PDB Chemical Component UMX
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 UMX
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.556 |
1.480 |
| O5' |
P |
1.580 |
1.610 |
| P |
OP1 |
1.567 |
1.610 |
| P |
OP3 |
1.611 |
1.610 |
| C2 |
N1 |
1.360 |
1.345 |
| C6 |
N1 |
1.353 |
1.368 |
| N1 |
C1' |
1.469 |
1.465 |
| N3 |
C2 |
1.357 |
1.346 |
| C2 |
O2 |
1.275 |
1.216 |
| C4 |
N3 |
1.324 |
1.349 |
| O4 |
C4 |
1.231 |
1.218 |
| C4 |
C5 |
1.436 |
1.416 |
| C5 |
C6 |
1.363 |
1.350 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.081 |
1.080 |
| C2' |
C1' |
1.516 |
1.561 |
| C1' |
O4' |
1.427 |
1.440 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
C3' |
1.483 |
1.572 |
| C2' |
C6' |
1.515 |
1.561 |
| C2' |
H2' |
1.100 |
1.090 |
| O3' |
C3' |
1.469 |
1.429 |
| C3' |
C4' |
1.510 |
1.569 |
| C3' |
H3' |
1.099 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| O4' |
C4' |
1.439 |
1.454 |
| C4' |
C5' |
1.518 |
1.529 |
| C4' |
C8' |
1.533 |
1.559 |
| O5' |
C5' |
1.447 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| C7' |
C6' |
1.495 |
1.531 |
| C6' |
C8' |
1.538 |
1.548 |
| C6' |
H6' |
1.100 |
1.090 |
| C7' |
H7' |
1.100 |
1.090 |
| C7' |
H7'A |
1.100 |
1.090 |
| C7' |
H7'B |
1.100 |
1.090 |
| C8' |
H8' |
1.100 |
1.089 |
| C8' |
H8'A |
1.100 |
1.090 |
| OP1 |
HOP1 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| N3 |
HN3 |
1.000 |
0.969 |
Bond Angles for UMX
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP3 |
112.8 |
109.5 |
| O5' |
P |
OP1 |
109.7 |
109.5 |
| O5' |
P |
OP3 |
103.5 |
109.4 |
| OP1 |
P |
OP3 |
108.7 |
109.5 |
| P |
OP1 |
HOP1 |
109.5 |
114.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| C2 |
N1 |
C1' |
118.5 |
119.7 |
| C6 |
N1 |
C1' |
122.5 |
119.7 |
| N1 |
C1' |
O4' |
109.2 |
110.2 |
| N1 |
C1' |
H1' |
104.1 |
110.2 |
| C4 |
N3 |
HN3 |
119.6 |
119.8 |
| O4 |
C4 |
C5 |
120.7 |
120.3 |
| C4 |
C5 |
C6 |
118.8 |
119.1 |
| C4 |
C5 |
H5 |
120.6 |
120.4 |
| C6 |
C5 |
H5 |
120.6 |
120.5 |
| C5 |
C6 |
H6 |
119.5 |
120.2 |
| C2' |
C1' |
O4' |
105.3 |
105.6 |
| C2' |
C1' |
H1' |
108.0 |
110.3 |
| O4' |
C1' |
H1' |
114.8 |
110.2 |
| C1' |
O4' |
C4' |
104.9 |
107.9 |
| C3' |
C2' |
C6' |
106.1 |
100.4 |
| C3' |
C2' |
H2' |
116.8 |
117.0 |
| C2' |
C3' |
C4' |
94.7 |
94.7 |
| C2' |
C3' |
H3' |
115.8 |
112.3 |
| C6' |
C2' |
H2' |
112.7 |
117.3 |
| C2' |
C6' |
C8' |
103.9 |
103.8 |
| C2' |
C6' |
H6' |
110.4 |
110.6 |
| O3' |
C3' |
C4' |
110.2 |
112.3 |
| O3' |
C3' |
H3' |
101.8 |
112.0 |
| C4' |
C3' |
H3' |
120.1 |
112.3 |
| C3' |
C4' |
C5' |
114.8 |
115.9 |
| C3' |
C4' |
C8' |
103.0 |
100.8 |
| O4' |
C4' |
C5' |
110.5 |
116.2 |
| O4' |
C4' |
C8' |
107.9 |
104.7 |
| C5' |
C4' |
C8' |
118.3 |
115.6 |
| C4' |
C5' |
H5' |
109.9 |
109.5 |
| C4' |
C5' |
H5'A |
109.9 |
109.5 |
| C4' |
C8' |
C6' |
100.7 |
104.4 |
| C4' |
C8' |
H8' |
112.5 |
110.5 |
| C4' |
C8' |
H8'A |
112.5 |
110.5 |
| O5' |
C5' |
H5' |
109.9 |
109.5 |
| O5' |
C5' |
H5'A |
109.9 |
109.4 |
| H5' |
C5' |
H5'A |
109.0 |
109.5 |
| C7' |
C6' |
C8' |
111.7 |
110.5 |
| C7' |
C6' |
H6' |
102.3 |
110.6 |
| C8' |
C6' |
H6' |
113.8 |
110.6 |
| C6' |
C8' |
H8' |
112.5 |
110.4 |
| C6' |
C8' |
H8'A |
112.5 |
110.4 |
| H7' |
C7' |
H7'A |
109.5 |
109.5 |
| H7' |
C7' |
H7'B |
109.5 |
109.5 |
| H7'A |
C7' |
H7'B |
109.5 |
109.4 |
| H8' |
C8' |
H8'A |
106.3 |
110.5 |
Torsion Angles for UMX
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP2 |
OP3 |
111.1 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
232.1 |
240.0 |
| OP2 |
P |
OP1 |
HOP1 |
360.0 |
180.0 |
| OP2 |
P |
OP3 |
HOP3 |
0.0 |
300.0 |
| OP2 |
P |
O5' |
OP3 |
242.3 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
115.9 |
120.0 |
| O5' |
P |
OP1 |
HOP1 |
117.6 |
300.0 |
| O5' |
P |
OP3 |
HOP3 |
249.1 |
180.0 |
| OP2 |
P |
OP1 |
OP3 |
129.8 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
247.4 |
240.0 |
| OP1 |
P |
OP3 |
HOP3 |
132.5 |
60.0 |
| O5' |
P |
OP3 |
OP1 |
116.6 |
120.0 |
| OP3 |
P |
OP1 |
HOP1 |
230.2 |
60.0 |
| C6 |
N1 |
C2 |
C1' |
182.0 |
180.3 |
| C2 |
N1 |
C1' |
O4' |
201.7 |
201.7 |
| C2 |
N1 |
C1' |
H1' |
324.7 |
323.6 |
| C2 |
N1 |
C6 |
C1' |
177.9 |
179.7 |
| C6 |
N1 |
C1' |
O4' |
19.6 |
21.3 |
| C6 |
N1 |
C1' |
H1' |
142.6 |
143.2 |
| C2' |
C1' |
N1 |
O4' |
241.4 |
243.9 |
| C2' |
C1' |
N1 |
H1' |
118.4 |
122.0 |
| O4' |
C1' |
N1 |
H1' |
237.0 |
238.1 |
| N1 |
C1' |
O4' |
C4' |
238.1 |
239.6 |
| N3 |
C2 |
N1 |
C1' |
177.1 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
357.5 |
360.0 |
| O4 |
C4 |
N3 |
HN3 |
358.2 |
0.1 |
| O4 |
C4 |
C5 |
C6 |
180.4 |
179.7 |
| O4 |
C4 |
C5 |
H5 |
0.4 |
359.9 |
| C5 |
C4 |
N3 |
HN3 |
180.3 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.8 |
| C4 |
C5 |
C6 |
H6 |
181.8 |
179.9 |
| C5 |
C6 |
N1 |
C1' |
181.6 |
179.7 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.2 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.8 |
| H5 |
C5 |
C6 |
H6 |
1.8 |
359.7 |
| H6 |
C6 |
N1 |
C1' |
1.6 |
0.3 |
| H6 |
C6 |
C5 |
H5 |
1.8 |
359.7 |
| N1 |
C1' |
C2' |
O4' |
120.7 |
119.0 |
| N1 |
C1' |
C2' |
H1' |
243.8 |
238.1 |
| O4' |
C1' |
C2' |
H1' |
123.1 |
119.1 |
| C2' |
C1' |
O4' |
C4' |
3.1 |
358.6 |
| N1 |
C1' |
O4' |
H1' |
116.4 |
121.9 |
| C2' |
C1' |
O4' |
H1' |
241.3 |
240.9 |
| C1' |
O4' |
C4' |
C5' |
154.8 |
161.6 |
| C1' |
O4' |
C4' |
C8' |
285.4 |
290.5 |
| N1 |
C1' |
H1' |
O4' |
240.8 |
238.1 |
| C2' |
C1' |
H1' |
O4' |
117.1 |
116.2 |
| H1' |
C1' |
O4' |
C4' |
121.7 |
117.7 |
| C3' |
C2' |
C1' |
O4' |
321.7 |
327.8 |
| C3' |
C2' |
C1' |
H1' |
198.6 |
208.7 |
| C6' |
C2' |
C3' |
H2' |
126.5 |
128.2 |
| C3' |
C2' |
C6' |
C8' |
25.1 |
36.1 |
| C3' |
C2' |
C6' |
H6' |
147.5 |
154.7 |
| O3' |
C3' |
C2' |
C4' |
114.9 |
116.4 |
| O3' |
C3' |
C2' |
H3' |
241.7 |
232.8 |
| C4' |
C3' |
C2' |
H3' |
126.8 |
116.4 |
| C2' |
C3' |
C4' |
C5' |
184.8 |
180.5 |
| C2' |
C3' |
C4' |
C8' |
54.8 |
54.8 |
| C6' |
C2' |
C1' |
O4' |
69.7 |
70.8 |
| C6' |
C2' |
C1' |
H1' |
306.6 |
311.7 |
| C3' |
C2' |
C6' |
H2' |
231.0 |
232.0 |
| C6' |
C2' |
C3' |
C4' |
311.4 |
304.3 |
| C6' |
C2' |
C3' |
H3' |
184.6 |
187.9 |
| C4' |
C8' |
C6' |
C2' |
9.6 |
358.6 |
| C7' |
C6' |
C2' |
C8' |
237.5 |
241.5 |
| C7' |
C6' |
C2' |
H6' |
115.1 |
122.8 |
| C8' |
C6' |
C2' |
H6' |
237.6 |
241.4 |
| C2' |
C6' |
C8' |
H8' |
249.6 |
239.9 |
| C2' |
C6' |
C8' |
H8'A |
129.6 |
117.4 |
| H2' |
C2' |
C1' |
O4' |
195.1 |
201.4 |
| H2' |
C2' |
C1' |
H1' |
72.0 |
82.3 |
| C3' |
C2' |
H2' |
C6' |
123.2 |
119.5 |
| H2' |
C2' |
C3' |
C4' |
184.8 |
176.1 |
| H2' |
C2' |
C3' |
H3' |
58.0 |
59.7 |
| H2' |
C2' |
C6' |
C8' |
154.1 |
164.1 |
| H2' |
C2' |
C6' |
H6' |
276.5 |
282.7 |
| O3' |
C3' |
C2' |
C6' |
66.2 |
60.7 |
| O3' |
C3' |
C2' |
H2' |
299.7 |
292.5 |
| C2' |
C3' |
O3' |
C4' |
254.5 |
254.8 |
| C2' |
C3' |
O3' |
H3' |
126.0 |
127.4 |
| C4' |
C3' |
O3' |
H3' |
231.5 |
232.6 |
| O3' |
C3' |
C4' |
C5' |
66.1 |
64.1 |
| O3' |
C3' |
C4' |
C8' |
296.1 |
298.4 |
| C1' |
O4' |
C4' |
C3' |
33.0 |
34.9 |
| C4' |
C3' |
C2' |
C6' |
311.4 |
304.3 |
| C4' |
C3' |
C2' |
H2' |
184.8 |
176.1 |
| C2' |
C3' |
C4' |
H3' |
236.5 |
243.6 |
| O3' |
C3' |
C4' |
H3' |
117.7 |
127.2 |
| O4' |
C4' |
C3' |
C5' |
118.6 |
126.8 |
| O4' |
C4' |
C3' |
C8' |
248.7 |
252.4 |
| C5' |
C4' |
C3' |
C8' |
130.0 |
125.6 |
| C3' |
C4' |
C5' |
H5' |
173.9 |
305.0 |
| C3' |
C4' |
C5' |
H5'A |
294.0 |
65.0 |
| C3' |
C4' |
C8' |
C6' |
319.3 |
326.0 |
| C3' |
C4' |
C8' |
H8' |
79.3 |
84.8 |
| C3' |
C4' |
C8' |
H8'A |
199.3 |
207.3 |
| H3' |
C3' |
C2' |
C6' |
184.6 |
187.9 |
| H3' |
C3' |
C2' |
H2' |
58.0 |
59.7 |
| C2' |
C3' |
H3' |
C4' |
112.7 |
105.2 |
| O3' |
C3' |
H3' |
C4' |
238.0 |
232.6 |
| H3' |
C3' |
C4' |
C5' |
308.4 |
296.9 |
| H3' |
C3' |
C4' |
C8' |
178.4 |
171.2 |
| HO3' |
O3' |
C3' |
C4' |
285.5 |
166.7 |
| HO3' |
O3' |
C3' |
H3' |
54.0 |
294.1 |
| C4' |
O4' |
C1' |
H1' |
121.7 |
117.7 |
| O4' |
C4' |
C3' |
H3' |
67.0 |
63.7 |
| C3' |
C4' |
O4' |
C5' |
238.2 |
233.4 |
| C3' |
C4' |
O4' |
C8' |
107.5 |
104.5 |
| C5' |
C4' |
O4' |
C8' |
229.3 |
231.1 |
| O4' |
C4' |
C5' |
H5' |
60.9 |
186.1 |
| O4' |
C4' |
C5' |
H5'A |
181.0 |
306.1 |
| O4' |
C4' |
C8' |
C6' |
65.2 |
71.0 |
| O4' |
C4' |
C8' |
H8' |
185.2 |
189.7 |
| O4' |
C4' |
C8' |
H8'A |
305.2 |
312.2 |
| C5' |
C4' |
C3' |
H3' |
308.4 |
296.9 |
| C3' |
C4' |
C5' |
C8' |
237.9 |
242.3 |
| O4' |
C4' |
C5' |
C8' |
124.9 |
123.4 |
| C5' |
C4' |
C8' |
C6' |
191.4 |
200.2 |
| C5' |
C4' |
C8' |
H8' |
311.4 |
318.9 |
| C5' |
C4' |
C8' |
H8'A |
71.4 |
81.4 |
| O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H5'A |
240.0 |
240.0 |
| C2' |
C6' |
C8' |
C4' |
9.6 |
358.6 |
| C8' |
C4' |
C3' |
H3' |
178.4 |
171.2 |
| C3' |
C4' |
C8' |
C5' |
127.9 |
125.8 |
| O4' |
C4' |
C8' |
C5' |
233.8 |
230.8 |
| C8' |
C4' |
C5' |
H5' |
296.0 |
62.7 |
| C8' |
C4' |
C5' |
H5'A |
56.0 |
182.7 |
| C7' |
C6' |
C8' |
C4' |
134.3 |
117.2 |
| C4' |
C8' |
C6' |
H6' |
249.5 |
240.0 |
| C6' |
C8' |
C4' |
H8' |
240.0 |
241.3 |
| C6' |
C8' |
C4' |
H8'A |
120.0 |
118.7 |
| H8' |
C8' |
C4' |
H8'A |
240.0 |
237.5 |
| C5' |
O5' |
P |
OP1 |
44.5 |
295.0 |
| C5' |
O5' |
P |
OP3 |
288.6 |
175.0 |
| O5' |
C5' |
C4' |
C8' |
176.0 |
302.7 |
| C4' |
C5' |
O5' |
H5' |
120.0 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
240.0 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
C8' |
296.0 |
62.7 |
| C4' |
C5' |
H5' |
H5'A |
120.6 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
239.5 |
240.0 |
| H5'A |
C5' |
C4' |
C8' |
56.0 |
182.7 |
| C4' |
C5' |
H5'A |
H5' |
239.4 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
120.5 |
120.0 |
| C7' |
C6' |
C2' |
H2' |
31.6 |
45.6 |
| C2' |
C6' |
C7' |
C8' |
118.2 |
114.4 |
| C2' |
C6' |
C7' |
H6' |
240.3 |
237.2 |
| C4' |
C8' |
C6' |
C7' |
134.3 |
117.2 |
| C8' |
C6' |
C7' |
H6' |
122.1 |
122.8 |
| C7' |
C6' |
C8' |
H8' |
14.3 |
358.4 |
| C7' |
C6' |
C8' |
H8'A |
254.3 |
235.9 |
| C8' |
C6' |
C2' |
H2' |
154.1 |
164.1 |
| C2' |
C6' |
C8' |
H6' |
120.1 |
118.6 |
| C4' |
C8' |
C6' |
H8' |
120.0 |
118.8 |
| C4' |
C8' |
C6' |
H8'A |
240.0 |
241.3 |
| C7' |
C6' |
C8' |
H6' |
244.8 |
237.2 |
| H8' |
C8' |
C6' |
H8'A |
120.0 |
122.5 |
| H6' |
C6' |
C2' |
H2' |
276.5 |
282.7 |
| C2' |
C6' |
H6' |
C8' |
243.7 |
245.6 |
| C7' |
C6' |
H6' |
C8' |
120.7 |
122.8 |
| H6' |
C6' |
C8' |
H8' |
129.5 |
121.3 |
| H6' |
C6' |
C8' |
H8'A |
9.5 |
358.8 |
| H7' |
C7' |
C6' |
C8' |
61.9 |
305.6 |
| H7' |
C7' |
C6' |
H6' |
299.7 |
182.8 |
| H7'A |
C7' |
H7' |
H7'B |
120.0 |
120.0 |
| H7'A |
C7' |
C6' |
C8' |
181.8 |
65.6 |
| H7'A |
C7' |
C6' |
H6' |
59.7 |
302.8 |
| H7' |
C7' |
H7'A |
H7'B |
240.0 |
239.9 |
| H7'B |
C7' |
C6' |
C8' |
301.8 |
185.5 |
| H7'B |
C7' |
C6' |
H6' |
179.7 |
62.7 |
| H7' |
C7' |
H7'B |
H7'A |
120.0 |
120.1 |
| C4' |
C8' |
H8' |
C6' |
247.1 |
245.0 |
| C4' |
C8' |
H8' |
H8'A |
123.5 |
122.5 |
| H8' |
C8' |
C6' |
H6' |
129.5 |
121.3 |
| C6' |
C8' |
H8' |
H8'A |
236.5 |
237.5 |
| C4' |
C8' |
H8'A |
C6' |
112.9 |
115.0 |
| C4' |
C8' |
H8'A |
H8' |
236.5 |
237.5 |
| H8'A |
C8' |
C6' |
H6' |
9.5 |
358.8 |
| C6' |
C8' |
H8'A |
H8' |
123.5 |
122.5 |
| HOP1 |
OP1 |
P |
OP3 |
230.2 |
60.0 |