PDB Chemical Component DNE
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 DNE
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.480 |
1.469 |
| N |
H |
1.000 |
1.010 |
| N |
H2 |
1.000 |
1.009 |
| CA |
C |
1.538 |
1.507 |
| CA |
CB |
1.535 |
1.530 |
| CA |
HA |
1.100 |
1.090 |
| C |
O |
1.229 |
1.209 |
| C |
OXT |
|
1.342 |
| CB |
CG |
1.535 |
1.530 |
| CB |
HB2 |
1.100 |
1.090 |
| CB |
HB3 |
1.100 |
1.090 |
| CG |
CD |
1.535 |
1.529 |
| CG |
HG2 |
1.100 |
1.090 |
| CG |
HG3 |
1.100 |
1.089 |
| CD |
CE |
1.532 |
1.530 |
| CD |
HD2 |
1.100 |
1.090 |
| CD |
HD3 |
1.100 |
1.090 |
| CE |
HE1 |
1.100 |
1.090 |
| CE |
HE2 |
1.100 |
1.090 |
| CE |
HE3 |
1.100 |
1.090 |
| OXT |
HXT |
|
0.967 |
Bond Angles for DNE
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
109.5 |
111.0 |
| CA |
N |
H2 |
109.5 |
111.0 |
| N |
CA |
C |
112.8 |
109.5 |
| N |
CA |
CB |
109.4 |
109.5 |
| N |
CA |
HA |
108.3 |
109.4 |
| H |
N |
H2 |
109.5 |
111.0 |
| C |
CA |
CB |
110.8 |
109.5 |
| C |
CA |
HA |
107.6 |
109.5 |
| CA |
C |
O |
119.7 |
120.0 |
| CA |
C |
OXT |
|
120.0 |
| CB |
CA |
HA |
107.7 |
109.5 |
| CA |
CB |
CG |
112.4 |
109.5 |
| CA |
CB |
HB2 |
108.7 |
109.5 |
| CA |
CB |
HB3 |
108.7 |
109.4 |
| O |
C |
OXT |
|
120.0 |
| C |
OXT |
HXT |
|
117.0 |
| CG |
CB |
HB2 |
108.8 |
109.5 |
| CG |
CB |
HB3 |
108.7 |
109.5 |
| CB |
CG |
CD |
112.0 |
109.4 |
| CB |
CG |
HG2 |
108.8 |
109.5 |
| CB |
CG |
HG3 |
108.8 |
109.5 |
| HB2 |
CB |
HB3 |
109.5 |
109.4 |
| CD |
CG |
HG2 |
108.8 |
109.5 |
| CD |
CG |
HG3 |
108.8 |
109.5 |
| CG |
CD |
CE |
112.7 |
109.5 |
| CG |
CD |
HD2 |
108.7 |
109.5 |
| CG |
CD |
HD3 |
108.7 |
109.5 |
| HG2 |
CG |
HG3 |
109.5 |
109.5 |
| CE |
CD |
HD2 |
108.7 |
109.4 |
| CE |
CD |
HD3 |
108.7 |
109.4 |
| CD |
CE |
HE1 |
109.5 |
109.4 |
| CD |
CE |
HE2 |
109.4 |
109.4 |
| CD |
CE |
HE3 |
109.5 |
109.5 |
| HD2 |
CD |
HD3 |
109.4 |
109.4 |
| HE1 |
CE |
HE2 |
109.5 |
109.4 |
| HE1 |
CE |
HE3 |
109.5 |
109.5 |
| HE2 |
CE |
HE3 |
109.5 |
109.5 |
Torsion Angles for DNE
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
240.0 |
236.1 |
| C |
CA |
N |
CB |
236.2 |
240.0 |
| C |
CA |
N |
HA |
119.1 |
120.0 |
| N |
CA |
C |
O |
177.9 |
20.0 |
| N |
CA |
C |
OXT |
|
200.1 |
| CB |
CA |
N |
HA |
242.9 |
240.0 |
| N |
CA |
CB |
CG |
63.2 |
65.0 |
| N |
CA |
CB |
HB2 |
183.6 |
185.0 |
| N |
CA |
CB |
HB3 |
302.8 |
304.9 |
| CA |
N |
H |
H2 |
120.0 |
123.9 |
| H |
N |
CA |
C |
180.0 |
300.0 |
| H |
N |
CA |
CB |
303.8 |
60.0 |
| H |
N |
CA |
HA |
60.9 |
180.0 |
| CA |
N |
H2 |
H |
239.9 |
236.1 |
| H2 |
N |
CA |
C |
300.0 |
63.9 |
| H2 |
N |
CA |
CB |
63.8 |
183.9 |
| H2 |
N |
CA |
HA |
180.9 |
303.9 |
| C |
CA |
N |
H |
180.0 |
300.0 |
| C |
CA |
N |
H2 |
300.0 |
63.9 |
| N |
CA |
C |
CB |
123.0 |
120.0 |
| N |
CA |
C |
HA |
240.5 |
240.0 |
| CB |
CA |
C |
HA |
117.5 |
120.0 |
| C |
CA |
CB |
CG |
188.2 |
185.0 |
| C |
CA |
CB |
HB2 |
308.6 |
305.0 |
| C |
CA |
CB |
HB3 |
67.8 |
65.0 |
| O |
C |
CA |
OXT |
|
179.9 |
| CA |
C |
OXT |
HXT |
|
180.0 |
| CB |
CA |
N |
H |
303.8 |
60.0 |
| CB |
CA |
N |
H2 |
63.8 |
183.9 |
| N |
CA |
CB |
C |
235.0 |
240.0 |
| N |
CA |
CB |
HA |
117.5 |
119.9 |
| C |
CA |
CB |
HA |
242.5 |
240.0 |
| CB |
CA |
C |
O |
54.9 |
260.0 |
| CB |
CA |
C |
OXT |
|
80.1 |
| CG |
CB |
CA |
HB2 |
239.6 |
240.0 |
| CG |
CB |
CA |
HB3 |
120.4 |
120.0 |
| CA |
CB |
CG |
CD |
182.9 |
180.0 |
| CA |
CB |
CG |
HG2 |
303.3 |
300.0 |
| CA |
CB |
CG |
HG3 |
62.5 |
60.0 |
| HB2 |
CB |
CA |
HB3 |
240.8 |
240.1 |
| HA |
CA |
N |
H |
60.9 |
180.0 |
| HA |
CA |
N |
H2 |
180.9 |
303.9 |
| N |
CA |
HA |
C |
122.3 |
120.0 |
| N |
CA |
HA |
CB |
241.8 |
240.0 |
| C |
CA |
HA |
CB |
119.5 |
120.0 |
| HA |
CA |
C |
O |
297.4 |
140.0 |
| HA |
CA |
C |
OXT |
|
320.0 |
| HA |
CA |
CB |
CG |
305.7 |
305.0 |
| HA |
CA |
CB |
HB2 |
66.1 |
65.0 |
| HA |
CA |
CB |
HB3 |
185.3 |
185.0 |
| O |
C |
CA |
CB |
54.9 |
260.0 |
| O |
C |
CA |
HA |
297.4 |
140.0 |
| CA |
C |
O |
OXT |
|
180.1 |
| O |
C |
OXT |
HXT |
|
0.1 |
| OXT |
C |
CA |
CB |
|
80.1 |
| OXT |
C |
CA |
HA |
|
320.0 |
| CA |
C |
OXT |
O |
|
179.9 |
| CG |
CB |
CA |
HA |
305.7 |
305.0 |
| CA |
CB |
CG |
HB2 |
120.4 |
120.0 |
| CA |
CB |
CG |
HB3 |
239.6 |
240.0 |
| HB2 |
CB |
CG |
HB3 |
119.2 |
120.0 |
| CD |
CG |
CB |
HG2 |
239.6 |
240.0 |
| CD |
CG |
CB |
HG3 |
120.4 |
120.0 |
| CB |
CG |
CD |
CE |
291.8 |
180.0 |
| CB |
CG |
CD |
HD2 |
52.3 |
300.0 |
| CB |
CG |
CD |
HD3 |
171.3 |
60.0 |
| HG2 |
CG |
CB |
HG3 |
240.8 |
240.0 |
| HB2 |
CB |
CA |
HA |
66.1 |
65.0 |
| CA |
CB |
HB2 |
CG |
237.4 |
240.0 |
| CA |
CB |
HB2 |
HB3 |
118.7 |
120.0 |
| CG |
CB |
HB2 |
HB3 |
241.3 |
240.0 |
| HB2 |
CB |
CG |
CD |
62.5 |
60.0 |
| HB2 |
CB |
CG |
HG2 |
182.9 |
180.0 |
| HB2 |
CB |
CG |
HG3 |
302.1 |
300.0 |
| HB3 |
CB |
CA |
HA |
185.3 |
185.0 |
| CA |
CB |
HB3 |
CG |
122.6 |
120.0 |
| CA |
CB |
HB3 |
HB2 |
241.3 |
240.0 |
| CG |
CB |
HB3 |
HB2 |
118.7 |
120.0 |
| HB3 |
CB |
CG |
CD |
303.3 |
300.0 |
| HB3 |
CB |
CG |
HG2 |
63.7 |
60.0 |
| HB3 |
CB |
CG |
HG3 |
182.9 |
180.0 |
| CD |
CG |
CB |
HB2 |
62.5 |
60.0 |
| CD |
CG |
CB |
HB3 |
303.3 |
300.0 |
| CB |
CG |
CD |
HG2 |
120.4 |
120.0 |
| CB |
CG |
CD |
HG3 |
239.6 |
240.0 |
| HG2 |
CG |
CD |
HG3 |
119.2 |
120.0 |
| CE |
CD |
CG |
HD2 |
239.5 |
240.0 |
| CE |
CD |
CG |
HD3 |
120.5 |
120.0 |
| CG |
CD |
CE |
HE1 |
180.0 |
300.0 |
| CG |
CD |
CE |
HE2 |
300.0 |
60.0 |
| CG |
CD |
CE |
HE3 |
60.0 |
180.0 |
| HD2 |
CD |
CG |
HD3 |
241.0 |
240.0 |
| HG2 |
CG |
CB |
HB2 |
182.9 |
180.0 |
| HG2 |
CG |
CB |
HB3 |
63.7 |
60.0 |
| CB |
CG |
HG2 |
CD |
237.6 |
240.0 |
| CB |
CG |
HG2 |
HG3 |
118.8 |
120.0 |
| CD |
CG |
HG2 |
HG3 |
241.1 |
240.0 |
| HG2 |
CG |
CD |
CE |
171.4 |
60.0 |
| HG2 |
CG |
CD |
HD2 |
291.9 |
180.0 |
| HG2 |
CG |
CD |
HD3 |
50.9 |
300.0 |
| HG3 |
CG |
CB |
HB2 |
302.1 |
300.0 |
| HG3 |
CG |
CB |
HB3 |
182.9 |
180.0 |
| CB |
CG |
HG3 |
CD |
122.3 |
120.0 |
| CB |
CG |
HG3 |
HG2 |
241.2 |
240.0 |
| CD |
CG |
HG3 |
HG2 |
118.8 |
120.0 |
| HG3 |
CG |
CD |
CE |
52.2 |
300.0 |
| HG3 |
CG |
CD |
HD2 |
172.6 |
60.0 |
| HG3 |
CG |
CD |
HD3 |
291.6 |
180.0 |
| CE |
CD |
CG |
HG2 |
171.4 |
60.0 |
| CE |
CD |
CG |
HG3 |
52.2 |
300.0 |
| CG |
CD |
CE |
HD2 |
120.5 |
120.0 |
| CG |
CD |
CE |
HD3 |
239.5 |
240.0 |
| HD2 |
CD |
CE |
HD3 |
119.0 |
119.9 |
| HE1 |
CE |
CD |
HE2 |
240.0 |
240.1 |
| HE1 |
CE |
CD |
HE3 |
120.0 |
120.0 |
| HE2 |
CE |
CD |
HE3 |
240.0 |
240.0 |
| HD2 |
CD |
CG |
HG2 |
291.9 |
180.0 |
| HD2 |
CD |
CG |
HG3 |
172.6 |
60.0 |
| CG |
CD |
HD2 |
CE |
237.1 |
240.0 |
| CG |
CD |
HD2 |
HD3 |
118.5 |
120.1 |
| CE |
CD |
HD2 |
HD3 |
241.5 |
240.1 |
| HD2 |
CD |
CE |
HE1 |
59.5 |
180.0 |
| HD2 |
CD |
CE |
HE2 |
179.5 |
299.9 |
| HD2 |
CD |
CE |
HE3 |
299.5 |
60.0 |
| HD3 |
CD |
CG |
HG2 |
50.9 |
300.0 |
| HD3 |
CD |
CG |
HG3 |
291.6 |
180.0 |
| CG |
CD |
HD3 |
CE |
123.0 |
120.0 |
| CG |
CD |
HD3 |
HD2 |
241.5 |
239.9 |
| CE |
CD |
HD3 |
HD2 |
118.5 |
119.9 |
| HD3 |
CD |
CE |
HE1 |
300.5 |
60.1 |
| HD3 |
CD |
CE |
HE2 |
60.5 |
180.0 |
| HD3 |
CD |
CE |
HE3 |
180.5 |
300.0 |
| HE1 |
CE |
CD |
HD2 |
59.5 |
180.0 |
| HE1 |
CE |
CD |
HD3 |
300.5 |
60.1 |
| CD |
CE |
HE1 |
HE2 |
120.0 |
119.9 |
| CD |
CE |
HE1 |
HE3 |
240.0 |
239.9 |
| HE2 |
CE |
HE1 |
HE3 |
120.0 |
120.0 |
| HE2 |
CE |
CD |
HD2 |
179.5 |
299.9 |
| HE2 |
CE |
CD |
HD3 |
60.5 |
180.0 |
| CD |
CE |
HE2 |
HE1 |
240.0 |
240.1 |
| CD |
CE |
HE2 |
HE3 |
120.0 |
120.1 |
| HE1 |
CE |
HE2 |
HE3 |
240.0 |
240.0 |
| HE3 |
CE |
CD |
HD2 |
299.5 |
60.0 |
| HE3 |
CE |
CD |
HD3 |
180.5 |
300.0 |
| CD |
CE |
HE3 |
HE1 |
120.0 |
120.0 |
| CD |
CE |
HE3 |
HE2 |
240.0 |
240.0 |
| HE1 |
CE |
HE3 |
HE2 |
120.0 |
120.0 |