
| HN61 |
N6 |
C6 |
HN62 |
125.3 |
180.4 |
| C1 |
C6 |
C5 |
C4 |
0.2 |
359.5 |
| C5 |
C6 |
C1 |
N6 |
180.2 |
180.3 |
| C1 |
C6 |
N6 |
HN61 |
0.2 |
0.1 |
| C1 |
C6 |
N6 |
HN62 |
235.0 |
179.7 |
| C2 |
C1 |
C6 |
H1 |
180.0 |
180.0 |
| C6 |
C1 |
C2 |
N3 |
0.0 |
360.0 |
| C6 |
C1 |
C2 |
H2 |
180.0 |
180.0 |
| HN61 |
N6 |
C6 |
C1 |
0.2 |
0.1 |
| C6 |
N6 |
HN61 |
HN62 |
234.7 |
179.6 |
| HN62 |
N6 |
C6 |
C1 |
235.0 |
179.7 |
| C6 |
N6 |
HN62 |
HN61 |
133.2 |
180.4 |
| C6 |
C1 |
C2 |
H1 |
180.0 |
180.0 |
| N3 |
C2 |
C1 |
H2 |
180.0 |
180.0 |
| C1 |
C2 |
N3 |
C4 |
359.8 |
0.0 |
| C6 |
C1 |
H1 |
C2 |
180.0 |
180.0 |
| H1 |
C1 |
C2 |
N3 |
180.0 |
180.0 |
| H1 |
C1 |
C2 |
H2 |
0.0 |
0.0 |
| N9 |
C4 |
N3 |
C2 |
182.5 |
179.9 |
| C5 |
C4 |
N3 |
C2 |
0.4 |
359.7 |
| N3 |
C2 |
C1 |
H1 |
180.0 |
180.0 |
| C1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
| H2 |
C2 |
C1 |
H1 |
0.0 |
0.0 |
| C1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
| H2 |
C2 |
N3 |
C4 |
179.8 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
182.1 |
180.2 |
| C4 |
N3 |
C2 |
H2 |
179.8 |
180.0 |