PDB Chemical Component OPY
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 OPY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O |
C |
1.229 |
1.213 |
| CA |
C |
1.533 |
1.507 |
| C |
NAM |
1.349 |
1.348 |
| N |
CA |
1.474 |
1.469 |
| N |
HN |
1.000 |
1.009 |
| N |
HNA |
1.000 |
1.009 |
| CA |
CB |
1.535 |
1.530 |
| CA |
HA |
1.100 |
1.090 |
| CB |
CAD |
1.543 |
1.530 |
| CB |
HB |
1.100 |
1.090 |
| CB |
HBA |
1.100 |
1.089 |
| CAD |
NAA |
1.467 |
1.469 |
| NAA |
HNAA |
1.000 |
1.009 |
| NAA |
HNAB |
1.000 |
1.009 |
| CAD |
HAD |
1.100 |
1.090 |
| CAD |
HADA |
1.100 |
1.090 |
| CAF |
CAE |
1.514 |
1.531 |
| CAG |
CAE |
1.534 |
1.530 |
| CAE |
HAE |
1.100 |
1.090 |
| CAE |
HAEA |
1.100 |
1.091 |
| CAI |
CAF |
1.535 |
1.533 |
| CAF |
HAF |
1.100 |
1.089 |
| CAF |
HAFA |
1.100 |
1.090 |
| CAJ |
CAG |
1.530 |
1.532 |
| CAG |
HAG |
1.100 |
1.090 |
| CAG |
HAGA |
1.100 |
1.090 |
| NAM |
CAI |
1.490 |
1.469 |
| CAI |
HAI |
1.100 |
1.090 |
| CAI |
HAIA |
1.101 |
1.089 |
| NAM |
CAJ |
1.488 |
1.469 |
| CAJ |
HAJ |
1.100 |
1.090 |
| CAJ |
HAJA |
1.100 |
1.090 |
Bond Angles for OPY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O |
C |
NAM |
120.0 |
120.0 |
| CA |
C |
NAM |
122.1 |
120.0 |
| C |
NAM |
CAI |
119.3 |
120.6 |
| C |
NAM |
CAJ |
121.0 |
120.6 |
| CA |
N |
HN |
109.5 |
111.0 |
| CA |
N |
HNA |
109.4 |
111.0 |
| N |
CA |
CB |
109.4 |
109.5 |
| N |
CA |
HA |
110.9 |
109.5 |
| HN |
N |
HNA |
109.5 |
111.0 |
| CB |
CA |
HA |
108.1 |
109.5 |
| CA |
CB |
CAD |
112.4 |
109.4 |
| CA |
CB |
HB |
108.5 |
109.5 |
| CA |
CB |
HBA |
108.5 |
109.5 |
| CAD |
CB |
HB |
108.5 |
109.4 |
| CAD |
CB |
HBA |
108.5 |
109.5 |
| CB |
CAD |
NAA |
109.7 |
109.4 |
| CB |
CAD |
HAD |
109.4 |
109.4 |
| CB |
CAD |
HADA |
109.4 |
109.6 |
| HB |
CB |
HBA |
110.4 |
109.5 |
| CAD |
NAA |
HNAA |
109.5 |
111.0 |
| CAD |
NAA |
HNAB |
109.5 |
111.0 |
| HNAA |
NAA |
HNAB |
109.5 |
111.0 |
| HAD |
CAD |
HADA |
109.6 |
109.5 |
| CAF |
CAE |
HAE |
109.5 |
109.4 |
| CAF |
CAE |
HAEA |
109.5 |
109.4 |
| CAG |
CAE |
HAE |
109.4 |
109.5 |
| CAG |
CAE |
HAEA |
109.4 |
109.5 |
| HAE |
CAE |
HAEA |
109.5 |
109.4 |
| CAI |
CAF |
HAF |
108.2 |
109.5 |
| CAI |
CAF |
HAFA |
108.3 |
109.5 |
| HAF |
CAF |
HAFA |
110.6 |
109.5 |
| CAJ |
CAG |
HAG |
109.3 |
109.5 |
| CAJ |
CAG |
HAGA |
109.3 |
109.5 |
| HAG |
CAG |
HAGA |
109.6 |
109.5 |
| NAM |
CAI |
HAI |
107.9 |
109.6 |
| NAM |
CAI |
HAIA |
107.9 |
109.7 |
| HAI |
CAI |
HAIA |
111.0 |
109.6 |
| NAM |
CAJ |
HAJ |
109.2 |
109.6 |
| NAM |
CAJ |
HAJA |
109.2 |
109.7 |
| HAJ |
CAJ |
HAJA |
109.8 |
109.6 |
Torsion Angles for OPY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
C |
O |
NAM |
177.8 |
180.3 |
| O |
C |
NAM |
CAI |
356.9 |
360.0 |
| O |
C |
NAM |
CAJ |
178.9 |
180.0 |
| O |
C |
CA |
NAM |
182.2 |
179.7 |
| CA |
C |
NAM |
CAI |
179.1 |
179.7 |
| CA |
C |
NAM |
CAJ |
1.1 |
359.8 |
| C |
NAM |
CAI |
HAI |
26.5 |
6.7 |
| C |
NAM |
CAI |
HAIA |
266.5 |
246.3 |
| C |
NAM |
CAJ |
HAJ |
101.3 |
113.8 |
| C |
NAM |
CAJ |
HAJA |
341.3 |
353.4 |
| N |
CA |
C |
NAM |
170.5 |
160.0 |
| HN |
N |
CA |
HNA |
240.0 |
236.1 |
| CB |
CA |
N |
HA |
119.2 |
120.1 |
| N |
CA |
CB |
CAD |
70.0 |
295.0 |
| N |
CA |
CB |
HB |
190.0 |
54.9 |
| N |
CA |
CB |
HBA |
310.0 |
175.0 |
| CA |
N |
HN |
HNA |
120.0 |
123.9 |
| HN |
N |
CA |
CB |
59.1 |
300.0 |
| HN |
N |
CA |
HA |
299.9 |
180.0 |
| CA |
N |
HNA |
HN |
240.0 |
236.1 |
| HNA |
N |
CA |
CB |
179.1 |
64.0 |
| HNA |
N |
CA |
HA |
59.9 |
303.9 |
| CB |
CA |
C |
NAM |
290.5 |
280.0 |
| CB |
CA |
N |
HN |
59.1 |
300.0 |
| CB |
CA |
N |
HNA |
179.1 |
64.0 |
| N |
CA |
CB |
HA |
239.1 |
239.9 |
| CAD |
CB |
CA |
HB |
240.0 |
240.1 |
| CAD |
CB |
CA |
HBA |
120.0 |
120.1 |
| CA |
CB |
CAD |
NAA |
187.1 |
180.0 |
| CA |
CB |
CAD |
HAD |
307.1 |
299.9 |
| CA |
CB |
CAD |
HADA |
67.1 |
60.0 |
| HB |
CB |
CA |
HBA |
240.0 |
240.0 |
| HA |
CA |
C |
NAM |
49.7 |
40.0 |
| HA |
CA |
N |
HN |
299.9 |
180.0 |
| HA |
CA |
N |
HNA |
59.9 |
303.9 |
| N |
CA |
HA |
CB |
120.0 |
120.1 |
| HA |
CA |
CB |
CAD |
190.9 |
55.1 |
| HA |
CA |
CB |
HB |
310.9 |
175.0 |
| HA |
CA |
CB |
HBA |
70.9 |
295.0 |
| CAD |
CB |
CA |
HA |
190.9 |
55.1 |
| CA |
CB |
CAD |
HB |
120.0 |
119.9 |
| CA |
CB |
CAD |
HBA |
240.0 |
240.0 |
| HB |
CB |
CAD |
HBA |
120.0 |
120.0 |
| CB |
CAD |
NAA |
HNAA |
180.0 |
56.1 |
| CB |
CAD |
NAA |
HNAB |
300.0 |
180.0 |
| HAD |
CAD |
CB |
HADA |
240.0 |
240.0 |
| HB |
CB |
CA |
HA |
310.9 |
175.0 |
| CA |
CB |
HB |
CAD |
237.6 |
240.1 |
| CA |
CB |
HB |
HBA |
118.8 |
120.0 |
| CAD |
CB |
HB |
HBA |
241.2 |
240.0 |
| HB |
CB |
CAD |
NAA |
67.1 |
60.1 |
| HB |
CB |
CAD |
HAD |
187.1 |
180.0 |
| HB |
CB |
CAD |
HADA |
307.1 |
300.0 |
| HBA |
CB |
CA |
HA |
70.9 |
295.0 |
| CA |
CB |
HBA |
CAD |
122.4 |
120.0 |
| CA |
CB |
HBA |
HB |
241.2 |
240.0 |
| CAD |
CB |
HBA |
HB |
118.8 |
120.0 |
| HBA |
CB |
CAD |
NAA |
307.1 |
300.0 |
| HBA |
CB |
CAD |
HAD |
67.1 |
60.0 |
| HBA |
CB |
CAD |
HADA |
187.1 |
180.0 |
| NAA |
CAD |
CB |
HB |
67.1 |
60.1 |
| NAA |
CAD |
CB |
HBA |
307.1 |
300.0 |
| CB |
CAD |
NAA |
HAD |
120.0 |
119.9 |
| CB |
CAD |
NAA |
HADA |
240.0 |
239.9 |
| HNAA |
NAA |
CAD |
HNAB |
240.0 |
236.1 |
| CAD |
NAA |
HNAA |
HNAB |
120.0 |
123.9 |
| CAD |
NAA |
HNAB |
HNAA |
240.0 |
236.0 |
| HAD |
CAD |
CB |
HB |
187.1 |
180.0 |
| HAD |
CAD |
CB |
HBA |
67.1 |
60.0 |
| CB |
CAD |
HAD |
NAA |
239.8 |
240.1 |
| CB |
CAD |
HAD |
HADA |
119.9 |
120.1 |
| HAD |
CAD |
NAA |
HNAA |
60.0 |
296.1 |
| HAD |
CAD |
NAA |
HNAB |
180.0 |
60.1 |
| HADA |
CAD |
CB |
HB |
307.1 |
300.0 |
| HADA |
CAD |
CB |
HBA |
187.1 |
180.0 |
| CB |
CAD |
HADA |
NAA |
120.2 |
120.0 |
| CB |
CAD |
HADA |
HAD |
240.1 |
240.0 |
| HADA |
CAD |
NAA |
HNAA |
300.0 |
176.1 |
| HADA |
CAD |
NAA |
HNAB |
60.0 |
300.1 |
| CAG |
CAE |
CAF |
HAE |
240.0 |
240.0 |
| CAG |
CAE |
CAF |
HAEA |
120.0 |
120.1 |
| HAE |
CAE |
CAF |
HAEA |
240.0 |
240.1 |
| CAF |
CAE |
CAG |
HAE |
120.0 |
120.0 |
| CAF |
CAE |
CAG |
HAEA |
240.0 |
240.0 |
| HAE |
CAE |
CAG |
HAEA |
120.0 |
120.0 |
| CAF |
CAE |
HAE |
HAEA |
120.0 |
119.9 |
| CAG |
CAE |
HAE |
HAEA |
240.0 |
240.0 |
| CAF |
CAE |
HAEA |
HAE |
240.0 |
240.1 |
| CAG |
CAE |
HAEA |
HAE |
120.0 |
120.0 |
| C |
NAM |
CAI |
CAF |
146.5 |
126.4 |
| CAI |
CAF |
CAE |
HAE |
65.4 |
58.7 |
| CAI |
CAF |
CAE |
HAEA |
185.5 |
178.6 |
| HAF |
CAF |
CAI |
HAFA |
120.0 |
120.1 |
| HAF |
CAF |
CAE |
HAE |
185.4 |
178.6 |
| HAF |
CAF |
CAE |
HAEA |
305.4 |
298.5 |
| CAI |
CAF |
HAF |
HAFA |
241.5 |
239.9 |
| HAFA |
CAF |
CAE |
HAE |
305.4 |
298.7 |
| HAFA |
CAF |
CAE |
HAEA |
65.4 |
58.7 |
| CAI |
CAF |
HAFA |
HAF |
118.5 |
120.1 |
| C |
NAM |
CAJ |
CAG |
221.3 |
233.6 |
| CAJ |
CAG |
CAE |
HAE |
303.2 |
301.4 |
| CAJ |
CAG |
CAE |
HAEA |
183.2 |
181.4 |
| HAG |
CAG |
CAJ |
HAGA |
119.9 |
120.1 |
| HAG |
CAG |
CAE |
HAE |
63.2 |
61.3 |
| HAG |
CAG |
CAE |
HAEA |
303.2 |
301.4 |
| CAJ |
CAG |
HAG |
HAGA |
240.3 |
239.9 |
| HAGA |
CAG |
CAE |
HAE |
183.2 |
181.4 |
| HAGA |
CAG |
CAE |
HAEA |
63.2 |
61.4 |
| CAJ |
CAG |
HAGA |
HAG |
119.7 |
120.1 |
| C |
NAM |
CAI |
CAJ |
181.9 |
180.1 |
| NAM |
CAI |
CAF |
HAF |
280.2 |
294.7 |
| NAM |
CAI |
CAF |
HAFA |
160.2 |
174.6 |
| HAI |
CAI |
NAM |
HAIA |
120.0 |
120.4 |
| HAI |
CAI |
CAF |
HAF |
40.2 |
54.4 |
| HAI |
CAI |
CAF |
HAFA |
280.2 |
294.3 |
| NAM |
CAI |
HAI |
HAIA |
242.0 |
239.5 |
| HAIA |
CAI |
CAF |
HAF |
160.1 |
174.8 |
| HAIA |
CAI |
CAF |
HAFA |
40.1 |
54.6 |
| NAM |
CAI |
HAIA |
HAI |
118.0 |
120.4 |
| C |
NAM |
CAJ |
CAI |
178.0 |
179.9 |
| NAM |
CAJ |
CAG |
HAG |
183.9 |
185.4 |
| NAM |
CAJ |
CAG |
HAGA |
64.0 |
65.3 |
| CAJ |
NAM |
CAI |
HAI |
204.6 |
186.6 |
| CAJ |
NAM |
CAI |
HAIA |
84.6 |
66.2 |
| HAJ |
CAJ |
NAM |
HAJA |
120.0 |
120.3 |
| HAJ |
CAJ |
CAG |
HAG |
303.9 |
305.2 |
| HAJ |
CAJ |
CAG |
HAGA |
184.0 |
185.1 |
| NAM |
CAJ |
HAJ |
HAJA |
240.3 |
239.6 |
| HAJA |
CAJ |
CAG |
HAG |
63.9 |
65.5 |
| HAJA |
CAJ |
CAG |
HAGA |
304.0 |
305.4 |
| NAM |
CAJ |
HAJA |
HAJ |
119.7 |
120.4 |