PDB Chemical Component 3MD
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 3MD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.477 |
1.468 |
| N |
H |
1.020 |
1.009 |
| N |
H2 |
1.020 |
1.008 |
| CB |
CG |
1.514 |
1.506 |
| CB |
CA |
1.561 |
1.529 |
| CB |
CB1 |
1.527 |
1.530 |
| CB |
HB |
1.115 |
1.091 |
| CG |
OD1 |
1.217 |
1.208 |
| CG |
OD2 |
1.230 |
1.342 |
| OD2 |
HD2 |
0.950 |
0.967 |
| CA |
C |
1.543 |
1.508 |
| CA |
HA |
1.115 |
1.090 |
| CB1 |
HB11 |
1.115 |
1.090 |
| CB1 |
HB12 |
1.115 |
1.089 |
| CB1 |
HB13 |
1.115 |
1.090 |
| C |
O |
1.234 |
1.207 |
| C |
OXT |
1.234 |
1.342 |
| OXT |
HXT |
0.949 |
0.967 |
Bond Angles for 3MD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
110.4 |
106.6 |
| CA |
N |
H2 |
114.3 |
106.8 |
| N |
CA |
CB |
114.3 |
109.5 |
| N |
CA |
C |
113.7 |
109.5 |
| N |
CA |
HA |
103.0 |
109.5 |
| H |
N |
H2 |
110.5 |
106.7 |
| CG |
CB |
CA |
111.7 |
109.5 |
| CG |
CB |
CB1 |
106.5 |
109.5 |
| CG |
CB |
HB |
113.2 |
109.5 |
| CB |
CG |
OD1 |
117.3 |
119.9 |
| CB |
CG |
OD2 |
122.7 |
120.1 |
| CA |
CB |
CB1 |
117.5 |
109.4 |
| CA |
CB |
HB |
101.1 |
109.5 |
| CB |
CA |
C |
109.9 |
109.5 |
| CB |
CA |
HA |
107.4 |
109.4 |
| CB1 |
CB |
HB |
106.9 |
109.4 |
| CB |
CB1 |
HB11 |
113.3 |
109.4 |
| CB |
CB1 |
HB12 |
106.5 |
109.5 |
| CB |
CB1 |
HB13 |
113.3 |
109.5 |
| OD1 |
CG |
OD2 |
119.9 |
120.0 |
| CG |
OD2 |
HD2 |
122.7 |
120.0 |
| C |
CA |
HA |
108.1 |
109.4 |
| CA |
C |
O |
119.8 |
120.0 |
| CA |
C |
OXT |
121.9 |
120.0 |
| HB11 |
CB1 |
HB12 |
113.4 |
109.5 |
| HB11 |
CB1 |
HB13 |
97.1 |
109.5 |
| HB12 |
CB1 |
HB13 |
113.3 |
109.5 |
| O |
C |
OXT |
118.2 |
120.0 |
| C |
OXT |
HXT |
122.0 |
120.0 |
Torsion Angles for 3MD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
234.7 |
246.2 |
| CG |
CB |
CA |
N |
300.5 |
300.1 |
| N |
CA |
CB |
CB1 |
64.0 |
60.1 |
| N |
CA |
CB |
HB |
179.8 |
180.0 |
| CB |
CA |
N |
C |
232.8 |
240.0 |
| CB |
CA |
N |
HA |
116.1 |
120.0 |
| C |
CA |
N |
HA |
243.3 |
240.0 |
| N |
CA |
C |
O |
156.0 |
330.1 |
| N |
CA |
C |
OXT |
335.4 |
149.9 |
| CA |
N |
H |
H2 |
127.4 |
113.8 |
| H |
N |
CA |
CB |
54.7 |
299.9 |
| H |
N |
CA |
C |
181.9 |
60.0 |
| H |
N |
CA |
HA |
298.6 |
180.0 |
| CA |
N |
H2 |
H |
234.7 |
246.3 |
| H2 |
N |
CA |
CB |
180.0 |
53.7 |
| H2 |
N |
CA |
C |
307.2 |
173.8 |
| H2 |
N |
CA |
HA |
63.9 |
293.8 |
| N |
CA |
CB |
CG |
300.5 |
300.1 |
| CA |
CB |
CG |
CB1 |
129.5 |
120.0 |
| CA |
CB |
CG |
HB |
246.7 |
240.0 |
| CG |
CB |
CA |
C |
171.4 |
180.0 |
| CG |
CB |
CA |
HA |
54.0 |
60.1 |
| CB1 |
CB |
CG |
HB |
117.2 |
120.0 |
| CG |
CB |
CB1 |
HB11 |
54.7 |
60.0 |
| CG |
CB |
CB1 |
HB12 |
180.0 |
180.1 |
| CG |
CB |
CB1 |
HB13 |
305.3 |
300.0 |
| OD1 |
CG |
CB |
OD2 |
177.6 |
179.9 |
| CB |
CG |
OD2 |
HD2 |
180.0 |
180.0 |
| CB |
CA |
N |
H |
54.7 |
299.9 |
| CB |
CA |
N |
H2 |
180.0 |
53.7 |
| N |
CA |
CB |
C |
129.2 |
120.1 |
| N |
CA |
CB |
HA |
246.5 |
240.0 |
| CG |
CB |
CA |
CB1 |
236.5 |
240.0 |
| CG |
CB |
CA |
HB |
120.7 |
120.0 |
| CA |
CB |
CG |
OD1 |
16.0 |
360.0 |
| CA |
CB |
CG |
OD2 |
198.5 |
180.0 |
| CB1 |
CB |
CA |
HB |
244.2 |
240.1 |
| CA |
CB |
CB1 |
HB11 |
288.6 |
300.0 |
| CA |
CB |
CB1 |
HB12 |
53.9 |
60.0 |
| CA |
CB |
CB1 |
HB13 |
179.2 |
180.0 |
| C |
CA |
CB |
HA |
117.3 |
119.9 |
| CB |
CA |
C |
O |
285.5 |
90.1 |
| CB |
CA |
C |
OXT |
104.9 |
270.0 |
| CG |
CB |
CB1 |
CA |
126.1 |
120.1 |
| CG |
CB |
CB1 |
HB |
238.7 |
240.0 |
| CB1 |
CB |
CG |
OD1 |
246.5 |
240.0 |
| CB1 |
CB |
CG |
OD2 |
68.9 |
60.0 |
| CA |
CB |
CB1 |
HB |
112.6 |
120.0 |
| CB1 |
CB |
CA |
C |
294.9 |
300.0 |
| CB1 |
CB |
CA |
HA |
177.5 |
180.1 |
| HB11 |
CB1 |
CB |
HB12 |
234.7 |
240.0 |
| HB11 |
CB1 |
CB |
HB13 |
109.4 |
120.0 |
| HB12 |
CB1 |
CB |
HB13 |
234.7 |
240.0 |
| CG |
CB |
HB |
CA |
240.4 |
239.9 |
| CG |
CB |
HB |
CB1 |
117.0 |
120.0 |
| HB |
CB |
CG |
OD1 |
129.3 |
120.0 |
| HB |
CB |
CG |
OD2 |
311.8 |
300.1 |
| CA |
CB |
HB |
CB1 |
236.6 |
240.1 |
| HB |
CB |
CA |
C |
50.7 |
60.0 |
| HB |
CB |
CA |
HA |
293.3 |
300.0 |
| HB |
CB |
CB1 |
HB11 |
176.0 |
180.0 |
| HB |
CB |
CB1 |
HB12 |
301.3 |
300.0 |
| HB |
CB |
CB1 |
HB13 |
66.6 |
60.0 |
| OD1 |
CG |
CB |
CA |
16.0 |
360.0 |
| OD1 |
CG |
CB |
CB1 |
246.5 |
240.0 |
| OD1 |
CG |
CB |
HB |
129.3 |
120.0 |
| CB |
CG |
OD1 |
OD2 |
182.4 |
180.1 |
| OD1 |
CG |
OD2 |
HD2 |
2.5 |
0.1 |
| OD2 |
CG |
CB |
CA |
198.5 |
180.0 |
| OD2 |
CG |
CB |
CB1 |
68.9 |
60.0 |
| OD2 |
CG |
CB |
HB |
311.8 |
300.1 |
| CB |
CG |
OD2 |
OD1 |
177.5 |
179.9 |
| C |
CA |
N |
H |
181.9 |
60.0 |
| C |
CA |
N |
H2 |
307.2 |
173.8 |
| N |
CA |
C |
CB |
230.5 |
239.9 |
| N |
CA |
C |
HA |
113.6 |
120.0 |
| C |
CA |
CB |
CB1 |
294.9 |
300.0 |
| C |
CA |
CB |
HB |
50.7 |
60.0 |
| CB |
CA |
C |
HA |
243.1 |
240.1 |
| O |
C |
CA |
OXT |
180.6 |
180.1 |
| CA |
C |
OXT |
HXT |
180.0 |
180.0 |
| HA |
CA |
N |
H |
298.6 |
180.0 |
| HA |
CA |
N |
H2 |
63.9 |
293.8 |
| N |
CA |
HA |
CB |
120.9 |
120.0 |
| N |
CA |
HA |
C |
239.4 |
240.0 |
| HA |
CA |
CB |
CB1 |
177.5 |
180.1 |
| HA |
CA |
CB |
HB |
293.3 |
300.0 |
| CB |
CA |
HA |
C |
118.5 |
120.0 |
| HA |
CA |
C |
O |
42.4 |
210.1 |
| HA |
CA |
C |
OXT |
221.8 |
29.9 |
| HB11 |
CB1 |
CB |
HB |
176.0 |
180.0 |
| CB |
CB1 |
HB11 |
HB12 |
121.5 |
120.0 |
| CB |
CB1 |
HB11 |
HB13 |
240.8 |
240.0 |
| HB12 |
CB1 |
HB11 |
HB13 |
119.3 |
120.0 |
| HB12 |
CB1 |
CB |
HB |
301.3 |
300.0 |
| CB |
CB1 |
HB12 |
HB11 |
234.7 |
240.0 |
| CB |
CB1 |
HB12 |
HB13 |
125.3 |
120.0 |
| HB11 |
CB1 |
HB12 |
HB13 |
250.5 |
240.0 |
| HB13 |
CB1 |
CB |
HB |
66.6 |
60.0 |
| CB |
CB1 |
HB13 |
HB11 |
119.2 |
119.9 |
| CB |
CB1 |
HB13 |
HB12 |
238.5 |
240.0 |
| HB11 |
CB1 |
HB13 |
HB12 |
119.3 |
120.1 |
| O |
C |
CA |
HA |
42.4 |
210.1 |
| CA |
C |
O |
OXT |
179.5 |
179.9 |
| O |
C |
OXT |
HXT |
359.5 |
359.9 |
| OXT |
C |
CA |
HA |
221.8 |
29.9 |
| CA |
C |
OXT |
O |
180.5 |
180.1 |