PDB Chemical Component NDF
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 NDF
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| CD1 |
CE1 |
1.401 |
1.382 |
| CD1 |
CG |
1.383 |
1.382 |
| CD1 |
HD1 |
1.104 |
1.080 |
| CE1 |
CZ |
1.383 |
1.382 |
| CE1 |
HE1 |
1.103 |
1.080 |
| CZ |
CE2 |
1.403 |
1.381 |
| CZ |
HZ |
1.103 |
1.081 |
| CE2 |
CD2 |
1.383 |
1.383 |
| CE2 |
HE2 |
1.103 |
1.080 |
| CD2 |
CG |
1.401 |
1.382 |
| CD2 |
HD2 |
1.102 |
1.080 |
| CG |
CB |
1.531 |
1.506 |
| CB |
CA |
1.529 |
1.529 |
| CB |
HB3 |
1.115 |
1.090 |
| CB |
HB2 |
1.115 |
1.090 |
| CA |
C |
1.527 |
1.507 |
| CA |
N |
1.470 |
1.464 |
| CA |
HA |
1.115 |
1.090 |
| C |
O |
1.227 |
1.208 |
| C |
OXT |
1.238 |
1.342 |
| OXT |
HXT |
0.950 |
0.968 |
| N |
C2 |
1.331 |
1.348 |
| N |
H |
1.020 |
0.970 |
| C2 |
O2' |
1.231 |
1.213 |
| C2 |
C1 |
1.529 |
1.494 |
| C1 |
O1 |
1.240 |
1.345 |
| C1 |
O2 |
1.221 |
1.212 |
| O1 |
HO1 |
0.950 |
0.966 |
Bond Angles for NDF
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CE1 |
CD1 |
CG |
120.0 |
120.0 |
| CE1 |
CD1 |
HD1 |
120.6 |
120.0 |
| CD1 |
CE1 |
CZ |
120.0 |
120.0 |
| CD1 |
CE1 |
HE1 |
120.6 |
120.0 |
| CG |
CD1 |
HD1 |
119.3 |
120.0 |
| CD1 |
CG |
CD2 |
120.1 |
120.0 |
| CD1 |
CG |
CB |
120.1 |
120.0 |
| CZ |
CE1 |
HE1 |
119.4 |
120.0 |
| CE1 |
CZ |
CE2 |
119.9 |
120.0 |
| CE1 |
CZ |
HZ |
119.3 |
120.0 |
| CE2 |
CZ |
HZ |
120.7 |
120.0 |
| CZ |
CE2 |
CD2 |
120.1 |
120.0 |
| CZ |
CE2 |
HE2 |
120.6 |
120.0 |
| CD2 |
CE2 |
HE2 |
119.3 |
120.0 |
| CE2 |
CD2 |
CG |
119.8 |
120.0 |
| CE2 |
CD2 |
HD2 |
119.5 |
120.0 |
| CG |
CD2 |
HD2 |
120.7 |
120.0 |
| CD2 |
CG |
CB |
119.8 |
120.0 |
| CG |
CB |
CA |
111.9 |
109.5 |
| CG |
CB |
HB3 |
111.3 |
109.5 |
| CG |
CB |
HB2 |
111.3 |
109.5 |
| CA |
CB |
HB3 |
111.3 |
109.5 |
| CA |
CB |
HB2 |
111.3 |
109.4 |
| CB |
CA |
C |
108.9 |
109.5 |
| CB |
CA |
N |
108.7 |
109.5 |
| CB |
CA |
HA |
110.8 |
109.5 |
| HB3 |
CB |
HB2 |
99.1 |
109.4 |
| C |
CA |
N |
110.7 |
109.5 |
| C |
CA |
HA |
108.8 |
109.4 |
| CA |
C |
O |
121.0 |
120.0 |
| CA |
C |
OXT |
119.8 |
119.9 |
| N |
CA |
HA |
109.0 |
109.4 |
| CA |
N |
C2 |
122.2 |
120.0 |
| CA |
N |
H |
124.0 |
120.0 |
| O |
C |
OXT |
119.2 |
120.1 |
| C |
OXT |
HXT |
119.8 |
119.9 |
| C2 |
N |
H |
113.8 |
120.0 |
| N |
C2 |
O2' |
123.0 |
120.0 |
| N |
C2 |
C1 |
119.0 |
120.0 |
| O2' |
C2 |
C1 |
117.9 |
120.0 |
| C2 |
C1 |
O1 |
119.6 |
120.1 |
| C2 |
C1 |
O2 |
120.6 |
120.0 |
| O1 |
C1 |
O2 |
119.8 |
119.9 |
| C1 |
O1 |
HO1 |
119.6 |
120.0 |
Torsion Angles for NDF
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CG |
CD1 |
CE1 |
HD1 |
180.0 |
179.9 |
| CE1 |
CD1 |
CG |
CD2 |
359.9 |
0.3 |
| CE1 |
CD1 |
CG |
CB |
178.8 |
180.0 |
| CZ |
CE1 |
CD1 |
HE1 |
180.0 |
180.1 |
| CD1 |
CE1 |
CZ |
CE2 |
360.0 |
360.0 |
| CD1 |
CE1 |
CZ |
HZ |
179.9 |
179.9 |
| CE1 |
CD1 |
CG |
HD1 |
180.0 |
180.1 |
| CG |
CD1 |
CE1 |
CZ |
0.1 |
360.0 |
| CG |
CD1 |
CE1 |
HE1 |
180.1 |
179.9 |
| CE2 |
CD2 |
CG |
CD1 |
0.0 |
359.4 |
| CD1 |
CG |
CD2 |
HD2 |
180.0 |
179.9 |
| CD2 |
CG |
CD1 |
CB |
181.1 |
180.4 |
| CD1 |
CG |
CB |
CA |
92.6 |
90.1 |
| CD1 |
CG |
CB |
HB3 |
327.3 |
330.0 |
| CD1 |
CG |
CB |
HB2 |
217.8 |
210.0 |
| CE1 |
CD1 |
HD1 |
CG |
180.0 |
179.9 |
| HD1 |
CD1 |
CE1 |
CZ |
180.1 |
180.0 |
| HD1 |
CD1 |
CE1 |
HE1 |
0.1 |
360.0 |
| HD1 |
CD1 |
CG |
CD2 |
179.9 |
180.2 |
| HD1 |
CD1 |
CG |
CB |
358.8 |
359.9 |
| CZ |
CE1 |
CD1 |
CG |
0.1 |
360.0 |
| CZ |
CE1 |
CD1 |
HD1 |
180.1 |
180.0 |
| CD1 |
CE1 |
CZ |
HE1 |
180.0 |
179.9 |
| CE2 |
CZ |
CE1 |
HZ |
180.0 |
180.1 |
| CE1 |
CZ |
CE2 |
CD2 |
359.9 |
359.8 |
| CE1 |
CZ |
CE2 |
HE2 |
180.0 |
180.0 |
| HE1 |
CE1 |
CD1 |
CG |
180.1 |
179.9 |
| HE1 |
CE1 |
CD1 |
HD1 |
0.1 |
360.0 |
| CD1 |
CE1 |
HE1 |
CZ |
180.0 |
180.1 |
| HE1 |
CE1 |
CZ |
CE2 |
180.0 |
180.0 |
| HE1 |
CE1 |
CZ |
HZ |
359.9 |
359.9 |
| CE2 |
CZ |
CE1 |
HE1 |
180.0 |
180.0 |
| CE1 |
CZ |
CE2 |
HZ |
180.0 |
179.9 |
| CD2 |
CE2 |
CZ |
HE2 |
180.0 |
179.8 |
| CZ |
CE2 |
CD2 |
CG |
0.1 |
0.5 |
| CZ |
CE2 |
CD2 |
HD2 |
180.1 |
180.0 |
| HZ |
CZ |
CE1 |
HE1 |
359.9 |
359.9 |
| CE1 |
CZ |
HZ |
CE2 |
180.0 |
180.1 |
| HZ |
CZ |
CE2 |
CD2 |
180.0 |
179.9 |
| HZ |
CZ |
CE2 |
HE2 |
360.0 |
0.1 |
| CD1 |
CG |
CD2 |
CE2 |
0.0 |
359.4 |
| CD2 |
CE2 |
CZ |
HZ |
180.0 |
179.9 |
| CZ |
CE2 |
CD2 |
HE2 |
180.0 |
180.2 |
| CG |
CD2 |
CE2 |
HD2 |
180.0 |
180.5 |
| CE2 |
CD2 |
CG |
CB |
181.1 |
179.8 |
| HE2 |
CE2 |
CZ |
HZ |
360.0 |
0.1 |
| CZ |
CE2 |
HE2 |
CD2 |
180.0 |
179.8 |
| HE2 |
CE2 |
CD2 |
CG |
180.0 |
180.3 |
| HE2 |
CE2 |
CD2 |
HD2 |
0.1 |
359.8 |
| CD2 |
CG |
CD1 |
HD1 |
179.9 |
180.2 |
| CD1 |
CG |
CD2 |
CB |
178.9 |
179.6 |
| CG |
CD2 |
CE2 |
HE2 |
180.0 |
180.3 |
| CE2 |
CD2 |
CG |
HD2 |
180.0 |
179.5 |
| CD2 |
CG |
CB |
CA |
271.5 |
269.7 |
| CD2 |
CG |
CB |
HB3 |
146.3 |
149.7 |
| CD2 |
CG |
CB |
HB2 |
36.8 |
29.7 |
| HD2 |
CD2 |
CE2 |
HE2 |
0.1 |
359.8 |
| CE2 |
CD2 |
HD2 |
CG |
180.0 |
180.5 |
| HD2 |
CD2 |
CG |
CB |
1.1 |
0.3 |
| CB |
CG |
CD1 |
HD1 |
358.8 |
359.9 |
| CD1 |
CG |
CB |
CD2 |
181.1 |
180.4 |
| CB |
CG |
CD2 |
HD2 |
1.1 |
0.3 |
| CA |
CB |
CG |
HB3 |
125.2 |
120.1 |
| CA |
CB |
CG |
HB2 |
234.7 |
240.0 |
| CG |
CB |
CA |
C |
180.4 |
180.0 |
| CG |
CB |
CA |
N |
59.7 |
59.9 |
| CG |
CB |
CA |
HA |
300.0 |
300.0 |
| HB3 |
CB |
CG |
HB2 |
109.5 |
120.0 |
| CG |
CB |
CA |
HB3 |
234.7 |
239.9 |
| CG |
CB |
CA |
HB2 |
125.3 |
120.0 |
| HB3 |
CB |
CA |
HB2 |
250.5 |
240.0 |
| C |
CA |
CB |
N |
120.7 |
120.1 |
| C |
CA |
CB |
HA |
240.4 |
240.0 |
| CB |
CA |
C |
O |
246.0 |
89.9 |
| CB |
CA |
C |
OXT |
65.9 |
270.0 |
| N |
CA |
CB |
HA |
119.7 |
119.9 |
| CB |
CA |
N |
C2 |
250.8 |
210.0 |
| CB |
CA |
N |
H |
70.9 |
30.0 |
| CG |
CB |
HB3 |
CA |
125.6 |
120.1 |
| CG |
CB |
HB3 |
HB2 |
242.8 |
240.0 |
| CA |
CB |
HB3 |
HB2 |
117.2 |
120.0 |
| HB3 |
CB |
CA |
C |
305.7 |
300.1 |
| HB3 |
CB |
CA |
N |
185.0 |
180.0 |
| HB3 |
CB |
CA |
HA |
65.3 |
60.1 |
| CG |
CB |
HB2 |
CA |
234.4 |
240.0 |
| CG |
CB |
HB2 |
HB3 |
117.2 |
120.0 |
| CA |
CB |
HB2 |
HB3 |
242.8 |
240.0 |
| HB2 |
CB |
CA |
C |
55.2 |
60.1 |
| HB2 |
CB |
CA |
N |
294.5 |
300.0 |
| HB2 |
CB |
CA |
HA |
174.8 |
180.1 |
| C |
CA |
CB |
HB3 |
305.7 |
300.1 |
| C |
CA |
CB |
HB2 |
55.2 |
60.1 |
| CB |
CA |
C |
N |
240.6 |
239.9 |
| CB |
CA |
C |
HA |
120.8 |
120.0 |
| N |
CA |
C |
HA |
240.2 |
240.1 |
| C |
CA |
N |
C2 |
131.3 |
89.9 |
| C |
CA |
N |
H |
311.3 |
269.9 |
| O |
C |
CA |
OXT |
180.1 |
179.9 |
| CA |
C |
OXT |
HXT |
180.0 |
180.0 |
| N |
CA |
CB |
HB3 |
185.0 |
180.0 |
| N |
CA |
CB |
HB2 |
294.5 |
300.0 |
| CB |
CA |
N |
C |
119.6 |
120.1 |
| CB |
CA |
N |
HA |
239.2 |
240.0 |
| C |
CA |
N |
HA |
119.6 |
119.9 |
| N |
CA |
C |
O |
5.4 |
210.0 |
| N |
CA |
C |
OXT |
185.3 |
30.1 |
| C2 |
N |
CA |
H |
180.0 |
180.0 |
| CA |
N |
C2 |
O2' |
357.7 |
0.0 |
| CA |
N |
C2 |
C1 |
178.8 |
180.0 |
| HA |
CA |
CB |
HB3 |
65.3 |
60.1 |
| HA |
CA |
CB |
HB2 |
174.8 |
180.1 |
| CB |
CA |
HA |
C |
240.3 |
240.0 |
| CB |
CA |
HA |
N |
119.5 |
120.0 |
| C |
CA |
HA |
N |
239.2 |
240.0 |
| HA |
CA |
C |
O |
125.2 |
329.9 |
| HA |
CA |
C |
OXT |
305.1 |
150.0 |
| HA |
CA |
N |
C2 |
11.7 |
330.0 |
| HA |
CA |
N |
H |
191.7 |
150.0 |
| O |
C |
CA |
N |
5.4 |
210.0 |
| O |
C |
CA |
HA |
125.2 |
329.9 |
| CA |
C |
O |
OXT |
179.9 |
180.1 |
| O |
C |
OXT |
HXT |
359.9 |
0.0 |
| OXT |
C |
CA |
N |
185.3 |
30.1 |
| OXT |
C |
CA |
HA |
305.1 |
150.0 |
| CA |
C |
OXT |
O |
180.1 |
179.9 |
| C2 |
N |
CA |
HA |
11.7 |
330.0 |
| CA |
N |
C2 |
H |
180.0 |
180.0 |
| O2' |
C2 |
N |
C1 |
178.8 |
180.0 |
| N |
C2 |
C1 |
O1 |
6.1 |
180.0 |
| N |
C2 |
C1 |
O2 |
186.7 |
360.0 |
| H |
N |
CA |
HA |
191.7 |
150.0 |
| CA |
N |
H |
C2 |
180.0 |
180.0 |
| H |
N |
C2 |
O2' |
177.7 |
180.0 |
| H |
N |
C2 |
C1 |
358.8 |
0.0 |
| O2' |
C2 |
N |
H |
177.7 |
180.0 |
| N |
C2 |
O2' |
C1 |
181.1 |
180.0 |
| O2' |
C2 |
C1 |
O1 |
187.2 |
360.0 |
| O2' |
C2 |
C1 |
O2 |
7.8 |
180.0 |
| C1 |
C2 |
N |
H |
358.8 |
0.0 |
| N |
C2 |
C1 |
O2' |
178.9 |
180.0 |
| O1 |
C1 |
C2 |
O2 |
179.3 |
180.0 |
| C2 |
C1 |
O1 |
HO1 |
180.0 |
180.0 |
| C2 |
C1 |
O1 |
O2 |
180.7 |
180.0 |
| C2 |
C1 |
O2 |
O1 |
179.3 |
180.0 |
| O2 |
C1 |
O1 |
HO1 |
359.3 |
0.0 |
| HO1 |
O1 |
C1 |
O2 |
359.3 |
0.0 |