PDB Chemical Component UMP
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 UMP
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.374 |
1.345 |
| N1 |
C6 |
1.346 |
1.369 |
| N1 |
C1' |
1.481 |
1.465 |
| C2 |
N3 |
1.378 |
1.347 |
| C2 |
O2 |
1.245 |
1.216 |
| N3 |
C4 |
1.367 |
1.349 |
| N3 |
HN3 |
1.000 |
0.970 |
| C4 |
C5 |
1.407 |
1.416 |
| C4 |
O4 |
1.255 |
1.218 |
| C5 |
C6 |
1.378 |
1.349 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| C1' |
C2' |
1.509 |
1.541 |
| C1' |
O4' |
1.425 |
1.437 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
C3' |
1.503 |
1.548 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'' |
1.100 |
1.090 |
| C3' |
C4' |
1.526 |
1.550 |
| C3' |
O3' |
1.434 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| C4' |
O4' |
1.443 |
1.444 |
| C4' |
C5' |
1.493 |
1.530 |
| C4' |
H4' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C5' |
O5' |
1.402 |
1.429 |
| C5' |
H5' |
1.099 |
1.090 |
| C5' |
H5'' |
1.100 |
1.090 |
| O5' |
P |
1.584 |
1.609 |
| P |
OP1 |
1.503 |
1.480 |
| P |
OP2 |
1.503 |
1.610 |
| P |
OP3 |
1.493 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for UMP
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
120.2 |
120.6 |
| C2 |
N1 |
C1' |
120.0 |
119.7 |
| N1 |
C2 |
N3 |
118.0 |
120.9 |
| N1 |
C2 |
O2 |
123.1 |
119.6 |
| C6 |
N1 |
C1' |
119.7 |
119.7 |
| N1 |
C6 |
C5 |
121.7 |
119.7 |
| N1 |
C6 |
H6 |
119.1 |
120.1 |
| N1 |
C1' |
C2' |
112.7 |
109.9 |
| N1 |
C1' |
O4' |
107.0 |
109.9 |
| N1 |
C1' |
H1' |
109.8 |
109.9 |
| N3 |
C2 |
O2 |
118.9 |
119.5 |
| C2 |
N3 |
C4 |
123.8 |
120.2 |
| C2 |
N3 |
HN3 |
118.1 |
119.9 |
| C4 |
N3 |
HN3 |
118.1 |
119.9 |
| N3 |
C4 |
C5 |
116.5 |
119.4 |
| N3 |
C4 |
O4 |
118.4 |
120.3 |
| C5 |
C4 |
O4 |
125.1 |
120.3 |
| C4 |
C5 |
C6 |
119.7 |
119.1 |
| C4 |
C5 |
H5 |
120.1 |
120.4 |
| C6 |
C5 |
H5 |
120.2 |
120.5 |
| C5 |
C6 |
H6 |
119.1 |
120.1 |
| C2' |
C1' |
O4' |
107.3 |
107.3 |
| C2' |
C1' |
H1' |
109.4 |
109.8 |
| C1' |
C2' |
C3' |
105.7 |
104.2 |
| C1' |
C2' |
H2' |
110.4 |
110.5 |
| C1' |
C2' |
H2'' |
110.4 |
110.5 |
| O4' |
C1' |
H1' |
110.6 |
110.0 |
| C1' |
O4' |
C4' |
109.4 |
107.0 |
| C3' |
C2' |
H2' |
110.4 |
110.5 |
| C3' |
C2' |
H2'' |
110.4 |
110.5 |
| C2' |
C3' |
C4' |
102.1 |
102.1 |
| C2' |
C3' |
O3' |
113.9 |
110.9 |
| C2' |
C3' |
H3' |
108.7 |
110.9 |
| H2' |
C2' |
H2'' |
109.4 |
110.5 |
| C4' |
C3' |
O3' |
113.7 |
110.9 |
| C4' |
C3' |
H3' |
108.4 |
110.9 |
| C3' |
C4' |
O4' |
106.6 |
103.5 |
| C3' |
C4' |
C5' |
116.9 |
110.6 |
| C3' |
C4' |
H4' |
107.7 |
110.6 |
| O3' |
C3' |
H3' |
109.6 |
110.8 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| O4' |
C4' |
C5' |
108.5 |
110.6 |
| O4' |
C4' |
H4' |
108.8 |
110.6 |
| C5' |
C4' |
H4' |
108.1 |
110.7 |
| C4' |
C5' |
O5' |
109.9 |
109.5 |
| C4' |
C5' |
H5' |
109.3 |
109.4 |
| C4' |
C5' |
H5'' |
109.3 |
109.5 |
| O5' |
C5' |
H5' |
109.4 |
109.5 |
| O5' |
C5' |
H5'' |
109.4 |
109.5 |
| C5' |
O5' |
P |
120.9 |
123.0 |
| H5' |
C5' |
H5'' |
109.5 |
109.5 |
| O5' |
P |
OP1 |
105.8 |
109.5 |
| O5' |
P |
OP2 |
108.5 |
109.5 |
| O5' |
P |
OP3 |
106.9 |
109.4 |
| OP1 |
P |
OP2 |
112.0 |
109.5 |
| OP1 |
P |
OP3 |
109.9 |
109.5 |
| OP2 |
P |
OP3 |
113.4 |
109.4 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
Torsion Angles for UMP
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
182.5 |
180.3 |
| C2 |
N1 |
C6 |
C5 |
356.7 |
0.0 |
| C2 |
N1 |
C6 |
H6 |
176.7 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
118.3 |
115.0 |
| C2 |
N1 |
C1' |
O4' |
236.0 |
232.8 |
| C2 |
N1 |
C1' |
H1' |
356.1 |
354.1 |
| N3 |
C2 |
N1 |
O2 |
180.9 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
359.0 |
360.0 |
| N1 |
C2 |
N3 |
HN3 |
178.9 |
180.0 |
| C2 |
N1 |
C6 |
C1' |
177.5 |
179.7 |
| C6 |
N1 |
C2 |
N3 |
2.0 |
0.0 |
| C6 |
N1 |
C2 |
O2 |
181.1 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
295.8 |
294.7 |
| C6 |
N1 |
C1' |
O4' |
53.5 |
52.6 |
| C6 |
N1 |
C1' |
H1' |
173.6 |
173.8 |
| C4 |
C5 |
C6 |
N1 |
3.5 |
0.0 |
| N1 |
C6 |
C5 |
H5 |
183.5 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.0 |
| C2 |
N1 |
C1' |
C6 |
182.5 |
180.3 |
| C1' |
N1 |
C2 |
N3 |
179.5 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
358.7 |
359.7 |
| C1' |
N1 |
C6 |
C5 |
179.2 |
180.3 |
| C1' |
N1 |
C6 |
H6 |
359.2 |
0.2 |
| C2' |
C1' |
N1 |
O4' |
242.3 |
242.2 |
| C2' |
C1' |
N1 |
H1' |
122.2 |
121.0 |
| N1 |
C1' |
C2' |
C3' |
99.8 |
121.5 |
| N1 |
C1' |
C2' |
H2' |
219.3 |
240.2 |
| N1 |
C1' |
C2' |
H2'' |
340.4 |
2.8 |
| O4' |
C1' |
N1 |
H1' |
240.0 |
238.8 |
| N1 |
C1' |
O4' |
C4' |
238.0 |
214.1 |
| N3 |
C2 |
N1 |
C6 |
2.0 |
0.0 |
| N3 |
C2 |
N1 |
C1' |
179.5 |
179.7 |
| N1 |
C2 |
N3 |
O2 |
179.2 |
180.0 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
1.2 |
0.1 |
| C2 |
N3 |
C4 |
O4 |
178.9 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
181.1 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
358.7 |
359.7 |
| N1 |
C2 |
O2 |
N3 |
180.9 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
179.8 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
359.8 |
360.0 |
| C4 |
N3 |
C2 |
O2 |
179.8 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
180.0 |
| C5 |
C4 |
N3 |
O4 |
182.3 |
180.1 |
| N3 |
C4 |
C5 |
C6 |
357.7 |
360.0 |
| N3 |
C4 |
C5 |
H5 |
177.7 |
180.0 |
| HN3 |
N3 |
C2 |
O2 |
359.8 |
360.0 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.0 |
| HN3 |
N3 |
C4 |
C5 |
181.2 |
180.0 |
| HN3 |
N3 |
C4 |
O4 |
359.0 |
360.0 |
| N1 |
C6 |
C5 |
C4 |
3.5 |
0.0 |
| C5 |
C4 |
N3 |
HN3 |
181.2 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
177.5 |
179.9 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
183.5 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
359.0 |
360.0 |
| N3 |
C4 |
O4 |
C5 |
182.5 |
180.1 |
| O4 |
C4 |
C5 |
C6 |
180.1 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
0.1 |
0.1 |
| C5 |
C6 |
N1 |
C1' |
179.2 |
180.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
O4 |
180.1 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.0 |
| H5 |
C5 |
C4 |
O4 |
0.1 |
0.1 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
3.5 |
0.0 |
| H6 |
C6 |
N1 |
C1' |
359.2 |
0.2 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
3.5 |
0.0 |
| N1 |
C1' |
C2' |
O4' |
117.6 |
119.5 |
| N1 |
C1' |
C2' |
H1' |
237.6 |
239.0 |
| O4' |
C1' |
C2' |
H1' |
120.0 |
119.6 |
| C2' |
C1' |
O4' |
C4' |
359.2 |
333.5 |
| C3' |
C2' |
C1' |
H2' |
240.6 |
241.3 |
| C3' |
C2' |
C1' |
H2'' |
119.4 |
118.7 |
| C1' |
C2' |
C3' |
C4' |
27.8 |
20.9 |
| C1' |
C2' |
C3' |
O3' |
150.8 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
273.3 |
262.7 |
| H2' |
C2' |
C1' |
H2'' |
238.9 |
237.4 |
| N1 |
C1' |
O4' |
C2' |
238.8 |
240.6 |
| N1 |
C1' |
O4' |
H1' |
119.5 |
121.1 |
| C2' |
C1' |
O4' |
H1' |
240.8 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
342.3 |
2.0 |
| O4' |
C1' |
C2' |
H2' |
101.7 |
120.7 |
| O4' |
C1' |
C2' |
H2'' |
222.9 |
243.3 |
| C3' |
C4' |
O4' |
C1' |
18.8 |
40.0 |
| C1' |
O4' |
C4' |
C5' |
145.5 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
262.9 |
281.6 |
| N1 |
C1' |
H1' |
C2' |
124.2 |
121.0 |
| N1 |
C1' |
H1' |
O4' |
242.2 |
238.8 |
| C2' |
C1' |
H1' |
O4' |
118.0 |
117.9 |
| H1' |
C1' |
C2' |
C3' |
222.3 |
242.5 |
| H1' |
C1' |
C2' |
H2' |
341.7 |
1.1 |
| H1' |
C1' |
C2' |
H2'' |
102.9 |
123.8 |
| H1' |
C1' |
O4' |
C4' |
118.4 |
92.9 |
| C3' |
C2' |
C1' |
O4' |
342.3 |
2.0 |
| C3' |
C2' |
C1' |
H1' |
222.3 |
242.5 |
| C1' |
C2' |
C3' |
H2' |
119.4 |
118.7 |
| C1' |
C2' |
C3' |
H2'' |
240.6 |
241.3 |
| H2' |
C2' |
C3' |
H2'' |
121.2 |
122.7 |
| C4' |
C3' |
C2' |
O3' |
237.0 |
241.8 |
| C4' |
C3' |
C2' |
H3' |
114.4 |
118.2 |
| C2' |
C3' |
C4' |
O4' |
331.3 |
323.0 |
| C2' |
C3' |
C4' |
C5' |
209.8 |
204.5 |
| C2' |
C3' |
C4' |
H4' |
87.9 |
81.5 |
| O3' |
C3' |
C2' |
H3' |
237.5 |
236.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.4 |
| H2' |
C2' |
C1' |
O4' |
101.7 |
120.7 |
| H2' |
C2' |
C1' |
H1' |
341.7 |
1.1 |
| C1' |
C2' |
H2' |
C3' |
243.5 |
245.3 |
| C1' |
C2' |
H2' |
H2'' |
121.7 |
122.6 |
| C3' |
C2' |
H2' |
H2'' |
238.2 |
237.3 |
| H2' |
C2' |
C3' |
C4' |
268.4 |
262.2 |
| H2' |
C2' |
C3' |
O3' |
31.4 |
20.4 |
| H2' |
C2' |
C3' |
H3' |
153.9 |
144.0 |
| H2'' |
C2' |
C1' |
O4' |
222.9 |
243.3 |
| H2'' |
C2' |
C1' |
H1' |
102.9 |
123.8 |
| C1' |
C2' |
H2'' |
C3' |
116.5 |
114.8 |
| C1' |
C2' |
H2'' |
H2' |
238.3 |
237.4 |
| C3' |
C2' |
H2'' |
H2' |
121.8 |
122.6 |
| H2'' |
C2' |
C3' |
C4' |
147.2 |
139.6 |
| H2'' |
C2' |
C3' |
O3' |
270.2 |
257.8 |
| H2'' |
C2' |
C3' |
H3' |
32.7 |
21.3 |
| C1' |
O4' |
C4' |
C3' |
18.8 |
40.0 |
| C4' |
C3' |
C2' |
H2' |
268.4 |
262.2 |
| C4' |
C3' |
C2' |
H2'' |
147.2 |
139.6 |
| C2' |
C3' |
C4' |
O3' |
123.1 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
245.4 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
122.2 |
123.6 |
| C4' |
C3' |
O3' |
HO3' |
296.5 |
174.2 |
| O4' |
C4' |
C3' |
C5' |
121.5 |
118.5 |
| O4' |
C4' |
C3' |
H4' |
243.4 |
241.5 |
| C5' |
C4' |
C3' |
H4' |
121.9 |
123.0 |
| C3' |
C4' |
C5' |
O5' |
59.0 |
185.0 |
| C3' |
C4' |
C5' |
H5' |
179.1 |
305.0 |
| C3' |
C4' |
C5' |
H5'' |
298.9 |
65.0 |
| O3' |
C3' |
C2' |
H2' |
31.4 |
20.4 |
| O3' |
C3' |
C2' |
H2'' |
270.2 |
257.8 |
| C2' |
C3' |
O3' |
C4' |
243.5 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
122.0 |
123.6 |
| C4' |
C3' |
O3' |
H3' |
238.4 |
236.4 |
| O3' |
C3' |
C4' |
O4' |
208.1 |
204.8 |
| O3' |
C3' |
C4' |
C5' |
86.7 |
86.3 |
| O3' |
C3' |
C4' |
H4' |
324.8 |
323.2 |
| H3' |
C3' |
C2' |
H2' |
153.9 |
144.0 |
| H3' |
C3' |
C2' |
H2'' |
32.7 |
21.3 |
| C2' |
C3' |
H3' |
C4' |
110.3 |
112.8 |
| C2' |
C3' |
H3' |
O3' |
234.9 |
236.4 |
| C4' |
C3' |
H3' |
O3' |
124.7 |
123.6 |
| H3' |
C3' |
C4' |
O4' |
85.9 |
81.2 |
| H3' |
C3' |
C4' |
C5' |
324.4 |
322.7 |
| H3' |
C3' |
C4' |
H4' |
202.5 |
199.7 |
| H3' |
C3' |
O3' |
HO3' |
58.0 |
297.8 |
| C4' |
O4' |
C1' |
H1' |
118.4 |
92.9 |
| O4' |
C4' |
C3' |
O3' |
208.1 |
204.8 |
| O4' |
C4' |
C3' |
H3' |
85.9 |
81.2 |
| C3' |
C4' |
O4' |
C5' |
233.3 |
241.5 |
| C3' |
C4' |
O4' |
H4' |
115.9 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
242.6 |
237.0 |
| O4' |
C4' |
C5' |
O5' |
298.5 |
70.9 |
| O4' |
C4' |
C5' |
H5' |
58.6 |
190.9 |
| O4' |
C4' |
C5' |
H5'' |
178.4 |
310.9 |
| C5' |
C4' |
C3' |
O3' |
86.7 |
86.3 |
| C5' |
C4' |
C3' |
H3' |
324.4 |
322.7 |
| C3' |
C4' |
C5' |
O4' |
120.5 |
114.0 |
| C3' |
C4' |
C5' |
H4' |
238.3 |
237.0 |
| O4' |
C4' |
C5' |
H4' |
117.8 |
123.0 |
| O5' |
C5' |
C4' |
H5' |
239.9 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
120.1 |
120.0 |
| C4' |
C5' |
O5' |
P |
185.6 |
180.0 |
| H5' |
C5' |
C4' |
H5'' |
240.2 |
240.0 |
| H4' |
C4' |
C3' |
O3' |
324.8 |
323.2 |
| H4' |
C4' |
C3' |
H3' |
202.5 |
199.7 |
| C3' |
C4' |
H4' |
O4' |
244.8 |
246.0 |
| C3' |
C4' |
H4' |
C5' |
127.2 |
123.0 |
| O4' |
C4' |
H4' |
C5' |
242.4 |
237.0 |
| H4' |
C4' |
C5' |
O5' |
180.7 |
308.0 |
| H4' |
C4' |
C5' |
H5' |
300.8 |
68.0 |
| H4' |
C4' |
C5' |
H5'' |
60.6 |
188.0 |
| HO3' |
O3' |
C3' |
H3' |
58.0 |
297.8 |
| O5' |
C5' |
C4' |
H4' |
180.7 |
308.0 |
| C4' |
C5' |
O5' |
H5' |
120.1 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
239.9 |
240.0 |
| H5' |
C5' |
O5' |
H5'' |
119.9 |
120.0 |
| C5' |
O5' |
P |
OP1 |
184.4 |
305.0 |
| C5' |
O5' |
P |
OP2 |
304.8 |
65.0 |
| C5' |
O5' |
P |
OP3 |
67.4 |
185.0 |
| H5' |
C5' |
C4' |
H4' |
300.8 |
68.0 |
| C4' |
C5' |
H5' |
O5' |
239.6 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
119.8 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
240.2 |
240.0 |
| H5' |
C5' |
O5' |
P |
65.5 |
60.0 |
| H5'' |
C5' |
C4' |
H4' |
60.6 |
188.0 |
| C4' |
C5' |
H5'' |
O5' |
120.4 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
240.2 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
119.8 |
120.0 |
| H5'' |
C5' |
O5' |
P |
305.7 |
300.0 |
| P |
O5' |
C5' |
H5' |
65.5 |
60.0 |
| P |
O5' |
C5' |
H5'' |
305.7 |
300.0 |
| OP1 |
P |
O5' |
OP2 |
239.7 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
117.1 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
237.4 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
243.6 |
60.0 |
| O5' |
P |
OP3 |
HOP3 |
114.4 |
180.0 |
| O5' |
P |
OP1 |
OP2 |
118.0 |
120.1 |
| O5' |
P |
OP1 |
OP3 |
244.9 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
126.9 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
360.0 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
60.0 |
| O5' |
P |
OP2 |
OP1 |
243.6 |
239.9 |
| O5' |
P |
OP2 |
OP3 |
118.6 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
235.0 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
233.9 |
300.0 |
| O5' |
P |
OP3 |
OP1 |
114.4 |
120.0 |
| O5' |
P |
OP3 |
OP2 |
240.5 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
126.1 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
125.0 |
300.0 |
| HOP2 |
OP2 |
P |
OP3 |
125.0 |
300.0 |