PDB Chemical Component FDJ
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 FDJ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2 |
C2 |
1.215 |
1.216 |
| C2 |
N3 |
1.312 |
1.346 |
| C2 |
N1 |
1.331 |
1.345 |
| N3 |
C4 |
1.344 |
1.348 |
| C2' |
C1' |
1.570 |
1.545 |
| C2' |
C3' |
1.279 |
1.545 |
| C1' |
N1 |
1.340 |
1.465 |
| C1' |
O4' |
1.537 |
1.444 |
| N1 |
C6 |
1.355 |
1.369 |
| C4 |
O4 |
1.220 |
1.219 |
| C4 |
C5 |
1.409 |
1.416 |
| O3' |
C3' |
1.474 |
1.429 |
| C3' |
C4' |
1.629 |
1.545 |
| O4' |
C4' |
1.276 |
1.445 |
| C6 |
C5 |
1.409 |
1.350 |
| C4' |
C5' |
1.531 |
1.530 |
| C5 |
C7 |
1.558 |
1.508 |
| O2B |
PB |
1.515 |
1.481 |
| C5' |
O5' |
1.433 |
1.429 |
| O5' |
PA |
1.588 |
1.610 |
| O3A |
PB |
1.585 |
1.610 |
| O3A |
PA |
1.591 |
1.611 |
| PB |
O1B |
1.487 |
1.610 |
| PB |
C3B |
1.814 |
1.823 |
| CL1 |
C3B |
1.759 |
1.803 |
| PA |
O2A |
1.496 |
1.480 |
| PA |
O1A |
1.495 |
1.610 |
| C3B |
PG |
1.814 |
1.823 |
| O3G |
PG |
1.519 |
1.480 |
| PG |
O1G |
1.497 |
1.610 |
| PG |
O2G |
1.512 |
1.611 |
| C6 |
H1 |
1.080 |
1.079 |
| C7 |
H2 |
1.100 |
1.090 |
| C7 |
H3 |
1.100 |
1.090 |
| C7 |
H4 |
1.100 |
1.090 |
| N3 |
H5 |
1.000 |
0.970 |
| C1' |
H6 |
1.101 |
1.091 |
| O1A |
H7 |
0.950 |
0.967 |
| O1G |
H8 |
0.950 |
0.967 |
| C2' |
H9 |
1.100 |
1.089 |
| C2' |
H10 |
1.100 |
1.091 |
| O1B |
H11 |
0.950 |
0.967 |
| O2G |
H12 |
0.950 |
0.968 |
| C3' |
H13 |
1.100 |
1.090 |
| O3' |
H14 |
0.950 |
0.968 |
| C3B |
H15 |
1.100 |
1.089 |
| C4' |
H16 |
1.100 |
1.089 |
| C5' |
H17 |
1.100 |
1.090 |
| C5' |
H18 |
1.100 |
1.090 |
Bond Angles for FDJ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2 |
C2 |
N3 |
117.5 |
119.5 |
| O2 |
C2 |
N1 |
119.3 |
119.6 |
| N1 |
C2 |
N3 |
123.2 |
121.0 |
| C2 |
N3 |
C4 |
120.5 |
120.2 |
| C2 |
N3 |
H5 |
119.8 |
119.9 |
| C2 |
N1 |
C6 |
119.2 |
120.6 |
| N3 |
C4 |
O4 |
119.2 |
120.3 |
| C2' |
C1' |
O4' |
103.5 |
104.9 |
| C2' |
C1' |
H6 |
109.0 |
110.4 |
| C2' |
C3' |
C4' |
102.5 |
104.1 |
| C3' |
C2' |
H9 |
110.5 |
110.5 |
| C3' |
C2' |
H10 |
110.5 |
110.5 |
| C2' |
C3' |
H13 |
111.7 |
110.5 |
| C1' |
O4' |
C4' |
106.1 |
105.3 |
| O4' |
C1' |
H6 |
109.4 |
110.4 |
| N1 |
C6 |
H1 |
119.7 |
120.2 |
| C5 |
C4 |
O4 |
120.4 |
120.3 |
| C4 |
C5 |
C7 |
122.2 |
120.4 |
| O3' |
C3' |
C4' |
110.5 |
110.5 |
| O3' |
C3' |
H13 |
108.7 |
110.6 |
| C3' |
C4' |
C5' |
108.7 |
110.4 |
| C4' |
C3' |
H13 |
106.9 |
110.5 |
| C3' |
C4' |
H16 |
107.4 |
110.4 |
| O4' |
C4' |
C5' |
112.5 |
110.4 |
| O4' |
C4' |
H16 |
112.5 |
110.5 |
| C6 |
C5 |
C7 |
121.6 |
120.4 |
| C4' |
C5' |
O5' |
109.6 |
109.5 |
| C5' |
C4' |
H16 |
108.5 |
110.4 |
| C4' |
C5' |
H17 |
109.4 |
109.5 |
| C4' |
C5' |
H18 |
109.4 |
109.5 |
| C5 |
C7 |
H2 |
109.5 |
109.4 |
| C5 |
C7 |
H3 |
109.4 |
109.5 |
| C5 |
C7 |
H4 |
109.5 |
109.5 |
| O2B |
PB |
O1B |
110.2 |
109.4 |
| O2B |
PB |
C3B |
109.4 |
109.5 |
| O5' |
C5' |
H17 |
109.4 |
109.5 |
| O5' |
C5' |
H18 |
109.4 |
109.4 |
| O3A |
PB |
C3B |
102.6 |
109.5 |
| O1B |
PB |
C3B |
113.5 |
109.5 |
| PB |
O1B |
H11 |
109.5 |
114.0 |
| PB |
C3B |
CL1 |
109.4 |
109.5 |
| PB |
C3B |
PG |
110.5 |
109.5 |
| PB |
C3B |
H15 |
108.4 |
109.5 |
| CL1 |
C3B |
H15 |
109.0 |
109.5 |
| O1A |
PA |
O2A |
112.4 |
109.5 |
| PA |
O1A |
H7 |
109.5 |
114.0 |
| O1G |
PG |
O2G |
109.1 |
109.5 |
| PG |
O1G |
H8 |
109.5 |
114.0 |
| PG |
O2G |
H12 |
109.5 |
113.9 |
| H2 |
C7 |
H3 |
109.5 |
109.4 |
| H2 |
C7 |
H4 |
109.5 |
109.5 |
| H3 |
C7 |
H4 |
109.5 |
109.5 |
| H9 |
C2' |
H10 |
109.5 |
110.6 |
| H17 |
C5' |
H18 |
109.4 |
109.5 |
Torsion Angles for FDJ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N1 |
C2 |
O2 |
N3 |
180.2 |
180.2 |
| O2 |
C2 |
N3 |
C4 |
180.7 |
180.3 |
| O2 |
C2 |
N3 |
H5 |
0.7 |
0.2 |
| O2 |
C2 |
N1 |
C6 |
179.9 |
179.8 |
| O2 |
C2 |
N3 |
N1 |
180.2 |
180.2 |
| N3 |
C2 |
N1 |
C6 |
0.1 |
360.0 |
| C2 |
N3 |
C4 |
O4 |
180.1 |
180.0 |
| O2 |
C2 |
N1 |
N3 |
179.8 |
179.8 |
| N1 |
C2 |
N3 |
C4 |
0.5 |
0.1 |
| N1 |
C2 |
N3 |
H5 |
180.5 |
180.0 |
| C2 |
N1 |
C6 |
H1 |
179.5 |
180.0 |
| C2 |
N3 |
C4 |
H5 |
180.0 |
179.9 |
| C5 |
C4 |
N3 |
O4 |
179.2 |
180.0 |
| C2' |
C1' |
O4' |
C4' |
355.6 |
319.5 |
| O4' |
C1' |
C2' |
H6 |
116.3 |
118.9 |
| C3' |
C2' |
C1' |
O4' |
337.0 |
24.0 |
| C3' |
C2' |
C1' |
H6 |
220.7 |
265.0 |
| O3' |
C3' |
C2' |
C4' |
120.5 |
118.6 |
| O3' |
C3' |
C2' |
H13 |
234.6 |
237.3 |
| C2' |
C3' |
C4' |
C5' |
197.1 |
217.2 |
| C4' |
C3' |
C2' |
H13 |
114.1 |
118.6 |
| C2' |
C3' |
C4' |
H16 |
79.9 |
94.9 |
| H9 |
C2' |
C3' |
H10 |
121.3 |
122.7 |
| C1' |
N1 |
C6 |
H1 |
358.5 |
360.0 |
| C2' |
C1' |
O4' |
H6 |
244.0 |
241.0 |
| C1' |
O4' |
C4' |
C5' |
143.6 |
159.3 |
| C1' |
O4' |
C4' |
H16 |
266.6 |
281.7 |
| C6 |
N1 |
C2 |
N3 |
0.1 |
360.0 |
| O4 |
C4 |
C5 |
C7 |
358.7 |
360.0 |
| C2 |
N3 |
C4 |
C5 |
359.3 |
359.9 |
| N3 |
C4 |
C5 |
O4 |
180.8 |
180.0 |
| C6 |
C5 |
C4 |
C7 |
180.8 |
180.0 |
| C4 |
C5 |
C7 |
H2 |
180.0 |
0.0 |
| C4 |
C5 |
C7 |
H3 |
300.0 |
120.0 |
| C4 |
C5 |
C7 |
H4 |
60.0 |
240.0 |
| C2' |
C3' |
O3' |
C4' |
243.9 |
245.3 |
| O3' |
C3' |
C2' |
H9 |
36.3 |
360.0 |
| O3' |
C3' |
C2' |
H10 |
275.0 |
237.2 |
| C2' |
C3' |
O3' |
H13 |
126.9 |
122.7 |
| O3' |
C3' |
C4' |
C5' |
72.8 |
98.5 |
| C4' |
C3' |
O3' |
H13 |
243.0 |
237.4 |
| O3' |
C3' |
C4' |
H16 |
315.6 |
336.3 |
| C4' |
C3' |
C2' |
H9 |
275.8 |
241.3 |
| C4' |
C3' |
C2' |
H10 |
154.5 |
118.6 |
| C2' |
C3' |
C4' |
H13 |
242.4 |
241.4 |
| C1' |
O4' |
C4' |
C3' |
24.3 |
40.5 |
| O3' |
C3' |
C4' |
H13 |
118.1 |
122.7 |
| O4' |
C4' |
C3' |
C5' |
121.8 |
118.8 |
| O4' |
C4' |
C3' |
H16 |
239.0 |
241.1 |
| C3' |
C4' |
C5' |
O5' |
70.6 |
185.0 |
| C5' |
C4' |
C3' |
H16 |
117.2 |
122.3 |
| C3' |
C4' |
C5' |
H17 |
190.7 |
305.0 |
| C3' |
C4' |
C5' |
H18 |
310.6 |
65.0 |
| C4' |
O4' |
C1' |
H6 |
111.7 |
78.4 |
| C3' |
C4' |
O4' |
C5' |
240.7 |
241.2 |
| O4' |
C4' |
C3' |
H13 |
76.4 |
94.6 |
| C3' |
C4' |
O4' |
H16 |
117.7 |
118.8 |
| O4' |
C4' |
C5' |
O5' |
312.3 |
69.6 |
| C5' |
C4' |
O4' |
H16 |
237.0 |
237.7 |
| O4' |
C4' |
C5' |
H17 |
72.3 |
189.6 |
| O4' |
C4' |
C5' |
H18 |
192.2 |
309.7 |
| C2 |
N1 |
C6 |
C5 |
359.5 |
360.0 |
| C6 |
C5 |
C4 |
O4 |
179.5 |
180.0 |
| C4 |
C5 |
C6 |
C7 |
179.2 |
180.0 |
| C6 |
C5 |
C7 |
H2 |
359.2 |
180.0 |
| C6 |
C5 |
C7 |
H3 |
119.2 |
299.9 |
| C6 |
C5 |
C7 |
H4 |
239.1 |
60.0 |
| C5' |
C4' |
C3' |
H13 |
314.7 |
335.8 |
| C3' |
C4' |
C5' |
H16 |
243.5 |
237.7 |
| O4' |
C4' |
C5' |
H16 |
125.2 |
122.4 |
| O5' |
C5' |
C4' |
H17 |
239.9 |
240.0 |
| O5' |
C5' |
C4' |
H18 |
120.0 |
119.9 |
| H17 |
C5' |
C4' |
H18 |
240.1 |
240.0 |
| C7 |
C5 |
C4 |
O4 |
358.7 |
360.0 |
| H2 |
C7 |
C5 |
H3 |
240.0 |
240.1 |
| H2 |
C7 |
C5 |
H4 |
120.0 |
120.0 |
| H3 |
C7 |
C5 |
H4 |
240.0 |
240.0 |
| O3A |
PB |
O2B |
C3B |
110.8 |
120.0 |
| O1B |
PB |
O2B |
C3B |
234.6 |
240.0 |
| O2B |
PB |
O1B |
H11 |
360.0 |
180.0 |
| O2B |
PB |
C3B |
CL1 |
345.4 |
60.0 |
| O2B |
PB |
C3B |
PG |
222.9 |
300.0 |
| O2B |
PB |
C3B |
H15 |
104.2 |
180.0 |
| O5' |
C5' |
C4' |
H16 |
187.1 |
307.2 |
| C4' |
C5' |
O5' |
H17 |
120.1 |
120.0 |
| C4' |
C5' |
O5' |
H18 |
240.0 |
240.0 |
| H17 |
C5' |
O5' |
H18 |
119.9 |
120.0 |
| O5' |
PA |
O1A |
H7 |
239.1 |
60.0 |
| O2B |
PB |
O3A |
C3B |
244.6 |
240.0 |
| O1B |
PB |
O3A |
C3B |
122.6 |
120.0 |
| O3A |
PB |
O1B |
H11 |
120.7 |
300.0 |
| O3A |
PB |
C3B |
CL1 |
231.1 |
300.0 |
| O3A |
PB |
C3B |
PG |
108.5 |
180.0 |
| O3A |
PB |
C3B |
H15 |
349.8 |
60.0 |
| O3A |
PA |
O1A |
H7 |
121.7 |
300.0 |
| O2B |
PB |
O1B |
C3B |
123.0 |
120.0 |
| O3A |
PB |
O1B |
C3B |
243.8 |
240.0 |
| O1B |
PB |
C3B |
CL1 |
108.9 |
180.0 |
| O1B |
PB |
C3B |
PG |
346.3 |
60.0 |
| O1B |
PB |
C3B |
H15 |
227.6 |
299.9 |
| O2B |
PB |
C3B |
O1B |
236.5 |
240.0 |
| C3B |
PB |
O1B |
H11 |
236.9 |
60.0 |
| CL1 |
C3B |
PB |
H15 |
241.3 |
240.0 |
| PB |
C3B |
CL1 |
PG |
237.8 |
240.0 |
| PB |
C3B |
CL1 |
H15 |
118.4 |
120.0 |
| O2A |
PA |
O1A |
H7 |
0.0 |
180.0 |
| PB |
C3B |
PG |
CL1 |
121.5 |
120.0 |
| PB |
C3B |
PG |
H15 |
241.3 |
240.0 |
| C3B |
PG |
O1G |
H8 |
118.7 |
59.9 |
| C3B |
PG |
O2G |
H12 |
239.3 |
180.0 |
| O3G |
PG |
O1G |
H8 |
0.0 |
179.9 |
| O3G |
PG |
O2G |
H12 |
360.0 |
60.0 |
| PB |
C3B |
PG |
O1G |
315.3 |
60.0 |
| O1G |
PG |
O2G |
H12 |
120.2 |
300.0 |
| PB |
C3B |
PG |
O2G |
195.7 |
180.0 |
| O2G |
PG |
O1G |
H8 |
239.3 |
300.0 |
| H1 |
C6 |
C5 |
C7 |
1.1 |
0.1 |
| C5 |
C7 |
H2 |
H3 |
120.0 |
119.9 |
| C5 |
C7 |
H2 |
H4 |
240.0 |
240.0 |
| H3 |
C7 |
H2 |
H4 |
120.0 |
120.0 |
| C5 |
C7 |
H3 |
H2 |
240.0 |
240.1 |
| C5 |
C7 |
H3 |
H4 |
120.0 |
120.0 |
| H2 |
C7 |
H3 |
H4 |
240.0 |
240.0 |
| C5 |
C7 |
H4 |
H2 |
120.0 |
120.0 |
| C5 |
C7 |
H4 |
H3 |
240.0 |
240.0 |
| H2 |
C7 |
H4 |
H3 |
120.0 |
120.0 |
| C2 |
N3 |
H5 |
C4 |
180.0 |
180.1 |
| H5 |
N3 |
C4 |
O4 |
0.1 |
0.0 |
| C2' |
C1' |
H6 |
O4' |
112.5 |
115.5 |
| H6 |
C1' |
O4' |
C4' |
111.7 |
78.4 |
| H7 |
O1A |
PA |
O2A |
0.0 |
180.0 |
| H8 |
O1G |
PG |
O2G |
239.3 |
300.0 |
| H9 |
C2' |
C1' |
O4' |
96.3 |
142.6 |
| H9 |
C2' |
C1' |
H6 |
340.0 |
23.7 |
| H9 |
C2' |
C3' |
C4' |
275.8 |
241.3 |
| C3' |
C2' |
H9 |
H10 |
238.1 |
237.3 |
| H9 |
C2' |
C3' |
H13 |
161.7 |
122.7 |
| H10 |
C2' |
C1' |
O4' |
217.6 |
265.4 |
| H10 |
C2' |
C1' |
H6 |
101.3 |
146.4 |
| H10 |
C2' |
C3' |
C4' |
154.5 |
118.6 |
| C3' |
C2' |
H10 |
H9 |
121.9 |
122.7 |
| H10 |
C2' |
C3' |
H13 |
40.4 |
360.0 |
| H11 |
O1B |
PB |
C3B |
236.9 |
60.0 |
| C2' |
C3' |
H13 |
C4' |
111.4 |
114.7 |
| H13 |
C3' |
C2' |
H9 |
161.7 |
122.7 |
| H13 |
C3' |
C2' |
H10 |
40.4 |
360.0 |
| O3' |
C3' |
H13 |
C4' |
240.7 |
237.4 |
| H13 |
C3' |
C4' |
C5' |
314.7 |
335.8 |
| H13 |
C3' |
C4' |
H16 |
197.4 |
213.6 |
| H14 |
O3' |
C3' |
C4' |
296.2 |
176.1 |
| H14 |
O3' |
C3' |
H13 |
53.1 |
298.8 |
| PB |
C3B |
H15 |
CL1 |
241.0 |
240.0 |
| PB |
C3B |
H15 |
PG |
120.0 |
120.0 |
| C3' |
C4' |
H16 |
C5' |
117.3 |
122.3 |
| H16 |
C4' |
C3' |
H13 |
197.4 |
213.6 |
| O4' |
C4' |
H16 |
C5' |
234.8 |
237.7 |
| H16 |
C4' |
C5' |
O5' |
187.1 |
307.2 |
| H16 |
C4' |
C5' |
H17 |
307.1 |
67.2 |
| H16 |
C4' |
C5' |
H18 |
67.1 |
187.3 |
| C4' |
C5' |
H17 |
O5' |
239.8 |
240.0 |
| H17 |
C5' |
C4' |
H16 |
307.1 |
67.2 |
| C4' |
C5' |
H17 |
H18 |
119.9 |
120.0 |
| O5' |
C5' |
H17 |
H18 |
240.1 |
240.0 |
| C4' |
C5' |
H18 |
O5' |
120.2 |
120.0 |
| H18 |
C5' |
C4' |
H16 |
67.1 |
187.3 |
| C4' |
C5' |
H18 |
H17 |
240.1 |
240.0 |
| O5' |
C5' |
H18 |
H17 |
119.9 |
120.0 |