PDB Chemical Component 5AL
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 5AL
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C |
O |
1.218 |
1.208 |
| N |
HN |
1.000 |
1.009 |
| P |
O5' |
1.607 |
1.610 |
| P |
O1A |
1.505 |
1.610 |
| C2 |
N1 |
1.341 |
1.320 |
| C2 |
H2 |
1.080 |
1.081 |
| N3 |
C2 |
1.340 |
1.316 |
| C4 |
N3 |
1.354 |
1.329 |
| C4 |
C5 |
1.428 |
1.406 |
| C5 |
C6 |
1.438 |
1.405 |
| C6 |
N1 |
1.349 |
1.329 |
| C6 |
N6 |
1.352 |
1.384 |
| N6 |
HN6 |
1.000 |
0.969 |
| N6 |
HN6A |
1.000 |
0.970 |
| N7 |
C5 |
1.344 |
1.355 |
| C8 |
N7 |
1.354 |
1.301 |
| C8 |
H8 |
1.081 |
1.081 |
| N9 |
C4 |
1.335 |
1.372 |
| N9 |
C8 |
1.343 |
1.363 |
| CA |
C |
1.485 |
1.507 |
| CA |
N |
1.459 |
1.469 |
| CB |
CA |
1.531 |
1.530 |
| CB |
HB |
1.100 |
1.090 |
| CB |
HBA |
1.100 |
1.090 |
| CB |
HBB |
1.100 |
1.090 |
| C1' |
N9 |
1.495 |
1.465 |
| C1' |
H1' |
1.100 |
1.090 |
| O1A |
HO1A |
0.950 |
0.968 |
| C2' |
C1' |
1.495 |
1.551 |
| C2' |
H2' |
1.101 |
1.090 |
| O2' |
C2' |
1.446 |
1.428 |
| O2' |
HO2' |
0.950 |
0.967 |
| O2A |
P |
1.508 |
1.480 |
| C3' |
C2' |
1.461 |
1.548 |
| C3' |
C4' |
1.471 |
1.541 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
C3' |
1.443 |
1.430 |
| O3' |
HO3' |
0.950 |
0.967 |
| O3A |
C |
1.457 |
1.342 |
| O3A |
P |
1.614 |
1.610 |
| C4' |
O4' |
1.437 |
1.439 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.440 |
1.443 |
| C5' |
C4' |
1.503 |
1.530 |
| C5' |
O5' |
1.422 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| N |
H18 |
1.000 |
1.009 |
| CA |
H19 |
1.099 |
1.090 |
Bond Angles for 5AL
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
HN |
109.5 |
111.0 |
| HN |
N |
H18 |
109.5 |
111.0 |
| O1A |
P |
O5' |
109.3 |
109.5 |
| O2A |
P |
O5' |
108.5 |
109.4 |
| O3A |
P |
O5' |
104.0 |
109.4 |
| P |
O5' |
C5' |
120.0 |
123.0 |
| P |
O1A |
HO1A |
109.5 |
114.0 |
| N3 |
C2 |
H2 |
118.6 |
118.7 |
| C4 |
C5 |
C6 |
118.3 |
118.1 |
| C5 |
C6 |
N6 |
121.4 |
120.7 |
| C6 |
N6 |
HN6 |
109.5 |
120.0 |
| C6 |
N6 |
HN6A |
109.5 |
120.0 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| N9 |
C8 |
H8 |
124.8 |
125.0 |
| CA |
N |
H18 |
109.5 |
111.0 |
| CB |
CA |
H19 |
100.4 |
109.4 |
| HB |
CB |
HBA |
109.5 |
109.5 |
| HB |
CB |
HBB |
109.5 |
109.5 |
| HBA |
CB |
HBB |
109.5 |
109.4 |
| C2' |
C1' |
H1' |
110.4 |
110.6 |
| O4' |
C1' |
H1' |
112.6 |
110.6 |
| O2' |
C2' |
H2' |
95.6 |
110.8 |
| C3' |
C2' |
H2' |
108.3 |
110.9 |
| C4' |
C3' |
H3' |
112.7 |
110.5 |
| O3' |
C3' |
C4' |
119.2 |
110.4 |
| C3' |
C4' |
O4' |
109.7 |
107.4 |
| C3' |
C4' |
H4' |
103.8 |
109.9 |
| O3' |
C3' |
H3' |
89.3 |
110.5 |
| O4' |
C4' |
H4' |
109.4 |
109.8 |
| C5' |
C4' |
H4' |
87.5 |
110.0 |
| O5' |
C5' |
H5' |
110.1 |
109.5 |
| O5' |
C5' |
H5'A |
110.0 |
109.5 |
| H5' |
C5' |
H5'A |
108.9 |
109.5 |
Torsion Angles for 5AL
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
HN |
H18 |
120.0 |
124.0 |
| O5' |
P |
O1A |
HO1A |
233.7 |
60.0 |
| P |
O5' |
C5' |
H5' |
118.8 |
60.0 |
| P |
O5' |
C5' |
H5'A |
358.8 |
300.0 |
| O2A |
P |
O1A |
O5' |
126.3 |
120.0 |
| O3A |
P |
O1A |
O5' |
247.1 |
240.0 |
| O1A |
P |
O5' |
C5' |
186.0 |
65.0 |
| C4 |
N3 |
C2 |
H2 |
179.9 |
180.0 |
| C4 |
C5 |
C6 |
N6 |
180.0 |
180.0 |
| C5 |
C6 |
N6 |
HN6 |
179.7 |
360.0 |
| C5 |
C6 |
N6 |
HN6A |
299.7 |
180.1 |
| HN6 |
N6 |
C6 |
HN6A |
240.0 |
179.9 |
| C6 |
N6 |
HN6 |
HN6A |
120.0 |
180.1 |
| C6 |
N6 |
HN6A |
HN6 |
240.0 |
179.9 |
| HN |
N |
CA |
H18 |
240.0 |
236.0 |
| CB |
CA |
N |
HN |
30.4 |
300.0 |
| CB |
CA |
N |
H18 |
150.3 |
63.9 |
| HB |
CB |
CA |
H19 |
75.2 |
300.0 |
| HBA |
CB |
HB |
HBB |
120.0 |
120.0 |
| HBA |
CB |
CA |
H19 |
195.2 |
60.1 |
| HB |
CB |
HBA |
HBB |
240.0 |
240.0 |
| HBB |
CB |
CA |
H19 |
315.2 |
179.9 |
| HB |
CB |
HBB |
HBA |
120.0 |
120.0 |
| C1' |
N9 |
C8 |
H8 |
0.4 |
0.0 |
| HO1A |
O1A |
P |
O5' |
233.7 |
60.0 |
| O4' |
C1' |
C2' |
H1' |
121.7 |
118.6 |
| H2' |
C2' |
C1' |
H1' |
99.5 |
160.2 |
| O2' |
C2' |
C1' |
H1' |
352.6 |
36.6 |
| C3' |
C2' |
O2' |
H2' |
245.9 |
236.3 |
| HO2' |
O2' |
C2' |
H2' |
65.8 |
56.4 |
| O1A |
P |
O2A |
O5' |
233.3 |
240.0 |
| O3A |
P |
O2A |
O5' |
110.8 |
119.9 |
| O2A |
P |
O5' |
C5' |
53.3 |
305.0 |
| O2A |
P |
O1A |
HO1A |
0.0 |
180.0 |
| C3' |
C2' |
C1' |
H1' |
216.5 |
278.4 |
| O2' |
C2' |
C3' |
H2' |
106.8 |
123.6 |
| C4' |
C3' |
C2' |
H2' |
139.7 |
97.3 |
| O3' |
C3' |
C4' |
H3' |
102.7 |
122.6 |
| O4' |
C4' |
C3' |
H4' |
243.1 |
240.7 |
| C5' |
C4' |
C3' |
H4' |
95.9 |
121.1 |
| H3' |
C3' |
C2' |
H2' |
19.0 |
338.6 |
| O3' |
C3' |
H3' |
C4' |
238.4 |
237.5 |
| H3' |
C3' |
C4' |
O4' |
103.3 |
116.8 |
| H3' |
C3' |
C4' |
H4' |
220.2 |
236.1 |
| O3' |
C3' |
C2' |
H2' |
277.1 |
216.0 |
| C4' |
C3' |
O3' |
H3' |
244.2 |
237.5 |
| O3' |
C3' |
C4' |
O4' |
206.0 |
239.4 |
| O3' |
C3' |
C4' |
H4' |
322.9 |
358.7 |
| HO3' |
O3' |
C3' |
C4' |
311.2 |
176.2 |
| HO3' |
O3' |
C3' |
H3' |
67.0 |
298.8 |
| O1A |
P |
O3A |
O5' |
116.3 |
120.0 |
| O2A |
P |
O3A |
O5' |
246.1 |
240.1 |
| O3A |
P |
O5' |
C5' |
301.8 |
185.0 |
| O3A |
P |
O1A |
HO1A |
120.9 |
300.0 |
| C4' |
O4' |
C1' |
H1' |
132.1 |
78.7 |
| O4' |
C4' |
C3' |
H3' |
103.3 |
116.8 |
| C3' |
C4' |
O4' |
H4' |
113.3 |
119.4 |
| C5' |
C4' |
O4' |
H4' |
261.7 |
238.9 |
| H4' |
C4' |
C3' |
H3' |
220.2 |
236.1 |
| C3' |
C4' |
H4' |
O4' |
242.9 |
242.2 |
| C2' |
C1' |
O4' |
H1' |
239.7 |
241.5 |
| P |
O5' |
C5' |
C4' |
238.8 |
180.0 |
| C5' |
C4' |
C3' |
H3' |
316.2 |
357.3 |
| C3' |
C4' |
C5' |
H4' |
255.2 |
238.9 |
| O4' |
C4' |
C5' |
H4' |
110.9 |
121.0 |
| O5' |
C5' |
C4' |
H4' |
182.3 |
306.0 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
302.4 |
66.1 |
| O5' |
C5' |
H5' |
H5'A |
239.3 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
62.4 |
186.1 |
| O5' |
C5' |
H5'A |
H5' |
120.7 |
120.0 |
| CA |
N |
H18 |
HN |
240.0 |
236.1 |
| H19 |
CA |
N |
HN |
284.0 |
180.0 |
| H19 |
CA |
N |
H18 |
44.0 |
304.0 |