PDB Chemical Component JDR
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 JDR
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.329 |
1.329 |
| N1 |
C6 |
1.328 |
1.320 |
| C2 |
N3 |
1.332 |
1.326 |
| C2 |
S21 |
1.761 |
1.761 |
| N3 |
C4 |
1.334 |
1.327 |
| C4 |
C5 |
1.395 |
1.415 |
| C4 |
N7 |
1.438 |
1.378 |
| C5 |
C6 |
1.394 |
1.405 |
| C5 |
C18 |
1.483 |
1.461 |
| C6 |
CL20 |
1.729 |
1.736 |
| N7 |
C23 |
1.447 |
1.465 |
| C8 |
C9 |
1.399 |
1.382 |
| C8 |
C13 |
1.382 |
1.382 |
| C8 |
C23 |
1.493 |
1.508 |
| C9 |
C10 |
1.400 |
1.383 |
| C10 |
C11 |
1.405 |
1.382 |
| C11 |
C12 |
1.387 |
1.382 |
| C11 |
S14 |
1.743 |
1.762 |
| C12 |
C13 |
1.387 |
1.383 |
| S14 |
O15 |
1.508 |
1.421 |
| S14 |
O16 |
1.524 |
1.420 |
| S14 |
N17 |
1.719 |
1.657 |
| C18 |
O19 |
1.233 |
1.214 |
| S21 |
C22 |
1.823 |
1.810 |
| N7 |
HN7 |
1.000 |
0.970 |
| C9 |
H9 |
1.080 |
1.080 |
| C10 |
H10 |
1.081 |
1.080 |
| C12 |
H12 |
1.080 |
1.080 |
| C13 |
H13 |
1.080 |
1.080 |
| N17 |
HN17 |
1.000 |
0.969 |
| N17 |
HN1A |
0.999 |
0.970 |
| C18 |
H18 |
1.080 |
1.080 |
| C22 |
H22 |
1.100 |
1.091 |
| C22 |
H22A |
1.100 |
1.091 |
| C22 |
H22B |
1.100 |
1.090 |
| C23 |
H23 |
1.100 |
1.090 |
| C23 |
H23A |
1.100 |
1.090 |
Bond Angles for JDR
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
120.5 |
121.2 |
| N1 |
C2 |
N3 |
122.2 |
122.1 |
| N1 |
C2 |
S21 |
120.5 |
119.0 |
| N1 |
C6 |
C5 |
119.7 |
119.0 |
| N1 |
C6 |
CL20 |
118.8 |
120.5 |
| N3 |
C2 |
S21 |
117.4 |
118.9 |
| C2 |
N3 |
C4 |
119.8 |
120.8 |
| C2 |
S21 |
C22 |
111.5 |
100.0 |
| N3 |
C4 |
C5 |
120.0 |
118.8 |
| N3 |
C4 |
N7 |
120.1 |
120.6 |
| C5 |
C4 |
N7 |
119.9 |
120.6 |
| C4 |
C5 |
C6 |
117.8 |
118.1 |
| C4 |
C5 |
C18 |
121.7 |
120.9 |
| C4 |
N7 |
C23 |
122.6 |
120.0 |
| C4 |
N7 |
HN7 |
105.3 |
120.0 |
| C6 |
C5 |
C18 |
120.6 |
121.0 |
| C5 |
C6 |
CL20 |
121.5 |
120.5 |
| C5 |
C18 |
O19 |
120.4 |
120.0 |
| C5 |
C18 |
H18 |
119.8 |
120.0 |
| N7 |
C23 |
C8 |
114.1 |
109.4 |
| C23 |
N7 |
HN7 |
105.3 |
120.0 |
| N7 |
C23 |
H23 |
108.0 |
109.5 |
| N7 |
C23 |
H23A |
108.0 |
109.5 |
| C9 |
C8 |
C13 |
121.0 |
120.0 |
| C9 |
C8 |
C23 |
124.9 |
120.0 |
| C8 |
C9 |
C10 |
119.2 |
120.0 |
| C8 |
C9 |
H9 |
120.4 |
120.0 |
| C13 |
C8 |
C23 |
114.1 |
120.0 |
| C8 |
C13 |
C12 |
119.9 |
120.0 |
| C8 |
C13 |
H13 |
120.0 |
120.0 |
| C8 |
C23 |
H23 |
108.0 |
109.4 |
| C8 |
C23 |
H23A |
108.0 |
109.4 |
| C9 |
C10 |
C11 |
119.4 |
120.0 |
| C10 |
C9 |
H9 |
120.4 |
120.0 |
| C9 |
C10 |
H10 |
120.3 |
120.0 |
| C10 |
C11 |
C12 |
120.5 |
120.0 |
| C10 |
C11 |
S14 |
122.0 |
120.0 |
| C11 |
C10 |
H10 |
120.3 |
120.0 |
| C12 |
C11 |
S14 |
117.5 |
120.0 |
| C11 |
C12 |
C13 |
120.0 |
120.0 |
| C11 |
C12 |
H12 |
120.0 |
120.0 |
| C11 |
S14 |
O15 |
108.1 |
106.3 |
| C11 |
S14 |
O16 |
107.0 |
106.4 |
| C11 |
S14 |
N17 |
108.1 |
107.2 |
| C13 |
C12 |
H12 |
120.0 |
120.0 |
| C12 |
C13 |
H13 |
120.1 |
120.0 |
| O15 |
S14 |
O16 |
116.5 |
123.2 |
| O15 |
S14 |
N17 |
108.0 |
106.4 |
| O16 |
S14 |
N17 |
109.0 |
106.4 |
| S14 |
N17 |
HN17 |
109.5 |
120.0 |
| S14 |
N17 |
HN1A |
109.5 |
120.0 |
| O19 |
C18 |
H18 |
119.8 |
120.0 |
| S21 |
C22 |
H22 |
109.5 |
109.5 |
| S21 |
C22 |
H22A |
109.4 |
109.5 |
| S21 |
C22 |
H22B |
109.5 |
109.5 |
| HN17 |
N17 |
HN1A |
109.5 |
120.0 |
| H22 |
C22 |
H22A |
109.5 |
109.4 |
| H22 |
C22 |
H22B |
109.5 |
109.4 |
| H22A |
C22 |
H22B |
109.5 |
109.5 |
| H23 |
C23 |
H23A |
110.9 |
109.5 |
Torsion Angles for JDR
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
C5 |
0.0 |
360.0 |
| C2 |
N1 |
C6 |
CL20 |
179.6 |
179.9 |
| N3 |
C2 |
N1 |
S21 |
179.4 |
180.1 |
| N1 |
C2 |
N3 |
C4 |
359.8 |
359.9 |
| N1 |
C2 |
S21 |
C22 |
166.5 |
0.0 |
| C6 |
N1 |
C2 |
N3 |
0.1 |
0.1 |
| C6 |
N1 |
C2 |
S21 |
180.7 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
360.0 |
360.0 |
| N1 |
C6 |
C5 |
C18 |
180.0 |
180.0 |
| C5 |
C6 |
N1 |
CL20 |
180.5 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
0.1 |
0.1 |
| N1 |
C2 |
N3 |
S21 |
180.6 |
179.9 |
| N3 |
C2 |
S21 |
C22 |
347.1 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
0.2 |
-0.0 |
| C2 |
N3 |
C4 |
N7 |
180.5 |
180.0 |
| S21 |
C2 |
N1 |
C6 |
180.7 |
180.0 |
| N1 |
C2 |
S21 |
N3 |
179.4 |
180.0 |
| S21 |
C2 |
N3 |
C4 |
179.2 |
180.0 |
| C2 |
S21 |
C22 |
H22 |
180.0 |
180.0 |
| C2 |
S21 |
C22 |
H22A |
300.0 |
300.0 |
| C2 |
S21 |
C22 |
H22B |
60.0 |
60.0 |
| C4 |
N3 |
C2 |
S21 |
179.2 |
180.0 |
| C5 |
C4 |
N3 |
N7 |
179.7 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
359.9 |
0.0 |
| N3 |
C4 |
C5 |
C18 |
179.9 |
180.0 |
| N3 |
C4 |
N7 |
C23 |
4.8 |
360.0 |
| N3 |
C4 |
N7 |
HN7 |
124.8 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
360.0 |
360.0 |
| N3 |
C4 |
C5 |
N7 |
180.3 |
180.0 |
| C5 |
C4 |
N7 |
C23 |
185.1 |
180.0 |
| C5 |
C4 |
N7 |
HN7 |
305.1 |
-0.0 |
| C6 |
C5 |
C4 |
C18 |
180.0 |
180.1 |
| C4 |
C5 |
C6 |
CL20 |
180.4 |
180.0 |
| C4 |
C5 |
C18 |
O19 |
26.0 |
180.0 |
| C4 |
C5 |
C18 |
H18 |
206.0 |
0.0 |
| N3 |
C4 |
N7 |
C5 |
179.7 |
180.0 |
| N7 |
C4 |
C5 |
C6 |
179.6 |
180.0 |
| N7 |
C4 |
C5 |
C18 |
359.6 |
360.0 |
| C4 |
N7 |
C23 |
C8 |
147.7 |
180.0 |
| C23 |
N7 |
C4 |
HN7 |
240.0 |
180.0 |
| C4 |
N7 |
C23 |
H23 |
267.7 |
300.0 |
| C4 |
N7 |
C23 |
H23A |
27.7 |
60.1 |
| N1 |
C6 |
C5 |
CL20 |
179.5 |
180.0 |
| C6 |
C5 |
C4 |
N7 |
179.6 |
180.0 |
| C4 |
C5 |
C6 |
C18 |
180.0 |
179.9 |
| C6 |
C5 |
C18 |
O19 |
206.0 |
359.9 |
| C6 |
C5 |
C18 |
H18 |
26.0 |
180.0 |
| C18 |
C5 |
C4 |
N7 |
359.6 |
360.0 |
| C4 |
C5 |
C18 |
C6 |
180.0 |
180.1 |
| C18 |
C5 |
C6 |
CL20 |
0.4 |
0.1 |
| O19 |
C18 |
C5 |
H18 |
180.0 |
180.0 |
| N1 |
C6 |
CL20 |
C5 |
180.5 |
180.0 |
| CL20 |
C6 |
C5 |
C18 |
0.4 |
0.1 |
| C4 |
N7 |
C23 |
HN7 |
120.0 |
180.0 |
| C9 |
C8 |
C23 |
N7 |
330.0 |
90.0 |
| C13 |
C8 |
C23 |
N7 |
150.0 |
269.7 |
| C8 |
C23 |
N7 |
H23 |
240.0 |
240.0 |
| C8 |
C23 |
N7 |
H23A |
120.0 |
119.9 |
| H23 |
C23 |
N7 |
H23A |
240.0 |
239.9 |
| N7 |
C23 |
C8 |
C9 |
330.0 |
90.0 |
| C13 |
C8 |
C9 |
C23 |
180.0 |
180.3 |
| C9 |
C8 |
C13 |
C12 |
0.2 |
0.0 |
| C9 |
C8 |
C13 |
H13 |
180.2 |
180.0 |
| C9 |
C8 |
C23 |
H23 |
210.0 |
330.0 |
| C9 |
C8 |
C23 |
H23A |
90.0 |
210.0 |
| C8 |
C9 |
C10 |
C11 |
0.0 |
360.0 |
| C10 |
C9 |
C8 |
H9 |
180.0 |
180.0 |
| C8 |
C9 |
C10 |
H10 |
180.0 |
180.0 |
| N7 |
C23 |
C8 |
C13 |
150.0 |
269.7 |
| C9 |
C8 |
C13 |
C23 |
180.0 |
179.7 |
| C13 |
C8 |
C9 |
C10 |
360.0 |
0.0 |
| C13 |
C8 |
C9 |
H9 |
180.0 |
180.0 |
| C13 |
C8 |
C23 |
H23 |
30.0 |
149.7 |
| C13 |
C8 |
C23 |
H23A |
270.0 |
29.7 |
| C11 |
C12 |
C13 |
C8 |
359.6 |
359.9 |
| C8 |
C13 |
C12 |
H12 |
179.6 |
180.0 |
| C12 |
C13 |
C8 |
H13 |
180.0 |
180.1 |
| C8 |
C23 |
N7 |
HN7 |
27.7 |
360.0 |
| N7 |
C23 |
C8 |
H23 |
120.0 |
120.0 |
| N7 |
C23 |
C8 |
H23A |
240.0 |
240.0 |
| C9 |
C8 |
C23 |
C13 |
180.0 |
180.3 |
| C23 |
C8 |
C9 |
C10 |
180.0 |
179.7 |
| C23 |
C8 |
C9 |
H9 |
360.0 |
359.7 |
| C23 |
C8 |
C13 |
C12 |
180.2 |
180.3 |
| C23 |
C8 |
C13 |
H13 |
0.2 |
0.3 |
| H23 |
C23 |
C8 |
H23A |
120.0 |
120.0 |
| C10 |
C9 |
C8 |
C13 |
360.0 |
0.0 |
| C10 |
C9 |
C8 |
C23 |
180.0 |
179.7 |
| C8 |
C9 |
C10 |
H9 |
180.0 |
180.0 |
| C9 |
C10 |
C11 |
C12 |
359.8 |
360.0 |
| C9 |
C10 |
C11 |
S14 |
180.0 |
180.0 |
| C11 |
C10 |
C9 |
H10 |
180.0 |
180.0 |
| C11 |
C10 |
C9 |
H9 |
180.0 |
180.0 |
| C9 |
C10 |
C11 |
H10 |
180.0 |
180.0 |
| C12 |
C11 |
C10 |
S14 |
179.8 |
180.0 |
| C10 |
C11 |
C12 |
C13 |
0.4 |
0.1 |
| C10 |
C11 |
C12 |
H12 |
180.4 |
180.0 |
| C10 |
C11 |
S14 |
O15 |
250.9 |
203.5 |
| C10 |
C11 |
S14 |
O16 |
17.1 |
336.5 |
| C10 |
C11 |
S14 |
N17 |
134.3 |
90.0 |
| C8 |
C13 |
C12 |
C11 |
359.6 |
359.9 |
| C10 |
C11 |
C12 |
S14 |
180.2 |
180.0 |
| C12 |
C11 |
C10 |
H10 |
179.8 |
180.0 |
| C12 |
C11 |
S14 |
O15 |
71.1 |
23.5 |
| C12 |
C11 |
S14 |
O16 |
197.3 |
156.4 |
| C12 |
C11 |
S14 |
N17 |
314.5 |
270.0 |
| C13 |
C12 |
C11 |
H12 |
180.0 |
180.1 |
| C11 |
C12 |
C13 |
H13 |
179.6 |
180.0 |
| C10 |
C11 |
S14 |
C12 |
179.8 |
180.0 |
| S14 |
C11 |
C10 |
H10 |
0.0 |
360.0 |
| S14 |
C11 |
C12 |
C13 |
180.2 |
180.1 |
| S14 |
C11 |
C12 |
H12 |
0.2 |
0.0 |
| O15 |
S14 |
C11 |
O16 |
233.8 |
227.1 |
| O15 |
S14 |
C11 |
N17 |
116.6 |
113.5 |
| O16 |
S14 |
C11 |
N17 |
242.8 |
246.4 |
| C11 |
S14 |
N17 |
HN17 |
180.0 |
150.0 |
| C11 |
S14 |
N17 |
HN1A |
300.0 |
330.0 |
| C12 |
C13 |
C8 |
C23 |
180.2 |
180.3 |
| C8 |
C13 |
C12 |
H13 |
180.0 |
179.9 |
| C13 |
C12 |
C11 |
S14 |
180.2 |
180.1 |
| C11 |
C12 |
C13 |
H12 |
180.0 |
179.9 |
| C11 |
S14 |
O15 |
O16 |
120.4 |
122.9 |
| C11 |
S14 |
O15 |
N17 |
243.3 |
245.9 |
| O16 |
S14 |
O15 |
N17 |
122.9 |
123.0 |
| O15 |
S14 |
N17 |
HN17 |
63.3 |
36.5 |
| O15 |
S14 |
N17 |
HN1A |
183.3 |
216.5 |
| C11 |
S14 |
O16 |
O15 |
239.0 |
237.1 |
| C11 |
S14 |
O16 |
N17 |
116.6 |
114.1 |
| O15 |
S14 |
O16 |
N17 |
237.6 |
237.0 |
| O16 |
S14 |
N17 |
HN17 |
295.9 |
263.5 |
| O16 |
S14 |
N17 |
HN1A |
55.9 |
83.5 |
| C11 |
S14 |
N17 |
O15 |
116.7 |
113.5 |
| C11 |
S14 |
N17 |
O16 |
244.1 |
246.4 |
| O15 |
S14 |
N17 |
O16 |
127.4 |
133.0 |
| HN17 |
N17 |
S14 |
HN1A |
240.0 |
180.0 |
| C5 |
C18 |
O19 |
H18 |
180.0 |
180.0 |
| H22 |
C22 |
S21 |
H22A |
240.0 |
240.0 |
| H22 |
C22 |
S21 |
H22B |
120.0 |
119.9 |
| H22A |
C22 |
S21 |
H22B |
240.0 |
239.9 |
| C4 |
N7 |
HN7 |
C23 |
229.2 |
180.0 |
| HN7 |
N7 |
C23 |
C8 |
27.7 |
360.0 |
| HN7 |
N7 |
C23 |
H23 |
147.7 |
119.9 |
| HN7 |
N7 |
C23 |
H23A |
267.7 |
240.0 |
| H9 |
C9 |
C8 |
C13 |
180.0 |
180.0 |
| H9 |
C9 |
C8 |
C23 |
360.0 |
359.7 |
| C8 |
C9 |
H9 |
C10 |
180.0 |
180.0 |
| H9 |
C9 |
C10 |
C11 |
180.0 |
180.0 |
| H9 |
C9 |
C10 |
H10 |
0.0 |
360.0 |
| C9 |
C10 |
H10 |
C11 |
180.0 |
180.0 |
| H10 |
C10 |
C9 |
H9 |
0.0 |
360.0 |
| H10 |
C10 |
C11 |
C12 |
179.8 |
180.0 |
| H10 |
C10 |
C11 |
S14 |
0.0 |
360.0 |
| H12 |
C12 |
C11 |
S14 |
0.2 |
0.0 |
| C11 |
C12 |
H12 |
C13 |
180.0 |
180.1 |
| H12 |
C12 |
C13 |
H13 |
359.6 |
0.1 |
| H13 |
C13 |
C8 |
C23 |
0.2 |
0.3 |
| C8 |
C13 |
H13 |
C12 |
180.0 |
180.1 |
| H13 |
C13 |
C12 |
H12 |
359.6 |
0.1 |
| S14 |
N17 |
HN17 |
HN1A |
120.0 |
180.0 |
| S14 |
N17 |
HN1A |
HN17 |
240.0 |
180.0 |
| C5 |
C18 |
H18 |
O19 |
180.0 |
180.0 |
| S21 |
C22 |
H22 |
H22A |
120.0 |
120.0 |
| S21 |
C22 |
H22 |
H22B |
240.0 |
240.0 |
| H22A |
C22 |
H22 |
H22B |
120.0 |
120.0 |
| S21 |
C22 |
H22A |
H22 |
240.0 |
240.0 |
| S21 |
C22 |
H22A |
H22B |
120.0 |
120.1 |
| H22 |
C22 |
H22A |
H22B |
240.0 |
240.0 |
| S21 |
C22 |
H22B |
H22 |
120.0 |
120.0 |
| S21 |
C22 |
H22B |
H22A |
240.0 |
239.9 |
| H22 |
C22 |
H22B |
H22A |
120.0 |
120.0 |
| N7 |
C23 |
H23 |
C8 |
236.2 |
240.0 |
| H23 |
C23 |
N7 |
HN7 |
147.7 |
119.9 |
| N7 |
C23 |
H23 |
H23A |
118.1 |
120.1 |
| C8 |
C23 |
H23 |
H23A |
241.9 |
240.0 |
| N7 |
C23 |
H23A |
C8 |
123.8 |
119.9 |
| H23A |
C23 |
N7 |
HN7 |
267.7 |
240.0 |
| N7 |
C23 |
H23A |
H23 |
241.9 |
239.9 |
| C8 |
C23 |
H23A |
H23 |
118.1 |
120.0 |