PDB Chemical Component 5Y9
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 5Y9
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C03 |
N02 |
1.456 |
1.465 |
| C01 |
N02 |
1.459 |
1.465 |
| N02 |
C04 |
1.429 |
1.348 |
| C04 |
O06 |
1.190 |
1.213 |
| C04 |
C05 |
1.522 |
1.507 |
| C01 |
H1 |
1.100 |
1.090 |
| C01 |
H2 |
1.100 |
1.090 |
| C01 |
H3 |
1.100 |
1.090 |
| C03 |
H4 |
1.100 |
1.090 |
| C03 |
H5 |
1.101 |
1.090 |
| C03 |
H6 |
1.100 |
1.090 |
| C05 |
H7 |
1.100 |
1.090 |
| C05 |
H8 |
1.100 |
1.090 |
| C05 |
H9 |
1.100 |
1.090 |
Bond Angles for 5Y9
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C03 |
N02 |
C04 |
118.4 |
120.0 |
| C01 |
N02 |
C04 |
120.7 |
120.0 |
| N02 |
C01 |
H1 |
109.5 |
109.5 |
| N02 |
C01 |
H2 |
109.5 |
109.5 |
| N02 |
C01 |
H3 |
109.5 |
109.5 |
| N02 |
C04 |
O06 |
118.9 |
120.0 |
| N02 |
C04 |
C05 |
118.8 |
120.0 |
| C05 |
C04 |
O06 |
122.3 |
120.0 |
| C04 |
C05 |
H7 |
109.5 |
109.5 |
| C04 |
C05 |
H8 |
109.4 |
109.4 |
| C04 |
C05 |
H9 |
109.5 |
109.5 |
| H1 |
C01 |
H2 |
109.5 |
109.5 |
| H1 |
C01 |
H3 |
109.4 |
109.5 |
| H2 |
C01 |
H3 |
109.4 |
109.5 |
| H4 |
C03 |
H5 |
109.5 |
109.5 |
| H4 |
C03 |
H6 |
109.4 |
109.5 |
| H5 |
C03 |
H6 |
109.5 |
109.5 |
| H7 |
C05 |
H8 |
109.5 |
109.5 |
| H7 |
C05 |
H9 |
109.5 |
109.5 |
| H8 |
C05 |
H9 |
109.4 |
109.5 |
Torsion Angles for 5Y9
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C01 |
N02 |
C03 |
C04 |
179.7 |
180.0 |
| C03 |
N02 |
C01 |
H1 |
180.0 |
270.0 |
| C03 |
N02 |
C01 |
H2 |
300.0 |
30.0 |
| C03 |
N02 |
C01 |
H3 |
60.0 |
150.0 |
| C03 |
N02 |
C04 |
O06 |
359.5 |
175.3 |
| C03 |
N02 |
C04 |
C05 |
180.1 |
355.3 |
| C03 |
N02 |
C01 |
C04 |
180.3 |
180.0 |
| C01 |
N02 |
C04 |
O06 |
179.8 |
355.3 |
| C01 |
N02 |
C04 |
C05 |
0.3 |
175.3 |
| H1 |
C01 |
N02 |
H2 |
240.0 |
240.0 |
| H1 |
C01 |
N02 |
H3 |
120.0 |
120.0 |
| H2 |
C01 |
N02 |
H3 |
240.0 |
240.0 |
| C04 |
N02 |
C01 |
H1 |
359.7 |
90.0 |
| C04 |
N02 |
C01 |
H2 |
119.8 |
210.0 |
| C04 |
N02 |
C01 |
H3 |
239.7 |
330.0 |
| C05 |
C04 |
N02 |
O06 |
180.5 |
180.0 |
| N02 |
C04 |
C05 |
H7 |
179.5 |
5.2 |
| N02 |
C04 |
C05 |
H8 |
299.5 |
125.2 |
| N02 |
C04 |
C05 |
H9 |
59.4 |
245.2 |
| N02 |
C04 |
O06 |
C05 |
180.6 |
180.0 |
| O06 |
C04 |
C05 |
H7 |
0.0 |
185.2 |
| O06 |
C04 |
C05 |
H8 |
120.0 |
305.2 |
| O06 |
C04 |
C05 |
H9 |
240.0 |
65.2 |
| N02 |
C04 |
C05 |
O06 |
179.4 |
180.0 |
| H7 |
C05 |
C04 |
H8 |
240.0 |
240.0 |
| H7 |
C05 |
C04 |
H9 |
120.1 |
120.0 |
| H8 |
C05 |
C04 |
H9 |
240.1 |
240.0 |
| H1 |
C01 |
N02 |
C04 |
359.7 |
90.0 |
| N02 |
C01 |
H1 |
H2 |
120.0 |
120.0 |
| N02 |
C01 |
H1 |
H3 |
240.0 |
240.0 |
| H2 |
C01 |
H1 |
H3 |
120.0 |
120.0 |
| H2 |
C01 |
N02 |
C04 |
119.8 |
210.0 |
| N02 |
C01 |
H2 |
H1 |
239.9 |
240.0 |
| N02 |
C01 |
H2 |
H3 |
120.0 |
120.0 |
| H1 |
C01 |
H2 |
H3 |
240.1 |
240.0 |
| H3 |
C01 |
N02 |
C04 |
239.7 |
330.0 |
| N02 |
C01 |
H3 |
H1 |
120.0 |
120.0 |
| N02 |
C01 |
H3 |
H2 |
240.0 |
240.0 |
| H1 |
C01 |
H3 |
H2 |
120.0 |
120.0 |
| H4 |
C03 |
N02 |
C04 |
0.2 |
275.5 |
| H5 |
C03 |
H4 |
H6 |
120.0 |
120.1 |
| H5 |
C03 |
N02 |
C04 |
120.3 |
35.5 |
| H4 |
C03 |
H5 |
H6 |
240.1 |
240.0 |
| H6 |
C03 |
N02 |
C04 |
240.3 |
155.5 |
| H4 |
C03 |
H6 |
H5 |
120.0 |
120.0 |
| H7 |
C05 |
C04 |
O06 |
0.0 |
185.2 |
| C04 |
C05 |
H7 |
H8 |
120.0 |
119.9 |
| C04 |
C05 |
H7 |
H9 |
240.0 |
240.0 |
| H8 |
C05 |
H7 |
H9 |
120.0 |
120.0 |
| H8 |
C05 |
C04 |
O06 |
120.0 |
305.2 |
| C04 |
C05 |
H8 |
H7 |
240.0 |
240.0 |
| C04 |
C05 |
H8 |
H9 |
120.0 |
120.0 |
| H7 |
C05 |
H8 |
H9 |
240.0 |
240.0 |
| H9 |
C05 |
C04 |
O06 |
240.0 |
65.2 |
| C04 |
C05 |
H9 |
H7 |
120.1 |
120.0 |
| C04 |
C05 |
H9 |
H8 |
240.1 |
240.0 |
| H7 |
C05 |
H9 |
H8 |
120.0 |
120.0 |