PDB Chemical Component FDY
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 FDY
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O2 |
C2 |
1.238 |
1.216 |
C2 |
N3 |
1.324 |
1.346 |
C2 |
N1 |
1.350 |
1.345 |
N3 |
C4 |
1.368 |
1.348 |
C2' |
C1' |
1.309 |
1.545 |
C2' |
C3' |
1.489 |
1.544 |
C1' |
N1 |
1.435 |
1.465 |
C1' |
O4' |
1.594 |
1.445 |
N1 |
C6 |
1.349 |
1.368 |
O3' |
C3' |
1.417 |
1.429 |
C4 |
O4 |
1.202 |
1.218 |
C4 |
C5 |
1.420 |
1.416 |
C3' |
C4' |
1.559 |
1.545 |
O4' |
C4' |
1.240 |
1.444 |
C6 |
C5 |
1.421 |
1.350 |
C4' |
C5' |
1.552 |
1.530 |
C5 |
C7 |
1.555 |
1.507 |
O2B |
PB |
1.536 |
1.480 |
C5' |
O5' |
1.488 |
1.429 |
O5' |
PA |
1.620 |
1.610 |
PB |
O3A |
1.543 |
1.610 |
PB |
O1B |
1.513 |
1.610 |
PB |
C3B |
1.887 |
1.822 |
F2B |
C3B |
1.333 |
1.399 |
O3A |
PA |
1.600 |
1.610 |
C3B |
PG |
1.793 |
1.823 |
PA |
O2A |
1.495 |
1.480 |
PA |
O1A |
1.498 |
1.610 |
O3G |
PG |
1.523 |
1.480 |
PG |
O1G |
1.514 |
1.610 |
PG |
O2G |
1.472 |
1.610 |
C6 |
H1 |
1.080 |
1.080 |
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 |
1.100 |
1.089 |
C2' |
H7 |
1.100 |
1.090 |
C2' |
H8 |
1.100 |
1.090 |
C3' |
H9 |
1.100 |
1.090 |
O3' |
H10 |
0.950 |
0.966 |
C4' |
H11 |
1.100 |
1.090 |
C5' |
H12 |
1.101 |
1.090 |
C5' |
H13 |
1.100 |
1.089 |
O1A |
H14 |
0.950 |
0.967 |
O1B |
H15 |
0.950 |
0.967 |
C3B |
H16 |
1.100 |
1.090 |
O2G |
H17 |
0.950 |
0.967 |
O1G |
H18 |
0.950 |
0.967 |
Bond Angles for FDY
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O2 |
C2 |
N1 |
119.0 |
119.6 |
N3 |
C2 |
N1 |
121.6 |
120.9 |
C2 |
N3 |
C4 |
121.1 |
120.3 |
C2 |
N3 |
H5 |
119.4 |
119.8 |
C2 |
N1 |
C6 |
120.6 |
120.6 |
C2' |
C1' |
O4' |
105.6 |
104.8 |
C2' |
C1' |
H6 |
112.2 |
110.5 |
C2' |
C3' |
C4' |
100.6 |
104.1 |
C3' |
C2' |
H7 |
110.0 |
110.5 |
C3' |
C2' |
H8 |
110.0 |
110.5 |
C2' |
C3' |
H9 |
108.7 |
110.5 |
C1' |
O4' |
C4' |
108.4 |
105.3 |
O4' |
C1' |
H6 |
108.1 |
110.4 |
N1 |
C6 |
H1 |
119.7 |
120.2 |
O3' |
C3' |
C4' |
111.5 |
110.5 |
O3' |
C3' |
H9 |
109.7 |
110.6 |
C5 |
C4 |
O4 |
119.5 |
120.3 |
C4 |
C5 |
C7 |
122.6 |
120.5 |
C3' |
C4' |
O4' |
104.4 |
104.8 |
C3' |
C4' |
C5' |
109.1 |
110.4 |
C4' |
C3' |
H9 |
107.9 |
110.5 |
C3' |
C4' |
H11 |
109.1 |
110.4 |
O4' |
C4' |
C5' |
110.4 |
110.4 |
O4' |
C4' |
H11 |
114.3 |
110.4 |
C6 |
C5 |
C7 |
121.2 |
120.4 |
C4' |
C5' |
O5' |
104.1 |
109.5 |
C5' |
C4' |
H11 |
109.2 |
110.4 |
C4' |
C5' |
H12 |
110.8 |
109.5 |
C4' |
C5' |
H13 |
110.8 |
109.5 |
C5 |
C7 |
H2 |
109.5 |
109.5 |
C5 |
C7 |
H3 |
109.5 |
109.5 |
C5 |
C7 |
H4 |
109.5 |
109.4 |
O2B |
PB |
O1B |
110.4 |
109.5 |
O2B |
PB |
C3B |
108.8 |
109.5 |
C5' |
O5' |
PA |
118.6 |
123.0 |
O5' |
C5' |
H12 |
110.8 |
109.5 |
O5' |
C5' |
H13 |
110.8 |
109.5 |
O5' |
PA |
O2A |
107.7 |
109.5 |
O5' |
PA |
O1A |
111.2 |
109.5 |
O1B |
PB |
C3B |
110.8 |
109.5 |
PB |
O1B |
H15 |
109.5 |
114.1 |
PB |
C3B |
PG |
109.9 |
109.5 |
PB |
C3B |
H16 |
106.0 |
109.5 |
F2B |
C3B |
PG |
112.4 |
109.4 |
F2B |
C3B |
H16 |
113.1 |
109.5 |
C3B |
PG |
O1G |
107.9 |
109.5 |
C3B |
PG |
O2G |
110.4 |
109.5 |
PG |
C3B |
H16 |
106.9 |
109.4 |
O1A |
PA |
O2A |
110.9 |
109.5 |
PA |
O1A |
H14 |
109.5 |
114.0 |
O3G |
PG |
O1G |
108.3 |
109.5 |
O3G |
PG |
O2G |
110.9 |
109.4 |
O2G |
PG |
O1G |
110.2 |
109.5 |
PG |
O1G |
H18 |
109.5 |
114.0 |
PG |
O2G |
H17 |
109.5 |
114.0 |
H2 |
C7 |
H3 |
109.5 |
109.5 |
H2 |
C7 |
H4 |
109.5 |
109.5 |
H3 |
C7 |
H4 |
109.5 |
109.5 |
H7 |
C2' |
H8 |
109.5 |
110.5 |
H12 |
C5' |
H13 |
109.4 |
109.5 |
Torsion Angles for FDY
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
N3 |
C2 |
O2 |
N1 |
180.4 |
179.7 |
O2 |
C2 |
N3 |
H5 |
1.5 |
0.2 |
O2 |
C2 |
N1 |
C6 |
179.0 |
179.7 |
O2 |
C2 |
N3 |
N1 |
179.6 |
180.3 |
N3 |
C2 |
N1 |
C6 |
358.6 |
0.0 |
N1 |
C2 |
N3 |
C4 |
1.9 |
0.0 |
N1 |
C2 |
N3 |
H5 |
181.9 |
179.9 |
C2 |
N1 |
C6 |
H1 |
180.8 |
180.0 |
C4 |
N3 |
C2 |
N1 |
1.9 |
0.0 |
C2 |
N3 |
C4 |
H5 |
180.0 |
179.9 |
C2' |
C1' |
O4' |
C4' |
351.0 |
319.4 |
O4' |
C1' |
C2' |
H6 |
117.6 |
118.9 |
C3' |
C2' |
C1' |
O4' |
343.6 |
24.0 |
C3' |
C2' |
C1' |
H6 |
226.1 |
265.1 |
O3' |
C3' |
C2' |
C4' |
121.3 |
118.7 |
O3' |
C3' |
C2' |
H9 |
234.5 |
237.3 |
C2' |
C3' |
C4' |
O4' |
322.6 |
336.0 |
C2' |
C3' |
C4' |
C5' |
204.5 |
217.2 |
C4' |
C3' |
C2' |
H9 |
113.2 |
118.6 |
C2' |
C3' |
C4' |
H11 |
85.2 |
94.8 |
H7 |
C2' |
C3' |
H8 |
120.7 |
122.7 |
C1' |
N1 |
C6 |
H1 |
357.6 |
0.1 |
C2' |
C1' |
O4' |
H6 |
239.7 |
241.0 |
C3' |
C4' |
O4' |
C1' |
28.3 |
40.5 |
C1' |
O4' |
C4' |
C5' |
145.5 |
159.4 |
C1' |
O4' |
C4' |
H11 |
269.2 |
281.7 |
C2' |
C3' |
O3' |
C4' |
244.5 |
245.3 |
O3' |
C3' |
C2' |
H7 |
33.3 |
0.0 |
O3' |
C3' |
C2' |
H8 |
272.6 |
237.3 |
C2' |
C3' |
O3' |
H9 |
125.0 |
122.7 |
O3' |
C3' |
C4' |
O4' |
197.0 |
217.4 |
O3' |
C3' |
C4' |
C5' |
78.9 |
98.5 |
C4' |
C3' |
O3' |
H9 |
240.5 |
237.4 |
O3' |
C3' |
C4' |
H11 |
319.6 |
336.2 |
C2 |
N3 |
C4 |
O4 |
179.0 |
179.9 |
O4 |
C4 |
C5 |
C7 |
359.6 |
0.1 |
C2 |
N3 |
C4 |
C5 |
358.3 |
359.9 |
C6 |
C5 |
C4 |
C7 |
180.7 |
180.0 |
C4 |
C5 |
C7 |
H2 |
180.0 |
360.0 |
C4 |
C5 |
C7 |
H3 |
300.0 |
120.0 |
C4 |
C5 |
C7 |
H4 |
60.0 |
240.0 |
C4' |
C3' |
C2' |
H7 |
271.9 |
241.4 |
C4' |
C3' |
C2' |
H8 |
151.3 |
118.7 |
C2' |
C3' |
C4' |
H9 |
246.2 |
241.3 |
C1' |
O4' |
C4' |
C3' |
28.3 |
40.5 |
O3' |
C3' |
C4' |
H9 |
120.6 |
122.7 |
O4' |
C4' |
C3' |
C5' |
118.1 |
118.8 |
O4' |
C4' |
C3' |
H11 |
237.4 |
241.2 |
C3' |
C4' |
C5' |
O5' |
56.9 |
185.0 |
C5' |
C4' |
C3' |
H11 |
119.3 |
122.3 |
C3' |
C4' |
C5' |
H12 |
176.1 |
305.0 |
C3' |
C4' |
C5' |
H13 |
297.7 |
65.0 |
C4' |
O4' |
C1' |
H6 |
111.3 |
78.4 |
C3' |
C4' |
O4' |
C5' |
242.8 |
241.2 |
O4' |
C4' |
C3' |
H9 |
76.4 |
94.7 |
C3' |
C4' |
O4' |
H11 |
119.2 |
118.8 |
O4' |
C4' |
C5' |
O5' |
302.7 |
69.6 |
C5' |
C4' |
O4' |
H11 |
236.4 |
237.6 |
O4' |
C4' |
C5' |
H12 |
61.8 |
189.6 |
O4' |
C4' |
C5' |
H13 |
183.5 |
309.7 |
C2 |
N1 |
C6 |
C5 |
0.8 |
359.9 |
C6 |
C5 |
C4 |
O4 |
180.3 |
180.0 |
C4 |
C5 |
C6 |
C7 |
179.3 |
180.0 |
C6 |
C5 |
C7 |
H2 |
359.3 |
180.0 |
C6 |
C5 |
C7 |
H3 |
119.3 |
300.0 |
C6 |
C5 |
C7 |
H4 |
239.3 |
60.0 |
C3' |
C4' |
C5' |
O4' |
114.2 |
115.4 |
C5' |
C4' |
C3' |
H9 |
318.3 |
335.8 |
C3' |
C4' |
C5' |
H11 |
240.8 |
237.7 |
O4' |
C4' |
C5' |
H11 |
126.5 |
122.3 |
C4' |
C5' |
O5' |
PA |
219.9 |
180.0 |
O5' |
C5' |
C4' |
H12 |
240.8 |
240.0 |
O5' |
C5' |
C4' |
H13 |
119.2 |
120.0 |
H12 |
C5' |
C4' |
H13 |
238.3 |
240.0 |
C7 |
C5 |
C4 |
O4 |
359.6 |
0.1 |
H2 |
C7 |
C5 |
H3 |
240.0 |
240.0 |
H2 |
C7 |
C5 |
H4 |
120.0 |
120.0 |
H3 |
C7 |
C5 |
H4 |
240.0 |
240.0 |
O1B |
PB |
O2B |
C3B |
238.2 |
240.0 |
O2B |
PB |
O1B |
H15 |
360.0 |
180.0 |
O2B |
PB |
C3B |
PG |
217.8 |
300.0 |
O2B |
PB |
C3B |
H16 |
102.6 |
180.0 |
O5' |
C5' |
C4' |
H11 |
176.1 |
307.3 |
C4' |
C5' |
O5' |
H12 |
119.2 |
120.0 |
C4' |
C5' |
O5' |
H13 |
240.8 |
240.0 |
C5' |
O5' |
PA |
O2A |
189.3 |
305.0 |
C5' |
O5' |
PA |
O1A |
311.1 |
65.0 |
H12 |
C5' |
O5' |
H13 |
121.7 |
120.0 |
PA |
O5' |
C5' |
H12 |
100.8 |
60.0 |
PA |
O5' |
C5' |
H13 |
339.1 |
300.0 |
O1A |
PA |
O5' |
O2A |
121.7 |
120.0 |
O5' |
PA |
O1A |
H14 |
240.1 |
60.0 |
O2B |
PB |
O1B |
C3B |
120.6 |
120.1 |
O1B |
PB |
C3B |
PG |
339.4 |
60.0 |
O1B |
PB |
C3B |
H16 |
224.2 |
300.1 |
O2B |
PB |
C3B |
O1B |
238.4 |
239.9 |
C3B |
PB |
O1B |
H15 |
239.4 |
59.9 |
F2B |
C3B |
PB |
PG |
123.1 |
120.0 |
F2B |
C3B |
PB |
H16 |
238.4 |
239.9 |
PB |
C3B |
PG |
O1G |
317.1 |
180.0 |
PB |
C3B |
PG |
O2G |
196.5 |
60.0 |
PG |
C3B |
PB |
H16 |
115.2 |
120.0 |
PB |
C3B |
F2B |
PG |
238.4 |
240.0 |
PB |
C3B |
F2B |
H16 |
117.2 |
120.1 |
F2B |
C3B |
PG |
O1G |
196.4 |
60.0 |
F2B |
C3B |
PG |
O2G |
75.8 |
300.0 |
PG |
C3B |
F2B |
H16 |
238.8 |
240.1 |
O3A |
PA |
O1A |
H14 |
117.8 |
300.0 |
PB |
C3B |
PG |
H16 |
245.4 |
240.0 |
F2B |
C3B |
PG |
H16 |
124.6 |
120.0 |
O3G |
PG |
C3B |
O1G |
117.4 |
120.0 |
O3G |
PG |
C3B |
O2G |
238.0 |
240.0 |
O2G |
PG |
C3B |
O1G |
239.5 |
240.0 |
C3B |
PG |
O1G |
H18 |
117.9 |
180.0 |
C3B |
PG |
O2G |
H17 |
239.1 |
60.1 |
O5' |
PA |
O2A |
O1A |
122.0 |
120.0 |
O2A |
PA |
O1A |
H14 |
360.0 |
180.0 |
O5' |
PA |
O1A |
O2A |
240.1 |
240.0 |
C3B |
PG |
O3G |
O1G |
242.8 |
240.0 |
C3B |
PG |
O3G |
O2G |
121.7 |
120.0 |
O3G |
PG |
C3B |
H16 |
189.2 |
60.0 |
O2G |
PG |
O3G |
O1G |
121.1 |
120.0 |
O3G |
PG |
O1G |
H18 |
0.0 |
59.9 |
O3G |
PG |
O2G |
H17 |
0.0 |
180.1 |
C3B |
PG |
O1G |
O2G |
239.4 |
240.0 |
O1G |
PG |
C3B |
H16 |
71.7 |
300.0 |
O3G |
PG |
O1G |
O2G |
121.5 |
120.0 |
O1G |
PG |
O2G |
H17 |
119.9 |
300.1 |
C3B |
PG |
O2G |
O1G |
119.1 |
120.0 |
O2G |
PG |
C3B |
H16 |
311.2 |
180.0 |
O3G |
PG |
O2G |
O1G |
240.1 |
240.0 |
O2G |
PG |
O1G |
H18 |
238.5 |
300.0 |
H1 |
C6 |
C5 |
C7 |
0.0 |
360.0 |
C5 |
C7 |
H2 |
H3 |
120.0 |
120.0 |
C5 |
C7 |
H2 |
H4 |
240.0 |
240.0 |
H3 |
C7 |
H2 |
H4 |
120.0 |
120.0 |
C5 |
C7 |
H3 |
H2 |
240.0 |
240.0 |
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 |
H5 |
N3 |
C2 |
N1 |
181.9 |
179.9 |
C2 |
N3 |
H5 |
C4 |
180.0 |
180.1 |
C2' |
C1' |
H6 |
O4' |
116.0 |
115.4 |
H6 |
C1' |
O4' |
C4' |
111.3 |
78.4 |
H7 |
C2' |
C1' |
O4' |
103.3 |
142.7 |
H7 |
C2' |
C1' |
H6 |
345.7 |
23.8 |
H7 |
C2' |
C3' |
C4' |
271.9 |
241.4 |
C3' |
C2' |
H7 |
H8 |
239.0 |
237.3 |
H7 |
C2' |
C3' |
H9 |
158.8 |
122.8 |
H8 |
C2' |
C1' |
O4' |
224.0 |
265.3 |
H8 |
C2' |
C1' |
H6 |
106.4 |
146.4 |
H8 |
C2' |
C3' |
C4' |
151.3 |
118.7 |
C3' |
C2' |
H8 |
H7 |
121.0 |
122.7 |
H8 |
C2' |
C3' |
H9 |
38.1 |
0.1 |
C2' |
C3' |
H9 |
C4' |
108.3 |
114.6 |
H9 |
C3' |
C2' |
H7 |
158.8 |
122.8 |
H9 |
C3' |
C2' |
H8 |
38.1 |
0.1 |
O3' |
C3' |
H9 |
C4' |
238.3 |
237.3 |
H9 |
C3' |
C4' |
O4' |
76.4 |
94.7 |
H9 |
C3' |
C4' |
C5' |
318.3 |
335.8 |
H9 |
C3' |
C4' |
H11 |
199.1 |
213.5 |
H10 |
O3' |
C3' |
C4' |
254.1 |
176.1 |
H10 |
O3' |
C3' |
H9 |
13.6 |
298.8 |
C3' |
C4' |
H11 |
O4' |
243.5 |
244.6 |
C3' |
C4' |
H11 |
C5' |
119.2 |
122.3 |
H11 |
C4' |
C3' |
H9 |
199.1 |
213.5 |
O4' |
C4' |
H11 |
C5' |
235.7 |
237.7 |
H11 |
C4' |
C5' |
O5' |
176.1 |
307.3 |
H11 |
C4' |
C5' |
H12 |
295.3 |
67.3 |
H11 |
C4' |
C5' |
H13 |
57.0 |
187.3 |
C4' |
C5' |
H12 |
O5' |
245.0 |
240.0 |
H12 |
C5' |
C4' |
H11 |
295.3 |
67.3 |
C4' |
C5' |
H12 |
H13 |
122.5 |
120.0 |
H12 |
C5' |
O5' |
PA |
100.8 |
60.0 |
O5' |
C5' |
H12 |
H13 |
237.5 |
240.0 |
C4' |
C5' |
H13 |
O5' |
115.0 |
120.0 |
H13 |
C5' |
C4' |
H11 |
57.0 |
187.3 |
C4' |
C5' |
H13 |
H12 |
237.5 |
240.0 |
H13 |
C5' |
O5' |
PA |
339.1 |
300.0 |
O5' |
C5' |
H13 |
H12 |
122.5 |
120.0 |
H14 |
O1A |
PA |
O2A |
360.0 |
180.0 |
H15 |
O1B |
PB |
C3B |
239.4 |
59.9 |
PB |
C3B |
H16 |
PG |
117.2 |
120.0 |
F2B |
C3B |
H16 |
PG |
235.8 |
240.1 |
H16 |
C3B |
PG |
O1G |
71.7 |
300.0 |
H16 |
C3B |
PG |
O2G |
311.2 |
180.0 |
H17 |
O2G |
PG |
O1G |
119.9 |
300.1 |