PDB Chemical Component JPD
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 JPD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O11 |
C10 |
1.452 |
1.429 |
| C09 |
C10 |
1.503 |
1.530 |
| C09 |
C08 |
1.536 |
1.530 |
| C12 |
C10 |
1.511 |
1.530 |
| C12 |
C13 |
1.555 |
1.529 |
| C10 |
C05 |
1.529 |
1.536 |
| C08 |
C07 |
1.509 |
1.533 |
| C02 |
C01 |
1.541 |
1.530 |
| C02 |
C03 |
1.531 |
1.531 |
| C13 |
C07 |
1.493 |
1.534 |
| C05 |
C03 |
1.589 |
1.530 |
| C05 |
N06 |
1.535 |
1.477 |
| C03 |
O04 |
1.346 |
1.429 |
| C07 |
N06 |
1.448 |
1.477 |
| N06 |
C14 |
1.452 |
1.348 |
| C14 |
O16 |
1.372 |
1.346 |
| C14 |
O15 |
1.191 |
1.216 |
| O16 |
C17 |
1.406 |
1.451 |
| C13 |
H132 |
1.100 |
1.090 |
| C13 |
H131 |
1.100 |
1.089 |
| C17 |
H171 |
1.100 |
1.090 |
| C17 |
H172 |
1.101 |
1.090 |
| C17 |
H173 |
1.100 |
1.090 |
| C01 |
H013 |
1.100 |
1.090 |
| C01 |
H011 |
1.100 |
1.090 |
| C01 |
H012 |
1.100 |
1.090 |
| C02 |
H021 |
1.100 |
1.089 |
| C02 |
H022 |
1.100 |
1.089 |
| C03 |
H031 |
1.100 |
1.089 |
| O04 |
H041 |
0.949 |
0.968 |
| C05 |
H051 |
1.100 |
1.090 |
| C07 |
H071 |
1.100 |
1.090 |
| C08 |
H081 |
1.100 |
1.090 |
| C08 |
H082 |
1.100 |
1.090 |
| C09 |
H092 |
1.100 |
1.090 |
| C09 |
H091 |
1.100 |
1.090 |
| O11 |
H111 |
0.950 |
0.968 |
| C12 |
H121 |
1.100 |
1.090 |
| C12 |
H122 |
1.100 |
1.090 |
Bond Angles for JPD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C09 |
C08 |
H081 |
110.0 |
109.4 |
| C09 |
C08 |
H082 |
110.0 |
109.5 |
| C12 |
C13 |
H132 |
109.6 |
109.5 |
| C12 |
C13 |
H131 |
109.6 |
109.5 |
| C10 |
C05 |
C03 |
109.6 |
110.0 |
| C10 |
C05 |
N06 |
108.0 |
106.7 |
| C10 |
C05 |
H051 |
106.3 |
110.0 |
| C08 |
C07 |
H071 |
111.0 |
111.0 |
| C02 |
C01 |
H013 |
109.5 |
109.5 |
| C02 |
C01 |
H011 |
109.4 |
109.5 |
| C02 |
C01 |
H012 |
109.5 |
109.4 |
| C02 |
C03 |
O04 |
111.8 |
109.5 |
| C03 |
C02 |
H021 |
108.1 |
109.4 |
| C03 |
C02 |
H022 |
108.1 |
109.5 |
| C02 |
C03 |
H031 |
106.7 |
109.5 |
| C13 |
C07 |
N06 |
106.7 |
108.0 |
| C07 |
C13 |
H132 |
109.6 |
109.4 |
| C07 |
C13 |
H131 |
109.6 |
109.4 |
| C13 |
C07 |
H071 |
111.3 |
110.5 |
| C05 |
C03 |
H031 |
106.1 |
109.5 |
| C05 |
N06 |
C14 |
120.7 |
122.1 |
| N06 |
C05 |
H051 |
106.2 |
110.1 |
| O04 |
C03 |
H031 |
109.1 |
109.5 |
| C03 |
O04 |
H041 |
109.5 |
114.1 |
| C07 |
N06 |
C14 |
125.7 |
122.1 |
| N06 |
C14 |
O16 |
113.5 |
120.0 |
| N06 |
C14 |
O15 |
126.0 |
120.0 |
| O15 |
C14 |
O16 |
120.6 |
120.0 |
| O16 |
C17 |
H171 |
109.5 |
109.5 |
| O16 |
C17 |
H172 |
109.5 |
109.5 |
| O16 |
C17 |
H173 |
109.4 |
109.5 |
| H132 |
C13 |
H131 |
109.5 |
109.5 |
| H171 |
C17 |
H172 |
109.5 |
109.5 |
| H171 |
C17 |
H173 |
109.5 |
109.5 |
| H172 |
C17 |
H173 |
109.5 |
109.4 |
| H013 |
C01 |
H011 |
109.5 |
109.5 |
| H013 |
C01 |
H012 |
109.5 |
109.5 |
| H011 |
C01 |
H012 |
109.5 |
109.5 |
| H021 |
C02 |
H022 |
109.5 |
109.5 |
| H081 |
C08 |
H082 |
109.5 |
109.5 |
| H092 |
C09 |
H091 |
109.5 |
109.3 |
| H121 |
C12 |
H122 |
109.5 |
109.2 |
Torsion Angles for JPD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O11 |
C10 |
C05 |
H051 |
82.5 |
61.0 |
| C09 |
C10 |
C05 |
H051 |
209.3 |
181.1 |
| C09 |
C08 |
C07 |
H071 |
196.5 |
182.2 |
| H081 |
C08 |
C09 |
H082 |
239.4 |
120.0 |
| C12 |
C10 |
C05 |
H051 |
320.3 |
300.2 |
| C07 |
C13 |
C12 |
H132 |
240.1 |
120.0 |
| C07 |
C13 |
C12 |
H131 |
119.9 |
240.0 |
| C12 |
C13 |
C07 |
H071 |
193.6 |
177.5 |
| H132 |
C13 |
C12 |
H131 |
239.9 |
120.0 |
| C10 |
C05 |
C03 |
H031 |
71.4 |
305.1 |
| C10 |
C05 |
N06 |
C14 |
168.6 |
180.0 |
| N06 |
C05 |
C10 |
H051 |
113.6 |
119.4 |
| C08 |
C07 |
C13 |
H132 |
193.2 |
59.7 |
| C08 |
C07 |
C13 |
H131 |
73.0 |
179.6 |
| C13 |
C07 |
C08 |
H071 |
240.4 |
238.2 |
| C08 |
C07 |
N06 |
C14 |
232.8 |
238.7 |
| H013 |
C01 |
C02 |
H011 |
240.0 |
240.0 |
| H013 |
C01 |
C02 |
H012 |
120.0 |
120.0 |
| H011 |
C01 |
C02 |
H012 |
240.0 |
240.0 |
| C10 |
C05 |
C03 |
C02 |
315.9 |
185.1 |
| C03 |
C02 |
C01 |
H013 |
180.0 |
180.0 |
| C03 |
C02 |
C01 |
H011 |
300.0 |
300.0 |
| C03 |
C02 |
C01 |
H012 |
60.0 |
60.0 |
| C05 |
C03 |
C02 |
H031 |
115.1 |
120.0 |
| O04 |
C03 |
C02 |
H031 |
240.8 |
240.0 |
| C02 |
C03 |
O04 |
H041 |
180.0 |
300.0 |
| H021 |
C02 |
C03 |
H022 |
118.4 |
120.0 |
| C12 |
C13 |
C07 |
H132 |
119.9 |
239.9 |
| C12 |
C13 |
C07 |
H131 |
240.1 |
120.0 |
| C08 |
C07 |
C13 |
H071 |
119.4 |
122.1 |
| C13 |
C07 |
N06 |
C14 |
120.1 |
121.4 |
| H132 |
C13 |
C07 |
H131 |
120.1 |
240.1 |
| C10 |
C05 |
C03 |
N06 |
233.9 |
242.7 |
| C10 |
C05 |
C03 |
H051 |
114.1 |
121.3 |
| C05 |
C03 |
C02 |
H021 |
81.8 |
66.1 |
| C05 |
C03 |
C02 |
H022 |
323.3 |
306.1 |
| C02 |
C03 |
C05 |
H031 |
244.5 |
240.0 |
| O04 |
C03 |
C05 |
H031 |
118.8 |
120.0 |
| C05 |
C03 |
O04 |
H041 |
305.2 |
60.0 |
| C10 |
C05 |
N06 |
C03 |
126.8 |
119.3 |
| C10 |
C05 |
N06 |
H051 |
246.4 |
240.7 |
| C13 |
C07 |
N06 |
C05 |
318.0 |
301.3 |
| N06 |
C05 |
C03 |
H031 |
197.5 |
62.4 |
| C07 |
N06 |
C05 |
C14 |
163.0 |
180.1 |
| C05 |
N06 |
C14 |
O16 |
314.0 |
189.0 |
| C05 |
N06 |
C14 |
O15 |
132.9 |
9.1 |
| C10 |
C05 |
C03 |
O04 |
190.3 |
65.2 |
| O04 |
C03 |
C02 |
H021 |
207.4 |
186.1 |
| O04 |
C03 |
C02 |
H022 |
89.0 |
66.1 |
| C02 |
C03 |
O04 |
H031 |
117.8 |
120.0 |
| C05 |
C03 |
O04 |
H031 |
243.0 |
240.0 |
| N06 |
C07 |
C13 |
H132 |
311.2 |
176.6 |
| N06 |
C07 |
C13 |
H131 |
191.1 |
296.5 |
| C13 |
C07 |
N06 |
H071 |
122.0 |
121.0 |
| C05 |
N06 |
C07 |
C14 |
198.0 |
179.9 |
| C07 |
N06 |
C05 |
H051 |
85.2 |
119.3 |
| C07 |
N06 |
C14 |
O16 |
153.6 |
9.0 |
| C07 |
N06 |
C14 |
O15 |
332.5 |
189.0 |
| C14 |
N06 |
C05 |
H051 |
282.2 |
299.3 |
| O15 |
C14 |
N06 |
O16 |
179.0 |
180.0 |
| N06 |
C14 |
O16 |
O15 |
179.0 |
180.0 |
| C14 |
O16 |
C17 |
H171 |
180.0 |
180.0 |
| C14 |
O16 |
C17 |
H172 |
300.0 |
300.0 |
| C14 |
O16 |
C17 |
H173 |
60.0 |
59.9 |
| N06 |
C14 |
O15 |
O16 |
181.1 |
180.0 |
| H171 |
C17 |
O16 |
H172 |
240.0 |
240.0 |
| H171 |
C17 |
O16 |
H173 |
120.0 |
120.0 |
| H172 |
C17 |
O16 |
H173 |
240.0 |
240.1 |
| C12 |
C13 |
H132 |
H131 |
120.2 |
240.0 |
| H132 |
C13 |
C07 |
N06 |
311.2 |
176.6 |
| C07 |
C13 |
H132 |
H131 |
239.8 |
119.9 |
| H132 |
C13 |
C07 |
H071 |
73.7 |
297.6 |
| C12 |
C13 |
H131 |
H132 |
239.8 |
120.0 |
| H131 |
C13 |
C07 |
N06 |
191.1 |
296.5 |
| C07 |
C13 |
H131 |
H132 |
120.2 |
240.1 |
| H131 |
C13 |
C07 |
H071 |
313.6 |
57.5 |
| O16 |
C17 |
H171 |
H172 |
120.0 |
120.0 |
| O16 |
C17 |
H171 |
H173 |
240.0 |
240.0 |
| H172 |
C17 |
H171 |
H173 |
120.0 |
120.0 |
| O16 |
C17 |
H172 |
H171 |
240.0 |
240.0 |
| O16 |
C17 |
H172 |
H173 |
120.0 |
120.0 |
| H171 |
C17 |
H172 |
H173 |
240.0 |
240.0 |
| O16 |
C17 |
H173 |
H171 |
120.0 |
120.1 |
| O16 |
C17 |
H173 |
H172 |
240.0 |
240.0 |
| H171 |
C17 |
H173 |
H172 |
120.0 |
120.0 |
| C02 |
C01 |
H013 |
H011 |
120.0 |
120.0 |
| C02 |
C01 |
H013 |
H012 |
240.0 |
240.0 |
| H011 |
C01 |
H013 |
H012 |
120.0 |
120.0 |
| C02 |
C01 |
H011 |
H013 |
240.0 |
240.0 |
| C02 |
C01 |
H011 |
H012 |
120.0 |
120.0 |
| H013 |
C01 |
H011 |
H012 |
240.0 |
240.0 |
| C02 |
C01 |
H012 |
H013 |
120.0 |
120.0 |
| C02 |
C01 |
H012 |
H011 |
240.0 |
240.0 |
| H013 |
C01 |
H012 |
H011 |
120.0 |
120.0 |
| H021 |
C02 |
C01 |
H013 |
300.7 |
299.9 |
| H021 |
C02 |
C01 |
H011 |
60.7 |
59.9 |
| H021 |
C02 |
C01 |
H012 |
180.7 |
180.0 |
| H021 |
C02 |
C03 |
O04 |
207.4 |
186.1 |
| C03 |
C02 |
H021 |
H022 |
242.4 |
240.0 |
| H021 |
C02 |
C03 |
H031 |
326.7 |
306.1 |
| H022 |
C02 |
C01 |
H013 |
59.2 |
60.0 |
| H022 |
C02 |
C01 |
H011 |
179.2 |
180.0 |
| H022 |
C02 |
C01 |
H012 |
299.2 |
300.0 |
| H022 |
C02 |
C03 |
O04 |
89.0 |
66.1 |
| C03 |
C02 |
H022 |
H021 |
117.6 |
120.0 |
| H022 |
C02 |
C03 |
H031 |
208.2 |
186.1 |
| C02 |
C03 |
H031 |
O04 |
239.0 |
240.0 |
| H031 |
C03 |
C02 |
H021 |
326.7 |
306.1 |
| H031 |
C03 |
C02 |
H022 |
208.2 |
186.1 |
| H031 |
C03 |
O04 |
H041 |
62.2 |
180.0 |
| H041 |
O04 |
C03 |
H031 |
62.2 |
180.0 |
| C10 |
C05 |
H051 |
C03 |
243.6 |
238.7 |
| C10 |
C05 |
H051 |
N06 |
114.9 |
117.3 |
| H051 |
C05 |
C03 |
H031 |
317.3 |
183.8 |
| H051 |
C05 |
N06 |
C14 |
282.2 |
299.3 |
| C13 |
C07 |
H071 |
N06 |
240.6 |
240.5 |
| H071 |
C07 |
C13 |
H132 |
73.7 |
297.6 |
| H071 |
C07 |
C13 |
H131 |
313.6 |
57.5 |
| H071 |
C07 |
N06 |
C14 |
358.0 |
0.3 |
| C09 |
C08 |
H081 |
H082 |
121.0 |
240.0 |
| H081 |
C08 |
C07 |
H071 |
76.9 |
302.2 |
| C09 |
C08 |
H082 |
H081 |
239.1 |
120.0 |
| H082 |
C08 |
C07 |
H071 |
316.2 |
62.2 |
| H092 |
C09 |
C08 |
H081 |
330.1 |
119.2 |
| H092 |
C09 |
C08 |
H082 |
90.8 |
359.2 |
| H091 |
C09 |
C08 |
H081 |
210.6 |
359.5 |
| H091 |
C09 |
C08 |
H082 |
331.2 |
239.5 |
| H121 |
C12 |
C13 |
H132 |
336.4 |
120.4 |
| H121 |
C12 |
C13 |
H131 |
96.6 |
0.4 |
| H122 |
C12 |
C13 |
H132 |
216.6 |
0.8 |
| H122 |
C12 |
C13 |
H131 |
336.7 |
240.8 |