PDB Chemical Component DBY
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 DBY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.467 |
1.468 |
| N |
H |
1.020 |
1.009 |
| N |
H2 |
1.019 |
1.009 |
| CA |
C |
1.525 |
1.507 |
| CA |
CB |
1.523 |
1.529 |
| CA |
HA |
1.116 |
1.091 |
| C |
O |
1.233 |
1.208 |
| C |
OXT |
1.332 |
1.343 |
| CB |
CG |
1.507 |
1.508 |
| CB |
HB2 |
1.114 |
1.089 |
| CB |
HB3 |
1.115 |
1.091 |
| CG |
CD1 |
1.394 |
1.381 |
| CG |
CD2 |
1.385 |
1.383 |
| CD1 |
CE1 |
1.388 |
1.382 |
| CD1 |
HD1 |
1.102 |
1.080 |
| CE1 |
CZ |
1.359 |
1.388 |
| CE1 |
BR1 |
1.836 |
1.891 |
| CD2 |
CE2 |
1.378 |
1.382 |
| CD2 |
HD2 |
1.104 |
1.081 |
| CE2 |
CZ |
1.372 |
1.386 |
| CE2 |
BR2 |
1.828 |
1.891 |
| CZ |
OH |
1.368 |
1.360 |
| OH |
HH |
0.951 |
0.966 |
| OXT |
HXT |
0.950 |
0.967 |
Bond Angles for DBY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
109.4 |
106.6 |
| CA |
N |
H2 |
112.2 |
106.7 |
| N |
CA |
C |
109.4 |
109.5 |
| N |
CA |
CB |
110.0 |
109.5 |
| N |
CA |
HA |
108.4 |
109.5 |
| H |
N |
H2 |
112.3 |
106.7 |
| C |
CA |
CB |
106.9 |
109.5 |
| C |
CA |
HA |
111.4 |
109.4 |
| CA |
C |
O |
119.7 |
120.0 |
| CA |
C |
OXT |
117.5 |
120.0 |
| CB |
CA |
HA |
110.8 |
109.5 |
| CA |
CB |
CG |
115.8 |
109.5 |
| CA |
CB |
HB2 |
109.9 |
109.5 |
| CA |
CB |
HB3 |
109.9 |
109.5 |
| O |
C |
OXT |
122.7 |
119.9 |
| C |
OXT |
HXT |
117.6 |
120.0 |
| CG |
CB |
HB2 |
109.9 |
109.5 |
| CG |
CB |
HB3 |
109.9 |
109.4 |
| CB |
CG |
CD1 |
121.1 |
119.9 |
| CB |
CG |
CD2 |
120.9 |
119.9 |
| HB2 |
CB |
HB3 |
100.3 |
109.5 |
| CD1 |
CG |
CD2 |
117.9 |
120.1 |
| CG |
CD1 |
CE1 |
120.7 |
120.1 |
| CG |
CD1 |
HD1 |
119.8 |
120.0 |
| CG |
CD2 |
CE2 |
120.8 |
120.0 |
| CG |
CD2 |
HD2 |
119.9 |
120.0 |
| CE1 |
CD1 |
HD1 |
119.4 |
119.9 |
| CD1 |
CE1 |
CZ |
120.0 |
119.9 |
| CD1 |
CE1 |
BR1 |
120.6 |
120.1 |
| CZ |
CE1 |
BR1 |
119.3 |
120.0 |
| CE1 |
CZ |
CE2 |
120.3 |
119.9 |
| CE1 |
CZ |
OH |
118.6 |
120.1 |
| CE2 |
CD2 |
HD2 |
119.3 |
120.0 |
| CD2 |
CE2 |
CZ |
120.3 |
120.0 |
| CD2 |
CE2 |
BR2 |
119.7 |
120.0 |
| CZ |
CE2 |
BR2 |
120.0 |
120.0 |
| CE2 |
CZ |
OH |
121.2 |
120.1 |
| CZ |
OH |
HH |
118.6 |
106.9 |
Torsion Angles for DBY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
125.3 |
246.2 |
| C |
CA |
N |
CB |
117.1 |
120.0 |
| C |
CA |
N |
HA |
238.4 |
240.0 |
| N |
CA |
C |
O |
320.6 |
330.0 |
| N |
CA |
C |
OXT |
142.3 |
149.9 |
| CB |
CA |
N |
HA |
121.3 |
120.0 |
| N |
CA |
CB |
CG |
284.2 |
300.0 |
| N |
CA |
CB |
HB2 |
49.4 |
60.1 |
| N |
CA |
CB |
HB3 |
159.0 |
180.1 |
| CA |
N |
H |
H2 |
234.7 |
113.7 |
| H |
N |
CA |
C |
180.0 |
60.0 |
| H |
N |
CA |
CB |
62.9 |
300.0 |
| H |
N |
CA |
HA |
301.7 |
180.0 |
| CA |
N |
H2 |
H |
123.7 |
246.3 |
| H2 |
N |
CA |
C |
54.7 |
173.8 |
| H2 |
N |
CA |
CB |
297.6 |
53.7 |
| H2 |
N |
CA |
HA |
176.3 |
293.7 |
| C |
CA |
N |
H |
180.0 |
60.0 |
| C |
CA |
N |
H2 |
54.7 |
173.8 |
| N |
CA |
C |
CB |
241.0 |
240.0 |
| N |
CA |
C |
HA |
119.8 |
120.0 |
| CB |
CA |
C |
HA |
238.8 |
240.0 |
| C |
CA |
CB |
CG |
165.5 |
180.0 |
| C |
CA |
CB |
HB2 |
290.8 |
300.0 |
| C |
CA |
CB |
HB3 |
40.3 |
60.0 |
| O |
C |
CA |
OXT |
178.3 |
180.1 |
| CA |
C |
OXT |
HXT |
180.0 |
180.0 |
| CB |
CA |
N |
H |
62.9 |
300.0 |
| CB |
CA |
N |
H2 |
297.6 |
53.7 |
| N |
CA |
CB |
C |
118.6 |
120.1 |
| N |
CA |
CB |
HA |
240.2 |
240.0 |
| C |
CA |
CB |
HA |
121.6 |
119.9 |
| CB |
CA |
C |
O |
79.7 |
90.0 |
| CB |
CA |
C |
OXT |
261.3 |
269.9 |
| CG |
CB |
CA |
HB2 |
234.8 |
240.0 |
| CG |
CB |
CA |
HB3 |
125.2 |
120.0 |
| CA |
CB |
CG |
CD1 |
107.1 |
90.0 |
| CA |
CB |
CG |
CD2 |
282.9 |
269.7 |
| HB2 |
CB |
CA |
HB3 |
250.5 |
240.0 |
| HA |
CA |
N |
H |
301.7 |
180.0 |
| HA |
CA |
N |
H2 |
176.3 |
293.7 |
| N |
CA |
HA |
C |
239.6 |
240.0 |
| N |
CA |
HA |
CB |
120.8 |
120.0 |
| C |
CA |
HA |
CB |
241.2 |
240.0 |
| HA |
CA |
C |
O |
200.8 |
210.0 |
| HA |
CA |
C |
OXT |
22.5 |
29.9 |
| HA |
CA |
CB |
CG |
44.0 |
60.0 |
| HA |
CA |
CB |
HB2 |
169.2 |
180.1 |
| HA |
CA |
CB |
HB3 |
278.8 |
300.1 |
| O |
C |
CA |
CB |
79.7 |
90.0 |
| O |
C |
CA |
HA |
200.8 |
210.0 |
| CA |
C |
O |
OXT |
181.7 |
179.9 |
| O |
C |
OXT |
HXT |
1.7 |
359.9 |
| OXT |
C |
CA |
CB |
261.3 |
269.9 |
| OXT |
C |
CA |
HA |
22.5 |
29.9 |
| CA |
C |
OXT |
O |
178.3 |
180.1 |
| CG |
CB |
CA |
HA |
44.0 |
60.0 |
| CA |
CB |
CG |
HB2 |
125.3 |
120.0 |
| CA |
CB |
CG |
HB3 |
234.8 |
240.0 |
| HB2 |
CB |
CG |
HB3 |
109.5 |
120.0 |
| CD1 |
CG |
CB |
CD2 |
184.2 |
180.3 |
| CB |
CG |
CD1 |
CE1 |
175.4 |
180.0 |
| CB |
CG |
CD1 |
HD1 |
355.4 |
359.9 |
| CB |
CG |
CD2 |
CE2 |
184.9 |
179.7 |
| CB |
CG |
CD2 |
HD2 |
5.0 |
0.3 |
| HB2 |
CB |
CA |
HA |
169.2 |
180.1 |
| CA |
CB |
HB2 |
CG |
231.4 |
240.0 |
| CA |
CB |
HB2 |
HB3 |
115.7 |
120.0 |
| CG |
CB |
HB2 |
HB3 |
244.3 |
240.1 |
| HB2 |
CB |
CG |
CD1 |
341.8 |
330.0 |
| HB2 |
CB |
CG |
CD2 |
157.6 |
149.7 |
| HB3 |
CB |
CA |
HA |
278.8 |
300.1 |
| CA |
CB |
HB3 |
CG |
128.6 |
120.0 |
| CA |
CB |
HB3 |
HB2 |
244.3 |
240.0 |
| CG |
CB |
HB3 |
HB2 |
115.7 |
120.0 |
| HB3 |
CB |
CG |
CD1 |
232.3 |
210.0 |
| HB3 |
CB |
CG |
CD2 |
48.1 |
29.7 |
| CD1 |
CG |
CB |
HB2 |
341.8 |
330.0 |
| CD1 |
CG |
CB |
HB3 |
232.3 |
210.0 |
| CB |
CG |
CD1 |
CD2 |
175.9 |
179.7 |
| CD1 |
CG |
CD2 |
CE2 |
0.9 |
359.4 |
| CD1 |
CG |
CD2 |
HD2 |
180.9 |
180.0 |
| CE1 |
CD1 |
CG |
HD1 |
180.0 |
180.0 |
| CG |
CD1 |
CE1 |
CZ |
359.6 |
0.0 |
| CG |
CD1 |
CE1 |
BR1 |
177.5 |
180.0 |
| CD2 |
CG |
CB |
HB2 |
157.6 |
149.7 |
| CD2 |
CG |
CB |
HB3 |
48.1 |
29.7 |
| CB |
CG |
CD2 |
CD1 |
184.1 |
180.3 |
| CD2 |
CG |
CD1 |
CE1 |
359.5 |
0.3 |
| CD2 |
CG |
CD1 |
HD1 |
179.5 |
180.3 |
| CE2 |
CD2 |
CG |
HD2 |
180.0 |
179.5 |
| CG |
CD2 |
CE2 |
CZ |
359.6 |
0.6 |
| CG |
CD2 |
CE2 |
BR2 |
179.5 |
180.2 |
| CE1 |
CD1 |
CG |
CD2 |
359.5 |
0.3 |
| CG |
CD1 |
CE1 |
HD1 |
180.0 |
180.0 |
| CZ |
CE1 |
CD1 |
BR1 |
182.1 |
180.0 |
| CD1 |
CE1 |
CZ |
CE2 |
0.9 |
360.0 |
| CD1 |
CE1 |
CZ |
OH |
182.4 |
180.1 |
| HD1 |
CD1 |
CG |
CD2 |
179.5 |
180.3 |
| CG |
CD1 |
HD1 |
CE1 |
180.0 |
180.0 |
| HD1 |
CD1 |
CE1 |
CZ |
179.7 |
180.0 |
| HD1 |
CD1 |
CE1 |
BR1 |
357.6 |
0.0 |
| CZ |
CE1 |
CD1 |
HD1 |
179.7 |
180.0 |
| CD1 |
CE1 |
CZ |
BR1 |
177.9 |
180.0 |
| CD2 |
CE2 |
CZ |
CE1 |
359.5 |
359.7 |
| CE1 |
CZ |
CE2 |
BR2 |
179.6 |
180.1 |
| CE2 |
CZ |
CE1 |
OH |
178.5 |
179.9 |
| CE1 |
CZ |
OH |
HH |
180.0 |
89.9 |
| BR1 |
CE1 |
CD1 |
HD1 |
357.6 |
0.0 |
| CD1 |
CE1 |
BR1 |
CZ |
182.1 |
180.0 |
| BR1 |
CE1 |
CZ |
CE2 |
182.9 |
180.0 |
| BR1 |
CE1 |
CZ |
OH |
4.5 |
0.1 |
| CG |
CD2 |
CE2 |
HD2 |
180.0 |
180.5 |
| CE1 |
CZ |
CE2 |
CD2 |
359.5 |
359.7 |
| CZ |
CE2 |
CD2 |
BR2 |
180.1 |
180.4 |
| CD2 |
CE2 |
CZ |
OH |
177.9 |
179.6 |
| CG |
CD2 |
HD2 |
CE2 |
180.0 |
179.5 |
| HD2 |
CD2 |
CE2 |
CZ |
179.6 |
180.0 |
| HD2 |
CD2 |
CE2 |
BR2 |
359.5 |
359.6 |
| CE2 |
CZ |
CE1 |
BR1 |
182.9 |
180.0 |
| CE1 |
CZ |
CE2 |
OH |
181.6 |
180.1 |
| CZ |
CE2 |
CD2 |
HD2 |
179.6 |
180.0 |
| CD2 |
CE2 |
CZ |
BR2 |
179.9 |
179.6 |
| CE2 |
CZ |
OH |
HH |
1.6 |
270.0 |
| BR2 |
CE2 |
CD2 |
HD2 |
359.5 |
359.6 |
| CD2 |
CE2 |
BR2 |
CZ |
180.1 |
180.4 |
| BR2 |
CE2 |
CZ |
OH |
358.0 |
0.0 |
| OH |
CZ |
CE1 |
BR1 |
4.5 |
0.1 |
| CE1 |
CZ |
OH |
CE2 |
178.4 |
179.9 |
| OH |
CZ |
CE2 |
BR2 |
358.0 |
0.0 |