PDB Chemical Component JBY
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 JBY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3 |
C3 |
1.229 |
1.208 |
| CB3 |
CA3 |
1.536 |
1.531 |
| C3 |
CA3 |
1.497 |
1.507 |
| N1 |
CA1 |
1.469 |
1.470 |
| CA3 |
N3 |
1.476 |
1.466 |
| CA1 |
C1 |
1.496 |
1.507 |
| N3 |
C1 |
1.353 |
1.366 |
| N3 |
C2 |
1.305 |
1.351 |
| C1 |
N2 |
1.357 |
1.295 |
| C2 |
O2 |
1.309 |
1.218 |
| C2 |
CA2 |
1.434 |
1.474 |
| N2 |
CA2 |
1.367 |
1.368 |
| CA2 |
CB2 |
1.453 |
1.378 |
| CB2 |
CG2 |
1.471 |
1.465 |
| CD1 |
CG2 |
1.411 |
1.402 |
| CD1 |
CE1 |
1.395 |
1.370 |
| CG2 |
CD2 |
1.351 |
1.402 |
| CE1 |
CZ |
1.380 |
1.390 |
| CD2 |
CE2 |
1.362 |
1.372 |
| CZ |
CE2 |
1.399 |
1.391 |
| CZ |
OH |
1.250 |
1.357 |
| CA3 |
HA31 |
1.100 |
1.090 |
| CB3 |
H5 |
1.100 |
1.090 |
| CB3 |
H6 |
1.100 |
1.090 |
| CB3 |
H7 |
1.100 |
1.090 |
| CA1 |
HA1 |
1.100 |
1.090 |
| CA1 |
HA2 |
1.100 |
1.090 |
| N1 |
H |
1.001 |
1.008 |
| N1 |
H2 |
1.000 |
1.009 |
| CB2 |
H13 |
1.080 |
1.080 |
| CD2 |
H14 |
1.079 |
1.079 |
| CE2 |
H16 |
1.080 |
1.080 |
| CE1 |
H17 |
1.080 |
1.081 |
| CD1 |
H18 |
1.080 |
1.080 |
| C3 |
OXT |
1.363 |
1.342 |
| OXT |
HXT |
0.950 |
0.967 |
| OH |
HOH |
0.950 |
0.967 |
Bond Angles for JBY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3 |
C3 |
CA3 |
112.6 |
120.0 |
| O3 |
C3 |
OXT |
127.9 |
120.0 |
| CB3 |
CA3 |
HA31 |
106.3 |
109.4 |
| C3 |
CA3 |
HA31 |
106.7 |
109.5 |
| CA3 |
C3 |
OXT |
119.4 |
120.0 |
| N1 |
CA1 |
HA1 |
110.2 |
109.4 |
| N1 |
CA1 |
HA2 |
110.2 |
109.5 |
| N3 |
C2 |
O2 |
127.1 |
127.4 |
| N3 |
C2 |
CA2 |
108.3 |
105.2 |
| C1 |
N2 |
CA2 |
106.0 |
109.3 |
| O2 |
C2 |
CA2 |
124.5 |
127.3 |
| C2 |
CA2 |
N2 |
106.5 |
105.7 |
| C2 |
CA2 |
CB2 |
122.1 |
127.1 |
| N2 |
CA2 |
CB2 |
131.4 |
127.2 |
| CA2 |
CB2 |
CG2 |
130.9 |
120.0 |
| CA2 |
CB2 |
H13 |
114.6 |
120.0 |
| CB2 |
CG2 |
CD2 |
115.9 |
120.1 |
| CG2 |
CB2 |
H13 |
114.6 |
120.0 |
| CD1 |
CE1 |
H17 |
119.2 |
119.9 |
| CG2 |
CD2 |
CE2 |
123.5 |
119.9 |
| CG2 |
CD2 |
H14 |
118.3 |
120.1 |
| CE2 |
CD2 |
H14 |
118.2 |
120.0 |
| CD2 |
CE2 |
H16 |
120.6 |
119.9 |
| CZ |
CE2 |
H16 |
120.6 |
120.0 |
| CZ |
OH |
HOH |
109.5 |
114.0 |
| H5 |
CB3 |
H6 |
109.4 |
109.4 |
| H5 |
CB3 |
H7 |
109.5 |
109.5 |
| H6 |
CB3 |
H7 |
109.5 |
109.5 |
| HA1 |
CA1 |
HA2 |
109.5 |
109.5 |
| H |
N1 |
H2 |
109.5 |
111.1 |
| C3 |
OXT |
HXT |
109.5 |
117.0 |
Torsion Angles for JBY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3 |
C3 |
CA3 |
HA31 |
61.3 |
240.0 |
| CA3 |
C3 |
O3 |
OXT |
184.6 |
179.9 |
| O3 |
C3 |
OXT |
HXT |
360.0 |
360.0 |
| C3 |
CA3 |
CB3 |
HA31 |
115.1 |
120.0 |
| CB3 |
CA3 |
C3 |
OXT |
130.7 |
300.0 |
| O3 |
C3 |
CA3 |
OXT |
175.8 |
180.1 |
| CB3 |
CA3 |
C3 |
HA31 |
245.2 |
240.0 |
| CA3 |
C3 |
OXT |
HXT |
175.1 |
180.0 |
| HA1 |
CA1 |
N1 |
HA2 |
239.0 |
120.0 |
| CA3 |
N3 |
C2 |
CA2 |
184.9 |
180.0 |
| CA1 |
C1 |
N2 |
CA2 |
177.2 |
179.7 |
| N3 |
C1 |
N2 |
CA2 |
358.9 |
360.0 |
| O2 |
C2 |
N3 |
CA2 |
183.9 |
179.9 |
| N3 |
C2 |
CA2 |
N2 |
3.4 |
360.0 |
| N3 |
C2 |
CA2 |
CB2 |
179.9 |
180.0 |
| C2 |
CA2 |
N2 |
C1 |
358.7 |
0.0 |
| C1 |
N2 |
CA2 |
CB2 |
182.6 |
180.1 |
| N3 |
C2 |
O2 |
CA2 |
175.5 |
180.1 |
| O2 |
C2 |
CA2 |
N2 |
179.5 |
180.1 |
| O2 |
C2 |
CA2 |
CB2 |
356.1 |
0.0 |
| N3 |
C2 |
CA2 |
O2 |
183.8 |
179.9 |
| C1 |
N2 |
CA2 |
C2 |
358.7 |
0.0 |
| N2 |
CA2 |
C2 |
CB2 |
183.5 |
180.0 |
| C2 |
CA2 |
CB2 |
CG2 |
184.3 |
174.8 |
| C2 |
CA2 |
CB2 |
H13 |
4.3 |
354.8 |
| C2 |
CA2 |
N2 |
CB2 |
176.1 |
180.0 |
| N2 |
CA2 |
CB2 |
CG2 |
359.8 |
354.7 |
| N2 |
CA2 |
CB2 |
H13 |
179.8 |
174.7 |
| C2 |
CA2 |
CB2 |
N2 |
184.4 |
180.1 |
| CA2 |
CB2 |
CG2 |
CD2 |
179.7 |
6.0 |
| CG2 |
CB2 |
CA2 |
H13 |
180.0 |
180.0 |
| CA2 |
CB2 |
CG2 |
H13 |
180.0 |
180.0 |
| CB2 |
CG2 |
CD2 |
CE2 |
180.3 |
179.9 |
| CB2 |
CG2 |
CD2 |
H14 |
0.3 |
360.0 |
| CD1 |
CG2 |
CB2 |
H13 |
189.9 |
5.8 |
| CD1 |
CG2 |
CD2 |
H14 |
170.8 |
180.2 |
| CD2 |
CG2 |
CB2 |
H13 |
359.6 |
186.0 |
| CE2 |
CD2 |
CG2 |
H14 |
180.0 |
180.0 |
| CG2 |
CD2 |
CE2 |
H16 |
186.5 |
180.0 |
| CE1 |
CZ |
CE2 |
H16 |
179.4 |
180.0 |
| CE1 |
CZ |
OH |
HOH |
180.0 |
270.0 |
| CG2 |
CD2 |
CE2 |
H14 |
180.0 |
180.0 |
| CZ |
CE2 |
CD2 |
H16 |
180.0 |
180.1 |
| CZ |
CE2 |
CD2 |
H14 |
186.5 |
180.1 |
| CD2 |
CE2 |
CZ |
H16 |
180.0 |
179.9 |
| OH |
CZ |
CE2 |
H16 |
357.1 |
0.0 |
| HA31 |
CA3 |
C3 |
OXT |
245.4 |
59.9 |
| H5 |
CB3 |
CA3 |
HA31 |
65.0 |
60.0 |
| H6 |
CB3 |
H5 |
H7 |
120.0 |
120.0 |
| H6 |
CB3 |
CA3 |
HA31 |
185.0 |
180.0 |
| H5 |
CB3 |
H6 |
H7 |
240.0 |
240.0 |
| H7 |
CB3 |
CA3 |
HA31 |
304.9 |
300.0 |
| H5 |
CB3 |
H7 |
H6 |
119.9 |
120.0 |
| N1 |
CA1 |
HA1 |
HA2 |
121.4 |
240.0 |
| N1 |
CA1 |
HA2 |
HA1 |
238.6 |
120.0 |
| H |
N1 |
CA1 |
HA1 |
299.5 |
60.0 |
| H |
N1 |
CA1 |
HA2 |
60.5 |
300.0 |
| H2 |
N1 |
CA1 |
HA1 |
59.5 |
184.0 |
| H2 |
N1 |
CA1 |
HA2 |
180.4 |
64.0 |
| CA2 |
CB2 |
H13 |
CG2 |
180.0 |
180.0 |
| H13 |
CB2 |
CG2 |
CD2 |
359.6 |
186.0 |
| CG2 |
CD2 |
H14 |
CE2 |
180.0 |
180.0 |
| H14 |
CD2 |
CE2 |
H16 |
6.5 |
360.0 |
| H16 |
CE2 |
CD2 |
H14 |
6.5 |
360.0 |
| H18 |
CD1 |
CE1 |
H17 |
359.6 |
0.0 |
| O3 |
C3 |
OXT |
CA3 |
184.9 |
179.9 |
| OXT |
C3 |
CA3 |
HA31 |
245.4 |
59.9 |