PDB Chemical Component UBI
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 UBI
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
P |
1.610 |
1.610 |
| OP1 |
P |
1.511 |
1.479 |
| P |
OP2 |
1.511 |
1.610 |
| P |
OP3 |
1.605 |
1.610 |
| C1' |
N1 |
1.461 |
1.465 |
| N1 |
C2 |
1.408 |
1.343 |
| N1 |
C6 |
1.331 |
1.359 |
| O2 |
C2 |
1.246 |
1.215 |
| C2 |
N3 |
1.351 |
1.344 |
| N3 |
C4 |
1.347 |
1.350 |
| N3 |
HN3 |
1.000 |
0.971 |
| C5 |
C4 |
1.490 |
1.471 |
| C4 |
O4 |
1.248 |
1.217 |
| C6 |
C5 |
1.385 |
1.381 |
| C5 |
C21 |
1.499 |
1.470 |
| C6 |
H6 |
1.080 |
1.080 |
| C2' |
C1' |
1.531 |
1.541 |
| O4' |
C1' |
1.425 |
1.437 |
| C1' |
H1' |
1.100 |
1.090 |
| C3' |
C2' |
1.515 |
1.547 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.091 |
| O22 |
C21 |
1.221 |
1.216 |
| C21 |
N23 |
1.332 |
1.349 |
| N23 |
C24 |
1.460 |
1.465 |
| N23 |
HN23 |
1.000 |
0.969 |
| C24 |
C25 |
1.530 |
1.531 |
| C24 |
H24 |
1.100 |
1.090 |
| C24 |
H24A |
1.101 |
1.090 |
| C26 |
C25 |
1.522 |
1.530 |
| C25 |
C27 |
1.515 |
1.530 |
| C25 |
H25 |
1.100 |
1.090 |
| C26 |
H26 |
1.100 |
1.090 |
| C26 |
H26A |
1.100 |
1.089 |
| C26 |
H26B |
1.100 |
1.091 |
| C27 |
H27 |
1.100 |
1.090 |
| C27 |
H27A |
1.100 |
1.091 |
| C27 |
H27B |
1.100 |
1.089 |
| O3' |
C3' |
1.427 |
1.429 |
| C3' |
C4' |
1.520 |
1.550 |
| C3' |
H3' |
1.100 |
1.091 |
| O3' |
HO3' |
0.950 |
0.967 |
| C5' |
C4' |
1.519 |
1.529 |
| C4' |
O4' |
1.425 |
1.446 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
O5' |
1.407 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for UBI
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP2 |
106.4 |
109.5 |
| O5' |
P |
OP3 |
98.5 |
109.5 |
| OP1 |
P |
OP2 |
121.5 |
109.5 |
| OP1 |
P |
OP3 |
108.8 |
109.5 |
| OP2 |
P |
OP3 |
108.8 |
109.4 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| C2 |
N1 |
C6 |
121.0 |
121.5 |
| N1 |
C2 |
N3 |
121.5 |
122.1 |
| N1 |
C6 |
C5 |
120.0 |
119.3 |
| N1 |
C6 |
H6 |
120.0 |
120.3 |
| O2 |
C2 |
N3 |
120.6 |
119.0 |
| C2 |
N3 |
C4 |
120.2 |
120.5 |
| C2 |
N3 |
HN3 |
119.9 |
119.7 |
| C4 |
N3 |
HN3 |
119.9 |
119.8 |
| N3 |
C4 |
O4 |
120.3 |
120.7 |
| C6 |
C5 |
C21 |
117.5 |
120.9 |
| C5 |
C21 |
N23 |
121.6 |
120.0 |
| C2' |
C1' |
H1' |
108.5 |
109.9 |
| O4' |
C1' |
H1' |
109.9 |
109.8 |
| C3' |
C2' |
H2' |
111.2 |
110.5 |
| C3' |
C2' |
H2'A |
111.1 |
110.6 |
| H2' |
C2' |
H2'A |
109.5 |
110.4 |
| O22 |
C21 |
N23 |
121.4 |
120.0 |
| C21 |
N23 |
C24 |
126.4 |
120.0 |
| C21 |
N23 |
HN23 |
116.8 |
120.0 |
| C24 |
N23 |
HN23 |
116.8 |
120.0 |
| N23 |
C24 |
C25 |
110.8 |
109.5 |
| N23 |
C24 |
H24 |
109.1 |
109.5 |
| N23 |
C24 |
H24A |
109.1 |
109.5 |
| C25 |
C24 |
H24 |
109.1 |
109.5 |
| C25 |
C24 |
H24A |
109.1 |
109.4 |
| C24 |
C25 |
C27 |
109.3 |
109.4 |
| C24 |
C25 |
H25 |
107.2 |
109.4 |
| H24 |
C24 |
H24A |
109.5 |
109.5 |
| C26 |
C25 |
C27 |
109.2 |
109.5 |
| C26 |
C25 |
H25 |
107.3 |
109.5 |
| C27 |
C25 |
H25 |
107.3 |
109.5 |
| C25 |
C27 |
H27 |
109.5 |
109.5 |
| C25 |
C27 |
H27A |
109.4 |
109.4 |
| C25 |
C27 |
H27B |
109.5 |
109.5 |
| H26 |
C26 |
H26A |
109.5 |
109.5 |
| H26 |
C26 |
H26B |
109.4 |
109.4 |
| H26A |
C26 |
H26B |
109.5 |
109.5 |
| H27 |
C27 |
H27A |
109.5 |
109.5 |
| H27 |
C27 |
H27B |
109.5 |
109.6 |
| H27A |
C27 |
H27B |
109.5 |
109.5 |
| O3' |
C3' |
C4' |
105.4 |
110.9 |
| O3' |
C3' |
H3' |
114.1 |
110.8 |
| C4' |
C3' |
H3' |
112.5 |
110.9 |
| C3' |
C4' |
O4' |
106.7 |
103.5 |
| C3' |
C4' |
H4' |
107.3 |
110.6 |
| C5' |
C4' |
H4' |
107.3 |
110.7 |
| O4' |
C4' |
H4' |
108.5 |
110.5 |
| O5' |
C5' |
H5' |
109.8 |
109.4 |
| O5' |
C5' |
H5'A |
109.8 |
109.4 |
| H5' |
C5' |
H5'A |
109.5 |
109.5 |
Torsion Angles for UBI
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
O5' |
OP2 |
226.3 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
113.7 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
247.4 |
240.1 |
| O5' |
P |
OP2 |
HOP2 |
232.6 |
60.0 |
| O5' |
P |
OP3 |
HOP3 |
115.1 |
180.1 |
| O5' |
P |
OP1 |
OP2 |
125.6 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
253.0 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
127.4 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
360.0 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
360.0 |
60.0 |
| O5' |
P |
OP2 |
OP3 |
105.2 |
119.9 |
| OP1 |
P |
OP2 |
OP3 |
232.6 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
225.7 |
300.0 |
| O5' |
P |
OP3 |
OP2 |
249.4 |
240.1 |
| OP1 |
P |
OP3 |
OP2 |
134.3 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
127.4 |
300.0 |
| C1' |
N1 |
C6 |
H6 |
0.1 |
0.2 |
| C2 |
N1 |
C6 |
C5 |
359.2 |
0.0 |
| C2 |
N1 |
C6 |
H6 |
179.1 |
180.0 |
| O2 |
C2 |
N1 |
N3 |
179.7 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
359.9 |
360.0 |
| N1 |
C2 |
N3 |
HN3 |
179.9 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
0.5 |
360.0 |
| N1 |
C6 |
C5 |
C21 |
180.8 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
180.2 |
179.9 |
| N1 |
C2 |
O2 |
N3 |
180.3 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
180.2 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
0.2 |
0.1 |
| N3 |
C2 |
N1 |
C6 |
0.5 |
360.0 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
O4 |
179.9 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
180.0 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.0 |
| HN3 |
N3 |
C4 |
O4 |
359.9 |
0.0 |
| N1 |
C6 |
C5 |
C4 |
0.8 |
360.0 |
| C5 |
C4 |
N3 |
HN3 |
180.0 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
359.9 |
0.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C21 |
N23 |
186.1 |
174.3 |
| O22 |
C21 |
C5 |
N23 |
181.0 |
180.0 |
| C5 |
C21 |
N23 |
C24 |
179.8 |
185.1 |
| C5 |
C21 |
N23 |
HN23 |
359.8 |
5.2 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
C21 |
0.8 |
0.0 |
| O4' |
C1' |
C2' |
H1' |
117.4 |
119.5 |
| C2' |
C1' |
O4' |
H1' |
243.6 |
240.5 |
| C3' |
C2' |
C1' |
H1' |
274.2 |
242.5 |
| H2' |
C2' |
C3' |
H2'A |
122.2 |
122.6 |
| H2' |
C2' |
C1' |
H1' |
33.2 |
1.2 |
| C3' |
C2' |
H2' |
H2'A |
236.8 |
237.3 |
| H2'A |
C2' |
C1' |
H1' |
155.3 |
123.6 |
| C3' |
C2' |
H2'A |
H2' |
123.2 |
122.7 |
| C5 |
C21 |
O22 |
N23 |
179.0 |
180.0 |
| O22 |
C21 |
N23 |
C24 |
358.7 |
5.1 |
| O22 |
C21 |
N23 |
HN23 |
178.7 |
185.1 |
| C24 |
N23 |
C21 |
HN23 |
180.0 |
179.9 |
| C21 |
N23 |
C24 |
C25 |
125.3 |
180.0 |
| C21 |
N23 |
C24 |
H24 |
245.5 |
300.0 |
| C21 |
N23 |
C24 |
H24A |
5.1 |
60.1 |
| C21 |
N23 |
C24 |
HN23 |
180.0 |
180.1 |
| C25 |
C24 |
N23 |
H24 |
239.8 |
240.0 |
| C25 |
C24 |
N23 |
H24A |
120.2 |
119.9 |
| N23 |
C24 |
C25 |
C27 |
243.1 |
295.0 |
| N23 |
C24 |
C25 |
H25 |
127.1 |
55.0 |
| H24 |
C24 |
N23 |
H24A |
240.4 |
239.9 |
| C21 |
N23 |
HN23 |
C24 |
180.0 |
179.9 |
| HN23 |
N23 |
C24 |
C25 |
305.3 |
359.9 |
| HN23 |
N23 |
C24 |
H24 |
65.5 |
119.9 |
| HN23 |
N23 |
C24 |
H24A |
185.1 |
240.0 |
| C25 |
C24 |
N23 |
HN23 |
305.3 |
359.9 |
| N23 |
C24 |
C25 |
H24 |
120.2 |
120.0 |
| N23 |
C24 |
C25 |
H24A |
239.8 |
240.0 |
| H24 |
C24 |
C25 |
H24A |
119.6 |
120.0 |
| C26 |
C25 |
C24 |
C27 |
124.1 |
240.0 |
| C26 |
C25 |
C24 |
H25 |
240.1 |
120.0 |
| C27 |
C25 |
C24 |
H25 |
116.0 |
240.0 |
| C24 |
C25 |
C27 |
H27 |
180.0 |
60.0 |
| C24 |
C25 |
C27 |
H27A |
300.0 |
180.0 |
| C24 |
C25 |
C27 |
H27B |
60.0 |
299.9 |
| H24 |
C24 |
N23 |
HN23 |
65.5 |
119.9 |
| N23 |
C24 |
H24 |
C25 |
238.7 |
240.0 |
| N23 |
C24 |
H24 |
H24A |
119.4 |
120.1 |
| C25 |
C24 |
H24 |
H24A |
240.6 |
240.0 |
| H24 |
C24 |
C25 |
C27 |
122.9 |
175.0 |
| H24 |
C24 |
C25 |
H25 |
6.9 |
295.0 |
| H24A |
C24 |
N23 |
HN23 |
185.1 |
240.0 |
| N23 |
C24 |
H24A |
C25 |
121.3 |
120.0 |
| N23 |
C24 |
H24A |
H24 |
240.6 |
239.9 |
| C25 |
C24 |
H24A |
H24 |
119.4 |
120.0 |
| H24A |
C24 |
C25 |
C27 |
3.3 |
55.0 |
| H24A |
C24 |
C25 |
H25 |
247.3 |
175.0 |
| C26 |
C25 |
C24 |
H24 |
247.0 |
55.0 |
| C26 |
C25 |
C24 |
H24A |
127.4 |
295.0 |
| C24 |
C25 |
C26 |
C27 |
235.9 |
120.0 |
| C24 |
C25 |
C26 |
H25 |
119.8 |
240.1 |
| C27 |
C25 |
C26 |
H25 |
244.0 |
120.1 |
| C26 |
C25 |
C27 |
H27 |
51.9 |
180.0 |
| C26 |
C25 |
C27 |
H27A |
171.9 |
300.0 |
| C26 |
C25 |
C27 |
H27B |
291.9 |
60.0 |
| C27 |
C25 |
C24 |
H24 |
122.9 |
175.0 |
| C27 |
C25 |
C24 |
H24A |
3.3 |
55.0 |
| C24 |
C25 |
C27 |
H25 |
244.1 |
119.9 |
| C26 |
C25 |
C27 |
H25 |
116.0 |
239.9 |
| H27 |
C27 |
C25 |
H27A |
240.0 |
240.0 |
| H27 |
C27 |
C25 |
H27B |
120.0 |
120.1 |
| H27A |
C27 |
C25 |
H27B |
240.0 |
240.1 |
| H25 |
C25 |
C24 |
H24 |
6.9 |
295.0 |
| H25 |
C25 |
C24 |
H24A |
247.3 |
175.0 |
| C24 |
C25 |
H25 |
C27 |
117.3 |
240.0 |
| C26 |
C25 |
H25 |
C27 |
242.8 |
120.1 |
| H25 |
C25 |
C27 |
H27 |
295.9 |
300.1 |
| H25 |
C25 |
C27 |
H27A |
55.9 |
60.1 |
| H25 |
C25 |
C27 |
H27B |
175.9 |
180.0 |
| H26 |
C26 |
C25 |
C27 |
304.1 |
300.0 |
| H26 |
C26 |
C25 |
H25 |
60.1 |
179.9 |
| H26A |
C26 |
H26 |
H26B |
120.0 |
120.0 |
| H26A |
C26 |
C25 |
C27 |
64.2 |
60.1 |
| H26A |
C26 |
C25 |
H25 |
180.2 |
300.0 |
| H26 |
C26 |
H26A |
H26B |
240.0 |
240.1 |
| H26B |
C26 |
C25 |
C27 |
184.2 |
180.1 |
| H26B |
C26 |
C25 |
H25 |
300.2 |
60.0 |
| H26 |
C26 |
H26B |
H26A |
120.0 |
120.0 |
| H27 |
C27 |
C25 |
H25 |
295.9 |
300.1 |
| C25 |
C27 |
H27 |
H27A |
120.0 |
119.9 |
| C25 |
C27 |
H27 |
H27B |
240.0 |
240.0 |
| H27A |
C27 |
H27 |
H27B |
120.0 |
120.0 |
| H27A |
C27 |
C25 |
H25 |
55.9 |
60.1 |
| C25 |
C27 |
H27A |
H27 |
240.0 |
240.0 |
| C25 |
C27 |
H27A |
H27B |
120.0 |
119.9 |
| H27 |
C27 |
H27A |
H27B |
240.0 |
239.9 |
| H27B |
C27 |
C25 |
H25 |
175.9 |
180.0 |
| C25 |
C27 |
H27B |
H27 |
120.0 |
120.0 |
| C25 |
C27 |
H27B |
H27A |
240.0 |
240.1 |
| H27 |
C27 |
H27B |
H27A |
120.0 |
120.1 |
| O3' |
C3' |
C2' |
H2' |
341.1 |
20.4 |
| O3' |
C3' |
C2' |
H2'A |
218.9 |
257.8 |
| C4' |
C3' |
O3' |
H3' |
236.1 |
236.4 |
| O3' |
C3' |
C4' |
O4' |
235.5 |
204.9 |
| O3' |
C3' |
C4' |
H4' |
351.6 |
323.2 |
| C4' |
C3' |
C2' |
H2' |
229.5 |
262.2 |
| C4' |
C3' |
C2' |
H2'A |
107.4 |
139.6 |
| O3' |
C3' |
C4' |
H3' |
124.9 |
123.5 |
| C5' |
C4' |
C3' |
H4' |
118.7 |
123.0 |
| O4' |
C4' |
C3' |
H4' |
243.9 |
241.6 |
| H3' |
C3' |
C2' |
H2' |
106.8 |
144.0 |
| H3' |
C3' |
C2' |
H2'A |
344.6 |
21.4 |
| O3' |
C3' |
H3' |
C4' |
240.0 |
236.4 |
| H3' |
C3' |
C4' |
O4' |
110.7 |
81.4 |
| H3' |
C3' |
C4' |
H4' |
226.8 |
199.7 |
| HO3' |
O3' |
C3' |
C4' |
291.3 |
174.3 |
| HO3' |
O3' |
C3' |
H3' |
55.2 |
297.8 |
| C5' |
C4' |
C3' |
H3' |
345.5 |
322.8 |
| C3' |
C4' |
C5' |
H4' |
241.3 |
237.0 |
| O4' |
C4' |
C5' |
H4' |
119.3 |
122.8 |
| C4' |
O4' |
C1' |
H1' |
75.9 |
93.2 |
| O4' |
C4' |
C3' |
H3' |
110.7 |
81.4 |
| C3' |
C4' |
O4' |
H4' |
115.3 |
118.4 |
| C5' |
C4' |
O4' |
H4' |
241.3 |
237.0 |
| H4' |
C4' |
C3' |
H3' |
226.8 |
199.7 |
| C3' |
C4' |
H4' |
O4' |
245.1 |
246.0 |
| C5' |
O5' |
P |
OP2 |
130.1 |
65.1 |
| C5' |
O5' |
P |
OP3 |
242.7 |
185.0 |
| O5' |
C5' |
C4' |
H4' |
183.8 |
308.0 |
| H5' |
C5' |
O5' |
H5'A |
120.4 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
303.7 |
67.9 |
| O5' |
C5' |
H5' |
H5'A |
239.5 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
64.0 |
188.0 |
| O5' |
C5' |
H5'A |
H5' |
120.5 |
120.0 |
| HOP2 |
OP2 |
P |
OP3 |
127.4 |
300.0 |