PDB Chemical Component JI2
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 JI2
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
C4 |
C5 |
1.448 |
1.383 |
C4 |
C3 |
1.457 |
1.389 |
C5 |
C6 |
1.442 |
1.391 |
C3 |
C2 |
1.448 |
1.380 |
C6 |
N6 |
1.325 |
1.390 |
C6 |
N1 |
1.381 |
1.323 |
C4' |
C5' |
1.556 |
1.544 |
C4' |
C7 |
1.591 |
1.530 |
C4' |
C3' |
1.539 |
1.543 |
C2 |
N1 |
1.389 |
1.320 |
C2 |
C7 |
1.557 |
1.507 |
C5' |
N1' |
1.491 |
1.485 |
C3' |
N8 |
1.468 |
1.469 |
C3' |
C2' |
1.561 |
1.544 |
N11 |
C10 |
1.488 |
1.470 |
N8 |
C9 |
1.487 |
1.468 |
N1' |
C2' |
1.507 |
1.485 |
C9 |
C10 |
1.514 |
1.530 |
N6 |
HN61 |
1.000 |
0.971 |
N6 |
HN62 |
1.000 |
0.970 |
C5 |
H5 |
1.080 |
1.080 |
C4 |
H4 |
1.080 |
1.080 |
C3 |
H3 |
1.080 |
1.080 |
N1' |
HN1' |
1.000 |
1.009 |
C2' |
H2'1 |
1.100 |
1.090 |
C2' |
H2'2 |
1.100 |
1.090 |
C3' |
H3' |
1.100 |
1.090 |
C4' |
H4' |
1.100 |
1.090 |
C5' |
H5'1 |
1.100 |
1.090 |
C5' |
H5'2 |
1.101 |
1.090 |
C7 |
H71 |
1.100 |
1.089 |
C7 |
H72 |
1.100 |
1.090 |
N8 |
HN8 |
1.001 |
1.009 |
C9 |
H91 |
1.100 |
1.090 |
C9 |
H92 |
1.101 |
1.090 |
C10 |
H101 |
1.100 |
1.089 |
C10 |
H102 |
1.100 |
1.090 |
N11 |
H111 |
1.000 |
1.009 |
N11 |
H112 |
1.000 |
1.009 |
Bond Angles for JI2
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
C4 |
C5 |
H5 |
120.7 |
120.4 |
C4 |
C3 |
C2 |
117.2 |
119.3 |
C3 |
C4 |
H4 |
119.5 |
120.8 |
C4 |
C3 |
H3 |
121.4 |
120.4 |
C5 |
C6 |
N1 |
119.3 |
120.6 |
C3 |
C2 |
N1 |
120.0 |
120.8 |
C3 |
C2 |
C7 |
121.3 |
119.6 |
C2 |
C3 |
H3 |
121.4 |
120.3 |
N6 |
C6 |
N1 |
120.0 |
119.7 |
C6 |
N6 |
HN61 |
109.5 |
120.0 |
C6 |
N6 |
HN62 |
109.5 |
120.0 |
C6 |
N1 |
C2 |
123.9 |
121.6 |
C5' |
C4' |
C7 |
111.8 |
110.3 |
C5' |
C4' |
H4' |
115.1 |
110.4 |
C4' |
C5' |
H5'1 |
110.9 |
110.4 |
C4' |
C5' |
H5'2 |
111.9 |
110.4 |
C2 |
C7 |
C4' |
113.2 |
109.5 |
C7 |
C4' |
H4' |
103.6 |
110.3 |
C4' |
C7 |
H71 |
108.3 |
109.5 |
C4' |
C7 |
H72 |
107.4 |
109.5 |
C4' |
C3' |
N8 |
113.2 |
110.3 |
C4' |
C3' |
H3' |
111.1 |
110.4 |
N1 |
C2 |
C7 |
118.7 |
119.6 |
C2 |
C7 |
H71 |
108.3 |
109.4 |
C2 |
C7 |
H72 |
107.4 |
109.4 |
C5' |
N1' |
HN1' |
109.6 |
111.0 |
C3' |
N8 |
C9 |
117.1 |
111.0 |
N8 |
C3' |
H3' |
105.3 |
110.3 |
C3' |
N8 |
HN8 |
107.0 |
111.0 |
C3' |
C2' |
H2'1 |
111.7 |
110.4 |
C3' |
C2' |
H2'2 |
113.0 |
110.5 |
N11 |
C10 |
H101 |
110.1 |
109.5 |
N11 |
C10 |
H102 |
110.4 |
109.5 |
N8 |
C9 |
C10 |
110.8 |
109.5 |
C9 |
N8 |
HN8 |
107.0 |
111.0 |
N8 |
C9 |
H91 |
109.0 |
109.4 |
N8 |
C9 |
H92 |
108.8 |
109.5 |
C2' |
N1' |
HN1' |
109.6 |
111.0 |
N1' |
C2' |
H2'1 |
111.7 |
110.4 |
N1' |
C2' |
H2'2 |
113.1 |
110.4 |
C10 |
C9 |
H91 |
109.1 |
109.5 |
C10 |
C9 |
H92 |
108.8 |
109.5 |
C9 |
C10 |
H101 |
110.0 |
109.4 |
C9 |
C10 |
H102 |
110.4 |
109.5 |
HN61 |
N6 |
HN62 |
109.4 |
120.0 |
H2'1 |
C2' |
H2'2 |
104.6 |
110.4 |
H5'1 |
C5' |
H5'2 |
106.1 |
110.5 |
H71 |
C7 |
H72 |
112.4 |
109.6 |
H91 |
C9 |
H92 |
110.5 |
109.4 |
H101 |
C10 |
H102 |
108.2 |
109.6 |
H111 |
N11 |
H112 |
109.4 |
111.0 |
Torsion Angles for JI2
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
C4 |
C5 |
C6 |
N1 |
0.2 |
0.2 |
C3 |
C4 |
C5 |
H5 |
179.9 |
180.0 |
C4 |
C3 |
C2 |
N1 |
360.0 |
359.8 |
C4 |
C3 |
C2 |
C7 |
180.0 |
180.0 |
C2 |
C3 |
C4 |
H3 |
180.0 |
180.0 |
N6 |
C6 |
C5 |
N1 |
180.1 |
179.7 |
C5 |
C6 |
N6 |
HN61 |
296.7 |
180.3 |
C5 |
C6 |
N6 |
HN62 |
56.6 |
0.2 |
C5 |
C6 |
N1 |
C2 |
359.8 |
359.5 |
C2 |
C3 |
C4 |
H4 |
180.0 |
180.1 |
C4 |
C3 |
C2 |
H3 |
180.0 |
180.0 |
C6 |
N1 |
C2 |
C3 |
0.1 |
0.5 |
C3 |
C2 |
C7 |
C4' |
86.7 |
125.0 |
N1 |
C2 |
C3 |
C7 |
180.0 |
179.7 |
C3 |
C2 |
C7 |
H71 |
326.6 |
245.0 |
C3 |
C2 |
C7 |
H72 |
205.1 |
5.0 |
C5 |
C6 |
N6 |
N1 |
179.9 |
180.3 |
N6 |
C6 |
N1 |
C2 |
179.7 |
179.7 |
HN61 |
N6 |
C6 |
HN62 |
240.1 |
180.0 |
C3 |
C2 |
N1 |
C6 |
0.1 |
0.5 |
N1 |
C6 |
N6 |
HN61 |
116.7 |
0.0 |
N1 |
C6 |
N6 |
HN62 |
236.7 |
180.0 |
C6 |
N1 |
C2 |
C7 |
180.1 |
180.3 |
C2 |
C7 |
C4' |
C5' |
64.5 |
66.5 |
C7 |
C4' |
C5' |
H4' |
242.1 |
237.9 |
C5' |
C4' |
C7 |
H71 |
184.6 |
306.5 |
C5' |
C4' |
C7 |
H72 |
306.2 |
186.4 |
C5' |
C4' |
C3' |
N8 |
162.1 |
118.9 |
C5' |
C4' |
C3' |
H3' |
280.4 |
241.1 |
C4' |
C5' |
N1' |
HN1' |
137.0 |
80.1 |
H5'1 |
C5' |
C4' |
H5'2 |
241.7 |
122.4 |
C5' |
C4' |
C7 |
H4' |
124.6 |
122.2 |
C7 |
C4' |
C5' |
H5'1 |
200.7 |
23.9 |
C7 |
C4' |
C5' |
H5'2 |
319.0 |
261.5 |
C7 |
C4' |
C3' |
N8 |
43.7 |
0.0 |
C7 |
C4' |
C3' |
H3' |
162.0 |
122.2 |
N1 |
C2 |
C7 |
C4' |
266.7 |
305.2 |
C2 |
C7 |
C4' |
H71 |
240.0 |
120.0 |
C2 |
C7 |
C4' |
H72 |
118.4 |
240.1 |
H71 |
C7 |
C4' |
H72 |
238.4 |
120.1 |
C2 |
C7 |
C4' |
C3' |
175.4 |
182.1 |
C4' |
C3' |
N8 |
C9 |
155.9 |
157.9 |
N8 |
C3' |
C4' |
H3' |
241.7 |
237.8 |
C4' |
C3' |
N8 |
HN8 |
275.9 |
281.9 |
C4' |
C3' |
C2' |
H2'1 |
85.3 |
217.4 |
C4' |
C3' |
C2' |
H2'2 |
202.9 |
95.0 |
C3 |
C2 |
N1 |
C7 |
180.0 |
180.3 |
N1 |
C2 |
C3 |
H3 |
180.0 |
179.8 |
N1 |
C2 |
C7 |
H71 |
146.6 |
65.2 |
N1 |
C2 |
C7 |
H72 |
25.1 |
185.3 |
C3 |
C2 |
C7 |
N1 |
180.0 |
179.8 |
C7 |
C2 |
C3 |
H3 |
360.0 |
0.0 |
C5' |
C4' |
C7 |
C2 |
64.5 |
66.5 |
C2 |
C7 |
C4' |
H4' |
299.9 |
304.3 |
C4' |
C7 |
C2 |
H71 |
120.0 |
240.0 |
C4' |
C7 |
C2 |
H72 |
241.6 |
120.0 |
H71 |
C7 |
C2 |
H72 |
121.6 |
240.0 |
C2' |
N1' |
C5' |
HN1' |
240.0 |
240.4 |
C5' |
N1' |
C2' |
H2'1 |
250.7 |
158.3 |
C5' |
N1' |
C2' |
H2'2 |
133.1 |
280.6 |
C4' |
C3' |
N8 |
H3' |
121.6 |
122.2 |
N8 |
C3' |
C2' |
H2'1 |
324.6 |
98.5 |
N8 |
C3' |
C2' |
H2'2 |
82.3 |
336.1 |
C3' |
N8 |
C9 |
C10 |
175.9 |
180.0 |
C9 |
N8 |
C3' |
HN8 |
240.0 |
236.1 |
C3' |
N8 |
C9 |
H91 |
295.9 |
300.0 |
C3' |
N8 |
C9 |
H92 |
56.4 |
60.0 |
C3' |
C2' |
N1' |
HN1' |
250.7 |
280.0 |
N1' |
C2' |
C3' |
H2'1 |
240.0 |
118.7 |
N1' |
C2' |
C3' |
H2'2 |
122.4 |
241.1 |
H2'1 |
C2' |
C3' |
H2'2 |
242.3 |
122.4 |
N11 |
C10 |
C9 |
H91 |
303.8 |
60.0 |
N11 |
C10 |
C9 |
H92 |
183.2 |
300.0 |
C9 |
C10 |
N11 |
H101 |
240.0 |
119.9 |
C9 |
C10 |
N11 |
H102 |
120.7 |
240.0 |
H101 |
C10 |
N11 |
H102 |
240.7 |
120.1 |
C9 |
N8 |
C3' |
H3' |
34.3 |
35.7 |
C3' |
N8 |
C9 |
HN8 |
120.0 |
124.0 |
C10 |
C9 |
N8 |
H91 |
240.0 |
240.0 |
C10 |
C9 |
N8 |
H92 |
119.5 |
120.0 |
N8 |
C9 |
C10 |
H101 |
303.8 |
299.9 |
N8 |
C9 |
C10 |
H102 |
184.4 |
60.0 |
H91 |
C9 |
N8 |
H92 |
239.5 |
240.0 |
C5' |
N1' |
C2' |
HN1' |
120.0 |
119.6 |
C3' |
C2' |
N1' |
H2'1 |
120.0 |
241.2 |
C3' |
C2' |
N1' |
H2'2 |
237.6 |
118.9 |
H2'1 |
C2' |
N1' |
H2'2 |
117.7 |
237.7 |
N11 |
C10 |
C9 |
H101 |
120.0 |
240.0 |
N11 |
C10 |
C9 |
H102 |
239.3 |
120.0 |
C10 |
C9 |
N8 |
HN8 |
55.9 |
56.1 |
N8 |
C9 |
C10 |
H91 |
120.0 |
120.0 |
N8 |
C9 |
C10 |
H92 |
240.5 |
240.0 |
H91 |
C9 |
C10 |
H92 |
120.5 |
120.0 |
H101 |
C10 |
C9 |
H102 |
119.3 |
239.9 |
HN61 |
N6 |
C6 |
N1 |
116.7 |
0.0 |
C6 |
N6 |
HN61 |
HN62 |
120.0 |
180.0 |
HN62 |
N6 |
C6 |
N1 |
236.7 |
180.0 |
C6 |
N6 |
HN62 |
HN61 |
240.0 |
180.0 |
H5 |
C5 |
C6 |
N1 |
180.2 |
180.2 |
H4 |
C4 |
C5 |
H5 |
360.0 |
359.9 |
H4 |
C4 |
C3 |
C2 |
180.0 |
180.1 |
H4 |
C4 |
C3 |
H3 |
359.9 |
0.0 |
C4 |
C3 |
H3 |
C2 |
180.0 |
180.0 |
H3 |
C3 |
C4 |
H4 |
359.9 |
0.0 |
H3 |
C3 |
C2 |
N1 |
180.0 |
179.8 |
H3 |
C3 |
C2 |
C7 |
360.0 |
0.0 |
HN1' |
N1' |
C2' |
H2'1 |
130.7 |
38.7 |
HN1' |
N1' |
C2' |
H2'2 |
13.1 |
161.0 |
C3' |
C2' |
H2'1 |
H2'2 |
122.6 |
237.5 |
H2'1 |
C2' |
N1' |
HN1' |
130.7 |
38.7 |
N1' |
C2' |
H2'1 |
H2'2 |
237.4 |
122.4 |
C3' |
C2' |
H2'2 |
H2'1 |
238.3 |
122.4 |
H2'2 |
C2' |
N1' |
HN1' |
13.1 |
161.0 |
N1' |
C2' |
H2'2 |
H2'1 |
121.7 |
237.7 |
C4' |
C3' |
H3' |
N8 |
237.0 |
237.8 |
H3' |
C3' |
N8 |
C9 |
34.3 |
35.7 |
H3' |
C3' |
N8 |
HN8 |
154.3 |
159.6 |
H3' |
C3' |
C2' |
H2'1 |
206.5 |
336.4 |
H3' |
C3' |
C2' |
H2'2 |
324.1 |
214.0 |
C5' |
C4' |
H4' |
C7 |
237.6 |
237.9 |
H4' |
C4' |
C5' |
H5'1 |
318.6 |
146.1 |
H4' |
C4' |
C5' |
H5'2 |
76.9 |
23.6 |
H4' |
C4' |
C7 |
H71 |
60.0 |
184.3 |
H4' |
C4' |
C7 |
H72 |
181.6 |
64.2 |
H4' |
C4' |
C3' |
N8 |
285.8 |
237.9 |
H4' |
C4' |
C3' |
H3' |
44.1 |
0.0 |
H5'1 |
C5' |
C4' |
C7 |
200.7 |
23.9 |
H5'1 |
C5' |
C4' |
H4' |
318.6 |
146.1 |
C4' |
C5' |
H5'1 |
H5'2 |
121.8 |
237.6 |
H5'1 |
C5' |
N1' |
HN1' |
17.0 |
198.8 |
H5'2 |
C5' |
C4' |
C7 |
319.0 |
261.5 |
H5'2 |
C5' |
C4' |
H4' |
76.9 |
23.6 |
C4' |
C5' |
H5'2 |
H5'1 |
238.8 |
122.4 |
H5'2 |
C5' |
N1' |
HN1' |
258.7 |
321.3 |
C2 |
C7 |
H71 |
C4' |
123.0 |
240.0 |
H71 |
C7 |
C4' |
H4' |
60.0 |
184.3 |
C4' |
C7 |
H71 |
H72 |
118.5 |
239.9 |
C2 |
C7 |
H71 |
H72 |
241.5 |
120.0 |
C2 |
C7 |
H72 |
C4' |
238.0 |
119.9 |
H72 |
C7 |
C4' |
H4' |
181.6 |
64.2 |
C4' |
C7 |
H72 |
H71 |
241.0 |
120.1 |
C2 |
C7 |
H72 |
H71 |
119.0 |
240.0 |
C3' |
N8 |
HN8 |
C9 |
233.8 |
236.0 |
HN8 |
N8 |
C3' |
H3' |
154.3 |
159.6 |
HN8 |
N8 |
C9 |
C10 |
55.9 |
56.1 |
HN8 |
N8 |
C9 |
H91 |
175.9 |
176.1 |
HN8 |
N8 |
C9 |
H92 |
296.4 |
296.0 |
N8 |
C9 |
H91 |
C10 |
238.9 |
240.0 |
H91 |
C9 |
N8 |
HN8 |
175.9 |
176.1 |
N8 |
C9 |
H91 |
H92 |
119.5 |
120.0 |
C10 |
C9 |
H91 |
H92 |
240.5 |
240.0 |
H91 |
C9 |
C10 |
H101 |
183.8 |
180.0 |
H91 |
C9 |
C10 |
H102 |
64.4 |
300.0 |
N8 |
C9 |
H92 |
C10 |
120.7 |
120.0 |
H92 |
C9 |
N8 |
HN8 |
296.4 |
296.0 |
N8 |
C9 |
H92 |
H91 |
240.4 |
240.1 |
C10 |
C9 |
H92 |
H91 |
119.7 |
120.0 |
H92 |
C9 |
C10 |
H101 |
63.2 |
60.0 |
H92 |
C9 |
C10 |
H102 |
303.9 |
180.0 |
N11 |
C10 |
H101 |
H102 |
120.7 |
240.0 |
H101 |
C10 |
C9 |
H91 |
183.8 |
180.0 |
H101 |
C10 |
C9 |
H92 |
63.2 |
60.0 |
C9 |
C10 |
H101 |
H102 |
239.3 |
120.0 |
N11 |
C10 |
H102 |
H101 |
239.5 |
120.1 |
H102 |
C10 |
C9 |
H91 |
64.4 |
300.0 |
H102 |
C10 |
C9 |
H92 |
303.9 |
180.0 |
C9 |
C10 |
H102 |
H101 |
120.4 |
240.0 |
H111 |
N11 |
C10 |
H101 |
315.8 |
60.1 |
H111 |
N11 |
C10 |
H102 |
75.2 |
300.0 |
H112 |
N11 |
C10 |
H101 |
75.8 |
184.0 |
H112 |
N11 |
C10 |
H102 |
195.2 |
63.9 |