PDB Chemical Component UPE
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 UPE
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP1 |
P |
1.514 |
1.480 |
O5' |
P |
1.616 |
1.610 |
OP3 |
P |
1.584 |
1.610 |
P |
OP2 |
1.511 |
1.610 |
C1' |
N1 |
1.471 |
1.464 |
C2 |
N1 |
1.415 |
1.342 |
N1 |
C6 |
1.334 |
1.359 |
O2 |
C2 |
1.244 |
1.216 |
C2 |
N3 |
1.341 |
1.344 |
N3 |
C4 |
1.337 |
1.350 |
N3 |
HN3 |
1.000 |
0.970 |
C4 |
O4 |
1.248 |
1.217 |
C4 |
C5 |
1.489 |
1.471 |
C6 |
C5 |
1.392 |
1.381 |
C5 |
C21 |
1.505 |
1.470 |
C6 |
H6 |
1.080 |
1.080 |
C2' |
C1' |
1.522 |
1.545 |
C1' |
O4' |
1.427 |
1.444 |
C1' |
H1' |
1.100 |
1.090 |
C2' |
C3' |
1.512 |
1.545 |
C2' |
H2' |
1.100 |
1.091 |
C2' |
H2'A |
1.100 |
1.090 |
C21 |
O22 |
1.232 |
1.217 |
C21 |
N23 |
1.337 |
1.348 |
N23 |
C24 |
1.464 |
1.465 |
N23 |
HN23 |
1.000 |
0.971 |
C24 |
C25 |
1.518 |
1.530 |
C24 |
H24 |
1.100 |
1.090 |
C24 |
H24A |
1.100 |
1.090 |
C25 |
C26 |
1.506 |
1.507 |
C25 |
H25 |
1.100 |
1.090 |
C25 |
H25A |
1.100 |
1.090 |
C31 |
C26 |
1.388 |
1.382 |
C26 |
C27 |
1.405 |
1.383 |
C27 |
C28 |
1.394 |
1.382 |
C27 |
H27 |
1.080 |
1.080 |
C29 |
C28 |
1.394 |
1.382 |
C28 |
H28 |
1.080 |
1.080 |
C30 |
C29 |
1.403 |
1.382 |
C29 |
H29 |
1.080 |
1.080 |
O3' |
C3' |
1.429 |
1.430 |
C3' |
C4' |
1.518 |
1.544 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.966 |
C31 |
C30 |
1.395 |
1.383 |
C30 |
H30 |
1.080 |
1.080 |
C31 |
H31 |
1.079 |
1.080 |
C4' |
O4' |
1.439 |
1.444 |
C4' |
C5' |
1.530 |
1.530 |
C4' |
H4' |
1.100 |
1.089 |
C5' |
O5' |
1.427 |
1.428 |
C5' |
H5' |
1.100 |
1.090 |
C5' |
H5'A |
1.100 |
1.090 |
OP2 |
HOP2 |
0.950 |
0.967 |
OP3 |
HOP3 |
0.950 |
0.968 |
Bond Angles for UPE
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
118.1 |
109.5 |
O5' |
P |
OP2 |
109.6 |
109.5 |
P |
OP2 |
HOP2 |
109.5 |
114.0 |
C2 |
N1 |
C6 |
119.5 |
121.5 |
N1 |
C6 |
C5 |
120.8 |
119.4 |
N1 |
C6 |
H6 |
119.6 |
120.3 |
O2 |
C2 |
N3 |
118.1 |
118.9 |
C2 |
N3 |
C4 |
121.0 |
120.4 |
C2 |
N3 |
HN3 |
119.5 |
119.8 |
C4 |
N3 |
HN3 |
119.5 |
119.8 |
N3 |
C4 |
O4 |
119.3 |
120.7 |
N3 |
C4 |
C5 |
118.5 |
118.5 |
O4 |
C4 |
C5 |
122.1 |
120.7 |
C4 |
C5 |
C21 |
124.4 |
121.0 |
C6 |
C5 |
C21 |
117.5 |
121.0 |
C5 |
C21 |
O22 |
117.0 |
120.0 |
C5 |
C21 |
N23 |
122.4 |
120.0 |
C2' |
C1' |
O4' |
105.2 |
104.8 |
C2' |
C1' |
H1' |
108.4 |
110.5 |
O4' |
C1' |
H1' |
109.7 |
110.4 |
C1' |
O4' |
C4' |
110.1 |
105.3 |
C3' |
C2' |
H2' |
110.8 |
110.5 |
C3' |
C2' |
H2'A |
110.7 |
110.5 |
C2' |
C3' |
C4' |
105.6 |
104.1 |
C2' |
C3' |
H3' |
111.6 |
110.5 |
H2' |
C2' |
H2'A |
109.5 |
110.6 |
O22 |
C21 |
N23 |
120.5 |
120.0 |
C21 |
N23 |
C24 |
120.2 |
120.0 |
C21 |
N23 |
HN23 |
119.9 |
119.9 |
C24 |
N23 |
HN23 |
119.9 |
120.0 |
N23 |
C24 |
C25 |
108.4 |
109.5 |
N23 |
C24 |
H24 |
109.7 |
109.5 |
N23 |
C24 |
H24A |
109.7 |
109.5 |
C25 |
C24 |
H24 |
109.7 |
109.4 |
C25 |
C24 |
H24A |
109.7 |
109.5 |
C24 |
C25 |
C26 |
114.5 |
109.5 |
C24 |
C25 |
H25 |
108.2 |
109.4 |
C24 |
C25 |
H25A |
108.2 |
109.5 |
H24 |
C24 |
H24A |
109.5 |
109.5 |
C26 |
C25 |
H25 |
108.2 |
109.5 |
C26 |
C25 |
H25A |
108.2 |
109.5 |
C25 |
C26 |
C27 |
117.6 |
120.0 |
H25 |
C25 |
H25A |
109.5 |
109.5 |
C26 |
C27 |
C28 |
120.5 |
120.0 |
C26 |
C27 |
H27 |
119.7 |
120.0 |
C28 |
C27 |
H27 |
119.7 |
120.0 |
C27 |
C28 |
H28 |
120.6 |
120.0 |
C29 |
C28 |
H28 |
120.5 |
120.0 |
C30 |
C29 |
H29 |
119.9 |
120.0 |
O3' |
C3' |
C4' |
107.1 |
110.5 |
O3' |
C3' |
H3' |
112.9 |
110.5 |
C4' |
C3' |
H3' |
111.5 |
110.6 |
C3' |
C4' |
O4' |
106.8 |
104.8 |
C3' |
C4' |
C5' |
112.8 |
110.4 |
C3' |
C4' |
H4' |
107.8 |
110.4 |
C31 |
C30 |
H30 |
119.5 |
120.0 |
O4' |
C4' |
C5' |
112.7 |
110.3 |
O4' |
C4' |
H4' |
108.9 |
110.4 |
C5' |
C4' |
H4' |
107.7 |
110.4 |
C4' |
C5' |
O5' |
110.2 |
109.5 |
C4' |
C5' |
H5' |
109.3 |
109.4 |
C4' |
C5' |
H5'A |
109.3 |
109.4 |
O5' |
C5' |
H5' |
109.3 |
109.5 |
O5' |
C5' |
H5'A |
109.3 |
109.5 |
H5' |
C5' |
H5'A |
109.5 |
109.4 |
Torsion Angles for UPE
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O5' |
P |
OP1 |
OP2 |
126.3 |
120.0 |
OP1 |
P |
OP2 |
HOP2 |
0.0 |
180.0 |
OP1 |
P |
O5' |
OP2 |
229.0 |
240.0 |
O5' |
P |
OP2 |
HOP2 |
233.7 |
60.0 |
OP3 |
P |
OP2 |
HOP2 |
121.4 |
300.0 |
C1' |
N1 |
C6 |
H6 |
0.7 |
0.2 |
C2 |
N1 |
C6 |
C5 |
359.9 |
360.0 |
C2 |
N1 |
C6 |
H6 |
179.9 |
180.0 |
N1 |
C6 |
C5 |
C21 |
179.2 |
180.0 |
O2 |
C2 |
N1 |
C6 |
179.9 |
180.0 |
O2 |
C2 |
N3 |
C4 |
180.3 |
180.0 |
O2 |
C2 |
N3 |
HN3 |
0.3 |
360.0 |
N3 |
C2 |
N1 |
C6 |
0.2 |
0.0 |
C4 |
N3 |
C2 |
HN3 |
180.0 |
180.0 |
C2 |
N3 |
C4 |
O4 |
180.2 |
180.0 |
C2 |
N3 |
C4 |
C5 |
359.7 |
0.0 |
C2 |
N3 |
C4 |
HN3 |
180.0 |
180.0 |
O4 |
C4 |
N3 |
C5 |
180.5 |
180.0 |
N3 |
C4 |
C5 |
C21 |
181.0 |
180.0 |
C2 |
N3 |
HN3 |
C4 |
180.0 |
180.0 |
HN3 |
N3 |
C4 |
O4 |
0.2 |
0.0 |
HN3 |
N3 |
C4 |
C5 |
179.7 |
180.0 |
O4 |
C4 |
N3 |
HN3 |
0.2 |
0.0 |
N3 |
C4 |
O4 |
C5 |
179.5 |
180.0 |
O4 |
C4 |
C5 |
C21 |
0.5 |
360.0 |
N1 |
C6 |
C5 |
C4 |
359.8 |
360.0 |
C5 |
C4 |
N3 |
HN3 |
179.7 |
180.0 |
N3 |
C4 |
C5 |
O4 |
180.5 |
180.0 |
C6 |
C5 |
C4 |
C21 |
179.4 |
180.0 |
C4 |
C5 |
C21 |
O22 |
182.1 |
174.3 |
C4 |
C5 |
C21 |
N23 |
3.6 |
354.3 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
C21 |
180.6 |
180.0 |
C6 |
C5 |
C21 |
O22 |
2.7 |
354.3 |
C6 |
C5 |
C21 |
N23 |
184.2 |
174.3 |
O22 |
C21 |
C5 |
N23 |
178.5 |
180.0 |
C5 |
C21 |
N23 |
C24 |
179.2 |
185.1 |
C5 |
C21 |
N23 |
HN23 |
359.2 |
5.1 |
N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
H6 |
C6 |
C5 |
C21 |
359.2 |
0.0 |
O4' |
C1' |
C2' |
H1' |
117.3 |
118.9 |
C2' |
C1' |
O4' |
C4' |
333.0 |
319.5 |
C2' |
C1' |
O4' |
H1' |
243.5 |
241.1 |
C3' |
C4' |
O4' |
C1' |
14.7 |
40.6 |
C1' |
O4' |
C4' |
C5' |
139.1 |
159.4 |
C1' |
O4' |
C4' |
H4' |
258.6 |
281.7 |
C2' |
C1' |
H1' |
O4' |
114.4 |
115.4 |
H1' |
C1' |
O4' |
C4' |
89.5 |
78.4 |
C3' |
C2' |
C1' |
O4' |
28.1 |
24.0 |
C3' |
C2' |
C1' |
H1' |
270.7 |
265.1 |
H2' |
C2' |
C3' |
H2'A |
121.7 |
122.7 |
O3' |
C3' |
C2' |
C4' |
114.2 |
118.6 |
O3' |
C3' |
C2' |
H3' |
235.5 |
237.3 |
C4' |
C3' |
C2' |
H3' |
121.3 |
118.7 |
C2' |
C3' |
C4' |
O4' |
3.7 |
336.0 |
C2' |
C3' |
C4' |
C5' |
239.3 |
217.2 |
C2' |
C3' |
C4' |
H4' |
120.5 |
94.9 |
H2' |
C2' |
C1' |
O4' |
147.2 |
142.6 |
H2' |
C2' |
C1' |
H1' |
29.9 |
23.7 |
C3' |
C2' |
H2' |
H2'A |
237.6 |
237.3 |
H2' |
C2' |
C3' |
C4' |
221.7 |
241.4 |
H2' |
C2' |
C3' |
H3' |
100.4 |
122.7 |
H2'A |
C2' |
C1' |
O4' |
268.9 |
265.3 |
H2'A |
C2' |
C1' |
H1' |
151.5 |
146.4 |
C3' |
C2' |
H2'A |
H2' |
122.4 |
122.7 |
H2'A |
C2' |
C3' |
C4' |
100.0 |
118.7 |
H2'A |
C2' |
C3' |
H3' |
338.7 |
360.0 |
C5 |
C21 |
O22 |
N23 |
181.5 |
180.0 |
O22 |
C21 |
N23 |
C24 |
0.8 |
5.1 |
O22 |
C21 |
N23 |
HN23 |
180.8 |
185.1 |
C5 |
C21 |
N23 |
O22 |
178.4 |
180.0 |
C24 |
N23 |
C21 |
HN23 |
180.0 |
180.0 |
C21 |
N23 |
C24 |
C25 |
153.9 |
180.0 |
C21 |
N23 |
C24 |
H24 |
273.7 |
300.0 |
C21 |
N23 |
C24 |
H24A |
34.0 |
60.0 |
C21 |
N23 |
C24 |
HN23 |
180.0 |
180.0 |
C25 |
C24 |
N23 |
H24 |
240.2 |
240.1 |
C25 |
C24 |
N23 |
H24A |
119.9 |
120.0 |
N23 |
C24 |
C25 |
C26 |
280.1 |
180.0 |
N23 |
C24 |
C25 |
H25 |
40.8 |
300.0 |
N23 |
C24 |
C25 |
H25A |
159.4 |
60.0 |
H24 |
C24 |
N23 |
H24A |
239.7 |
240.0 |
C21 |
N23 |
HN23 |
C24 |
180.0 |
180.0 |
HN23 |
N23 |
C24 |
C25 |
333.9 |
0.0 |
HN23 |
N23 |
C24 |
H24 |
93.7 |
120.0 |
HN23 |
N23 |
C24 |
H24A |
214.0 |
240.0 |
C25 |
C24 |
N23 |
HN23 |
333.9 |
0.0 |
N23 |
C24 |
C25 |
H24 |
119.8 |
120.0 |
N23 |
C24 |
C25 |
H24A |
240.2 |
240.0 |
H24 |
C24 |
C25 |
H24A |
120.3 |
120.0 |
C26 |
C25 |
C24 |
H25 |
239.3 |
240.0 |
C26 |
C25 |
C24 |
H25A |
120.7 |
120.0 |
C24 |
C25 |
C26 |
C27 |
166.6 |
89.9 |
H25 |
C25 |
C24 |
H25A |
241.4 |
240.0 |
H24 |
C24 |
N23 |
HN23 |
93.7 |
120.0 |
N23 |
C24 |
H24 |
C25 |
240.9 |
240.0 |
N23 |
C24 |
H24 |
H24A |
120.5 |
120.0 |
C25 |
C24 |
H24 |
H24A |
239.5 |
240.0 |
H24 |
C24 |
C25 |
C26 |
160.3 |
60.0 |
H24 |
C24 |
C25 |
H25 |
281.0 |
180.0 |
H24 |
C24 |
C25 |
H25A |
39.6 |
300.0 |
H24A |
C24 |
N23 |
HN23 |
214.0 |
240.0 |
N23 |
C24 |
H24A |
C25 |
119.1 |
120.0 |
N23 |
C24 |
H24A |
H24 |
239.6 |
240.0 |
C25 |
C24 |
H24A |
H24 |
120.5 |
120.0 |
H24A |
C24 |
C25 |
C26 |
39.9 |
300.0 |
H24A |
C24 |
C25 |
H25 |
160.6 |
60.0 |
H24A |
C24 |
C25 |
H25A |
279.2 |
180.0 |
C26 |
C25 |
C24 |
H24 |
160.3 |
60.0 |
C26 |
C25 |
C24 |
H24A |
39.9 |
300.0 |
C24 |
C25 |
C26 |
H25 |
120.7 |
120.0 |
C24 |
C25 |
C26 |
H25A |
239.3 |
240.0 |
H25 |
C25 |
C26 |
H25A |
118.6 |
120.0 |
C25 |
C26 |
C27 |
C28 |
180.7 |
180.0 |
C25 |
C26 |
C27 |
H27 |
0.7 |
0.0 |
H25 |
C25 |
C24 |
H24 |
281.0 |
180.0 |
H25 |
C25 |
C24 |
H24A |
160.6 |
60.0 |
C24 |
C25 |
H25 |
C26 |
235.5 |
240.0 |
C24 |
C25 |
H25 |
H25A |
117.7 |
120.0 |
C26 |
C25 |
H25 |
H25A |
242.3 |
240.0 |
H25 |
C25 |
C26 |
C27 |
45.9 |
330.0 |
H25A |
C25 |
C24 |
H24 |
39.6 |
300.0 |
H25A |
C25 |
C24 |
H24A |
279.2 |
180.0 |
C24 |
C25 |
H25A |
C26 |
124.5 |
120.0 |
C24 |
C25 |
H25A |
H25 |
242.3 |
240.0 |
C26 |
C25 |
H25A |
H25 |
117.7 |
120.0 |
H25A |
C25 |
C26 |
C27 |
287.3 |
210.0 |
C31 |
C26 |
C25 |
H25 |
226.4 |
149.8 |
C31 |
C26 |
C25 |
H25A |
107.9 |
29.7 |
C31 |
C26 |
C27 |
H27 |
180.1 |
180.3 |
C27 |
C26 |
C25 |
H25 |
45.9 |
330.0 |
C27 |
C26 |
C25 |
H25A |
287.3 |
210.0 |
C28 |
C27 |
C26 |
H27 |
180.0 |
180.0 |
C26 |
C27 |
C28 |
H28 |
179.7 |
180.0 |
C26 |
C27 |
C28 |
H27 |
180.0 |
180.0 |
C29 |
C28 |
C27 |
H28 |
180.0 |
180.0 |
C26 |
C27 |
H27 |
C28 |
180.0 |
180.0 |
H27 |
C27 |
C28 |
H28 |
359.7 |
0.0 |
C29 |
C28 |
C27 |
H27 |
179.7 |
180.0 |
C27 |
C28 |
C29 |
H28 |
180.0 |
180.0 |
H28 |
C28 |
C27 |
H27 |
359.7 |
0.0 |
C30 |
C29 |
C28 |
H28 |
180.7 |
180.0 |
H29 |
C29 |
C28 |
H28 |
0.7 |
359.9 |
O3' |
C3' |
C2' |
H2' |
335.9 |
0.1 |
O3' |
C3' |
C2' |
H2'A |
214.2 |
237.3 |
C2' |
C3' |
O3' |
C4' |
246.8 |
245.4 |
C2' |
C3' |
O3' |
H3' |
123.7 |
122.7 |
C4' |
C3' |
O3' |
H3' |
236.9 |
237.3 |
O3' |
C3' |
C4' |
O4' |
249.0 |
217.3 |
O3' |
C3' |
C4' |
C5' |
124.6 |
98.6 |
O3' |
C3' |
C4' |
H4' |
5.8 |
336.2 |
C1' |
O4' |
C4' |
C3' |
14.7 |
40.6 |
C4' |
C3' |
C2' |
H2' |
221.7 |
241.4 |
C4' |
C3' |
C2' |
H2'A |
100.0 |
118.7 |
C2' |
C3' |
C4' |
H3' |
238.6 |
241.3 |
O3' |
C3' |
C4' |
H3' |
123.9 |
122.7 |
O4' |
C4' |
C3' |
C5' |
124.4 |
118.8 |
O4' |
C4' |
C3' |
H4' |
243.2 |
241.1 |
C5' |
C4' |
C3' |
H4' |
118.8 |
122.3 |
C3' |
C4' |
C5' |
O5' |
158.7 |
185.0 |
C3' |
C4' |
C5' |
H5' |
278.8 |
305.0 |
C3' |
C4' |
C5' |
H5'A |
38.5 |
64.9 |
H3' |
C3' |
C2' |
H2' |
100.4 |
122.7 |
H3' |
C3' |
C2' |
H2'A |
338.7 |
360.0 |
C2' |
C3' |
H3' |
C4' |
117.8 |
114.7 |
O3' |
C3' |
H3' |
C4' |
239.4 |
237.3 |
H3' |
C3' |
C4' |
O4' |
125.0 |
94.7 |
H3' |
C3' |
C4' |
C5' |
0.7 |
335.9 |
H3' |
C3' |
C4' |
H4' |
241.9 |
213.5 |
HO3' |
O3' |
C3' |
C4' |
293.2 |
176.1 |
HO3' |
O3' |
C3' |
H3' |
56.2 |
298.8 |
C31 |
C30 |
C29 |
H29 |
179.0 |
179.8 |
H30 |
C30 |
C29 |
H29 |
359.0 |
360.0 |
H31 |
C31 |
C30 |
H30 |
0.8 |
0.1 |
C4' |
O4' |
C1' |
H1' |
89.5 |
78.4 |
O4' |
C4' |
C3' |
H3' |
125.0 |
94.7 |
C3' |
C4' |
O4' |
C5' |
235.6 |
241.2 |
C3' |
C4' |
O4' |
H4' |
116.2 |
118.9 |
C5' |
C4' |
O4' |
H4' |
240.5 |
237.7 |
O4' |
C4' |
C5' |
O5' |
37.6 |
69.6 |
O4' |
C4' |
C5' |
H5' |
157.7 |
189.7 |
O4' |
C4' |
C5' |
H5'A |
277.5 |
309.6 |
C5' |
C4' |
C3' |
H3' |
0.7 |
335.9 |
C3' |
C4' |
C5' |
O4' |
121.0 |
115.3 |
C3' |
C4' |
C5' |
H4' |
241.1 |
237.7 |
O4' |
C4' |
C5' |
H4' |
120.1 |
122.3 |
O5' |
C5' |
C4' |
H5' |
239.9 |
240.0 |
O5' |
C5' |
C4' |
H5'A |
120.1 |
120.0 |
H5' |
C5' |
C4' |
H5'A |
240.2 |
240.1 |
H4' |
C4' |
C3' |
H3' |
241.9 |
213.5 |
C3' |
C4' |
H4' |
O4' |
244.5 |
244.6 |
C3' |
C4' |
H4' |
C5' |
122.0 |
122.3 |
O4' |
C4' |
H4' |
C5' |
237.5 |
237.7 |
H4' |
C4' |
C5' |
O5' |
277.5 |
307.3 |
H4' |
C4' |
C5' |
H5' |
37.6 |
67.4 |
H4' |
C4' |
C5' |
H5'A |
157.4 |
187.3 |
C5' |
O5' |
P |
OP2 |
134.8 |
65.0 |
O5' |
C5' |
C4' |
H4' |
277.5 |
307.3 |
C4' |
C5' |
O5' |
H5' |
120.1 |
120.0 |
C4' |
C5' |
O5' |
H5'A |
239.9 |
240.0 |
H5' |
C5' |
O5' |
H5'A |
119.8 |
120.0 |
H5' |
C5' |
C4' |
H4' |
37.6 |
67.4 |
C4' |
C5' |
H5' |
O5' |
239.3 |
239.9 |
C4' |
C5' |
H5' |
H5'A |
119.7 |
119.9 |
O5' |
C5' |
H5' |
H5'A |
240.3 |
240.0 |
H5'A |
C5' |
C4' |
H4' |
157.4 |
187.3 |
C4' |
C5' |
H5'A |
O5' |
120.7 |
120.1 |
C4' |
C5' |
H5'A |
H5' |
240.4 |
240.1 |
O5' |
C5' |
H5'A |
H5' |
119.7 |
120.0 |