PDB Chemical Component 2BY
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 2BY
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
C8 |
1.457 |
1.469 |
| C8 |
C7 |
1.534 |
1.530 |
| C7 |
C9 |
1.522 |
1.530 |
| C7 |
C6 |
1.474 |
1.507 |
| C9 |
P |
1.800 |
1.823 |
| O3 |
P |
1.610 |
1.481 |
| O1 |
P |
1.491 |
1.610 |
| C6 |
C5 |
1.394 |
1.383 |
| C6 |
C1 |
1.395 |
1.382 |
| C5 |
C4 |
1.403 |
1.382 |
| P |
O2 |
1.608 |
1.610 |
| C1 |
C2 |
1.388 |
1.382 |
| C4 |
C3 |
1.395 |
1.384 |
| C2 |
C3 |
1.391 |
1.384 |
| C3 |
CL |
1.794 |
1.736 |
| C2 |
H1 |
1.080 |
1.080 |
| C4 |
H2 |
1.080 |
1.081 |
| C5 |
H3 |
1.080 |
1.080 |
| C1 |
H4 |
1.080 |
1.080 |
| C7 |
H5 |
1.100 |
1.090 |
| C8 |
H6 |
1.100 |
1.090 |
| C8 |
H7 |
1.100 |
1.090 |
| N |
H8 |
1.000 |
1.009 |
| N |
H9 |
1.000 |
1.009 |
| C9 |
H11 |
1.101 |
1.089 |
| C9 |
H12 |
1.100 |
1.090 |
| O1 |
H13 |
0.950 |
0.967 |
| O2 |
H14 |
0.950 |
0.968 |
Bond Angles for 2BY
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N |
C8 |
H6 |
109.2 |
109.5 |
| N |
C8 |
H7 |
109.3 |
109.5 |
| C8 |
C7 |
C9 |
108.4 |
109.5 |
| C8 |
C7 |
H5 |
109.6 |
109.5 |
| C7 |
C9 |
P |
111.8 |
109.4 |
| C9 |
C7 |
H5 |
109.8 |
109.5 |
| C7 |
C9 |
H11 |
108.9 |
109.5 |
| C7 |
C9 |
H12 |
108.9 |
109.5 |
| C9 |
P |
O2 |
110.8 |
109.5 |
| P |
C9 |
H11 |
108.9 |
109.5 |
| P |
C9 |
H12 |
108.9 |
109.4 |
| O3 |
P |
O2 |
110.4 |
109.4 |
| O1 |
P |
O2 |
107.6 |
109.5 |
| C6 |
C5 |
H3 |
120.2 |
120.0 |
| C6 |
C1 |
H4 |
120.1 |
120.0 |
| C5 |
C4 |
H2 |
120.3 |
120.0 |
| P |
O2 |
H14 |
109.5 |
114.0 |
| C1 |
C2 |
H1 |
120.0 |
120.0 |
| H6 |
C8 |
H7 |
109.5 |
109.4 |
| H8 |
N |
H9 |
109.5 |
111.1 |
| H11 |
C9 |
H12 |
109.5 |
109.5 |
Torsion Angles for 2BY
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N |
C8 |
C7 |
C9 |
171.3 |
185.0 |
| N |
C8 |
C7 |
H5 |
291.1 |
305.1 |
| H6 |
C8 |
N |
H7 |
240.2 |
120.0 |
| C8 |
C7 |
C9 |
P |
171.1 |
75.0 |
| C9 |
C7 |
C8 |
H5 |
240.2 |
239.9 |
| C8 |
C7 |
C9 |
H11 |
291.4 |
195.0 |
| C8 |
C7 |
C9 |
H12 |
50.8 |
315.1 |
| C8 |
C7 |
C9 |
H5 |
119.7 |
120.1 |
| C7 |
C9 |
P |
O2 |
95.6 |
65.0 |
| P |
C9 |
C7 |
H11 |
239.7 |
240.0 |
| P |
C9 |
C7 |
H12 |
120.3 |
120.0 |
| H11 |
C9 |
C7 |
H12 |
240.7 |
239.9 |
| C7 |
C6 |
C5 |
H3 |
0.9 |
0.0 |
| C7 |
C6 |
C1 |
H4 |
358.3 |
0.3 |
| P |
C9 |
C7 |
H5 |
51.4 |
315.0 |
| C7 |
C9 |
P |
H11 |
120.3 |
120.0 |
| C7 |
C9 |
P |
H12 |
239.7 |
240.0 |
| O3 |
P |
C9 |
O2 |
236.6 |
240.0 |
| O1 |
P |
C9 |
O2 |
117.2 |
120.0 |
| C9 |
P |
O2 |
H14 |
236.0 |
60.0 |
| H11 |
C9 |
P |
H12 |
119.3 |
120.0 |
| C9 |
P |
O3 |
O2 |
123.6 |
120.0 |
| O3 |
P |
C9 |
H11 |
211.9 |
185.0 |
| O3 |
P |
C9 |
H12 |
92.5 |
65.0 |
| O1 |
P |
O3 |
O2 |
241.9 |
240.0 |
| O3 |
P |
O2 |
H14 |
360.0 |
180.0 |
| C9 |
P |
O1 |
O2 |
240.7 |
239.9 |
| O1 |
P |
C9 |
H11 |
92.5 |
65.0 |
| O1 |
P |
C9 |
H12 |
333.2 |
305.0 |
| O3 |
P |
O1 |
O2 |
119.8 |
120.0 |
| O1 |
P |
O2 |
H14 |
118.9 |
299.9 |
| C6 |
C5 |
C4 |
H2 |
179.9 |
180.1 |
| C1 |
C6 |
C5 |
H3 |
180.8 |
180.3 |
| C6 |
C1 |
C2 |
H1 |
181.6 |
180.0 |
| O2 |
P |
C9 |
H11 |
335.2 |
305.0 |
| O2 |
P |
C9 |
H12 |
215.9 |
185.0 |
| H3 |
C5 |
C4 |
H2 |
359.9 |
0.1 |
| H4 |
C1 |
C2 |
H1 |
1.6 |
359.8 |
| C8 |
C7 |
H5 |
C9 |
241.0 |
239.9 |
| H5 |
C7 |
C9 |
P |
51.4 |
315.0 |
| H5 |
C7 |
C9 |
H11 |
171.8 |
74.9 |
| H5 |
C7 |
C9 |
H12 |
291.1 |
195.0 |
| N |
C8 |
H6 |
H7 |
119.6 |
239.9 |
| H6 |
C8 |
C7 |
C9 |
51.2 |
305.0 |
| H6 |
C8 |
C7 |
H5 |
171.0 |
65.1 |
| N |
C8 |
H7 |
H6 |
240.4 |
120.1 |
| H7 |
C8 |
C7 |
C9 |
291.5 |
64.9 |
| H7 |
C8 |
C7 |
H5 |
51.3 |
185.0 |
| H8 |
N |
C8 |
H6 |
300.1 |
296.0 |
| H8 |
N |
C8 |
H7 |
59.9 |
176.0 |
| H9 |
N |
C8 |
H6 |
60.1 |
60.1 |
| H9 |
N |
C8 |
H7 |
179.8 |
300.1 |
| C7 |
C9 |
H11 |
P |
237.9 |
240.0 |
| H11 |
C9 |
C7 |
H5 |
171.8 |
74.9 |
| C7 |
C9 |
H11 |
H12 |
118.9 |
120.0 |
| H11 |
C9 |
P |
O2 |
335.2 |
305.0 |
| P |
C9 |
H11 |
H12 |
241.0 |
240.0 |
| C7 |
C9 |
H12 |
P |
122.1 |
120.0 |
| H12 |
C9 |
C7 |
H5 |
291.1 |
195.0 |
| C7 |
C9 |
H12 |
H11 |
241.1 |
239.9 |
| H12 |
C9 |
P |
O2 |
215.9 |
185.0 |
| P |
C9 |
H12 |
H11 |
119.0 |
120.0 |
| H13 |
O1 |
P |
O2 |
240.2 |
300.0 |