PDB Chemical Component 5IU
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 5IU
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
N1 |
C2 |
1.391 |
1.345 |
N1 |
C6 |
1.370 |
1.369 |
N1 |
C1' |
1.514 |
1.464 |
C2 |
N3 |
1.363 |
1.346 |
C2 |
O2 |
1.222 |
1.216 |
N3 |
C4 |
1.379 |
1.348 |
N3 |
HN3 |
1.021 |
0.971 |
C4 |
C5 |
1.428 |
1.416 |
C4 |
O4 |
1.255 |
1.217 |
C5 |
C6 |
1.427 |
1.350 |
C5 |
I5 |
2.118 |
2.095 |
C6 |
H6 |
1.102 |
1.079 |
C1' |
C2' |
1.525 |
1.545 |
C1' |
O4' |
1.452 |
1.443 |
C1' |
H1' |
1.116 |
1.091 |
C2' |
C3' |
1.513 |
1.545 |
C2' |
H2' |
1.116 |
1.090 |
C2' |
H2'' |
1.115 |
1.089 |
C3' |
C4' |
1.490 |
1.544 |
C3' |
O3' |
1.417 |
1.429 |
C3' |
H3' |
1.115 |
1.090 |
C4' |
O4' |
1.450 |
1.447 |
C4' |
C5' |
1.532 |
1.529 |
C4' |
H4' |
1.115 |
1.091 |
O3' |
HO3' |
0.950 |
0.967 |
C5' |
O5' |
1.449 |
1.429 |
C5' |
H5' |
1.116 |
1.090 |
C5' |
H5'' |
1.115 |
1.089 |
O5' |
P |
1.639 |
1.610 |
P |
OP1 |
1.482 |
1.479 |
P |
OP2 |
1.492 |
1.610 |
P |
OP3 |
1.462 |
1.610 |
OP2 |
HOP2 |
0.950 |
0.967 |
OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for 5IU
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
C2 |
N1 |
C6 |
121.0 |
120.6 |
C2 |
N1 |
C1' |
119.6 |
119.7 |
N1 |
C2 |
N3 |
118.9 |
120.9 |
N1 |
C2 |
O2 |
122.6 |
119.5 |
C6 |
N1 |
C1' |
119.3 |
119.7 |
N1 |
C6 |
C5 |
120.1 |
119.7 |
N1 |
C6 |
H6 |
117.9 |
120.1 |
N1 |
C1' |
C2' |
115.3 |
110.4 |
N1 |
C1' |
O4' |
104.4 |
110.5 |
N1 |
C1' |
H1' |
107.6 |
110.3 |
N3 |
C2 |
O2 |
118.5 |
119.5 |
C2 |
N3 |
C4 |
123.6 |
120.3 |
C2 |
N3 |
HN3 |
117.6 |
119.8 |
C4 |
N3 |
HN3 |
118.9 |
119.8 |
N3 |
C4 |
C5 |
117.8 |
119.4 |
N3 |
C4 |
O4 |
119.3 |
120.4 |
C5 |
C4 |
O4 |
122.9 |
120.3 |
C4 |
C5 |
C6 |
118.6 |
119.1 |
C4 |
C5 |
I5 |
119.5 |
120.4 |
C6 |
C5 |
I5 |
121.8 |
120.5 |
C5 |
C6 |
H6 |
122.0 |
120.1 |
C2' |
C1' |
O4' |
104.3 |
104.8 |
C2' |
C1' |
H1' |
107.6 |
110.4 |
C1' |
C2' |
C3' |
101.0 |
104.0 |
C1' |
C2' |
H2' |
115.4 |
110.5 |
C1' |
C2' |
H2'' |
115.4 |
110.5 |
O4' |
C1' |
H1' |
118.0 |
110.4 |
C1' |
O4' |
C4' |
109.9 |
105.4 |
C3' |
C2' |
H2' |
115.4 |
110.6 |
C3' |
C2' |
H2'' |
115.5 |
110.6 |
C2' |
C3' |
C4' |
102.6 |
104.2 |
C2' |
C3' |
O3' |
114.0 |
110.5 |
C2' |
C3' |
H3' |
110.6 |
110.5 |
H2' |
C2' |
H2'' |
95.0 |
110.5 |
C4' |
C3' |
O3' |
107.7 |
110.5 |
C4' |
C3' |
H3' |
116.6 |
110.5 |
C3' |
C4' |
O4' |
104.4 |
104.7 |
C3' |
C4' |
C5' |
115.8 |
110.7 |
C3' |
C4' |
H4' |
108.7 |
110.3 |
O3' |
C3' |
H3' |
105.6 |
110.5 |
C3' |
O3' |
HO3' |
114.1 |
106.8 |
O4' |
C4' |
C5' |
109.4 |
110.4 |
O4' |
C4' |
H4' |
115.3 |
110.3 |
C5' |
C4' |
H4' |
103.7 |
110.3 |
C4' |
C5' |
O5' |
110.6 |
109.5 |
C4' |
C5' |
H5' |
111.7 |
109.5 |
C4' |
C5' |
H5'' |
111.7 |
109.5 |
O5' |
C5' |
H5' |
111.8 |
109.4 |
O5' |
C5' |
H5'' |
111.8 |
109.5 |
C5' |
O5' |
P |
122.7 |
106.8 |
H5' |
C5' |
H5'' |
98.6 |
109.5 |
O5' |
P |
OP1 |
108.2 |
109.5 |
O5' |
P |
OP2 |
109.8 |
109.5 |
O5' |
P |
OP3 |
109.8 |
109.5 |
OP1 |
P |
OP2 |
109.8 |
109.5 |
OP1 |
P |
OP3 |
109.6 |
109.5 |
OP2 |
P |
OP3 |
109.6 |
109.5 |
P |
OP2 |
HOP2 |
109.9 |
106.8 |
P |
OP3 |
HOP3 |
109.8 |
106.8 |
Torsion Angles for 5IU
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
C6 |
N1 |
C2 |
C1' |
183.0 |
179.7 |
C2 |
N1 |
C6 |
C5 |
358.3 |
0.3 |
C2 |
N1 |
C6 |
H6 |
178.3 |
180.2 |
C2 |
N1 |
C1' |
C2' |
103.1 |
299.7 |
C2 |
N1 |
C1' |
O4' |
216.9 |
55.2 |
C2 |
N1 |
C1' |
H1' |
343.0 |
177.5 |
N3 |
C2 |
N1 |
O2 |
180.6 |
179.3 |
N1 |
C2 |
N3 |
C4 |
1.1 |
0.6 |
N1 |
C2 |
N3 |
HN3 |
181.1 |
180.3 |
C2 |
N1 |
C6 |
C1' |
177.0 |
180.3 |
C6 |
N1 |
C2 |
N3 |
0.2 |
359.4 |
C6 |
N1 |
C2 |
O2 |
179.6 |
180.1 |
C6 |
N1 |
C1' |
C2' |
280.1 |
120.0 |
C6 |
N1 |
C1' |
O4' |
33.9 |
235.5 |
C6 |
N1 |
C1' |
H1' |
160.1 |
357.7 |
C4 |
C5 |
C6 |
N1 |
1.9 |
360.0 |
N1 |
C6 |
C5 |
I5 |
181.4 |
180.0 |
C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
C2 |
N1 |
C1' |
C6 |
182.9 |
179.7 |
C1' |
N1 |
C2 |
N3 |
177.2 |
179.6 |
C1' |
N1 |
C2 |
O2 |
356.6 |
0.3 |
C1' |
N1 |
C6 |
C5 |
181.3 |
180.1 |
C1' |
N1 |
C6 |
H6 |
1.3 |
360.0 |
C2' |
C1' |
N1 |
O4' |
246.2 |
244.5 |
C2' |
C1' |
N1 |
H1' |
120.1 |
122.2 |
N1 |
C1' |
C2' |
C3' |
146.4 |
142.9 |
N1 |
C1' |
C2' |
H2' |
271.6 |
24.3 |
N1 |
C1' |
C2' |
H2'' |
21.1 |
261.6 |
O4' |
C1' |
N1 |
H1' |
233.8 |
237.7 |
N1 |
C1' |
O4' |
C4' |
227.4 |
200.7 |
N3 |
C2 |
N1 |
C6 |
0.2 |
359.4 |
N3 |
C2 |
N1 |
C1' |
177.2 |
179.6 |
N1 |
C2 |
N3 |
O2 |
179.4 |
180.7 |
C4 |
N3 |
C2 |
HN3 |
180.0 |
180.4 |
C2 |
N3 |
C4 |
C5 |
359.2 |
359.7 |
C2 |
N3 |
C4 |
O4 |
179.1 |
179.6 |
O2 |
C2 |
N1 |
C6 |
179.6 |
180.1 |
O2 |
C2 |
N1 |
C1' |
356.6 |
0.3 |
N1 |
C2 |
O2 |
N3 |
180.6 |
179.3 |
O2 |
C2 |
N3 |
C4 |
181.7 |
180.0 |
O2 |
C2 |
N3 |
HN3 |
1.7 |
359.6 |
C4 |
N3 |
C2 |
O2 |
181.7 |
180.0 |
C2 |
N3 |
C4 |
HN3 |
180.0 |
179.6 |
C5 |
C4 |
N3 |
O4 |
180.1 |
180.0 |
N3 |
C4 |
C5 |
C6 |
359.3 |
0.0 |
N3 |
C4 |
C5 |
I5 |
179.8 |
180.0 |
HN3 |
N3 |
C2 |
O2 |
1.7 |
359.6 |
C2 |
N3 |
HN3 |
C4 |
180.0 |
180.4 |
HN3 |
N3 |
C4 |
C5 |
179.2 |
180.0 |
HN3 |
N3 |
C4 |
O4 |
359.1 |
360.0 |
N1 |
C6 |
C5 |
C4 |
1.9 |
360.0 |
C5 |
C4 |
N3 |
HN3 |
179.2 |
180.0 |
N3 |
C4 |
C5 |
O4 |
179.9 |
180.0 |
C6 |
C5 |
C4 |
I5 |
179.5 |
180.0 |
C4 |
C5 |
C6 |
H6 |
181.9 |
180.1 |
O4 |
C4 |
N3 |
HN3 |
359.1 |
360.0 |
N3 |
C4 |
O4 |
C5 |
180.1 |
180.0 |
O4 |
C4 |
C5 |
C6 |
179.4 |
180.1 |
O4 |
C4 |
C5 |
I5 |
359.9 |
0.0 |
C5 |
C6 |
N1 |
C1' |
181.3 |
180.1 |
N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
C6 |
C5 |
C4 |
O4 |
179.4 |
180.1 |
C4 |
C5 |
C6 |
I5 |
180.5 |
180.0 |
I5 |
C5 |
C4 |
O4 |
359.9 |
0.0 |
C4 |
C5 |
I5 |
C6 |
179.5 |
180.0 |
I5 |
C5 |
C6 |
H6 |
1.4 |
0.1 |
H6 |
C6 |
N1 |
C1' |
1.3 |
360.0 |
N1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
H6 |
C6 |
C5 |
I5 |
1.4 |
0.1 |
N1 |
C1' |
C2' |
O4' |
113.8 |
119.0 |
N1 |
C1' |
C2' |
H1' |
240.0 |
237.8 |
O4' |
C1' |
C2' |
H1' |
126.1 |
118.9 |
C2' |
C1' |
O4' |
C4' |
348.8 |
319.6 |
C3' |
C2' |
C1' |
H2' |
234.8 |
118.7 |
C3' |
C2' |
C1' |
H2'' |
125.3 |
241.3 |
C1' |
C2' |
C3' |
C4' |
318.2 |
359.9 |
C1' |
C2' |
C3' |
O3' |
74.3 |
118.7 |
C1' |
C2' |
C3' |
H3' |
193.2 |
241.2 |
H2' |
C2' |
C1' |
H2'' |
250.6 |
122.6 |
N1 |
C1' |
O4' |
C2' |
238.7 |
241.1 |
N1 |
C1' |
O4' |
H1' |
119.3 |
122.2 |
C2' |
C1' |
O4' |
H1' |
240.7 |
241.2 |
O4' |
C1' |
C2' |
C3' |
32.6 |
23.9 |
O4' |
C1' |
C2' |
H2' |
157.8 |
265.3 |
O4' |
C1' |
C2' |
H2'' |
267.2 |
142.6 |
C3' |
C4' |
O4' |
C1' |
344.7 |
40.3 |
C1' |
O4' |
C4' |
C5' |
109.2 |
159.5 |
C1' |
O4' |
C4' |
H4' |
225.5 |
281.6 |
N1 |
C1' |
H1' |
C2' |
124.8 |
122.2 |
N1 |
C1' |
H1' |
O4' |
242.4 |
237.7 |
C2' |
C1' |
H1' |
O4' |
117.6 |
115.4 |
H1' |
C1' |
C2' |
C3' |
266.4 |
265.1 |
H1' |
C1' |
C2' |
H2' |
31.7 |
146.4 |
H1' |
C1' |
C2' |
H2'' |
141.1 |
23.8 |
H1' |
C1' |
O4' |
C4' |
108.1 |
78.5 |
C3' |
C2' |
C1' |
O4' |
32.6 |
23.9 |
C3' |
C2' |
C1' |
H1' |
266.4 |
265.1 |
C1' |
C2' |
C3' |
H2' |
125.2 |
241.4 |
C1' |
C2' |
C3' |
H2'' |
234.7 |
118.7 |
H2' |
C2' |
C3' |
H2'' |
109.5 |
237.3 |
C4' |
C3' |
C2' |
O3' |
243.9 |
241.2 |
C4' |
C3' |
C2' |
H3' |
125.0 |
118.7 |
C2' |
C3' |
C4' |
O4' |
35.7 |
336.2 |
C2' |
C3' |
C4' |
C5' |
275.5 |
217.3 |
C2' |
C3' |
C4' |
H4' |
159.2 |
94.9 |
O3' |
C3' |
C2' |
H3' |
241.2 |
237.5 |
C2' |
C3' |
O3' |
HO3' |
179.9 |
63.3 |
H2' |
C2' |
C1' |
O4' |
157.8 |
265.3 |
H2' |
C2' |
C1' |
H1' |
31.7 |
146.4 |
C1' |
C2' |
H2' |
C3' |
242.6 |
114.6 |
C1' |
C2' |
H2' |
H2'' |
121.3 |
237.3 |
C3' |
C2' |
H2' |
H2'' |
238.7 |
122.7 |
H2' |
C2' |
C3' |
C4' |
193.0 |
118.5 |
H2' |
C2' |
C3' |
O3' |
309.1 |
237.3 |
H2' |
C2' |
C3' |
H3' |
67.9 |
359.8 |
H2'' |
C2' |
C1' |
O4' |
267.2 |
142.6 |
H2'' |
C2' |
C1' |
H1' |
141.1 |
23.8 |
C1' |
C2' |
H2'' |
C3' |
117.5 |
245.4 |
C1' |
C2' |
H2'' |
H2' |
238.8 |
122.6 |
C3' |
C2' |
H2'' |
H2' |
121.3 |
237.3 |
H2'' |
C2' |
C3' |
C4' |
83.5 |
241.3 |
H2'' |
C2' |
C3' |
O3' |
199.6 |
0.0 |
H2'' |
C2' |
C3' |
H3' |
318.5 |
122.5 |
C1' |
O4' |
C4' |
C3' |
344.7 |
40.3 |
C4' |
C3' |
C2' |
H2' |
193.0 |
118.5 |
C4' |
C3' |
C2' |
H2'' |
83.5 |
241.3 |
C2' |
C3' |
C4' |
O3' |
120.6 |
118.7 |
C2' |
C3' |
C4' |
H3' |
239.0 |
241.3 |
O3' |
C3' |
C4' |
H3' |
118.5 |
122.6 |
C4' |
C3' |
O3' |
HO3' |
293.0 |
178.1 |
O4' |
C4' |
C3' |
C5' |
120.2 |
119.0 |
O4' |
C4' |
C3' |
H4' |
236.5 |
241.3 |
C5' |
C4' |
C3' |
H4' |
116.2 |
122.4 |
C3' |
C4' |
C5' |
O5' |
283.7 |
176.9 |
C3' |
C4' |
C5' |
H5' |
49.0 |
296.9 |
C3' |
C4' |
C5' |
H5'' |
158.4 |
56.9 |
O3' |
C3' |
C2' |
H2' |
309.1 |
237.3 |
O3' |
C3' |
C2' |
H2'' |
199.6 |
0.0 |
C2' |
C3' |
O3' |
C4' |
246.9 |
245.2 |
C2' |
C3' |
O3' |
H3' |
121.6 |
122.5 |
C4' |
C3' |
O3' |
H3' |
234.7 |
237.4 |
O3' |
C3' |
C4' |
O4' |
275.1 |
217.5 |
O3' |
C3' |
C4' |
C5' |
154.9 |
98.6 |
O3' |
C3' |
C4' |
H4' |
38.6 |
336.2 |
H3' |
C3' |
C2' |
H2' |
67.9 |
359.8 |
H3' |
C3' |
C2' |
H2'' |
318.5 |
122.5 |
C2' |
C3' |
H3' |
C4' |
116.6 |
114.8 |
C2' |
C3' |
H3' |
O3' |
236.2 |
237.5 |
C4' |
C3' |
H3' |
O3' |
119.6 |
122.7 |
H3' |
C3' |
C4' |
O4' |
156.7 |
94.9 |
H3' |
C3' |
C4' |
C5' |
36.4 |
336.0 |
H3' |
C3' |
C4' |
H4' |
280.2 |
213.6 |
H3' |
C3' |
O3' |
HO3' |
58.3 |
300.8 |
C4' |
O4' |
C1' |
H1' |
108.1 |
78.5 |
O4' |
C4' |
C3' |
O3' |
275.1 |
217.5 |
O4' |
C4' |
C3' |
H3' |
156.7 |
94.9 |
C3' |
C4' |
O4' |
C5' |
235.5 |
240.8 |
C3' |
C4' |
O4' |
H4' |
119.2 |
118.6 |
C5' |
C4' |
O4' |
H4' |
243.7 |
237.8 |
O4' |
C4' |
C5' |
O5' |
166.2 |
61.4 |
O4' |
C4' |
C5' |
H5' |
291.5 |
181.4 |
O4' |
C4' |
C5' |
H5'' |
40.9 |
301.4 |
C5' |
C4' |
C3' |
O3' |
154.9 |
98.6 |
C5' |
C4' |
C3' |
H3' |
36.4 |
336.0 |
C3' |
C4' |
C5' |
O4' |
117.5 |
115.5 |
C3' |
C4' |
C5' |
H4' |
241.0 |
237.7 |
O4' |
C4' |
C5' |
H4' |
123.5 |
122.2 |
O5' |
C5' |
C4' |
H5' |
234.7 |
240.0 |
O5' |
C5' |
C4' |
H5'' |
125.3 |
120.0 |
C4' |
C5' |
O5' |
P |
134.8 |
180.0 |
H5' |
C5' |
C4' |
H5'' |
250.6 |
240.0 |
H4' |
C4' |
C3' |
O3' |
38.6 |
336.2 |
H4' |
C4' |
C3' |
H3' |
280.2 |
213.6 |
C3' |
C4' |
H4' |
O4' |
243.3 |
244.8 |
C3' |
C4' |
H4' |
C5' |
123.8 |
122.6 |
O4' |
C4' |
H4' |
C5' |
240.5 |
237.8 |
H4' |
C4' |
C5' |
O5' |
42.7 |
299.3 |
H4' |
C4' |
C5' |
H5' |
168.0 |
59.2 |
H4' |
C4' |
C5' |
H5'' |
277.4 |
179.2 |
HO3' |
O3' |
C3' |
H3' |
58.3 |
300.8 |
O5' |
C5' |
C4' |
H4' |
42.7 |
299.3 |
C4' |
C5' |
O5' |
H5' |
125.2 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
234.8 |
240.0 |
H5' |
C5' |
O5' |
H5'' |
109.5 |
120.0 |
C5' |
O5' |
P |
OP1 |
25.8 |
60.0 |
C5' |
O5' |
P |
OP2 |
266.0 |
180.0 |
C5' |
O5' |
P |
OP3 |
145.4 |
299.9 |
H5' |
C5' |
C4' |
H4' |
168.0 |
59.2 |
C4' |
C5' |
H5' |
O5' |
235.4 |
240.0 |
C4' |
C5' |
H5' |
H5'' |
117.6 |
120.0 |
O5' |
C5' |
H5' |
H5'' |
242.2 |
240.0 |
H5' |
C5' |
O5' |
P |
9.6 |
60.0 |
H5'' |
C5' |
C4' |
H4' |
277.4 |
179.2 |
C4' |
C5' |
H5'' |
O5' |
124.6 |
120.0 |
C4' |
C5' |
H5'' |
H5' |
242.4 |
240.0 |
O5' |
C5' |
H5'' |
H5' |
117.7 |
120.0 |
H5'' |
C5' |
O5' |
P |
260.1 |
300.0 |
P |
O5' |
C5' |
H5' |
9.6 |
60.0 |
P |
O5' |
C5' |
H5'' |
260.1 |
300.0 |
OP1 |
P |
O5' |
OP2 |
119.9 |
240.0 |
OP1 |
P |
O5' |
OP3 |
240.4 |
120.0 |
OP2 |
P |
O5' |
OP3 |
120.6 |
240.0 |
O5' |
P |
OP2 |
HOP2 |
180.0 |
180.0 |
O5' |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
O5' |
P |
OP1 |
OP2 |
240.1 |
120.0 |
O5' |
P |
OP1 |
OP3 |
119.7 |
240.0 |
OP2 |
P |
OP1 |
OP3 |
239.6 |
120.0 |
OP1 |
P |
OP2 |
HOP2 |
61.1 |
300.0 |
OP1 |
P |
OP3 |
HOP3 |
298.7 |
180.0 |
O5' |
P |
OP2 |
OP1 |
118.9 |
240.0 |
O5' |
P |
OP2 |
OP3 |
239.3 |
120.0 |
OP1 |
P |
OP2 |
OP3 |
120.4 |
240.0 |
OP2 |
P |
OP3 |
HOP3 |
59.2 |
60.0 |
O5' |
P |
OP3 |
OP1 |
241.3 |
120.0 |
O5' |
P |
OP3 |
OP2 |
120.7 |
240.0 |
OP1 |
P |
OP3 |
OP2 |
239.5 |
120.0 |
OP3 |
P |
OP2 |
HOP2 |
300.7 |
60.0 |
HOP2 |
OP2 |
P |
OP3 |
300.7 |
60.0 |