PDB Chemical Component 5LD
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 5LD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O12 |
P9 |
1.524 |
1.481 |
| O10 |
P9 |
1.517 |
1.611 |
| P9 |
O11 |
1.534 |
1.610 |
| P9 |
C8 |
1.795 |
1.823 |
| C8 |
C7 |
1.540 |
1.530 |
| C6 |
C7 |
1.523 |
1.530 |
| C6 |
N2 |
1.468 |
1.465 |
| C7 |
O13 |
1.426 |
1.428 |
| C3 |
N2 |
1.315 |
1.344 |
| C3 |
N4 |
1.360 |
1.308 |
| N2 |
N1 |
1.404 |
1.404 |
| N4 |
C5 |
1.354 |
1.332 |
| N1 |
C5 |
1.362 |
1.307 |
| O10 |
H1 |
0.950 |
0.967 |
| O11 |
H2 |
0.950 |
0.967 |
| C8 |
H3 |
1.100 |
1.090 |
| C8 |
H4 |
1.100 |
1.090 |
| C7 |
H5 |
1.100 |
1.091 |
| O13 |
H6 |
0.950 |
0.967 |
| C6 |
H7 |
1.100 |
1.090 |
| C6 |
H8 |
1.100 |
1.090 |
| C5 |
H9 |
1.080 |
1.080 |
| C3 |
H10 |
1.080 |
1.080 |
Bond Angles for 5LD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O12 |
P9 |
C8 |
110.5 |
109.4 |
| O10 |
P9 |
O11 |
111.3 |
109.5 |
| O10 |
P9 |
C8 |
105.8 |
109.5 |
| P9 |
O10 |
H1 |
109.5 |
114.0 |
| O11 |
P9 |
C8 |
107.1 |
109.5 |
| P9 |
O11 |
H2 |
109.5 |
114.0 |
| P9 |
C8 |
C7 |
116.5 |
109.5 |
| P9 |
C8 |
H3 |
107.7 |
109.4 |
| P9 |
C8 |
H4 |
107.7 |
109.5 |
| C8 |
C7 |
O13 |
110.3 |
109.5 |
| C7 |
C8 |
H3 |
107.7 |
109.5 |
| C7 |
C8 |
H4 |
107.7 |
109.5 |
| C8 |
C7 |
H5 |
109.2 |
109.5 |
| C6 |
C7 |
H5 |
109.4 |
109.4 |
| C6 |
N2 |
N1 |
119.1 |
126.8 |
| N2 |
C6 |
H7 |
108.4 |
109.5 |
| N2 |
C6 |
H8 |
108.4 |
109.5 |
| O13 |
C7 |
H5 |
110.8 |
109.5 |
| C7 |
O13 |
H6 |
109.5 |
114.0 |
| N2 |
N1 |
C5 |
103.2 |
106.8 |
| N4 |
C5 |
H9 |
124.9 |
125.5 |
| N1 |
C5 |
H9 |
124.8 |
125.5 |
| H3 |
C8 |
H4 |
109.5 |
109.4 |
| H7 |
C6 |
H8 |
109.5 |
109.5 |
Torsion Angles for 5LD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O10 |
P9 |
O12 |
C8 |
117.0 |
120.0 |
| O12 |
P9 |
O10 |
H1 |
0.0 |
180.0 |
| O11 |
P9 |
O12 |
C8 |
241.3 |
240.0 |
| O12 |
P9 |
O11 |
H2 |
360.0 |
300.1 |
| O12 |
P9 |
C8 |
C7 |
285.4 |
55.0 |
| O12 |
P9 |
C8 |
H3 |
46.5 |
175.0 |
| O12 |
P9 |
C8 |
H4 |
164.4 |
295.0 |
| O12 |
P9 |
O10 |
C8 |
240.2 |
240.1 |
| O11 |
P9 |
O10 |
C8 |
116.0 |
120.0 |
| O10 |
P9 |
O11 |
H2 |
124.0 |
60.0 |
| O10 |
P9 |
C8 |
C7 |
165.3 |
295.0 |
| O10 |
P9 |
C8 |
H3 |
286.4 |
55.0 |
| O10 |
P9 |
C8 |
H4 |
44.3 |
175.0 |
| O12 |
P9 |
O11 |
C8 |
120.7 |
120.0 |
| O10 |
P9 |
O11 |
C8 |
244.8 |
240.0 |
| O11 |
P9 |
O10 |
H1 |
235.8 |
60.0 |
| O11 |
P9 |
C8 |
C7 |
46.5 |
175.0 |
| O11 |
P9 |
C8 |
H3 |
167.5 |
295.0 |
| O11 |
P9 |
C8 |
H4 |
285.5 |
55.0 |
| O10 |
P9 |
C8 |
O11 |
118.8 |
120.0 |
| C8 |
P9 |
O10 |
H1 |
119.8 |
300.0 |
| C8 |
P9 |
O11 |
H2 |
239.3 |
180.1 |
| P9 |
C8 |
C7 |
O13 |
184.1 |
295.0 |
| C7 |
C8 |
P9 |
H3 |
239.0 |
240.0 |
| C7 |
C8 |
P9 |
H4 |
121.0 |
120.0 |
| P9 |
C8 |
C7 |
H5 |
306.1 |
55.0 |
| H3 |
C8 |
P9 |
H4 |
242.0 |
240.0 |
| P9 |
C8 |
C7 |
H3 |
121.0 |
120.0 |
| P9 |
C8 |
C7 |
H4 |
239.0 |
240.0 |
| C6 |
C7 |
C8 |
H5 |
121.9 |
119.9 |
| O13 |
C7 |
C8 |
H5 |
238.0 |
239.9 |
| C8 |
C7 |
O13 |
H6 |
180.0 |
300.0 |
| H3 |
C8 |
C7 |
H4 |
118.0 |
120.0 |
| C6 |
C7 |
C8 |
H3 |
306.9 |
55.0 |
| C6 |
C7 |
C8 |
H4 |
188.9 |
295.0 |
| C8 |
C7 |
C6 |
H5 |
238.2 |
240.0 |
| O13 |
C7 |
C6 |
H5 |
118.6 |
120.0 |
| C6 |
C7 |
O13 |
H6 |
301.3 |
60.0 |
| N2 |
C6 |
C7 |
H5 |
322.7 |
305.0 |
| C6 |
N2 |
N1 |
C5 |
181.1 |
180.0 |
| H7 |
C6 |
N2 |
H8 |
118.8 |
120.0 |
| O13 |
C7 |
C8 |
H3 |
63.0 |
175.0 |
| O13 |
C7 |
C8 |
H4 |
305.1 |
55.0 |
| C8 |
C7 |
O13 |
H5 |
121.0 |
120.0 |
| C6 |
C7 |
O13 |
H5 |
242.3 |
240.0 |
| C3 |
N2 |
C6 |
H7 |
10.1 |
4.7 |
| C3 |
N2 |
C6 |
H8 |
251.3 |
244.7 |
| C3 |
N4 |
C5 |
H9 |
182.6 |
179.8 |
| N1 |
N2 |
C6 |
H7 |
189.8 |
185.0 |
| N1 |
N2 |
C6 |
H8 |
70.9 |
65.0 |
| N2 |
N1 |
C5 |
H9 |
177.9 |
180.0 |
| N1 |
C5 |
N4 |
H9 |
180.0 |
180.0 |
| N4 |
C5 |
N1 |
H9 |
180.0 |
180.0 |
| H1 |
O10 |
P9 |
O11 |
235.8 |
60.0 |
| H1 |
O10 |
P9 |
C8 |
119.8 |
300.0 |
| H2 |
O11 |
P9 |
C8 |
239.3 |
180.1 |
| P9 |
C8 |
H3 |
C7 |
233.6 |
240.0 |
| P9 |
C8 |
H3 |
H4 |
116.8 |
120.0 |
| H3 |
C8 |
C7 |
O13 |
63.0 |
175.0 |
| C7 |
C8 |
H3 |
H4 |
243.2 |
240.0 |
| H3 |
C8 |
C7 |
H5 |
185.0 |
295.1 |
| P9 |
C8 |
H4 |
C7 |
126.4 |
120.0 |
| P9 |
C8 |
H4 |
H3 |
243.2 |
240.0 |
| H4 |
C8 |
C7 |
O13 |
305.1 |
55.0 |
| C7 |
C8 |
H4 |
H3 |
116.8 |
120.0 |
| H4 |
C8 |
C7 |
H5 |
67.1 |
175.1 |
| C8 |
C7 |
H5 |
O13 |
238.3 |
240.0 |
| H5 |
C7 |
C8 |
H3 |
185.0 |
295.1 |
| H5 |
C7 |
C8 |
H4 |
67.1 |
175.1 |
| H5 |
C7 |
O13 |
H6 |
58.9 |
180.0 |
| H6 |
O13 |
C7 |
H5 |
58.9 |
180.0 |
| H7 |
C6 |
C7 |
H5 |
83.3 |
65.0 |
| H7 |
C6 |
N2 |
N1 |
189.8 |
185.0 |
| N2 |
C6 |
H7 |
H8 |
241.9 |
240.0 |
| H8 |
C6 |
C7 |
H5 |
202.1 |
184.9 |
| H8 |
C6 |
N2 |
N1 |
70.9 |
65.0 |
| N2 |
C6 |
H8 |
H7 |
118.1 |
120.0 |