PDB Chemical Component 5FD
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 5FD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2' |
C2' |
1.440 |
1.429 |
| O2' |
HO2 |
0.950 |
0.967 |
| C2' |
C3' |
1.533 |
1.548 |
| C2' |
C1' |
1.546 |
1.550 |
| C2' |
H2' |
1.100 |
1.090 |
| C3' |
O3' |
1.440 |
1.429 |
| C3' |
C4' |
1.533 |
1.541 |
| C3' |
H3'' |
1.100 |
1.089 |
| O3' |
HO3 |
0.950 |
0.968 |
| C4' |
C5' |
1.491 |
1.530 |
| C4' |
O4' |
1.413 |
1.437 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
F19 |
1.356 |
1.400 |
| C5' |
H5'1 |
1.099 |
1.089 |
| C5' |
H5'2 |
1.100 |
1.090 |
| O4' |
C1' |
1.394 |
1.444 |
| C1' |
N9 |
1.432 |
1.465 |
| C1' |
H1' |
1.100 |
1.090 |
| N9 |
C8 |
1.343 |
1.362 |
| N9 |
C4 |
1.314 |
1.372 |
| C8 |
N7 |
1.329 |
1.302 |
| C8 |
HC8 |
1.080 |
1.080 |
| N7 |
C5 |
1.328 |
1.354 |
| C5 |
C4 |
1.396 |
1.404 |
| C5 |
C6 |
1.371 |
1.405 |
| C4 |
N3 |
1.348 |
1.329 |
| N3 |
C2 |
1.320 |
1.316 |
| C2 |
N1 |
1.398 |
1.321 |
| C2 |
HC2 |
1.080 |
1.080 |
| N1 |
C6 |
1.416 |
1.329 |
| C6 |
N6 |
1.332 |
1.384 |
| HN2 |
N6 |
1.000 |
0.970 |
| N6 |
H1 |
1.000 |
0.970 |
Bond Angles for 5FD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2' |
O2' |
HO2 |
109.5 |
114.0 |
| O2' |
C2' |
C3' |
110.5 |
110.9 |
| O2' |
C2' |
C1' |
110.3 |
110.9 |
| O2' |
C2' |
H2' |
111.9 |
110.8 |
| C3' |
C2' |
C1' |
102.9 |
102.1 |
| C3' |
C2' |
H2' |
110.5 |
110.9 |
| C2' |
C3' |
O3' |
110.4 |
110.5 |
| C2' |
C3' |
C4' |
101.8 |
104.2 |
| C2' |
C3' |
H3'' |
110.9 |
110.5 |
| C1' |
C2' |
H2' |
110.3 |
111.0 |
| C2' |
C1' |
O4' |
106.0 |
103.5 |
| C2' |
C1' |
N9 |
110.7 |
110.6 |
| C2' |
C1' |
H1' |
110.0 |
110.6 |
| O3' |
C3' |
C4' |
110.2 |
110.5 |
| O3' |
C3' |
H3'' |
112.2 |
110.4 |
| C3' |
O3' |
HO3 |
109.5 |
114.0 |
| C4' |
C3' |
H3'' |
110.9 |
110.6 |
| C3' |
C4' |
C5' |
114.4 |
109.9 |
| C3' |
C4' |
O4' |
102.7 |
107.3 |
| C3' |
C4' |
H4' |
111.0 |
109.9 |
| C5' |
C4' |
O4' |
103.9 |
109.9 |
| C5' |
C4' |
H4' |
111.5 |
109.9 |
| C4' |
C5' |
F19 |
110.5 |
109.4 |
| C4' |
C5' |
H5'1 |
109.2 |
109.5 |
| C4' |
C5' |
H5'2 |
109.2 |
109.5 |
| O4' |
C4' |
H4' |
112.8 |
110.0 |
| C4' |
O4' |
C1' |
104.6 |
107.0 |
| F19 |
C5' |
H5'1 |
109.2 |
109.5 |
| F19 |
C5' |
H5'2 |
109.2 |
109.4 |
| H5'1 |
C5' |
H5'2 |
109.5 |
109.5 |
| O4' |
C1' |
N9 |
105.9 |
110.7 |
| O4' |
C1' |
H1' |
112.3 |
110.6 |
| N9 |
C1' |
H1' |
111.7 |
110.7 |
| C1' |
N9 |
C8 |
126.8 |
126.2 |
| C1' |
N9 |
C4 |
124.7 |
126.3 |
| C8 |
N9 |
C4 |
108.6 |
107.5 |
| N9 |
C8 |
N7 |
110.5 |
109.9 |
| N9 |
C8 |
HC8 |
124.7 |
125.1 |
| N9 |
C4 |
C5 |
105.6 |
106.0 |
| N9 |
C4 |
N3 |
131.5 |
134.9 |
| N7 |
C8 |
HC8 |
124.7 |
125.0 |
| C8 |
N7 |
C5 |
105.6 |
109.4 |
| N7 |
C5 |
C4 |
109.7 |
107.1 |
| N7 |
C5 |
C6 |
131.8 |
134.7 |
| C4 |
C5 |
C6 |
118.5 |
118.1 |
| C5 |
C4 |
N3 |
122.9 |
119.1 |
| C5 |
C6 |
N1 |
117.3 |
118.5 |
| C5 |
C6 |
N6 |
119.8 |
120.8 |
| C4 |
N3 |
C2 |
120.6 |
120.7 |
| N3 |
C2 |
N1 |
119.2 |
122.4 |
| N3 |
C2 |
HC2 |
120.4 |
118.8 |
| N1 |
C2 |
HC2 |
120.4 |
118.7 |
| C2 |
N1 |
C6 |
121.6 |
121.2 |
| N1 |
C6 |
N6 |
122.9 |
120.7 |
| C6 |
N6 |
H1 |
109.5 |
120.0 |
| HN2 |
N6 |
H1 |
109.5 |
119.9 |
Torsion Angles for 5FD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C3' |
C2' |
O2' |
C1' |
113.1 |
112.7 |
| C3' |
C2' |
O2' |
H2' |
236.4 |
236.4 |
| O2' |
C2' |
C3' |
O3' |
13.1 |
339.6 |
| O2' |
C2' |
C3' |
C4' |
256.2 |
221.0 |
| O2' |
C2' |
C3' |
H3'' |
138.2 |
102.1 |
| C1' |
C2' |
O2' |
H2' |
123.3 |
123.7 |
| O2' |
C2' |
C1' |
O4' |
131.9 |
155.2 |
| O2' |
C2' |
C1' |
N9 |
246.3 |
273.7 |
| O2' |
C2' |
C1' |
H1' |
10.2 |
36.7 |
| HO2 |
O2' |
C2' |
C3' |
180.0 |
298.6 |
| HO2 |
O2' |
C2' |
C1' |
66.8 |
185.9 |
| HO2 |
O2' |
C2' |
H2' |
303.6 |
62.2 |
| C3' |
C2' |
O2' |
HO2 |
180.0 |
298.6 |
| O2' |
C2' |
C3' |
C1' |
242.2 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
124.4 |
123.6 |
| C1' |
C2' |
C3' |
H2' |
242.2 |
241.7 |
| C3' |
C2' |
C1' |
O4' |
13.9 |
37.0 |
| C3' |
C2' |
C1' |
N9 |
128.3 |
155.5 |
| C3' |
C2' |
C1' |
H1' |
252.3 |
278.5 |
| O3' |
C3' |
C2' |
C4' |
117.0 |
118.7 |
| O3' |
C3' |
C2' |
H3'' |
234.9 |
237.5 |
| C2' |
C3' |
O3' |
HO3 |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
H3'' |
118.0 |
118.8 |
| C2' |
C3' |
C4' |
C5' |
210.7 |
238.5 |
| C2' |
C3' |
C4' |
O4' |
322.6 |
358.0 |
| C2' |
C3' |
C4' |
H4' |
83.4 |
117.6 |
| C1' |
C2' |
O2' |
HO2 |
66.8 |
185.9 |
| O2' |
C2' |
C1' |
C3' |
117.9 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
235.8 |
236.4 |
| C3' |
C2' |
C1' |
H2' |
117.9 |
118.2 |
| C1' |
C2' |
C3' |
O3' |
130.9 |
97.8 |
| C1' |
C2' |
C3' |
C4' |
14.0 |
339.1 |
| C1' |
C2' |
C3' |
H3'' |
256.0 |
220.3 |
| C4' |
O4' |
C1' |
C2' |
320.9 |
319.9 |
| O4' |
C1' |
C2' |
N9 |
245.6 |
241.5 |
| O4' |
C1' |
C2' |
H1' |
121.6 |
118.5 |
| N9 |
C1' |
C2' |
H1' |
236.0 |
237.0 |
| C2' |
C1' |
N9 |
C8 |
311.1 |
265.0 |
| C2' |
C1' |
N9 |
C4 |
130.2 |
84.7 |
| H2' |
C2' |
O2' |
HO2 |
303.6 |
62.2 |
| O2' |
C2' |
H2' |
C3' |
236.4 |
236.4 |
| O2' |
C2' |
H2' |
C1' |
123.3 |
123.6 |
| C3' |
C2' |
H2' |
C1' |
246.9 |
247.2 |
| H2' |
C2' |
C3' |
O3' |
248.7 |
216.1 |
| H2' |
C2' |
C3' |
C4' |
131.8 |
97.4 |
| H2' |
C2' |
C3' |
H3'' |
13.8 |
338.6 |
| H2' |
C2' |
C1' |
O4' |
256.0 |
278.8 |
| H2' |
C2' |
C1' |
N9 |
10.4 |
37.3 |
| H2' |
C2' |
C1' |
H1' |
134.4 |
160.3 |
| O3' |
C3' |
C2' |
C1' |
130.9 |
97.8 |
| O3' |
C3' |
C2' |
H2' |
248.7 |
216.1 |
| C2' |
C3' |
O3' |
C4' |
248.4 |
245.2 |
| C2' |
C3' |
O3' |
H3'' |
124.3 |
122.6 |
| C4' |
C3' |
O3' |
H3'' |
235.9 |
237.3 |
| O3' |
C3' |
C4' |
C5' |
93.5 |
119.9 |
| O3' |
C3' |
C4' |
O4' |
205.4 |
239.3 |
| O3' |
C3' |
C4' |
H4' |
326.2 |
358.9 |
| C4' |
C3' |
C2' |
C1' |
14.0 |
339.1 |
| C4' |
C3' |
C2' |
H2' |
131.8 |
97.4 |
| C2' |
C3' |
C4' |
O3' |
117.2 |
118.7 |
| C2' |
C3' |
C4' |
H3'' |
242.0 |
241.2 |
| O3' |
C3' |
C4' |
H3'' |
124.9 |
122.5 |
| C4' |
C3' |
O3' |
HO3 |
291.6 |
294.8 |
| C5' |
C4' |
C3' |
O4' |
248.1 |
240.6 |
| C5' |
C4' |
C3' |
H4' |
127.2 |
121.0 |
| C3' |
C4' |
C5' |
F19 |
284.7 |
185.0 |
| C3' |
C4' |
C5' |
H5'1 |
44.9 |
305.0 |
| C3' |
C4' |
C5' |
H5'2 |
164.6 |
65.0 |
| O4' |
C4' |
C3' |
H4' |
239.2 |
240.4 |
| C3' |
C4' |
O4' |
C1' |
48.4 |
26.5 |
| H3'' |
C3' |
C2' |
C1' |
256.0 |
220.3 |
| H3'' |
C3' |
C2' |
H2' |
13.8 |
338.6 |
| C2' |
C3' |
H3'' |
O3' |
236.0 |
237.4 |
| C2' |
C3' |
H3'' |
C4' |
112.3 |
114.9 |
| O3' |
C3' |
H3'' |
C4' |
236.3 |
237.4 |
| H3'' |
C3' |
O3' |
HO3 |
55.7 |
57.5 |
| H3'' |
C3' |
C4' |
C5' |
328.6 |
357.3 |
| H3'' |
C3' |
C4' |
O4' |
80.6 |
116.7 |
| H3'' |
C3' |
C4' |
H4' |
201.4 |
236.3 |
| HO3 |
O3' |
C3' |
C4' |
291.6 |
294.8 |
| HO3 |
O3' |
C3' |
H3'' |
55.7 |
57.5 |
| C5' |
C4' |
C3' |
H3'' |
328.6 |
357.3 |
| C3' |
C4' |
C5' |
O4' |
111.2 |
117.8 |
| C3' |
C4' |
C5' |
H4' |
233.1 |
239.0 |
| O4' |
C4' |
C5' |
H4' |
121.9 |
121.2 |
| C5' |
C4' |
O4' |
C1' |
167.9 |
145.9 |
| F19 |
C5' |
C4' |
H5'1 |
239.9 |
240.0 |
| F19 |
C5' |
C4' |
H5'2 |
120.2 |
119.9 |
| H5'1 |
C5' |
C4' |
H5'2 |
240.3 |
240.0 |
| C2' |
C1' |
O4' |
C4' |
320.9 |
319.9 |
| O4' |
C4' |
C3' |
H3'' |
80.6 |
116.7 |
| C3' |
C4' |
O4' |
C5' |
240.5 |
240.6 |
| C3' |
C4' |
O4' |
H4' |
119.5 |
119.5 |
| C5' |
C4' |
O4' |
H4' |
239.0 |
238.9 |
| O4' |
C4' |
C5' |
F19 |
173.5 |
67.2 |
| O4' |
C4' |
C5' |
H5'1 |
293.6 |
187.2 |
| O4' |
C4' |
C5' |
H5'2 |
53.3 |
307.2 |
| C4' |
O4' |
C1' |
N9 |
203.2 |
201.4 |
| C4' |
O4' |
C1' |
H1' |
81.0 |
78.4 |
| H4' |
C4' |
C3' |
H3'' |
201.4 |
236.3 |
| C3' |
C4' |
H4' |
C5' |
128.8 |
121.0 |
| C3' |
C4' |
H4' |
O4' |
245.3 |
242.1 |
| C5' |
C4' |
H4' |
O4' |
116.6 |
121.1 |
| H4' |
C4' |
C5' |
F19 |
51.6 |
306.0 |
| H4' |
C4' |
C5' |
H5'1 |
171.8 |
66.0 |
| H4' |
C4' |
C5' |
H5'2 |
291.5 |
186.0 |
| H4' |
C4' |
O4' |
C1' |
288.9 |
267.0 |
| F19 |
C5' |
C4' |
O4' |
173.5 |
67.2 |
| F19 |
C5' |
C4' |
H4' |
51.6 |
306.0 |
| C4' |
C5' |
F19 |
H5'1 |
120.1 |
120.1 |
| C4' |
C5' |
F19 |
H5'2 |
239.9 |
240.0 |
| H5'1 |
C5' |
F19 |
H5'2 |
119.7 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
293.6 |
187.2 |
| H5'1 |
C5' |
C4' |
H4' |
171.8 |
66.0 |
| C4' |
C5' |
H5'1 |
F19 |
239.1 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
119.5 |
120.0 |
| F19 |
C5' |
H5'1 |
H5'2 |
240.4 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
53.3 |
307.2 |
| H5'2 |
C5' |
C4' |
H4' |
291.5 |
186.0 |
| C4' |
C5' |
H5'2 |
F19 |
120.9 |
119.9 |
| C4' |
C5' |
H5'2 |
H5'1 |
240.5 |
239.9 |
| F19 |
C5' |
H5'2 |
H5'1 |
119.6 |
120.0 |
| O4' |
C1' |
C2' |
H2' |
256.0 |
278.8 |
| C2' |
C1' |
O4' |
N9 |
117.6 |
118.5 |
| C2' |
C1' |
O4' |
H1' |
239.8 |
241.5 |
| C1' |
O4' |
C4' |
H4' |
288.9 |
267.0 |
| N9 |
C1' |
O4' |
H1' |
122.2 |
123.0 |
| O4' |
C1' |
N9 |
C8 |
65.6 |
19.1 |
| O4' |
C1' |
N9 |
C4 |
244.6 |
198.8 |
| N9 |
C1' |
C2' |
H2' |
10.4 |
37.3 |
| C2' |
C1' |
N9 |
O4' |
245.6 |
245.9 |
| C2' |
C1' |
N9 |
H1' |
123.0 |
123.0 |
| O4' |
C1' |
N9 |
H1' |
237.4 |
237.0 |
| C8 |
N9 |
C1' |
C4 |
181.0 |
180.3 |
| C1' |
N9 |
C8 |
N7 |
179.4 |
180.0 |
| C1' |
N9 |
C8 |
HC8 |
359.4 |
359.9 |
| C1' |
N9 |
C4 |
C5 |
181.2 |
179.9 |
| C1' |
N9 |
C4 |
N3 |
0.3 |
359.9 |
| H1' |
C1' |
C2' |
H2' |
134.4 |
160.3 |
| C2' |
C1' |
H1' |
O4' |
117.8 |
114.1 |
| C2' |
C1' |
H1' |
N9 |
236.6 |
237.1 |
| O4' |
C1' |
H1' |
N9 |
118.9 |
123.0 |
| H1' |
C1' |
N9 |
C8 |
188.1 |
142.0 |
| H1' |
C1' |
N9 |
C4 |
7.2 |
321.8 |
| C8 |
N9 |
C1' |
H1' |
188.1 |
142.0 |
| C1' |
N9 |
C8 |
C4 |
179.2 |
179.8 |
| C8 |
N9 |
C4 |
C5 |
0.3 |
359.6 |
| C8 |
N9 |
C4 |
N3 |
179.5 |
179.7 |
| N7 |
C8 |
N9 |
HC8 |
180.0 |
180.1 |
| N9 |
C8 |
N7 |
C5 |
359.3 |
360.0 |
| C4 |
N9 |
C1' |
H1' |
7.2 |
321.8 |
| C1' |
N9 |
C4 |
C8 |
180.8 |
180.2 |
| C4 |
N9 |
C8 |
N7 |
0.2 |
0.3 |
| C4 |
N9 |
C8 |
HC8 |
180.2 |
180.1 |
| N7 |
C5 |
C4 |
N9 |
359.2 |
0.3 |
| N9 |
C4 |
C5 |
C6 |
179.8 |
180.1 |
| C5 |
C4 |
N9 |
N3 |
180.8 |
180.0 |
| N9 |
C4 |
N3 |
C2 |
180.2 |
180.0 |
| N7 |
C8 |
N9 |
C4 |
0.2 |
0.3 |
| N9 |
C8 |
N7 |
HC8 |
180.0 |
179.9 |
| C8 |
N7 |
C5 |
C4 |
0.9 |
359.8 |
| C8 |
N7 |
C5 |
C6 |
180.2 |
180.0 |
| HC8 |
C8 |
N9 |
C4 |
180.2 |
180.1 |
| N9 |
C8 |
HC8 |
N7 |
180.0 |
180.1 |
| HC8 |
C8 |
N7 |
C5 |
179.3 |
180.1 |
| N9 |
C4 |
C5 |
N7 |
359.2 |
0.3 |
| C5 |
N7 |
C8 |
HC8 |
179.3 |
180.1 |
| C4 |
C5 |
N7 |
C6 |
180.7 |
179.8 |
| N7 |
C5 |
C4 |
N3 |
179.9 |
180.3 |
| N7 |
C5 |
C6 |
N1 |
180.9 |
179.3 |
| N7 |
C5 |
C6 |
N6 |
0.8 |
360.0 |
| N9 |
C4 |
C5 |
N3 |
179.2 |
180.0 |
| N7 |
C5 |
C4 |
C6 |
179.4 |
180.2 |
| C4 |
C5 |
C6 |
N1 |
0.1 |
359.5 |
| C4 |
C5 |
C6 |
N6 |
180.0 |
180.2 |
| C5 |
C4 |
N3 |
C2 |
359.2 |
0.1 |
| N7 |
C5 |
C6 |
C4 |
180.8 |
179.7 |
| C6 |
C5 |
C4 |
N3 |
0.6 |
0.1 |
| C2 |
N1 |
C6 |
C5 |
359.4 |
0.7 |
| N1 |
C6 |
C5 |
N6 |
180.1 |
179.3 |
| C5 |
C6 |
N6 |
H1 |
300.1 |
0.0 |
| N9 |
C4 |
N3 |
C5 |
181.0 |
179.9 |
| N3 |
C4 |
C5 |
C6 |
0.6 |
0.1 |
| C4 |
N3 |
C2 |
N1 |
0.3 |
0.1 |
| C4 |
N3 |
C2 |
HC2 |
180.3 |
180.0 |
| N1 |
C2 |
N3 |
HC2 |
180.0 |
180.1 |
| N3 |
C2 |
N1 |
C6 |
0.4 |
359.5 |
| C5 |
C6 |
N1 |
C2 |
359.4 |
0.7 |
| N3 |
C2 |
N1 |
HC2 |
180.0 |
179.9 |
| C2 |
N1 |
C6 |
N6 |
179.5 |
180.0 |
| N3 |
C2 |
HC2 |
N1 |
180.0 |
180.1 |
| HC2 |
C2 |
N1 |
C6 |
180.4 |
179.6 |
| C5 |
C6 |
N1 |
N6 |
179.9 |
180.7 |
| C6 |
N1 |
C2 |
HC2 |
180.4 |
179.6 |
| N1 |
C6 |
N6 |
H1 |
120.0 |
180.7 |
| C5 |
C6 |
N6 |
N1 |
180.1 |
179.3 |
| HN2 |
N6 |
C6 |
H1 |
240.0 |
180.0 |
| C6 |
N6 |
HN2 |
H1 |
120.0 |
180.0 |