PDB Chemical Component OMD
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 OMD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1 |
C2 |
1.536 |
1.506 |
| C1 |
O1 |
1.225 |
1.209 |
| C1 |
O2 |
1.233 |
1.342 |
| C2 |
C1' |
1.509 |
1.507 |
| C2 |
H21 |
1.115 |
1.090 |
| C2 |
H22 |
1.115 |
1.089 |
| C1' |
C2' |
1.391 |
1.381 |
| C1' |
C6' |
1.388 |
1.387 |
| C2' |
C3' |
1.375 |
1.387 |
| C2' |
H2' |
1.103 |
1.079 |
| C3' |
O3' |
1.375 |
1.360 |
| C3' |
C4' |
1.391 |
1.386 |
| O3' |
HO3 |
0.950 |
0.966 |
| C4' |
C5' |
1.369 |
1.381 |
| C4' |
H4' |
1.104 |
1.079 |
| C5' |
C6' |
1.380 |
1.387 |
| C5' |
H5' |
1.104 |
1.081 |
| C6' |
O6' |
1.093 |
1.359 |
| O6' |
HO6 |
0.950 |
0.966 |
| O2 |
HO2 |
0.950 |
0.966 |
Bond Angles for OMD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C1 |
O1 |
120.1 |
120.0 |
| C2 |
C1 |
O2 |
121.9 |
120.1 |
| C1 |
C2 |
C1' |
114.6 |
109.5 |
| C1 |
C2 |
H21 |
110.4 |
109.5 |
| C1 |
C2 |
H22 |
110.4 |
109.4 |
| O1 |
C1 |
O2 |
118.0 |
120.0 |
| C1 |
O2 |
HO2 |
122.0 |
120.1 |
| C1' |
C2 |
H21 |
110.3 |
109.4 |
| C1' |
C2 |
H22 |
110.3 |
109.5 |
| C2 |
C1' |
C2' |
120.0 |
120.0 |
| C2 |
C1' |
C6' |
122.5 |
119.9 |
| H21 |
C2 |
H22 |
99.9 |
109.5 |
| C2' |
C1' |
C6' |
117.5 |
120.0 |
| C1' |
C2' |
C3' |
118.9 |
120.0 |
| C1' |
C2' |
H2' |
121.2 |
120.0 |
| C1' |
C6' |
C5' |
122.9 |
119.9 |
| C1' |
C6' |
O6' |
123.2 |
120.1 |
| C3' |
C2' |
H2' |
120.0 |
120.0 |
| C2' |
C3' |
O3' |
125.6 |
120.0 |
| C2' |
C3' |
C4' |
123.5 |
120.0 |
| O3' |
C3' |
C4' |
110.9 |
120.0 |
| C3' |
O3' |
HO3 |
125.5 |
106.8 |
| C3' |
C4' |
C5' |
117.3 |
120.0 |
| C3' |
C4' |
H4' |
122.1 |
120.0 |
| C5' |
C4' |
H4' |
120.6 |
120.0 |
| C4' |
C5' |
C6' |
119.9 |
120.0 |
| C4' |
C5' |
H5' |
119.7 |
120.0 |
| C6' |
C5' |
H5' |
120.4 |
120.0 |
| C5' |
C6' |
O6' |
113.9 |
120.0 |
| C6' |
O6' |
HO6 |
123.1 |
106.8 |
Torsion Angles for OMD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1 |
C1 |
C2 |
O2 |
177.5 |
180.0 |
| C2 |
C1 |
O2 |
HO2 |
180.0 |
180.0 |
| C1' |
C2 |
C1 |
H21 |
234.7 |
240.0 |
| C1' |
C2 |
C1 |
H22 |
125.2 |
120.1 |
| C1 |
C2 |
C1' |
C2' |
33.9 |
90.0 |
| C1 |
C2 |
C1' |
C6' |
213.7 |
269.7 |
| H21 |
C2 |
C1 |
H22 |
250.5 |
240.1 |
| C2 |
C1 |
O1 |
O2 |
182.4 |
180.0 |
| O1 |
C1 |
C2 |
C1' |
181.2 |
360.0 |
| O1 |
C1 |
C2 |
H21 |
306.4 |
120.0 |
| O1 |
C1 |
C2 |
H22 |
55.9 |
239.9 |
| O1 |
C1 |
O2 |
HO2 |
2.5 |
0.0 |
| C2 |
C1 |
O2 |
O1 |
177.5 |
180.0 |
| O2 |
C1 |
C2 |
C1' |
3.7 |
180.0 |
| O2 |
C1 |
C2 |
H21 |
129.0 |
300.0 |
| O2 |
C1 |
C2 |
H22 |
238.5 |
60.0 |
| C1' |
C2 |
C1 |
O1 |
181.2 |
360.0 |
| C1' |
C2 |
C1 |
O2 |
3.7 |
180.0 |
| C1 |
C2 |
C1' |
H21 |
125.3 |
120.0 |
| C1 |
C2 |
C1' |
H22 |
234.7 |
240.0 |
| H21 |
C2 |
C1' |
H22 |
109.4 |
120.0 |
| C2' |
C1' |
C2 |
C6' |
180.2 |
180.3 |
| C2 |
C1' |
C2' |
C3' |
180.5 |
180.0 |
| C2 |
C1' |
C2' |
H2' |
0.5 |
360.0 |
| C2 |
C1' |
C6' |
C5' |
178.4 |
179.8 |
| C2 |
C1' |
C6' |
O6' |
359.5 |
0.3 |
| H21 |
C2 |
C1 |
O1 |
306.4 |
120.0 |
| H21 |
C2 |
C1 |
O2 |
129.0 |
300.0 |
| C1 |
C2 |
H21 |
C1' |
232.3 |
240.0 |
| C1 |
C2 |
H21 |
H22 |
116.2 |
119.9 |
| C1' |
C2 |
H21 |
H22 |
243.9 |
240.0 |
| H21 |
C2 |
C1' |
C2' |
268.6 |
330.0 |
| H21 |
C2 |
C1' |
C6' |
88.4 |
149.7 |
| H22 |
C2 |
C1 |
O1 |
55.9 |
239.9 |
| H22 |
C2 |
C1 |
O2 |
238.5 |
60.0 |
| C1 |
C2 |
H22 |
C1' |
127.7 |
120.1 |
| C1 |
C2 |
H22 |
H21 |
243.8 |
240.0 |
| C1' |
C2 |
H22 |
H21 |
116.1 |
120.0 |
| H22 |
C2 |
C1' |
C2' |
159.2 |
210.0 |
| H22 |
C2 |
C1' |
C6' |
339.0 |
29.7 |
| C2' |
C1' |
C2 |
H21 |
268.6 |
330.0 |
| C2' |
C1' |
C2 |
H22 |
159.2 |
210.0 |
| C2 |
C1' |
C2' |
C6' |
179.8 |
179.7 |
| C2' |
C1' |
C6' |
C5' |
358.2 |
359.5 |
| C2' |
C1' |
C6' |
O6' |
179.3 |
180.0 |
| C3' |
C2' |
C1' |
H2' |
179.9 |
180.0 |
| C1' |
C2' |
C3' |
O3' |
180.1 |
180.1 |
| C1' |
C2' |
C3' |
C4' |
0.1 |
360.0 |
| C6' |
C1' |
C2 |
H21 |
88.4 |
149.7 |
| C6' |
C1' |
C2 |
H22 |
339.0 |
29.7 |
| C2 |
C1' |
C6' |
C2' |
180.2 |
180.3 |
| C6' |
C1' |
C2' |
C3' |
0.6 |
0.2 |
| C6' |
C1' |
C2' |
H2' |
180.7 |
180.2 |
| C4' |
C5' |
C6' |
C1' |
2.1 |
0.6 |
| C1' |
C6' |
C5' |
H5' |
182.1 |
180.3 |
| C5' |
C6' |
C1' |
O6' |
178.9 |
179.5 |
| C1' |
C6' |
O6' |
HO6 |
180.0 |
269.5 |
| C3' |
C2' |
C1' |
C6' |
0.6 |
0.2 |
| C1' |
C2' |
C3' |
H2' |
180.1 |
180.0 |
| O3' |
C3' |
C2' |
C4' |
180.0 |
180.1 |
| C2' |
C3' |
O3' |
HO3 |
180.0 |
90.0 |
| C2' |
C3' |
C4' |
C5' |
0.2 |
0.1 |
| C2' |
C3' |
C4' |
H4' |
180.2 |
180.0 |
| H2' |
C2' |
C1' |
C6' |
180.7 |
180.2 |
| C1' |
C2' |
H2' |
C3' |
179.9 |
180.0 |
| H2' |
C2' |
C3' |
O3' |
0.0 |
0.1 |
| H2' |
C2' |
C3' |
C4' |
180.0 |
180.0 |
| O3' |
C3' |
C2' |
H2' |
0.0 |
0.1 |
| C2' |
C3' |
O3' |
C4' |
180.0 |
179.9 |
| O3' |
C3' |
C4' |
C5' |
180.2 |
180.0 |
| O3' |
C3' |
C4' |
H4' |
0.3 |
359.9 |
| C4' |
C3' |
C2' |
H2' |
180.0 |
180.0 |
| C2' |
C3' |
C4' |
O3' |
180.0 |
180.1 |
| C4' |
C3' |
O3' |
HO3 |
359.9 |
270.1 |
| C5' |
C4' |
C3' |
H4' |
180.0 |
180.1 |
| C3' |
C4' |
C5' |
C6' |
358.7 |
359.7 |
| C3' |
C4' |
C5' |
H5' |
178.7 |
179.9 |
| HO3 |
O3' |
C3' |
C4' |
359.9 |
270.1 |
| C1' |
C6' |
C5' |
C4' |
2.1 |
0.6 |
| C3' |
C4' |
C5' |
H4' |
180.0 |
179.9 |
| C6' |
C5' |
C4' |
H5' |
180.0 |
179.7 |
| C4' |
C5' |
C6' |
O6' |
181.1 |
180.0 |
| C3' |
C4' |
H4' |
C5' |
180.0 |
180.1 |
| H4' |
C4' |
C5' |
C6' |
178.7 |
179.7 |
| H4' |
C4' |
C5' |
H5' |
358.7 |
0.0 |
| C1' |
C6' |
C5' |
O6' |
181.0 |
180.5 |
| C6' |
C5' |
C4' |
H4' |
178.7 |
179.7 |
| C4' |
C5' |
C6' |
H5' |
180.0 |
180.3 |
| C5' |
C6' |
O6' |
HO6 |
1.0 |
90.0 |
| H5' |
C5' |
C4' |
H4' |
358.7 |
0.0 |
| C4' |
C5' |
H5' |
C6' |
180.0 |
179.7 |
| H5' |
C5' |
C6' |
O6' |
1.1 |
359.8 |
| C1' |
C6' |
O6' |
C5' |
179.0 |
179.5 |
| O6' |
C6' |
C5' |
H5' |
1.1 |
359.8 |