PDB Chemical Component U6M
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 U6M
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C7 |
C6 |
1.512 |
1.507 |
| C6 |
C5 |
1.393 |
1.351 |
| C6 |
N1 |
1.444 |
1.369 |
| C5 |
C4 |
1.387 |
1.416 |
| O4' |
C1' |
1.451 |
1.444 |
| O4' |
C4' |
1.444 |
1.437 |
| O4 |
C4 |
1.262 |
1.218 |
| C4 |
N3 |
1.341 |
1.348 |
| N1 |
C1' |
1.483 |
1.466 |
| N1 |
C2 |
1.384 |
1.345 |
| C1' |
C2' |
1.497 |
1.550 |
| C4' |
C5' |
1.525 |
1.530 |
| C4' |
C3' |
1.512 |
1.541 |
| N3 |
C2 |
1.354 |
1.346 |
| C2 |
O2 |
1.243 |
1.216 |
| O3' |
C3' |
1.441 |
1.429 |
| C5' |
O5' |
1.440 |
1.429 |
| C3' |
C2' |
1.510 |
1.548 |
| C2' |
O2' |
1.423 |
1.429 |
| O3P |
P |
1.489 |
1.480 |
| O5' |
P |
1.616 |
1.610 |
| P |
O1P |
1.486 |
1.610 |
| P |
O2P |
1.510 |
1.610 |
| N3 |
H1 |
1.000 |
0.970 |
| C5 |
H2 |
1.080 |
1.080 |
| C7 |
H5 |
1.100 |
1.090 |
| C7 |
H6 |
1.100 |
1.090 |
| C7 |
H7 |
1.100 |
1.089 |
| C1' |
H8 |
1.100 |
1.090 |
| C2' |
H9 |
1.100 |
1.089 |
| O2' |
H10 |
0.950 |
0.967 |
| C3' |
H11 |
1.100 |
1.090 |
| O3' |
H12 |
0.950 |
0.967 |
| C4' |
H13 |
1.100 |
1.090 |
| C5' |
H14 |
1.100 |
1.090 |
| C5' |
H15 |
1.100 |
1.089 |
| O1P |
H16 |
0.950 |
0.967 |
| O2P |
H17 |
0.950 |
0.967 |
Bond Angles for U6M
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C7 |
C6 |
N1 |
122.4 |
120.2 |
| C6 |
C5 |
H2 |
119.4 |
120.4 |
| C6 |
N1 |
C1' |
121.2 |
119.7 |
| O4' |
C1' |
C2' |
105.8 |
103.5 |
| O4' |
C1' |
H8 |
109.9 |
110.7 |
| O4' |
C4' |
C5' |
107.7 |
109.9 |
| O4' |
C4' |
C3' |
106.0 |
107.3 |
| O4' |
C4' |
H13 |
110.2 |
109.9 |
| C4 |
N3 |
H1 |
119.7 |
119.9 |
| N1 |
C1' |
C2' |
116.7 |
110.6 |
| N1 |
C1' |
H8 |
109.5 |
110.6 |
| C1' |
C2' |
O2' |
107.6 |
110.9 |
| C2' |
C1' |
H8 |
109.3 |
110.7 |
| C1' |
C2' |
H9 |
111.5 |
110.9 |
| C4' |
C5' |
O5' |
103.8 |
109.5 |
| C5' |
C4' |
H13 |
109.1 |
109.9 |
| C4' |
C5' |
H14 |
110.9 |
109.4 |
| C4' |
C5' |
H15 |
110.9 |
109.5 |
| C4' |
C3' |
H11 |
111.9 |
110.5 |
| O3' |
C3' |
H11 |
113.1 |
110.4 |
| C5' |
O5' |
P |
120.5 |
123.0 |
| O5' |
C5' |
H14 |
110.9 |
109.5 |
| O5' |
C5' |
H15 |
110.9 |
109.5 |
| C3' |
C2' |
H9 |
111.3 |
110.9 |
| O2' |
C2' |
H9 |
112.7 |
110.8 |
| C2' |
O2' |
H10 |
109.5 |
114.0 |
| O3P |
P |
O1P |
110.2 |
109.5 |
| O3P |
P |
O2P |
113.6 |
109.4 |
| O5' |
P |
O1P |
109.6 |
109.5 |
| O5' |
P |
O2P |
102.9 |
109.5 |
| O1P |
P |
O2P |
113.1 |
109.4 |
| P |
O1P |
H16 |
109.5 |
114.0 |
| P |
O2P |
H17 |
109.5 |
114.1 |
| H5 |
C7 |
H6 |
109.5 |
109.4 |
| H5 |
C7 |
H7 |
109.5 |
109.5 |
| H6 |
C7 |
H7 |
109.5 |
109.5 |
| H14 |
C5' |
H15 |
109.5 |
109.5 |
Torsion Angles for U6M
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C7 |
C6 |
C5 |
H2 |
333.8 |
360.0 |
| C7 |
C6 |
N1 |
C1' |
30.2 |
359.8 |
| N1 |
C6 |
C5 |
H2 |
171.8 |
179.8 |
| C6 |
N1 |
C1' |
C2' |
138.5 |
115.0 |
| C6 |
N1 |
C1' |
H8 |
13.8 |
352.1 |
| C5 |
C4 |
N3 |
H1 |
195.0 |
180.0 |
| N1 |
C1' |
O4' |
C2' |
235.8 |
241.5 |
| N1 |
C1' |
O4' |
H8 |
117.9 |
122.9 |
| O4' |
C1' |
C2' |
O2' |
150.0 |
155.2 |
| C2' |
C1' |
O4' |
H8 |
242.1 |
241.4 |
| O4' |
C1' |
C2' |
H9 |
274.0 |
278.8 |
| C4' |
O4' |
C1' |
C2' |
344.1 |
319.9 |
| C4' |
O4' |
C1' |
H8 |
102.0 |
78.6 |
| O4' |
C4' |
C5' |
O5' |
168.0 |
66.5 |
| C5' |
C4' |
O4' |
H13 |
241.0 |
239.0 |
| O4' |
C4' |
C5' |
H14 |
287.1 |
186.4 |
| O4' |
C4' |
C5' |
H15 |
48.9 |
306.4 |
| O4' |
C4' |
C3' |
H11 |
148.7 |
116.7 |
| O4 |
C4 |
N3 |
H1 |
356.6 |
0.0 |
| O4' |
C1' |
N1 |
C2' |
117.1 |
114.1 |
| O4' |
C1' |
N1 |
H8 |
241.8 |
237.0 |
| N1 |
C1' |
C2' |
O2' |
266.9 |
273.7 |
| C2' |
C1' |
N1 |
H8 |
124.7 |
123.0 |
| N1 |
C1' |
C2' |
H9 |
30.9 |
37.3 |
| O4' |
C1' |
C2' |
H8 |
118.3 |
118.7 |
| N1 |
C1' |
C2' |
H8 |
235.2 |
237.1 |
| C3' |
C2' |
C1' |
H9 |
119.0 |
118.2 |
| O2' |
C2' |
C1' |
H9 |
236.0 |
236.4 |
| C1' |
C2' |
O2' |
H10 |
180.0 |
180.0 |
| O4' |
C4' |
C5' |
C3' |
242.5 |
242.2 |
| O4' |
C4' |
C5' |
H13 |
119.7 |
121.0 |
| C5' |
C4' |
C3' |
H11 |
30.2 |
357.3 |
| C4' |
C5' |
O5' |
P |
178.5 |
180.0 |
| O5' |
C5' |
C4' |
H14 |
240.9 |
240.0 |
| O5' |
C5' |
C4' |
H15 |
119.1 |
120.0 |
| H14 |
C5' |
C4' |
H15 |
238.2 |
240.0 |
| O4' |
C4' |
C3' |
C5' |
118.5 |
119.4 |
| O4' |
C4' |
C3' |
H13 |
241.2 |
240.5 |
| O3' |
C3' |
C4' |
H11 |
124.6 |
122.6 |
| C4' |
C3' |
C2' |
H9 |
82.1 |
97.3 |
| O4' |
C4' |
C3' |
O3' |
273.2 |
239.2 |
| C4' |
C3' |
O3' |
H11 |
236.1 |
237.4 |
| O3' |
C3' |
C2' |
H9 |
195.7 |
216.1 |
| O5' |
C5' |
C4' |
H13 |
48.3 |
305.4 |
| C4' |
C5' |
O5' |
H14 |
119.1 |
120.0 |
| C4' |
C5' |
O5' |
H15 |
240.9 |
240.0 |
| C5' |
O5' |
P |
O1P |
325.4 |
65.0 |
| C5' |
O5' |
P |
O2P |
204.8 |
185.0 |
| H14 |
C5' |
O5' |
H15 |
121.8 |
120.0 |
| O4' |
C4' |
C3' |
C2' |
28.3 |
358.0 |
| C3' |
C2' |
C1' |
H8 |
274.8 |
278.4 |
| C1' |
C2' |
C3' |
H9 |
240.8 |
241.8 |
| O2' |
C2' |
C3' |
H9 |
126.3 |
123.6 |
| C3' |
C2' |
O2' |
H10 |
291.1 |
292.7 |
| O2' |
C2' |
C1' |
H8 |
31.7 |
36.6 |
| C1' |
C2' |
O2' |
H9 |
123.3 |
123.6 |
| C3' |
C2' |
O2' |
H9 |
234.5 |
236.3 |
| O5' |
P |
O3P |
O1P |
241.0 |
120.0 |
| O5' |
P |
O3P |
O2P |
112.9 |
239.9 |
| O1P |
P |
O3P |
O2P |
231.9 |
119.9 |
| O3P |
P |
O1P |
H16 |
0.0 |
180.0 |
| O3P |
P |
O2P |
H17 |
0.0 |
60.0 |
| P |
O5' |
C5' |
H14 |
59.4 |
60.0 |
| P |
O5' |
C5' |
H15 |
297.6 |
300.0 |
| O3P |
P |
O5' |
O1P |
119.4 |
240.0 |
| O3P |
P |
O5' |
O2P |
240.0 |
120.0 |
| O1P |
P |
O5' |
O2P |
120.6 |
240.0 |
| O5' |
P |
O1P |
H16 |
117.5 |
60.0 |
| O5' |
P |
O2P |
H17 |
244.7 |
180.0 |
| O3P |
P |
O1P |
O2P |
128.4 |
240.1 |
| O5' |
P |
O1P |
O2P |
245.8 |
120.1 |
| O1P |
P |
O2P |
H17 |
126.6 |
300.0 |
| O3P |
P |
O2P |
O1P |
233.5 |
120.0 |
| O5' |
P |
O2P |
O1P |
118.1 |
240.0 |
| O2P |
P |
O1P |
H16 |
231.6 |
300.0 |
| H5 |
C7 |
C6 |
N1 |
340.9 |
180.2 |
| H6 |
C7 |
H5 |
H7 |
120.0 |
120.0 |
| H6 |
C7 |
C6 |
N1 |
101.0 |
300.1 |
| H5 |
C7 |
H6 |
H7 |
240.0 |
240.0 |
| H7 |
C7 |
C6 |
N1 |
220.9 |
60.2 |
| H5 |
C7 |
H7 |
H6 |
120.0 |
120.0 |
| O4' |
C1' |
H8 |
C2' |
244.3 |
245.8 |
| N1 |
C1' |
H8 |
C2' |
128.9 |
122.9 |
| H8 |
C1' |
C2' |
O2' |
31.7 |
36.6 |
| H8 |
C1' |
C2' |
H9 |
155.7 |
160.2 |
| C1' |
C2' |
H9 |
O2' |
238.9 |
236.4 |
| H9 |
C2' |
C1' |
H8 |
155.7 |
160.2 |
| H9 |
C2' |
O2' |
H10 |
56.7 |
56.4 |
| H10 |
O2' |
C2' |
H9 |
56.7 |
56.4 |
| H11 |
C3' |
C2' |
H9 |
321.7 |
338.6 |
| H12 |
O3' |
C3' |
H11 |
303.8 |
298.9 |
| O4' |
C4' |
H13 |
C5' |
241.9 |
239.0 |
| O4' |
C4' |
H13 |
C3' |
116.1 |
117.9 |
| H13 |
C4' |
C5' |
O5' |
48.3 |
305.4 |
| H13 |
C4' |
C5' |
H14 |
167.4 |
65.4 |
| H13 |
C4' |
C5' |
H15 |
289.2 |
185.4 |
| H13 |
C4' |
C3' |
H11 |
267.5 |
236.2 |
| C4' |
C5' |
H14 |
O5' |
245.3 |
240.0 |
| H14 |
C5' |
C4' |
H13 |
167.4 |
65.4 |
| C4' |
C5' |
H14 |
H15 |
122.6 |
120.0 |
| H14 |
C5' |
O5' |
P |
59.4 |
60.0 |
| O5' |
C5' |
H14 |
H15 |
237.4 |
240.0 |
| C4' |
C5' |
H15 |
O5' |
114.7 |
120.0 |
| H15 |
C5' |
C4' |
H13 |
289.2 |
185.4 |
| C4' |
C5' |
H15 |
H14 |
237.4 |
240.0 |
| H15 |
C5' |
O5' |
P |
297.6 |
300.0 |
| O5' |
C5' |
H15 |
H14 |
122.6 |
120.0 |
| H16 |
O1P |
P |
O2P |
231.6 |
300.0 |