PDB Chemical Component F3O
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 F3O
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.543 |
1.479 |
| OP1 |
P |
1.525 |
1.611 |
| P |
O5' |
1.594 |
1.610 |
| C2 |
N3 |
1.300 |
1.317 |
| C2 |
N1 |
1.311 |
1.320 |
| N |
CA |
1.446 |
1.468 |
| N3 |
C4 |
1.346 |
1.329 |
| O5' |
C5' |
1.428 |
1.429 |
| CE2 |
CD2 |
1.412 |
1.383 |
| CE2 |
CZ |
1.397 |
1.383 |
| N1 |
C6 |
1.332 |
1.328 |
| O4' |
C4' |
1.449 |
1.437 |
| O4' |
C1' |
1.398 |
1.444 |
| CD2 |
CG |
1.414 |
1.382 |
| C4' |
C5' |
1.503 |
1.530 |
| C4' |
C3' |
1.530 |
1.541 |
| O3' |
C |
1.415 |
1.342 |
| O3' |
C3' |
1.433 |
1.452 |
| CA |
C |
1.524 |
1.506 |
| CA |
CB |
1.569 |
1.530 |
| C4 |
N9 |
1.345 |
1.373 |
| C4 |
C5 |
1.385 |
1.406 |
| C1' |
N9 |
1.446 |
1.465 |
| C1' |
C2' |
1.516 |
1.550 |
| CZ |
CE1 |
1.410 |
1.382 |
| C |
O |
1.197 |
1.208 |
| C6 |
C5 |
1.399 |
1.406 |
| C6 |
N6 |
1.371 |
1.383 |
| C3' |
C2' |
1.531 |
1.548 |
| N9 |
C8 |
1.333 |
1.363 |
| CG |
CB |
1.550 |
1.507 |
| CG |
CD1 |
1.403 |
1.382 |
| C5 |
N7 |
1.375 |
1.355 |
| C2' |
O2' |
1.412 |
1.429 |
| CE1 |
CD1 |
1.400 |
1.382 |
| C8 |
N7 |
1.337 |
1.301 |
| OP1 |
H1 |
0.950 |
0.967 |
| C1' |
H3 |
1.100 |
1.090 |
| C2' |
H4 |
1.100 |
1.090 |
| O2' |
H5 |
0.950 |
0.967 |
| C3' |
H6 |
1.100 |
1.091 |
| C4' |
H7 |
1.100 |
1.091 |
| C5' |
H8 |
1.100 |
1.089 |
| C5' |
H9 |
1.100 |
1.090 |
| C8 |
H10 |
1.080 |
1.080 |
| N6 |
H11 |
1.000 |
0.971 |
| N6 |
H12 |
1.001 |
0.970 |
| C2 |
H13 |
1.080 |
1.080 |
| CA |
H14 |
1.100 |
1.090 |
| N |
H15 |
1.000 |
1.010 |
| N |
H16 |
1.001 |
1.009 |
| CB |
H18 |
1.100 |
1.090 |
| CB |
H19 |
1.100 |
1.090 |
| CD1 |
H20 |
1.080 |
1.080 |
| CE1 |
H21 |
1.080 |
1.081 |
| CZ |
H22 |
1.080 |
1.079 |
| CE2 |
H23 |
1.080 |
1.079 |
| CD2 |
H24 |
1.080 |
1.080 |
| P |
OP3 |
|
1.610 |
| OP3 |
H2 |
|
0.968 |
Bond Angles for F3O
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
O5' |
108.4 |
109.5 |
| OP2 |
P |
OP3 |
|
109.5 |
| OP1 |
P |
O5' |
112.4 |
109.4 |
| OP1 |
P |
OP3 |
|
109.5 |
| P |
O5' |
C5' |
122.1 |
123.0 |
| O5' |
P |
OP3 |
|
109.5 |
| N1 |
C2 |
H13 |
119.1 |
118.8 |
| N |
CA |
CB |
116.2 |
109.5 |
| N |
CA |
H14 |
107.5 |
109.5 |
| O5' |
C5' |
H8 |
108.9 |
109.5 |
| O5' |
C5' |
H9 |
109.0 |
109.5 |
| CD2 |
CE2 |
H23 |
120.7 |
120.0 |
| CE2 |
CD2 |
H24 |
118.8 |
120.0 |
| CE2 |
CZ |
H22 |
120.4 |
120.0 |
| O4' |
C4' |
C5' |
107.9 |
109.9 |
| O4' |
C4' |
H7 |
109.2 |
110.0 |
| O4' |
C1' |
N9 |
107.8 |
110.6 |
| O4' |
C1' |
H3 |
111.0 |
110.8 |
| C5' |
C4' |
H7 |
108.5 |
109.9 |
| C4' |
C5' |
H8 |
109.0 |
109.4 |
| C4' |
C5' |
H9 |
108.9 |
109.5 |
| C4' |
C3' |
H6 |
111.0 |
110.5 |
| O3' |
C |
O |
118.6 |
120.0 |
| O3' |
C3' |
H6 |
112.5 |
110.4 |
| CB |
CA |
H14 |
106.1 |
109.4 |
| CA |
CB |
H18 |
107.9 |
109.5 |
| CA |
CB |
H19 |
107.9 |
109.5 |
| C2' |
C1' |
N9 |
112.8 |
110.6 |
| C1' |
N9 |
C8 |
127.7 |
126.3 |
| N9 |
C1' |
H3 |
110.2 |
110.5 |
| C1' |
C2' |
O2' |
110.9 |
110.9 |
| C2' |
C1' |
H3 |
109.3 |
110.6 |
| C1' |
C2' |
H4 |
108.8 |
110.9 |
| CZ |
CE1 |
H21 |
118.9 |
120.0 |
| N6 |
C6 |
C5 |
119.8 |
120.7 |
| C6 |
N6 |
H11 |
109.5 |
120.0 |
| C6 |
N6 |
H12 |
109.5 |
120.0 |
| C3' |
C2' |
H4 |
108.6 |
111.0 |
| N9 |
C8 |
N7 |
108.3 |
110.0 |
| N9 |
C8 |
H10 |
125.9 |
125.0 |
| CG |
CB |
H18 |
107.9 |
109.4 |
| CG |
CB |
H19 |
107.9 |
109.5 |
| CG |
CD1 |
H20 |
120.4 |
120.0 |
| O2' |
C2' |
H4 |
110.3 |
110.8 |
| C2' |
O2' |
H5 |
109.5 |
114.0 |
| CE1 |
CD1 |
H20 |
120.4 |
120.0 |
| N7 |
C8 |
H10 |
125.8 |
125.0 |
| H8 |
C5' |
H9 |
109.4 |
109.5 |
| H11 |
N6 |
H12 |
109.4 |
120.0 |
| H15 |
N |
H16 |
109.4 |
111.0 |
| H18 |
CB |
H19 |
109.5 |
109.5 |
| P |
OP3 |
H2 |
|
114.0 |
Torsion Angles for F3O
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
O5' |
121.7 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
|
240.0 |
| OP2 |
P |
O5' |
C5' |
120.2 |
54.9 |
| O5' |
P |
OP2 |
OP3 |
|
120.0 |
| OP2 |
P |
OP3 |
H2 |
|
300.0 |
| OP2 |
P |
OP1 |
O5' |
240.8 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
|
120.0 |
| OP1 |
P |
O5' |
C5' |
1.5 |
294.9 |
| O5' |
P |
OP1 |
OP3 |
|
240.0 |
| OP1 |
P |
OP3 |
H2 |
|
60.0 |
| OP2 |
P |
O5' |
OP3 |
|
240.0 |
| OP1 |
P |
O5' |
OP3 |
|
120.0 |
| P |
O5' |
C5' |
H8 |
168.1 |
60.1 |
| P |
O5' |
C5' |
H9 |
287.5 |
300.1 |
| O5' |
P |
OP3 |
H2 |
|
180.0 |
| CB |
CA |
N |
H14 |
118.6 |
120.0 |
| N |
CA |
CB |
H18 |
63.1 |
55.0 |
| N |
CA |
CB |
H19 |
181.3 |
175.0 |
| C5' |
O5' |
P |
OP3 |
|
175.0 |
| O5' |
C5' |
C4' |
H7 |
310.9 |
306.0 |
| C4' |
C5' |
O5' |
H8 |
239.7 |
120.0 |
| C4' |
C5' |
O5' |
H9 |
120.3 |
240.0 |
| H8 |
C5' |
O5' |
H9 |
240.6 |
120.0 |
| CD2 |
CE2 |
CZ |
H22 |
179.7 |
179.7 |
| CE2 |
CZ |
CE1 |
H21 |
179.7 |
180.0 |
| N1 |
C6 |
N6 |
H11 |
0.0 |
180.7 |
| N1 |
C6 |
N6 |
H12 |
120.0 |
0.8 |
| C4' |
O4' |
C1' |
N9 |
211.8 |
201.4 |
| C4' |
O4' |
C1' |
H3 |
91.1 |
78.5 |
| C5' |
C4' |
O4' |
H7 |
242.2 |
238.9 |
| O4' |
C4' |
C5' |
H8 |
308.8 |
187.1 |
| O4' |
C4' |
C5' |
H9 |
189.4 |
307.1 |
| O4' |
C4' |
C3' |
H6 |
136.5 |
116.7 |
| C2' |
C1' |
O4' |
N9 |
120.9 |
118.5 |
| O4' |
C1' |
N9 |
C8 |
75.5 |
19.2 |
| N9 |
C1' |
O4' |
H3 |
120.8 |
122.9 |
| C2' |
C1' |
O4' |
H3 |
241.6 |
241.4 |
| O4' |
C1' |
C2' |
H4 |
283.0 |
278.8 |
| CD2 |
CG |
CB |
H18 |
218.6 |
149.8 |
| CD2 |
CG |
CB |
H19 |
100.4 |
29.8 |
| CD2 |
CG |
CD1 |
H20 |
179.5 |
180.3 |
| P |
O5' |
C5' |
C4' |
47.8 |
180.0 |
| O5' |
C5' |
C4' |
H8 |
120.3 |
240.0 |
| O5' |
C5' |
C4' |
H9 |
239.7 |
120.0 |
| O4' |
C4' |
C5' |
H7 |
118.2 |
121.2 |
| C5' |
C4' |
C3' |
H6 |
16.2 |
357.2 |
| H8 |
C5' |
C4' |
H9 |
119.4 |
240.0 |
| O3' |
C3' |
C4' |
H6 |
124.3 |
122.5 |
| C4' |
C3' |
C2' |
H4 |
82.0 |
97.3 |
| C |
O3' |
C3' |
H6 |
312.9 |
328.9 |
| C4' |
C3' |
O3' |
H6 |
236.6 |
237.4 |
| O3' |
C3' |
C2' |
H4 |
198.0 |
216.2 |
| N |
CA |
CB |
H14 |
240.6 |
240.0 |
| CG |
CB |
CA |
H18 |
239.1 |
240.1 |
| CG |
CB |
CA |
H19 |
120.9 |
120.1 |
| H18 |
CB |
CA |
H19 |
241.8 |
240.0 |
| C4 |
N9 |
C1' |
H3 |
14.9 |
321.8 |
| C4 |
N9 |
C8 |
H10 |
180.1 |
180.3 |
| O4' |
C1' |
N9 |
H3 |
238.8 |
236.9 |
| N9 |
C1' |
C2' |
O2' |
279.0 |
273.7 |
| C2' |
C1' |
N9 |
H3 |
122.5 |
122.9 |
| N9 |
C1' |
C2' |
H4 |
40.5 |
37.3 |
| C1' |
N9 |
C8 |
N7 |
178.4 |
180.0 |
| C1' |
N9 |
C8 |
H10 |
358.4 |
359.9 |
| O4' |
C1' |
C2' |
N9 |
242.5 |
241.5 |
| O4' |
C1' |
C2' |
H3 |
119.5 |
118.7 |
| C2' |
C1' |
N9 |
C8 |
319.2 |
265.1 |
| N9 |
C1' |
C2' |
H3 |
237.0 |
237.2 |
| C3' |
C2' |
C1' |
H4 |
114.4 |
118.3 |
| O2' |
C2' |
C1' |
H4 |
238.5 |
236.4 |
| C1' |
C2' |
O2' |
H5 |
224.2 |
61.5 |
| CZ |
CE1 |
CD1 |
H20 |
180.7 |
180.0 |
| C5 |
C6 |
N6 |
H11 |
180.7 |
359.9 |
| C5 |
C6 |
N6 |
H12 |
300.7 |
180.0 |
| H11 |
N6 |
C6 |
H12 |
240.0 |
179.9 |
| C3' |
C2' |
C1' |
N9 |
154.9 |
155.6 |
| C3' |
C2' |
C1' |
H3 |
277.9 |
278.4 |
| C1' |
C2' |
C3' |
H4 |
245.4 |
241.8 |
| O2' |
C2' |
C3' |
H4 |
125.0 |
123.6 |
| C3' |
C2' |
O2' |
H5 |
339.4 |
174.1 |
| C8 |
N9 |
C1' |
H3 |
196.8 |
142.2 |
| N7 |
C8 |
N9 |
H10 |
180.0 |
180.1 |
| CG |
CB |
CA |
H14 |
61.6 |
55.1 |
| CA |
CB |
CG |
H18 |
120.9 |
120.0 |
| CA |
CB |
CG |
H19 |
239.1 |
239.9 |
| H18 |
CB |
CG |
H19 |
118.2 |
120.0 |
| CD1 |
CG |
CB |
H18 |
37.5 |
329.9 |
| CD1 |
CG |
CB |
H19 |
279.3 |
210.0 |
| CE1 |
CD1 |
CG |
H20 |
180.0 |
180.0 |
| C5 |
N7 |
C8 |
H10 |
179.6 |
180.1 |
| O2' |
C2' |
C1' |
N9 |
279.0 |
273.7 |
| O2' |
C2' |
C1' |
H3 |
42.0 |
36.5 |
| C1' |
C2' |
O2' |
H4 |
120.6 |
123.6 |
| C3' |
C2' |
O2' |
H4 |
235.8 |
236.3 |
| CG |
CD1 |
CE1 |
H20 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
H10 |
180.0 |
179.9 |
| H1 |
OP1 |
P |
O5' |
119.2 |
300.0 |
| H1 |
OP1 |
P |
OP3 |
|
60.0 |
| O4' |
C1' |
H3 |
N9 |
119.3 |
123.0 |
| C2' |
C1' |
H3 |
N9 |
235.5 |
237.1 |
| H3 |
C1' |
N9 |
C8 |
196.8 |
142.2 |
| H3 |
C1' |
C2' |
O2' |
42.0 |
36.5 |
| H3 |
C1' |
C2' |
H4 |
163.5 |
160.1 |
| H4 |
C2' |
C1' |
N9 |
40.5 |
37.3 |
| C1' |
C2' |
H4 |
O2' |
238.2 |
236.4 |
| H4 |
C2' |
C1' |
H3 |
163.5 |
160.1 |
| H4 |
C2' |
O2' |
H5 |
103.6 |
297.8 |
| H5 |
O2' |
C2' |
H4 |
103.6 |
297.8 |
| H6 |
C3' |
C2' |
H4 |
323.3 |
338.6 |
| O4' |
C4' |
H7 |
C5' |
242.6 |
238.9 |
| H7 |
C4' |
C5' |
H8 |
190.6 |
66.0 |
| H7 |
C4' |
C5' |
H9 |
71.2 |
186.0 |
| H7 |
C4' |
C3' |
H6 |
253.7 |
236.2 |
| O5' |
C5' |
H8 |
H9 |
119.1 |
240.0 |
| H8 |
C5' |
C4' |
H7 |
190.6 |
66.0 |
| C4' |
C5' |
H8 |
H9 |
241.0 |
120.0 |
| O5' |
C5' |
H9 |
H8 |
241.0 |
120.0 |
| H9 |
C5' |
C4' |
H7 |
71.2 |
186.0 |
| C4' |
C5' |
H9 |
H8 |
119.1 |
240.0 |
| N9 |
C8 |
H10 |
N7 |
180.0 |
180.1 |
| H11 |
N6 |
C6 |
C5 |
180.7 |
359.9 |
| C6 |
N6 |
H11 |
H12 |
120.0 |
180.1 |
| H12 |
N6 |
C6 |
C5 |
300.7 |
180.0 |
| C6 |
N6 |
H12 |
H11 |
240.0 |
179.9 |
| N |
CA |
H14 |
CB |
125.0 |
120.0 |
| H14 |
CA |
CB |
H18 |
182.5 |
175.0 |
| H14 |
CA |
CB |
H19 |
300.7 |
295.0 |
| H15 |
N |
CA |
CB |
54.4 |
176.0 |
| H15 |
N |
CA |
H14 |
295.8 |
56.0 |
| H16 |
N |
CA |
CB |
174.4 |
299.9 |
| H16 |
N |
CA |
H14 |
55.7 |
180.0 |
| H18 |
CB |
CA |
H14 |
182.5 |
175.0 |
| CA |
CB |
H18 |
H19 |
117.1 |
120.1 |
| CG |
CB |
H18 |
H19 |
242.9 |
240.0 |
| H19 |
CB |
CA |
H14 |
300.7 |
295.0 |
| CA |
CB |
H19 |
H18 |
242.9 |
240.0 |
| CG |
CB |
H19 |
H18 |
117.1 |
119.9 |
| H21 |
CE1 |
CD1 |
H20 |
0.7 |
360.0 |
| H22 |
CZ |
CE1 |
H21 |
359.8 |
359.9 |
| H23 |
CE2 |
CD2 |
H24 |
0.4 |
359.4 |
| H23 |
CE2 |
CZ |
H22 |
359.7 |
0.4 |
| H24 |
CD2 |
CE2 |
H23 |
0.4 |
359.4 |
| OP2 |
P |
OP3 |
O5' |
|
120.0 |
| OP1 |
P |
OP3 |
O5' |
|
240.1 |
| OP3 |
P |
O5' |
C5' |
|
175.0 |