PDB Chemical Component APD
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 APD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C |
O |
1.230 |
1.208 |
| C |
CA |
1.512 |
1.506 |
| C |
OXT |
1.333 |
1.342 |
| CA |
N |
1.449 |
1.469 |
| CA |
CB |
1.527 |
1.529 |
| CA |
HA |
1.115 |
1.090 |
| N |
H |
1.020 |
1.009 |
| N |
H2 |
1.020 |
1.009 |
| CB |
CG |
1.515 |
1.506 |
| CB |
HBC1 |
1.115 |
1.091 |
| CB |
HBC2 |
1.115 |
1.089 |
| CG |
CD1 |
1.401 |
1.382 |
| CG |
CD2 |
1.392 |
1.381 |
| CD1 |
CE1 |
1.400 |
1.382 |
| CD1 |
HD1 |
1.103 |
1.080 |
| CD2 |
CE2 |
1.397 |
1.382 |
| CD2 |
HD2 |
1.103 |
1.080 |
| CE1 |
CZ |
1.394 |
1.382 |
| CE1 |
HE1 |
1.103 |
1.080 |
| CE2 |
CZ |
1.397 |
1.382 |
| CE2 |
C5 |
1.499 |
1.507 |
| CZ |
HZ |
1.103 |
1.080 |
| C5 |
H5C1 |
1.115 |
1.088 |
| C5 |
H5C2 |
1.115 |
1.090 |
| C5 |
H5C3 |
1.115 |
1.090 |
| OXT |
HXT |
0.950 |
0.967 |
Bond Angles for APD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O |
C |
CA |
119.8 |
120.0 |
| O |
C |
OXT |
124.1 |
120.0 |
| CA |
C |
OXT |
116.1 |
120.0 |
| C |
CA |
N |
110.0 |
109.5 |
| C |
CA |
CB |
110.8 |
109.5 |
| C |
CA |
HA |
108.7 |
109.5 |
| C |
OXT |
HXT |
124.1 |
120.0 |
| N |
CA |
CB |
110.0 |
109.4 |
| N |
CA |
HA |
108.7 |
109.4 |
| CA |
N |
H |
110.0 |
106.6 |
| CA |
N |
H2 |
112.0 |
106.7 |
| CB |
CA |
HA |
108.7 |
109.5 |
| CA |
CB |
CG |
111.3 |
109.5 |
| CA |
CB |
HBC1 |
111.5 |
109.4 |
| CA |
CB |
HBC2 |
111.5 |
109.5 |
| H |
N |
H2 |
112.0 |
106.7 |
| CG |
CB |
HBC1 |
111.5 |
109.4 |
| CG |
CB |
HBC2 |
111.5 |
109.6 |
| CB |
CG |
CD1 |
120.9 |
119.9 |
| CB |
CG |
CD2 |
120.4 |
120.1 |
| HBC1 |
CB |
HBC2 |
98.8 |
109.4 |
| CD1 |
CG |
CD2 |
118.6 |
120.0 |
| CG |
CD1 |
CE1 |
120.8 |
120.0 |
| CG |
CD1 |
HD1 |
119.6 |
120.0 |
| CG |
CD2 |
CE2 |
121.6 |
120.0 |
| CG |
CD2 |
HD2 |
119.2 |
120.0 |
| CE1 |
CD1 |
HD1 |
119.6 |
120.0 |
| CD1 |
CE1 |
CZ |
119.3 |
120.0 |
| CD1 |
CE1 |
HE1 |
120.4 |
120.0 |
| CE2 |
CD2 |
HD2 |
119.2 |
120.0 |
| CD2 |
CE2 |
CZ |
118.8 |
120.0 |
| CD2 |
CE2 |
C5 |
120.3 |
120.0 |
| CZ |
CE1 |
HE1 |
120.3 |
120.0 |
| CE1 |
CZ |
CE2 |
120.8 |
120.0 |
| CE1 |
CZ |
HZ |
119.6 |
120.0 |
| CZ |
CE2 |
C5 |
120.9 |
120.0 |
| CE2 |
CZ |
HZ |
119.6 |
120.0 |
| CE2 |
C5 |
H5C1 |
120.9 |
109.5 |
| CE2 |
C5 |
H5C2 |
108.1 |
109.4 |
| CE2 |
C5 |
H5C3 |
108.1 |
109.5 |
| H5C1 |
C5 |
H5C2 |
108.1 |
109.5 |
| H5C1 |
C5 |
H5C3 |
108.1 |
109.5 |
| H5C2 |
C5 |
H5C3 |
101.8 |
109.5 |
Torsion Angles for APD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
C |
O |
OXT |
180.1 |
180.0 |
| O |
C |
CA |
N |
322.3 |
330.0 |
| O |
C |
CA |
CB |
84.1 |
90.0 |
| O |
C |
CA |
HA |
203.5 |
210.0 |
| O |
C |
OXT |
HXT |
180.0 |
359.9 |
| O |
C |
CA |
OXT |
179.9 |
180.0 |
| CA |
C |
OXT |
HXT |
359.9 |
180.0 |
| N |
CA |
C |
CB |
238.2 |
240.0 |
| N |
CA |
C |
HA |
118.8 |
119.9 |
| C |
CA |
N |
H |
180.0 |
60.0 |
| C |
CA |
N |
H2 |
54.7 |
173.8 |
| CB |
CA |
C |
HA |
240.7 |
240.0 |
| C |
CA |
CB |
CG |
175.3 |
179.9 |
| C |
CA |
CB |
HBC1 |
50.1 |
60.0 |
| C |
CA |
CB |
HBC2 |
300.6 |
300.1 |
| O |
C |
OXT |
CA |
180.1 |
180.0 |
| OXT |
C |
CA |
N |
142.4 |
149.9 |
| OXT |
C |
CA |
CB |
264.2 |
269.9 |
| OXT |
C |
CA |
HA |
23.6 |
30.0 |
| N |
CA |
C |
OXT |
142.4 |
149.9 |
| C |
CA |
N |
CB |
122.3 |
120.1 |
| C |
CA |
N |
HA |
241.2 |
240.0 |
| CB |
CA |
N |
HA |
118.9 |
119.9 |
| N |
CA |
CB |
CG |
297.1 |
300.0 |
| N |
CA |
CB |
HBC1 |
171.9 |
180.1 |
| N |
CA |
CB |
HBC2 |
62.4 |
60.1 |
| H |
N |
CA |
H2 |
125.3 |
246.2 |
| CB |
CA |
C |
OXT |
264.2 |
269.9 |
| C |
CA |
CB |
N |
238.2 |
240.0 |
| C |
CA |
CB |
HA |
119.3 |
120.0 |
| N |
CA |
CB |
HA |
241.1 |
240.1 |
| CB |
CA |
N |
H |
57.7 |
299.9 |
| CB |
CA |
N |
H2 |
292.4 |
53.7 |
| CG |
CB |
CA |
HBC1 |
125.3 |
119.9 |
| CG |
CB |
CA |
HBC2 |
234.7 |
239.8 |
| CA |
CB |
CG |
CD1 |
272.8 |
90.0 |
| CA |
CB |
CG |
CD2 |
89.9 |
270.2 |
| HBC1 |
CB |
CA |
HBC2 |
109.5 |
119.9 |
| HA |
CA |
C |
OXT |
23.6 |
30.0 |
| C |
CA |
HA |
N |
119.6 |
120.0 |
| C |
CA |
HA |
CB |
239.4 |
239.9 |
| N |
CA |
HA |
CB |
119.7 |
119.9 |
| HA |
CA |
N |
H |
298.8 |
180.0 |
| HA |
CA |
N |
H2 |
173.6 |
293.8 |
| HA |
CA |
CB |
CG |
56.0 |
59.9 |
| HA |
CA |
CB |
HBC1 |
290.7 |
300.0 |
| HA |
CA |
CB |
HBC2 |
181.3 |
180.0 |
| H |
N |
CA |
CB |
57.7 |
299.9 |
| H |
N |
CA |
HA |
298.8 |
180.0 |
| CA |
N |
H |
H2 |
234.7 |
113.8 |
| H2 |
N |
CA |
CB |
292.4 |
53.7 |
| H2 |
N |
CA |
HA |
173.6 |
293.8 |
| CA |
N |
H2 |
H |
124.2 |
246.3 |
| CG |
CB |
CA |
HA |
56.0 |
59.9 |
| CA |
CB |
CG |
HBC1 |
234.7 |
240.1 |
| CA |
CB |
CG |
HBC2 |
125.3 |
120.1 |
| HBC1 |
CB |
CG |
HBC2 |
250.6 |
240.0 |
| CD1 |
CG |
CB |
CD2 |
182.9 |
179.8 |
| CB |
CG |
CD1 |
CE1 |
176.7 |
180.0 |
| CB |
CG |
CD1 |
HD1 |
356.7 |
0.0 |
| CB |
CG |
CD2 |
CE2 |
183.2 |
180.3 |
| CB |
CG |
CD2 |
HD2 |
3.3 |
359.8 |
| HBC1 |
CB |
CA |
HA |
290.7 |
300.0 |
| CA |
CB |
HBC1 |
CG |
125.1 |
120.0 |
| CA |
CB |
HBC1 |
HBC2 |
242.6 |
240.0 |
| CG |
CB |
HBC1 |
HBC2 |
117.4 |
120.0 |
| HBC1 |
CB |
CG |
CD1 |
38.1 |
210.0 |
| HBC1 |
CB |
CG |
CD2 |
215.2 |
30.2 |
| HBC2 |
CB |
CA |
HA |
181.3 |
180.0 |
| CA |
CB |
HBC2 |
CG |
234.9 |
239.8 |
| CA |
CB |
HBC2 |
HBC1 |
117.4 |
119.9 |
| CG |
CB |
HBC2 |
HBC1 |
242.6 |
240.1 |
| HBC2 |
CB |
CG |
CD1 |
147.6 |
329.9 |
| HBC2 |
CB |
CG |
CD2 |
324.7 |
150.1 |
| CD1 |
CG |
CB |
HBC1 |
38.1 |
210.0 |
| CD1 |
CG |
CB |
HBC2 |
147.6 |
329.9 |
| CB |
CG |
CD1 |
CD2 |
177.1 |
180.2 |
| CD1 |
CG |
CD2 |
CE2 |
0.4 |
0.5 |
| CD1 |
CG |
CD2 |
HD2 |
180.4 |
180.0 |
| CE1 |
CD1 |
CG |
HD1 |
180.0 |
180.0 |
| CG |
CD1 |
CE1 |
CZ |
0.2 |
360.0 |
| CG |
CD1 |
CE1 |
HE1 |
180.2 |
180.0 |
| CD2 |
CG |
CB |
HBC1 |
215.2 |
30.2 |
| CD2 |
CG |
CB |
HBC2 |
324.7 |
150.1 |
| CB |
CG |
CD2 |
CD1 |
182.8 |
179.8 |
| CD2 |
CG |
CD1 |
CE1 |
359.6 |
359.8 |
| CD2 |
CG |
CD1 |
HD1 |
179.6 |
179.8 |
| CE2 |
CD2 |
CG |
HD2 |
180.0 |
180.5 |
| CG |
CD2 |
CE2 |
CZ |
359.9 |
359.5 |
| CG |
CD2 |
CE2 |
C5 |
179.7 |
179.8 |
| CE1 |
CD1 |
CG |
CD2 |
359.6 |
359.8 |
| CG |
CD1 |
CE1 |
HD1 |
180.0 |
180.0 |
| CZ |
CE1 |
CD1 |
HE1 |
180.0 |
180.0 |
| CD1 |
CE1 |
CZ |
CE2 |
0.2 |
-0.0 |
| CD1 |
CE1 |
CZ |
HZ |
180.2 |
180.0 |
| HD1 |
CD1 |
CG |
CD2 |
179.6 |
179.8 |
| CG |
CD1 |
HD1 |
CE1 |
180.0 |
180.0 |
| HD1 |
CD1 |
CE1 |
CZ |
180.1 |
179.9 |
| HD1 |
CD1 |
CE1 |
HE1 |
0.1 |
360.0 |
| CG |
CD2 |
CE2 |
HD2 |
180.0 |
179.5 |
| CE1 |
CZ |
CE2 |
CD2 |
359.8 |
0.3 |
| CZ |
CE2 |
CD2 |
C5 |
180.2 |
179.7 |
| CD2 |
CE2 |
CZ |
HZ |
179.8 |
180.3 |
| CD2 |
CE2 |
C5 |
H5C1 |
0.2 |
269.7 |
| CD2 |
CE2 |
C5 |
H5C2 |
235.0 |
29.7 |
| CD2 |
CE2 |
C5 |
H5C3 |
125.5 |
149.7 |
| CG |
CD2 |
HD2 |
CE2 |
180.0 |
180.5 |
| HD2 |
CD2 |
CE2 |
CZ |
179.9 |
180.0 |
| HD2 |
CD2 |
CE2 |
C5 |
359.7 |
0.3 |
| CZ |
CE1 |
CD1 |
HD1 |
180.1 |
179.9 |
| CD1 |
CE1 |
CZ |
HE1 |
180.0 |
180.0 |
| CD2 |
CE2 |
CZ |
CE1 |
359.8 |
0.3 |
| CE1 |
CZ |
CE2 |
C5 |
180.0 |
180.0 |
| CE2 |
CZ |
CE1 |
HZ |
180.0 |
180.0 |
| HE1 |
CE1 |
CD1 |
HD1 |
0.1 |
360.0 |
| CD1 |
CE1 |
HE1 |
CZ |
180.0 |
180.0 |
| HE1 |
CE1 |
CZ |
CE2 |
180.2 |
180.0 |
| HE1 |
CE1 |
CZ |
HZ |
0.2 |
360.0 |
| CZ |
CE2 |
CD2 |
HD2 |
179.9 |
180.0 |
| CD2 |
CE2 |
CZ |
C5 |
179.8 |
180.3 |
| CE2 |
CZ |
CE1 |
HE1 |
180.2 |
180.0 |
| CE1 |
CZ |
CE2 |
HZ |
180.0 |
180.0 |
| CZ |
CE2 |
C5 |
H5C1 |
180.0 |
90.0 |
| CZ |
CE2 |
C5 |
H5C2 |
54.8 |
210.0 |
| CZ |
CE2 |
C5 |
H5C3 |
305.3 |
330.0 |
| C5 |
CE2 |
CD2 |
HD2 |
359.7 |
0.3 |
| CD2 |
CE2 |
C5 |
CZ |
180.2 |
179.7 |
| C5 |
CE2 |
CZ |
HZ |
360.0 |
360.0 |
| H5C1 |
C5 |
CE2 |
H5C2 |
125.3 |
240.0 |
| H5C1 |
C5 |
CE2 |
H5C3 |
234.7 |
120.0 |
| H5C2 |
C5 |
CE2 |
H5C3 |
109.5 |
240.0 |
| HZ |
CZ |
CE1 |
HE1 |
0.2 |
360.0 |
| CE1 |
CZ |
HZ |
CE2 |
180.0 |
180.0 |
| HZ |
CZ |
CE2 |
C5 |
360.0 |
360.0 |
| CE2 |
C5 |
H5C1 |
H5C2 |
234.7 |
119.9 |
| CE2 |
C5 |
H5C1 |
H5C3 |
125.3 |
240.0 |
| H5C2 |
C5 |
H5C1 |
H5C3 |
250.5 |
120.0 |
| CE2 |
C5 |
H5C2 |
H5C1 |
132.5 |
240.0 |
| CE2 |
C5 |
H5C2 |
H5C3 |
246.3 |
120.0 |
| H5C1 |
C5 |
H5C2 |
H5C3 |
113.8 |
240.0 |
| CE2 |
C5 |
H5C3 |
H5C1 |
227.5 |
120.0 |
| CE2 |
C5 |
H5C3 |
H5C2 |
113.8 |
240.0 |
| H5C1 |
C5 |
H5C3 |
H5C2 |
246.2 |
120.0 |