PDB Chemical Component APA
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 APA
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1 |
O1 |
1.262 |
1.209 |
| C1 |
OXT |
1.256 |
1.342 |
| C1 |
C2 |
1.550 |
1.507 |
| OXT |
HXT |
0.950 |
0.968 |
| C2 |
O2 |
1.311 |
1.429 |
| C2 |
C3 |
1.547 |
1.529 |
| C3 |
C1' |
1.551 |
1.508 |
| C3 |
H31 |
1.100 |
1.090 |
| C3 |
H32 |
1.101 |
1.090 |
| C1' |
C2' |
1.389 |
1.383 |
| C1' |
C6' |
1.377 |
1.384 |
| C2' |
C3' |
1.395 |
1.380 |
| C2' |
H2' |
1.080 |
1.080 |
| C3' |
C4' |
1.363 |
1.395 |
| C3' |
H3' |
1.080 |
1.079 |
| C4' |
C5' |
1.392 |
1.395 |
| C4' |
C |
1.398 |
1.481 |
| C5' |
C6' |
1.408 |
1.379 |
| C5' |
H5' |
1.080 |
1.080 |
| C6' |
H6' |
1.080 |
1.080 |
| C |
N1 |
1.300 |
1.378 |
| C |
N2 |
1.333 |
1.302 |
| N1 |
HN11 |
1.000 |
0.970 |
| N1 |
HN12 |
1.000 |
0.969 |
| N2 |
HN2 |
1.000 |
0.970 |
| C2 |
H11 |
1.100 |
1.090 |
| O2 |
H12 |
0.950 |
0.967 |
Bond Angles for APA
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1 |
C1 |
OXT |
122.7 |
120.0 |
| O1 |
C1 |
C2 |
117.6 |
120.0 |
| OXT |
C1 |
C2 |
119.6 |
120.0 |
| C1 |
OXT |
HXT |
109.5 |
117.0 |
| C1 |
C2 |
O2 |
111.7 |
109.5 |
| C1 |
C2 |
C3 |
111.1 |
109.5 |
| C1 |
C2 |
H11 |
112.7 |
109.5 |
| O2 |
C2 |
C3 |
121.7 |
109.5 |
| O2 |
C2 |
H11 |
98.6 |
109.4 |
| C2 |
O2 |
H12 |
109.5 |
114.0 |
| C2 |
C3 |
C1' |
114.9 |
109.5 |
| C2 |
C3 |
H31 |
107.7 |
109.5 |
| C2 |
C3 |
H32 |
107.7 |
109.5 |
| C3 |
C2 |
H11 |
99.4 |
109.5 |
| C1' |
C3 |
H31 |
107.7 |
109.4 |
| C1' |
C3 |
H32 |
107.7 |
109.5 |
| C3 |
C1' |
C2' |
120.0 |
119.9 |
| C3 |
C1' |
C6' |
121.3 |
119.8 |
| H31 |
C3 |
H32 |
111.2 |
109.4 |
| C2' |
C1' |
C6' |
118.7 |
120.3 |
| C1' |
C2' |
C3' |
121.8 |
120.2 |
| C1' |
C2' |
H2' |
119.1 |
120.0 |
| C1' |
C6' |
C5' |
118.8 |
120.1 |
| C1' |
C6' |
H6' |
120.6 |
120.0 |
| C3' |
C2' |
H2' |
119.1 |
119.9 |
| C2' |
C3' |
C4' |
120.2 |
119.8 |
| C2' |
C3' |
H3' |
119.9 |
120.1 |
| C4' |
C3' |
H3' |
119.9 |
120.1 |
| C3' |
C4' |
C5' |
118.2 |
119.7 |
| C3' |
C4' |
C |
119.8 |
120.1 |
| C5' |
C4' |
C |
121.9 |
120.1 |
| C4' |
C5' |
C6' |
122.1 |
119.9 |
| C4' |
C5' |
H5' |
118.9 |
120.0 |
| C4' |
C |
N1 |
117.9 |
120.0 |
| C4' |
C |
N2 |
123.1 |
120.0 |
| C6' |
C5' |
H5' |
118.9 |
120.1 |
| C5' |
C6' |
H6' |
120.7 |
119.9 |
| N1 |
C |
N2 |
116.1 |
120.0 |
| C |
N1 |
HN11 |
120.0 |
119.9 |
| C |
N1 |
HN12 |
120.0 |
120.0 |
| C |
N2 |
HN2 |
112.0 |
120.0 |
| HN11 |
N1 |
HN12 |
120.0 |
120.0 |
Torsion Angles for APA
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OXT |
C1 |
O1 |
C2 |
177.2 |
180.2 |
| O1 |
C1 |
OXT |
HXT |
0.0 |
0.0 |
| O1 |
C1 |
C2 |
O2 |
151.0 |
355.0 |
| O1 |
C1 |
C2 |
C3 |
290.4 |
115.0 |
| O1 |
C1 |
C2 |
H11 |
41.0 |
235.0 |
| O1 |
C1 |
OXT |
C2 |
182.9 |
179.8 |
| OXT |
C1 |
C2 |
O2 |
333.7 |
174.7 |
| OXT |
C1 |
C2 |
C3 |
113.2 |
294.7 |
| OXT |
C1 |
C2 |
H11 |
223.7 |
54.8 |
| O1 |
C1 |
C2 |
OXT |
177.3 |
180.2 |
| C2 |
C1 |
OXT |
HXT |
177.2 |
180.2 |
| O2 |
C2 |
C1 |
C3 |
220.5 |
240.0 |
| O2 |
C2 |
C1 |
H11 |
110.0 |
119.9 |
| C1 |
C2 |
O2 |
H12 |
180.0 |
60.0 |
| C1 |
C2 |
C3 |
C1' |
189.6 |
175.0 |
| C1 |
C2 |
C3 |
H31 |
309.6 |
295.0 |
| C1 |
C2 |
C3 |
H32 |
69.6 |
55.0 |
| C3 |
C2 |
C1 |
H11 |
249.4 |
240.0 |
| HXT |
OXT |
C1 |
C2 |
177.2 |
180.2 |
| C1 |
C2 |
O2 |
C3 |
134.6 |
120.0 |
| C1 |
C2 |
O2 |
H11 |
241.3 |
240.0 |
| O2 |
C2 |
C3 |
C1' |
324.4 |
295.0 |
| O2 |
C2 |
C3 |
H31 |
84.4 |
55.0 |
| O2 |
C2 |
C3 |
H32 |
204.4 |
175.0 |
| C3 |
C2 |
O2 |
H11 |
106.7 |
120.0 |
| C1 |
C2 |
C3 |
O2 |
225.2 |
240.0 |
| C1 |
C2 |
C3 |
H11 |
118.9 |
120.0 |
| O2 |
C2 |
C3 |
H11 |
253.7 |
240.0 |
| C3 |
C2 |
O2 |
H12 |
45.4 |
300.0 |
| C1' |
C3 |
C2 |
H31 |
240.0 |
240.0 |
| C1' |
C3 |
C2 |
H32 |
120.0 |
120.1 |
| C2 |
C3 |
C1' |
C2' |
132.9 |
90.0 |
| C2 |
C3 |
C1' |
C6' |
312.0 |
269.7 |
| H31 |
C3 |
C2 |
H32 |
240.0 |
240.0 |
| C2 |
C3 |
C1' |
H31 |
120.0 |
120.0 |
| C2 |
C3 |
C1' |
H32 |
240.0 |
239.9 |
| C1' |
C3 |
C2 |
H11 |
70.7 |
55.0 |
| H31 |
C3 |
C1' |
H32 |
120.0 |
119.9 |
| C2' |
C1' |
C3 |
C6' |
181.0 |
180.2 |
| C3 |
C1' |
C2' |
C3' |
183.8 |
180.0 |
| C3 |
C1' |
C2' |
H2' |
3.8 |
360.0 |
| C3 |
C1' |
C6' |
C5' |
176.9 |
179.8 |
| C3 |
C1' |
C6' |
H6' |
356.9 |
360.0 |
| C2 |
C3 |
H31 |
C1' |
235.5 |
240.0 |
| C2 |
C3 |
H31 |
H32 |
117.8 |
120.0 |
| H31 |
C3 |
C2 |
H11 |
190.7 |
175.0 |
| C1' |
C3 |
H31 |
H32 |
242.2 |
240.0 |
| H31 |
C3 |
C1' |
C2' |
13.0 |
330.0 |
| H31 |
C3 |
C1' |
C6' |
192.0 |
149.7 |
| C2 |
C3 |
H32 |
C1' |
124.5 |
120.1 |
| C2 |
C3 |
H32 |
H31 |
242.2 |
240.0 |
| H32 |
C3 |
C2 |
H11 |
310.7 |
294.9 |
| C1' |
C3 |
H32 |
H31 |
117.8 |
119.9 |
| H32 |
C3 |
C1' |
C2' |
253.0 |
210.0 |
| H32 |
C3 |
C1' |
C6' |
72.0 |
29.8 |
| C2' |
C1' |
C3 |
H31 |
13.0 |
330.0 |
| C2' |
C1' |
C3 |
H32 |
253.0 |
210.0 |
| C3 |
C1' |
C2' |
C6' |
179.1 |
179.8 |
| C2' |
C1' |
C6' |
C5' |
355.9 |
359.5 |
| C2' |
C1' |
C6' |
H6' |
176.0 |
179.7 |
| C3' |
C2' |
C1' |
H2' |
180.0 |
180.0 |
| C1' |
C2' |
C3' |
C4' |
358.8 |
359.9 |
| C1' |
C2' |
C3' |
H3' |
178.8 |
180.0 |
| C6' |
C1' |
C3 |
H31 |
192.0 |
149.7 |
| C6' |
C1' |
C3 |
H32 |
72.0 |
29.8 |
| C3 |
C1' |
C6' |
C2' |
180.9 |
180.2 |
| C6' |
C1' |
C2' |
C3' |
4.7 |
0.3 |
| C6' |
C1' |
C2' |
H2' |
184.7 |
180.2 |
| C4' |
C5' |
C6' |
C1' |
0.1 |
0.4 |
| C1' |
C6' |
C5' |
H5' |
180.1 |
180.3 |
| C5' |
C6' |
C1' |
H6' |
180.0 |
179.8 |
| C3' |
C2' |
C1' |
C6' |
4.7 |
0.3 |
| C1' |
C2' |
C3' |
H2' |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
H3' |
180.0 |
180.0 |
| C2' |
C3' |
C4' |
C5' |
357.3 |
0.0 |
| C2' |
C3' |
C4' |
C |
180.5 |
180.0 |
| H2' |
C2' |
C1' |
C6' |
184.7 |
180.2 |
| C1' |
C2' |
H2' |
C3' |
180.0 |
180.0 |
| H2' |
C2' |
C3' |
C4' |
178.8 |
180.0 |
| H2' |
C2' |
C3' |
H3' |
358.8 |
0.0 |
| C4' |
C3' |
C2' |
H2' |
178.8 |
180.0 |
| C2' |
C3' |
C4' |
H3' |
180.0 |
180.0 |
| C5' |
C4' |
C3' |
C |
176.8 |
180.0 |
| C3' |
C4' |
C5' |
C6' |
3.3 |
359.8 |
| C3' |
C4' |
C5' |
H5' |
183.3 |
179.9 |
| C3' |
C4' |
C |
N1 |
354.5 |
180.0 |
| C3' |
C4' |
C |
N2 |
194.5 |
360.0 |
| H3' |
C3' |
C2' |
H2' |
358.8 |
0.0 |
| C2' |
C3' |
H3' |
C4' |
180.0 |
180.0 |
| H3' |
C3' |
C4' |
C5' |
177.3 |
180.0 |
| H3' |
C3' |
C4' |
C |
0.5 |
360.0 |
| C1' |
C6' |
C5' |
C4' |
0.1 |
0.4 |
| C5' |
C4' |
C3' |
H3' |
177.3 |
180.0 |
| C3' |
C4' |
C5' |
C |
183.3 |
180.0 |
| C5' |
C4' |
C |
N1 |
177.8 |
0.0 |
| C5' |
C4' |
C |
N2 |
17.9 |
180.0 |
| C6' |
C5' |
C4' |
H5' |
180.0 |
179.9 |
| C4' |
C5' |
C6' |
H6' |
180.1 |
180.2 |
| C |
C4' |
C3' |
H3' |
0.5 |
360.0 |
| C3' |
C4' |
C |
C5' |
176.7 |
180.0 |
| C |
C4' |
C5' |
C6' |
180.0 |
179.8 |
| C |
C4' |
C5' |
H5' |
0.0 |
359.9 |
| N1 |
C |
C4' |
N2 |
159.9 |
180.1 |
| C4' |
C |
N1 |
HN11 |
198.7 |
360.0 |
| C4' |
C |
N1 |
HN12 |
18.7 |
180.0 |
| C4' |
C |
N2 |
HN2 |
160.3 |
180.0 |
| C1' |
C6' |
C5' |
H6' |
180.0 |
180.2 |
| C6' |
C5' |
C4' |
C |
180.0 |
179.8 |
| C4' |
C5' |
C6' |
H5' |
180.0 |
180.1 |
| H5' |
C5' |
C4' |
C |
0.0 |
359.9 |
| C4' |
C5' |
H5' |
C6' |
180.0 |
179.9 |
| H5' |
C5' |
C6' |
H6' |
0.1 |
0.1 |
| C1' |
C6' |
H6' |
C5' |
180.0 |
179.8 |
| H6' |
C6' |
C5' |
H5' |
0.1 |
0.1 |
| C4' |
C |
N1 |
N2 |
198.6 |
179.9 |
| N1 |
C |
N2 |
HN2 |
360.0 |
360.0 |
| HN11 |
N1 |
C |
HN12 |
180.0 |
179.9 |
| C4' |
C |
N2 |
N1 |
160.3 |
180.1 |
| N2 |
C |
N1 |
HN11 |
0.0 |
180.0 |
| N2 |
C |
N1 |
HN12 |
180.0 |
0.1 |
| HN11 |
N1 |
C |
N2 |
0.0 |
180.0 |
| C |
N1 |
HN11 |
HN12 |
180.0 |
180.1 |
| HN12 |
N1 |
C |
N2 |
180.0 |
0.1 |
| C |
N1 |
HN12 |
HN11 |
180.0 |
179.9 |
| C1 |
C2 |
H11 |
O2 |
118.0 |
120.0 |
| C1 |
C2 |
H11 |
C3 |
242.3 |
239.9 |
| O2 |
C2 |
H11 |
C3 |
124.3 |
120.0 |
| H11 |
C2 |
O2 |
H12 |
298.7 |
180.0 |
| H11 |
C2 |
C3 |
C1' |
70.7 |
55.0 |
| H11 |
C2 |
C3 |
H31 |
190.7 |
175.0 |
| H11 |
C2 |
C3 |
H32 |
310.7 |
294.9 |
| H12 |
O2 |
C2 |
C3 |
45.4 |
300.0 |
| H12 |
O2 |
C2 |
H11 |
298.7 |
180.0 |