PDB Chemical Component TR5
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 TR5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2' |
C2' |
1.440 |
1.429 |
| C2 |
N3 |
1.489 |
1.321 |
| C2 |
N1 |
1.500 |
1.330 |
| O3' |
C3' |
1.441 |
1.429 |
| N3 |
C4 |
1.350 |
1.337 |
| N1 |
C6 |
1.349 |
1.329 |
| C2' |
C3' |
1.542 |
1.548 |
| C2' |
C1' |
1.561 |
1.551 |
| C3' |
C4' |
1.520 |
1.540 |
| C4 |
C5 |
1.330 |
1.381 |
| C4 |
N9 |
1.338 |
1.364 |
| C6 |
C5 |
1.332 |
1.383 |
| C6 |
N61 |
1.357 |
1.372 |
| C62 |
N61 |
1.485 |
1.465 |
| C1' |
N9 |
1.505 |
1.465 |
| C1' |
O4' |
1.454 |
1.444 |
| C5 |
C7 |
1.323 |
1.461 |
| N9 |
C8 |
1.345 |
1.386 |
| N61 |
N71 |
1.309 |
1.402 |
| C4' |
C5' |
1.525 |
1.530 |
| C4' |
O4' |
1.429 |
1.438 |
| C5' |
O5' |
1.430 |
1.429 |
| C7 |
C8 |
1.337 |
1.347 |
| C7 |
C72 |
1.345 |
1.474 |
| N71 |
C72 |
1.354 |
1.309 |
| C72 |
N73 |
1.336 |
1.391 |
| O5' |
PB |
1.614 |
1.609 |
| O2 |
PB |
1.596 |
1.480 |
| O1 |
PB |
1.480 |
1.611 |
| PB |
O3 |
1.475 |
1.610 |
| O3 |
H1 |
0.950 |
0.968 |
| O1 |
H2 |
0.950 |
0.967 |
| C5' |
H3 |
1.100 |
1.090 |
| C5' |
H4 |
1.100 |
1.089 |
| C4' |
H5 |
1.100 |
1.090 |
| C3' |
H6 |
1.100 |
1.091 |
| O3' |
H7 |
0.950 |
0.967 |
| C2' |
H8 |
1.100 |
1.090 |
| O2' |
H9 |
0.950 |
0.967 |
| C1' |
H10 |
1.100 |
1.091 |
| C8 |
H11 |
1.080 |
1.079 |
| C2 |
H12 |
1.080 |
1.079 |
| C62 |
H13 |
1.100 |
1.090 |
| C62 |
H14 |
1.100 |
1.089 |
| C62 |
H15 |
1.100 |
1.090 |
| N73 |
H16 |
1.000 |
0.970 |
| N73 |
H17 |
1.000 |
0.969 |
Bond Angles for TR5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2' |
C2' |
C1' |
112.5 |
110.9 |
| O2' |
C2' |
H8 |
110.0 |
110.9 |
| C2 |
N1 |
C6 |
121.9 |
119.0 |
| N1 |
C2 |
H12 |
123.7 |
117.2 |
| O3' |
C3' |
H6 |
110.1 |
110.4 |
| N1 |
C6 |
N61 |
122.9 |
127.8 |
| C2' |
C3' |
H6 |
108.7 |
110.4 |
| C2' |
C1' |
N9 |
110.4 |
110.6 |
| C1' |
C2' |
H8 |
108.4 |
110.8 |
| C2' |
C1' |
H10 |
110.0 |
110.6 |
| C3' |
C4' |
H5 |
110.2 |
110.0 |
| C6 |
N61 |
N71 |
119.8 |
120.7 |
| C62 |
N61 |
N71 |
119.2 |
119.7 |
| C1' |
N9 |
C8 |
127.3 |
124.5 |
| N9 |
C1' |
H10 |
110.8 |
110.5 |
| C5 |
C7 |
C72 |
117.8 |
114.6 |
| N9 |
C8 |
H11 |
125.7 |
125.1 |
| N61 |
N71 |
C72 |
120.9 |
125.2 |
| C4' |
C5' |
H3 |
109.7 |
109.5 |
| C4' |
C5' |
H4 |
109.7 |
109.5 |
| O4' |
C4' |
H5 |
111.5 |
109.9 |
| C7 |
C8 |
H11 |
125.7 |
125.0 |
| C7 |
C72 |
N71 |
120.0 |
118.5 |
| C7 |
C72 |
N73 |
117.5 |
120.8 |
| N71 |
C72 |
N73 |
122.5 |
120.7 |
| C72 |
N73 |
H16 |
120.0 |
119.9 |
| C72 |
N73 |
H17 |
120.0 |
120.0 |
| O2 |
PB |
O3 |
109.9 |
109.5 |
| PB |
O3 |
H1 |
109.5 |
114.0 |
| H3 |
C5' |
H4 |
109.5 |
109.5 |
| H13 |
C62 |
H14 |
109.5 |
109.5 |
| H13 |
C62 |
H15 |
109.5 |
109.4 |
| H14 |
C62 |
H15 |
109.5 |
109.5 |
| H16 |
N73 |
H17 |
120.0 |
120.0 |
Torsion Angles for TR5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2' |
C2' |
C3' |
H6 |
124.7 |
102.3 |
| O2' |
C2' |
C1' |
N9 |
226.5 |
273.8 |
| C1' |
C2' |
O2' |
H8 |
120.9 |
123.6 |
| O2' |
C2' |
C1' |
H10 |
349.0 |
36.6 |
| C2 |
N1 |
C6 |
N61 |
180.3 |
180.0 |
| C2' |
C3' |
O3' |
H6 |
121.7 |
122.6 |
| O3' |
C3' |
C4' |
H5 |
5.1 |
358.6 |
| C6 |
N1 |
C2 |
H12 |
180.0 |
180.2 |
| N1 |
C6 |
N61 |
N71 |
180.1 |
180.0 |
| O3' |
C3' |
C2' |
H6 |
237.5 |
237.4 |
| C2' |
C3' |
C4' |
H5 |
127.6 |
117.4 |
| O2' |
C2' |
C1' |
H8 |
238.2 |
236.4 |
| C1' |
C2' |
C3' |
H6 |
247.2 |
220.4 |
| C2' |
C1' |
N9 |
C8 |
245.9 |
265.0 |
| N9 |
C1' |
C2' |
H10 |
237.5 |
237.2 |
| C3' |
C4' |
C5' |
H3 |
283.5 |
64.3 |
| C3' |
C4' |
C5' |
H4 |
43.8 |
304.3 |
| O4' |
C4' |
C3' |
H5 |
238.0 |
240.5 |
| C4 |
C5 |
C7 |
C72 |
179.9 |
179.8 |
| C4 |
N9 |
C1' |
H10 |
301.8 |
321.8 |
| C4 |
N9 |
C8 |
H11 |
180.0 |
180.2 |
| C6 |
C5 |
C7 |
C72 |
0.1 |
360.0 |
| C62 |
N61 |
C6 |
N71 |
179.9 |
180.1 |
| C6 |
N61 |
N71 |
C72 |
359.9 |
359.6 |
| C6 |
N61 |
C62 |
N71 |
180.1 |
179.9 |
| C62 |
N61 |
N71 |
C72 |
180.0 |
179.5 |
| N9 |
C1' |
C2' |
H8 |
348.3 |
37.3 |
| C2' |
C1' |
N9 |
H10 |
122.1 |
122.8 |
| C1' |
N9 |
C8 |
H11 |
358.2 |
359.9 |
| C1' |
O4' |
C4' |
H5 |
224.2 |
266.9 |
| C5 |
C7 |
C8 |
H11 |
179.9 |
180.0 |
| C5 |
C7 |
C72 |
N71 |
0.3 |
360.0 |
| C5 |
C7 |
C72 |
N73 |
179.7 |
180.0 |
| C8 |
N9 |
C1' |
H10 |
123.8 |
142.2 |
| C7 |
C8 |
N9 |
H11 |
180.0 |
180.1 |
| C7 |
C72 |
N71 |
N61 |
359.8 |
0.3 |
| N61 |
N71 |
C72 |
N73 |
180.4 |
180.2 |
| H3 |
C5' |
C4' |
H4 |
239.7 |
120.0 |
| C3' |
C4' |
O4' |
H5 |
121.2 |
119.6 |
| O4' |
C4' |
C5' |
H3 |
166.4 |
306.5 |
| O4' |
C4' |
C5' |
H4 |
286.7 |
186.5 |
| N9 |
C8 |
C7 |
H11 |
180.0 |
179.9 |
| N61 |
N71 |
C72 |
C7 |
359.8 |
0.3 |
| C72 |
C7 |
C8 |
H11 |
0.3 |
0.0 |
| N71 |
C72 |
C7 |
N73 |
180.6 |
180.0 |
| C7 |
C72 |
N73 |
H16 |
180.6 |
0.1 |
| C7 |
C72 |
N73 |
H17 |
0.6 |
179.9 |
| C7 |
C72 |
N71 |
N73 |
179.4 |
180.0 |
| N71 |
C72 |
N73 |
H16 |
360.0 |
180.1 |
| N71 |
C72 |
N73 |
H17 |
180.0 |
360.0 |
| C7 |
C72 |
N73 |
N71 |
180.6 |
180.0 |
| H16 |
N73 |
C72 |
H17 |
180.0 |
180.1 |
| O5' |
PB |
O3 |
H1 |
111.1 |
180.0 |
| O2 |
PB |
O3 |
H1 |
0.0 |
59.9 |
| O1 |
PB |
O3 |
H1 |
234.9 |
300.0 |
| C4' |
C5' |
H3 |
H4 |
120.4 |
240.0 |
| C4' |
C5' |
H4 |
H3 |
239.6 |
120.0 |
| H5 |
C4' |
C5' |
H3 |
44.8 |
185.5 |
| H5 |
C4' |
C5' |
H4 |
165.1 |
65.5 |
| H6 |
C3' |
C4' |
H5 |
244.6 |
236.1 |
| H7 |
O3' |
C3' |
H6 |
58.3 |
302.6 |
| O2' |
C2' |
H8 |
C1' |
123.4 |
123.6 |
| H8 |
C2' |
C3' |
H6 |
3.3 |
338.6 |
| H8 |
C2' |
C1' |
N9 |
348.3 |
37.3 |
| H8 |
C2' |
C1' |
H10 |
110.8 |
160.2 |
| H9 |
O2' |
C2' |
C1' |
61.5 |
185.8 |
| H9 |
O2' |
C2' |
H8 |
300.6 |
62.3 |
| C2' |
C1' |
H10 |
N9 |
237.7 |
237.1 |
| H10 |
C1' |
C2' |
H8 |
110.8 |
160.2 |
| H10 |
C1' |
N9 |
C8 |
123.8 |
142.2 |
| H12 |
C2 |
N1 |
C6 |
180.0 |
180.2 |
| H13 |
C62 |
N61 |
N71 |
360.0 |
270.0 |
| H14 |
C62 |
H13 |
H15 |
120.0 |
120.0 |
| H14 |
C62 |
N61 |
N71 |
120.0 |
30.0 |
| H13 |
C62 |
H14 |
H15 |
240.0 |
240.0 |
| H15 |
C62 |
N61 |
N71 |
240.0 |
150.0 |
| H13 |
C62 |
H15 |
H14 |
120.0 |
120.0 |
| C72 |
N73 |
H16 |
H17 |
180.0 |
179.9 |
| C72 |
N73 |
H17 |
H16 |
180.0 |
180.1 |