PDB Chemical Component JRR
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 JRR
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2 |
C1 |
1.520 |
1.530 |
| C1 |
O1 |
1.432 |
1.429 |
| C1 |
H1 |
1.100 |
1.090 |
| C1 |
H1A |
1.100 |
1.090 |
| O1 |
C3' |
1.438 |
1.429 |
| C2 |
N2 |
1.451 |
1.469 |
| C2 |
H2 |
1.100 |
1.090 |
| C2 |
H2A |
1.100 |
1.090 |
| C3 |
N2 |
1.449 |
1.469 |
| N2 |
HN2 |
1.000 |
1.009 |
| C3 |
C4 |
1.524 |
1.530 |
| C3 |
H3 |
1.100 |
1.090 |
| C3 |
H3A |
1.100 |
1.091 |
| C11 |
C4 |
1.509 |
1.507 |
| C4 |
H4 |
1.100 |
1.090 |
| C4 |
H4A |
1.100 |
1.090 |
| C2' |
N1' |
1.450 |
1.486 |
| C5' |
N1' |
1.471 |
1.485 |
| N1' |
HN1' |
1.000 |
1.009 |
| C12 |
C11 |
1.392 |
1.382 |
| C11 |
C16 |
1.408 |
1.383 |
| C13 |
C12 |
1.391 |
1.385 |
| C12 |
H12 |
1.080 |
1.080 |
| F13 |
C13 |
1.349 |
1.351 |
| C13 |
C14 |
1.407 |
1.384 |
| C14 |
C15 |
1.405 |
1.383 |
| C14 |
H14 |
1.080 |
1.079 |
| C15 |
C16 |
1.396 |
1.382 |
| C15 |
H15 |
1.080 |
1.080 |
| C16 |
H16 |
1.080 |
1.079 |
| C2A |
N1A |
1.359 |
1.319 |
| N1A |
C6A |
1.362 |
1.325 |
| C3' |
C2' |
1.529 |
1.543 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| C7A |
C2A |
1.513 |
1.507 |
| C2A |
C3A |
1.398 |
1.382 |
| C3' |
C4' |
1.526 |
1.543 |
| C3' |
H3' |
1.100 |
1.090 |
| C3A |
C4A |
1.395 |
1.388 |
| C3A |
H3AA |
1.080 |
1.080 |
| C7A |
C4' |
1.532 |
1.530 |
| C4' |
C5' |
1.533 |
1.544 |
| C4' |
H4' |
1.100 |
1.090 |
| C4A |
C5A |
1.394 |
1.383 |
| C4A |
C8A |
1.510 |
1.507 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| C6A |
C5A |
1.401 |
1.391 |
| C5A |
H5A |
1.081 |
1.080 |
| N6A |
C6A |
1.361 |
1.390 |
| N6A |
HN6A |
1.000 |
0.970 |
| N6A |
HN6B |
1.000 |
0.970 |
| C7A |
H7A |
1.100 |
1.089 |
| C7A |
H7AA |
1.100 |
1.090 |
| C8A |
H8A |
1.100 |
1.090 |
| C8A |
H8AA |
1.100 |
1.090 |
| C8A |
H8AB |
1.100 |
1.090 |
Bond Angles for JRR
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C1 |
H1 |
109.5 |
109.5 |
| C2 |
C1 |
H1A |
109.5 |
109.5 |
| O1 |
C1 |
H1 |
109.5 |
109.5 |
| O1 |
C1 |
H1A |
109.5 |
109.5 |
| C1 |
O1 |
C3' |
113.6 |
114.0 |
| H1 |
C1 |
H1A |
109.4 |
109.5 |
| O1 |
C3' |
C2' |
110.5 |
110.3 |
| O1 |
C3' |
C4' |
108.0 |
110.3 |
| O1 |
C3' |
H3' |
108.2 |
110.3 |
| N2 |
C2 |
H2 |
108.2 |
109.5 |
| N2 |
C2 |
H2A |
108.2 |
109.5 |
| C2 |
N2 |
HN2 |
106.9 |
111.0 |
| H2 |
C2 |
H2A |
110.7 |
109.4 |
| C3 |
N2 |
HN2 |
106.9 |
111.0 |
| C4 |
C3 |
H3 |
108.8 |
109.5 |
| C4 |
C3 |
H3A |
108.8 |
109.5 |
| C3 |
C4 |
H4 |
109.2 |
109.5 |
| C3 |
C4 |
H4A |
109.2 |
109.4 |
| H3 |
C3 |
H3A |
110.1 |
109.5 |
| C11 |
C4 |
H4 |
109.2 |
109.4 |
| C11 |
C4 |
H4A |
109.2 |
109.5 |
| H4 |
C4 |
H4A |
109.7 |
109.5 |
| C2' |
N1' |
HN1' |
108.4 |
110.9 |
| C5' |
N1' |
HN1' |
108.4 |
111.0 |
| C12 |
C11 |
C16 |
120.4 |
120.1 |
| C11 |
C16 |
C15 |
119.5 |
120.0 |
| C11 |
C16 |
H16 |
120.3 |
120.0 |
| C13 |
C12 |
H12 |
119.8 |
120.1 |
| F13 |
C13 |
C14 |
121.9 |
120.0 |
| C13 |
C14 |
C15 |
119.9 |
119.9 |
| C13 |
C14 |
H14 |
120.0 |
120.0 |
| C15 |
C14 |
H14 |
120.0 |
120.1 |
| C14 |
C15 |
C16 |
120.1 |
120.1 |
| C14 |
C15 |
H15 |
120.0 |
119.9 |
| C16 |
C15 |
H15 |
120.0 |
120.0 |
| C15 |
C16 |
H16 |
120.3 |
120.0 |
| C2A |
N1A |
C6A |
121.7 |
121.6 |
| N1A |
C6A |
C5A |
119.6 |
120.6 |
| C3' |
C2' |
H2' |
111.5 |
110.4 |
| C3' |
C2' |
H2'A |
111.5 |
110.5 |
| H2' |
C2' |
H2'A |
107.3 |
110.3 |
| C2A |
C3A |
C4A |
119.0 |
119.3 |
| C2A |
C3A |
H3AA |
120.5 |
120.3 |
| C4' |
C3' |
H3' |
114.2 |
110.5 |
| C3' |
C4' |
C5' |
104.1 |
105.0 |
| C3' |
C4' |
H4' |
111.6 |
110.3 |
| C4A |
C3A |
H3AA |
120.5 |
120.4 |
| C3A |
C4A |
C5A |
119.9 |
118.6 |
| C3A |
C4A |
C8A |
119.6 |
120.7 |
| C7A |
C4' |
H4' |
102.3 |
110.3 |
| C5' |
C4' |
H4' |
112.4 |
110.4 |
| C4' |
C5' |
H5' |
111.3 |
110.4 |
| C4' |
C5' |
H5'A |
111.4 |
110.4 |
| C5A |
C4A |
C8A |
120.5 |
120.7 |
| C4A |
C5A |
H5A |
120.2 |
120.5 |
| C4A |
C8A |
H8A |
109.5 |
109.5 |
| C4A |
C8A |
H8AA |
109.5 |
109.5 |
| C4A |
C8A |
H8AB |
109.4 |
109.5 |
| H5' |
C5' |
H5'A |
107.5 |
110.4 |
| C6A |
C5A |
H5A |
120.3 |
120.4 |
| HN6A |
N6A |
HN6B |
109.4 |
120.0 |
| H7A |
C7A |
H7AA |
109.3 |
109.5 |
| H8A |
C8A |
H8AA |
109.4 |
109.4 |
| H8A |
C8A |
H8AB |
109.5 |
109.5 |
| H8AA |
C8A |
H8AB |
109.5 |
109.4 |
Torsion Angles for JRR
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1 |
C1 |
C2 |
H1 |
240.0 |
120.0 |
| O1 |
C1 |
C2 |
H1A |
120.0 |
240.0 |
| C2 |
C1 |
O1 |
C3' |
177.1 |
180.0 |
| H1 |
C1 |
C2 |
H1A |
240.0 |
120.0 |
| C2 |
C1 |
O1 |
H1 |
120.0 |
240.0 |
| C2 |
C1 |
O1 |
H1A |
240.0 |
120.0 |
| H1 |
C1 |
O1 |
H1A |
120.0 |
240.0 |
| C1 |
O1 |
C3' |
C2' |
74.8 |
91.5 |
| C1 |
O1 |
C3' |
C4' |
188.1 |
207.1 |
| C1 |
O1 |
C3' |
H3' |
312.2 |
329.4 |
| C2 |
C1 |
H1 |
H1A |
120.1 |
240.0 |
| O1 |
C1 |
H1 |
H1A |
240.0 |
120.0 |
| H1 |
C1 |
O1 |
C3' |
57.1 |
300.0 |
| C2 |
C1 |
H1A |
H1 |
239.9 |
120.0 |
| O1 |
C1 |
H1A |
H1 |
120.0 |
240.0 |
| H1A |
C1 |
O1 |
C3' |
297.1 |
60.0 |
| C3' |
O1 |
C1 |
H1 |
57.1 |
300.0 |
| C3' |
O1 |
C1 |
H1A |
297.1 |
60.0 |
| O1 |
C3' |
C2' |
H2' |
325.3 |
23.9 |
| O1 |
C3' |
C2' |
H2'A |
205.3 |
261.6 |
| C4' |
C3' |
O1 |
H3' |
236.0 |
237.7 |
| O1 |
C3' |
C4' |
C5' |
276.6 |
241.1 |
| O1 |
C3' |
C4' |
H4' |
155.2 |
122.2 |
| N2 |
C2 |
C1 |
H1 |
181.9 |
305.0 |
| N2 |
C2 |
C1 |
H1A |
302.0 |
185.0 |
| H2 |
C2 |
N2 |
H2A |
120.0 |
120.0 |
| C3 |
N2 |
C2 |
HN2 |
240.0 |
236.0 |
| H2 |
C2 |
C1 |
H1 |
301.9 |
65.0 |
| H2 |
C2 |
C1 |
H1A |
62.0 |
305.0 |
| N2 |
C2 |
H2 |
H2A |
241.6 |
240.0 |
| H2 |
C2 |
N2 |
HN2 |
148.0 |
184.0 |
| H2A |
C2 |
C1 |
H1 |
61.9 |
185.0 |
| H2A |
C2 |
C1 |
H1A |
182.0 |
65.0 |
| N2 |
C2 |
H2A |
H2 |
118.4 |
120.0 |
| H2A |
C2 |
N2 |
HN2 |
28.0 |
64.0 |
| C3 |
N2 |
C2 |
H2 |
28.0 |
60.0 |
| C3 |
N2 |
C2 |
H2A |
268.0 |
300.0 |
| C2 |
N2 |
C3 |
HN2 |
120.0 |
124.0 |
| HN2 |
N2 |
C2 |
H2 |
148.0 |
184.0 |
| HN2 |
N2 |
C2 |
H2A |
28.0 |
64.0 |
| C4 |
C3 |
N2 |
HN2 |
37.7 |
55.9 |
| H3 |
C3 |
C4 |
H3A |
120.0 |
120.0 |
| C11 |
C4 |
C3 |
H4 |
240.0 |
240.0 |
| C11 |
C4 |
C3 |
H4A |
120.0 |
120.0 |
| H4 |
C4 |
C3 |
H4A |
240.0 |
240.0 |
| H3 |
C3 |
N2 |
HN2 |
157.7 |
176.0 |
| C4 |
C3 |
H3 |
H3A |
240.8 |
239.9 |
| H3 |
C3 |
C4 |
H4 |
181.5 |
180.0 |
| H3 |
C3 |
C4 |
H4A |
301.5 |
300.0 |
| H3A |
C3 |
N2 |
HN2 |
277.8 |
295.9 |
| C4 |
C3 |
H3A |
H3 |
119.2 |
120.1 |
| H3A |
C3 |
C4 |
H4 |
61.5 |
60.0 |
| H3A |
C3 |
C4 |
H4A |
181.5 |
180.0 |
| C11 |
C4 |
C3 |
H3 |
61.5 |
60.0 |
| C11 |
C4 |
C3 |
H3A |
301.5 |
300.0 |
| C3 |
C4 |
C11 |
H4 |
120.0 |
120.0 |
| C3 |
C4 |
C11 |
H4A |
240.0 |
240.0 |
| H4 |
C4 |
C11 |
H4A |
120.0 |
120.0 |
| H4 |
C4 |
C3 |
H3 |
181.5 |
180.0 |
| H4 |
C4 |
C3 |
H3A |
61.5 |
60.0 |
| C3 |
C4 |
H4 |
H4A |
119.7 |
120.0 |
| C11 |
C4 |
H4 |
H4A |
240.3 |
240.0 |
| H4A |
C4 |
C3 |
H3 |
301.5 |
300.0 |
| H4A |
C4 |
C3 |
H3A |
181.5 |
180.0 |
| C3 |
C4 |
H4A |
H4 |
240.3 |
240.0 |
| C11 |
C4 |
H4A |
H4 |
119.7 |
120.0 |
| O1 |
C3' |
C2' |
N1' |
85.3 |
142.8 |
| C5' |
N1' |
C2' |
HN1' |
240.0 |
240.5 |
| C2' |
N1' |
C5' |
HN1' |
120.0 |
119.5 |
| C12 |
C11 |
C4 |
H4 |
341.5 |
150.3 |
| C12 |
C11 |
C4 |
H4A |
221.5 |
30.3 |
| C12 |
C11 |
C16 |
C15 |
359.6 |
359.4 |
| C12 |
C11 |
C16 |
H16 |
179.6 |
179.7 |
| C16 |
C11 |
C4 |
H4 |
161.0 |
329.9 |
| C16 |
C11 |
C4 |
H4A |
41.0 |
209.9 |
| C14 |
C15 |
C16 |
C11 |
0.4 |
0.6 |
| C11 |
C16 |
C15 |
H15 |
180.3 |
180.3 |
| C15 |
C16 |
C11 |
H16 |
180.0 |
179.7 |
| C13 |
C12 |
C11 |
C16 |
0.3 |
0.3 |
| H12 |
C12 |
C11 |
C16 |
180.3 |
180.2 |
| F13 |
C13 |
C12 |
H12 |
359.8 |
0.0 |
| F13 |
C13 |
C14 |
C15 |
180.2 |
180.0 |
| F13 |
C13 |
C14 |
H14 |
0.2 |
360.0 |
| C14 |
C13 |
C12 |
H12 |
179.8 |
180.0 |
| C15 |
C14 |
C13 |
H14 |
180.0 |
180.0 |
| C13 |
C14 |
C15 |
C16 |
359.7 |
359.7 |
| C13 |
C14 |
C15 |
H15 |
179.7 |
180.0 |
| C11 |
C16 |
C15 |
C14 |
0.4 |
0.6 |
| C13 |
C14 |
C15 |
H14 |
180.0 |
180.0 |
| C16 |
C15 |
C14 |
H15 |
180.0 |
179.7 |
| C14 |
C15 |
C16 |
H16 |
180.4 |
180.3 |
| C13 |
C14 |
H14 |
C15 |
180.0 |
180.0 |
| H14 |
C14 |
C15 |
C16 |
179.7 |
179.7 |
| H14 |
C14 |
C15 |
H15 |
359.7 |
0.0 |
| C11 |
C16 |
C15 |
H16 |
180.0 |
180.3 |
| C16 |
C15 |
C14 |
H14 |
179.7 |
179.7 |
| C14 |
C15 |
C16 |
H15 |
180.0 |
180.3 |
| H15 |
C15 |
C14 |
H14 |
359.7 |
0.0 |
| C14 |
C15 |
H15 |
C16 |
180.0 |
179.7 |
| H15 |
C15 |
C16 |
H16 |
0.4 |
0.0 |
| C11 |
C16 |
H16 |
C15 |
180.0 |
179.7 |
| H16 |
C16 |
C15 |
H15 |
0.4 |
0.0 |
| C2A |
N1A |
C6A |
C5A |
0.9 |
0.0 |
| N1A |
C6A |
C5A |
H5A |
179.1 |
180.1 |
| O1 |
C3' |
C2' |
C4' |
115.7 |
118.9 |
| O1 |
C3' |
C2' |
H3' |
239.4 |
237.9 |
| C3' |
C2' |
N1' |
HN1' |
135.6 |
80.0 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.3 |
| H2' |
C2' |
N1' |
HN1' |
255.6 |
198.9 |
| C3' |
C2' |
H2' |
H2'A |
237.6 |
237.6 |
| H2'A |
C2' |
N1' |
HN1' |
15.6 |
321.1 |
| C3' |
C2' |
H2'A |
H2' |
122.4 |
122.4 |
| C7A |
C2A |
C3A |
H3AA |
359.4 |
359.9 |
| C3A |
C2A |
N1A |
C6A |
359.1 |
360.0 |
| C4A |
C3A |
C2A |
H3AA |
180.0 |
180.0 |
| C2A |
C3A |
C4A |
C5A |
359.2 |
360.0 |
| C2A |
C3A |
C4A |
C8A |
179.5 |
180.0 |
| O1 |
C3' |
C4' |
C2' |
242.5 |
241.1 |
| O1 |
C3' |
C4' |
H3' |
120.4 |
122.2 |
| C4' |
C3' |
C2' |
H2' |
209.6 |
265.0 |
| C4' |
C3' |
C2' |
H2'A |
89.6 |
142.7 |
| C7A |
C4' |
C3' |
H4' |
244.8 |
237.9 |
| C5' |
C4' |
C3' |
H4' |
121.4 |
118.9 |
| C3' |
C4' |
C5' |
H5' |
215.6 |
217.4 |
| C3' |
C4' |
C5' |
H5'A |
95.6 |
95.0 |
| O1 |
C3' |
H3' |
C2' |
121.9 |
122.1 |
| O1 |
C3' |
H3' |
C4' |
239.8 |
237.8 |
| H3' |
C3' |
C2' |
H2' |
85.9 |
146.0 |
| H3' |
C3' |
C2' |
H2'A |
325.9 |
23.7 |
| H3' |
C3' |
C4' |
C5' |
156.2 |
118.9 |
| H3' |
C3' |
C4' |
H4' |
34.8 |
0.0 |
| C2A |
C3A |
C4A |
H3AA |
180.0 |
180.0 |
| C5A |
C4A |
C3A |
C8A |
179.7 |
180.0 |
| C3A |
C4A |
C5A |
H5A |
180.8 |
179.9 |
| C3A |
C4A |
C8A |
H8A |
89.9 |
90.0 |
| C3A |
C4A |
C8A |
H8AA |
209.8 |
210.0 |
| C3A |
C4A |
C8A |
H8AB |
329.8 |
329.9 |
| C2A |
C3A |
H3AA |
C4A |
180.0 |
180.0 |
| H3AA |
C3A |
C4A |
C5A |
179.2 |
180.0 |
| H3AA |
C3A |
C4A |
C8A |
359.5 |
0.0 |
| C7A |
C4' |
C3' |
H3' |
279.7 |
237.9 |
| C3' |
C4' |
C7A |
H4' |
120.5 |
122.1 |
| C5' |
C4' |
C7A |
H4' |
238.9 |
237.7 |
| C7A |
C4' |
C5' |
H5' |
91.6 |
98.5 |
| C7A |
C4' |
C5' |
H5'A |
331.6 |
336.1 |
| C4' |
C5' |
N1' |
HN1' |
245.6 |
280.0 |
| C5' |
C4' |
C3' |
H3' |
156.2 |
118.9 |
| C3' |
C4' |
C5' |
H4' |
239.1 |
241.1 |
| C7A |
C4' |
C5' |
H4' |
115.2 |
122.2 |
| H5' |
C5' |
C4' |
H5'A |
120.0 |
122.4 |
| H4' |
C4' |
C3' |
H3' |
34.8 |
0.0 |
| C3' |
C4' |
H4' |
C5' |
116.4 |
115.6 |
| H4' |
C4' |
C5' |
H5' |
336.4 |
336.2 |
| H4' |
C4' |
C5' |
H5'A |
216.4 |
213.8 |
| N1A |
C6A |
C5A |
C4A |
359.1 |
360.0 |
| C5A |
C4A |
C3A |
H3AA |
179.2 |
180.0 |
| C3A |
C4A |
C5A |
C8A |
180.3 |
180.0 |
| C5A |
C4A |
C8A |
H8A |
270.2 |
270.0 |
| C5A |
C4A |
C8A |
H8AA |
30.1 |
30.0 |
| C5A |
C4A |
C8A |
H8AB |
150.2 |
149.9 |
| C6A |
C5A |
C4A |
H5A |
180.0 |
180.1 |
| C8A |
C4A |
C3A |
H3AA |
359.5 |
0.0 |
| C3A |
C4A |
C8A |
C5A |
179.7 |
180.0 |
| C8A |
C4A |
C5A |
H5A |
0.5 |
359.9 |
| H8A |
C8A |
C4A |
H8AA |
240.0 |
240.0 |
| H8A |
C8A |
C4A |
H8AB |
120.0 |
120.1 |
| H8AA |
C8A |
C4A |
H8AB |
240.0 |
240.1 |
| H5' |
C5' |
N1' |
HN1' |
5.5 |
38.8 |
| H5' |
C5' |
C4' |
H4' |
336.4 |
336.2 |
| C4' |
C5' |
H5' |
H5'A |
237.8 |
237.6 |
| H5'A |
C5' |
N1' |
HN1' |
125.5 |
161.2 |
| H5'A |
C5' |
C4' |
H4' |
216.4 |
213.8 |
| C4' |
C5' |
H5'A |
H5' |
122.2 |
122.4 |
| C6A |
C5A |
C4A |
C8A |
180.5 |
180.0 |
| C4A |
C5A |
C6A |
H5A |
180.0 |
179.9 |
| H5A |
C5A |
C4A |
C8A |
0.5 |
359.9 |
| N6A |
C6A |
C5A |
H5A |
359.1 |
0.1 |
| H7A |
C7A |
C4' |
H4' |
298.0 |
292.9 |
| H7AA |
C7A |
C4' |
H4' |
178.0 |
172.8 |
| C4A |
C8A |
H8A |
H8AA |
120.0 |
120.0 |
| C4A |
C8A |
H8A |
H8AB |
240.0 |
239.9 |
| H8AA |
C8A |
H8A |
H8AB |
120.0 |
119.9 |
| C4A |
C8A |
H8AA |
H8A |
240.0 |
239.9 |
| C4A |
C8A |
H8AA |
H8AB |
120.0 |
120.0 |
| H8A |
C8A |
H8AA |
H8AB |
240.0 |
240.1 |
| C4A |
C8A |
H8AB |
H8A |
120.0 |
120.1 |
| C4A |
C8A |
H8AB |
H8AA |
240.0 |
240.0 |
| H8A |
C8A |
H8AB |
H8AA |
120.0 |
119.9 |