PDB Chemical Component 5AD
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 5AD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.333 |
1.320 |
| N1 |
C6 |
1.349 |
1.328 |
| C2 |
N3 |
1.314 |
1.317 |
| C2 |
H2 |
1.103 |
1.080 |
| N3 |
C4 |
1.341 |
1.329 |
| C4 |
N9 |
1.362 |
1.372 |
| C4 |
C5 |
1.383 |
1.405 |
| N9 |
C8 |
1.367 |
1.363 |
| N9 |
C1' |
1.452 |
1.464 |
| C8 |
N7 |
1.311 |
1.302 |
| C8 |
H8 |
1.103 |
1.078 |
| N7 |
C5 |
1.384 |
1.354 |
| C5 |
C6 |
1.401 |
1.405 |
| C6 |
N6 |
1.320 |
1.384 |
| N6 |
HN61 |
1.019 |
0.970 |
| N6 |
HN62 |
1.020 |
0.969 |
| C1' |
C2' |
1.504 |
1.541 |
| C1' |
O4' |
1.430 |
1.437 |
| C1' |
H1' |
1.116 |
1.090 |
| C2' |
C3' |
1.512 |
1.549 |
| C2' |
O2' |
1.409 |
1.429 |
| C2' |
H2' |
1.115 |
1.090 |
| C3' |
C4' |
1.534 |
1.549 |
| C3' |
O3' |
1.421 |
1.429 |
| C3' |
H3' |
1.114 |
1.089 |
| C4' |
C5' |
1.511 |
1.531 |
| C4' |
O4' |
1.443 |
1.443 |
| C4' |
H4' |
1.114 |
1.089 |
| C5' |
H5'1 |
1.114 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.090 |
| C5' |
H5'3 |
1.115 |
1.089 |
| O2' |
HO2' |
0.950 |
0.966 |
| O3' |
HO3' |
0.949 |
0.967 |
Bond Angles for 5AD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
117.7 |
121.2 |
| N1 |
C2 |
N3 |
133.7 |
122.5 |
| N1 |
C2 |
H2 |
114.1 |
118.8 |
| N1 |
C6 |
C5 |
116.7 |
118.5 |
| N1 |
C6 |
N6 |
117.7 |
120.8 |
| N3 |
C2 |
H2 |
112.1 |
118.7 |
| C2 |
N3 |
C4 |
105.3 |
120.6 |
| N3 |
C4 |
N9 |
124.1 |
134.9 |
| N3 |
C4 |
C5 |
130.7 |
119.0 |
| N9 |
C4 |
C5 |
105.2 |
106.0 |
| C4 |
N9 |
C8 |
107.7 |
107.5 |
| C4 |
N9 |
C1' |
122.6 |
126.3 |
| C4 |
C5 |
N7 |
110.3 |
107.1 |
| C4 |
C5 |
C6 |
115.8 |
118.2 |
| C8 |
N9 |
C1' |
129.7 |
126.2 |
| N9 |
C8 |
N7 |
111.9 |
109.9 |
| N9 |
C8 |
H8 |
125.8 |
125.1 |
| N9 |
C1' |
C2' |
112.6 |
110.0 |
| N9 |
C1' |
O4' |
103.8 |
109.9 |
| N9 |
C1' |
H1' |
109.6 |
109.9 |
| N7 |
C8 |
H8 |
122.3 |
125.0 |
| C8 |
N7 |
C5 |
105.0 |
109.5 |
| N7 |
C5 |
C6 |
133.9 |
134.7 |
| C5 |
C6 |
N6 |
125.6 |
120.8 |
| C6 |
N6 |
HN61 |
117.7 |
120.0 |
| C6 |
N6 |
HN62 |
109.2 |
120.0 |
| HN61 |
N6 |
HN62 |
109.2 |
120.0 |
| C2' |
C1' |
O4' |
104.2 |
107.3 |
| C2' |
C1' |
H1' |
109.2 |
109.9 |
| C1' |
C2' |
C3' |
103.4 |
104.3 |
| C1' |
C2' |
O2' |
109.7 |
110.5 |
| C1' |
C2' |
H2' |
114.2 |
110.4 |
| O4' |
C1' |
H1' |
117.3 |
109.9 |
| C1' |
O4' |
C4' |
105.4 |
107.0 |
| C3' |
C2' |
O2' |
112.3 |
110.5 |
| C3' |
C2' |
H2' |
111.7 |
110.6 |
| C2' |
C3' |
C4' |
104.6 |
102.0 |
| C2' |
C3' |
O3' |
112.8 |
110.9 |
| C2' |
C3' |
H3' |
110.5 |
110.9 |
| O2' |
C2' |
H2' |
105.7 |
110.4 |
| C2' |
O2' |
HO2' |
109.7 |
106.8 |
| C4' |
C3' |
O3' |
109.2 |
111.1 |
| C4' |
C3' |
H3' |
114.0 |
110.9 |
| C3' |
C4' |
C5' |
110.6 |
110.6 |
| C3' |
C4' |
O4' |
105.7 |
103.6 |
| C3' |
C4' |
H4' |
112.1 |
110.6 |
| O3' |
C3' |
H3' |
106.0 |
110.8 |
| C3' |
O3' |
HO3' |
112.8 |
106.8 |
| C5' |
C4' |
O4' |
111.9 |
110.6 |
| C5' |
C4' |
H4' |
105.9 |
110.5 |
| C4' |
C5' |
H5'1 |
110.6 |
109.5 |
| C4' |
C5' |
H5'2 |
111.7 |
109.5 |
| C4' |
C5' |
H5'3 |
111.8 |
109.5 |
| O4' |
C4' |
H4' |
110.8 |
110.7 |
| H5'1 |
C5' |
H5'2 |
111.9 |
109.6 |
| H5'1 |
C5' |
H5'3 |
111.8 |
109.4 |
| H5'2 |
C5' |
H5'3 |
98.6 |
109.5 |
Torsion Angles for 5AD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
C5 |
0.6 |
0.1 |
| C2 |
N1 |
C6 |
N6 |
180.0 |
180.0 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.3 |
359.7 |
| C6 |
N1 |
C2 |
N3 |
359.4 |
360.0 |
| C6 |
N1 |
C2 |
H2 |
179.4 |
179.9 |
| C4 |
C5 |
C6 |
N1 |
359.6 |
0.2 |
| N7 |
C5 |
C6 |
N1 |
179.5 |
180.0 |
| C5 |
C6 |
N1 |
N6 |
180.6 |
180.1 |
| N1 |
C6 |
N6 |
HN61 |
180.0 |
0.0 |
| N1 |
C6 |
N6 |
HN62 |
54.8 |
180.1 |
| N3 |
C2 |
N1 |
C6 |
359.4 |
360.0 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
N9 |
180.1 |
179.6 |
| C2 |
N3 |
C4 |
C5 |
359.9 |
0.6 |
| H2 |
C2 |
N1 |
C6 |
179.4 |
179.9 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
| H2 |
C2 |
N3 |
C4 |
180.3 |
179.7 |
| C4 |
N3 |
C2 |
H2 |
180.3 |
179.7 |
| N9 |
C4 |
N3 |
C5 |
180.2 |
179.0 |
| N3 |
C4 |
N9 |
C8 |
179.9 |
180.6 |
| N3 |
C4 |
N9 |
C1' |
359.2 |
0.8 |
| N3 |
C4 |
C5 |
N7 |
180.3 |
179.6 |
| N3 |
C4 |
C5 |
C6 |
0.2 |
359.5 |
| N3 |
C4 |
N9 |
C5 |
179.8 |
180.9 |
| N9 |
C4 |
C5 |
N7 |
0.1 |
0.4 |
| N9 |
C4 |
C5 |
C6 |
180.1 |
180.2 |
| C8 |
N9 |
C4 |
C1' |
180.7 |
179.8 |
| C4 |
N9 |
C8 |
N7 |
359.9 |
0.2 |
| C4 |
N9 |
C8 |
H8 |
179.8 |
180.3 |
| C4 |
N9 |
C1' |
C2' |
123.5 |
90.3 |
| C4 |
N9 |
C1' |
O4' |
235.6 |
208.3 |
| C4 |
N9 |
C1' |
H1' |
1.7 |
329.3 |
| N1 |
C6 |
C5 |
C4 |
359.6 |
0.2 |
| N3 |
C4 |
C5 |
N9 |
180.2 |
179.2 |
| C5 |
C4 |
N9 |
C8 |
0.0 |
359.6 |
| C5 |
C4 |
N9 |
C1' |
179.3 |
179.8 |
| C8 |
N7 |
C5 |
C4 |
359.8 |
359.7 |
| N7 |
C5 |
C4 |
C6 |
180.0 |
180.2 |
| C4 |
C5 |
C6 |
N6 |
180.2 |
180.3 |
| C8 |
N9 |
C4 |
C5 |
0.0 |
359.6 |
| C4 |
N9 |
C8 |
C1' |
179.2 |
180.2 |
| C8 |
N9 |
C1' |
C2' |
302.7 |
270.6 |
| C8 |
N9 |
C1' |
O4' |
54.7 |
28.5 |
| C8 |
N9 |
C1' |
H1' |
180.8 |
149.5 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
179.9 |
| N9 |
C8 |
N7 |
C5 |
0.2 |
0.1 |
| C1' |
N9 |
C4 |
C5 |
179.3 |
179.8 |
| C4 |
N9 |
C1' |
C8 |
180.9 |
179.7 |
| C1' |
N9 |
C8 |
N7 |
180.6 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
0.6 |
0.1 |
| C2' |
C1' |
N9 |
O4' |
247.9 |
242.1 |
| C2' |
C1' |
N9 |
H1' |
121.8 |
121.0 |
| N9 |
C1' |
C2' |
C3' |
76.3 |
121.7 |
| N9 |
C1' |
C2' |
O2' |
196.3 |
240.4 |
| N9 |
C1' |
C2' |
H2' |
314.7 |
2.8 |
| O4' |
C1' |
N9 |
H1' |
233.9 |
239.0 |
| N9 |
C1' |
O4' |
C4' |
284.0 |
213.9 |
| C4 |
C5 |
N7 |
C8 |
359.8 |
359.7 |
| N7 |
C8 |
N9 |
C1' |
180.6 |
180.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.1 |
| C8 |
N7 |
C5 |
C6 |
179.9 |
179.9 |
| H8 |
C8 |
N9 |
C1' |
0.6 |
0.1 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
179.9 |
| H8 |
C8 |
N7 |
C5 |
180.2 |
180.0 |
| N1 |
C6 |
C5 |
N7 |
179.5 |
180.0 |
| C4 |
C5 |
N7 |
C6 |
180.0 |
179.8 |
| C5 |
N7 |
C8 |
H8 |
180.2 |
180.0 |
| N7 |
C5 |
C6 |
N6 |
0.1 |
0.1 |
| N1 |
C6 |
C5 |
N6 |
179.4 |
179.9 |
| C4 |
C5 |
C6 |
N7 |
180.0 |
180.2 |
| C5 |
C6 |
N6 |
HN61 |
359.3 |
179.9 |
| C5 |
C6 |
N6 |
HN62 |
234.1 |
359.9 |
| N1 |
C6 |
N6 |
C5 |
180.6 |
180.1 |
| HN61 |
N6 |
C6 |
HN62 |
125.2 |
180.0 |
| C6 |
N6 |
HN61 |
HN62 |
234.8 |
180.0 |
| C6 |
N6 |
HN62 |
HN61 |
130.0 |
180.0 |
| N9 |
C1' |
C2' |
O4' |
111.8 |
119.6 |
| N9 |
C1' |
C2' |
H1' |
238.0 |
239.0 |
| O4' |
C1' |
C2' |
H1' |
126.1 |
119.4 |
| C2' |
C1' |
O4' |
C4' |
42.0 |
333.5 |
| C3' |
C2' |
C1' |
O2' |
240.0 |
241.3 |
| C3' |
C2' |
C1' |
H2' |
121.6 |
118.9 |
| C1' |
C2' |
C3' |
C4' |
16.0 |
20.7 |
| C1' |
C2' |
C3' |
O3' |
134.6 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
253.0 |
262.6 |
| O2' |
C2' |
C1' |
H2' |
241.6 |
237.5 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| N9 |
C1' |
O4' |
C2' |
241.9 |
240.4 |
| N9 |
C1' |
O4' |
H1' |
121.0 |
121.0 |
| C2' |
C1' |
O4' |
H1' |
239.1 |
240.6 |
| O4' |
C1' |
C2' |
C3' |
324.5 |
2.1 |
| O4' |
C1' |
C2' |
O2' |
84.5 |
120.8 |
| O4' |
C1' |
C2' |
H2' |
202.9 |
243.3 |
| C3' |
C4' |
O4' |
C1' |
328.7 |
40.0 |
| C5' |
C4' |
O4' |
C1' |
89.2 |
158.5 |
| C1' |
O4' |
C4' |
H4' |
207.2 |
281.4 |
| N9 |
C1' |
H1' |
C2' |
123.8 |
121.1 |
| N9 |
C1' |
H1' |
O4' |
242.0 |
238.9 |
| C2' |
C1' |
H1' |
O4' |
118.2 |
117.8 |
| H1' |
C1' |
C2' |
C3' |
198.3 |
242.7 |
| H1' |
C1' |
C2' |
O2' |
318.3 |
1.4 |
| H1' |
C1' |
C2' |
H2' |
76.7 |
123.9 |
| H1' |
C1' |
O4' |
C4' |
162.9 |
92.9 |
| C3' |
C2' |
C1' |
O4' |
324.5 |
2.1 |
| C3' |
C2' |
C1' |
H1' |
198.3 |
242.7 |
| C1' |
C2' |
C3' |
O2' |
118.2 |
118.7 |
| C1' |
C2' |
C3' |
H2' |
236.7 |
241.3 |
| O2' |
C2' |
C3' |
H2' |
118.5 |
122.6 |
| C3' |
C2' |
O2' |
HO2' |
294.4 |
294.8 |
| C4' |
C3' |
C2' |
O3' |
241.5 |
241.6 |
| C4' |
C3' |
C2' |
H3' |
123.1 |
118.1 |
| C2' |
C3' |
C4' |
C5' |
247.1 |
204.6 |
| C2' |
C3' |
C4' |
O4' |
8.4 |
323.1 |
| C2' |
C3' |
C4' |
H4' |
129.2 |
81.8 |
| O3' |
C3' |
C2' |
H3' |
241.6 |
236.5 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| O2' |
C2' |
C1' |
O4' |
84.5 |
120.8 |
| O2' |
C2' |
C1' |
H1' |
318.3 |
1.4 |
| C1' |
C2' |
O2' |
C3' |
245.6 |
245.2 |
| C1' |
C2' |
O2' |
H2' |
123.5 |
122.5 |
| C3' |
C2' |
O2' |
H2' |
238.0 |
237.3 |
| O2' |
C2' |
C3' |
C4' |
257.8 |
262.0 |
| O2' |
C2' |
C3' |
O3' |
16.4 |
20.4 |
| O2' |
C2' |
C3' |
H3' |
134.8 |
143.9 |
| H2' |
C2' |
C1' |
O4' |
202.9 |
243.3 |
| H2' |
C2' |
C1' |
H1' |
76.7 |
123.9 |
| C1' |
C2' |
H2' |
C3' |
117.0 |
114.9 |
| C1' |
C2' |
H2' |
O2' |
239.3 |
237.5 |
| C3' |
C2' |
H2' |
O2' |
122.4 |
122.6 |
| H2' |
C2' |
C3' |
C4' |
139.3 |
139.4 |
| H2' |
C2' |
C3' |
O3' |
257.9 |
257.9 |
| H2' |
C2' |
C3' |
H3' |
16.2 |
21.4 |
| H2' |
C2' |
O2' |
HO2' |
56.5 |
57.5 |
| C1' |
O4' |
C4' |
C3' |
328.7 |
40.0 |
| C4' |
C3' |
C2' |
O2' |
257.8 |
262.0 |
| C4' |
C3' |
C2' |
H2' |
139.3 |
139.4 |
| C2' |
C3' |
C4' |
O3' |
121.0 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
239.2 |
241.9 |
| O3' |
C3' |
C4' |
H3' |
118.3 |
123.6 |
| C4' |
C3' |
O3' |
HO3' |
295.9 |
292.7 |
| C5' |
C4' |
C3' |
O4' |
238.7 |
241.4 |
| C5' |
C4' |
C3' |
H4' |
117.9 |
122.8 |
| C3' |
C4' |
C5' |
H5'1 |
180.0 |
177.8 |
| C3' |
C4' |
C5' |
H5'2 |
305.3 |
297.9 |
| C3' |
C4' |
C5' |
H5'3 |
54.8 |
57.8 |
| O4' |
C4' |
C3' |
H4' |
239.2 |
241.4 |
| O3' |
C3' |
C2' |
O2' |
16.4 |
20.4 |
| O3' |
C3' |
C2' |
H2' |
257.9 |
257.9 |
| C2' |
C3' |
O3' |
C4' |
244.2 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
121.0 |
123.6 |
| C4' |
C3' |
O3' |
H3' |
236.8 |
236.3 |
| O3' |
C3' |
C4' |
C5' |
126.2 |
86.3 |
| O3' |
C3' |
C4' |
O4' |
247.5 |
204.9 |
| O3' |
C3' |
C4' |
H4' |
8.2 |
323.5 |
| H3' |
C3' |
C2' |
O2' |
134.8 |
143.9 |
| H3' |
C3' |
C2' |
H2' |
16.2 |
21.4 |
| C2' |
C3' |
H3' |
C4' |
117.4 |
112.6 |
| C2' |
C3' |
H3' |
O3' |
237.5 |
236.4 |
| C4' |
C3' |
H3' |
O3' |
120.1 |
123.9 |
| H3' |
C3' |
C4' |
C5' |
7.9 |
322.7 |
| H3' |
C3' |
C4' |
O4' |
129.2 |
81.3 |
| H3' |
C3' |
C4' |
H4' |
250.0 |
199.9 |
| H3' |
C3' |
O3' |
HO3' |
59.0 |
56.5 |
| C1' |
O4' |
C4' |
C5' |
89.2 |
158.5 |
| C5' |
C4' |
C3' |
O3' |
126.2 |
86.3 |
| C5' |
C4' |
C3' |
H3' |
7.9 |
322.7 |
| C3' |
C4' |
C5' |
O4' |
117.5 |
114.2 |
| C3' |
C4' |
C5' |
H4' |
238.4 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
120.8 |
122.9 |
| H5'1 |
C5' |
C4' |
H5'2 |
234.7 |
239.9 |
| H5'1 |
C5' |
C4' |
H5'3 |
125.2 |
119.9 |
| H5'2 |
C5' |
C4' |
H5'3 |
250.5 |
240.0 |
| C4' |
O4' |
C1' |
H1' |
162.9 |
92.9 |
| O4' |
C4' |
C3' |
O3' |
247.5 |
204.9 |
| O4' |
C4' |
C3' |
H3' |
129.2 |
81.3 |
| C3' |
C4' |
O4' |
C5' |
239.5 |
241.5 |
| C3' |
C4' |
O4' |
H4' |
121.6 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
242.1 |
237.2 |
| O4' |
C4' |
C5' |
H5'1 |
62.5 |
63.5 |
| O4' |
C4' |
C5' |
H5'2 |
187.8 |
183.6 |
| O4' |
C4' |
C5' |
H5'3 |
297.2 |
303.6 |
| H4' |
C4' |
C3' |
O3' |
8.2 |
323.5 |
| H4' |
C4' |
C3' |
H3' |
250.0 |
199.9 |
| C3' |
C4' |
H4' |
C5' |
120.7 |
122.8 |
| C3' |
C4' |
H4' |
O4' |
242.3 |
245.7 |
| C5' |
C4' |
H4' |
O4' |
121.5 |
122.9 |
| H4' |
C4' |
C5' |
H5'1 |
301.6 |
300.6 |
| H4' |
C4' |
C5' |
H5'2 |
66.9 |
60.7 |
| H4' |
C4' |
C5' |
H5'3 |
176.4 |
180.7 |
| H5'1 |
C5' |
C4' |
O4' |
62.5 |
63.5 |
| H5'1 |
C5' |
C4' |
H4' |
301.6 |
300.6 |
| C4' |
C5' |
H5'1 |
H5'2 |
125.2 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'3 |
234.8 |
240.0 |
| H5'2 |
C5' |
H5'1 |
H5'3 |
109.6 |
120.0 |
| H5'2 |
C5' |
C4' |
O4' |
187.8 |
183.6 |
| H5'2 |
C5' |
C4' |
H4' |
66.9 |
60.7 |
| C4' |
C5' |
H5'2 |
H5'1 |
235.4 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'3 |
117.7 |
120.0 |
| H5'1 |
C5' |
H5'2 |
H5'3 |
242.3 |
240.0 |
| H5'3 |
C5' |
C4' |
O4' |
297.2 |
303.6 |
| H5'3 |
C5' |
C4' |
H4' |
176.4 |
180.7 |
| C4' |
C5' |
H5'3 |
H5'1 |
124.6 |
119.9 |
| C4' |
C5' |
H5'3 |
H5'2 |
242.4 |
240.0 |
| H5'1 |
C5' |
H5'3 |
H5'2 |
117.8 |
120.1 |
| HO2' |
O2' |
C2' |
H2' |
56.5 |
57.5 |
| HO3' |
O3' |
C3' |
H3' |
59.0 |
56.5 |