PDB Chemical Component IC
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 IC
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP1 |
1.479 |
1.480 |
P |
OP2 |
1.477 |
1.610 |
P |
OP3 |
1.617 |
1.609 |
P |
O5' |
1.614 |
1.610 |
OP2 |
HOP2 |
0.950 |
0.967 |
OP3 |
HOP3 |
0.950 |
0.967 |
O5' |
C5' |
1.414 |
1.427 |
O3' |
C3' |
1.419 |
1.430 |
O3' |
HO3' |
0.950 |
0.966 |
C1' |
C2' |
1.524 |
1.543 |
C1' |
O4' |
1.423 |
1.444 |
C1' |
N1 |
1.492 |
1.465 |
C1' |
H1' |
1.091 |
1.090 |
C2' |
C3' |
1.526 |
1.545 |
C2' |
O2' |
1.416 |
1.429 |
C2' |
H2' |
1.088 |
1.091 |
C3' |
C4' |
1.529 |
1.544 |
C3' |
H3' |
1.092 |
1.090 |
C4' |
C5' |
1.534 |
1.529 |
C4' |
O4' |
1.424 |
1.445 |
C4' |
H4' |
1.090 |
1.090 |
C5' |
H5' |
1.090 |
1.090 |
C5' |
H5'' |
1.091 |
1.090 |
O2' |
HO2' |
0.962 |
0.967 |
N2 |
C2 |
1.337 |
1.370 |
N2 |
H21 |
1.007 |
0.970 |
N2 |
H22 |
1.016 |
0.971 |
C4 |
N3 |
1.364 |
1.339 |
C4 |
O4 |
1.224 |
1.222 |
C4 |
C5 |
1.450 |
1.418 |
N3 |
C2 |
1.336 |
1.318 |
C2 |
N1 |
1.396 |
1.358 |
N1 |
C6 |
1.373 |
1.365 |
C6 |
C5 |
1.354 |
1.351 |
C6 |
H6 |
1.079 |
1.080 |
C5 |
H5 |
1.079 |
1.080 |
Bond Angles for IC
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
120.0 |
109.5 |
OP1 |
P |
OP3 |
107.7 |
109.5 |
OP1 |
P |
O5' |
108.3 |
109.4 |
OP2 |
P |
OP3 |
108.0 |
109.4 |
OP2 |
P |
O5' |
107.8 |
109.5 |
P |
OP2 |
HOP2 |
119.9 |
106.8 |
OP3 |
P |
O5' |
104.0 |
109.5 |
P |
OP3 |
HOP3 |
107.7 |
106.8 |
P |
O5' |
C5' |
122.1 |
106.8 |
O5' |
C5' |
C4' |
110.8 |
109.5 |
O5' |
C5' |
H5' |
109.5 |
109.5 |
O5' |
C5' |
H5'' |
109.7 |
109.5 |
C3' |
O3' |
HO3' |
110.8 |
106.8 |
O3' |
C3' |
C2' |
110.9 |
110.5 |
O3' |
C3' |
C4' |
113.7 |
110.5 |
O3' |
C3' |
H3' |
111.8 |
110.4 |
C2' |
C1' |
O4' |
106.6 |
104.9 |
C2' |
C1' |
N1 |
110.2 |
110.4 |
C2' |
C1' |
H1' |
109.1 |
110.4 |
C1' |
C2' |
C3' |
102.9 |
104.0 |
C1' |
C2' |
O2' |
108.0 |
110.8 |
C1' |
C2' |
H2' |
112.3 |
110.4 |
O4' |
C1' |
N1 |
114.0 |
110.4 |
O4' |
C1' |
H1' |
108.0 |
110.4 |
C1' |
O4' |
C4' |
109.6 |
105.2 |
N1 |
C1' |
H1' |
108.7 |
110.3 |
C1' |
N1 |
C2 |
120.1 |
119.9 |
C1' |
N1 |
C6 |
122.1 |
119.8 |
C3' |
C2' |
O2' |
112.0 |
110.5 |
C3' |
C2' |
H2' |
111.1 |
110.5 |
C2' |
C3' |
C4' |
100.0 |
104.1 |
C2' |
C3' |
H3' |
110.3 |
110.6 |
O2' |
C2' |
H2' |
110.3 |
110.5 |
C2' |
O2' |
HO2' |
106.7 |
106.8 |
C4' |
C3' |
H3' |
109.6 |
110.5 |
C3' |
C4' |
C5' |
114.3 |
110.6 |
C3' |
C4' |
O4' |
106.1 |
104.8 |
C3' |
C4' |
H4' |
107.9 |
110.3 |
C5' |
C4' |
O4' |
111.5 |
110.4 |
C5' |
C4' |
H4' |
108.5 |
110.3 |
C4' |
C5' |
H5' |
108.8 |
109.5 |
C4' |
C5' |
H5'' |
109.4 |
109.5 |
O4' |
C4' |
H4' |
108.3 |
110.3 |
H5' |
C5' |
H5'' |
108.7 |
109.4 |
C2 |
N2 |
H21 |
121.1 |
120.0 |
C2 |
N2 |
H22 |
118.8 |
120.0 |
N2 |
C2 |
N3 |
115.8 |
119.4 |
N2 |
C2 |
N1 |
122.3 |
119.4 |
H21 |
N2 |
H22 |
119.9 |
120.0 |
N3 |
C4 |
O4 |
120.5 |
120.2 |
N3 |
C4 |
C5 |
114.7 |
119.6 |
C4 |
N3 |
C2 |
123.0 |
120.6 |
O4 |
C4 |
C5 |
124.7 |
120.2 |
C4 |
C5 |
C6 |
122.3 |
118.9 |
C4 |
C5 |
H5 |
118.1 |
120.6 |
N3 |
C2 |
N1 |
121.9 |
121.2 |
C2 |
N1 |
C6 |
117.8 |
120.4 |
N1 |
C6 |
C5 |
120.1 |
119.3 |
N1 |
C6 |
H6 |
120.7 |
120.4 |
C5 |
C6 |
H6 |
119.3 |
120.3 |
C6 |
C5 |
H5 |
119.6 |
120.5 |
Torsion Angles for IC
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
OP3 |
124.0 |
120.0 |
OP2 |
P |
OP1 |
O5' |
235.8 |
240.0 |
OP1 |
P |
OP2 |
HOP2 |
180.0 |
300.0 |
OP3 |
P |
OP1 |
O5' |
111.9 |
120.0 |
OP1 |
P |
OP3 |
HOP3 |
180.1 |
180.0 |
OP1 |
P |
O5' |
C5' |
34.4 |
60.0 |
OP1 |
P |
OP2 |
OP3 |
236.2 |
240.0 |
OP1 |
P |
OP2 |
O5' |
124.4 |
120.0 |
OP3 |
P |
OP2 |
O5' |
248.2 |
240.0 |
OP2 |
P |
OP3 |
HOP3 |
49.1 |
60.0 |
OP2 |
P |
O5' |
C5' |
165.6 |
180.0 |
OP1 |
P |
OP3 |
OP2 |
130.9 |
120.0 |
OP1 |
P |
OP3 |
O5' |
245.3 |
240.0 |
OP2 |
P |
OP3 |
O5' |
114.3 |
120.0 |
OP3 |
P |
OP2 |
HOP2 |
303.8 |
60.1 |
OP3 |
P |
O5' |
C5' |
280.1 |
300.0 |
OP1 |
P |
O5' |
OP2 |
228.8 |
240.0 |
OP1 |
P |
O5' |
OP3 |
114.3 |
120.1 |
OP2 |
P |
O5' |
OP3 |
245.5 |
240.0 |
O5' |
P |
OP2 |
HOP2 |
55.6 |
180.1 |
O5' |
P |
OP3 |
HOP3 |
294.8 |
300.0 |
P |
O5' |
C5' |
C4' |
171.6 |
180.0 |
P |
O5' |
C5' |
H5' |
51.7 |
60.0 |
P |
O5' |
C5' |
H5'' |
292.5 |
300.0 |
HOP2 |
OP2 |
P |
OP3 |
303.8 |
60.1 |
HOP2 |
OP2 |
P |
O5' |
55.6 |
180.1 |
HOP3 |
OP3 |
P |
O5' |
294.8 |
300.0 |
C3' |
C4' |
C5' |
O5' |
68.5 |
176.9 |
O5' |
C5' |
C4' |
O4' |
308.1 |
61.4 |
O5' |
C5' |
C4' |
H4' |
188.9 |
299.2 |
C4' |
C5' |
O5' |
H5' |
119.9 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
239.1 |
240.0 |
H5' |
C5' |
O5' |
H5'' |
119.1 |
119.9 |
C1' |
C2' |
C3' |
O3' |
156.5 |
118.9 |
O3' |
C3' |
C2' |
O2' |
40.7 |
359.9 |
O3' |
C3' |
C2' |
H2' |
276.9 |
237.4 |
C2' |
C3' |
O3' |
C4' |
248.3 |
245.3 |
C2' |
C3' |
O3' |
H3' |
123.5 |
122.7 |
C4' |
C3' |
O3' |
H3' |
235.2 |
237.4 |
O3' |
C3' |
C4' |
C5' |
82.7 |
98.3 |
O3' |
C3' |
C4' |
O4' |
206.0 |
217.2 |
O3' |
C3' |
C4' |
H4' |
321.9 |
336.0 |
HO3' |
O3' |
C3' |
C2' |
180.0 |
65.3 |
HO3' |
O3' |
C3' |
C4' |
291.8 |
180.1 |
HO3' |
O3' |
C3' |
H3' |
56.6 |
302.6 |
O3' |
C3' |
C2' |
C1' |
156.5 |
118.9 |
O4' |
C1' |
C2' |
N1 |
235.8 |
241.1 |
O4' |
C1' |
C2' |
H1' |
116.5 |
118.9 |
C2' |
C1' |
O4' |
C4' |
2.9 |
319.6 |
N1 |
C1' |
C2' |
H1' |
240.7 |
237.8 |
C2' |
C1' |
N1 |
C2 |
79.4 |
90.4 |
C2' |
C1' |
N1 |
C6 |
260.3 |
270.9 |
C3' |
C2' |
C1' |
O2' |
241.4 |
241.2 |
C3' |
C2' |
C1' |
H2' |
119.5 |
118.5 |
C1' |
C2' |
C3' |
C4' |
36.2 |
0.2 |
C1' |
C2' |
C3' |
H3' |
280.8 |
241.5 |
O2' |
C2' |
C1' |
H2' |
238.1 |
237.3 |
C1' |
C2' |
O2' |
HO2' |
209.9 |
183.8 |
C2' |
C1' |
O4' |
N1 |
121.8 |
118.9 |
C2' |
C1' |
O4' |
H1' |
242.8 |
241.1 |
O4' |
C1' |
C2' |
C3' |
334.5 |
23.8 |
O4' |
C1' |
C2' |
O2' |
93.0 |
142.6 |
O4' |
C1' |
C2' |
H2' |
214.9 |
265.3 |
N1 |
C1' |
O4' |
H1' |
121.0 |
122.1 |
O4' |
C1' |
N1 |
C2 |
199.2 |
206.0 |
O4' |
C1' |
N1 |
C6 |
20.2 |
26.4 |
C3' |
C4' |
O4' |
C1' |
21.2 |
40.5 |
C5' |
C4' |
O4' |
C1' |
146.3 |
159.5 |
C1' |
O4' |
C4' |
H4' |
265.6 |
281.7 |
C2' |
C1' |
N1 |
O4' |
240.1 |
244.4 |
C2' |
C1' |
N1 |
H1' |
119.6 |
122.2 |
N1 |
C1' |
C2' |
C3' |
98.7 |
142.8 |
N1 |
C1' |
C2' |
O2' |
217.3 |
261.5 |
N1 |
C1' |
C2' |
H2' |
339.2 |
24.2 |
O4' |
C1' |
N1 |
H1' |
239.4 |
237.8 |
N1 |
C1' |
O4' |
C4' |
241.0 |
200.7 |
N2 |
C2 |
N1 |
C1' |
354.6 |
0.2 |
N3 |
C2 |
N1 |
C1' |
176.1 |
180.0 |
C2 |
N1 |
C1' |
C6 |
179.1 |
179.6 |
C1' |
N1 |
C6 |
C5 |
183.4 |
180.0 |
C1' |
N1 |
C6 |
H6 |
3.1 |
359.8 |
C2' |
C1' |
H1' |
O4' |
115.6 |
115.5 |
C2' |
C1' |
H1' |
N1 |
239.8 |
237.8 |
H1' |
C1' |
C2' |
C3' |
218.0 |
264.9 |
H1' |
C1' |
C2' |
O2' |
336.6 |
23.7 |
H1' |
C1' |
C2' |
H2' |
98.5 |
146.4 |
O4' |
C1' |
H1' |
N1 |
124.2 |
122.2 |
H1' |
C1' |
O4' |
C4' |
120.1 |
78.5 |
H1' |
C1' |
N1 |
C2 |
319.8 |
328.2 |
H1' |
C1' |
N1 |
C6 |
140.8 |
148.6 |
C2' |
C3' |
O3' |
HO3' |
180.0 |
65.3 |
O3' |
C3' |
C2' |
C4' |
120.3 |
118.7 |
O3' |
C3' |
C2' |
H3' |
235.7 |
237.4 |
C3' |
C2' |
C1' |
O4' |
334.5 |
23.8 |
C3' |
C2' |
C1' |
N1 |
98.7 |
142.8 |
C3' |
C2' |
C1' |
H1' |
218.0 |
264.9 |
C1' |
C2' |
C3' |
O2' |
115.8 |
119.0 |
C1' |
C2' |
C3' |
H2' |
239.6 |
241.5 |
O2' |
C2' |
C3' |
H2' |
123.8 |
122.5 |
C3' |
C2' |
O2' |
HO2' |
322.5 |
298.6 |
C4' |
C3' |
C2' |
H3' |
115.4 |
118.7 |
C2' |
C3' |
C4' |
C5' |
200.9 |
217.0 |
C2' |
C3' |
C4' |
O4' |
324.2 |
335.9 |
C2' |
C3' |
C4' |
H4' |
80.1 |
94.7 |
O2' |
C2' |
C1' |
O4' |
93.0 |
142.6 |
O2' |
C2' |
C1' |
N1 |
217.3 |
261.5 |
O2' |
C2' |
C1' |
H1' |
336.6 |
23.7 |
C1' |
C2' |
O2' |
C3' |
247.4 |
245.3 |
C1' |
C2' |
O2' |
H2' |
123.1 |
122.7 |
C3' |
C2' |
O2' |
H2' |
235.8 |
237.5 |
O2' |
C2' |
C3' |
C4' |
280.5 |
241.2 |
O2' |
C2' |
C3' |
H3' |
165.0 |
122.5 |
H2' |
C2' |
C1' |
O4' |
214.9 |
265.3 |
H2' |
C2' |
C1' |
N1 |
339.2 |
24.2 |
H2' |
C2' |
C1' |
H1' |
98.5 |
146.4 |
C1' |
C2' |
H2' |
C3' |
114.7 |
114.5 |
C1' |
C2' |
H2' |
O2' |
239.4 |
237.1 |
C3' |
C2' |
H2' |
O2' |
124.7 |
122.6 |
H2' |
C2' |
C3' |
C4' |
156.6 |
118.6 |
H2' |
C2' |
C3' |
H3' |
41.2 |
360.0 |
H2' |
C2' |
O2' |
HO2' |
86.8 |
61.1 |
O5' |
C5' |
C4' |
C3' |
68.5 |
176.9 |
C4' |
C3' |
O3' |
HO3' |
291.8 |
180.1 |
O3' |
C3' |
C4' |
C2' |
241.8 |
241.3 |
O3' |
C3' |
C4' |
H3' |
125.9 |
122.5 |
C1' |
O4' |
C4' |
C3' |
21.2 |
40.5 |
C4' |
C3' |
C2' |
O2' |
280.5 |
241.2 |
C4' |
C3' |
C2' |
H2' |
156.6 |
118.6 |
C2' |
C3' |
C4' |
H3' |
244.1 |
241.2 |
C5' |
C4' |
C3' |
O4' |
236.7 |
241.1 |
C5' |
C4' |
C3' |
H4' |
120.8 |
122.3 |
C3' |
C4' |
C5' |
H5' |
188.8 |
296.9 |
C3' |
C4' |
C5' |
H5'' |
307.4 |
56.8 |
O4' |
C4' |
C3' |
H4' |
244.1 |
241.2 |
H3' |
C3' |
O3' |
HO3' |
56.6 |
302.6 |
O3' |
C3' |
H3' |
C2' |
123.8 |
122.7 |
O3' |
C3' |
H3' |
C4' |
233.0 |
237.4 |
H3' |
C3' |
C2' |
O2' |
165.0 |
122.5 |
H3' |
C3' |
C2' |
H2' |
41.2 |
360.0 |
C2' |
C3' |
H3' |
C4' |
109.2 |
114.7 |
H3' |
C3' |
C4' |
C5' |
316.7 |
335.8 |
H3' |
C3' |
C4' |
O4' |
80.1 |
94.7 |
H3' |
C3' |
C4' |
H4' |
195.9 |
213.5 |
O5' |
C5' |
C4' |
H5' |
239.6 |
240.0 |
O5' |
C5' |
C4' |
H5'' |
121.0 |
120.1 |
C1' |
O4' |
C4' |
C5' |
146.3 |
159.5 |
C5' |
C4' |
C3' |
H3' |
316.7 |
335.8 |
C3' |
C4' |
C5' |
O4' |
120.4 |
115.5 |
C3' |
C4' |
C5' |
H4' |
239.6 |
237.7 |
O4' |
C4' |
C5' |
H4' |
119.2 |
122.2 |
H5' |
C5' |
C4' |
H5'' |
241.4 |
240.1 |
C4' |
O4' |
C1' |
N1 |
241.0 |
200.7 |
C4' |
O4' |
C1' |
H1' |
120.1 |
78.5 |
O4' |
C4' |
C3' |
H3' |
80.1 |
94.7 |
C3' |
C4' |
O4' |
C5' |
234.9 |
241.0 |
C3' |
C4' |
O4' |
H4' |
115.6 |
118.8 |
C5' |
C4' |
O4' |
H4' |
240.7 |
237.8 |
O4' |
C4' |
C5' |
H5' |
68.5 |
181.5 |
O4' |
C4' |
C5' |
H5'' |
187.1 |
301.4 |
H4' |
C4' |
C3' |
H3' |
195.9 |
213.5 |
C3' |
C4' |
H4' |
C5' |
124.4 |
122.5 |
C3' |
C4' |
H4' |
O4' |
245.6 |
244.7 |
C5' |
C4' |
H4' |
O4' |
121.2 |
122.2 |
H4' |
C4' |
C5' |
H5' |
309.3 |
59.3 |
H4' |
C4' |
C5' |
H5'' |
67.9 |
179.2 |
O5' |
C5' |
H5' |
C4' |
121.2 |
120.1 |
O5' |
C5' |
H5' |
H5'' |
240.3 |
240.0 |
H5' |
C5' |
C4' |
O4' |
68.5 |
181.5 |
H5' |
C5' |
C4' |
H4' |
309.3 |
59.3 |
C4' |
C5' |
H5' |
H5'' |
119.1 |
119.9 |
O5' |
C5' |
H5'' |
C4' |
238.3 |
239.9 |
O5' |
C5' |
H5'' |
H5' |
119.6 |
120.0 |
H5'' |
C5' |
C4' |
O4' |
187.1 |
301.4 |
H5'' |
C5' |
C4' |
H4' |
67.9 |
179.2 |
C4' |
C5' |
H5'' |
H5' |
241.3 |
240.1 |
HO2' |
O2' |
C2' |
H2' |
86.8 |
61.1 |
C1' |
N1 |
C2 |
N2 |
354.6 |
0.2 |
H21 |
N2 |
C2 |
H22 |
175.9 |
180.3 |
C4 |
N3 |
C2 |
N2 |
183.2 |
179.9 |
N3 |
C2 |
N2 |
N1 |
178.6 |
180.2 |
N2 |
C2 |
N1 |
C6 |
173.7 |
179.8 |
C2 |
N2 |
H21 |
H22 |
184.2 |
179.7 |
H21 |
N2 |
C2 |
N3 |
175.9 |
348.1 |
H21 |
N2 |
C2 |
N1 |
357.3 |
167.9 |
C2 |
N2 |
H22 |
H21 |
175.9 |
180.3 |
H22 |
N2 |
C2 |
N3 |
0.1 |
167.8 |
H22 |
N2 |
C2 |
N1 |
181.5 |
347.6 |
N2 |
C2 |
N3 |
C4 |
183.2 |
179.9 |
O4 |
C4 |
N3 |
C5 |
180.0 |
179.9 |
N3 |
C4 |
C5 |
C6 |
358.0 |
359.9 |
N3 |
C4 |
C5 |
H5 |
177.9 |
180.0 |
C4 |
N3 |
C2 |
N1 |
1.8 |
0.2 |
N3 |
C4 |
O4 |
C5 |
179.9 |
180.1 |
O4 |
C4 |
N3 |
C2 |
181.6 |
180.0 |
O4 |
C4 |
C5 |
C6 |
177.9 |
180.0 |
O4 |
C4 |
C5 |
H5 |
357.9 |
0.1 |
N3 |
C4 |
C5 |
O4 |
180.0 |
179.9 |
C5 |
C4 |
N3 |
C2 |
1.6 |
0.1 |
N1 |
C6 |
C5 |
C4 |
359.0 |
359.8 |
C4 |
C5 |
C6 |
H6 |
179.3 |
180.0 |
C6 |
C5 |
C4 |
H5 |
180.1 |
179.9 |
C1' |
N1 |
C2 |
N3 |
176.1 |
180.0 |
N3 |
C2 |
N2 |
H21 |
175.9 |
348.1 |
N3 |
C2 |
N2 |
H22 |
0.1 |
167.8 |
N2 |
C2 |
N3 |
N1 |
181.4 |
179.8 |
C2 |
N3 |
C4 |
O4 |
181.6 |
180.0 |
C2 |
N3 |
C4 |
C5 |
1.6 |
0.1 |
N3 |
C2 |
N1 |
C6 |
355.2 |
359.6 |
C2 |
N1 |
C1' |
H1' |
319.8 |
328.2 |
C1' |
N1 |
C2 |
C6 |
180.9 |
180.4 |
N1 |
C2 |
N2 |
H21 |
357.3 |
167.9 |
N1 |
C2 |
N2 |
H22 |
181.5 |
347.6 |
N2 |
C2 |
N1 |
N3 |
178.5 |
180.2 |
C2 |
N1 |
C6 |
C5 |
4.3 |
0.5 |
C2 |
N1 |
C6 |
H6 |
184.0 |
180.3 |
C6 |
N1 |
C1' |
H1' |
140.8 |
148.6 |
C1' |
N1 |
C6 |
C2 |
179.1 |
179.6 |
C4 |
C5 |
C6 |
N1 |
359.0 |
359.8 |
C5 |
C6 |
N1 |
H6 |
180.3 |
180.2 |
N1 |
C6 |
C5 |
H5 |
179.1 |
179.7 |
C4 |
C5 |
C6 |
H5 |
179.9 |
180.1 |
N1 |
C6 |
C5 |
H6 |
179.7 |
179.8 |
N1 |
C6 |
H6 |
C5 |
180.3 |
180.2 |
H6 |
C6 |
C5 |
H5 |
359.4 |
359.9 |
C4 |
C5 |
H5 |
C6 |
180.1 |
179.9 |
H5 |
C5 |
C6 |
H6 |
359.4 |
359.9 |