PDB Chemical Component 5N5
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 5N5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N6 |
C6 |
1.336 |
1.384 |
| N7 |
C5 |
1.334 |
1.355 |
| N7 |
C8 |
1.336 |
1.302 |
| C6 |
C5 |
1.395 |
1.405 |
| C6 |
N1 |
1.342 |
1.329 |
| C5 |
C4 |
1.391 |
1.405 |
| C8 |
N9 |
1.343 |
1.364 |
| C2' |
O2' |
1.423 |
1.429 |
| C2' |
C3' |
1.536 |
1.548 |
| C2' |
C1' |
1.533 |
1.550 |
| N1 |
C2 |
1.327 |
1.321 |
| O3' |
C3' |
1.441 |
1.429 |
| C3' |
C4' |
1.525 |
1.540 |
| C4 |
N9 |
1.332 |
1.372 |
| C4 |
N3 |
1.347 |
1.329 |
| N9 |
C1' |
1.502 |
1.465 |
| C2 |
N3 |
1.329 |
1.316 |
| C1' |
O4' |
1.454 |
1.444 |
| C4' |
O4' |
1.446 |
1.438 |
| C4' |
C5' |
1.533 |
1.531 |
| C5' |
N5' |
1.472 |
1.469 |
| O2' |
H1 |
0.950 |
0.967 |
| C2' |
H2 |
1.100 |
1.090 |
| C3' |
H3 |
1.100 |
1.091 |
| O3' |
H4 |
0.950 |
0.967 |
| C4' |
H5 |
1.100 |
1.090 |
| C5' |
H6 |
1.100 |
1.090 |
| C5' |
H7 |
1.100 |
1.090 |
| N5' |
H8 |
1.000 |
1.009 |
| N5' |
H9 |
1.000 |
1.008 |
| C1' |
H11 |
1.100 |
1.089 |
| C8 |
H12 |
1.080 |
1.080 |
| C2 |
H13 |
1.080 |
1.080 |
| N6 |
H14 |
1.000 |
0.970 |
| N6 |
H15 |
1.000 |
0.970 |
Bond Angles for 5N5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N7 |
C5 |
C4 |
107.4 |
107.2 |
| N7 |
C8 |
H12 |
125.2 |
125.0 |
| C5 |
C4 |
N3 |
119.4 |
119.1 |
| C2' |
O2' |
H1 |
109.5 |
114.0 |
| C3' |
C2' |
C1' |
104.5 |
102.1 |
| C2' |
C3' |
C4' |
102.0 |
104.2 |
| C3' |
C2' |
H2 |
110.3 |
110.9 |
| C2' |
C3' |
H3 |
110.0 |
110.5 |
| C2' |
C1' |
O4' |
105.5 |
103.5 |
| C1' |
C2' |
H2 |
110.3 |
110.9 |
| C2' |
C1' |
H11 |
109.4 |
110.6 |
| N1 |
C2 |
H13 |
118.9 |
118.7 |
| O3' |
C3' |
C4' |
111.0 |
110.5 |
| O3' |
C3' |
H3 |
111.4 |
110.5 |
| C3' |
C4' |
O4' |
102.2 |
107.3 |
| C3' |
C4' |
C5' |
110.4 |
109.9 |
| C4' |
C3' |
H3 |
110.2 |
110.5 |
| C3' |
C4' |
H5 |
111.1 |
109.9 |
| N9 |
C1' |
H11 |
109.8 |
110.7 |
| C5' |
C4' |
O4' |
109.6 |
109.9 |
| O4' |
C4' |
H5 |
112.3 |
109.9 |
| C4' |
C5' |
N5' |
109.3 |
109.5 |
| C5' |
C4' |
H5 |
111.0 |
110.0 |
| C4' |
C5' |
H6 |
109.5 |
109.4 |
| C4' |
C5' |
H7 |
109.5 |
109.5 |
| N5' |
C5' |
H6 |
109.5 |
109.5 |
| N5' |
C5' |
H7 |
109.5 |
109.5 |
| C5' |
N5' |
H8 |
109.5 |
110.9 |
| C5' |
N5' |
H9 |
109.5 |
111.0 |
| H6 |
C5' |
H7 |
109.5 |
109.5 |
| H8 |
N5' |
H9 |
109.5 |
111.0 |
| H14 |
N6 |
H15 |
109.4 |
120.1 |
Torsion Angles for 5N5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5 |
N7 |
C8 |
H12 |
180.1 |
180.1 |
| N7 |
C5 |
C4 |
N3 |
179.9 |
180.0 |
| C6 |
N1 |
C2 |
H13 |
179.7 |
180.3 |
| C8 |
N9 |
C1' |
H11 |
167.7 |
142.1 |
| C3' |
C2' |
O2' |
H1 |
180.0 |
298.6 |
| C3' |
C2' |
C1' |
O4' |
5.3 |
37.0 |
| C1' |
C2' |
C3' |
H2 |
241.4 |
241.8 |
| C3' |
C2' |
C1' |
H11 |
246.5 |
278.5 |
| O3' |
C3' |
C2' |
C4' |
118.7 |
118.7 |
| O3' |
C3' |
C2' |
H3 |
235.6 |
237.4 |
| C2' |
C3' |
C4' |
O4' |
319.4 |
358.0 |
| C2' |
C3' |
C4' |
C5' |
202.9 |
238.5 |
| C4' |
C3' |
C2' |
H3 |
116.9 |
118.7 |
| C2' |
C3' |
C4' |
H5 |
79.3 |
117.4 |
| C1' |
C2' |
O2' |
H1 |
65.8 |
185.9 |
| C1' |
C2' |
C3' |
C4' |
21.2 |
339.1 |
| C3' |
C2' |
C1' |
H2 |
118.6 |
118.2 |
| C1' |
C2' |
C3' |
H3 |
264.3 |
220.4 |
| N9 |
C1' |
C2' |
H11 |
239.3 |
237.0 |
| O3' |
C3' |
C2' |
C1' |
139.9 |
97.8 |
| C2' |
C3' |
O3' |
C4' |
246.7 |
245.2 |
| O3' |
C3' |
C2' |
H2 |
258.6 |
216.0 |
| C2' |
C3' |
O3' |
H3 |
123.6 |
122.6 |
| O3' |
C3' |
C4' |
O4' |
200.1 |
239.3 |
| O3' |
C3' |
C4' |
C5' |
83.6 |
119.9 |
| C4' |
C3' |
O3' |
H3 |
236.8 |
237.4 |
| O3' |
C3' |
C4' |
H5 |
320.0 |
358.7 |
| C4' |
C3' |
C2' |
C1' |
21.2 |
339.1 |
| C4' |
C3' |
C2' |
H2 |
139.9 |
97.4 |
| C2' |
C3' |
C4' |
H3 |
243.2 |
241.3 |
| O3' |
C3' |
C4' |
H3 |
123.9 |
122.6 |
| C5' |
C4' |
C3' |
O4' |
243.5 |
240.6 |
| O4' |
C4' |
C3' |
H5 |
240.1 |
240.6 |
| C3' |
C4' |
C5' |
N5' |
191.0 |
185.0 |
| C5' |
C4' |
C3' |
H5 |
123.6 |
121.2 |
| C3' |
C4' |
C5' |
H6 |
311.0 |
305.0 |
| C3' |
C4' |
C5' |
H7 |
71.0 |
65.0 |
| C4 |
N9 |
C1' |
H11 |
348.1 |
321.8 |
| N9 |
C1' |
C2' |
H2 |
7.2 |
37.3 |
| C2' |
C1' |
N9 |
H11 |
120.4 |
122.9 |
| O4' |
C1' |
C2' |
H2 |
246.6 |
278.8 |
| C2' |
C1' |
O4' |
H11 |
241.9 |
241.5 |
| C1' |
O4' |
C4' |
H5 |
286.6 |
267.1 |
| C2' |
C1' |
O4' |
C4' |
328.2 |
319.9 |
| C3' |
C4' |
O4' |
C5' |
242.9 |
240.6 |
| O4' |
C4' |
C3' |
H3 |
76.2 |
116.7 |
| C3' |
C4' |
O4' |
H5 |
119.1 |
119.5 |
| O4' |
C4' |
C5' |
N5' |
79.2 |
67.1 |
| C5' |
C4' |
O4' |
H5 |
236.2 |
238.9 |
| O4' |
C4' |
C5' |
H6 |
199.2 |
187.2 |
| O4' |
C4' |
C5' |
H7 |
319.3 |
307.1 |
| C3' |
C4' |
C5' |
O4' |
111.8 |
117.8 |
| C5' |
C4' |
C3' |
H3 |
319.7 |
357.2 |
| C3' |
C4' |
C5' |
H5 |
236.4 |
238.9 |
| O4' |
C4' |
C5' |
H5 |
124.6 |
121.0 |
| N5' |
C5' |
C4' |
H6 |
240.0 |
240.0 |
| N5' |
C5' |
C4' |
H7 |
120.0 |
120.0 |
| C4' |
C5' |
N5' |
H8 |
180.0 |
56.0 |
| C4' |
C5' |
N5' |
H9 |
300.0 |
180.0 |
| H6 |
C5' |
C4' |
H7 |
239.9 |
240.0 |
| N5' |
C5' |
C4' |
O4' |
79.2 |
67.1 |
| N5' |
C5' |
C4' |
H5 |
314.6 |
306.1 |
| C4' |
C5' |
N5' |
H6 |
120.0 |
120.0 |
| C4' |
C5' |
N5' |
H7 |
240.0 |
240.0 |
| H6 |
C5' |
N5' |
H7 |
120.0 |
120.1 |
| H8 |
N5' |
C5' |
H9 |
240.0 |
236.1 |
| H2 |
C2' |
O2' |
H1 |
303.7 |
62.2 |
| C3' |
C2' |
H2 |
C1' |
245.0 |
247.3 |
| H2 |
C2' |
C3' |
C4' |
139.9 |
97.4 |
| H2 |
C2' |
C3' |
H3 |
22.9 |
338.6 |
| H2 |
C2' |
C1' |
O4' |
246.6 |
278.8 |
| H2 |
C2' |
C1' |
H11 |
127.8 |
160.4 |
| H3 |
C3' |
C2' |
C1' |
264.3 |
220.4 |
| C2' |
C3' |
H3 |
C4' |
111.7 |
114.8 |
| H3 |
C3' |
C2' |
H2 |
22.9 |
338.6 |
| O3' |
C3' |
H3 |
C4' |
236.4 |
237.4 |
| H3 |
C3' |
C4' |
O4' |
76.2 |
116.7 |
| H3 |
C3' |
C4' |
C5' |
319.7 |
357.2 |
| H3 |
C3' |
C4' |
H5 |
196.1 |
236.1 |
| H4 |
O3' |
C3' |
C4' |
293.3 |
176.2 |
| H4 |
O3' |
C3' |
H3 |
56.4 |
298.8 |
| C3' |
C4' |
H5 |
O4' |
246.3 |
242.1 |
| C3' |
C4' |
H5 |
C5' |
123.2 |
121.1 |
| H5 |
C4' |
C3' |
H3 |
196.1 |
236.1 |
| C5' |
C4' |
H5 |
O4' |
123.1 |
121.0 |
| H5 |
C4' |
C5' |
N5' |
314.6 |
306.1 |
| H5 |
C4' |
C5' |
H6 |
74.6 |
66.1 |
| H5 |
C4' |
C5' |
H7 |
194.7 |
186.1 |
| H6 |
C5' |
C4' |
O4' |
199.2 |
187.2 |
| C4' |
C5' |
H6 |
N5' |
240.1 |
240.0 |
| H6 |
C5' |
C4' |
H5 |
74.6 |
66.1 |
| C4' |
C5' |
H6 |
H7 |
120.1 |
120.0 |
| N5' |
C5' |
H6 |
H7 |
240.0 |
240.0 |
| H6 |
C5' |
N5' |
H8 |
60.0 |
296.1 |
| H6 |
C5' |
N5' |
H9 |
180.0 |
60.0 |
| H7 |
C5' |
C4' |
O4' |
319.3 |
307.1 |
| C4' |
C5' |
H7 |
N5' |
119.9 |
120.0 |
| H7 |
C5' |
C4' |
H5 |
194.7 |
186.1 |
| C4' |
C5' |
H7 |
H6 |
239.9 |
240.1 |
| N5' |
C5' |
H7 |
H6 |
120.0 |
120.1 |
| H7 |
C5' |
N5' |
H8 |
299.9 |
176.0 |
| H7 |
C5' |
N5' |
H9 |
60.0 |
300.0 |
| H8 |
N5' |
C5' |
H6 |
60.0 |
296.1 |
| H8 |
N5' |
C5' |
H7 |
299.9 |
176.0 |
| C5' |
N5' |
H8 |
H9 |
120.0 |
123.9 |
| H9 |
N5' |
C5' |
H6 |
180.0 |
60.0 |
| H9 |
N5' |
C5' |
H7 |
60.0 |
300.0 |
| C5' |
N5' |
H9 |
H8 |
239.9 |
236.1 |
| C2' |
C1' |
H11 |
O4' |
115.7 |
114.1 |
| H11 |
C1' |
C2' |
H2 |
127.8 |
160.4 |