PDB Chemical Component JI4
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 JI4
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C1 |
1.460 |
1.469 |
| C2 |
C1 |
1.528 |
1.530 |
| C1 |
H1 |
1.100 |
1.090 |
| C1 |
H1A |
1.099 |
1.090 |
| N1 |
C3' |
1.460 |
1.469 |
| N1 |
HN1 |
0.999 |
1.009 |
| N2 |
C2 |
1.457 |
1.469 |
| C2 |
H2 |
1.100 |
1.090 |
| C2 |
H2A |
1.100 |
1.089 |
| C3 |
N2 |
1.459 |
1.469 |
| N2 |
HN2 |
1.000 |
1.009 |
| C4 |
C3 |
1.517 |
1.530 |
| C3 |
H3 |
1.100 |
1.089 |
| C3 |
H3A |
1.099 |
1.090 |
| C11 |
C4 |
1.510 |
1.507 |
| C4 |
H4 |
1.100 |
1.090 |
| C4 |
H4A |
1.100 |
1.090 |
| C2' |
N1' |
1.445 |
1.486 |
| N1' |
C5' |
1.452 |
1.486 |
| N1' |
HN1' |
0.999 |
1.009 |
| C12 |
C11 |
1.397 |
1.382 |
| C16 |
C11 |
1.397 |
1.383 |
| C13 |
C12 |
1.395 |
1.385 |
| C12 |
H12 |
1.080 |
1.080 |
| F13 |
C13 |
1.342 |
1.351 |
| C14 |
C13 |
1.400 |
1.385 |
| C14 |
C15 |
1.392 |
1.381 |
| C14 |
H14 |
1.080 |
1.080 |
| C15 |
C16 |
1.397 |
1.382 |
| C15 |
H15 |
1.080 |
1.080 |
| C16 |
H16 |
1.080 |
1.080 |
| N11 |
C21 |
1.354 |
1.320 |
| N11 |
C61 |
1.362 |
1.324 |
| C2' |
C3' |
1.536 |
1.544 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| C71 |
C21 |
1.531 |
1.506 |
| C21 |
C31 |
1.390 |
1.380 |
| C3' |
C4' |
1.546 |
1.543 |
| C3' |
H3' |
1.100 |
1.090 |
| C31 |
C41 |
1.394 |
1.389 |
| C31 |
H31 |
1.080 |
1.080 |
| C71 |
C4' |
1.533 |
1.531 |
| C4' |
C5' |
1.537 |
1.543 |
| C4' |
H4' |
1.100 |
1.090 |
| C51 |
C41 |
1.400 |
1.384 |
| C41 |
C81 |
1.511 |
1.507 |
| C5' |
H5' |
1.099 |
1.089 |
| C5' |
H5'A |
1.100 |
1.090 |
| C61 |
C51 |
1.400 |
1.391 |
| C51 |
H51 |
1.080 |
1.079 |
| N61 |
C61 |
1.354 |
1.390 |
| N61 |
HN61 |
1.000 |
0.969 |
| N61 |
HN6A |
1.000 |
0.970 |
| C71 |
H71 |
1.100 |
1.090 |
| C71 |
H71A |
1.100 |
1.090 |
| C81 |
H81 |
1.100 |
1.090 |
| C81 |
H81A |
1.100 |
1.090 |
| C81 |
H81B |
1.100 |
1.090 |
Bond Angles for JI4
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N1 |
C1 |
H1 |
108.9 |
109.4 |
| N1 |
C1 |
H1A |
109.0 |
109.5 |
| C2 |
C1 |
H1 |
108.9 |
109.4 |
| C2 |
C1 |
H1A |
108.9 |
109.5 |
| H1 |
C1 |
H1A |
110.0 |
109.4 |
| C3' |
N1 |
HN1 |
105.6 |
111.0 |
| N1 |
C3' |
C2' |
110.0 |
110.3 |
| N1 |
C3' |
C4' |
116.6 |
110.3 |
| N1 |
C3' |
H3' |
102.6 |
110.3 |
| N2 |
C2 |
H2 |
108.1 |
109.4 |
| N2 |
C2 |
H2A |
108.1 |
109.5 |
| H2 |
C2 |
H2A |
110.8 |
109.4 |
| C3 |
N2 |
HN2 |
106.6 |
111.0 |
| C4 |
C3 |
H3 |
108.9 |
109.5 |
| C4 |
C3 |
H3A |
108.8 |
109.5 |
| H3 |
C3 |
H3A |
110.1 |
109.5 |
| C11 |
C4 |
H4 |
108.7 |
109.4 |
| C11 |
C4 |
H4A |
108.7 |
109.5 |
| H4 |
C4 |
H4A |
110.2 |
109.5 |
| C2' |
N1' |
C5' |
112.8 |
104.2 |
| C2' |
N1' |
HN1' |
108.4 |
110.9 |
| C5' |
N1' |
HN1' |
108.4 |
111.1 |
| N1' |
C5' |
C4' |
104.0 |
104.6 |
| N1' |
C5' |
H5' |
111.3 |
110.4 |
| N1' |
C5' |
H5'A |
111.3 |
110.4 |
| C13 |
C12 |
H12 |
120.5 |
120.0 |
| C15 |
C14 |
H14 |
120.1 |
120.0 |
| C14 |
C15 |
C16 |
119.7 |
120.0 |
| C14 |
C15 |
H15 |
120.2 |
120.0 |
| C16 |
C15 |
H15 |
120.2 |
120.0 |
| C15 |
C16 |
H16 |
119.9 |
120.0 |
| C21 |
N11 |
C61 |
122.4 |
121.6 |
| N11 |
C21 |
C31 |
119.2 |
120.9 |
| N11 |
C61 |
C51 |
120.3 |
120.6 |
| C3' |
C2' |
H2' |
111.4 |
110.4 |
| C3' |
C2' |
H2'A |
111.5 |
110.4 |
| C2' |
C3' |
C4' |
104.3 |
105.0 |
| C2' |
C3' |
H3' |
115.3 |
110.3 |
| H2' |
C2' |
H2'A |
107.4 |
110.5 |
| C21 |
C31 |
C41 |
119.8 |
119.3 |
| C21 |
C31 |
H31 |
120.1 |
120.3 |
| C4' |
C3' |
H3' |
108.5 |
110.4 |
| C3' |
C4' |
C5' |
100.9 |
105.1 |
| C3' |
C4' |
H4' |
114.7 |
110.3 |
| C41 |
C31 |
H31 |
120.1 |
120.3 |
| C31 |
C41 |
C81 |
118.6 |
120.8 |
| C71 |
C4' |
H4' |
102.6 |
110.4 |
| C5' |
C4' |
H4' |
113.6 |
110.4 |
| C4' |
C5' |
H5' |
111.3 |
110.4 |
| C4' |
C5' |
H5'A |
111.4 |
110.4 |
| C51 |
C41 |
C81 |
120.9 |
120.7 |
| C41 |
C81 |
H81 |
109.5 |
109.4 |
| C41 |
C81 |
H81A |
109.5 |
109.5 |
| C41 |
C81 |
H81B |
109.4 |
109.4 |
| H5' |
C5' |
H5'A |
107.5 |
110.5 |
| C61 |
C51 |
H51 |
121.1 |
120.5 |
| HN61 |
N61 |
HN6A |
109.4 |
120.0 |
| H71 |
C71 |
H71A |
110.8 |
109.4 |
| H81 |
C81 |
H81A |
109.4 |
109.5 |
| H81 |
C81 |
H81B |
109.5 |
109.5 |
| H81A |
C81 |
H81B |
109.5 |
109.5 |
Torsion Angles for JI4
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C1 |
N1 |
H1 |
240.0 |
240.0 |
| C2 |
C1 |
N1 |
H1A |
120.0 |
120.1 |
| H1 |
C1 |
N1 |
H1A |
240.0 |
240.0 |
| N1 |
C1 |
C2 |
H1 |
120.0 |
120.0 |
| N1 |
C1 |
C2 |
H1A |
240.0 |
239.9 |
| H1 |
C1 |
C2 |
H1A |
120.0 |
120.0 |
| N1 |
C1 |
H1 |
H1A |
119.4 |
120.0 |
| C2 |
C1 |
H1 |
H1A |
240.7 |
240.0 |
| N1 |
C1 |
H1A |
H1 |
240.6 |
240.0 |
| C2 |
C1 |
H1A |
H1 |
119.3 |
120.0 |
| C3' |
N1 |
C1 |
H1 |
238.0 |
300.0 |
| C3' |
N1 |
C1 |
H1A |
358.0 |
59.9 |
| N1 |
C3' |
C2' |
H2' |
87.6 |
98.5 |
| N1 |
C3' |
C2' |
H2'A |
327.6 |
336.1 |
| C2' |
C3' |
N1 |
C4' |
118.4 |
115.6 |
| C2' |
C3' |
N1 |
H3' |
236.8 |
237.8 |
| C4' |
C3' |
N1 |
H3' |
118.4 |
122.2 |
| N1 |
C3' |
C4' |
C5' |
158.6 |
118.9 |
| N1 |
C3' |
C4' |
H4' |
281.1 |
237.8 |
| HN1 |
N1 |
C1 |
H1 |
358.0 |
64.0 |
| HN1 |
N1 |
C1 |
H1A |
118.0 |
183.9 |
| HN1 |
N1 |
C3' |
C2' |
59.9 |
161.0 |
| HN1 |
N1 |
C3' |
C4' |
301.4 |
45.4 |
| HN1 |
N1 |
C3' |
H3' |
183.1 |
283.2 |
| N2 |
C2 |
C1 |
H1 |
299.2 |
60.0 |
| N2 |
C2 |
C1 |
H1A |
179.2 |
300.1 |
| H2 |
C2 |
N2 |
H2A |
120.0 |
120.0 |
| H2 |
C2 |
C1 |
H1 |
59.2 |
180.0 |
| H2 |
C2 |
C1 |
H1A |
299.2 |
60.0 |
| N2 |
C2 |
H2 |
H2A |
241.8 |
240.0 |
| H2A |
C2 |
C1 |
H1 |
179.2 |
300.0 |
| H2A |
C2 |
C1 |
H1A |
59.2 |
180.0 |
| N2 |
C2 |
H2A |
H2 |
118.2 |
120.0 |
| C3 |
N2 |
C2 |
H2 |
30.9 |
60.0 |
| C3 |
N2 |
C2 |
H2A |
270.9 |
300.0 |
| HN2 |
N2 |
C2 |
H2 |
150.9 |
184.0 |
| HN2 |
N2 |
C2 |
H2A |
30.9 |
64.0 |
| C4 |
C3 |
N2 |
HN2 |
50.2 |
56.0 |
| H3 |
C3 |
C4 |
H3A |
120.0 |
120.1 |
| H3 |
C3 |
N2 |
HN2 |
170.3 |
176.1 |
| C4 |
C3 |
H3 |
H3A |
240.8 |
239.9 |
| H3A |
C3 |
N2 |
HN2 |
290.3 |
296.0 |
| C4 |
C3 |
H3A |
H3 |
119.3 |
120.1 |
| C11 |
C4 |
C3 |
H3 |
58.3 |
60.0 |
| C11 |
C4 |
C3 |
H3A |
298.3 |
300.0 |
| H4 |
C4 |
C11 |
H4A |
120.0 |
120.1 |
| H4 |
C4 |
C3 |
H3 |
178.3 |
180.0 |
| H4 |
C4 |
C3 |
H3A |
58.3 |
59.9 |
| C11 |
C4 |
H4 |
H4A |
241.0 |
239.9 |
| H4A |
C4 |
C3 |
H3 |
298.3 |
300.0 |
| H4A |
C4 |
C3 |
H3A |
178.3 |
180.0 |
| C11 |
C4 |
H4A |
H4 |
119.0 |
120.0 |
| N1 |
C3' |
C2' |
N1' |
207.7 |
217.3 |
| C5' |
N1' |
C2' |
HN1' |
240.0 |
240.4 |
| C2' |
N1' |
C5' |
C4' |
18.8 |
320.5 |
| C2' |
N1' |
C5' |
H5' |
138.8 |
79.3 |
| C2' |
N1' |
C5' |
H5'A |
258.8 |
201.8 |
| C2' |
N1' |
C5' |
HN1' |
120.0 |
119.5 |
| C3' |
C4' |
C5' |
N1' |
326.2 |
23.9 |
| N1' |
C5' |
C4' |
H4' |
203.0 |
265.0 |
| C4' |
C5' |
N1' |
H5' |
240.0 |
241.2 |
| C4' |
C5' |
N1' |
H5'A |
120.0 |
118.7 |
| H5' |
C5' |
N1' |
H5'A |
240.0 |
237.5 |
| C2' |
N1' |
HN1' |
C5' |
237.3 |
244.5 |
| HN1' |
N1' |
C5' |
C4' |
258.8 |
201.0 |
| HN1' |
N1' |
C5' |
H5' |
18.8 |
319.7 |
| HN1' |
N1' |
C5' |
H5'A |
138.8 |
82.2 |
| C12 |
C11 |
C4 |
H4 |
159.0 |
330.1 |
| C12 |
C11 |
C4 |
H4A |
39.0 |
210.0 |
| C16 |
C11 |
C4 |
H4 |
340.3 |
149.8 |
| C16 |
C11 |
C4 |
H4A |
220.3 |
29.7 |
| F13 |
C13 |
C12 |
H12 |
0.5 |
0.1 |
| C14 |
C13 |
C12 |
H12 |
180.3 |
180.0 |
| C16 |
C15 |
C14 |
H15 |
180.0 |
179.8 |
| C14 |
C15 |
C16 |
H16 |
179.9 |
180.0 |
| H14 |
C14 |
C15 |
C16 |
179.8 |
179.7 |
| H14 |
C14 |
C15 |
H15 |
359.8 |
360.0 |
| C16 |
C15 |
C14 |
H14 |
179.8 |
179.7 |
| C14 |
C15 |
C16 |
H15 |
180.0 |
180.2 |
| H15 |
C15 |
C14 |
H14 |
359.8 |
360.0 |
| C14 |
C15 |
H15 |
C16 |
180.0 |
179.8 |
| H15 |
C15 |
C16 |
H16 |
359.9 |
359.7 |
| H16 |
C16 |
C15 |
H15 |
359.9 |
359.7 |
| C21 |
N11 |
C61 |
C51 |
358.8 |
360.0 |
| N11 |
C21 |
C31 |
C41 |
0.5 |
359.9 |
| N11 |
C21 |
C31 |
H31 |
180.5 |
179.9 |
| C61 |
N11 |
C21 |
C31 |
0.2 |
0.1 |
| N11 |
C61 |
C51 |
H51 |
181.5 |
180.0 |
| C2' |
C3' |
N1 |
HN1 |
59.9 |
161.0 |
| N1 |
C3' |
C2' |
C4' |
234.2 |
241.1 |
| N1 |
C3' |
C2' |
H3' |
115.4 |
122.1 |
| C3' |
C2' |
N1' |
C5' |
4.9 |
39.5 |
| C3' |
C2' |
N1' |
HN1' |
124.9 |
159.1 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.4 |
| C4' |
C3' |
C2' |
H3' |
241.2 |
241.0 |
| C2' |
C3' |
C4' |
C5' |
37.1 |
360.0 |
| C2' |
C3' |
C4' |
H4' |
159.6 |
118.9 |
| H2' |
C2' |
N1' |
C5' |
124.9 |
158.2 |
| H2' |
C2' |
N1' |
HN1' |
244.9 |
277.9 |
| C3' |
C2' |
H2' |
H2'A |
237.6 |
237.6 |
| H2' |
C2' |
C3' |
C4' |
213.4 |
217.4 |
| H2' |
C2' |
C3' |
H3' |
332.2 |
336.3 |
| H2'A |
C2' |
N1' |
C5' |
244.9 |
280.7 |
| H2'A |
C2' |
N1' |
HN1' |
4.9 |
40.4 |
| C3' |
C2' |
H2'A |
H2' |
122.4 |
122.4 |
| H2'A |
C2' |
C3' |
C4' |
93.4 |
94.9 |
| H2'A |
C2' |
C3' |
H3' |
212.2 |
213.9 |
| C71 |
C21 |
C31 |
H31 |
1.4 |
360.0 |
| C31 |
C21 |
N11 |
C61 |
0.2 |
0.1 |
| C41 |
C31 |
C21 |
H31 |
180.0 |
180.0 |
| C21 |
C31 |
C41 |
C81 |
179.2 |
180.0 |
| C4' |
C3' |
N1 |
HN1 |
301.4 |
45.4 |
| N1 |
C3' |
C4' |
C2' |
121.5 |
118.9 |
| N1 |
C3' |
C4' |
H3' |
244.9 |
237.8 |
| N1' |
C5' |
C4' |
C3' |
326.2 |
23.9 |
| C4' |
C3' |
C2' |
H2' |
213.4 |
217.4 |
| C4' |
C3' |
C2' |
H2'A |
93.4 |
94.9 |
| C2' |
C3' |
C4' |
H3' |
123.3 |
118.9 |
| C71 |
C4' |
C3' |
H4' |
116.6 |
122.2 |
| C5' |
C4' |
C3' |
H4' |
237.5 |
241.1 |
| C3' |
C4' |
C5' |
H5' |
206.2 |
265.1 |
| C3' |
C4' |
C5' |
H5'A |
86.2 |
142.6 |
| H3' |
C3' |
N1 |
HN1 |
183.1 |
283.2 |
| N1 |
C3' |
H3' |
C2' |
240.4 |
237.8 |
| N1 |
C3' |
H3' |
C4' |
124.0 |
122.2 |
| H3' |
C3' |
C2' |
H2' |
332.2 |
336.3 |
| H3' |
C3' |
C2' |
H2'A |
212.2 |
213.9 |
| C2' |
C3' |
H3' |
C4' |
243.6 |
244.3 |
| H3' |
C3' |
C4' |
C5' |
273.8 |
241.0 |
| H3' |
C3' |
C4' |
H4' |
36.3 |
360.0 |
| C21 |
C31 |
C41 |
H31 |
180.0 |
180.0 |
| C51 |
C41 |
C31 |
C81 |
180.7 |
180.0 |
| C31 |
C41 |
C81 |
H81 |
90.4 |
90.0 |
| C31 |
C41 |
C81 |
H81A |
210.3 |
210.0 |
| C31 |
C41 |
C81 |
H81B |
330.3 |
330.0 |
| C21 |
C31 |
H31 |
C41 |
180.0 |
180.0 |
| H31 |
C31 |
C41 |
C81 |
359.2 |
0.0 |
| C71 |
C4' |
C3' |
H3' |
152.9 |
122.2 |
| C3' |
C4' |
C71 |
H4' |
236.4 |
237.8 |
| C5' |
C4' |
C71 |
H4' |
122.9 |
122.2 |
| C71 |
C4' |
C5' |
H5' |
326.3 |
24.0 |
| C71 |
C4' |
C5' |
H5'A |
206.3 |
261.5 |
| C4' |
C5' |
N1' |
HN1' |
258.8 |
201.0 |
| N1' |
C5' |
C4' |
H5' |
120.0 |
118.8 |
| N1' |
C5' |
C4' |
H5'A |
240.0 |
241.3 |
| C5' |
C4' |
C3' |
H3' |
273.8 |
241.0 |
| C3' |
C4' |
C5' |
H4' |
123.2 |
118.9 |
| C71 |
C4' |
C5' |
H4' |
243.4 |
237.8 |
| H5' |
C5' |
C4' |
H5'A |
120.0 |
122.5 |
| H4' |
C4' |
C3' |
H3' |
36.3 |
360.0 |
| C3' |
C4' |
H4' |
C5' |
244.6 |
244.3 |
| H4' |
C4' |
C5' |
H5' |
83.0 |
146.2 |
| H4' |
C4' |
C5' |
H5'A |
323.0 |
23.7 |
| N11 |
C61 |
C51 |
C41 |
1.5 |
359.9 |
| C51 |
C41 |
C31 |
H31 |
179.9 |
180.0 |
| C31 |
C41 |
C51 |
C81 |
179.3 |
180.0 |
| C51 |
C41 |
C81 |
H81 |
269.7 |
270.0 |
| C51 |
C41 |
C81 |
H81A |
29.6 |
30.0 |
| C51 |
C41 |
C81 |
H81B |
149.6 |
150.0 |
| C81 |
C41 |
C31 |
H31 |
359.2 |
0.0 |
| H81 |
C81 |
C41 |
H81A |
240.0 |
240.0 |
| H81 |
C81 |
C41 |
H81B |
120.0 |
120.0 |
| H81A |
C81 |
C41 |
H81B |
240.0 |
240.0 |
| H5' |
C5' |
N1' |
HN1' |
18.8 |
319.7 |
| N1' |
C5' |
H5' |
C4' |
244.4 |
244.8 |
| N1' |
C5' |
H5' |
H5'A |
122.2 |
122.4 |
| H5' |
C5' |
C4' |
H4' |
83.0 |
146.2 |
| C4' |
C5' |
H5' |
H5'A |
237.8 |
237.6 |
| H5'A |
C5' |
N1' |
HN1' |
138.8 |
82.2 |
| N1' |
C5' |
H5'A |
C4' |
115.6 |
115.1 |
| N1' |
C5' |
H5'A |
H5' |
237.8 |
237.6 |
| H5'A |
C5' |
C4' |
H4' |
323.0 |
23.7 |
| C4' |
C5' |
H5'A |
H5' |
122.2 |
122.5 |
| C61 |
C51 |
C41 |
C81 |
179.9 |
180.1 |
| H51 |
C51 |
C41 |
C81 |
359.9 |
360.0 |
| N61 |
C61 |
C51 |
H51 |
0.3 |
0.1 |
| H71 |
C71 |
C4' |
H4' |
175.4 |
186.4 |
| H71A |
C71 |
C4' |
H4' |
55.4 |
66.4 |
| C41 |
C81 |
H81 |
H81A |
120.0 |
120.0 |
| C41 |
C81 |
H81 |
H81B |
240.0 |
240.1 |
| H81A |
C81 |
H81 |
H81B |
120.0 |
120.1 |
| C41 |
C81 |
H81A |
H81 |
240.0 |
240.0 |
| C41 |
C81 |
H81A |
H81B |
120.0 |
120.0 |
| H81 |
C81 |
H81A |
H81B |
240.0 |
239.9 |
| C41 |
C81 |
H81B |
H81 |
120.0 |
119.9 |
| C41 |
C81 |
H81B |
H81A |
240.0 |
240.0 |
| H81 |
C81 |
H81B |
H81A |
120.0 |
120.1 |