PDB Chemical Component JI1
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 JI1
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C4 |
C3 |
1.413 |
1.383 |
| C4 |
C5 |
1.417 |
1.389 |
| C3 |
C2 |
1.414 |
1.391 |
| C5 |
C6 |
1.418 |
1.381 |
| C2 |
N2 |
1.314 |
1.390 |
| C2 |
N1 |
1.347 |
1.324 |
| C5' |
C4' |
1.539 |
1.544 |
| C5' |
N1' |
1.472 |
1.486 |
| C4' |
C3' |
1.563 |
1.543 |
| C4' |
C7 |
1.577 |
1.530 |
| C6 |
N1 |
1.345 |
1.319 |
| C6 |
C7 |
1.543 |
1.507 |
| C3' |
N8 |
1.490 |
1.468 |
| C3' |
C2' |
1.548 |
1.544 |
| N1' |
C2' |
1.496 |
1.485 |
| N8 |
C9 |
1.482 |
1.468 |
| C9 |
C10 |
1.539 |
1.530 |
| O12 |
C11 |
1.430 |
1.429 |
| C10 |
C11 |
1.546 |
1.530 |
| N2 |
HN21 |
1.000 |
0.970 |
| N2 |
HN22 |
1.000 |
0.970 |
| C3 |
H3 |
1.080 |
1.079 |
| C4 |
H4 |
1.080 |
1.080 |
| C5 |
H5 |
1.080 |
1.080 |
| N1' |
HN1' |
1.000 |
1.009 |
| C2' |
H2'1 |
1.100 |
1.090 |
| C2' |
H2'2 |
1.100 |
1.091 |
| C3' |
H3' |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C7 |
H71 |
1.100 |
1.090 |
| C7 |
H72 |
1.101 |
1.090 |
| N8 |
HN8 |
1.000 |
1.010 |
| C9 |
H91 |
1.100 |
1.090 |
| C9 |
H92 |
1.100 |
1.090 |
| C10 |
H101 |
1.099 |
1.090 |
| C10 |
H102 |
1.100 |
1.089 |
| C11 |
H111 |
1.100 |
1.090 |
| C11 |
H112 |
1.100 |
1.090 |
| O12 |
HO12 |
0.950 |
0.967 |
Bond Angles for JI1
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4 |
C3 |
H3 |
120.8 |
120.5 |
| C4 |
C5 |
C6 |
118.3 |
119.3 |
| C5 |
C4 |
H4 |
120.1 |
120.7 |
| C4 |
C5 |
H5 |
120.8 |
120.3 |
| C5 |
C6 |
C7 |
120.9 |
119.5 |
| C6 |
C5 |
H5 |
120.8 |
120.3 |
| C2 |
N2 |
HN21 |
109.5 |
120.0 |
| C2 |
N2 |
HN22 |
109.5 |
120.0 |
| C5' |
C4' |
C7 |
110.7 |
110.3 |
| C5' |
C4' |
H4' |
114.4 |
110.4 |
| C5' |
N1' |
HN1' |
109.6 |
111.0 |
| C4' |
C3' |
N8 |
113.5 |
110.3 |
| C4' |
C3' |
H3' |
111.1 |
110.4 |
| C6 |
C7 |
C4' |
111.3 |
109.4 |
| C7 |
C4' |
H4' |
104.6 |
110.3 |
| C4' |
C7 |
H71 |
108.9 |
109.4 |
| C4' |
C7 |
H72 |
108.5 |
109.5 |
| C6 |
C7 |
H71 |
108.8 |
109.4 |
| C6 |
C7 |
H72 |
108.5 |
109.5 |
| C3' |
N8 |
C9 |
120.7 |
111.0 |
| N8 |
C3' |
H3' |
104.7 |
110.3 |
| C3' |
N8 |
HN8 |
105.9 |
111.0 |
| C3' |
C2' |
H2'1 |
110.6 |
110.4 |
| C3' |
C2' |
H2'2 |
111.2 |
110.5 |
| C2' |
N1' |
HN1' |
109.6 |
111.0 |
| N1' |
C2' |
H2'1 |
110.5 |
110.4 |
| N1' |
C2' |
H2'2 |
111.3 |
110.4 |
| N8 |
C9 |
C10 |
111.6 |
109.5 |
| C9 |
N8 |
HN8 |
105.9 |
111.0 |
| N8 |
C9 |
H91 |
108.8 |
109.5 |
| N8 |
C9 |
H92 |
108.3 |
109.5 |
| C9 |
C10 |
C11 |
109.9 |
109.5 |
| C10 |
C9 |
H91 |
108.7 |
109.5 |
| C10 |
C9 |
H92 |
108.3 |
109.5 |
| C9 |
C10 |
H101 |
109.3 |
109.4 |
| C9 |
C10 |
H102 |
109.2 |
109.5 |
| O12 |
C11 |
H111 |
110.0 |
109.5 |
| O12 |
C11 |
H112 |
110.3 |
109.5 |
| C11 |
C10 |
H101 |
109.3 |
109.5 |
| C11 |
C10 |
H102 |
109.2 |
109.5 |
| C10 |
C11 |
H111 |
110.0 |
109.5 |
| C10 |
C11 |
H112 |
110.3 |
109.5 |
| HN21 |
N2 |
HN22 |
109.5 |
120.1 |
| H2'1 |
C2' |
H2'2 |
107.0 |
110.4 |
| H5'1 |
C5' |
H5'2 |
106.5 |
110.5 |
| H71 |
C7 |
H72 |
110.9 |
109.5 |
| H91 |
C9 |
H92 |
111.2 |
109.4 |
| H101 |
C10 |
H102 |
109.8 |
109.5 |
| H111 |
C11 |
H112 |
108.3 |
109.4 |
Torsion Angles for JI1
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5 |
C4 |
C3 |
H3 |
179.6 |
180.1 |
| C4 |
C5 |
C6 |
C7 |
181.0 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| C3 |
C2 |
N2 |
HN21 |
299.8 |
180.0 |
| C3 |
C2 |
N2 |
HN22 |
59.8 |
0.0 |
| C6 |
C5 |
C4 |
H4 |
180.0 |
180.1 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| C5 |
C6 |
C7 |
C4' |
87.3 |
125.0 |
| C5 |
C6 |
C7 |
H71 |
327.3 |
244.9 |
| C5 |
C6 |
C7 |
H72 |
206.5 |
5.0 |
| HN21 |
N2 |
C2 |
HN22 |
240.0 |
180.0 |
| C4' |
C5' |
N1' |
HN1' |
142.5 |
80.1 |
| C5' |
C4' |
C3' |
N8 |
153.6 |
118.9 |
| C5' |
C4' |
C3' |
H3' |
271.3 |
241.1 |
| C6 |
C7 |
C4' |
C5' |
64.8 |
69.3 |
| C7 |
C4' |
C5' |
H4' |
242.2 |
237.8 |
| C5' |
C4' |
C7 |
H71 |
184.8 |
309.4 |
| C5' |
C4' |
C7 |
H72 |
305.5 |
189.4 |
| C2' |
N1' |
C5' |
HN1' |
240.0 |
240.4 |
| C5' |
N1' |
C2' |
H2'1 |
240.1 |
158.2 |
| C5' |
N1' |
C2' |
H2'2 |
121.3 |
280.6 |
| C6 |
C7 |
C4' |
C3' |
178.3 |
185.0 |
| C4' |
C3' |
N8 |
C9 |
166.2 |
157.9 |
| N8 |
C3' |
C4' |
H3' |
242.3 |
237.8 |
| C4' |
C3' |
N8 |
HN8 |
286.2 |
281.9 |
| C4' |
C3' |
C2' |
H2'1 |
98.0 |
217.4 |
| C4' |
C3' |
C2' |
H2'2 |
216.7 |
95.0 |
| C5' |
C4' |
C7 |
H4' |
123.7 |
122.2 |
| C7 |
C4' |
C3' |
N8 |
34.9 |
360.0 |
| C7 |
C4' |
C3' |
H3' |
152.6 |
122.2 |
| C6 |
C7 |
C4' |
H71 |
240.0 |
119.9 |
| C6 |
C7 |
C4' |
H72 |
119.2 |
240.0 |
| H71 |
C7 |
C4' |
H72 |
239.2 |
120.0 |
| C7 |
C6 |
C5 |
H5 |
0.9 |
360.0 |
| C5' |
C4' |
C7 |
C6 |
64.8 |
69.3 |
| C6 |
C7 |
C4' |
H4' |
301.1 |
307.1 |
| C4' |
C7 |
C6 |
H71 |
120.0 |
240.1 |
| C4' |
C7 |
C6 |
H72 |
240.8 |
120.0 |
| H71 |
C7 |
C6 |
H72 |
120.7 |
240.0 |
| C4' |
C3' |
N8 |
H3' |
121.3 |
122.2 |
| N8 |
C3' |
C2' |
H2'1 |
336.6 |
98.5 |
| N8 |
C3' |
C2' |
H2'2 |
95.3 |
336.1 |
| C3' |
N8 |
C9 |
C10 |
163.0 |
180.0 |
| C9 |
N8 |
C3' |
HN8 |
240.0 |
236.0 |
| C3' |
N8 |
C9 |
H91 |
283.0 |
300.0 |
| C3' |
N8 |
C9 |
H92 |
43.9 |
60.0 |
| C3' |
C2' |
N1' |
HN1' |
240.1 |
279.9 |
| N1' |
C2' |
C3' |
H2'1 |
240.0 |
118.8 |
| N1' |
C2' |
C3' |
H2'2 |
121.3 |
241.1 |
| H2'1 |
C2' |
C3' |
H2'2 |
241.2 |
122.4 |
| C5' |
N1' |
C2' |
HN1' |
120.0 |
119.5 |
| C3' |
C2' |
N1' |
H2'1 |
120.0 |
241.3 |
| C3' |
C2' |
N1' |
H2'2 |
238.8 |
118.9 |
| H2'1 |
C2' |
N1' |
H2'2 |
118.8 |
237.7 |
| C9 |
N8 |
C3' |
H3' |
44.9 |
35.7 |
| C3' |
N8 |
C9 |
HN8 |
120.0 |
124.0 |
| N8 |
C9 |
C10 |
C11 |
198.4 |
180.0 |
| C10 |
C9 |
N8 |
H91 |
240.0 |
240.0 |
| C10 |
C9 |
N8 |
H92 |
119.1 |
120.0 |
| N8 |
C9 |
C10 |
H101 |
318.4 |
300.0 |
| N8 |
C9 |
C10 |
H102 |
78.6 |
60.0 |
| H91 |
C9 |
N8 |
H92 |
239.1 |
240.0 |
| C10 |
C9 |
N8 |
HN8 |
42.9 |
56.0 |
| N8 |
C9 |
C10 |
H91 |
120.0 |
120.0 |
| N8 |
C9 |
C10 |
H92 |
240.9 |
240.0 |
| C11 |
C10 |
C9 |
H101 |
240.0 |
240.0 |
| C11 |
C10 |
C9 |
H102 |
119.8 |
120.0 |
| C9 |
C10 |
C11 |
H111 |
177.0 |
300.0 |
| C9 |
C10 |
C11 |
H112 |
57.5 |
60.0 |
| H91 |
C9 |
C10 |
H92 |
120.9 |
120.0 |
| H101 |
C10 |
C9 |
H102 |
239.8 |
240.0 |
| O12 |
C11 |
C10 |
H101 |
177.0 |
60.0 |
| O12 |
C11 |
C10 |
H102 |
56.7 |
300.0 |
| C10 |
C11 |
O12 |
H111 |
240.0 |
120.0 |
| C10 |
C11 |
O12 |
H112 |
120.6 |
240.0 |
| H111 |
C11 |
O12 |
H112 |
240.6 |
120.0 |
| C11 |
C10 |
C9 |
H91 |
78.4 |
60.0 |
| C11 |
C10 |
C9 |
H92 |
317.5 |
300.0 |
| C9 |
C10 |
C11 |
H101 |
120.0 |
120.0 |
| C9 |
C10 |
C11 |
H102 |
240.2 |
240.0 |
| O12 |
C11 |
C10 |
H111 |
120.0 |
240.0 |
| O12 |
C11 |
C10 |
H112 |
239.4 |
120.0 |
| H101 |
C10 |
C11 |
H102 |
120.2 |
120.0 |
| H111 |
C11 |
C10 |
H112 |
119.4 |
240.0 |
| C2 |
N2 |
HN21 |
HN22 |
120.0 |
180.0 |
| C2 |
N2 |
HN22 |
HN21 |
240.0 |
180.0 |
| H4 |
C4 |
C3 |
H3 |
359.6 |
359.9 |
| H4 |
C4 |
C5 |
C6 |
180.0 |
180.1 |
| H4 |
C4 |
C5 |
H5 |
0.0 |
0.2 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.9 |
| H5 |
C5 |
C4 |
H4 |
0.0 |
0.2 |
| H5 |
C5 |
C6 |
C7 |
0.9 |
360.0 |
| HN1' |
N1' |
C2' |
H2'1 |
120.0 |
38.7 |
| HN1' |
N1' |
C2' |
H2'2 |
1.3 |
161.0 |
| C3' |
C2' |
H2'1 |
H2'2 |
121.3 |
237.6 |
| H2'1 |
C2' |
N1' |
HN1' |
120.0 |
38.7 |
| N1' |
C2' |
H2'1 |
H2'2 |
238.7 |
122.4 |
| C3' |
C2' |
H2'2 |
H2'1 |
239.1 |
122.4 |
| H2'2 |
C2' |
N1' |
HN1' |
1.3 |
161.0 |
| N1' |
C2' |
H2'2 |
H2'1 |
120.8 |
237.7 |
| C4' |
C3' |
H3' |
N8 |
237.1 |
237.8 |
| H3' |
C3' |
N8 |
C9 |
44.9 |
35.7 |
| H3' |
C3' |
N8 |
HN8 |
164.9 |
159.7 |
| H3' |
C3' |
C2' |
H2'1 |
219.0 |
336.3 |
| H3' |
C3' |
C2' |
H2'2 |
337.8 |
214.0 |
| C5' |
C4' |
H4' |
C7 |
238.7 |
237.8 |
| H4' |
C4' |
C3' |
N8 |
276.9 |
237.9 |
| H4' |
C4' |
C3' |
H3' |
34.6 |
0.1 |
| H4' |
C4' |
C7 |
H71 |
61.1 |
187.2 |
| H4' |
C4' |
C7 |
H72 |
181.8 |
67.1 |
| H5'1 |
C5' |
C4' |
C7 |
204.4 |
24.0 |
| H5'1 |
C5' |
C4' |
H4' |
322.2 |
146.1 |
| H5'1 |
C5' |
N1' |
HN1' |
22.5 |
198.9 |
| H5'2 |
C5' |
C4' |
C7 |
322.9 |
261.5 |
| H5'2 |
C5' |
C4' |
H4' |
80.7 |
23.7 |
| H5'2 |
C5' |
N1' |
HN1' |
264.0 |
321.3 |
| C6 |
C7 |
H71 |
C4' |
121.5 |
240.1 |
| H71 |
C7 |
C4' |
H4' |
61.1 |
187.2 |
| C4' |
C7 |
H71 |
H72 |
119.3 |
240.0 |
| C6 |
C7 |
H71 |
H72 |
240.8 |
120.0 |
| C6 |
C7 |
H72 |
C4' |
239.0 |
120.0 |
| H72 |
C7 |
C4' |
H4' |
181.8 |
67.1 |
| C4' |
C7 |
H72 |
H71 |
240.5 |
120.0 |
| C6 |
C7 |
H72 |
H71 |
119.5 |
240.0 |
| C3' |
N8 |
HN8 |
C9 |
230.7 |
236.0 |
| HN8 |
N8 |
C3' |
H3' |
164.9 |
159.7 |
| HN8 |
N8 |
C9 |
C10 |
42.9 |
56.0 |
| HN8 |
N8 |
C9 |
H91 |
162.9 |
176.1 |
| HN8 |
N8 |
C9 |
H92 |
283.9 |
296.0 |
| N8 |
C9 |
H91 |
C10 |
238.2 |
240.0 |
| H91 |
C9 |
N8 |
HN8 |
162.9 |
176.1 |
| N8 |
C9 |
H91 |
H92 |
119.1 |
120.0 |
| H91 |
C9 |
C10 |
C11 |
78.4 |
60.0 |
| C10 |
C9 |
H91 |
H92 |
240.9 |
240.0 |
| H91 |
C9 |
C10 |
H101 |
198.4 |
180.0 |
| H91 |
C9 |
C10 |
H102 |
318.6 |
300.0 |
| N8 |
C9 |
H92 |
C10 |
121.2 |
120.0 |
| H92 |
C9 |
N8 |
HN8 |
283.9 |
296.0 |
| N8 |
C9 |
H92 |
H91 |
240.6 |
240.0 |
| H92 |
C9 |
C10 |
C11 |
317.5 |
300.0 |
| C10 |
C9 |
H92 |
H91 |
119.4 |
120.0 |
| H92 |
C9 |
C10 |
H101 |
77.5 |
60.0 |
| H92 |
C9 |
C10 |
H102 |
197.7 |
180.0 |
| C9 |
C10 |
H101 |
C11 |
239.6 |
240.0 |
| H101 |
C10 |
C9 |
H91 |
198.4 |
180.0 |
| H101 |
C10 |
C9 |
H92 |
77.5 |
60.0 |
| C9 |
C10 |
H101 |
H102 |
119.8 |
120.0 |
| C11 |
C10 |
H101 |
H102 |
240.2 |
240.0 |
| H101 |
C10 |
C11 |
H111 |
57.0 |
180.1 |
| H101 |
C10 |
C11 |
H112 |
297.5 |
300.0 |
| C9 |
C10 |
H102 |
C11 |
120.2 |
120.0 |
| H102 |
C10 |
C9 |
H91 |
318.6 |
300.0 |
| H102 |
C10 |
C9 |
H92 |
197.7 |
180.0 |
| C9 |
C10 |
H102 |
H101 |
240.1 |
240.0 |
| C11 |
C10 |
H102 |
H101 |
119.9 |
120.0 |
| H102 |
C10 |
C11 |
H111 |
296.7 |
60.0 |
| H102 |
C10 |
C11 |
H112 |
177.3 |
180.0 |
| O12 |
C11 |
H111 |
H112 |
120.6 |
240.0 |
| H111 |
C11 |
C10 |
H101 |
57.0 |
180.1 |
| H111 |
C11 |
C10 |
H102 |
296.7 |
60.0 |
| C10 |
C11 |
H111 |
H112 |
239.4 |
120.0 |
| O12 |
C11 |
H112 |
H111 |
239.6 |
120.0 |
| H112 |
C11 |
C10 |
H101 |
297.5 |
300.0 |
| H112 |
C11 |
C10 |
H102 |
177.3 |
180.0 |
| C10 |
C11 |
H112 |
H111 |
120.4 |
240.0 |
| HO12 |
O12 |
C11 |
H111 |
309.9 |
60.0 |
| HO12 |
O12 |
C11 |
H112 |
69.4 |
300.0 |