PDB Chemical Component UPV
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 UPV
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP3 |
1.480 |
1.611 |
| N1 |
C6 |
1.365 |
1.368 |
| N1 |
C1' |
1.476 |
1.465 |
| C2 |
N1 |
1.383 |
1.346 |
| O2 |
C2 |
1.230 |
1.215 |
| N3 |
C2 |
1.388 |
1.346 |
| N3 |
C4 |
1.387 |
1.349 |
| C4 |
C5 |
1.445 |
1.415 |
| O4 |
C4 |
1.228 |
1.218 |
| C5 |
H5 |
1.080 |
1.080 |
| C5 |
C6 |
1.350 |
1.350 |
| C6 |
H6 |
1.080 |
1.080 |
| CA |
HAA |
1.100 |
1.091 |
| CA |
O2' |
1.531 |
1.429 |
| CB |
OB1 |
1.319 |
1.342 |
| CB |
OB2 |
1.229 |
1.208 |
| CG |
CB |
1.531 |
1.507 |
| C1' |
O4' |
1.429 |
1.444 |
| C1' |
C2' |
1.525 |
1.545 |
| C2' |
O2' |
1.430 |
1.429 |
| C2' |
C3' |
1.525 |
1.545 |
| C3' |
O3' |
1.428 |
1.429 |
| O3' |
HO3' |
0.950 |
0.968 |
| C4' |
C3' |
1.525 |
1.545 |
| C4' |
C5' |
1.525 |
1.530 |
| C4' |
H4' |
1.100 |
1.091 |
| O4' |
C4' |
1.430 |
1.443 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
P |
1.611 |
1.610 |
| O5' |
C5' |
1.430 |
1.429 |
| OB1 |
CA |
1.530 |
1.452 |
| CD1 |
CG |
1.529 |
1.530 |
| CD1 |
HD1B |
1.100 |
1.090 |
| CD1 |
HD1A |
1.099 |
1.090 |
| CD2 |
CG |
1.529 |
1.531 |
| CD2 |
HD2B |
1.100 |
1.090 |
| CD2 |
HD2 |
1.100 |
1.089 |
| CD3 |
CG |
1.530 |
1.530 |
| CD3 |
HD3 |
1.101 |
1.090 |
| CD3 |
HD3B |
1.100 |
1.090 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| OP2 |
P |
1.479 |
1.609 |
| OP2 |
HOP2 |
0.949 |
0.967 |
| HN3 |
N3 |
1.000 |
0.970 |
| H5' |
C5' |
1.100 |
1.089 |
| H1' |
C1' |
1.100 |
1.091 |
| HD1 |
CD1 |
1.100 |
1.090 |
| H2' |
C2' |
1.100 |
1.091 |
| HD2A |
CD2 |
1.100 |
1.090 |
| H3' |
C3' |
1.100 |
1.090 |
| HD3A |
CD3 |
1.100 |
1.091 |
| HA |
CA |
1.100 |
1.090 |
| P |
OP1 |
1.470 |
1.480 |
Bond Angles for UPV
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP3 |
108.4 |
109.5 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| OP3 |
P |
OP1 |
73.9 |
109.5 |
| C6 |
N1 |
C1' |
121.0 |
119.7 |
| C2 |
N1 |
C6 |
121.5 |
120.6 |
| N1 |
C6 |
C5 |
121.7 |
119.7 |
| N1 |
C6 |
H6 |
119.2 |
120.1 |
| C2 |
N1 |
C1' |
117.5 |
119.6 |
| N1 |
C1' |
O4' |
111.0 |
110.4 |
| N1 |
C1' |
C2' |
110.5 |
110.4 |
| N3 |
C4 |
C5 |
113.8 |
119.4 |
| O4 |
C4 |
C5 |
125.5 |
120.3 |
| C4 |
C5 |
H5 |
119.5 |
120.4 |
| C4 |
C5 |
C6 |
121.0 |
119.1 |
| C6 |
C5 |
H5 |
119.5 |
120.4 |
| C5 |
C6 |
H6 |
119.1 |
120.2 |
| O2' |
CA |
HAA |
109.2 |
109.5 |
| OB1 |
CA |
HAA |
109.3 |
109.5 |
| HA |
CA |
HAA |
109.5 |
109.5 |
| CA |
O2' |
C2' |
111.3 |
114.1 |
| OB1 |
CB |
OB2 |
119.9 |
120.0 |
| CG |
CB |
OB1 |
120.2 |
120.0 |
| CG |
CB |
OB2 |
119.9 |
120.0 |
| C2' |
C1' |
O4' |
107.9 |
104.8 |
| C1' |
O4' |
C4' |
107.8 |
105.3 |
| C1' |
C2' |
O2' |
111.2 |
110.5 |
| C1' |
C2' |
C3' |
100.8 |
104.1 |
| O2' |
C2' |
C3' |
112.0 |
110.5 |
| C2' |
C3' |
O3' |
112.8 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| C5' |
C4' |
H4' |
108.5 |
110.3 |
| O4' |
C4' |
C5' |
112.0 |
110.4 |
| C4' |
C5' |
H5'A |
108.8 |
109.4 |
| O4' |
C4' |
H4' |
109.8 |
110.4 |
| O5' |
C5' |
H5'A |
108.8 |
109.5 |
| H5' |
C5' |
H5'A |
109.5 |
109.6 |
| O5' |
P |
OP1 |
99.1 |
109.5 |
| HD1A |
CD1 |
HD1B |
109.5 |
109.5 |
| HD1 |
CD1 |
HD1B |
109.5 |
109.5 |
| HD1 |
CD1 |
HD1A |
109.5 |
109.5 |
| HD2 |
CD2 |
HD2B |
109.5 |
109.5 |
| HD2A |
CD2 |
HD2B |
109.5 |
109.5 |
| HD3 |
CD3 |
HD3B |
109.4 |
109.5 |
| HD3A |
CD3 |
HD3B |
109.5 |
109.5 |
| OP2 |
P |
OP1 |
142.2 |
109.5 |
Torsion Angles for UPV
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP3 |
OP1 |
265.6 |
240.0 |
| OP2 |
P |
OP3 |
OP1 |
141.4 |
120.0 |
| C2 |
N1 |
C6 |
C1' |
179.9 |
179.8 |
| C6 |
N1 |
C1' |
O4' |
20.7 |
233.6 |
| C6 |
N1 |
C1' |
C2' |
261.1 |
118.2 |
| C4 |
C5 |
C6 |
N1 |
359.3 |
360.0 |
| N1 |
C6 |
C5 |
H5 |
179.3 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.3 |
| C2 |
N1 |
C1' |
C6 |
180.1 |
180.2 |
| C1' |
N1 |
C6 |
C5 |
180.7 |
180.3 |
| C1' |
N1 |
C6 |
H6 |
0.7 |
360.0 |
| C2' |
C1' |
N1 |
O4' |
240.3 |
244.6 |
| N1 |
C1' |
O4' |
C4' |
248.4 |
200.7 |
| N1 |
C1' |
C2' |
O2' |
209.7 |
261.5 |
| N1 |
C1' |
C2' |
C3' |
90.8 |
142.8 |
| C6 |
N1 |
C2 |
C1' |
180.1 |
180.2 |
| C2 |
N1 |
C6 |
C5 |
0.6 |
0.1 |
| C2 |
N1 |
C6 |
H6 |
180.6 |
179.7 |
| C2 |
N1 |
C1' |
O4' |
200.8 |
53.8 |
| C2 |
N1 |
C1' |
C2' |
81.1 |
298.4 |
| O2 |
C2 |
N1 |
C6 |
179.4 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
359.3 |
359.8 |
| N3 |
C2 |
N1 |
C6 |
359.9 |
359.9 |
| N3 |
C2 |
N1 |
C1' |
179.8 |
179.7 |
| O4 |
C4 |
N3 |
C5 |
180.0 |
180.0 |
| N3 |
C4 |
C5 |
H5 |
180.3 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.3 |
360.0 |
| N1 |
C6 |
C5 |
C4 |
359.3 |
360.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
179.3 |
180.3 |
| N3 |
C4 |
O4 |
C5 |
180.0 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
0.3 |
0.0 |
| O4 |
C4 |
C5 |
C6 |
180.3 |
180.0 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
359.3 |
0.3 |
| C5 |
C6 |
N1 |
C1' |
180.7 |
180.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.7 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| H6 |
C6 |
N1 |
C1' |
0.7 |
360.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.3 |
| H6 |
C6 |
C5 |
H5 |
359.3 |
0.3 |
| HAA |
CA |
O2' |
C2' |
19.7 |
314.1 |
| OB1 |
CA |
O2' |
HAA |
239.9 |
120.0 |
| HA |
CA |
O2' |
HAA |
119.8 |
240.0 |
| C1' |
C2' |
O2' |
CA |
73.6 |
140.1 |
| CA |
O2' |
C2' |
C3' |
185.6 |
254.8 |
| CB |
OB1 |
CA |
HAA |
84.3 |
195.5 |
| CG |
CB |
OB1 |
OB2 |
180.1 |
180.0 |
| CG |
CB |
OB2 |
OB1 |
179.9 |
180.0 |
| OB1 |
CB |
CG |
OB2 |
179.9 |
180.0 |
| N1 |
C1' |
O4' |
C2' |
238.8 |
241.1 |
| O4' |
C1' |
C2' |
O2' |
88.2 |
142.6 |
| O4' |
C1' |
C2' |
C3' |
329.2 |
23.9 |
| C1' |
O4' |
C4' |
C5' |
137.6 |
159.3 |
| C1' |
O4' |
C4' |
H4' |
258.3 |
281.6 |
| N1 |
C1' |
C2' |
O4' |
121.6 |
118.9 |
| CA |
O2' |
C2' |
C1' |
73.6 |
140.1 |
| C2' |
C1' |
O4' |
C4' |
9.6 |
319.5 |
| O2' |
C2' |
C1' |
C3' |
118.9 |
118.7 |
| C1' |
C2' |
C3' |
O3' |
157.1 |
118.6 |
| C2' |
O2' |
CA |
HAA |
19.7 |
314.1 |
| O2' |
C2' |
C1' |
O4' |
88.2 |
142.6 |
| C1' |
C2' |
O2' |
C3' |
248.0 |
245.3 |
| O2' |
C2' |
C3' |
O3' |
38.7 |
359.9 |
| C3' |
C2' |
C1' |
O4' |
329.2 |
23.9 |
| C1' |
C2' |
C3' |
O2' |
118.4 |
118.7 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
181.9 |
| C1' |
O4' |
C4' |
C3' |
16.0 |
40.5 |
| C4' |
C3' |
O3' |
HO3' |
292.5 |
296.4 |
| O4' |
C4' |
C5' |
H4' |
121.4 |
122.4 |
| O5' |
C5' |
C4' |
H5'A |
239.6 |
120.0 |
| H5' |
C5' |
C4' |
H5'A |
119.2 |
239.9 |
| O4' |
C4' |
H4' |
C5' |
237.2 |
237.6 |
| H4' |
C4' |
C5' |
H5'A |
297.7 |
187.3 |
| C5' |
C4' |
O4' |
H4' |
239.3 |
237.7 |
| O4' |
C4' |
C5' |
H5'A |
59.1 |
309.7 |
| H5'A |
C5' |
C4' |
H4' |
297.7 |
187.3 |
| O5' |
P |
OP3 |
HOP3 |
265.6 |
180.0 |
| OP3 |
P |
O5' |
OP1 |
75.9 |
120.0 |
| OP2 |
P |
O5' |
OP1 |
206.7 |
240.0 |
| C5' |
O5' |
P |
OP3 |
47.5 |
175.0 |
| O5' |
C5' |
C4' |
H4' |
177.3 |
307.2 |
| C4' |
C5' |
O5' |
H5'A |
120.4 |
240.1 |
| H5' |
C5' |
O5' |
H5'A |
240.8 |
120.1 |
| C5' |
O5' |
P |
OP1 |
331.5 |
55.0 |
| O2' |
CA |
OB1 |
HAA |
120.1 |
240.0 |
| HA |
CA |
OB1 |
HAA |
240.2 |
120.0 |
| HD1 |
CD1 |
HD1B |
HD1A |
240.0 |
120.0 |
| HD1 |
CD1 |
HD1A |
HD1B |
120.0 |
240.0 |
| HD2A |
CD2 |
HD2 |
HD2B |
120.0 |
120.0 |
| HD3A |
CD3 |
HD3 |
HD3B |
240.1 |
120.0 |
| HOP3 |
OP3 |
P |
OP1 |
0.0 |
300.0 |
| OP2 |
P |
OP3 |
HOP3 |
141.4 |
60.0 |
| OP3 |
P |
OP2 |
OP1 |
258.1 |
240.0 |
| O5' |
P |
OP2 |
OP1 |
133.7 |
120.0 |
| HOP2 |
OP2 |
P |
OP1 |
360.0 |
180.0 |
| H5' |
C5' |
C4' |
H4' |
56.9 |
67.2 |
| C4' |
C5' |
H5' |
H5'A |
241.2 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
118.8 |
240.0 |
| HD1A |
CD1 |
HD1 |
HD1B |
240.0 |
120.0 |
| HD2 |
CD2 |
HD2A |
HD2B |
240.0 |
239.9 |
| H3' |
C3' |
O3' |
HO3' |
55.8 |
59.2 |
| HD3 |
CD3 |
HD3A |
HD3B |
119.9 |
240.0 |
| O2' |
CA |
HA |
HAA |
240.4 |
120.0 |
| OB1 |
CA |
HA |
HAA |
119.6 |
240.0 |
| O5' |
P |
OP1 |
OP3 |
106.6 |
120.0 |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
300.0 |