PDB Chemical Component APM
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 APM
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.463 |
1.468 |
| N |
H |
1.020 |
1.009 |
| N |
H2 |
1.020 |
1.009 |
| CA |
C |
1.543 |
1.507 |
| CA |
CB |
1.539 |
1.529 |
| CA |
HA |
1.116 |
1.090 |
| C |
O |
1.243 |
1.207 |
| C |
OXT |
1.346 |
1.342 |
| CB |
CG |
1.534 |
1.506 |
| CB |
HB2 |
1.116 |
1.090 |
| CB |
HB3 |
1.115 |
1.089 |
| CG |
CD1 |
1.381 |
1.379 |
| CG |
CD2 |
1.382 |
1.383 |
| CD1 |
CE1 |
1.382 |
1.394 |
| CD1 |
HD1 |
1.102 |
1.080 |
| CD2 |
CE2 |
1.375 |
1.384 |
| CD2 |
HD2 |
1.104 |
1.079 |
| CE1 |
CZ |
1.397 |
1.394 |
| CE1 |
CF |
1.405 |
1.481 |
| CE2 |
CZ |
1.380 |
1.380 |
| CE2 |
HE2 |
1.103 |
1.080 |
| CZ |
HZ |
1.102 |
1.080 |
| CF |
NG1 |
1.345 |
1.302 |
| CF |
NG2 |
1.348 |
1.378 |
| NG1 |
HG1 |
1.020 |
0.970 |
| NG2 |
HG21 |
1.020 |
0.970 |
| NG2 |
HG22 |
1.020 |
0.969 |
| OXT |
HXT |
0.950 |
0.968 |
Bond Angles for APM
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
112.4 |
106.7 |
| CA |
N |
H2 |
111.1 |
106.7 |
| N |
CA |
C |
112.5 |
109.5 |
| N |
CA |
CB |
109.2 |
109.5 |
| N |
CA |
HA |
108.2 |
109.4 |
| H |
N |
H2 |
111.1 |
106.7 |
| C |
CA |
CB |
111.0 |
109.5 |
| C |
CA |
HA |
106.2 |
109.4 |
| CA |
C |
O |
118.4 |
120.0 |
| CA |
C |
OXT |
120.6 |
120.0 |
| CB |
CA |
HA |
109.7 |
109.4 |
| CA |
CB |
CG |
116.4 |
109.5 |
| CA |
CB |
HB2 |
109.7 |
109.4 |
| CA |
CB |
HB3 |
109.7 |
109.5 |
| O |
C |
OXT |
120.9 |
120.0 |
| C |
OXT |
HXT |
120.6 |
120.0 |
| CG |
CB |
HB2 |
109.7 |
109.5 |
| CG |
CB |
HB3 |
109.7 |
109.5 |
| CB |
CG |
CD1 |
121.3 |
120.0 |
| CB |
CG |
CD2 |
120.6 |
119.9 |
| HB2 |
CB |
HB3 |
100.4 |
109.5 |
| CD1 |
CG |
CD2 |
118.1 |
120.1 |
| CG |
CD1 |
CE1 |
124.4 |
119.9 |
| CG |
CD1 |
HD1 |
117.8 |
120.0 |
| CG |
CD2 |
CE2 |
119.1 |
120.3 |
| CG |
CD2 |
HD2 |
120.8 |
119.9 |
| CE1 |
CD1 |
HD1 |
117.8 |
120.1 |
| CD1 |
CE1 |
CZ |
116.0 |
119.7 |
| CD1 |
CE1 |
CF |
122.4 |
120.1 |
| CE2 |
CD2 |
HD2 |
120.2 |
119.8 |
| CD2 |
CE2 |
CZ |
122.0 |
120.1 |
| CD2 |
CE2 |
HE2 |
118.8 |
119.9 |
| CZ |
CE1 |
CF |
121.5 |
120.1 |
| CE1 |
CZ |
CE2 |
120.4 |
119.8 |
| CE1 |
CZ |
HZ |
120.4 |
120.1 |
| CE1 |
CF |
NG1 |
119.2 |
120.0 |
| CE1 |
CF |
NG2 |
120.1 |
120.0 |
| CZ |
CE2 |
HE2 |
119.2 |
120.0 |
| CE2 |
CZ |
HZ |
119.2 |
120.1 |
| NG1 |
CF |
NG2 |
120.7 |
120.0 |
| CF |
NG1 |
HG1 |
112.5 |
120.0 |
| CF |
NG2 |
HG21 |
120.1 |
120.0 |
| CF |
NG2 |
HG22 |
108.3 |
120.0 |
| HG21 |
NG2 |
HG22 |
108.4 |
120.0 |
Torsion Angles for APM
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
125.3 |
113.7 |
| C |
CA |
N |
CB |
123.6 |
120.1 |
| C |
CA |
N |
HA |
243.0 |
240.0 |
| N |
CA |
C |
O |
328.9 |
330.0 |
| N |
CA |
C |
OXT |
151.6 |
149.9 |
| CB |
CA |
N |
HA |
119.4 |
120.0 |
| N |
CA |
CB |
CG |
89.4 |
300.1 |
| N |
CA |
CB |
HB2 |
214.7 |
60.0 |
| N |
CA |
CB |
HB3 |
324.1 |
180.0 |
| CA |
N |
H |
H2 |
234.8 |
246.3 |
| H |
N |
CA |
C |
180.0 |
173.8 |
| H |
N |
CA |
CB |
56.4 |
53.7 |
| H |
N |
CA |
HA |
297.0 |
293.7 |
| CA |
N |
H2 |
H |
126.0 |
113.8 |
| H2 |
N |
CA |
C |
54.8 |
60.0 |
| H2 |
N |
CA |
CB |
291.1 |
300.0 |
| H2 |
N |
CA |
HA |
171.8 |
180.0 |
| C |
CA |
N |
H |
180.0 |
173.8 |
| C |
CA |
N |
H2 |
54.8 |
60.0 |
| N |
CA |
C |
CB |
237.4 |
239.9 |
| N |
CA |
C |
HA |
118.2 |
120.0 |
| CB |
CA |
C |
HA |
240.8 |
240.1 |
| C |
CA |
CB |
CG |
324.9 |
180.0 |
| C |
CA |
CB |
HB2 |
90.2 |
300.0 |
| C |
CA |
CB |
HB3 |
199.6 |
59.9 |
| O |
C |
CA |
OXT |
177.3 |
180.1 |
| CA |
C |
OXT |
HXT |
180.0 |
180.0 |
| CB |
CA |
N |
H |
56.4 |
53.7 |
| CB |
CA |
N |
H2 |
291.1 |
300.0 |
| N |
CA |
CB |
C |
124.5 |
120.1 |
| N |
CA |
CB |
HA |
241.6 |
240.0 |
| C |
CA |
CB |
HA |
117.1 |
120.0 |
| CB |
CA |
C |
O |
91.5 |
90.1 |
| CB |
CA |
C |
OXT |
274.2 |
270.0 |
| CG |
CB |
CA |
HB2 |
234.7 |
240.0 |
| CG |
CB |
CA |
HB3 |
125.3 |
120.0 |
| CA |
CB |
CG |
CD1 |
271.6 |
269.7 |
| CA |
CB |
CG |
CD2 |
93.6 |
90.0 |
| HB2 |
CB |
CA |
HB3 |
250.6 |
240.0 |
| HA |
CA |
N |
H |
297.0 |
293.7 |
| HA |
CA |
N |
H2 |
171.8 |
180.0 |
| N |
CA |
HA |
C |
239.0 |
240.0 |
| N |
CA |
HA |
CB |
119.0 |
120.0 |
| C |
CA |
HA |
CB |
240.0 |
240.0 |
| HA |
CA |
C |
O |
210.7 |
210.0 |
| HA |
CA |
C |
OXT |
33.4 |
29.9 |
| HA |
CA |
CB |
CG |
207.8 |
60.0 |
| HA |
CA |
CB |
HB2 |
333.1 |
180.0 |
| HA |
CA |
CB |
HB3 |
82.5 |
300.0 |
| O |
C |
CA |
CB |
91.5 |
90.1 |
| O |
C |
CA |
HA |
210.7 |
210.0 |
| CA |
C |
O |
OXT |
182.7 |
179.9 |
| O |
C |
OXT |
HXT |
2.7 |
359.9 |
| OXT |
C |
CA |
CB |
274.2 |
270.0 |
| OXT |
C |
CA |
HA |
33.4 |
29.9 |
| CA |
C |
OXT |
O |
177.2 |
180.1 |
| CG |
CB |
CA |
HA |
207.8 |
60.0 |
| CA |
CB |
CG |
HB2 |
125.3 |
120.0 |
| CA |
CB |
CG |
HB3 |
234.7 |
240.0 |
| HB2 |
CB |
CG |
HB3 |
109.4 |
120.0 |
| CD1 |
CG |
CB |
CD2 |
178.0 |
179.7 |
| CB |
CG |
CD1 |
CE1 |
182.2 |
179.7 |
| CB |
CG |
CD1 |
HD1 |
2.1 |
0.2 |
| CB |
CG |
CD2 |
CE2 |
178.1 |
180.0 |
| CB |
CG |
CD2 |
HD2 |
358.2 |
360.0 |
| HB2 |
CB |
CA |
HA |
333.1 |
180.0 |
| CA |
CB |
HB2 |
CG |
231.0 |
240.0 |
| CA |
CB |
HB2 |
HB3 |
115.5 |
120.0 |
| CG |
CB |
HB2 |
HB3 |
244.5 |
240.0 |
| HB2 |
CB |
CG |
CD1 |
146.3 |
149.7 |
| HB2 |
CB |
CG |
CD2 |
328.4 |
330.0 |
| HB3 |
CB |
CA |
HA |
82.5 |
300.0 |
| CA |
CB |
HB3 |
CG |
129.1 |
120.0 |
| CA |
CB |
HB3 |
HB2 |
244.5 |
240.0 |
| CG |
CB |
HB3 |
HB2 |
115.5 |
120.0 |
| HB3 |
CB |
CG |
CD1 |
36.9 |
29.7 |
| HB3 |
CB |
CG |
CD2 |
218.9 |
210.0 |
| CD1 |
CG |
CB |
HB2 |
146.3 |
149.7 |
| CD1 |
CG |
CB |
HB3 |
36.9 |
29.7 |
| CB |
CG |
CD1 |
CD2 |
182.0 |
180.3 |
| CD1 |
CG |
CD2 |
CE2 |
0.1 |
0.2 |
| CD1 |
CG |
CD2 |
HD2 |
180.1 |
180.2 |
| CE1 |
CD1 |
CG |
HD1 |
180.0 |
179.5 |
| CG |
CD1 |
CE1 |
CZ |
359.6 |
0.6 |
| CG |
CD1 |
CE1 |
CF |
178.7 |
180.3 |
| CD2 |
CG |
CB |
HB2 |
328.4 |
330.0 |
| CD2 |
CG |
CB |
HB3 |
218.9 |
210.0 |
| CB |
CG |
CD2 |
CD1 |
178.0 |
179.7 |
| CD2 |
CG |
CD1 |
CE1 |
0.2 |
359.5 |
| CD2 |
CG |
CD1 |
HD1 |
180.2 |
180.0 |
| CE2 |
CD2 |
CG |
HD2 |
180.0 |
180.0 |
| CG |
CD2 |
CE2 |
CZ |
359.8 |
360.0 |
| CG |
CD2 |
CE2 |
HE2 |
179.8 |
180.0 |
| CE1 |
CD1 |
CG |
CD2 |
0.2 |
359.5 |
| CG |
CD1 |
CE1 |
HD1 |
180.0 |
180.5 |
| CZ |
CE1 |
CD1 |
CF |
180.9 |
180.3 |
| CD1 |
CE1 |
CZ |
CE2 |
0.3 |
359.7 |
| CD1 |
CE1 |
CZ |
HZ |
180.3 |
179.7 |
| CD1 |
CE1 |
CF |
NG1 |
180.6 |
0.3 |
| CD1 |
CE1 |
CF |
NG2 |
1.6 |
180.2 |
| HD1 |
CD1 |
CG |
CD2 |
180.2 |
180.0 |
| CG |
CD1 |
HD1 |
CE1 |
180.0 |
179.5 |
| HD1 |
CD1 |
CE1 |
CZ |
179.6 |
180.1 |
| HD1 |
CD1 |
CE1 |
CF |
358.7 |
359.8 |
| CG |
CD2 |
CE2 |
HD2 |
180.0 |
180.0 |
| CE1 |
CZ |
CE2 |
CD2 |
360.0 |
0.1 |
| CZ |
CE2 |
CD2 |
HE2 |
179.9 |
179.9 |
| CD2 |
CE2 |
CZ |
HZ |
180.0 |
180.0 |
| CG |
CD2 |
HD2 |
CE2 |
180.0 |
180.0 |
| HD2 |
CD2 |
CE2 |
CZ |
179.8 |
180.0 |
| HD2 |
CD2 |
CE2 |
HE2 |
359.8 |
0.0 |
| CZ |
CE1 |
CD1 |
HD1 |
179.6 |
180.1 |
| CD1 |
CE1 |
CZ |
CF |
179.1 |
179.7 |
| CD2 |
CE2 |
CZ |
CE1 |
360.0 |
0.1 |
| CZ |
CE1 |
CF |
NG1 |
359.6 |
180.0 |
| CZ |
CE1 |
CF |
NG2 |
180.7 |
359.9 |
| CE1 |
CZ |
CE2 |
HE2 |
179.9 |
180.0 |
| CE2 |
CZ |
CE1 |
HZ |
180.0 |
179.9 |
| CF |
CE1 |
CD1 |
HD1 |
358.7 |
359.8 |
| CD1 |
CE1 |
CF |
CZ |
181.0 |
180.3 |
| CF |
CE1 |
CZ |
CE2 |
181.2 |
180.0 |
| CF |
CE1 |
CZ |
HZ |
1.2 |
0.0 |
| NG1 |
CF |
CE1 |
NG2 |
178.9 |
180.1 |
| CE1 |
CF |
NG1 |
HG1 |
328.4 |
180.0 |
| CE1 |
CF |
NG2 |
HG21 |
180.0 |
180.0 |
| CE1 |
CF |
NG2 |
HG22 |
54.7 |
0.1 |
| CZ |
CE2 |
CD2 |
HD2 |
179.8 |
180.0 |
| CD2 |
CE2 |
CZ |
HE2 |
180.1 |
180.1 |
| CE2 |
CZ |
CE1 |
CF |
181.2 |
180.0 |
| CE1 |
CZ |
CE2 |
HZ |
180.0 |
180.1 |
| HE2 |
CE2 |
CD2 |
HD2 |
359.8 |
0.0 |
| CD2 |
CE2 |
HE2 |
CZ |
179.9 |
179.9 |
| HE2 |
CE2 |
CZ |
HZ |
360.0 |
359.9 |
| HZ |
CZ |
CE1 |
CF |
1.2 |
0.0 |
| CE1 |
CZ |
HZ |
CE2 |
180.0 |
179.9 |
| HZ |
CZ |
CE2 |
HE2 |
360.0 |
359.9 |
| CE1 |
CF |
NG1 |
NG2 |
181.1 |
179.9 |
| NG1 |
CF |
NG2 |
HG21 |
1.1 |
359.9 |
| NG1 |
CF |
NG2 |
HG22 |
235.8 |
180.0 |
| CE1 |
CF |
NG2 |
NG1 |
178.9 |
180.1 |
| NG2 |
CF |
NG1 |
HG1 |
147.3 |
0.1 |
| HG21 |
NG2 |
CF |
HG22 |
125.3 |
179.9 |
| HG1 |
NG1 |
CF |
NG2 |
147.3 |
0.1 |
| CF |
NG2 |
HG21 |
HG22 |
234.8 |
180.1 |
| CF |
NG2 |
HG22 |
HG21 |
131.9 |
179.9 |