PDB Chemical Component 2FD
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 2FD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.428 |
1.430 |
| O5' |
H5' |
0.950 |
0.966 |
| C5' |
C4' |
1.544 |
1.530 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.089 |
| C4' |
O4' |
1.474 |
1.446 |
| C4' |
C3' |
1.527 |
1.550 |
| C4' |
H4' |
1.115 |
1.091 |
| O4' |
C1' |
1.443 |
1.437 |
| C1' |
N9 |
1.516 |
1.465 |
| C1' |
C2' |
1.551 |
1.541 |
| C1' |
H1' |
1.115 |
1.090 |
| N9 |
C4 |
1.398 |
1.373 |
| N9 |
C8 |
1.332 |
1.364 |
| C4 |
N3 |
1.360 |
1.329 |
| C4 |
C5 |
1.369 |
1.405 |
| N3 |
C2 |
1.349 |
1.319 |
| C2 |
F |
1.304 |
1.352 |
| C2 |
N1 |
1.330 |
1.322 |
| N1 |
C6 |
1.340 |
1.329 |
| C6 |
N6 |
1.314 |
1.384 |
| C6 |
C5 |
1.417 |
1.405 |
| N6 |
HN61 |
1.020 |
0.969 |
| N6 |
HN62 |
1.020 |
0.970 |
| C5 |
N7 |
1.370 |
1.354 |
| N7 |
C8 |
1.293 |
1.301 |
| C8 |
H8 |
1.103 |
1.079 |
| C2' |
C3' |
1.549 |
1.548 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.115 |
1.089 |
| C3' |
O3' |
1.405 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
H1 |
0.950 |
0.967 |
Bond Angles for 2FD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
H5' |
111.0 |
106.8 |
| O5' |
C5' |
C4' |
111.0 |
109.4 |
| O5' |
C5' |
H5'1 |
111.7 |
109.5 |
| O5' |
C5' |
H5'2 |
111.6 |
109.5 |
| C4' |
C5' |
H5'1 |
111.6 |
109.4 |
| C4' |
C5' |
H5'2 |
111.6 |
109.4 |
| C5' |
C4' |
O4' |
115.4 |
110.8 |
| C5' |
C4' |
C3' |
113.5 |
110.6 |
| C5' |
C4' |
H4' |
101.0 |
110.5 |
| H5'1 |
C5' |
H5'2 |
98.8 |
109.5 |
| O4' |
C4' |
C3' |
105.2 |
103.6 |
| O4' |
C4' |
H4' |
110.0 |
110.5 |
| C4' |
O4' |
C1' |
111.3 |
106.8 |
| C3' |
C4' |
H4' |
112.0 |
110.6 |
| C4' |
C3' |
C2' |
101.3 |
102.1 |
| C4' |
C3' |
O3' |
106.9 |
110.9 |
| C4' |
C3' |
H3' |
117.4 |
110.9 |
| O4' |
C1' |
N9 |
106.5 |
109.9 |
| O4' |
C1' |
C2' |
102.7 |
107.5 |
| O4' |
C1' |
H1' |
117.7 |
109.9 |
| N9 |
C1' |
C2' |
115.4 |
109.8 |
| N9 |
C1' |
H1' |
105.6 |
109.9 |
| C1' |
N9 |
C4 |
133.2 |
126.3 |
| C1' |
N9 |
C8 |
124.7 |
126.3 |
| C2' |
C1' |
H1' |
109.2 |
109.9 |
| C1' |
C2' |
C3' |
109.4 |
104.2 |
| C1' |
C2' |
H2'1 |
112.2 |
110.5 |
| C1' |
C2' |
H2'2 |
112.2 |
110.5 |
| C4 |
N9 |
C8 |
102.1 |
107.4 |
| N9 |
C4 |
N3 |
128.7 |
134.9 |
| N9 |
C4 |
C5 |
106.8 |
106.0 |
| N9 |
C8 |
N7 |
118.4 |
109.9 |
| N9 |
C8 |
H8 |
122.2 |
125.0 |
| N3 |
C4 |
C5 |
124.5 |
119.1 |
| C4 |
N3 |
C2 |
113.6 |
120.6 |
| C4 |
C5 |
C6 |
116.9 |
118.2 |
| C4 |
C5 |
N7 |
110.6 |
107.2 |
| N3 |
C2 |
F |
118.4 |
118.8 |
| N3 |
C2 |
N1 |
126.8 |
122.4 |
| F |
C2 |
N1 |
114.9 |
118.8 |
| C2 |
N1 |
C6 |
118.8 |
121.2 |
| N1 |
C6 |
N6 |
118.1 |
120.7 |
| N1 |
C6 |
C5 |
119.4 |
118.5 |
| N6 |
C6 |
C5 |
122.5 |
120.8 |
| C6 |
N6 |
HN61 |
109.1 |
120.0 |
| C6 |
N6 |
HN62 |
118.1 |
120.0 |
| C6 |
C5 |
N7 |
132.4 |
134.6 |
| HN61 |
N6 |
HN62 |
109.1 |
120.0 |
| C5 |
N7 |
C8 |
102.1 |
109.5 |
| N7 |
C8 |
H8 |
119.3 |
125.1 |
| C3' |
C2' |
H2'1 |
112.2 |
110.5 |
| C3' |
C2' |
H2'2 |
112.2 |
110.5 |
| C2' |
C3' |
O3' |
113.1 |
110.9 |
| C2' |
C3' |
H3' |
111.7 |
110.9 |
| H2'1 |
C2' |
H2'2 |
98.2 |
110.5 |
| O3' |
C3' |
H3' |
106.6 |
110.8 |
| C3' |
O3' |
H1 |
106.9 |
106.8 |
Torsion Angles for 2FD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.8 |
240.1 |
| O5' |
C5' |
C4' |
O4' |
57.6 |
70.7 |
| O5' |
C5' |
C4' |
C3' |
179.1 |
185.0 |
| O5' |
C5' |
C4' |
H4' |
299.1 |
307.9 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
120.1 |
| H5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| H5' |
O5' |
C5' |
H5'1 |
54.7 |
60.0 |
| H5' |
O5' |
C5' |
H5'2 |
305.3 |
299.9 |
| C4' |
C5' |
O5' |
H5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
238.5 |
245.7 |
| O4' |
C4' |
C5' |
H4' |
118.5 |
122.8 |
| C5' |
C4' |
O4' |
C1' |
92.9 |
158.5 |
| C3' |
C4' |
C5' |
H4' |
240.0 |
237.1 |
| C5' |
C4' |
C3' |
C2' |
262.0 |
204.3 |
| C5' |
C4' |
C3' |
O3' |
143.4 |
86.1 |
| C5' |
C4' |
C3' |
H3' |
23.9 |
322.5 |
| H5'1 |
C5' |
O5' |
H5' |
54.7 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
124.9 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
242.4 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
117.5 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
182.9 |
190.7 |
| H5'1 |
C5' |
C4' |
C3' |
304.4 |
305.0 |
| H5'1 |
C5' |
C4' |
H4' |
64.4 |
67.9 |
| H5'2 |
C5' |
O5' |
H5' |
305.3 |
299.9 |
| O5' |
C5' |
H5'2 |
C4' |
235.1 |
240.1 |
| O5' |
C5' |
H5'2 |
H5'1 |
117.6 |
120.1 |
| C4' |
C5' |
H5'2 |
H5'1 |
242.5 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
292.3 |
310.7 |
| H5'2 |
C5' |
C4' |
C3' |
53.8 |
65.0 |
| H5'2 |
C5' |
C4' |
H4' |
173.8 |
187.9 |
| O4' |
C4' |
C5' |
H5'1 |
182.9 |
190.7 |
| O4' |
C4' |
C5' |
H5'2 |
292.3 |
310.7 |
| C5' |
C4' |
O4' |
C3' |
125.9 |
118.7 |
| C5' |
C4' |
O4' |
H4' |
246.6 |
237.1 |
| C3' |
C4' |
O4' |
H4' |
120.7 |
118.5 |
| O4' |
C4' |
C3' |
C2' |
29.0 |
323.1 |
| O4' |
C4' |
C3' |
O3' |
270.4 |
204.9 |
| O4' |
C4' |
C3' |
H3' |
150.9 |
81.2 |
| C4' |
O4' |
C1' |
N9 |
259.0 |
214.2 |
| C4' |
O4' |
C1' |
C2' |
20.7 |
333.6 |
| C4' |
O4' |
C1' |
H1' |
140.7 |
93.2 |
| C3' |
C4' |
C5' |
H5'1 |
304.4 |
305.0 |
| C3' |
C4' |
C5' |
H5'2 |
53.8 |
65.0 |
| C5' |
C4' |
C3' |
O4' |
233.0 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
113.6 |
122.8 |
| O4' |
C4' |
C3' |
H4' |
240.6 |
241.6 |
| C3' |
C4' |
O4' |
C1' |
327.0 |
39.9 |
| C1' |
C2' |
C3' |
C4' |
342.6 |
20.8 |
| C4' |
C3' |
C2' |
H2'1 |
107.9 |
262.2 |
| C4' |
C3' |
C2' |
H2'2 |
217.3 |
139.5 |
| C2' |
C3' |
C4' |
O3' |
118.6 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
238.1 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
119.5 |
123.6 |
| C4' |
C3' |
O3' |
H1 |
180.0 |
174.2 |
| H4' |
C4' |
C5' |
H5'1 |
64.4 |
67.9 |
| H4' |
C4' |
C5' |
H5'2 |
173.8 |
187.9 |
| C5' |
C4' |
H4' |
O4' |
122.4 |
123.0 |
| C5' |
C4' |
H4' |
C3' |
238.9 |
237.1 |
| O4' |
C4' |
H4' |
C3' |
116.6 |
114.1 |
| H4' |
C4' |
O4' |
C1' |
206.3 |
281.4 |
| H4' |
C4' |
C3' |
C2' |
148.4 |
81.5 |
| H4' |
C4' |
C3' |
O3' |
29.8 |
323.3 |
| H4' |
C4' |
C3' |
H3' |
270.3 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
327.0 |
39.9 |
| C1' |
O4' |
C4' |
H4' |
206.3 |
281.4 |
| N9 |
C1' |
O4' |
C2' |
238.3 |
240.5 |
| N9 |
C1' |
O4' |
H1' |
118.3 |
121.0 |
| O4' |
C1' |
N9 |
C4 |
100.2 |
203.3 |
| O4' |
C1' |
N9 |
C8 |
280.4 |
23.3 |
| C2' |
C1' |
O4' |
H1' |
240.0 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
359.0 |
2.0 |
| O4' |
C1' |
C2' |
H2'1 |
233.8 |
120.7 |
| O4' |
C1' |
C2' |
H2'2 |
124.3 |
243.3 |
| O4' |
C1' |
N9 |
C2' |
113.3 |
118.0 |
| O4' |
C1' |
N9 |
H1' |
234.0 |
239.0 |
| C2' |
C1' |
N9 |
H1' |
120.8 |
121.0 |
| N9 |
C1' |
C2' |
C3' |
114.5 |
121.5 |
| N9 |
C1' |
C2' |
H2'1 |
349.2 |
240.1 |
| N9 |
C1' |
C2' |
H2'2 |
239.8 |
2.8 |
| C4 |
N9 |
C1' |
C8 |
179.8 |
180.1 |
| C1' |
N9 |
C4 |
N3 |
0.2 |
359.9 |
| C1' |
N9 |
C4 |
C5 |
180.3 |
180.2 |
| C1' |
N9 |
C8 |
N7 |
179.8 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
359.8 |
360.0 |
| C4' |
C3' |
C2' |
C1' |
342.6 |
20.8 |
| O4' |
C1' |
C2' |
N9 |
244.5 |
240.5 |
| O4' |
C1' |
C2' |
H1' |
125.7 |
119.6 |
| N9 |
C1' |
C2' |
H1' |
241.2 |
239.0 |
| C2' |
C1' |
N9 |
C4 |
346.9 |
85.3 |
| C2' |
C1' |
N9 |
C8 |
167.2 |
265.3 |
| C3' |
C2' |
C1' |
H2'1 |
125.3 |
241.3 |
| C3' |
C2' |
C1' |
H2'2 |
234.7 |
118.7 |
| C1' |
C2' |
C3' |
O3' |
96.7 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
216.8 |
262.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
109.4 |
237.3 |
| O4' |
C1' |
H1' |
N9 |
118.8 |
121.0 |
| O4' |
C1' |
H1' |
C2' |
243.5 |
241.9 |
| N9 |
C1' |
H1' |
C2' |
124.7 |
121.0 |
| H1' |
C1' |
N9 |
C4 |
226.2 |
324.4 |
| H1' |
C1' |
N9 |
C8 |
46.4 |
144.3 |
| H1' |
C1' |
C2' |
C3' |
233.3 |
242.4 |
| H1' |
C1' |
C2' |
H2'1 |
108.0 |
1.1 |
| H1' |
C1' |
C2' |
H2'2 |
358.6 |
123.7 |
| C4 |
N9 |
C1' |
C2' |
346.9 |
85.3 |
| C4 |
N9 |
C1' |
H1' |
226.2 |
324.4 |
| C1' |
N9 |
C4 |
C8 |
180.2 |
180.0 |
| C4 |
N9 |
C8 |
N7 |
360.0 |
360.0 |
| C4 |
N9 |
C8 |
H8 |
180.0 |
179.9 |
| N3 |
C4 |
N9 |
C5 |
179.9 |
179.7 |
| N9 |
C4 |
N3 |
C2 |
180.1 |
180.1 |
| N9 |
C4 |
C5 |
C6 |
179.8 |
180.3 |
| N9 |
C4 |
C5 |
N7 |
359.9 |
359.6 |
| C8 |
N9 |
C1' |
C2' |
167.2 |
265.3 |
| C8 |
N9 |
C1' |
H1' |
46.4 |
144.3 |
| C1' |
N9 |
C8 |
C4 |
179.8 |
180.0 |
| C8 |
N9 |
C4 |
N3 |
180.0 |
180.0 |
| C8 |
N9 |
C4 |
C5 |
0.1 |
0.3 |
| C5 |
N7 |
C8 |
N9 |
360.0 |
359.8 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N3 |
C4 |
N9 |
C8 |
180.0 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
180.1 |
180.3 |
| N3 |
C4 |
C5 |
C6 |
359.9 |
0.5 |
| N3 |
C4 |
C5 |
N7 |
180.0 |
179.8 |
| C4 |
N3 |
C2 |
F |
179.8 |
180.0 |
| C4 |
N3 |
C2 |
N1 |
0.0 |
360.0 |
| C5 |
C4 |
N9 |
C8 |
0.1 |
0.3 |
| N9 |
C4 |
C5 |
N3 |
179.9 |
179.7 |
| C5 |
C4 |
N3 |
C2 |
0.0 |
359.7 |
| N1 |
C6 |
C5 |
C4 |
0.1 |
359.5 |
| N6 |
C6 |
C5 |
C4 |
180.0 |
179.8 |
| C6 |
C5 |
C4 |
N7 |
179.9 |
180.7 |
| C4 |
C5 |
N7 |
C8 |
0.0 |
0.4 |
| C2 |
N3 |
C4 |
C5 |
0.0 |
359.7 |
| F |
C2 |
N3 |
N1 |
179.8 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
0.0 |
0.1 |
| N3 |
C2 |
F |
N1 |
180.2 |
180.0 |
| F |
C2 |
N1 |
C6 |
180.2 |
180.0 |
| N3 |
C2 |
N1 |
F |
179.8 |
180.0 |
| C2 |
N1 |
C6 |
N6 |
180.0 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
359.9 |
0.2 |
| C4 |
C5 |
C6 |
N1 |
0.1 |
359.5 |
| N6 |
C6 |
N1 |
C5 |
180.1 |
179.7 |
| N1 |
C6 |
N6 |
HN61 |
54.7 |
360.0 |
| N1 |
C6 |
N6 |
HN62 |
180.0 |
179.7 |
| N1 |
C6 |
C5 |
N7 |
180.0 |
180.4 |
| C4 |
C5 |
C6 |
N6 |
180.0 |
179.8 |
| N1 |
C6 |
N6 |
C5 |
179.9 |
180.3 |
| N6 |
C6 |
C5 |
N7 |
359.9 |
0.7 |
| HN61 |
N6 |
C6 |
HN62 |
234.8 |
180.3 |
| C4 |
C5 |
C6 |
N7 |
180.1 |
179.1 |
| N1 |
C6 |
C5 |
N6 |
180.1 |
179.7 |
| C5 |
C6 |
N6 |
HN61 |
234.8 |
179.7 |
| C5 |
C6 |
N6 |
HN62 |
0.0 |
359.4 |
| C6 |
C5 |
N7 |
C8 |
180.1 |
179.5 |
| HN61 |
N6 |
C6 |
C5 |
234.8 |
179.7 |
| C6 |
N6 |
HN61 |
HN62 |
130.3 |
179.7 |
| HN62 |
N6 |
C6 |
C5 |
0.0 |
359.4 |
| C6 |
N6 |
HN62 |
HN61 |
234.7 |
180.3 |
| N9 |
C8 |
N7 |
C5 |
360.0 |
359.8 |
| C4 |
C5 |
N7 |
C6 |
179.9 |
180.9 |
| C5 |
N7 |
C8 |
H8 |
180.0 |
179.8 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| C2' |
C3' |
C4' |
H4' |
148.4 |
81.5 |
| C4' |
C3' |
C2' |
O3' |
245.9 |
241.7 |
| C4' |
C3' |
C2' |
H3' |
125.8 |
118.2 |
| C3' |
C2' |
C1' |
H1' |
233.3 |
242.4 |
| C1' |
C2' |
C3' |
H2'1 |
234.7 |
118.7 |
| C1' |
C2' |
C3' |
H2'2 |
125.3 |
241.3 |
| H2'1 |
C2' |
C3' |
H2'2 |
250.5 |
122.6 |
| O3' |
C3' |
C2' |
H3' |
239.8 |
236.4 |
| C2' |
C3' |
O3' |
H1 |
69.3 |
61.5 |
| H2'1 |
C2' |
C1' |
H1' |
108.0 |
1.1 |
| C1' |
C2' |
H2'1 |
C3' |
123.7 |
245.3 |
| C1' |
C2' |
H2'1 |
H2'2 |
241.9 |
122.6 |
| C3' |
C2' |
H2'1 |
H2'2 |
118.1 |
237.4 |
| H2'1 |
C2' |
C3' |
O3' |
221.9 |
20.4 |
| H2'1 |
C2' |
C3' |
H3' |
342.1 |
144.0 |
| H2'2 |
C2' |
C1' |
H1' |
358.6 |
123.7 |
| C1' |
C2' |
H2'2 |
C3' |
236.3 |
114.8 |
| C1' |
C2' |
H2'2 |
H2'1 |
118.1 |
237.4 |
| C3' |
C2' |
H2'2 |
H2'1 |
241.8 |
122.6 |
| H2'2 |
C2' |
C3' |
O3' |
331.4 |
257.8 |
| H2'2 |
C2' |
C3' |
H3' |
91.6 |
21.4 |
| O3' |
C3' |
C4' |
H4' |
29.8 |
323.3 |
| C4' |
C3' |
O3' |
C2' |
110.7 |
112.7 |
| C4' |
C3' |
O3' |
H3' |
233.7 |
236.3 |
| O3' |
C3' |
C2' |
H2'1 |
221.9 |
20.4 |
| O3' |
C3' |
C2' |
H2'2 |
331.4 |
257.8 |
| C2' |
C3' |
O3' |
H3' |
123.1 |
123.6 |
| H3' |
C3' |
C4' |
H4' |
270.3 |
199.7 |
| C4' |
C3' |
H3' |
C2' |
243.6 |
247.3 |
| C4' |
C3' |
H3' |
O3' |
119.7 |
123.7 |
| H3' |
C3' |
C2' |
H2'1 |
342.1 |
144.0 |
| H3' |
C3' |
C2' |
H2'2 |
91.6 |
21.4 |
| C2' |
C3' |
H3' |
O3' |
236.1 |
236.4 |
| H3' |
C3' |
O3' |
H1 |
306.3 |
297.8 |
| H1 |
O3' |
C3' |
H3' |
306.3 |
297.8 |