PDB Chemical Component PYB
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 PYB
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.375 |
1.349 |
| N |
H |
1.020 |
1.031 |
| N |
HN2 |
1.020 |
1.031 |
| CA |
CB1 |
1.414 |
1.417 |
| CA |
CB |
1.398 |
1.378 |
| CB1 |
CG1 |
1.404 |
1.377 |
| CB1 |
HB1 |
1.104 |
1.082 |
| CB |
NG2 |
1.418 |
1.370 |
| CB |
HB |
1.102 |
1.083 |
| CG1 |
NG2 |
1.427 |
1.370 |
| CG1 |
C |
1.470 |
1.432 |
| NG2 |
CD |
1.484 |
1.447 |
| CD |
HD1 |
1.115 |
1.093 |
| CD |
HD2 |
1.115 |
1.094 |
| CD |
HD3 |
1.115 |
1.094 |
| C |
O |
1.229 |
1.249 |
| C |
OXT |
|
1.371 |
| OXT |
HXT |
|
0.980 |
Bond Angles for PYB
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
125.8 |
122.1 |
| CA |
N |
HN2 |
106.5 |
122.2 |
| N |
CA |
CB1 |
125.8 |
126.6 |
| N |
CA |
CB |
126.6 |
126.1 |
| H |
N |
HN2 |
106.5 |
115.4 |
| CB1 |
CA |
CB |
107.6 |
107.4 |
| CA |
CB1 |
CG1 |
108.4 |
107.4 |
| CA |
CB1 |
HB1 |
126.1 |
126.9 |
| CA |
CB |
NG2 |
109.2 |
107.8 |
| CA |
CB |
HB |
124.8 |
131.3 |
| CG1 |
CB1 |
HB1 |
125.5 |
125.7 |
| CB1 |
CG1 |
NG2 |
108.2 |
107.8 |
| CB1 |
CG1 |
C |
129.5 |
127.5 |
| NG2 |
CB |
HB |
126.0 |
120.9 |
| CB |
NG2 |
CG1 |
106.6 |
109.6 |
| CB |
NG2 |
CD |
122.5 |
124.6 |
| NG2 |
CG1 |
C |
122.3 |
124.6 |
| CG1 |
NG2 |
CD |
131.0 |
125.8 |
| CG1 |
C |
O |
115.1 |
126.3 |
| CG1 |
C |
OXT |
|
113.4 |
| NG2 |
CD |
HD1 |
122.4 |
108.0 |
| NG2 |
CD |
HD2 |
107.5 |
109.4 |
| NG2 |
CD |
HD3 |
107.6 |
109.3 |
| HD1 |
CD |
HD2 |
107.6 |
110.5 |
| HD1 |
CD |
HD3 |
107.7 |
110.6 |
| HD2 |
CD |
HD3 |
102.2 |
109.1 |
| O |
C |
OXT |
|
120.3 |
| C |
OXT |
HXT |
|
114.0 |
Torsion Angles for PYB
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
HN2 |
125.3 |
173.9 |
| CB1 |
CA |
N |
CB |
178.4 |
179.9 |
| N |
CA |
CB1 |
CG1 |
181.3 |
180.1 |
| N |
CA |
CB1 |
HB1 |
1.3 |
0.0 |
| N |
CA |
CB |
NG2 |
178.7 |
180.0 |
| N |
CA |
CB |
HB |
358.6 |
359.9 |
| CA |
N |
H |
HN2 |
234.6 |
185.7 |
| H |
N |
CA |
CB1 |
180.0 |
214.9 |
| H |
N |
CA |
CB |
1.6 |
34.9 |
| CA |
N |
HN2 |
H |
136.4 |
174.2 |
| HN2 |
N |
CA |
CB1 |
54.7 |
41.0 |
| HN2 |
N |
CA |
CB |
236.3 |
221.1 |
| CB1 |
CA |
N |
H |
180.0 |
214.9 |
| CB1 |
CA |
N |
HN2 |
54.7 |
41.0 |
| N |
CA |
CB1 |
CB |
181.3 |
180.1 |
| CB1 |
CA |
CB |
NG2 |
0.0 |
0.0 |
| CB1 |
CA |
CB |
HB |
180.0 |
180.0 |
| CG1 |
CB1 |
CA |
HB1 |
180.0 |
180.0 |
| CA |
CB1 |
CG1 |
NG2 |
360.0 |
360.0 |
| CA |
CB1 |
CG1 |
C |
179.5 |
180.0 |
| CB |
CA |
N |
H |
1.6 |
34.9 |
| CB |
CA |
N |
HN2 |
236.3 |
221.1 |
| N |
CA |
CB |
CB1 |
178.6 |
179.9 |
| CB |
CA |
CB1 |
CG1 |
360.0 |
0.0 |
| CB |
CA |
CB1 |
HB1 |
180.0 |
180.0 |
| NG2 |
CB |
CA |
HB |
180.0 |
180.1 |
| CA |
CB |
NG2 |
CG1 |
359.9 |
359.9 |
| CA |
CB |
NG2 |
CD |
180.1 |
180.0 |
| CG1 |
CB1 |
CA |
CB |
360.0 |
0.0 |
| CA |
CB1 |
CG1 |
HB1 |
180.0 |
180.0 |
| CB |
NG2 |
CG1 |
CB1 |
0.1 |
0.1 |
| NG2 |
CG1 |
CB1 |
C |
180.5 |
180.0 |
| CB1 |
CG1 |
NG2 |
CD |
179.9 |
180.0 |
| CB1 |
CG1 |
C |
O |
190.3 |
150.0 |
| CB1 |
CG1 |
C |
OXT |
|
329.9 |
| HB1 |
CB1 |
CA |
CB |
180.0 |
180.0 |
| CA |
CB1 |
HB1 |
CG1 |
180.0 |
180.0 |
| HB1 |
CB1 |
CG1 |
NG2 |
179.9 |
180.0 |
| HB1 |
CB1 |
CG1 |
C |
359.5 |
0.0 |
| CA |
CB |
NG2 |
HB |
180.0 |
179.9 |
| CB1 |
CG1 |
NG2 |
CB |
0.1 |
0.1 |
| CB |
NG2 |
CG1 |
C |
180.5 |
180.0 |
| CG1 |
NG2 |
CB |
CD |
179.8 |
180.0 |
| CB |
NG2 |
CD |
HD1 |
180.0 |
175.8 |
| CB |
NG2 |
CD |
HD2 |
305.2 |
296.1 |
| CB |
NG2 |
CD |
HD3 |
54.7 |
55.4 |
| CA |
CB |
HB |
NG2 |
180.1 |
180.1 |
| HB |
CB |
NG2 |
CG1 |
180.0 |
180.0 |
| HB |
CB |
NG2 |
CD |
0.1 |
0.0 |
| NG2 |
CG1 |
CB1 |
HB1 |
179.9 |
180.0 |
| CB1 |
CG1 |
NG2 |
C |
179.6 |
180.0 |
| CG1 |
NG2 |
CB |
HB |
180.0 |
180.0 |
| CB |
NG2 |
CG1 |
CD |
180.2 |
180.0 |
| NG2 |
CG1 |
C |
O |
9.8 |
330.1 |
| NG2 |
CG1 |
C |
OXT |
|
149.9 |
| CG1 |
NG2 |
CD |
HD1 |
0.2 |
355.8 |
| CG1 |
NG2 |
CD |
HD2 |
125.4 |
116.1 |
| CG1 |
NG2 |
CD |
HD3 |
234.9 |
235.5 |
| C |
CG1 |
CB1 |
HB1 |
359.5 |
0.0 |
| CB1 |
CG1 |
C |
NG2 |
180.5 |
179.9 |
| C |
CG1 |
NG2 |
CD |
0.3 |
360.0 |
| O |
C |
CG1 |
OXT |
|
180.1 |
| CG1 |
C |
OXT |
HXT |
|
180.1 |
| CD |
NG2 |
CB |
HB |
0.1 |
0.0 |
| CB |
NG2 |
CD |
CG1 |
179.8 |
180.0 |
| CD |
NG2 |
CG1 |
C |
0.3 |
360.0 |
| HD1 |
CD |
NG2 |
HD2 |
234.8 |
239.7 |
| HD1 |
CD |
NG2 |
HD3 |
125.3 |
120.3 |
| HD2 |
CD |
NG2 |
HD3 |
250.5 |
240.6 |
| NG2 |
CD |
HD1 |
HD2 |
125.2 |
119.6 |
| NG2 |
CD |
HD1 |
HD3 |
234.7 |
240.5 |
| HD2 |
CD |
HD1 |
HD3 |
109.5 |
120.9 |
| NG2 |
CD |
HD2 |
HD1 |
226.4 |
241.2 |
| NG2 |
CD |
HD2 |
HD3 |
113.1 |
119.5 |
| HD1 |
CD |
HD2 |
HD3 |
246.8 |
238.3 |
| NG2 |
CD |
HD3 |
HD1 |
133.7 |
118.7 |
| NG2 |
CD |
HD3 |
HD2 |
246.9 |
240.4 |
| HD1 |
CD |
HD3 |
HD2 |
113.2 |
121.7 |
| CG1 |
C |
O |
OXT |
|
179.9 |
| O |
C |
OXT |
HXT |
|
360.0 |
| CG1 |
C |
OXT |
O |
|
180.1 |