PDB Chemical Component UPS
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 UPS
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP3 |
1.599 |
1.610 |
| S1P |
P |
1.483 |
1.864 |
| P |
OP2 |
1.478 |
1.610 |
| P |
O5' |
1.601 |
1.611 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| C5' |
O5' |
1.412 |
1.429 |
| C5' |
C4' |
1.505 |
1.530 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| C4' |
C3' |
1.529 |
1.544 |
| C4' |
O4' |
1.442 |
1.444 |
| C4' |
H4' |
1.100 |
1.091 |
| O4' |
C1' |
1.407 |
1.444 |
| C2' |
C1' |
1.529 |
1.545 |
| C1' |
N1 |
1.529 |
1.465 |
| C1' |
H1' |
1.100 |
1.090 |
| N1 |
C6 |
1.393 |
1.368 |
| N1 |
C2 |
1.399 |
1.345 |
| O2 |
C2 |
1.222 |
1.216 |
| C2 |
N3 |
1.384 |
1.346 |
| N3 |
C4 |
1.394 |
1.348 |
| C5 |
C4 |
1.452 |
1.416 |
| C4 |
O4 |
1.231 |
1.217 |
| C6 |
C5 |
1.346 |
1.350 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.081 |
1.081 |
| C3' |
C2' |
1.536 |
1.545 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| O3' |
C3' |
1.460 |
1.429 |
| C3' |
H3' |
1.100 |
1.091 |
| O3' |
HO3' |
0.950 |
0.967 |
| N3 |
HN3 |
0.999 |
0.970 |
Bond Angles for UPS
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| S1P |
P |
OP2 |
118.7 |
109.4 |
| S1P |
P |
O5' |
110.2 |
109.4 |
| OP2 |
P |
O5' |
108.2 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| C4' |
C5' |
H5' |
109.4 |
109.5 |
| C4' |
C5' |
H5'A |
109.3 |
109.5 |
| C5' |
C4' |
C3' |
115.2 |
110.4 |
| C5' |
C4' |
O4' |
107.8 |
110.4 |
| C5' |
C4' |
H4' |
105.9 |
110.3 |
| H5' |
C5' |
H5'A |
109.7 |
109.5 |
| O4' |
C4' |
C3' |
106.7 |
104.8 |
| C3' |
C4' |
H4' |
107.1 |
110.4 |
| C4' |
C3' |
C2' |
102.9 |
104.1 |
| C4' |
C3' |
H3' |
115.7 |
110.5 |
| O4' |
C4' |
H4' |
114.5 |
110.4 |
| C4' |
O4' |
C1' |
106.3 |
105.3 |
| O4' |
C1' |
N1 |
109.7 |
110.4 |
| O4' |
C1' |
H1' |
116.1 |
110.4 |
| C2' |
C1' |
H1' |
107.7 |
110.5 |
| N1 |
C1' |
H1' |
101.9 |
110.3 |
| C1' |
N1 |
C6 |
120.2 |
119.7 |
| C1' |
N1 |
C2 |
119.3 |
119.7 |
| C2 |
N1 |
C6 |
120.5 |
120.6 |
| N1 |
C6 |
C5 |
123.1 |
119.7 |
| N1 |
C6 |
H6 |
118.5 |
120.1 |
| N1 |
C2 |
N3 |
115.7 |
121.0 |
| O2 |
C2 |
N3 |
120.6 |
119.5 |
| C2 |
N3 |
C4 |
126.3 |
120.3 |
| C2 |
N3 |
HN3 |
116.9 |
119.9 |
| N3 |
C4 |
O4 |
119.3 |
120.3 |
| C4 |
N3 |
HN3 |
116.8 |
119.9 |
| C6 |
C5 |
H5 |
120.4 |
120.5 |
| C3' |
C2' |
H2' |
111.1 |
110.5 |
| C3' |
C2' |
H2'A |
112.0 |
110.7 |
| H2' |
C2' |
H2'A |
105.9 |
110.4 |
| O3' |
C3' |
H3' |
103.8 |
110.6 |
Torsion Angles for UPS
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| S1P |
P |
OP3 |
HOP3 |
177.4 |
180.0 |
| OP2 |
P |
S1P |
O5' |
234.5 |
120.0 |
| S1P |
P |
OP2 |
HOP2 |
17.6 |
60.1 |
| OP2 |
P |
OP3 |
HOP3 |
47.9 |
300.0 |
| S1P |
P |
OP2 |
O5' |
126.5 |
240.0 |
| O5' |
P |
OP3 |
HOP3 |
293.4 |
60.0 |
| S1P |
P |
O5' |
OP2 |
228.7 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
251.2 |
180.0 |
| HOP2 |
OP2 |
P |
O5' |
251.2 |
180.0 |
| H5' |
C5' |
C4' |
H5'A |
120.1 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
241.0 |
244.6 |
| C3' |
C4' |
C5' |
H4' |
241.9 |
237.7 |
| C5' |
C4' |
C3' |
C2' |
226.0 |
217.2 |
| C5' |
C4' |
C3' |
H3' |
346.3 |
335.8 |
| O4' |
C4' |
C5' |
H4' |
123.0 |
122.3 |
| C5' |
C4' |
O4' |
C1' |
159.0 |
159.4 |
| C4' |
C5' |
H5' |
H5'A |
240.1 |
240.0 |
| H5' |
C5' |
C4' |
C3' |
315.7 |
65.0 |
| H5' |
C5' |
C4' |
O4' |
196.7 |
309.6 |
| H5' |
C5' |
C4' |
H4' |
73.8 |
187.3 |
| C4' |
C5' |
H5'A |
H5' |
119.9 |
120.0 |
| H5'A |
C5' |
C4' |
C3' |
195.6 |
305.0 |
| H5'A |
C5' |
C4' |
O4' |
76.6 |
189.6 |
| H5'A |
C5' |
C4' |
H4' |
313.7 |
67.3 |
| C3' |
C4' |
C5' |
H5' |
315.7 |
65.0 |
| C3' |
C4' |
C5' |
H5'A |
195.6 |
305.0 |
| C5' |
C4' |
C3' |
O4' |
240.4 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
117.4 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
237.0 |
241.1 |
| C3' |
C4' |
O4' |
C1' |
34.8 |
40.5 |
| C4' |
C3' |
C2' |
H2' |
231.1 |
241.4 |
| C4' |
C3' |
C2' |
H2'A |
112.9 |
118.7 |
| O3' |
C3' |
C4' |
H3' |
116.8 |
122.7 |
| O4' |
C4' |
C5' |
H5' |
196.7 |
309.6 |
| O4' |
C4' |
C5' |
H5'A |
76.6 |
189.6 |
| C5' |
C4' |
O4' |
C3' |
124.2 |
118.9 |
| C5' |
C4' |
O4' |
H4' |
242.5 |
237.7 |
| C3' |
C4' |
O4' |
H4' |
118.2 |
118.9 |
| O4' |
C4' |
C3' |
C2' |
345.6 |
336.1 |
| O4' |
C4' |
C3' |
H3' |
105.9 |
94.7 |
| C4' |
O4' |
C1' |
N1 |
193.0 |
200.7 |
| C4' |
O4' |
C1' |
H1' |
78.2 |
78.4 |
| H4' |
C4' |
C5' |
H5' |
73.8 |
187.3 |
| H4' |
C4' |
C5' |
H5'A |
313.7 |
67.3 |
| C5' |
C4' |
H4' |
C3' |
236.6 |
237.7 |
| C5' |
C4' |
H4' |
O4' |
118.6 |
122.3 |
| O4' |
C4' |
H4' |
C3' |
118.0 |
115.4 |
| H4' |
C4' |
C3' |
C2' |
108.6 |
94.9 |
| H4' |
C4' |
C3' |
H3' |
228.9 |
213.6 |
| H4' |
C4' |
O4' |
C1' |
276.5 |
281.6 |
| C1' |
O4' |
C4' |
C3' |
34.8 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
276.5 |
281.6 |
| C2' |
C1' |
O4' |
H1' |
241.8 |
241.1 |
| N1 |
C1' |
O4' |
H1' |
114.8 |
122.2 |
| O4' |
C1' |
N1 |
C6 |
50.2 |
233.5 |
| O4' |
C1' |
N1 |
C2 |
231.2 |
53.8 |
| C4' |
C3' |
C2' |
C1' |
351.1 |
360.0 |
| O4' |
C1' |
C2' |
H1' |
123.8 |
118.9 |
| N1 |
C1' |
C2' |
H1' |
245.6 |
237.7 |
| O4' |
C1' |
N1 |
H1' |
236.4 |
237.7 |
| C2' |
C1' |
N1 |
H1' |
117.6 |
122.4 |
| C2 |
N1 |
C1' |
C6 |
181.0 |
180.3 |
| C1' |
N1 |
C6 |
C5 |
180.4 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
0.4 |
0.0 |
| C1' |
N1 |
C2 |
N3 |
179.2 |
180.0 |
| O4' |
C1' |
H1' |
N1 |
119.1 |
122.3 |
| H1' |
C1' |
N1 |
C6 |
173.8 |
355.8 |
| H1' |
C1' |
N1 |
C2 |
354.8 |
176.1 |
| C6 |
N1 |
C1' |
H1' |
173.8 |
355.8 |
| C1' |
N1 |
C6 |
C2 |
181.0 |
180.3 |
| C6 |
N1 |
C2 |
N3 |
0.2 |
0.2 |
| N1 |
C6 |
C5 |
H5 |
180.8 |
180.2 |
| C2 |
N1 |
C1' |
H1' |
354.8 |
176.1 |
| C1' |
N1 |
C2 |
C6 |
179.0 |
179.7 |
| C2 |
N1 |
C6 |
C5 |
359.4 |
359.5 |
| C2 |
N1 |
C6 |
H6 |
179.4 |
179.8 |
| O2 |
C2 |
N1 |
N3 |
179.8 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.0 |
0.0 |
| N1 |
C2 |
N3 |
HN3 |
180.0 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
180.0 |
180.3 |
| N1 |
C2 |
O2 |
N3 |
180.2 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
180.2 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
0.2 |
0.0 |
| N3 |
C2 |
N1 |
C6 |
0.2 |
0.2 |
| C2 |
N3 |
C4 |
O4 |
179.6 |
180.0 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.8 |
0.5 |
| C5 |
C4 |
N3 |
HN3 |
180.1 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
359.6 |
0.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.3 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.7 |
| H6 |
C6 |
C5 |
H5 |
0.8 |
360.0 |
| C2' |
C3' |
C4' |
H4' |
108.6 |
94.9 |
| C4' |
C3' |
C2' |
H3' |
124.0 |
118.7 |
| C3' |
C2' |
C1' |
H1' |
266.0 |
265.1 |
| H2' |
C2' |
C3' |
H2'A |
118.2 |
122.7 |
| H2' |
C2' |
C1' |
H1' |
26.0 |
23.8 |
| C3' |
C2' |
H2' |
H2'A |
238.1 |
237.2 |
| H2'A |
C2' |
C1' |
H1' |
144.3 |
146.3 |
| C3' |
C2' |
H2'A |
H2' |
121.2 |
122.7 |
| O3' |
C3' |
C4' |
H4' |
345.7 |
336.3 |
| C4' |
C3' |
O3' |
H3' |
235.9 |
237.3 |
| O3' |
C3' |
C2' |
H2' |
350.2 |
0.0 |
| O3' |
C3' |
C2' |
H2'A |
231.9 |
237.4 |
| H3' |
C3' |
C4' |
H4' |
228.9 |
213.6 |
| C4' |
C3' |
H3' |
C2' |
243.8 |
245.3 |
| H3' |
C3' |
C2' |
H2' |
107.1 |
122.7 |
| H3' |
C3' |
C2' |
H2'A |
348.8 |
0.0 |
| HO3' |
O3' |
C3' |
H3' |
52.6 |
302.7 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.0 |
| HN3 |
N3 |
C4 |
O4 |
359.6 |
0.0 |