PDB Chemical Component N5M
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 N5M
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O4 |
N5 |
1.223 |
1.218 |
N5 |
O3 |
1.222 |
1.219 |
N5 |
C5 |
1.447 |
1.480 |
C5 |
C4 |
1.393 |
1.409 |
C5 |
C6 |
1.390 |
1.354 |
C4 |
N4 |
1.356 |
1.376 |
C4 |
N3 |
1.354 |
1.327 |
N3 |
C2 |
1.355 |
1.332 |
C2 |
O2 |
1.253 |
1.220 |
C2 |
N1 |
1.356 |
1.345 |
C6 |
N1 |
1.344 |
1.362 |
N1 |
C1' |
1.472 |
1.465 |
C1' |
O4' |
1.437 |
1.444 |
C1' |
C2' |
1.525 |
1.545 |
O4' |
C4' |
1.433 |
1.444 |
C2' |
O2' |
1.430 |
1.429 |
C2' |
C3' |
1.517 |
1.545 |
C3' |
O3' |
1.432 |
1.429 |
C3' |
C4' |
1.518 |
1.545 |
C4' |
C5' |
1.527 |
1.529 |
C5' |
O5' |
1.429 |
1.429 |
O5' |
P |
1.616 |
1.611 |
P |
OP2 |
1.512 |
1.480 |
P |
OP1 |
1.513 |
1.610 |
P |
OP3 |
1.600 |
1.610 |
N4 |
HN4 |
1.000 |
0.970 |
N4 |
HN4A |
1.000 |
0.970 |
C6 |
H6 |
1.080 |
1.080 |
C1' |
H1' |
1.100 |
1.090 |
C2' |
H2' |
1.100 |
1.090 |
O2' |
HO2' |
0.950 |
0.967 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.967 |
C4' |
H4' |
1.100 |
1.091 |
C5' |
H5' |
1.100 |
1.090 |
C5' |
H5'A |
1.100 |
1.090 |
OP1 |
HOP1 |
0.950 |
0.968 |
OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for N5M
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O4 |
N5 |
O3 |
119.2 |
119.9 |
O4 |
N5 |
C5 |
119.3 |
120.1 |
O3 |
N5 |
C5 |
121.5 |
120.0 |
N5 |
C5 |
C4 |
123.2 |
120.5 |
N5 |
C5 |
C6 |
118.4 |
120.5 |
C4 |
C5 |
C6 |
118.4 |
119.0 |
C5 |
C4 |
N4 |
121.8 |
120.2 |
C5 |
C4 |
N3 |
119.1 |
119.6 |
C5 |
C6 |
N1 |
121.0 |
119.3 |
C5 |
C6 |
H6 |
119.5 |
120.4 |
N4 |
C4 |
N3 |
119.0 |
120.2 |
C4 |
N4 |
HN4 |
109.8 |
120.0 |
C4 |
N4 |
HN4A |
125.1 |
120.0 |
C4 |
N3 |
C2 |
121.2 |
120.7 |
N3 |
C2 |
O2 |
118.3 |
119.4 |
N3 |
C2 |
N1 |
120.6 |
121.1 |
O2 |
C2 |
N1 |
121.2 |
119.5 |
C2 |
N1 |
C6 |
119.8 |
120.4 |
C2 |
N1 |
C1' |
121.6 |
119.8 |
C6 |
N1 |
C1' |
118.6 |
119.8 |
N1 |
C6 |
H6 |
119.5 |
120.4 |
N1 |
C1' |
O4' |
111.4 |
110.4 |
N1 |
C1' |
C2' |
109.9 |
110.4 |
N1 |
C1' |
H1' |
107.1 |
110.4 |
O4' |
C1' |
C2' |
106.9 |
104.8 |
C1' |
O4' |
C4' |
110.0 |
105.3 |
O4' |
C1' |
H1' |
110.0 |
110.3 |
C1' |
C2' |
O2' |
108.8 |
110.6 |
C1' |
C2' |
C3' |
105.4 |
104.1 |
C2' |
C1' |
H1' |
111.6 |
110.4 |
C1' |
C2' |
H2' |
113.2 |
110.5 |
O4' |
C4' |
C3' |
105.8 |
104.8 |
O4' |
C4' |
C5' |
112.7 |
110.4 |
O4' |
C4' |
H4' |
111.1 |
110.3 |
O2' |
C2' |
C3' |
111.2 |
110.6 |
O2' |
C2' |
H2' |
107.5 |
110.5 |
C2' |
O2' |
HO2' |
109.5 |
114.0 |
C2' |
C3' |
O3' |
111.7 |
110.5 |
C2' |
C3' |
C4' |
103.8 |
104.1 |
C3' |
C2' |
H2' |
110.9 |
110.6 |
C2' |
C3' |
H3' |
112.2 |
110.5 |
O3' |
C3' |
C4' |
110.9 |
110.5 |
O3' |
C3' |
H3' |
105.3 |
110.4 |
C3' |
O3' |
HO3' |
109.5 |
114.0 |
C3' |
C4' |
C5' |
112.9 |
110.4 |
C4' |
C3' |
H3' |
113.0 |
110.7 |
C3' |
C4' |
H4' |
110.9 |
110.4 |
C4' |
C5' |
O5' |
112.2 |
109.4 |
C5' |
C4' |
H4' |
103.6 |
110.4 |
C4' |
C5' |
H5' |
108.6 |
109.5 |
C4' |
C5' |
H5'A |
108.0 |
109.5 |
C5' |
O5' |
P |
115.9 |
123.0 |
O5' |
C5' |
H5' |
108.6 |
109.5 |
O5' |
C5' |
H5'A |
107.9 |
109.5 |
O5' |
P |
OP2 |
85.2 |
109.5 |
O5' |
P |
OP1 |
115.9 |
109.5 |
O5' |
P |
OP3 |
105.7 |
109.4 |
OP2 |
P |
OP1 |
129.4 |
109.5 |
OP2 |
P |
OP3 |
110.0 |
109.5 |
OP1 |
P |
OP3 |
107.4 |
109.5 |
P |
OP1 |
HOP1 |
109.5 |
114.0 |
P |
OP3 |
HOP3 |
109.5 |
114.0 |
HN4 |
N4 |
HN4A |
125.1 |
120.0 |
H5' |
C5' |
H5'A |
111.7 |
109.4 |
Torsion Angles for N5M
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O3 |
N5 |
O4 |
C5 |
180.3 |
180.3 |
O4 |
N5 |
C5 |
C4 |
159.3 |
174.6 |
O4 |
N5 |
C5 |
C6 |
339.4 |
354.3 |
O4 |
N5 |
O3 |
C5 |
179.7 |
179.7 |
O3 |
N5 |
C5 |
C4 |
339.0 |
354.3 |
O3 |
N5 |
C5 |
C6 |
159.2 |
174.0 |
O4 |
N5 |
C5 |
O3 |
180.3 |
180.3 |
C4 |
C5 |
N5 |
C6 |
179.8 |
180.3 |
N5 |
C5 |
C4 |
N4 |
0.1 |
0.0 |
N5 |
C5 |
C4 |
N3 |
180.1 |
180.0 |
N5 |
C5 |
C6 |
N1 |
179.8 |
179.8 |
N5 |
C5 |
C6 |
H6 |
359.8 |
359.9 |
N5 |
C5 |
C4 |
C6 |
180.2 |
179.7 |
C4 |
C5 |
C6 |
N1 |
360.0 |
359.5 |
C4 |
C5 |
C6 |
H6 |
180.0 |
179.7 |
N4 |
C4 |
C5 |
N3 |
180.0 |
180.1 |
C5 |
C4 |
N4 |
HN4 |
180.0 |
5.5 |
C5 |
C4 |
N4 |
HN4A |
0.0 |
185.4 |
C5 |
C4 |
N3 |
C2 |
0.1 |
0.1 |
N5 |
C5 |
C6 |
C4 |
179.8 |
180.3 |
C6 |
C5 |
C4 |
N4 |
179.9 |
180.3 |
C6 |
C5 |
C4 |
N3 |
359.9 |
0.2 |
C2 |
N1 |
C6 |
C5 |
0.1 |
0.5 |
C5 |
C6 |
N1 |
C1' |
179.8 |
180.2 |
N1 |
C6 |
C5 |
H6 |
180.0 |
179.8 |
N4 |
C4 |
C5 |
C6 |
179.9 |
180.3 |
C5 |
C4 |
N4 |
N3 |
180.0 |
179.9 |
N4 |
C4 |
N3 |
C2 |
180.1 |
180.0 |
HN4 |
N4 |
C4 |
HN4A |
180.0 |
180.1 |
N3 |
C4 |
C5 |
C6 |
359.9 |
0.2 |
C5 |
C4 |
N3 |
N4 |
180.0 |
180.1 |
N3 |
C4 |
N4 |
HN4 |
360.0 |
185.5 |
N3 |
C4 |
N4 |
HN4A |
180.0 |
5.5 |
C4 |
N3 |
C2 |
O2 |
179.9 |
180.0 |
C4 |
N3 |
C2 |
N1 |
359.9 |
359.9 |
O2 |
C2 |
N3 |
N1 |
180.0 |
180.1 |
N3 |
C2 |
N1 |
C6 |
360.0 |
359.8 |
N3 |
C2 |
N1 |
C1' |
180.2 |
180.1 |
N3 |
C2 |
O2 |
N1 |
180.0 |
179.9 |
O2 |
C2 |
N1 |
C6 |
180.0 |
179.8 |
O2 |
C2 |
N1 |
C1' |
0.2 |
360.0 |
C5 |
C6 |
N1 |
C2 |
0.1 |
0.5 |
N3 |
C2 |
N1 |
O2 |
180.0 |
180.1 |
C6 |
N1 |
C2 |
C1' |
179.8 |
179.8 |
C2 |
N1 |
C6 |
H6 |
180.1 |
180.3 |
C2 |
N1 |
C1' |
O4' |
200.3 |
53.6 |
C2 |
N1 |
C1' |
C2' |
82.0 |
298.2 |
C2 |
N1 |
C1' |
H1' |
320.6 |
175.8 |
C5 |
C6 |
N1 |
H6 |
180.0 |
180.2 |
C2 |
N1 |
C6 |
C1' |
180.2 |
180.2 |
C6 |
N1 |
C1' |
O4' |
20.5 |
233.8 |
C6 |
N1 |
C1' |
C2' |
262.2 |
118.4 |
C6 |
N1 |
C1' |
H1' |
140.9 |
356.0 |
C2 |
N1 |
C1' |
C6 |
179.8 |
179.8 |
C1' |
N1 |
C6 |
H6 |
359.8 |
0.1 |
O4' |
C1' |
N1 |
C2' |
118.3 |
115.4 |
N1 |
C1' |
O4' |
C4' |
228.7 |
200.7 |
O4' |
C1' |
N1 |
H1' |
239.6 |
237.8 |
N1 |
C1' |
C2' |
O2' |
232.9 |
261.5 |
N1 |
C1' |
C2' |
C3' |
113.6 |
142.8 |
C2' |
C1' |
N1 |
H1' |
121.4 |
122.4 |
N1 |
C1' |
C2' |
H2' |
352.4 |
24.0 |
N1 |
C1' |
O4' |
C2' |
240.0 |
241.1 |
N1 |
C1' |
O4' |
H1' |
118.6 |
122.3 |
O4' |
C1' |
C2' |
O2' |
111.9 |
142.6 |
O4' |
C1' |
C2' |
C3' |
352.6 |
23.9 |
C2' |
C1' |
O4' |
H1' |
238.7 |
241.1 |
O4' |
C1' |
C2' |
H2' |
231.3 |
265.2 |
C1' |
O4' |
C4' |
C3' |
25.5 |
40.5 |
C1' |
O4' |
C4' |
C5' |
149.4 |
159.3 |
C1' |
O4' |
C4' |
H4' |
265.1 |
281.7 |
N1 |
C1' |
C2' |
O4' |
121.1 |
118.9 |
N1 |
C1' |
C2' |
H1' |
241.4 |
237.7 |
C2' |
C1' |
O4' |
C4' |
348.7 |
319.6 |
O4' |
C1' |
C2' |
H1' |
120.3 |
118.8 |
O2' |
C2' |
C1' |
C3' |
119.3 |
118.7 |
O2' |
C2' |
C1' |
H2' |
240.6 |
237.4 |
C1' |
C2' |
O2' |
HO2' |
200.2 |
180.0 |
C1' |
C2' |
C3' |
O3' |
141.4 |
118.7 |
C1' |
C2' |
C3' |
C4' |
21.9 |
0.0 |
C3' |
C2' |
C1' |
H2' |
121.3 |
118.7 |
C1' |
C2' |
C3' |
H3' |
259.5 |
241.2 |
C4' |
O4' |
C1' |
C2' |
348.7 |
319.6 |
C4' |
O4' |
C1' |
H1' |
110.0 |
78.4 |
C2' |
C3' |
C4' |
O4' |
331.1 |
336.0 |
O3' |
C3' |
C4' |
O4' |
210.9 |
217.4 |
C3' |
C4' |
O4' |
C5' |
236.1 |
241.2 |
O4' |
C4' |
C3' |
H3' |
92.9 |
94.7 |
C3' |
C4' |
O4' |
H4' |
120.4 |
118.8 |
O4' |
C4' |
C5' |
O5' |
311.5 |
66.4 |
C5' |
C4' |
O4' |
H4' |
244.3 |
237.7 |
O4' |
C4' |
C5' |
H5' |
71.5 |
186.4 |
O4' |
C4' |
C5' |
H5'A |
192.7 |
306.5 |
C1' |
C2' |
O2' |
C3' |
244.4 |
245.3 |
O2' |
C2' |
C1' |
H1' |
351.5 |
23.8 |
C1' |
C2' |
O2' |
H2' |
122.9 |
122.6 |
O2' |
C2' |
C3' |
O3' |
23.7 |
360.0 |
O2' |
C2' |
C3' |
C4' |
264.2 |
241.3 |
C3' |
C2' |
O2' |
H2' |
238.5 |
237.3 |
O2' |
C2' |
C3' |
H3' |
141.8 |
122.5 |
C1' |
C2' |
C3' |
O2' |
117.7 |
118.7 |
C3' |
C2' |
C1' |
H1' |
232.3 |
265.1 |
C1' |
C2' |
C3' |
H2' |
237.2 |
241.4 |
O4' |
C4' |
C3' |
C2' |
331.1 |
336.0 |
O2' |
C2' |
C3' |
H2' |
119.5 |
122.7 |
C3' |
C2' |
O2' |
HO2' |
315.8 |
294.7 |
O3' |
C3' |
C2' |
C4' |
119.5 |
118.7 |
O3' |
C3' |
C2' |
H3' |
241.9 |
237.5 |
C2' |
C3' |
O3' |
HO3' |
147.4 |
61.5 |
C2' |
C3' |
C4' |
C5' |
207.3 |
217.1 |
C4' |
C3' |
C2' |
H3' |
122.4 |
118.8 |
C2' |
C3' |
C4' |
H4' |
91.6 |
94.8 |
O4' |
C4' |
C3' |
O3' |
210.9 |
217.4 |
C2' |
C3' |
O3' |
C4' |
244.7 |
245.4 |
O3' |
C3' |
C2' |
H2' |
264.2 |
237.3 |
C2' |
C3' |
O3' |
H3' |
122.1 |
122.5 |
O3' |
C3' |
C4' |
C5' |
87.2 |
98.5 |
C4' |
C3' |
O3' |
H3' |
237.4 |
237.2 |
O3' |
C3' |
C4' |
H4' |
331.5 |
336.2 |
O4' |
C4' |
C3' |
C5' |
123.8 |
118.9 |
O4' |
C4' |
C3' |
H4' |
239.5 |
241.2 |
C2' |
C3' |
C4' |
O3' |
120.1 |
118.6 |
C4' |
C3' |
C2' |
H2' |
144.6 |
118.7 |
C2' |
C3' |
C4' |
H3' |
238.1 |
241.3 |
O3' |
C3' |
C4' |
H3' |
118.0 |
122.7 |
C4' |
C3' |
O3' |
HO3' |
262.7 |
176.1 |
C3' |
C4' |
C5' |
O5' |
71.3 |
181.8 |
C5' |
C4' |
C3' |
H4' |
115.7 |
122.3 |
C3' |
C4' |
C5' |
H5' |
191.3 |
301.8 |
C3' |
C4' |
C5' |
H5'A |
312.5 |
61.9 |
O4' |
C4' |
C5' |
C3' |
240.2 |
244.6 |
O4' |
C4' |
C5' |
H4' |
120.2 |
122.3 |
C5' |
C4' |
C3' |
H3' |
329.2 |
335.9 |
C3' |
C4' |
C5' |
H4' |
240.0 |
237.7 |
C4' |
C5' |
O5' |
P |
178.6 |
180.0 |
O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
O5' |
C5' |
C4' |
H5'A |
118.8 |
120.0 |
H5' |
C5' |
C4' |
H5'A |
238.8 |
240.0 |
O5' |
C5' |
C4' |
H4' |
191.3 |
304.1 |
C4' |
C5' |
O5' |
H5' |
120.0 |
120.1 |
C4' |
C5' |
O5' |
H5'A |
241.2 |
240.0 |
C5' |
O5' |
P |
OP2 |
171.1 |
55.0 |
C5' |
O5' |
P |
OP1 |
39.3 |
175.0 |
C5' |
O5' |
P |
OP3 |
280.5 |
295.0 |
H5' |
C5' |
O5' |
H5'A |
121.2 |
119.9 |
P |
O5' |
C5' |
H5' |
58.6 |
60.0 |
P |
O5' |
C5' |
H5'A |
297.4 |
300.0 |
OP2 |
P |
O5' |
OP1 |
131.8 |
240.0 |
OP2 |
P |
O5' |
OP3 |
250.6 |
120.0 |
OP1 |
P |
O5' |
OP3 |
118.7 |
240.0 |
O5' |
P |
OP1 |
HOP1 |
166.3 |
180.0 |
O5' |
P |
OP3 |
HOP3 |
152.2 |
300.0 |
O5' |
P |
OP2 |
OP1 |
240.2 |
120.0 |
O5' |
P |
OP2 |
OP3 |
105.0 |
240.0 |
OP1 |
P |
OP2 |
OP3 |
224.8 |
120.0 |
OP2 |
P |
OP1 |
HOP1 |
60.3 |
300.0 |
OP2 |
P |
OP3 |
HOP3 |
242.7 |
180.0 |
O5' |
P |
OP1 |
OP2 |
106.1 |
240.0 |
O5' |
P |
OP1 |
OP3 |
242.2 |
119.9 |
OP2 |
P |
OP1 |
OP3 |
136.1 |
240.0 |
OP1 |
P |
OP3 |
HOP3 |
28.0 |
59.9 |
O5' |
P |
OP3 |
OP2 |
269.5 |
120.0 |
O5' |
P |
OP3 |
OP1 |
124.2 |
240.0 |
OP2 |
P |
OP3 |
OP1 |
214.8 |
120.0 |
OP3 |
P |
OP1 |
HOP1 |
284.2 |
60.1 |
HN4 |
N4 |
C4 |
N3 |
360.0 |
185.5 |
C4 |
N4 |
HN4 |
HN4A |
180.0 |
179.9 |
HN4A |
N4 |
C4 |
N3 |
180.0 |
5.5 |
C4 |
N4 |
HN4A |
HN4 |
180.0 |
180.1 |
C5 |
C6 |
H6 |
N1 |
180.0 |
179.8 |
H6 |
C6 |
N1 |
C1' |
359.8 |
0.1 |
N1 |
C1' |
H1' |
O4' |
238.7 |
237.7 |
N1 |
C1' |
H1' |
C2' |
120.3 |
122.4 |
O4' |
C1' |
H1' |
C2' |
241.5 |
244.6 |
H1' |
C1' |
O4' |
C4' |
110.0 |
78.4 |
H1' |
C1' |
C2' |
O2' |
351.5 |
23.8 |
H1' |
C1' |
C2' |
C3' |
232.3 |
265.1 |
H1' |
C1' |
C2' |
H2' |
111.0 |
146.4 |
C1' |
C2' |
H2' |
O2' |
239.8 |
237.4 |
C1' |
C2' |
H2' |
C3' |
118.1 |
114.7 |
H2' |
C2' |
C1' |
H1' |
111.0 |
146.4 |
O2' |
C2' |
H2' |
C3' |
238.3 |
237.3 |
H2' |
C2' |
O2' |
HO2' |
77.3 |
57.5 |
H2' |
C2' |
C3' |
O3' |
264.2 |
237.3 |
H2' |
C2' |
C3' |
C4' |
144.6 |
118.7 |
H2' |
C2' |
C3' |
H3' |
22.2 |
359.8 |
HO2' |
O2' |
C2' |
C3' |
315.8 |
294.7 |
HO2' |
O2' |
C2' |
H2' |
77.3 |
57.5 |
C2' |
C3' |
H3' |
O3' |
238.2 |
237.5 |
C2' |
C3' |
H3' |
C4' |
117.0 |
114.8 |
H3' |
C3' |
C2' |
H2' |
22.2 |
359.8 |
O3' |
C3' |
H3' |
C4' |
238.8 |
237.3 |
H3' |
C3' |
O3' |
HO3' |
25.3 |
298.9 |
H3' |
C3' |
C4' |
C5' |
329.2 |
335.9 |
H3' |
C3' |
C4' |
H4' |
213.4 |
213.5 |
HO3' |
O3' |
C3' |
C4' |
262.7 |
176.1 |
HO3' |
O3' |
C3' |
H3' |
25.3 |
298.9 |
O4' |
C4' |
H4' |
C3' |
117.3 |
115.4 |
O4' |
C4' |
H4' |
C5' |
238.7 |
237.6 |
C3' |
C4' |
H4' |
C5' |
121.4 |
122.3 |
H4' |
C4' |
C3' |
H3' |
213.4 |
213.5 |
H4' |
C4' |
C5' |
O5' |
191.3 |
304.1 |
H4' |
C4' |
C5' |
H5' |
311.3 |
64.1 |
H4' |
C4' |
C5' |
H5'A |
72.5 |
184.2 |
C4' |
C5' |
H5' |
O5' |
237.8 |
240.0 |
H5' |
C5' |
C4' |
H4' |
311.3 |
64.1 |
C4' |
C5' |
H5' |
H5'A |
118.9 |
120.0 |
H5' |
C5' |
O5' |
P |
58.6 |
60.0 |
O5' |
C5' |
H5' |
H5'A |
241.1 |
240.0 |
C4' |
C5' |
H5'A |
O5' |
121.5 |
120.0 |
H5'A |
C5' |
C4' |
H4' |
72.5 |
184.2 |
C4' |
C5' |
H5'A |
H5' |
240.7 |
239.9 |
H5'A |
C5' |
O5' |
P |
297.4 |
300.0 |
O5' |
C5' |
H5'A |
H5' |
119.2 |
120.0 |
HOP1 |
OP1 |
P |
OP3 |
284.2 |
60.1 |