PDB Chemical Component 3XB
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 3XB
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O1 |
C1 |
1.420 |
1.430 |
| C2 |
C1 |
1.506 |
1.530 |
| C1 |
H1 |
1.100 |
1.089 |
| C1 |
H1A |
1.100 |
1.090 |
| C3' |
O1 |
1.436 |
1.429 |
| C2 |
N2 |
1.451 |
1.469 |
| C2 |
H2 |
1.100 |
1.091 |
| C2 |
H2A |
1.100 |
1.090 |
| N2 |
C3 |
1.462 |
1.469 |
| N2 |
HN2 |
1.000 |
1.009 |
| C3 |
C4 |
1.523 |
1.530 |
| C3 |
H3 |
1.100 |
1.090 |
| C3 |
H3A |
1.101 |
1.090 |
| F6 |
C4 |
1.324 |
1.399 |
| C4 |
C11 |
1.509 |
1.506 |
| C4 |
F5 |
1.320 |
1.400 |
| N1' |
C5' |
1.454 |
1.485 |
| N1' |
C2' |
1.455 |
1.486 |
| N1' |
HN1' |
1.000 |
1.009 |
| C16 |
C11 |
1.385 |
1.382 |
| C11 |
C12 |
1.377 |
1.383 |
| C12 |
C13 |
1.366 |
1.384 |
| C12 |
H12 |
1.080 |
1.080 |
| C14 |
C13 |
1.377 |
1.385 |
| C13 |
F13 |
1.326 |
1.351 |
| C15 |
C14 |
1.377 |
1.382 |
| C14 |
H14 |
1.080 |
1.080 |
| C16 |
C15 |
1.380 |
1.382 |
| C15 |
H15 |
1.080 |
1.080 |
| C16 |
H16 |
1.080 |
1.080 |
| C6A |
N1A |
1.351 |
1.325 |
| C2A |
N1A |
1.350 |
1.320 |
| C2' |
C3' |
1.538 |
1.544 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.101 |
1.089 |
| C3A |
C2A |
1.390 |
1.380 |
| C2A |
C7A |
1.487 |
1.506 |
| C4' |
C3' |
1.515 |
1.543 |
| C3' |
H3' |
1.100 |
1.090 |
| C4A |
C3A |
1.394 |
1.389 |
| C3A |
H3AA |
1.080 |
1.080 |
| C5' |
C4' |
1.532 |
1.544 |
| C4' |
C7A |
1.526 |
1.530 |
| C4' |
H4' |
1.100 |
1.090 |
| C8A |
C4A |
1.516 |
1.507 |
| C4A |
C5A |
1.408 |
1.383 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.101 |
1.090 |
| C5A |
C6A |
1.409 |
1.391 |
| C5A |
H5A |
1.080 |
1.080 |
| C6A |
N6A |
1.353 |
1.389 |
| N6A |
HN6A |
1.000 |
0.969 |
| N6A |
HN6B |
1.000 |
0.971 |
| C7A |
H7A |
1.100 |
1.090 |
| 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 3XB
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1 |
C1 |
H1 |
111.1 |
109.5 |
| O1 |
C1 |
H1A |
111.1 |
109.5 |
| C2 |
C1 |
H1 |
111.1 |
109.5 |
| C2 |
C1 |
H1A |
111.1 |
109.5 |
| H1 |
C1 |
H1A |
107.7 |
109.5 |
| N2 |
C2 |
H2 |
109.2 |
109.5 |
| N2 |
C2 |
H2A |
109.2 |
109.5 |
| C2 |
N2 |
C3 |
119.4 |
111.0 |
| C2 |
N2 |
HN2 |
106.3 |
111.0 |
| H2 |
C2 |
H2A |
109.8 |
109.5 |
| C3 |
N2 |
HN2 |
106.3 |
111.0 |
| N2 |
C3 |
C4 |
108.3 |
109.5 |
| N2 |
C3 |
H3 |
109.9 |
109.4 |
| N2 |
C3 |
H3A |
109.9 |
109.5 |
| C4 |
C3 |
H3 |
109.9 |
109.5 |
| C4 |
C3 |
H3A |
109.9 |
109.5 |
| C3 |
C4 |
C11 |
116.2 |
109.5 |
| C3 |
C4 |
F5 |
106.3 |
109.5 |
| H3 |
C3 |
H3A |
109.1 |
109.5 |
| F6 |
C4 |
C11 |
111.5 |
109.5 |
| F5 |
C4 |
C11 |
107.9 |
109.5 |
| C4 |
C11 |
C12 |
119.2 |
120.0 |
| C2' |
N1' |
C5' |
113.9 |
104.2 |
| C5' |
N1' |
HN1' |
108.0 |
111.0 |
| N1' |
C5' |
C4' |
104.5 |
104.6 |
| N1' |
C5' |
H5' |
111.1 |
110.4 |
| N1' |
C5' |
H5'A |
111.2 |
110.4 |
| C2' |
N1' |
HN1' |
108.0 |
111.0 |
| N1' |
C2' |
C3' |
105.0 |
104.6 |
| N1' |
C2' |
H2' |
111.0 |
110.4 |
| N1' |
C2' |
H2'A |
111.0 |
110.4 |
| C11 |
C12 |
C13 |
120.0 |
120.0 |
| C11 |
C12 |
H12 |
120.0 |
120.0 |
| C13 |
C12 |
H12 |
120.0 |
120.0 |
| C12 |
C13 |
F13 |
118.3 |
120.0 |
| C15 |
C14 |
H14 |
120.2 |
120.1 |
| C16 |
C15 |
H15 |
120.6 |
120.0 |
| C3' |
C2' |
H2' |
111.0 |
110.4 |
| C3' |
C2' |
H2'A |
111.0 |
110.4 |
| C2' |
C3' |
H3' |
107.2 |
110.3 |
| H2' |
C2' |
H2'A |
107.9 |
110.5 |
| C3A |
C2A |
C7A |
120.5 |
119.6 |
| C2A |
C7A |
C4' |
106.1 |
109.5 |
| C2A |
C7A |
H7A |
110.6 |
109.5 |
| C2A |
C7A |
H7AA |
110.6 |
109.5 |
| C4' |
C3' |
H3' |
116.7 |
110.4 |
| C4A |
C3A |
H3AA |
120.5 |
120.3 |
| C5' |
C4' |
C7A |
114.2 |
110.3 |
| C5' |
C4' |
H4' |
108.2 |
110.4 |
| C7A |
C4' |
H4' |
104.9 |
110.3 |
| C4' |
C7A |
H7A |
110.6 |
109.5 |
| C4' |
C7A |
H7AA |
110.6 |
109.5 |
| C4A |
C5A |
C6A |
119.6 |
119.1 |
| C4A |
C5A |
H5A |
120.2 |
120.5 |
| H5' |
C5' |
H5'A |
107.8 |
110.5 |
| C6A |
C5A |
H5A |
120.2 |
120.5 |
| C5A |
C6A |
N6A |
122.5 |
119.7 |
| C6A |
N6A |
HN6A |
109.5 |
120.1 |
| C6A |
N6A |
HN6B |
109.5 |
120.0 |
| HN6A |
N6A |
HN6B |
109.5 |
120.0 |
| H7A |
C7A |
H7AA |
108.3 |
109.5 |
| H8A |
C8A |
H8AA |
109.5 |
109.5 |
| H8A |
C8A |
H8AB |
109.4 |
109.5 |
| H8AA |
C8A |
H8AB |
109.5 |
109.5 |
Torsion Angles for 3XB
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C1 |
O1 |
H1 |
240.0 |
240.0 |
| C2 |
C1 |
O1 |
H1A |
120.0 |
120.0 |
| H1 |
C1 |
O1 |
H1A |
240.0 |
240.0 |
| O1 |
C1 |
C2 |
H1 |
120.0 |
120.0 |
| O1 |
C1 |
C2 |
H1A |
240.0 |
240.0 |
| H1 |
C1 |
C2 |
H1A |
120.0 |
120.0 |
| O1 |
C1 |
H1 |
H1A |
122.0 |
120.0 |
| C2 |
C1 |
H1 |
H1A |
238.0 |
240.0 |
| O1 |
C1 |
H1A |
H1 |
238.0 |
240.0 |
| C2 |
C1 |
H1A |
H1 |
122.0 |
120.0 |
| C3' |
O1 |
C1 |
H1 |
6.7 |
300.0 |
| C3' |
O1 |
C1 |
H1A |
126.7 |
60.0 |
| N2 |
C2 |
C1 |
H1 |
201.1 |
305.0 |
| N2 |
C2 |
C1 |
H1A |
81.1 |
185.0 |
| H2 |
C2 |
N2 |
H2A |
120.0 |
120.0 |
| C3 |
N2 |
C2 |
HN2 |
240.0 |
236.1 |
| C2 |
N2 |
C3 |
C4 |
24.5 |
180.0 |
| C2 |
N2 |
C3 |
H3 |
144.5 |
300.0 |
| C2 |
N2 |
C3 |
H3A |
264.5 |
60.0 |
| H2 |
C2 |
C1 |
H1 |
321.1 |
65.0 |
| H2 |
C2 |
C1 |
H1A |
201.1 |
305.0 |
| N2 |
C2 |
H2 |
H2A |
240.3 |
240.0 |
| H2 |
C2 |
N2 |
C3 |
85.6 |
60.0 |
| H2 |
C2 |
N2 |
HN2 |
205.6 |
183.9 |
| H2A |
C2 |
C1 |
H1 |
81.1 |
185.0 |
| H2A |
C2 |
C1 |
H1A |
321.1 |
65.0 |
| N2 |
C2 |
H2A |
H2 |
119.7 |
120.0 |
| H2A |
C2 |
N2 |
C3 |
325.6 |
300.0 |
| H2A |
C2 |
N2 |
HN2 |
85.6 |
63.9 |
| C3 |
N2 |
C2 |
H2 |
85.6 |
60.0 |
| C3 |
N2 |
C2 |
H2A |
325.6 |
300.0 |
| C2 |
N2 |
C3 |
HN2 |
120.0 |
123.9 |
| C4 |
C3 |
N2 |
H3 |
240.0 |
240.0 |
| C4 |
C3 |
N2 |
H3A |
120.0 |
120.0 |
| N2 |
C3 |
C4 |
C11 |
174.8 |
180.0 |
| N2 |
C3 |
C4 |
F5 |
54.8 |
300.0 |
| H3 |
C3 |
N2 |
H3A |
240.0 |
240.0 |
| HN2 |
N2 |
C2 |
H2 |
205.6 |
183.9 |
| HN2 |
N2 |
C2 |
H2A |
85.6 |
63.9 |
| C2 |
N2 |
HN2 |
C3 |
231.8 |
236.0 |
| HN2 |
N2 |
C3 |
C4 |
264.5 |
56.1 |
| HN2 |
N2 |
C3 |
H3 |
24.5 |
176.0 |
| HN2 |
N2 |
C3 |
H3A |
144.5 |
296.0 |
| C4 |
C3 |
N2 |
HN2 |
264.5 |
56.1 |
| N2 |
C3 |
C4 |
H3 |
120.0 |
119.9 |
| N2 |
C3 |
C4 |
H3A |
240.0 |
240.0 |
| H3 |
C3 |
C4 |
H3A |
120.0 |
120.1 |
| F6 |
C4 |
C3 |
C11 |
127.1 |
240.0 |
| F5 |
C4 |
C3 |
C11 |
239.9 |
120.0 |
| C3 |
C4 |
C11 |
C12 |
269.5 |
90.0 |
| H3 |
C3 |
N2 |
HN2 |
24.5 |
176.0 |
| N2 |
C3 |
H3 |
C4 |
240.9 |
240.1 |
| N2 |
C3 |
H3 |
H3A |
120.5 |
120.0 |
| C4 |
C3 |
H3 |
H3A |
239.5 |
239.9 |
| H3 |
C3 |
C4 |
C11 |
54.8 |
60.0 |
| H3 |
C3 |
C4 |
F5 |
294.7 |
180.0 |
| H3A |
C3 |
N2 |
HN2 |
144.5 |
296.0 |
| N2 |
C3 |
H3A |
C4 |
119.1 |
120.0 |
| N2 |
C3 |
H3A |
H3 |
239.5 |
240.0 |
| C4 |
C3 |
H3A |
H3 |
120.5 |
120.0 |
| H3A |
C3 |
C4 |
C11 |
294.8 |
300.0 |
| H3A |
C3 |
C4 |
F5 |
174.7 |
60.0 |
| F6 |
C4 |
C3 |
H3 |
181.9 |
300.0 |
| F6 |
C4 |
C3 |
H3A |
61.9 |
180.0 |
| C3 |
C4 |
F6 |
C11 |
230.2 |
120.0 |
| F5 |
C4 |
F6 |
C11 |
116.5 |
240.0 |
| F6 |
C4 |
C11 |
C12 |
143.5 |
210.0 |
| C11 |
C4 |
C3 |
H3 |
54.8 |
60.0 |
| C11 |
C4 |
C3 |
H3A |
294.8 |
300.0 |
| C3 |
C4 |
C11 |
F5 |
240.8 |
120.0 |
| C4 |
C11 |
C12 |
C13 |
182.1 |
180.0 |
| C4 |
C11 |
C12 |
H12 |
2.1 |
0.0 |
| F5 |
C4 |
C3 |
H3 |
294.7 |
180.0 |
| F5 |
C4 |
C3 |
H3A |
174.7 |
60.0 |
| C3 |
C4 |
F5 |
C11 |
125.3 |
240.0 |
| F6 |
C4 |
F5 |
C11 |
241.0 |
120.0 |
| F5 |
C4 |
C11 |
C12 |
28.7 |
330.0 |
| C2' |
N1' |
C5' |
HN1' |
240.0 |
240.5 |
| C5' |
N1' |
C2' |
C3' |
5.5 |
320.5 |
| C5' |
N1' |
C2' |
H2' |
125.5 |
79.3 |
| C5' |
N1' |
C2' |
H2'A |
245.5 |
201.8 |
| N1' |
C5' |
C4' |
C7A |
221.4 |
217.3 |
| N1' |
C5' |
C4' |
H4' |
105.0 |
95.1 |
| H5' |
C5' |
N1' |
H5'A |
240.0 |
237.5 |
| C5' |
N1' |
C2' |
HN1' |
120.0 |
119.6 |
| C2' |
N1' |
C5' |
C4' |
6.7 |
39.5 |
| C2' |
N1' |
C5' |
H5' |
126.7 |
158.2 |
| C2' |
N1' |
C5' |
H5'A |
246.7 |
280.7 |
| C3' |
C2' |
N1' |
H2' |
240.0 |
241.3 |
| C3' |
C2' |
N1' |
H2'A |
120.0 |
118.8 |
| N1' |
C2' |
C3' |
H3' |
219.3 |
264.8 |
| H2' |
C2' |
N1' |
H2'A |
240.0 |
237.5 |
| C2' |
N1' |
HN1' |
C5' |
123.6 |
115.4 |
| HN1' |
N1' |
C5' |
C4' |
126.7 |
159.0 |
| HN1' |
N1' |
C5' |
H5' |
246.7 |
277.8 |
| HN1' |
N1' |
C5' |
H5'A |
6.7 |
40.2 |
| HN1' |
N1' |
C2' |
C3' |
245.5 |
201.0 |
| HN1' |
N1' |
C2' |
H2' |
5.5 |
319.7 |
| HN1' |
N1' |
C2' |
H2'A |
125.5 |
82.2 |
| C16 |
C11 |
C12 |
H12 |
178.2 |
180.2 |
| C13 |
C12 |
C11 |
H12 |
180.0 |
180.0 |
| C11 |
C12 |
C13 |
F13 |
179.7 |
180.0 |
| C11 |
C12 |
C13 |
H12 |
180.0 |
180.0 |
| C11 |
C12 |
H12 |
C13 |
180.0 |
180.0 |
| H12 |
C12 |
C13 |
F13 |
359.7 |
0.0 |
| C14 |
C13 |
C12 |
H12 |
180.6 |
180.0 |
| F13 |
C13 |
C12 |
H12 |
359.7 |
0.0 |
| C16 |
C15 |
C14 |
H14 |
179.8 |
179.7 |
| H15 |
C15 |
C14 |
H14 |
359.8 |
0.1 |
| H16 |
C16 |
C15 |
H15 |
358.8 |
359.9 |
| C3' |
C2' |
N1' |
C5' |
5.5 |
320.5 |
| C3' |
C2' |
N1' |
HN1' |
245.5 |
201.0 |
| N1' |
C2' |
C3' |
H2' |
120.0 |
118.7 |
| N1' |
C2' |
C3' |
H2'A |
240.0 |
241.2 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.5 |
| C4' |
C3' |
C2' |
H3' |
125.2 |
119.0 |
| H2' |
C2' |
N1' |
C5' |
125.5 |
79.3 |
| H2' |
C2' |
N1' |
HN1' |
5.5 |
319.7 |
| N1' |
C2' |
H2' |
C3' |
243.7 |
244.9 |
| N1' |
C2' |
H2' |
H2'A |
121.8 |
122.5 |
| C3' |
C2' |
H2' |
H2'A |
238.1 |
237.5 |
| H2' |
C2' |
C3' |
H3' |
99.3 |
146.1 |
| H2'A |
C2' |
N1' |
C5' |
245.5 |
201.8 |
| H2'A |
C2' |
N1' |
HN1' |
125.5 |
82.2 |
| N1' |
C2' |
H2'A |
C3' |
116.4 |
115.1 |
| N1' |
C2' |
H2'A |
H2' |
238.2 |
237.6 |
| C3' |
C2' |
H2'A |
H2' |
121.9 |
122.4 |
| H2'A |
C2' |
C3' |
H3' |
339.3 |
23.6 |
| C3A |
C2A |
C7A |
C4' |
300.7 |
125.0 |
| C3A |
C2A |
C7A |
H7A |
60.7 |
245.0 |
| C3A |
C2A |
C7A |
H7AA |
180.7 |
5.0 |
| C5' |
C4' |
C7A |
C2A |
292.3 |
290.6 |
| C2A |
C7A |
C4' |
H4' |
50.7 |
52.9 |
| C4' |
C7A |
C2A |
H7A |
240.0 |
240.0 |
| C4' |
C7A |
C2A |
H7AA |
120.0 |
120.0 |
| H7A |
C7A |
C2A |
H7AA |
240.0 |
240.0 |
| N1' |
C5' |
C4' |
C3' |
343.6 |
336.1 |
| C4' |
C3' |
C2' |
H2' |
224.5 |
265.1 |
| C4' |
C3' |
C2' |
H2'A |
104.5 |
142.6 |
| C2' |
C3' |
C4' |
H3' |
240.9 |
241.1 |
| C2A |
C7A |
C4' |
C3' |
171.8 |
175.0 |
| H3' |
C3' |
C2' |
H2' |
99.3 |
146.1 |
| H3' |
C3' |
C2' |
H2'A |
339.3 |
23.6 |
| C4A |
C3A |
C2A |
C7A |
178.9 |
180.0 |
| H3AA |
C3A |
C2A |
C7A |
358.8 |
360.0 |
| C4' |
C5' |
N1' |
HN1' |
126.7 |
159.0 |
| N1' |
C5' |
C4' |
H5' |
120.0 |
118.8 |
| N1' |
C5' |
C4' |
H5'A |
240.0 |
241.2 |
| C2A |
C7A |
C4' |
C5' |
292.3 |
290.6 |
| C5' |
C4' |
C3' |
H3' |
139.0 |
119.0 |
| C7A |
C4' |
C5' |
H4' |
116.4 |
122.2 |
| C5' |
C4' |
C7A |
H7A |
172.3 |
170.6 |
| C5' |
C4' |
C7A |
H7AA |
52.3 |
50.6 |
| C2A |
C7A |
C4' |
H7A |
120.0 |
120.0 |
| C2A |
C7A |
C4' |
H7AA |
240.0 |
240.0 |
| C7A |
C4' |
C3' |
H3' |
263.6 |
237.8 |
| C5' |
C4' |
C7A |
H4' |
241.7 |
237.7 |
| H7A |
C7A |
C4' |
H7AA |
120.0 |
120.0 |
| H4' |
C4' |
C3' |
H3' |
20.3 |
360.0 |
| C5' |
C4' |
H4' |
C7A |
122.3 |
122.2 |
| H4' |
C4' |
C7A |
H7A |
290.7 |
292.9 |
| H4' |
C4' |
C7A |
H7AA |
170.7 |
172.9 |
| C8A |
C4A |
C3A |
H3AA |
359.6 |
0.1 |
| C8A |
C4A |
C5A |
H5A |
0.3 |
0.0 |
| C5A |
C4A |
C3A |
H3AA |
180.0 |
180.0 |
| C6A |
C5A |
C4A |
H5A |
180.0 |
179.9 |
| C4A |
C5A |
C6A |
N6A |
179.9 |
180.0 |
| H5' |
C5' |
N1' |
HN1' |
246.7 |
277.8 |
| N1' |
C5' |
H5' |
C4' |
244.1 |
244.8 |
| N1' |
C5' |
H5' |
H5'A |
122.0 |
122.4 |
| H5' |
C5' |
C4' |
C7A |
101.4 |
98.5 |
| H5' |
C5' |
C4' |
H4' |
345.0 |
336.3 |
| H5'A |
C5' |
N1' |
HN1' |
6.7 |
40.2 |
| N1' |
C5' |
H5'A |
C4' |
115.9 |
115.2 |
| N1' |
C5' |
H5'A |
H5' |
238.0 |
237.6 |
| H5'A |
C5' |
C4' |
C7A |
341.4 |
336.0 |
| H5'A |
C5' |
C4' |
H4' |
225.0 |
213.8 |
| C4A |
C5A |
C6A |
H5A |
180.0 |
180.1 |
| C5A |
C6A |
N6A |
HN6A |
180.0 |
0.1 |
| C5A |
C6A |
N6A |
HN6B |
300.0 |
180.1 |
| C4A |
C5A |
H5A |
C6A |
180.0 |
179.9 |
| H5A |
C5A |
C6A |
N6A |
359.9 |
359.9 |
| N6A |
C6A |
C5A |
H5A |
359.9 |
359.9 |
| HN6A |
N6A |
C6A |
HN6B |
240.0 |
180.0 |
| C6A |
N6A |
HN6A |
HN6B |
120.0 |
180.0 |
| C6A |
N6A |
HN6B |
HN6A |
240.0 |
180.0 |
| C2A |
C7A |
H7A |
C4' |
242.8 |
240.0 |
| C2A |
C7A |
H7A |
H7AA |
121.4 |
120.0 |
| H7A |
C7A |
C4' |
H4' |
290.7 |
292.9 |
| C4' |
C7A |
H7A |
H7AA |
238.6 |
240.0 |
| C2A |
C7A |
H7AA |
C4' |
117.2 |
120.0 |
| C2A |
C7A |
H7AA |
H7A |
238.6 |
240.0 |
| H7AA |
C7A |
C4' |
H4' |
170.7 |
172.9 |
| C4' |
C7A |
H7AA |
H7A |
121.4 |
120.0 |
| H8AA |
C8A |
H8A |
H8AB |
120.0 |
120.0 |
| H8A |
C8A |
H8AA |
H8AB |
240.0 |
240.0 |
| H8A |
C8A |
H8AB |
H8AA |
120.0 |
120.0 |