PDB Chemical Component IU
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 IU
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP1 |
1.490 |
1.501 |
P |
OP2 |
1.489 |
1.617 |
P |
OP3 |
|
1.618 |
P |
O5' |
1.590 |
1.619 |
OP2 |
HOP2 |
0.950 |
0.980 |
OP3 |
HOP3 |
|
0.980 |
O5' |
C5' |
1.421 |
1.416 |
C5' |
C4' |
1.503 |
1.523 |
C5' |
H5' |
1.115 |
1.092 |
C5' |
H5'' |
1.116 |
1.091 |
C4' |
O4' |
1.426 |
1.444 |
C4' |
C3' |
1.525 |
1.523 |
C4' |
H4' |
1.115 |
1.095 |
O4' |
C1' |
1.396 |
1.437 |
C3' |
O3' |
1.435 |
1.427 |
C3' |
C2' |
1.535 |
1.514 |
C3' |
H3' |
1.115 |
1.093 |
O3' |
HO3' |
0.949 |
0.969 |
C2' |
O2' |
1.414 |
1.413 |
C2' |
C1' |
1.532 |
1.519 |
C2' |
H2' |
1.115 |
1.097 |
O2' |
HO2' |
0.949 |
0.973 |
C1' |
N1 |
1.460 |
1.435 |
C1' |
H1' |
1.115 |
1.094 |
N1 |
C2 |
1.379 |
1.412 |
N1 |
C6 |
1.354 |
1.391 |
C2 |
O2 |
1.223 |
1.232 |
C2 |
N3 |
1.362 |
1.399 |
N3 |
C4 |
1.377 |
1.388 |
N3 |
H3 |
1.019 |
1.017 |
C4 |
O4 |
1.225 |
1.228 |
C4 |
C5 |
1.427 |
1.488 |
C5 |
C6 |
1.312 |
1.339 |
C5 |
I5 |
2.086 |
2.048 |
C6 |
H6 |
1.103 |
1.086 |
Bond Angles for IU
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
119.1 |
115.3 |
OP1 |
P |
OP3 |
|
114.9 |
OP1 |
P |
O5' |
108.7 |
115.0 |
OP2 |
P |
OP3 |
|
103.3 |
OP2 |
P |
O5' |
106.2 |
103.8 |
P |
OP2 |
HOP2 |
119.1 |
119.0 |
OP3 |
P |
O5' |
|
102.9 |
P |
OP3 |
HOP3 |
|
119.0 |
P |
O5' |
C5' |
122.5 |
118.5 |
O5' |
C5' |
C4' |
108.3 |
108.6 |
O5' |
C5' |
H5' |
112.7 |
109.2 |
O5' |
C5' |
H5'' |
112.6 |
109.3 |
C4' |
C5' |
H5' |
112.6 |
110.1 |
C4' |
C5' |
H5'' |
112.6 |
110.1 |
C5' |
C4' |
O4' |
105.7 |
108.2 |
C5' |
C4' |
C3' |
113.0 |
113.3 |
C5' |
C4' |
H4' |
108.9 |
109.3 |
H5' |
C5' |
H5'' |
97.7 |
109.6 |
O4' |
C4' |
C3' |
107.3 |
105.9 |
O4' |
C4' |
H4' |
114.5 |
107.7 |
C4' |
O4' |
C1' |
109.3 |
109.2 |
C3' |
C4' |
H4' |
107.5 |
112.2 |
C4' |
C3' |
O3' |
105.4 |
107.9 |
C4' |
C3' |
C2' |
105.8 |
102.1 |
C4' |
C3' |
H3' |
115.8 |
114.5 |
O4' |
C1' |
C2' |
109.2 |
106.5 |
O4' |
C1' |
N1 |
107.9 |
109.0 |
O4' |
C1' |
H1' |
113.8 |
108.9 |
O3' |
C3' |
C2' |
113.3 |
110.3 |
O3' |
C3' |
H3' |
108.6 |
107.8 |
C3' |
O3' |
HO3' |
105.4 |
106.4 |
C2' |
C3' |
H3' |
108.2 |
114.0 |
C3' |
C2' |
O2' |
116.9 |
112.3 |
C3' |
C2' |
C1' |
103.3 |
102.0 |
C3' |
C2' |
H2' |
109.2 |
110.1 |
O2' |
C2' |
C1' |
110.8 |
112.6 |
O2' |
C2' |
H2' |
101.6 |
108.6 |
C2' |
O2' |
HO2' |
116.9 |
107.1 |
C1' |
C2' |
H2' |
115.5 |
111.1 |
C2' |
C1' |
N1 |
117.4 |
112.5 |
C2' |
C1' |
H1' |
103.7 |
112.6 |
N1 |
C1' |
H1' |
105.0 |
107.3 |
C1' |
N1 |
C2 |
117.6 |
121.2 |
C1' |
N1 |
C6 |
120.6 |
118.6 |
C2 |
N1 |
C6 |
121.8 |
120.2 |
N1 |
C2 |
O2 |
123.3 |
123.7 |
N1 |
C2 |
N3 |
114.6 |
115.1 |
N1 |
C6 |
C5 |
122.7 |
124.4 |
N1 |
C6 |
H6 |
120.3 |
114.2 |
O2 |
C2 |
N3 |
122.1 |
121.1 |
C2 |
N3 |
C4 |
126.3 |
127.2 |
C2 |
N3 |
H3 |
116.3 |
116.4 |
C4 |
N3 |
H3 |
117.4 |
116.4 |
N3 |
C4 |
O4 |
119.4 |
122.9 |
N3 |
C4 |
C5 |
114.8 |
114.5 |
O4 |
C4 |
C5 |
125.8 |
122.6 |
C4 |
C5 |
C6 |
119.8 |
118.6 |
C4 |
C5 |
I5 |
120.4 |
119.4 |
C6 |
C5 |
I5 |
119.5 |
122.0 |
C5 |
C6 |
H6 |
117.0 |
121.4 |
Torsion Angles for IU
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
OP3 |
|
240.0 |
OP2 |
P |
OP1 |
O5' |
238.3 |
120.7 |
OP1 |
P |
OP2 |
HOP2 |
180.0 |
48.7 |
OP3 |
P |
OP1 |
O5' |
|
240.7 |
OP1 |
P |
OP3 |
HOP3 |
|
312.0 |
OP1 |
P |
O5' |
C5' |
50.4 |
180.1 |
OP1 |
P |
OP2 |
OP3 |
|
126.2 |
OP1 |
P |
OP2 |
O5' |
122.9 |
233.4 |
OP3 |
P |
OP2 |
O5' |
|
107.1 |
OP2 |
P |
OP3 |
HOP3 |
|
78.5 |
OP2 |
P |
O5' |
C5' |
179.6 |
53.2 |
OP1 |
P |
OP3 |
OP2 |
|
233.5 |
OP1 |
P |
OP3 |
O5' |
|
125.8 |
OP2 |
P |
OP3 |
O5' |
|
252.3 |
OP3 |
P |
OP2 |
HOP2 |
|
282.5 |
OP3 |
P |
O5' |
C5' |
|
305.8 |
OP1 |
P |
O5' |
OP2 |
230.8 |
126.9 |
OP1 |
P |
O5' |
OP3 |
|
234.2 |
OP2 |
P |
O5' |
OP3 |
|
107.4 |
O5' |
P |
OP2 |
HOP2 |
57.1 |
175.4 |
O5' |
P |
OP3 |
HOP3 |
|
186.2 |
P |
O5' |
C5' |
C4' |
184.6 |
180.0 |
P |
O5' |
C5' |
H5' |
309.9 |
300.1 |
P |
O5' |
C5' |
H5'' |
59.3 |
59.9 |
HOP2 |
OP2 |
P |
OP3 |
|
282.5 |
HOP2 |
OP2 |
P |
O5' |
57.1 |
175.4 |
HOP3 |
OP3 |
P |
O5' |
|
186.2 |
C4' |
C5' |
O5' |
H5' |
234.7 |
239.9 |
C4' |
C5' |
O5' |
H5'' |
125.3 |
120.1 |
O5' |
C5' |
C4' |
O4' |
303.0 |
62.4 |
O5' |
C5' |
C4' |
C3' |
60.0 |
179.5 |
O5' |
C5' |
C4' |
H4' |
179.4 |
305.4 |
H5' |
C5' |
O5' |
H5'' |
250.6 |
240.2 |
O5' |
C5' |
C4' |
H5' |
125.3 |
119.5 |
O5' |
C5' |
C4' |
H5'' |
234.7 |
240.4 |
H5' |
C5' |
C4' |
H5'' |
109.4 |
120.9 |
O4' |
C4' |
C5' |
C3' |
242.9 |
242.9 |
O4' |
C4' |
C5' |
H4' |
123.5 |
117.0 |
C5' |
C4' |
O4' |
C1' |
143.1 |
109.0 |
C3' |
C4' |
C5' |
H4' |
240.6 |
234.1 |
C5' |
C4' |
C3' |
O3' |
111.2 |
156.8 |
C5' |
C4' |
C3' |
C2' |
231.5 |
273.1 |
C5' |
C4' |
C3' |
H3' |
351.2 |
36.8 |
O5' |
C5' |
H5' |
C4' |
237.1 |
240.8 |
O5' |
C5' |
H5' |
H5'' |
118.5 |
119.6 |
C4' |
C5' |
H5' |
H5'' |
241.5 |
238.8 |
H5' |
C5' |
C4' |
O4' |
177.6 |
302.9 |
H5' |
C5' |
C4' |
C3' |
294.7 |
60.0 |
H5' |
C5' |
C4' |
H4' |
54.1 |
185.9 |
O5' |
C5' |
H5'' |
C4' |
122.9 |
119.2 |
O5' |
C5' |
H5'' |
H5' |
241.5 |
240.4 |
C4' |
C5' |
H5'' |
H5' |
118.5 |
121.2 |
H5'' |
C5' |
C4' |
O4' |
68.2 |
182.0 |
H5'' |
C5' |
C4' |
C3' |
185.3 |
299.1 |
H5'' |
C5' |
C4' |
H4' |
304.7 |
65.0 |
O4' |
C4' |
C5' |
H5' |
177.6 |
302.9 |
O4' |
C4' |
C5' |
H5'' |
68.2 |
182.0 |
C5' |
C4' |
O4' |
C3' |
120.9 |
121.7 |
C5' |
C4' |
O4' |
H4' |
240.1 |
241.9 |
C3' |
C4' |
O4' |
H4' |
119.2 |
120.2 |
O4' |
C4' |
C3' |
O3' |
227.4 |
275.3 |
O4' |
C4' |
C3' |
C2' |
347.7 |
31.5 |
O4' |
C4' |
C3' |
H3' |
107.4 |
155.2 |
C4' |
O4' |
C1' |
C2' |
336.7 |
348.7 |
C4' |
O4' |
C1' |
N1 |
208.1 |
227.1 |
C4' |
O4' |
C1' |
H1' |
92.0 |
110.3 |
C3' |
C4' |
C5' |
H5' |
294.7 |
60.0 |
C3' |
C4' |
C5' |
H5'' |
185.3 |
299.1 |
C5' |
C4' |
C3' |
O4' |
243.8 |
241.6 |
C5' |
C4' |
C3' |
H4' |
120.2 |
124.4 |
O4' |
C4' |
C3' |
H4' |
236.4 |
242.8 |
C3' |
C4' |
O4' |
C1' |
22.2 |
347.2 |
O3' |
C3' |
C4' |
C2' |
239.7 |
243.7 |
O3' |
C3' |
C4' |
H3' |
120.0 |
120.1 |
C4' |
C3' |
O3' |
HO3' |
180.0 |
15.2 |
C2' |
C3' |
C4' |
H3' |
240.3 |
236.3 |
C4' |
C3' |
C2' |
O2' |
237.1 |
202.0 |
C4' |
C3' |
C2' |
C1' |
359.1 |
322.9 |
C4' |
C3' |
C2' |
H2' |
122.5 |
80.9 |
H4' |
C4' |
C5' |
H5' |
54.1 |
185.9 |
H4' |
C4' |
C5' |
H5'' |
304.7 |
65.0 |
C5' |
C4' |
H4' |
O4' |
118.1 |
117.3 |
C5' |
C4' |
H4' |
C3' |
237.2 |
233.5 |
O4' |
C4' |
H4' |
C3' |
119.1 |
116.2 |
H4' |
C4' |
O4' |
C1' |
263.0 |
227.0 |
H4' |
C4' |
C3' |
O3' |
351.0 |
32.5 |
H4' |
C4' |
C3' |
C2' |
111.3 |
148.7 |
H4' |
C4' |
C3' |
H3' |
231.0 |
272.4 |
C1' |
O4' |
C4' |
C3' |
22.2 |
347.2 |
C1' |
O4' |
C4' |
H4' |
263.0 |
227.0 |
C3' |
C2' |
C1' |
O4' |
14.4 |
30.7 |
O2' |
C2' |
C1' |
O4' |
140.4 |
151.3 |
O4' |
C1' |
C2' |
H2' |
255.1 |
273.4 |
C2' |
C1' |
O4' |
N1 |
128.6 |
121.6 |
C2' |
C1' |
O4' |
H1' |
244.7 |
238.4 |
N1 |
C1' |
O4' |
H1' |
116.1 |
116.8 |
O4' |
C1' |
N1 |
C2 |
222.5 |
212.2 |
O4' |
C1' |
N1 |
C6 |
41.9 |
32.2 |
O3' |
C3' |
C4' |
H4' |
351.0 |
32.5 |
C4' |
C3' |
O3' |
C2' |
115.2 |
110.7 |
C4' |
C3' |
O3' |
H3' |
235.4 |
235.8 |
C2' |
C3' |
O3' |
H3' |
120.2 |
125.1 |
O3' |
C3' |
C2' |
O2' |
352.0 |
316.5 |
O3' |
C3' |
C2' |
C1' |
114.0 |
77.4 |
O3' |
C3' |
C2' |
H2' |
237.5 |
195.4 |
C2' |
C3' |
C4' |
H4' |
111.3 |
148.7 |
C4' |
C3' |
C2' |
O3' |
245.1 |
245.5 |
C4' |
C3' |
C2' |
H3' |
124.6 |
124.0 |
O4' |
C1' |
C2' |
C3' |
14.4 |
30.7 |
O3' |
C3' |
C2' |
H3' |
239.5 |
238.5 |
C2' |
C3' |
O3' |
HO3' |
64.9 |
264.4 |
O2' |
C2' |
C3' |
C1' |
238.0 |
239.2 |
O2' |
C2' |
C3' |
H2' |
114.5 |
121.1 |
C3' |
C2' |
O2' |
HO2' |
180.0 |
168.8 |
C1' |
C2' |
C3' |
H2' |
236.5 |
242.0 |
C3' |
C2' |
C1' |
N1 |
137.5 |
150.0 |
C3' |
C2' |
C1' |
H1' |
252.7 |
271.5 |
H3' |
C3' |
C4' |
H4' |
231.0 |
272.4 |
C4' |
C3' |
H3' |
O3' |
118.2 |
120.1 |
C4' |
C3' |
H3' |
C2' |
241.6 |
243.0 |
O3' |
C3' |
H3' |
C2' |
123.4 |
122.8 |
H3' |
C3' |
O3' |
HO3' |
304.6 |
139.4 |
H3' |
C3' |
C2' |
O2' |
112.5 |
78.0 |
H3' |
C3' |
C2' |
C1' |
234.5 |
198.9 |
H3' |
C3' |
C2' |
H2' |
357.9 |
316.9 |
HO3' |
O3' |
C3' |
C2' |
64.9 |
264.4 |
HO3' |
O3' |
C3' |
H3' |
304.6 |
139.4 |
O4' |
C1' |
C2' |
O2' |
140.4 |
151.3 |
O2' |
C2' |
C3' |
H3' |
112.5 |
78.0 |
C3' |
C2' |
O2' |
C1' |
118.0 |
114.5 |
C3' |
C2' |
O2' |
H2' |
241.2 |
238.0 |
C1' |
C2' |
O2' |
H2' |
123.2 |
123.5 |
O2' |
C2' |
C1' |
N1 |
263.5 |
270.6 |
O2' |
C2' |
C1' |
H1' |
18.7 |
32.1 |
O4' |
C1' |
C2' |
N1 |
236.8 |
240.7 |
O4' |
C1' |
C2' |
H1' |
121.7 |
119.3 |
C1' |
C2' |
C3' |
H3' |
234.5 |
198.9 |
C3' |
C2' |
C1' |
O2' |
234.0 |
239.4 |
C3' |
C2' |
C1' |
H2' |
119.2 |
117.3 |
O2' |
C2' |
C1' |
H2' |
245.3 |
237.9 |
C1' |
C2' |
O2' |
HO2' |
61.9 |
54.3 |
N1 |
C1' |
C2' |
H1' |
244.8 |
238.6 |
C2' |
C1' |
N1 |
C2 |
98.7 |
94.3 |
C2' |
C1' |
N1 |
C6 |
278.1 |
274.3 |
H2' |
C2' |
C3' |
H3' |
357.9 |
316.9 |
C3' |
C2' |
H2' |
O2' |
124.1 |
123.3 |
C3' |
C2' |
H2' |
C1' |
244.1 |
247.7 |
O2' |
C2' |
H2' |
C1' |
120.0 |
124.4 |
H2' |
C2' |
O2' |
HO2' |
298.7 |
290.8 |
H2' |
C2' |
C1' |
N1 |
18.3 |
32.7 |
H2' |
C2' |
C1' |
H1' |
133.5 |
154.2 |
HO2' |
O2' |
C2' |
C1' |
61.9 |
54.3 |
HO2' |
O2' |
C2' |
H2' |
298.7 |
290.8 |
O4' |
C1' |
N1 |
C2' |
123.8 |
117.9 |
O4' |
C1' |
N1 |
H1' |
238.3 |
242.3 |
N1 |
C1' |
C2' |
H2' |
18.3 |
32.7 |
C2' |
C1' |
N1 |
H1' |
114.5 |
124.4 |
C2 |
N1 |
C1' |
C6 |
180.5 |
180.0 |
C1' |
N1 |
C2 |
O2 |
1.1 |
359.9 |
C1' |
N1 |
C2 |
N3 |
179.9 |
180.0 |
C1' |
N1 |
C6 |
C5 |
180.1 |
180.0 |
C1' |
N1 |
C6 |
H6 |
0.1 |
0.1 |
O4' |
C1' |
H1' |
C2' |
241.5 |
242.1 |
O4' |
C1' |
H1' |
N1 |
117.8 |
117.8 |
H1' |
C1' |
C2' |
H2' |
133.5 |
154.2 |
C2' |
C1' |
H1' |
N1 |
236.3 |
235.7 |
H1' |
C1' |
N1 |
C2 |
344.2 |
330.0 |
H1' |
C1' |
N1 |
C6 |
163.7 |
150.0 |
C2 |
N1 |
C1' |
H1' |
344.2 |
330.0 |
C1' |
N1 |
C2 |
C6 |
179.5 |
180.0 |
C2 |
N1 |
C6 |
C5 |
359.5 |
360.0 |
C2 |
N1 |
C6 |
H6 |
179.5 |
180.1 |
O2 |
C2 |
N1 |
N3 |
181.2 |
180.0 |
N1 |
C2 |
N3 |
C4 |
359.6 |
0.0 |
N1 |
C2 |
N3 |
H3 |
179.6 |
180.0 |
C6 |
N1 |
C1' |
H1' |
163.7 |
150.0 |
C1' |
N1 |
C6 |
C2 |
180.6 |
180.0 |
C6 |
N1 |
C2 |
O2 |
181.6 |
179.9 |
C6 |
N1 |
C2 |
N3 |
0.4 |
360.0 |
C4 |
C5 |
C6 |
N1 |
0.5 |
0.1 |
N1 |
C6 |
C5 |
I5 |
186.9 |
180.0 |
C5 |
C6 |
N1 |
H6 |
180.0 |
179.9 |
O2 |
C2 |
N1 |
C6 |
181.6 |
179.9 |
N1 |
C2 |
O2 |
N3 |
178.7 |
180.0 |
O2 |
C2 |
N3 |
C4 |
178.4 |
180.1 |
O2 |
C2 |
N3 |
H3 |
358.4 |
0.1 |
N3 |
C2 |
N1 |
C6 |
0.4 |
360.0 |
N1 |
C2 |
N3 |
O2 |
181.2 |
180.0 |
C4 |
N3 |
C2 |
H3 |
180.0 |
180.0 |
C2 |
N3 |
C4 |
O4 |
181.7 |
179.9 |
C2 |
N3 |
C4 |
C5 |
0.5 |
0.0 |
C2 |
N3 |
C4 |
H3 |
180.0 |
180.0 |
O4 |
C4 |
N3 |
C5 |
181.2 |
179.9 |
N3 |
C4 |
C5 |
C6 |
359.5 |
359.9 |
N3 |
C4 |
C5 |
I5 |
173.0 |
180.0 |
C2 |
N3 |
H3 |
C4 |
180.0 |
180.0 |
H3 |
N3 |
C4 |
O4 |
1.6 |
359.9 |
H3 |
N3 |
C4 |
C5 |
180.4 |
180.0 |
O4 |
C4 |
N3 |
H3 |
1.6 |
359.9 |
N3 |
C4 |
O4 |
C5 |
178.7 |
180.1 |
O4 |
C4 |
C5 |
C6 |
178.2 |
180.0 |
O4 |
C4 |
C5 |
I5 |
351.7 |
0.1 |
N1 |
C6 |
C5 |
C4 |
0.5 |
0.1 |
C5 |
C4 |
N3 |
H3 |
180.4 |
180.0 |
N3 |
C4 |
C5 |
O4 |
181.3 |
179.9 |
C6 |
C5 |
C4 |
I5 |
186.5 |
179.9 |
C4 |
C5 |
C6 |
H6 |
180.5 |
180.0 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.1 |
C4 |
C5 |
C6 |
I5 |
173.6 |
180.1 |
C4 |
C5 |
I5 |
C6 |
186.5 |
179.9 |
I5 |
C5 |
C6 |
H6 |
7.0 |
359.9 |
N1 |
C6 |
H6 |
C5 |
180.0 |
179.9 |
H6 |
C6 |
C5 |
I5 |
7.0 |
359.9 |