PDB Chemical Component UMC
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 UMC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
P |
1.622 |
1.610 |
| O2P |
P |
1.501 |
1.481 |
| P |
O1P |
1.512 |
1.610 |
| P |
O3P |
1.524 |
1.610 |
| C2 |
N1 |
1.331 |
1.343 |
| C1' |
N1 |
1.470 |
1.465 |
| N1 |
C6 |
1.463 |
1.464 |
| O2 |
C2 |
1.235 |
1.215 |
| C2 |
N3 |
1.343 |
1.343 |
| HN3 |
N3 |
1.000 |
0.970 |
| N3 |
C4 |
1.344 |
1.346 |
| O4 |
C4 |
1.239 |
1.213 |
| C4 |
C5 |
1.508 |
1.507 |
| H5A |
C5 |
1.100 |
1.090 |
| C5 |
C6 |
1.521 |
1.530 |
| C5 |
H5 |
1.100 |
1.090 |
| C6 |
H6 |
1.100 |
1.090 |
| C6 |
H6A |
1.100 |
1.090 |
| H1' |
C1' |
1.100 |
1.090 |
| C1' |
C2' |
1.528 |
1.541 |
| C1' |
O4' |
1.430 |
1.437 |
| O1P |
HO1P |
0.950 |
0.967 |
| H2'A |
C2' |
1.100 |
1.091 |
| C2' |
C3' |
1.521 |
1.548 |
| C2' |
H2' |
1.100 |
1.090 |
| O3' |
C3' |
1.433 |
1.429 |
| C3' |
H3' |
1.100 |
1.091 |
| C3' |
C4' |
1.516 |
1.551 |
| HO3' |
O3' |
0.950 |
0.967 |
| O3P |
HO3P |
0.950 |
0.967 |
| O4' |
C4' |
1.430 |
1.443 |
| H4' |
C4' |
1.100 |
1.090 |
| C4' |
C5' |
1.520 |
1.530 |
| C5' |
H5' |
1.100 |
1.091 |
| C5' |
H5'A |
1.100 |
1.090 |
| C5' |
O5' |
1.432 |
1.429 |
Bond Angles for UMC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2P |
P |
O3P |
114.2 |
109.5 |
| O1P |
P |
O3P |
114.1 |
109.5 |
| P |
O1P |
HO1P |
109.5 |
114.0 |
| P |
O3P |
HO3P |
109.5 |
114.0 |
| C2 |
N1 |
C6 |
125.1 |
120.9 |
| N1 |
C6 |
C5 |
111.0 |
109.5 |
| N1 |
C6 |
H6 |
109.1 |
109.5 |
| N1 |
C6 |
H6A |
109.1 |
109.4 |
| O2 |
C2 |
N3 |
121.0 |
119.2 |
| C2 |
N3 |
C4 |
124.5 |
121.0 |
| N3 |
C4 |
C5 |
120.0 |
120.0 |
| O4 |
C4 |
C5 |
119.9 |
120.0 |
| C4 |
C5 |
C6 |
112.5 |
109.2 |
| C4 |
C5 |
H5 |
108.7 |
109.5 |
| C6 |
C5 |
H5 |
108.7 |
109.5 |
| C5 |
C6 |
H6 |
109.1 |
109.5 |
| C5 |
C6 |
H6A |
109.1 |
109.5 |
| H6 |
C6 |
H6A |
109.4 |
109.4 |
| C2' |
C1' |
O4' |
104.5 |
107.3 |
| C1' |
C2' |
C3' |
101.2 |
104.2 |
| C1' |
C2' |
H2' |
111.5 |
110.5 |
| C1' |
O4' |
C4' |
111.0 |
107.0 |
| C3' |
C2' |
H2' |
111.5 |
110.5 |
| C2' |
C3' |
H3' |
110.6 |
110.9 |
| C2' |
C3' |
C4' |
102.2 |
102.1 |
| O3' |
C3' |
H3' |
112.0 |
110.8 |
| O3' |
C3' |
C4' |
109.6 |
110.9 |
| C4' |
C3' |
H3' |
110.7 |
110.9 |
| C3' |
C4' |
C5' |
111.1 |
110.6 |
| O4' |
C4' |
C5' |
108.1 |
110.6 |
| C4' |
C5' |
H5' |
108.9 |
109.4 |
| C4' |
C5' |
H5'A |
108.9 |
109.5 |
| C4' |
C5' |
O5' |
111.7 |
109.5 |
| H5' |
C5' |
H5'A |
109.5 |
109.4 |
| O5' |
C5' |
H5' |
108.9 |
109.5 |
| O5' |
C5' |
H5'A |
108.9 |
109.5 |
Torsion Angles for UMC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
O1P |
HO1P |
113.3 |
60.0 |
| O5' |
P |
O3P |
HO3P |
243.6 |
179.9 |
| O1P |
P |
O2P |
O3P |
227.1 |
120.0 |
| O2P |
P |
O1P |
HO1P |
0.0 |
180.0 |
| O2P |
P |
O3P |
HO3P |
0.0 |
59.9 |
| O2P |
P |
O1P |
O3P |
132.9 |
240.0 |
| O1P |
P |
O3P |
HO3P |
132.5 |
300.0 |
| O3P |
P |
O1P |
HO1P |
227.1 |
300.0 |
| C2 |
N1 |
C6 |
C5 |
29.6 |
324.1 |
| C2 |
N1 |
C6 |
H6 |
149.9 |
84.1 |
| C2 |
N1 |
C6 |
H6A |
269.3 |
204.1 |
| C1' |
N1 |
C6 |
H6 |
327.9 |
264.4 |
| C1' |
N1 |
C6 |
H6A |
87.4 |
24.4 |
| C4 |
C5 |
C6 |
N1 |
327.5 |
46.7 |
| N1 |
C6 |
C5 |
H5 |
88.0 |
286.8 |
| C5 |
C6 |
N1 |
H6 |
239.8 |
240.0 |
| C5 |
C6 |
N1 |
H6A |
120.3 |
120.0 |
| H6 |
C6 |
N1 |
H6A |
240.5 |
240.0 |
| O2 |
C2 |
N1 |
C6 |
171.4 |
185.8 |
| O2 |
C2 |
N3 |
C4 |
171.4 |
192.0 |
| N3 |
C2 |
N1 |
C6 |
351.1 |
5.7 |
| C2 |
N3 |
C4 |
C5 |
1.1 |
4.4 |
| O4 |
C4 |
N3 |
C5 |
182.3 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
20.4 |
325.8 |
| N3 |
C4 |
C5 |
H5 |
259.9 |
85.7 |
| N3 |
C4 |
O4 |
C5 |
177.7 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
198.1 |
145.7 |
| O4 |
C4 |
C5 |
H5 |
77.6 |
265.7 |
| N1 |
C6 |
C5 |
C4 |
327.5 |
46.7 |
| C6 |
C5 |
C4 |
H5 |
120.5 |
240.0 |
| C4 |
C5 |
C6 |
H6 |
207.2 |
286.7 |
| C4 |
C5 |
C6 |
H6A |
87.7 |
166.7 |
| H5A |
C5 |
C6 |
H6A |
327.3 |
286.6 |
| N1 |
C6 |
C5 |
H6 |
120.2 |
120.0 |
| N1 |
C6 |
C5 |
H6A |
239.7 |
240.0 |
| C4 |
C5 |
C6 |
H5 |
239.5 |
119.9 |
| H6 |
C6 |
C5 |
H6A |
119.5 |
120.0 |
| C4 |
C5 |
H5 |
C6 |
122.8 |
240.2 |
| H5 |
C5 |
C6 |
H6 |
327.7 |
166.7 |
| H5 |
C5 |
C6 |
H6A |
208.2 |
46.8 |
| N1 |
C6 |
H6 |
C5 |
238.6 |
240.0 |
| N1 |
C6 |
H6 |
H6A |
119.3 |
119.9 |
| H6 |
C6 |
C5 |
H5 |
327.7 |
166.7 |
| C5 |
C6 |
H6 |
H6A |
240.7 |
240.0 |
| N1 |
C6 |
H6A |
C5 |
121.4 |
120.0 |
| N1 |
C6 |
H6A |
H6 |
240.7 |
240.0 |
| H6A |
C6 |
C5 |
H5 |
208.2 |
46.8 |
| C5 |
C6 |
H6A |
H6 |
119.3 |
120.0 |
| C2' |
C1' |
O4' |
C4' |
343.5 |
333.5 |
| C3' |
C2' |
C1' |
H2' |
118.6 |
241.3 |
| C1' |
C2' |
C3' |
H3' |
203.3 |
262.8 |
| C1' |
C2' |
C3' |
C4' |
321.2 |
20.9 |
| O4' |
C1' |
C2' |
C3' |
34.4 |
2.0 |
| O4' |
C1' |
C2' |
H2' |
275.7 |
120.7 |
| C1' |
O4' |
C4' |
C5' |
110.3 |
158.5 |
| HO1P |
O1P |
P |
O3P |
227.1 |
300.0 |
| H2'A |
C2' |
C3' |
H3' |
84.6 |
21.4 |
| C3' |
C2' |
C1' |
O4' |
34.4 |
2.0 |
| C1' |
C2' |
C3' |
H2' |
241.4 |
118.7 |
| O3' |
C3' |
C2' |
H3' |
234.8 |
236.4 |
| O3' |
C3' |
C2' |
C4' |
116.9 |
118.2 |
| C4' |
C3' |
C2' |
H3' |
117.9 |
118.2 |
| C2' |
C3' |
C4' |
C5' |
273.2 |
204.5 |
| H2' |
C2' |
C1' |
O4' |
275.7 |
120.7 |
| C1' |
C2' |
H2' |
C3' |
112.3 |
245.2 |
| H2' |
C2' |
C3' |
H3' |
321.9 |
144.0 |
| H2' |
C2' |
C3' |
C4' |
79.8 |
262.2 |
| O3' |
C3' |
C2' |
H2' |
196.7 |
20.4 |
| C2' |
C3' |
O3' |
H3' |
124.4 |
123.7 |
| C2' |
C3' |
O3' |
C4' |
247.6 |
247.3 |
| C4' |
C3' |
O3' |
H3' |
236.8 |
236.4 |
| O3' |
C3' |
C4' |
C5' |
155.0 |
86.2 |
| H3' |
C3' |
C2' |
H2' |
321.9 |
144.0 |
| C2' |
C3' |
H3' |
C4' |
112.6 |
112.7 |
| O3' |
C3' |
H3' |
C4' |
237.4 |
236.4 |
| H3' |
C3' |
C4' |
C5' |
31.0 |
322.7 |
| C1' |
O4' |
C4' |
C3' |
351.4 |
40.0 |
| C4' |
C3' |
C2' |
H2' |
79.8 |
262.2 |
| C2' |
C3' |
C4' |
H3' |
242.2 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
124.0 |
123.5 |
| O4' |
C4' |
C3' |
C5' |
116.9 |
118.5 |
| C3' |
C4' |
C5' |
H5' |
44.1 |
305.0 |
| C3' |
C4' |
C5' |
H5'A |
163.4 |
65.0 |
| C3' |
C4' |
C5' |
O5' |
283.8 |
185.0 |
| O4' |
C4' |
C3' |
H3' |
147.9 |
81.2 |
| C3' |
C4' |
O4' |
C5' |
241.1 |
241.5 |
| O4' |
C4' |
C5' |
H5' |
289.0 |
191.0 |
| O4' |
C4' |
C5' |
H5'A |
48.3 |
310.9 |
| O4' |
C4' |
C5' |
O5' |
168.7 |
71.0 |
| C5' |
C4' |
C3' |
H3' |
31.0 |
322.7 |
| H5' |
C5' |
C4' |
H5'A |
240.7 |
240.0 |
| O5' |
C5' |
C4' |
H5' |
239.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
120.3 |
120.1 |
| C4' |
C5' |
H5' |
H5'A |
119.0 |
120.0 |
| C4' |
C5' |
H5' |
O5' |
238.0 |
240.0 |
| O5' |
C5' |
H5' |
H5'A |
241.0 |
240.0 |
| C4' |
C5' |
H5'A |
H5' |
241.0 |
240.0 |
| C4' |
C5' |
H5'A |
O5' |
122.0 |
120.0 |
| O5' |
C5' |
H5'A |
H5' |
119.0 |
120.0 |
| C4' |
C5' |
O5' |
H5' |
120.4 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
239.7 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
119.3 |
120.0 |