PDB Chemical Component C6D
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 C6D
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.461 |
1.469 |
| C03 |
O2 |
1.394 |
1.429 |
| C03 |
C01 |
1.498 |
1.530 |
| C01 |
C02 |
1.502 |
1.530 |
| CA |
C |
1.528 |
1.507 |
| CA |
CB |
1.545 |
1.530 |
| C02 |
NH2 |
1.458 |
1.465 |
| CG |
CB |
1.523 |
1.530 |
| CG |
CD |
1.511 |
1.530 |
| C |
O |
1.226 |
1.209 |
| NE |
CD |
1.452 |
1.465 |
| NE |
CZ |
1.322 |
1.375 |
| NH2 |
CZ |
1.329 |
1.375 |
| CZ |
NH1 |
1.324 |
1.303 |
| N |
H |
1.000 |
1.009 |
| N |
H2 |
1.000 |
1.009 |
| CA |
HA |
1.100 |
1.090 |
| CB |
H6 |
1.100 |
1.090 |
| CB |
H7 |
1.100 |
1.090 |
| CG |
H8 |
1.100 |
1.090 |
| CG |
H9 |
1.100 |
1.090 |
| CD |
H10 |
1.100 |
1.090 |
| CD |
H11 |
1.100 |
1.090 |
| NE |
H12 |
1.000 |
0.970 |
| NH1 |
H13 |
1.000 |
0.970 |
| NH2 |
H14 |
1.000 |
0.970 |
| C01 |
H15 |
1.100 |
1.090 |
| C01 |
H16 |
1.100 |
1.090 |
| C02 |
H17 |
1.100 |
1.091 |
| C02 |
H18 |
1.100 |
1.090 |
| C03 |
H19 |
1.100 |
1.090 |
| C03 |
H20 |
1.100 |
1.090 |
| O2 |
H21 |
0.950 |
0.967 |
| C |
OXT |
1.325 |
1.343 |
| OXT |
HXT |
0.950 |
0.967 |
Bond Angles for C6D
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N |
CA |
C |
110.1 |
109.5 |
| N |
CA |
CB |
111.4 |
109.5 |
| CA |
N |
H |
109.5 |
111.0 |
| CA |
N |
H2 |
109.5 |
111.0 |
| N |
CA |
HA |
108.9 |
109.4 |
| O2 |
C03 |
H19 |
109.6 |
109.5 |
| O2 |
C03 |
H20 |
109.6 |
109.5 |
| C03 |
O2 |
H21 |
109.5 |
114.0 |
| C03 |
C01 |
H15 |
109.2 |
109.5 |
| C03 |
C01 |
H16 |
109.2 |
109.5 |
| C02 |
C01 |
H15 |
109.2 |
109.5 |
| C02 |
C01 |
H16 |
109.2 |
109.4 |
| C01 |
C02 |
H17 |
109.8 |
109.4 |
| C01 |
C02 |
H18 |
109.8 |
109.4 |
| C |
CA |
CB |
110.3 |
109.5 |
| CA |
C |
O |
120.8 |
120.0 |
| C |
CA |
HA |
108.1 |
109.4 |
| CA |
C |
OXT |
116.3 |
120.0 |
| CB |
CA |
HA |
107.9 |
109.5 |
| CA |
CB |
H6 |
108.4 |
109.4 |
| CA |
CB |
H7 |
108.4 |
109.5 |
| C02 |
NH2 |
H14 |
119.1 |
120.0 |
| CG |
CB |
H6 |
108.4 |
109.5 |
| CG |
CB |
H7 |
108.4 |
109.4 |
| CD |
CG |
H8 |
109.4 |
109.5 |
| CD |
CG |
H9 |
109.4 |
109.5 |
| CG |
CD |
H10 |
108.8 |
109.5 |
| CG |
CD |
H11 |
108.8 |
109.5 |
| O |
C |
OXT |
122.9 |
119.9 |
| NE |
CD |
H10 |
108.8 |
109.4 |
| NE |
CD |
H11 |
108.8 |
109.5 |
| NE |
CZ |
NH1 |
117.3 |
120.0 |
| CZ |
NE |
H12 |
118.4 |
120.0 |
| CZ |
NH1 |
H13 |
112.0 |
120.0 |
| H |
N |
H2 |
109.4 |
111.0 |
| H6 |
CB |
H7 |
109.5 |
109.5 |
| H8 |
CG |
H9 |
109.5 |
109.5 |
| H10 |
CD |
H11 |
109.4 |
109.5 |
| H15 |
C01 |
H16 |
109.5 |
109.4 |
| H17 |
C02 |
H18 |
109.4 |
109.5 |
| H19 |
C03 |
H20 |
109.5 |
109.5 |
| C |
OXT |
HXT |
109.5 |
117.0 |
Torsion Angles for C6D
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C |
CA |
N |
CB |
122.7 |
120.0 |
| N |
CA |
C |
O |
215.3 |
339.9 |
| C |
CA |
N |
HA |
241.6 |
240.1 |
| N |
CA |
C |
OXT |
35.4 |
160.0 |
| CB |
CA |
N |
HA |
118.9 |
120.0 |
| N |
CA |
CB |
H6 |
66.4 |
55.0 |
| N |
CA |
CB |
H7 |
185.1 |
175.0 |
| H |
N |
CA |
H2 |
240.0 |
236.1 |
| O2 |
C03 |
C01 |
H15 |
5.1 |
60.0 |
| O2 |
C03 |
C01 |
H16 |
124.7 |
300.0 |
| H19 |
C03 |
O2 |
H20 |
239.9 |
120.1 |
| C02 |
C01 |
C03 |
H15 |
239.8 |
120.0 |
| C02 |
C01 |
C03 |
H16 |
120.2 |
240.0 |
| C03 |
C01 |
C02 |
H17 |
290.8 |
60.0 |
| C03 |
C01 |
C02 |
H18 |
51.2 |
300.0 |
| H15 |
C01 |
C03 |
H16 |
240.3 |
120.0 |
| C03 |
C01 |
C02 |
H15 |
120.2 |
240.0 |
| C03 |
C01 |
C02 |
H16 |
239.9 |
120.0 |
| C01 |
C02 |
NH2 |
H14 |
340.7 |
360.0 |
| H15 |
C01 |
C02 |
H16 |
119.7 |
240.1 |
| H17 |
C02 |
C01 |
H18 |
239.7 |
119.9 |
| N |
CA |
C |
CB |
236.7 |
240.0 |
| C |
CA |
N |
H |
180.0 |
296.1 |
| C |
CA |
N |
H2 |
300.0 |
60.0 |
| N |
CA |
C |
HA |
118.9 |
119.9 |
| CB |
CA |
C |
HA |
242.2 |
239.9 |
| C |
CA |
CB |
H6 |
303.8 |
295.0 |
| C |
CA |
CB |
H7 |
62.5 |
55.0 |
| O |
C |
CA |
OXT |
179.8 |
179.9 |
| CA |
C |
OXT |
HXT |
179.8 |
180.0 |
| N |
CA |
CB |
C |
122.5 |
120.0 |
| CB |
CA |
N |
H |
57.3 |
176.1 |
| CB |
CA |
N |
H2 |
177.3 |
300.0 |
| N |
CA |
CB |
HA |
240.5 |
240.0 |
| CB |
CA |
C |
O |
338.6 |
100.0 |
| C |
CA |
CB |
HA |
117.9 |
120.0 |
| CB |
CA |
C |
OXT |
158.8 |
280.0 |
| CG |
CB |
CA |
H6 |
239.3 |
240.0 |
| CG |
CB |
CA |
H7 |
120.6 |
120.0 |
| H6 |
CB |
CA |
H7 |
241.3 |
240.0 |
| CG |
CB |
CA |
HA |
65.2 |
55.0 |
| CA |
CB |
CG |
H6 |
120.6 |
120.0 |
| CA |
CB |
CG |
H7 |
239.3 |
240.0 |
| H6 |
CB |
CG |
H7 |
118.7 |
120.0 |
| CD |
CG |
CB |
H6 |
82.6 |
60.0 |
| CD |
CG |
CB |
H7 |
323.9 |
300.0 |
| NE |
CD |
CG |
H10 |
239.6 |
240.0 |
| NE |
CD |
CG |
H11 |
120.4 |
120.0 |
| H8 |
CG |
CD |
H9 |
119.9 |
120.0 |
| H10 |
CD |
CG |
H11 |
240.8 |
240.0 |
| O |
C |
CA |
CB |
338.6 |
100.0 |
| O |
C |
CA |
HA |
96.4 |
220.0 |
| CA |
C |
O |
OXT |
180.2 |
180.1 |
| O |
C |
OXT |
HXT |
360.0 |
0.0 |
| NE |
CD |
CG |
H8 |
61.9 |
60.0 |
| NE |
CD |
CG |
H9 |
302.0 |
300.0 |
| CG |
CD |
NE |
H10 |
120.4 |
120.0 |
| CG |
CD |
NE |
H11 |
239.6 |
240.0 |
| H10 |
CD |
NE |
H11 |
119.2 |
120.0 |
| CZ |
NE |
CD |
H10 |
55.3 |
60.0 |
| CZ |
NE |
CD |
H11 |
296.1 |
300.0 |
| NE |
CZ |
NH1 |
H13 |
180.1 |
180.0 |
| NH2 |
CZ |
NE |
H12 |
359.7 |
0.0 |
| NH2 |
CZ |
NH1 |
H13 |
360.0 |
360.0 |
| NH1 |
CZ |
NE |
H12 |
179.6 |
180.0 |
| H |
N |
CA |
C |
180.0 |
296.1 |
| H |
N |
CA |
CB |
57.3 |
176.1 |
| CA |
N |
H |
H2 |
120.0 |
123.9 |
| H |
N |
CA |
HA |
298.4 |
56.0 |
| H2 |
N |
CA |
C |
300.0 |
60.0 |
| H2 |
N |
CA |
CB |
177.3 |
300.0 |
| CA |
N |
H2 |
H |
240.0 |
236.1 |
| H2 |
N |
CA |
HA |
58.4 |
180.0 |
| N |
CA |
HA |
C |
240.4 |
240.1 |
| N |
CA |
HA |
CB |
121.1 |
120.0 |
| HA |
CA |
N |
H |
298.4 |
56.0 |
| HA |
CA |
N |
H2 |
58.4 |
180.0 |
| C |
CA |
HA |
CB |
240.7 |
240.0 |
| HA |
CA |
C |
O |
96.4 |
220.0 |
| HA |
CA |
C |
OXT |
276.5 |
40.1 |
| HA |
CA |
CB |
H6 |
185.9 |
175.0 |
| HA |
CA |
CB |
H7 |
304.6 |
295.0 |
| H6 |
CB |
CA |
HA |
185.9 |
175.0 |
| CA |
CB |
H6 |
H7 |
118.0 |
120.0 |
| CG |
CB |
H6 |
H7 |
242.0 |
240.0 |
| H7 |
CB |
CA |
HA |
304.6 |
295.0 |
| CA |
CB |
H7 |
H6 |
242.0 |
240.0 |
| CG |
CB |
H7 |
H6 |
118.0 |
120.0 |
| H8 |
CG |
CB |
H6 |
202.6 |
180.0 |
| H8 |
CG |
CB |
H7 |
83.9 |
60.0 |
| CD |
CG |
H8 |
H9 |
240.1 |
240.0 |
| H8 |
CG |
CD |
H10 |
182.3 |
180.0 |
| H8 |
CG |
CD |
H11 |
301.5 |
300.0 |
| H9 |
CG |
CB |
H6 |
322.5 |
300.0 |
| H9 |
CG |
CB |
H7 |
203.8 |
180.0 |
| CD |
CG |
H9 |
H8 |
119.9 |
120.0 |
| H9 |
CG |
CD |
H10 |
62.4 |
60.0 |
| H9 |
CG |
CD |
H11 |
181.6 |
180.0 |
| H10 |
CD |
CG |
H8 |
182.3 |
180.0 |
| H10 |
CD |
CG |
H9 |
62.4 |
60.0 |
| CG |
CD |
H10 |
H11 |
118.8 |
120.0 |
| NE |
CD |
H10 |
H11 |
241.2 |
240.0 |
| H11 |
CD |
CG |
H8 |
301.5 |
300.0 |
| H11 |
CD |
CG |
H9 |
181.6 |
180.0 |
| CG |
CD |
H11 |
H10 |
241.2 |
240.0 |
| NE |
CD |
H11 |
H10 |
118.8 |
120.0 |
| H12 |
NE |
CD |
H10 |
235.3 |
240.0 |
| H12 |
NE |
CD |
H11 |
116.1 |
120.0 |
| H12 |
NE |
CZ |
NH1 |
179.6 |
180.0 |
| C03 |
C01 |
H15 |
H16 |
119.5 |
240.0 |
| C02 |
C01 |
H15 |
H16 |
240.5 |
119.9 |
| H15 |
C01 |
C02 |
H17 |
170.7 |
180.0 |
| H15 |
C01 |
C02 |
H18 |
291.0 |
60.1 |
| C03 |
C01 |
H16 |
H15 |
240.5 |
120.0 |
| C02 |
C01 |
H16 |
H15 |
119.5 |
240.0 |
| H16 |
C01 |
C02 |
H17 |
51.0 |
299.9 |
| H16 |
C01 |
C02 |
H18 |
171.3 |
180.0 |
| H17 |
C02 |
C01 |
H15 |
170.7 |
180.0 |
| H17 |
C02 |
C01 |
H16 |
51.0 |
299.9 |
| C01 |
C02 |
H17 |
H18 |
120.6 |
240.1 |
| H17 |
C02 |
NH2 |
H14 |
220.8 |
120.0 |
| H18 |
C02 |
C01 |
H15 |
291.0 |
60.1 |
| H18 |
C02 |
C01 |
H16 |
171.3 |
180.0 |
| C01 |
C02 |
H18 |
H17 |
239.4 |
119.9 |
| H18 |
C02 |
NH2 |
H14 |
100.5 |
240.0 |
| O2 |
C03 |
H19 |
H20 |
120.2 |
239.9 |
| H19 |
C03 |
O2 |
H21 |
299.9 |
60.0 |
| H19 |
C03 |
C01 |
H15 |
245.1 |
179.9 |
| H19 |
C03 |
C01 |
H16 |
4.8 |
60.0 |
| O2 |
C03 |
H20 |
H19 |
239.8 |
120.0 |
| H20 |
C03 |
O2 |
H21 |
60.1 |
300.0 |
| H20 |
C03 |
C01 |
H15 |
125.0 |
300.0 |
| H20 |
C03 |
C01 |
H16 |
244.7 |
180.0 |
| H21 |
O2 |
C03 |
H19 |
299.9 |
60.0 |
| H21 |
O2 |
C03 |
H20 |
60.1 |
300.0 |
| OXT |
C |
CA |
CB |
158.8 |
280.0 |
| CA |
C |
OXT |
O |
179.8 |
179.9 |
| OXT |
C |
CA |
HA |
276.5 |
40.1 |