PDB Chemical Component 3XD
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 3XD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2 |
C1 |
1.521 |
1.530 |
| C1 |
O1 |
1.421 |
1.430 |
| C1 |
H1 |
1.100 |
1.090 |
| C1 |
H1A |
1.100 |
1.090 |
| O1 |
C3' |
1.429 |
1.428 |
| C2 |
N2 |
1.453 |
1.469 |
| C2 |
H2 |
1.100 |
1.089 |
| C2 |
H2A |
1.100 |
1.090 |
| C3 |
N2 |
1.452 |
1.469 |
| N2 |
HN2 |
1.000 |
1.009 |
| C4 |
C3 |
1.530 |
1.530 |
| C3 |
H3 |
1.100 |
1.089 |
| C3 |
H3A |
1.100 |
1.089 |
| F5 |
C4 |
1.325 |
1.399 |
| C11 |
C4 |
1.517 |
1.508 |
| C4 |
F6 |
1.324 |
1.399 |
| C2' |
N1' |
1.448 |
1.485 |
| C5' |
N1' |
1.464 |
1.486 |
| N1' |
HN1' |
1.000 |
1.008 |
| C12 |
C11 |
1.393 |
1.382 |
| C11 |
C16 |
1.400 |
1.382 |
| C13 |
C12 |
1.399 |
1.383 |
| C12 |
H12 |
1.080 |
1.080 |
| C13 |
C14 |
1.395 |
1.382 |
| C13 |
H13 |
1.080 |
1.080 |
| C14 |
C15 |
1.391 |
1.382 |
| C14 |
H14 |
1.080 |
1.080 |
| C15 |
C16 |
1.397 |
1.383 |
| C15 |
H15 |
1.080 |
1.080 |
| C16 |
H16 |
1.080 |
1.080 |
| N1A |
C2A |
1.368 |
1.319 |
| N1A |
C6A |
1.363 |
1.325 |
| C3' |
C2' |
1.522 |
1.544 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| C7A |
C2A |
1.519 |
1.508 |
| C2A |
C3A |
1.396 |
1.381 |
| C3' |
C4' |
1.530 |
1.542 |
| C3' |
H3' |
1.100 |
1.090 |
| C3A |
C4A |
1.393 |
1.388 |
| C3A |
H3AA |
1.080 |
1.081 |
| C7A |
C4' |
1.545 |
1.529 |
| C4' |
C5' |
1.534 |
1.544 |
| C4' |
H4' |
1.100 |
1.090 |
| C5A |
C4A |
1.400 |
1.384 |
| C4A |
C8A |
1.513 |
1.506 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| C6A |
C5A |
1.398 |
1.391 |
| C5A |
H5A |
1.080 |
1.080 |
| N6A |
C6A |
1.376 |
1.390 |
| N6A |
HN6A |
1.000 |
0.970 |
| N6A |
HN6B |
1.000 |
0.970 |
| C7A |
H7A |
1.100 |
1.090 |
| C7A |
H7AA |
1.100 |
1.090 |
| C8A |
H8A |
1.100 |
1.091 |
| C8A |
H8AA |
1.100 |
1.089 |
| C8A |
H8AB |
1.100 |
1.091 |
Bond Angles for 3XD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C1 |
H1 |
110.1 |
109.5 |
| C2 |
C1 |
H1A |
110.1 |
109.5 |
| O1 |
C1 |
H1 |
110.1 |
109.4 |
| O1 |
C1 |
H1A |
110.1 |
109.5 |
| C1 |
O1 |
C3' |
113.8 |
114.0 |
| H1 |
C1 |
H1A |
108.8 |
109.5 |
| O1 |
C3' |
C2' |
109.6 |
110.3 |
| O1 |
C3' |
C4' |
107.3 |
110.3 |
| O1 |
C3' |
H3' |
109.1 |
110.3 |
| N2 |
C2 |
H2 |
109.3 |
109.5 |
| N2 |
C2 |
H2A |
109.3 |
109.5 |
| C2 |
N2 |
HN2 |
106.1 |
111.0 |
| H2 |
C2 |
H2A |
109.6 |
109.5 |
| C3 |
N2 |
HN2 |
106.1 |
111.0 |
| C4 |
C3 |
H3 |
109.7 |
109.5 |
| C4 |
C3 |
H3A |
109.7 |
109.5 |
| H3 |
C3 |
H3A |
109.2 |
109.5 |
| F5 |
C4 |
F6 |
108.5 |
109.5 |
| C2' |
N1' |
HN1' |
108.2 |
111.0 |
| C5' |
N1' |
HN1' |
108.2 |
111.1 |
| C12 |
C11 |
C16 |
119.6 |
120.0 |
| C11 |
C16 |
C15 |
120.3 |
120.0 |
| C11 |
C16 |
H16 |
119.9 |
119.9 |
| C13 |
C12 |
H12 |
119.6 |
120.0 |
| C14 |
C13 |
H13 |
120.7 |
120.0 |
| C13 |
C14 |
C15 |
121.5 |
120.0 |
| C13 |
C14 |
H14 |
119.3 |
120.0 |
| C15 |
C14 |
H14 |
119.2 |
119.9 |
| C14 |
C15 |
C16 |
119.2 |
120.0 |
| C14 |
C15 |
H15 |
120.4 |
120.1 |
| C16 |
C15 |
H15 |
120.4 |
120.0 |
| C15 |
C16 |
H16 |
119.9 |
120.1 |
| C2A |
N1A |
C6A |
122.2 |
121.6 |
| N1A |
C2A |
C3A |
120.6 |
120.9 |
| N1A |
C6A |
C5A |
118.3 |
120.6 |
| C3' |
C2' |
H2' |
112.3 |
110.4 |
| C3' |
C2' |
H2'A |
112.3 |
110.5 |
| H2' |
C2' |
H2'A |
106.5 |
110.4 |
| C2A |
C3A |
C4A |
118.6 |
119.4 |
| C2A |
C3A |
H3AA |
120.7 |
120.3 |
| C4' |
C3' |
H3' |
114.3 |
110.4 |
| C3' |
C4' |
C5' |
103.0 |
105.0 |
| C3' |
C4' |
H4' |
112.1 |
110.3 |
| C4A |
C3A |
H3AA |
120.7 |
120.3 |
| C3A |
C4A |
C8A |
119.7 |
120.8 |
| C7A |
C4' |
H4' |
99.8 |
110.4 |
| C5' |
C4' |
H4' |
112.7 |
110.3 |
| C4' |
C5' |
H5' |
111.5 |
110.4 |
| C4' |
C5' |
H5'A |
111.5 |
110.4 |
| C5A |
C4A |
C8A |
120.6 |
120.7 |
| C4A |
C8A |
H8A |
109.5 |
109.5 |
| C4A |
C8A |
H8AA |
109.5 |
109.5 |
| C4A |
C8A |
H8AB |
109.4 |
109.4 |
| H5' |
C5' |
H5'A |
107.4 |
110.5 |
| C6A |
C5A |
H5A |
119.6 |
120.5 |
| HN6A |
N6A |
HN6B |
109.5 |
120.0 |
| H7A |
C7A |
H7AA |
109.6 |
109.5 |
| H8A |
C8A |
H8AA |
109.5 |
109.5 |
| H8A |
C8A |
H8AB |
109.4 |
109.4 |
| H8AA |
C8A |
H8AB |
109.5 |
109.5 |
Torsion Angles for 3XD
| 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' |
185.4 |
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' |
98.2 |
91.5 |
| C1 |
O1 |
C3' |
C4' |
210.5 |
207.1 |
| C1 |
O1 |
C3' |
H3' |
334.9 |
329.4 |
| C2 |
C1 |
H1 |
H1A |
120.7 |
240.0 |
| O1 |
C1 |
H1 |
H1A |
239.2 |
120.0 |
| H1 |
C1 |
O1 |
C3' |
65.4 |
300.0 |
| C2 |
C1 |
H1A |
H1 |
239.3 |
120.0 |
| O1 |
C1 |
H1A |
H1 |
120.8 |
240.0 |
| H1A |
C1 |
O1 |
C3' |
305.3 |
60.0 |
| C3' |
O1 |
C1 |
H1 |
65.4 |
300.0 |
| C3' |
O1 |
C1 |
H1A |
305.3 |
60.0 |
| O1 |
C3' |
C2' |
H2' |
318.2 |
23.9 |
| O1 |
C3' |
C2' |
H2'A |
198.2 |
261.6 |
| C4' |
C3' |
O1 |
H3' |
235.6 |
237.8 |
| O1 |
C3' |
C4' |
C5' |
281.1 |
241.1 |
| O1 |
C3' |
C4' |
H4' |
159.7 |
122.2 |
| N2 |
C2 |
C1 |
H1 |
189.4 |
305.0 |
| N2 |
C2 |
C1 |
H1A |
309.4 |
185.0 |
| H2 |
C2 |
N2 |
H2A |
120.0 |
120.0 |
| C3 |
N2 |
C2 |
HN2 |
240.0 |
236.1 |
| H2 |
C2 |
C1 |
H1 |
309.4 |
65.0 |
| H2 |
C2 |
C1 |
H1A |
69.4 |
305.0 |
| N2 |
C2 |
H2 |
H2A |
240.1 |
240.0 |
| H2 |
C2 |
N2 |
HN2 |
197.1 |
183.9 |
| H2A |
C2 |
C1 |
H1 |
69.4 |
185.0 |
| H2A |
C2 |
C1 |
H1A |
189.4 |
65.0 |
| N2 |
C2 |
H2A |
H2 |
119.8 |
120.0 |
| H2A |
C2 |
N2 |
HN2 |
77.0 |
64.0 |
| C3 |
N2 |
C2 |
H2 |
77.1 |
60.0 |
| C3 |
N2 |
C2 |
H2A |
317.0 |
300.0 |
| C2 |
N2 |
C3 |
HN2 |
120.0 |
123.9 |
| HN2 |
N2 |
C2 |
H2 |
197.1 |
183.9 |
| HN2 |
N2 |
C2 |
H2A |
77.0 |
64.0 |
| C4 |
C3 |
N2 |
HN2 |
166.2 |
56.1 |
| H3 |
C3 |
C4 |
H3A |
120.0 |
120.1 |
| H3 |
C3 |
N2 |
HN2 |
286.2 |
176.0 |
| C4 |
C3 |
H3 |
H3A |
239.7 |
240.0 |
| H3A |
C3 |
N2 |
HN2 |
46.2 |
296.1 |
| C4 |
C3 |
H3A |
H3 |
120.3 |
120.0 |
| F5 |
C4 |
C3 |
H3 |
307.8 |
180.0 |
| F5 |
C4 |
C3 |
H3A |
187.8 |
59.9 |
| C11 |
C4 |
C3 |
H3 |
67.9 |
60.0 |
| C11 |
C4 |
C3 |
H3A |
307.8 |
300.0 |
| F6 |
C4 |
C3 |
H3 |
189.9 |
300.0 |
| F6 |
C4 |
C3 |
H3A |
69.9 |
180.0 |
| O1 |
C3' |
C2' |
N1' |
78.2 |
142.8 |
| C5' |
N1' |
C2' |
HN1' |
240.0 |
240.3 |
| C2' |
N1' |
C5' |
HN1' |
120.0 |
119.6 |
| C12 |
C11 |
C16 |
C15 |
0.3 |
359.5 |
| C12 |
C11 |
C16 |
H16 |
180.2 |
179.7 |
| C14 |
C15 |
C16 |
C11 |
359.5 |
0.5 |
| C11 |
C16 |
C15 |
H15 |
179.5 |
180.3 |
| C15 |
C16 |
C11 |
H16 |
180.0 |
179.7 |
| C13 |
C12 |
C11 |
C16 |
0.3 |
0.4 |
| H12 |
C12 |
C11 |
C16 |
180.3 |
180.3 |
| C14 |
C13 |
C12 |
H12 |
179.5 |
180.0 |
| C15 |
C14 |
C13 |
H14 |
180.0 |
180.0 |
| C13 |
C14 |
C15 |
C16 |
0.3 |
359.8 |
| C13 |
C14 |
C15 |
H15 |
180.2 |
180.0 |
| H13 |
C13 |
C12 |
H12 |
359.5 |
0.0 |
| H13 |
C13 |
C14 |
C15 |
180.3 |
180.0 |
| H13 |
C13 |
C14 |
H14 |
0.3 |
0.0 |
| C11 |
C16 |
C15 |
C14 |
359.5 |
0.5 |
| C15 |
C14 |
C13 |
H13 |
180.3 |
180.0 |
| C13 |
C14 |
C15 |
H14 |
180.0 |
180.0 |
| C16 |
C15 |
C14 |
H15 |
180.0 |
179.9 |
| C14 |
C15 |
C16 |
H16 |
179.5 |
180.2 |
| H14 |
C14 |
C13 |
H13 |
0.3 |
0.0 |
| C13 |
C14 |
H14 |
C15 |
180.0 |
180.0 |
| H14 |
C14 |
C15 |
C16 |
180.3 |
179.8 |
| H14 |
C14 |
C15 |
H15 |
0.2 |
359.9 |
| C11 |
C16 |
C15 |
H16 |
180.0 |
180.3 |
| C16 |
C15 |
C14 |
H14 |
180.3 |
179.8 |
| C14 |
C15 |
C16 |
H15 |
180.0 |
180.1 |
| H15 |
C15 |
C14 |
H14 |
0.2 |
359.9 |
| C14 |
C15 |
H15 |
C16 |
180.0 |
179.9 |
| H15 |
C15 |
C16 |
H16 |
359.5 |
0.0 |
| C11 |
C16 |
H16 |
C15 |
180.0 |
179.7 |
| H16 |
C16 |
C15 |
H15 |
359.5 |
0.0 |
| C2A |
N1A |
C6A |
C5A |
0.4 |
360.0 |
| N1A |
C2A |
C3A |
C4A |
359.6 |
359.9 |
| N1A |
C2A |
C3A |
H3AA |
179.6 |
180.0 |
| C6A |
N1A |
C2A |
C3A |
359.9 |
0.1 |
| N1A |
C6A |
C5A |
H5A |
179.8 |
180.0 |
| O1 |
C3' |
C2' |
C4' |
114.5 |
118.9 |
| O1 |
C3' |
C2' |
H3' |
238.6 |
237.9 |
| C3' |
C2' |
N1' |
HN1' |
142.6 |
80.1 |
| H2' |
C2' |
C3' |
H2'A |
120.0 |
122.3 |
| H2' |
C2' |
N1' |
HN1' |
262.6 |
198.9 |
| C3' |
C2' |
H2' |
H2'A |
236.7 |
237.6 |
| H2'A |
C2' |
N1' |
HN1' |
22.6 |
321.3 |
| C3' |
C2' |
H2'A |
H2' |
123.3 |
122.3 |
| C7A |
C2A |
C3A |
H3AA |
359.5 |
0.1 |
| C3A |
C2A |
N1A |
C6A |
359.9 |
0.1 |
| C4A |
C3A |
C2A |
H3AA |
180.0 |
180.0 |
| C2A |
C3A |
C4A |
C8A |
180.3 |
180.0 |
| O1 |
C3' |
C4' |
C2' |
243.9 |
241.1 |
| O1 |
C3' |
C4' |
H3' |
121.2 |
122.1 |
| C4' |
C3' |
C2' |
H2' |
203.8 |
265.0 |
| C4' |
C3' |
C2' |
H2'A |
83.8 |
142.7 |
| C7A |
C4' |
C3' |
H4' |
246.8 |
237.7 |
| C5' |
C4' |
C3' |
H4' |
121.4 |
118.9 |
| C3' |
C4' |
C5' |
H5' |
216.9 |
217.4 |
| C3' |
C4' |
C5' |
H5'A |
96.9 |
95.0 |
| O1 |
C3' |
H3' |
C2' |
121.7 |
122.1 |
| O1 |
C3' |
H3' |
C4' |
239.8 |
237.8 |
| H3' |
C3' |
C2' |
H2' |
79.7 |
146.0 |
| H3' |
C3' |
C2' |
H2'A |
319.7 |
23.7 |
| H3' |
C3' |
C4' |
C5' |
160.0 |
118.9 |
| H3' |
C3' |
C4' |
H4' |
38.6 |
0.1 |
| C2A |
C3A |
C4A |
H3AA |
180.0 |
180.0 |
| C5A |
C4A |
C3A |
C8A |
180.3 |
180.0 |
| C3A |
C4A |
C8A |
H8A |
90.1 |
90.0 |
| C3A |
C4A |
C8A |
H8AA |
210.1 |
210.0 |
| C3A |
C4A |
C8A |
H8AB |
330.2 |
330.0 |
| C2A |
C3A |
H3AA |
C4A |
180.0 |
180.0 |
| H3AA |
C3A |
C4A |
C8A |
0.2 |
360.0 |
| C7A |
C4' |
C3' |
H3' |
285.4 |
237.8 |
| C3' |
C4' |
C7A |
H4' |
120.2 |
122.2 |
| C5' |
C4' |
C7A |
H4' |
239.3 |
237.8 |
| C7A |
C4' |
C5' |
H5' |
91.1 |
98.5 |
| C7A |
C4' |
C5' |
H5'A |
331.1 |
336.1 |
| C4' |
C5' |
N1' |
HN1' |
240.3 |
279.9 |
| C5' |
C4' |
C3' |
H3' |
160.0 |
118.9 |
| C3' |
C4' |
C5' |
H4' |
239.0 |
241.1 |
| C7A |
C4' |
C5' |
H4' |
113.2 |
122.2 |
| H5' |
C5' |
C4' |
H5'A |
120.0 |
122.4 |
| H4' |
C4' |
C3' |
H3' |
38.6 |
0.1 |
| C3' |
C4' |
H4' |
C5' |
115.6 |
115.6 |
| H4' |
C4' |
C5' |
H5' |
337.9 |
336.3 |
| H4' |
C4' |
C5' |
H5'A |
217.8 |
213.8 |
| N1A |
C6A |
C5A |
C4A |
359.8 |
359.9 |
| C5A |
C4A |
C3A |
H3AA |
180.5 |
180.0 |
| C3A |
C4A |
C5A |
C8A |
179.7 |
180.0 |
| C5A |
C4A |
C8A |
H8A |
269.8 |
270.0 |
| C5A |
C4A |
C8A |
H8AA |
29.9 |
30.0 |
| C5A |
C4A |
C8A |
H8AB |
149.9 |
150.1 |
| C8A |
C4A |
C3A |
H3AA |
0.2 |
360.0 |
| H8A |
C8A |
C4A |
H8AA |
240.0 |
239.9 |
| H8A |
C8A |
C4A |
H8AB |
120.0 |
119.9 |
| H8AA |
C8A |
C4A |
H8AB |
240.0 |
240.0 |
| H5' |
C5' |
N1' |
HN1' |
0.3 |
38.6 |
| H5' |
C5' |
C4' |
H4' |
337.9 |
336.3 |
| C4' |
C5' |
H5' |
H5'A |
237.6 |
237.6 |
| H5'A |
C5' |
N1' |
HN1' |
120.3 |
161.1 |
| H5'A |
C5' |
C4' |
H4' |
217.8 |
213.8 |
| C4' |
C5' |
H5'A |
H5' |
122.4 |
122.4 |
| C6A |
C5A |
C4A |
C8A |
180.0 |
180.1 |
| H5A |
C5A |
C4A |
C8A |
0.0 |
359.9 |
| N6A |
C6A |
C5A |
H5A |
359.3 |
0.1 |
| H7A |
C7A |
C4' |
H4' |
299.1 |
292.8 |
| H7AA |
C7A |
C4' |
H4' |
179.2 |
172.8 |
| C4A |
C8A |
H8A |
H8AA |
120.0 |
120.1 |
| C4A |
C8A |
H8A |
H8AB |
240.0 |
240.1 |
| H8AA |
C8A |
H8A |
H8AB |
120.0 |
120.0 |
| 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 |
120.0 |
| C4A |
C8A |
H8AB |
H8AA |
240.0 |
240.0 |
| H8A |
C8A |
H8AB |
H8AA |
120.0 |
120.0 |