PDB Chemical Component N8M
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 N8M
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N2 |
CG |
1.476 |
1.469 |
| CG |
HG |
1.100 |
1.090 |
| CG |
HGA |
1.101 |
1.090 |
| CG |
HGB |
1.100 |
1.091 |
| CE |
N2 |
1.480 |
1.469 |
| N2 |
C5' |
1.476 |
1.469 |
| CE |
HE |
1.100 |
1.090 |
| CE |
HEA |
1.100 |
1.090 |
| CE |
HEB |
1.100 |
1.090 |
| C4' |
C5' |
1.521 |
1.529 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| O4' |
C4' |
1.465 |
1.444 |
| C4' |
C3' |
1.524 |
1.544 |
| C4' |
H4' |
1.100 |
1.090 |
| C1' |
O4' |
1.422 |
1.444 |
| N9 |
C1' |
1.467 |
1.465 |
| C1' |
C2' |
1.524 |
1.545 |
| C1' |
H1' |
1.100 |
1.090 |
| C8 |
N9 |
1.376 |
1.363 |
| N9 |
C4 |
1.383 |
1.372 |
| C5 |
C4 |
1.388 |
1.405 |
| C4 |
N3 |
1.362 |
1.329 |
| N3 |
C2 |
1.348 |
1.316 |
| N1 |
C2 |
1.352 |
1.321 |
| C2 |
H2 |
1.080 |
1.080 |
| C6 |
N1 |
1.373 |
1.329 |
| C5 |
C6 |
1.428 |
1.406 |
| N6 |
C6 |
1.346 |
1.384 |
| N6 |
HN6 |
1.000 |
0.970 |
| N6 |
HN6A |
1.000 |
0.970 |
| N7 |
C5 |
1.386 |
1.355 |
| C8 |
N7 |
1.308 |
1.301 |
| C9 |
C8 |
1.499 |
1.507 |
| O2' |
C2' |
1.412 |
1.428 |
| C2' |
C3' |
1.514 |
1.545 |
| C2' |
H2' |
1.100 |
1.090 |
| O2' |
HO2' |
0.950 |
0.967 |
| O3' |
C3' |
1.415 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.951 |
0.967 |
| C9 |
H9 |
1.100 |
1.090 |
| C9 |
H9A |
1.100 |
1.091 |
| C9 |
H9B |
1.100 |
1.090 |
Bond Angles for N8M
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N2 |
CG |
HG |
109.5 |
109.5 |
| N2 |
CG |
HGA |
109.4 |
109.5 |
| N2 |
CG |
HGB |
109.5 |
109.5 |
| HG |
CG |
HGA |
109.5 |
109.5 |
| HG |
CG |
HGB |
109.5 |
109.5 |
| HGA |
CG |
HGB |
109.5 |
109.4 |
| CE |
N2 |
C5' |
110.3 |
111.0 |
| N2 |
C5' |
H5' |
108.2 |
109.5 |
| N2 |
C5' |
H5'A |
107.3 |
109.4 |
| HE |
CE |
HEA |
109.5 |
109.5 |
| HE |
CE |
HEB |
109.5 |
109.5 |
| HEA |
CE |
HEB |
109.5 |
109.5 |
| C4' |
C5' |
H5' |
108.2 |
109.5 |
| C4' |
C5' |
H5'A |
107.4 |
109.5 |
| H5' |
C5' |
H5'A |
112.5 |
109.5 |
| O4' |
C4' |
C3' |
105.9 |
104.8 |
| O4' |
C4' |
H4' |
114.1 |
110.4 |
| C3' |
C4' |
H4' |
109.2 |
110.4 |
| C4' |
C3' |
C2' |
102.4 |
104.1 |
| C4' |
C3' |
H3' |
114.4 |
110.5 |
| N9 |
C1' |
C2' |
113.8 |
110.4 |
| N9 |
C1' |
H1' |
106.9 |
110.4 |
| C2' |
C1' |
H1' |
108.9 |
110.4 |
| C1' |
C2' |
C3' |
101.6 |
104.0 |
| C1' |
C2' |
H2' |
115.3 |
110.5 |
| N9 |
C4 |
N3 |
127.7 |
134.9 |
| C4 |
N3 |
C2 |
111.6 |
120.6 |
| N3 |
C2 |
H2 |
115.8 |
118.7 |
| N1 |
C2 |
H2 |
115.8 |
118.8 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| O2' |
C2' |
C3' |
116.2 |
110.6 |
| O2' |
C2' |
H2' |
100.3 |
110.6 |
| C3' |
C2' |
H2' |
111.6 |
110.5 |
| C2' |
C3' |
H3' |
113.7 |
110.5 |
| O3' |
C3' |
H3' |
107.9 |
110.5 |
| H9 |
C9 |
H9A |
109.5 |
109.4 |
| H9 |
C9 |
H9B |
109.4 |
109.5 |
| H9A |
C9 |
H9B |
109.5 |
109.4 |
Torsion Angles for N8M
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| HG |
CG |
N2 |
HGA |
240.0 |
240.0 |
| HG |
CG |
N2 |
HGB |
120.0 |
120.0 |
| HGA |
CG |
N2 |
HGB |
240.0 |
240.0 |
| N2 |
CG |
HG |
HGA |
120.0 |
120.0 |
| N2 |
CG |
HG |
HGB |
240.0 |
240.0 |
| HGA |
CG |
HG |
HGB |
120.0 |
120.0 |
| N2 |
CG |
HGA |
HG |
240.0 |
240.0 |
| N2 |
CG |
HGA |
HGB |
120.0 |
120.0 |
| HG |
CG |
HGA |
HGB |
240.0 |
240.0 |
| N2 |
CG |
HGB |
HG |
120.0 |
120.0 |
| N2 |
CG |
HGB |
HGA |
240.0 |
240.0 |
| HG |
CG |
HGB |
HGA |
120.0 |
120.0 |
| CE |
N2 |
CG |
HG |
101.3 |
296.0 |
| CE |
N2 |
CG |
HGA |
221.3 |
56.1 |
| CE |
N2 |
CG |
HGB |
341.3 |
176.0 |
| CE |
N2 |
C5' |
H5' |
181.0 |
54.0 |
| CE |
N2 |
C5' |
H5'A |
302.6 |
174.0 |
| C5' |
N2 |
CG |
HG |
341.0 |
60.0 |
| C5' |
N2 |
CG |
HGA |
101.0 |
180.0 |
| C5' |
N2 |
CG |
HGB |
221.0 |
300.0 |
| C4' |
C5' |
N2 |
H5' |
240.0 |
240.0 |
| C4' |
C5' |
N2 |
H5'A |
118.4 |
120.0 |
| H5' |
C5' |
N2 |
H5'A |
238.4 |
240.0 |
| HE |
CE |
N2 |
C5' |
272.7 |
296.1 |
| HEA |
CE |
HE |
HEB |
120.0 |
120.1 |
| HEA |
CE |
N2 |
C5' |
32.7 |
56.0 |
| HE |
CE |
HEA |
HEB |
240.0 |
239.9 |
| HEB |
CE |
N2 |
C5' |
152.7 |
176.0 |
| HE |
CE |
HEB |
HEA |
120.0 |
120.0 |
| N2 |
C5' |
C4' |
H5' |
120.0 |
120.0 |
| N2 |
C5' |
C4' |
H5'A |
241.7 |
240.0 |
| H5' |
C5' |
C4' |
H5'A |
121.7 |
120.0 |
| N2 |
C5' |
H5' |
H5'A |
118.4 |
120.0 |
| C4' |
C5' |
H5' |
H5'A |
241.5 |
240.0 |
| N2 |
C5' |
H5'A |
H5' |
241.1 |
240.0 |
| C4' |
C5' |
H5'A |
H5' |
119.0 |
120.0 |
| O4' |
C4' |
C5' |
H5' |
278.8 |
309.6 |
| O4' |
C4' |
C5' |
H5'A |
157.1 |
189.6 |
| C3' |
C4' |
O4' |
H4' |
120.1 |
118.9 |
| O4' |
C4' |
C3' |
C2' |
25.2 |
336.0 |
| O4' |
C4' |
C3' |
H3' |
148.7 |
94.7 |
| C3' |
C4' |
C5' |
H5' |
35.2 |
64.9 |
| C3' |
C4' |
C5' |
H5'A |
273.5 |
304.9 |
| O4' |
C4' |
C3' |
H4' |
236.8 |
241.1 |
| C1' |
C2' |
C3' |
C4' |
322.2 |
0.0 |
| O2' |
C2' |
C3' |
C4' |
199.7 |
241.4 |
| C4' |
C3' |
C2' |
H2' |
85.5 |
118.6 |
| C2' |
C3' |
C4' |
H3' |
236.5 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
120.6 |
122.7 |
| H4' |
C4' |
C5' |
H5' |
155.5 |
187.3 |
| H4' |
C4' |
C5' |
H5'A |
33.8 |
67.3 |
| O4' |
C4' |
H4' |
C3' |
118.2 |
115.4 |
| H4' |
C4' |
C3' |
C2' |
148.5 |
94.9 |
| H4' |
C4' |
C3' |
H3' |
272.0 |
213.6 |
| C1' |
O4' |
C4' |
C3' |
358.4 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
238.3 |
281.6 |
| C2' |
C1' |
N9 |
H1' |
120.2 |
122.3 |
| N9 |
C1' |
C2' |
C3' |
154.7 |
142.8 |
| N9 |
C1' |
C2' |
H2' |
33.9 |
24.2 |
| C4' |
C3' |
C2' |
C1' |
322.2 |
0.0 |
| N9 |
C1' |
C2' |
H1' |
240.9 |
237.7 |
| O2' |
C2' |
C1' |
C3' |
125.0 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
245.7 |
237.3 |
| C3' |
C2' |
C1' |
H2' |
120.8 |
118.6 |
| C1' |
C2' |
C3' |
H3' |
198.3 |
241.4 |
| N9 |
C1' |
H1' |
C2' |
123.3 |
122.3 |
| H1' |
C1' |
C2' |
C3' |
273.8 |
265.1 |
| H1' |
C1' |
C2' |
H2' |
153.0 |
146.5 |
| C8 |
N9 |
C1' |
C2' |
103.8 |
287.8 |
| C8 |
N9 |
C1' |
H1' |
343.5 |
165.5 |
| C4 |
N9 |
C1' |
C2' |
284.2 |
108.2 |
| C4 |
N9 |
C1' |
H1' |
163.9 |
345.9 |
| N9 |
C4 |
N3 |
C2 |
179.9 |
180.0 |
| C4 |
N3 |
C2 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
180.1 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
179.9 |
| C6 |
N1 |
C2 |
H2 |
179.9 |
180.0 |
| C4' |
C3' |
C2' |
O2' |
199.7 |
241.4 |
| O2' |
C2' |
C1' |
H1' |
38.7 |
23.8 |
| C1' |
C2' |
O2' |
C3' |
243.5 |
245.4 |
| C1' |
C2' |
O2' |
H2' |
123.1 |
122.7 |
| C3' |
C2' |
O2' |
H2' |
239.6 |
237.3 |
| O2' |
C2' |
C3' |
H3' |
75.8 |
122.7 |
| C2' |
C3' |
C4' |
H4' |
148.5 |
94.9 |
| C4' |
C3' |
C2' |
H3' |
124.0 |
118.7 |
| C3' |
C2' |
C1' |
H1' |
273.8 |
265.1 |
| C1' |
C2' |
C3' |
H2' |
236.7 |
241.4 |
| O2' |
C2' |
C3' |
H2' |
114.2 |
122.8 |
| O3' |
C3' |
C2' |
H3' |
239.2 |
237.3 |
| H2' |
C2' |
C1' |
H1' |
153.0 |
146.5 |
| C1' |
C2' |
H2' |
C3' |
115.1 |
114.6 |
| O2' |
C2' |
H2' |
C3' |
236.3 |
237.3 |
| H2' |
C2' |
C3' |
H3' |
321.6 |
359.9 |
| HO2' |
O2' |
C2' |
C3' |
266.5 |
294.7 |
| HO2' |
O2' |
C2' |
H2' |
26.9 |
57.4 |
| O3' |
C3' |
C4' |
H4' |
32.6 |
336.3 |
| C4' |
C3' |
O3' |
H3' |
235.4 |
237.4 |
| O3' |
C3' |
C2' |
H2' |
200.8 |
237.3 |
| C2' |
C3' |
O3' |
H3' |
124.2 |
122.7 |
| H3' |
C3' |
C4' |
H4' |
272.0 |
213.6 |
| C4' |
C3' |
H3' |
C2' |
242.8 |
245.3 |
| H3' |
C3' |
C2' |
H2' |
321.6 |
359.9 |
| HO3' |
O3' |
C3' |
H3' |
178.7 |
302.7 |
| H9A |
C9 |
H9 |
H9B |
120.0 |
119.9 |
| H9 |
C9 |
H9A |
H9B |
240.0 |
240.1 |
| H9 |
C9 |
H9B |
H9A |
120.0 |
119.9 |