PDB Chemical Component NUP
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 NUP
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O4 |
C4 |
1.231 |
1.219 |
C4 |
N2 |
1.334 |
1.349 |
C4 |
C5 |
1.398 |
1.404 |
N2 |
C2 |
1.341 |
1.346 |
N2 |
HN2 |
1.000 |
0.969 |
C2 |
O2 |
1.246 |
1.216 |
C2 |
N1 |
1.413 |
1.345 |
C5 |
C6 |
1.383 |
1.367 |
C5 |
H5 |
1.080 |
1.079 |
C6 |
N1 |
1.415 |
1.374 |
C6 |
N3 |
1.341 |
1.371 |
N3 |
HN31 |
1.000 |
0.969 |
N3 |
HN32 |
1.000 |
0.971 |
N1 |
C1' |
1.470 |
1.465 |
C1' |
C2' |
1.533 |
1.551 |
C1' |
O4' |
1.438 |
1.443 |
C1' |
H1' |
1.100 |
1.090 |
O4' |
C4' |
1.421 |
1.438 |
C2' |
O2' |
1.439 |
1.429 |
C2' |
C3' |
1.515 |
1.547 |
C2' |
H2' |
1.100 |
1.090 |
O2' |
HO2' |
0.950 |
0.967 |
C3' |
O3' |
1.437 |
1.429 |
C3' |
C4' |
1.530 |
1.541 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.967 |
C4' |
C5' |
1.532 |
1.530 |
C4' |
H4' |
1.100 |
1.090 |
C5' |
O5' |
1.427 |
1.429 |
C5' |
H5'1 |
1.100 |
1.090 |
C5' |
H5'2 |
1.099 |
1.090 |
O5' |
P |
1.619 |
1.610 |
P |
O1P |
1.494 |
1.480 |
P |
O2P |
1.512 |
1.610 |
P |
O3P |
1.521 |
1.610 |
O2P |
HO2P |
0.950 |
0.967 |
O3P |
HO3P |
0.950 |
0.967 |
Bond Angles for NUP
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O4 |
C4 |
N2 |
116.1 |
120.2 |
O4 |
C4 |
C5 |
120.6 |
120.2 |
N2 |
C4 |
C5 |
123.3 |
119.6 |
C4 |
N2 |
C2 |
121.3 |
120.5 |
C4 |
N2 |
HN2 |
119.3 |
119.8 |
C4 |
C5 |
C6 |
116.3 |
119.1 |
C4 |
C5 |
H5 |
121.8 |
120.4 |
C2 |
N2 |
HN2 |
119.4 |
119.7 |
N2 |
C2 |
O2 |
118.7 |
119.5 |
N2 |
C2 |
N1 |
119.7 |
121.0 |
O2 |
C2 |
N1 |
121.6 |
119.5 |
C2 |
N1 |
C6 |
118.2 |
120.4 |
C2 |
N1 |
C1' |
119.9 |
119.8 |
C6 |
C5 |
H5 |
121.8 |
120.5 |
C5 |
C6 |
N1 |
121.1 |
119.4 |
C5 |
C6 |
N3 |
117.4 |
120.3 |
N3 |
C6 |
N1 |
121.5 |
120.3 |
C6 |
N1 |
C1' |
121.8 |
119.8 |
C6 |
N3 |
HN31 |
109.5 |
120.0 |
C6 |
N3 |
HN32 |
109.5 |
120.0 |
HN31 |
N3 |
HN32 |
109.5 |
120.0 |
N1 |
C1' |
C2' |
114.5 |
110.6 |
N1 |
C1' |
O4' |
109.7 |
110.7 |
N1 |
C1' |
H1' |
104.9 |
110.5 |
O4' |
C1' |
C2' |
106.6 |
103.5 |
C2' |
C1' |
H1' |
108.2 |
110.6 |
C1' |
C2' |
O2' |
118.0 |
110.9 |
C1' |
C2' |
C3' |
100.3 |
102.1 |
C1' |
C2' |
H2' |
111.3 |
110.8 |
O4' |
C1' |
H1' |
113.1 |
110.8 |
C1' |
O4' |
C4' |
110.8 |
107.0 |
O4' |
C4' |
C3' |
104.8 |
107.3 |
O4' |
C4' |
C5' |
111.2 |
109.9 |
O4' |
C4' |
H4' |
112.7 |
109.9 |
O2' |
C2' |
C3' |
112.3 |
111.0 |
O2' |
C2' |
H2' |
98.9 |
110.8 |
C2' |
O2' |
HO2' |
109.5 |
114.0 |
C3' |
C2' |
H2' |
117.0 |
111.0 |
C2' |
C3' |
O3' |
108.8 |
110.5 |
C2' |
C3' |
C4' |
104.2 |
104.2 |
C2' |
C3' |
H3' |
113.7 |
110.5 |
O3' |
C3' |
C4' |
110.5 |
110.4 |
O3' |
C3' |
H3' |
107.7 |
110.4 |
C3' |
O3' |
HO3' |
109.5 |
114.0 |
C4' |
C3' |
H3' |
112.0 |
110.6 |
C3' |
C4' |
C5' |
112.9 |
109.9 |
C3' |
C4' |
H4' |
111.0 |
109.9 |
C5' |
C4' |
H4' |
104.5 |
110.0 |
C4' |
C5' |
O5' |
107.5 |
109.5 |
C4' |
C5' |
H5'1 |
110.1 |
109.5 |
C4' |
C5' |
H5'2 |
110.6 |
109.5 |
O5' |
C5' |
H5'1 |
110.1 |
109.4 |
O5' |
C5' |
H5'2 |
110.6 |
109.5 |
C5' |
O5' |
P |
123.8 |
123.0 |
H5'1 |
C5' |
H5'2 |
108.0 |
109.5 |
O5' |
P |
O1P |
100.4 |
109.5 |
O5' |
P |
O2P |
104.9 |
109.5 |
O5' |
P |
O3P |
104.1 |
109.4 |
O1P |
P |
O2P |
118.9 |
109.5 |
O1P |
P |
O3P |
111.5 |
109.5 |
O2P |
P |
O3P |
114.4 |
109.5 |
P |
O2P |
HO2P |
109.5 |
114.0 |
P |
O3P |
HO3P |
109.5 |
113.9 |
Torsion Angles for NUP
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
N2 |
C4 |
O4 |
C5 |
180.9 |
180.2 |
O4 |
C4 |
N2 |
C2 |
179.8 |
180.0 |
O4 |
C4 |
N2 |
HN2 |
359.8 |
360.0 |
O4 |
C4 |
C5 |
C6 |
179.9 |
180.0 |
O4 |
C4 |
C5 |
H5 |
359.9 |
0.0 |
O4 |
C4 |
N2 |
C5 |
179.1 |
179.8 |
N2 |
C4 |
C5 |
C6 |
359.0 |
359.8 |
N2 |
C4 |
C5 |
H5 |
179.0 |
179.8 |
C2 |
N2 |
C4 |
HN2 |
180.0 |
180.0 |
C4 |
N2 |
C2 |
O2 |
180.7 |
180.0 |
C4 |
N2 |
C2 |
N1 |
0.3 |
360.0 |
O4 |
C4 |
C5 |
N2 |
181.0 |
180.2 |
C5 |
C4 |
N2 |
C2 |
0.7 |
0.3 |
C5 |
C4 |
N2 |
HN2 |
180.7 |
180.2 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
N1 |
0.2 |
360.0 |
C4 |
C5 |
C6 |
N3 |
179.4 |
180.1 |
C2 |
N2 |
C4 |
C5 |
0.7 |
0.3 |
C4 |
N2 |
C2 |
HN2 |
180.0 |
180.0 |
O2 |
C2 |
N2 |
N1 |
180.3 |
180.0 |
N2 |
C2 |
N1 |
C6 |
358.9 |
359.8 |
N2 |
C2 |
N1 |
C1' |
180.5 |
180.0 |
HN2 |
N2 |
C4 |
C5 |
180.7 |
180.2 |
C4 |
N2 |
HN2 |
C2 |
180.0 |
180.0 |
HN2 |
N2 |
C2 |
O2 |
0.7 |
0.0 |
HN2 |
N2 |
C2 |
N1 |
180.4 |
180.0 |
O2 |
C2 |
N2 |
HN2 |
0.7 |
0.0 |
N2 |
C2 |
O2 |
N1 |
179.7 |
180.0 |
O2 |
C2 |
N1 |
C6 |
178.6 |
179.7 |
O2 |
C2 |
N1 |
C1' |
0.2 |
0.0 |
N1 |
C2 |
N2 |
HN2 |
180.4 |
180.0 |
N2 |
C2 |
N1 |
O2 |
180.3 |
180.0 |
C5 |
C6 |
N1 |
C2 |
0.8 |
0.3 |
N3 |
C6 |
N1 |
C2 |
181.6 |
180.2 |
C6 |
N1 |
C2 |
C1' |
178.4 |
179.7 |
C2 |
N1 |
C1' |
C2' |
307.9 |
291.7 |
C2 |
N1 |
C1' |
O4' |
67.7 |
45.8 |
C2 |
N1 |
C1' |
H1' |
189.5 |
168.9 |
C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
C2 |
N1 |
C6 |
C5 |
0.8 |
0.3 |
N3 |
C6 |
C5 |
N1 |
179.2 |
180.1 |
C5 |
C6 |
N1 |
C1' |
179.2 |
180.0 |
C5 |
C6 |
N3 |
HN31 |
117.3 |
352.7 |
C5 |
C6 |
N3 |
HN32 |
237.3 |
172.6 |
C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
H5 |
C5 |
C6 |
N1 |
180.3 |
179.9 |
H5 |
C5 |
C6 |
N3 |
359.5 |
0.0 |
C2 |
N1 |
C6 |
C1' |
181.6 |
180.3 |
N1 |
C6 |
C5 |
H5 |
180.3 |
179.9 |
C5 |
C6 |
N1 |
N3 |
179.2 |
180.1 |
N1 |
C6 |
N3 |
HN31 |
296.5 |
172.8 |
N1 |
C6 |
N3 |
HN32 |
56.5 |
352.7 |
C6 |
N1 |
C1' |
C2' |
129.5 |
112.0 |
C6 |
N1 |
C1' |
O4' |
249.3 |
226.1 |
C6 |
N1 |
C1' |
H1' |
11.1 |
349.2 |
C2 |
N1 |
C6 |
N3 |
181.6 |
180.2 |
N3 |
C6 |
C5 |
H5 |
359.5 |
0.0 |
C5 |
C6 |
N3 |
N1 |
180.8 |
179.9 |
N3 |
C6 |
N1 |
C1' |
0.0 |
359.9 |
HN31 |
N3 |
C6 |
HN32 |
240.0 |
180.0 |
HN31 |
N3 |
C6 |
N1 |
296.5 |
172.8 |
C6 |
N3 |
HN31 |
HN32 |
120.0 |
180.0 |
HN32 |
N3 |
C6 |
N1 |
56.5 |
352.7 |
C6 |
N3 |
HN32 |
HN31 |
239.9 |
180.0 |
C2 |
N1 |
C1' |
C6 |
178.4 |
179.7 |
O4' |
C1' |
N1 |
C2' |
119.8 |
114.1 |
C2' |
C1' |
N1 |
H1' |
118.4 |
122.8 |
N1 |
C1' |
C2' |
O2' |
273.8 |
273.8 |
N1 |
C1' |
C2' |
C3' |
151.6 |
155.5 |
N1 |
C1' |
C2' |
H2' |
27.1 |
37.3 |
O4' |
C1' |
N1 |
H1' |
238.3 |
236.9 |
N1 |
C1' |
O4' |
C4' |
223.1 |
201.4 |
N1 |
C1' |
C2' |
O4' |
121.5 |
118.6 |
N1 |
C1' |
C2' |
H1' |
243.4 |
237.2 |
O4' |
C1' |
C2' |
H1' |
121.9 |
118.7 |
C2' |
C1' |
O4' |
C4' |
347.6 |
320.0 |
O2' |
C2' |
C1' |
C3' |
122.2 |
118.2 |
O2' |
C2' |
C1' |
H2' |
246.7 |
236.5 |
C1' |
C2' |
O2' |
HO2' |
44.3 |
180.0 |
C3' |
C2' |
C1' |
H2' |
124.5 |
118.3 |
C1' |
C2' |
C3' |
O3' |
82.0 |
97.8 |
C1' |
C2' |
C3' |
C4' |
324.1 |
339.2 |
C1' |
C2' |
C3' |
H3' |
201.9 |
220.3 |
N1 |
C1' |
O4' |
C2' |
235.5 |
241.5 |
N1 |
C1' |
O4' |
H1' |
116.8 |
123.0 |
C2' |
C1' |
O4' |
H1' |
241.3 |
241.5 |
O4' |
C1' |
C2' |
O2' |
152.3 |
155.2 |
O4' |
C1' |
C2' |
C3' |
30.0 |
37.0 |
O4' |
C1' |
C2' |
H2' |
265.5 |
278.7 |
C1' |
O4' |
C4' |
C3' |
349.1 |
26.5 |
C1' |
O4' |
C4' |
C5' |
111.4 |
145.9 |
C1' |
O4' |
C4' |
H4' |
228.4 |
267.0 |
N1 |
C1' |
H1' |
C2' |
122.6 |
122.8 |
N1 |
C1' |
H1' |
O4' |
240.5 |
237.0 |
O4' |
C1' |
H1' |
C2' |
242.2 |
245.9 |
H1' |
C1' |
C2' |
O2' |
30.4 |
36.6 |
H1' |
C1' |
C2' |
C3' |
268.2 |
278.3 |
H1' |
C1' |
C2' |
H2' |
143.7 |
160.1 |
H1' |
C1' |
O4' |
C4' |
106.3 |
78.5 |
C4' |
O4' |
C1' |
C2' |
347.6 |
320.0 |
C4' |
O4' |
C1' |
H1' |
106.3 |
78.5 |
C2' |
C3' |
C4' |
O4' |
30.1 |
358.0 |
O3' |
C3' |
C4' |
O4' |
273.4 |
239.3 |
O4' |
C4' |
C3' |
H3' |
153.3 |
116.8 |
C3' |
C4' |
O4' |
C5' |
237.7 |
240.6 |
C3' |
C4' |
O4' |
H4' |
120.7 |
119.5 |
C5' |
C4' |
O4' |
H4' |
243.1 |
238.9 |
O4' |
C4' |
C5' |
O5' |
172.6 |
66.5 |
O4' |
C4' |
C5' |
H5'1 |
292.6 |
186.4 |
O4' |
C4' |
C5' |
H5'2 |
51.8 |
306.5 |
O2' |
C2' |
C1' |
H1' |
30.4 |
36.6 |
C1' |
C2' |
O2' |
C3' |
244.1 |
247.3 |
C1' |
C2' |
O2' |
H2' |
119.9 |
123.5 |
C3' |
C2' |
O2' |
H2' |
235.8 |
236.2 |
O2' |
C2' |
C3' |
O3' |
315.9 |
339.6 |
O2' |
C2' |
C3' |
C4' |
198.0 |
221.0 |
O2' |
C2' |
C3' |
H3' |
75.8 |
102.1 |
C3' |
C2' |
C1' |
H1' |
268.2 |
278.3 |
C1' |
C2' |
C3' |
O2' |
126.1 |
118.2 |
C1' |
C2' |
C3' |
H2' |
239.6 |
241.9 |
O4' |
C4' |
C3' |
C2' |
30.1 |
358.0 |
O2' |
C2' |
C3' |
H2' |
113.5 |
123.7 |
C3' |
C2' |
O2' |
HO2' |
160.2 |
292.7 |
O3' |
C3' |
C2' |
C4' |
117.9 |
118.6 |
O3' |
C3' |
C2' |
H3' |
240.1 |
237.5 |
C2' |
C3' |
O3' |
HO3' |
87.4 |
61.5 |
C4' |
C3' |
C2' |
H3' |
122.2 |
118.9 |
C2' |
C3' |
C4' |
C5' |
268.9 |
238.6 |
C2' |
C3' |
C4' |
H4' |
151.9 |
117.4 |
H2' |
C2' |
C1' |
H1' |
143.7 |
160.1 |
C1' |
C2' |
H2' |
O2' |
235.2 |
236.5 |
C1' |
C2' |
H2' |
C3' |
114.4 |
112.7 |
O2' |
C2' |
H2' |
C3' |
239.2 |
236.2 |
H2' |
C2' |
O2' |
HO2' |
284.4 |
56.5 |
H2' |
C2' |
C3' |
O3' |
202.4 |
215.9 |
H2' |
C2' |
C3' |
C4' |
84.5 |
97.3 |
H2' |
C2' |
C3' |
H3' |
322.3 |
338.5 |
HO2' |
O2' |
C2' |
C3' |
160.2 |
292.7 |
HO2' |
O2' |
C2' |
H2' |
284.4 |
56.5 |
O4' |
C4' |
C3' |
O3' |
273.4 |
239.3 |
O3' |
C3' |
C2' |
H2' |
202.4 |
215.9 |
C2' |
C3' |
O3' |
C4' |
246.2 |
245.2 |
C2' |
C3' |
O3' |
H3' |
123.6 |
122.6 |
C4' |
C3' |
O3' |
H3' |
237.4 |
237.4 |
O3' |
C3' |
C4' |
C5' |
152.2 |
119.9 |
O3' |
C3' |
C4' |
H4' |
35.2 |
358.7 |
O4' |
C4' |
C3' |
C5' |
121.2 |
119.4 |
O4' |
C4' |
C3' |
H4' |
238.1 |
240.5 |
C4' |
C3' |
C2' |
H2' |
84.5 |
97.3 |
C2' |
C3' |
C4' |
O3' |
116.7 |
118.7 |
C2' |
C3' |
C4' |
H3' |
236.7 |
241.2 |
O3' |
C3' |
C4' |
H3' |
120.1 |
122.5 |
C4' |
C3' |
O3' |
HO3' |
201.2 |
176.2 |
C5' |
C4' |
C3' |
H4' |
117.0 |
121.2 |
C3' |
C4' |
C5' |
O5' |
290.1 |
184.3 |
C3' |
C4' |
C5' |
H5'1 |
50.1 |
304.2 |
C3' |
C4' |
C5' |
H5'2 |
169.3 |
64.3 |
H3' |
C3' |
C2' |
H2' |
322.3 |
338.5 |
C2' |
C3' |
H3' |
O3' |
239.5 |
237.4 |
C2' |
C3' |
H3' |
C4' |
117.7 |
114.9 |
O3' |
C3' |
H3' |
C4' |
238.3 |
237.5 |
H3' |
C3' |
O3' |
HO3' |
323.8 |
298.9 |
H3' |
C3' |
C4' |
C5' |
32.2 |
357.4 |
H3' |
C3' |
C4' |
H4' |
275.2 |
236.2 |
HO3' |
O3' |
C3' |
C4' |
201.2 |
176.2 |
HO3' |
O3' |
C3' |
H3' |
323.8 |
298.9 |
O4' |
C4' |
C5' |
C3' |
242.5 |
242.2 |
O4' |
C4' |
C5' |
H4' |
121.8 |
121.1 |
C5' |
C4' |
C3' |
H3' |
32.2 |
357.4 |
C3' |
C4' |
C5' |
H4' |
239.3 |
238.9 |
O5' |
C5' |
C4' |
H5'1 |
240.0 |
240.1 |
O5' |
C5' |
C4' |
H5'2 |
120.8 |
120.0 |
C4' |
C5' |
O5' |
P |
180.2 |
180.0 |
H5'1 |
C5' |
C4' |
H5'2 |
240.8 |
239.9 |
O4' |
C4' |
H4' |
C3' |
117.1 |
117.8 |
O4' |
C4' |
H4' |
C5' |
239.1 |
238.9 |
H4' |
C4' |
C3' |
H3' |
275.2 |
236.2 |
C3' |
C4' |
H4' |
C5' |
122.0 |
121.1 |
H4' |
C4' |
C5' |
O5' |
50.8 |
305.4 |
H4' |
C4' |
C5' |
H5'1 |
170.8 |
65.3 |
H4' |
C4' |
C5' |
H5'2 |
290.0 |
185.4 |
O5' |
C5' |
C4' |
H4' |
50.8 |
305.4 |
C4' |
C5' |
O5' |
H5'1 |
120.0 |
120.0 |
C4' |
C5' |
O5' |
H5'2 |
239.2 |
240.0 |
H5'1 |
C5' |
O5' |
H5'2 |
119.3 |
120.0 |
C5' |
O5' |
P |
O1P |
197.4 |
305.0 |
C5' |
O5' |
P |
O2P |
321.3 |
65.0 |
C5' |
O5' |
P |
O3P |
81.9 |
185.0 |
H5'1 |
C5' |
C4' |
H4' |
170.8 |
65.3 |
C4' |
C5' |
H5'1 |
O5' |
241.6 |
240.0 |
C4' |
C5' |
H5'1 |
H5'2 |
120.8 |
120.0 |
O5' |
C5' |
H5'1 |
H5'2 |
239.1 |
240.0 |
H5'1 |
C5' |
O5' |
P |
60.3 |
60.0 |
H5'2 |
C5' |
C4' |
H4' |
290.0 |
185.4 |
C4' |
C5' |
H5'2 |
O5' |
118.9 |
120.0 |
C4' |
C5' |
H5'2 |
H5'1 |
239.5 |
240.0 |
O5' |
C5' |
H5'2 |
H5'1 |
120.6 |
120.0 |
H5'2 |
C5' |
O5' |
P |
301.0 |
300.0 |
P |
O5' |
C5' |
H5'1 |
60.3 |
60.0 |
P |
O5' |
C5' |
H5'2 |
301.0 |
300.0 |
O1P |
P |
O5' |
O2P |
236.1 |
240.0 |
O1P |
P |
O5' |
O3P |
115.5 |
120.0 |
O2P |
P |
O5' |
O3P |
239.5 |
240.0 |
O5' |
P |
O2P |
HO2P |
89.7 |
60.0 |
O5' |
P |
O3P |
HO3P |
114.0 |
180.0 |
O5' |
P |
O1P |
O2P |
113.6 |
120.0 |
O5' |
P |
O1P |
O3P |
250.2 |
240.0 |
O2P |
P |
O1P |
O3P |
136.6 |
120.0 |
O1P |
P |
O2P |
HO2P |
200.9 |
180.0 |
O1P |
P |
O3P |
HO3P |
6.6 |
60.0 |
O5' |
P |
O2P |
O1P |
248.8 |
240.0 |
O5' |
P |
O2P |
O3P |
113.4 |
120.0 |
O1P |
P |
O2P |
O3P |
224.6 |
240.0 |
O2P |
P |
O3P |
HO3P |
227.9 |
300.0 |
O5' |
P |
O3P |
O1P |
107.4 |
120.0 |
O5' |
P |
O3P |
O2P |
246.1 |
240.0 |
O1P |
P |
O3P |
O2P |
138.7 |
120.0 |
O3P |
P |
O2P |
HO2P |
336.3 |
300.0 |
HO2P |
O2P |
P |
O3P |
336.3 |
300.0 |