PDB Chemical Component THU
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 THU
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.350 |
1.343 |
| N1 |
C6 |
1.403 |
1.464 |
| N1 |
C1' |
1.638 |
1.465 |
| C2 |
O2 |
1.225 |
1.215 |
| C2 |
N3 |
1.354 |
1.344 |
| N3 |
C4 |
1.461 |
1.345 |
| N3 |
HN3 |
1.000 |
0.970 |
| C4 |
O4 |
1.425 |
1.212 |
| C4 |
C5 |
1.555 |
1.508 |
| C5 |
C6 |
1.540 |
1.530 |
| C5 |
H51 |
1.100 |
1.090 |
| C5 |
H52 |
1.100 |
1.090 |
| C6 |
H61 |
1.100 |
1.090 |
| C6 |
H62 |
1.100 |
1.090 |
| C1' |
C2' |
1.497 |
1.550 |
| C1' |
O4' |
1.420 |
1.436 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
C3' |
1.479 |
1.554 |
| C2' |
H2'1 |
1.100 |
1.090 |
| C2' |
H2'2 |
1.100 |
1.090 |
| C3' |
O3' |
1.398 |
1.430 |
| C3' |
C4' |
1.532 |
1.544 |
| C3' |
H3' |
1.099 |
1.090 |
| O3' |
HO3' |
0.950 |
0.966 |
| C4' |
O4' |
1.423 |
1.432 |
| C4' |
C5' |
1.497 |
1.530 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
O5' |
1.431 |
1.429 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| O5' |
HO5' |
0.950 |
0.967 |
Bond Angles for THU
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
123.0 |
121.0 |
| C2 |
N1 |
C1' |
114.3 |
119.5 |
| N1 |
C2 |
O2 |
120.9 |
119.2 |
| N1 |
C2 |
N3 |
118.7 |
121.6 |
| C6 |
N1 |
C1' |
105.3 |
119.5 |
| N1 |
C6 |
C5 |
109.5 |
109.5 |
| N1 |
C6 |
H61 |
109.5 |
109.4 |
| N1 |
C6 |
H62 |
109.5 |
109.5 |
| N1 |
C1' |
C2' |
144.3 |
110.3 |
| N1 |
C1' |
O4' |
98.2 |
110.3 |
| N1 |
C1' |
H1' |
96.3 |
110.3 |
| O2 |
C2 |
N3 |
120.3 |
119.3 |
| C2 |
N3 |
C4 |
122.5 |
120.9 |
| C2 |
N3 |
HN3 |
118.8 |
119.5 |
| C4 |
N3 |
HN3 |
118.8 |
119.6 |
| N3 |
C4 |
O4 |
113.7 |
120.0 |
| N3 |
C4 |
C5 |
115.5 |
120.0 |
| O4 |
C4 |
C5 |
106.7 |
120.0 |
| C4 |
C5 |
C6 |
109.5 |
109.2 |
| C4 |
C5 |
H51 |
109.5 |
109.5 |
| C4 |
C5 |
H52 |
109.4 |
109.5 |
| C6 |
C5 |
H51 |
109.5 |
109.5 |
| C6 |
C5 |
H52 |
109.5 |
109.6 |
| C5 |
C6 |
H61 |
109.5 |
109.5 |
| C5 |
C6 |
H62 |
109.5 |
109.5 |
| H51 |
C5 |
H52 |
109.5 |
109.6 |
| H61 |
C6 |
H62 |
109.5 |
109.5 |
| C2' |
C1' |
O4' |
117.5 |
105.1 |
| C2' |
C1' |
H1' |
48.1 |
110.3 |
| C1' |
C2' |
C3' |
99.8 |
100.9 |
| C1' |
C2' |
H2'1 |
112.8 |
111.1 |
| C1' |
C2' |
H2'2 |
114.8 |
111.1 |
| O4' |
C1' |
H1' |
165.5 |
110.3 |
| C1' |
O4' |
C4' |
103.5 |
110.0 |
| C3' |
C2' |
H2'1 |
112.8 |
111.1 |
| C3' |
C2' |
H2'2 |
114.8 |
111.1 |
| C2' |
C3' |
O3' |
111.9 |
110.8 |
| C2' |
C3' |
C4' |
108.7 |
102.2 |
| C2' |
C3' |
H3' |
108.7 |
110.8 |
| H2'1 |
C2' |
H2'2 |
102.3 |
111.0 |
| O3' |
C3' |
C4' |
110.3 |
110.8 |
| O3' |
C3' |
H3' |
106.9 |
111.0 |
| C3' |
O3' |
HO3' |
109.5 |
106.8 |
| C4' |
C3' |
H3' |
110.3 |
110.9 |
| C3' |
C4' |
O4' |
109.4 |
107.6 |
| C3' |
C4' |
C5' |
114.0 |
109.8 |
| C3' |
C4' |
H4' |
107.5 |
109.9 |
| O4' |
C4' |
C5' |
112.4 |
109.9 |
| O4' |
C4' |
H4' |
109.2 |
109.8 |
| C5' |
C4' |
H4' |
104.0 |
109.8 |
| C4' |
C5' |
O5' |
106.6 |
109.5 |
| C4' |
C5' |
H5'1 |
110.4 |
109.5 |
| C4' |
C5' |
H5'2 |
111.1 |
109.5 |
| O5' |
C5' |
H5'1 |
110.4 |
109.4 |
| O5' |
C5' |
H5'2 |
111.1 |
109.5 |
| C5' |
O5' |
HO5' |
109.5 |
106.8 |
| H5'1 |
C5' |
H5'2 |
107.3 |
109.5 |
Torsion Angles for THU
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
129.6 |
179.7 |
| C2 |
N1 |
C6 |
C5 |
49.2 |
324.4 |
| C2 |
N1 |
C6 |
H61 |
169.2 |
84.4 |
| C2 |
N1 |
C6 |
H62 |
289.2 |
204.4 |
| C2 |
N1 |
C1' |
C2' |
47.9 |
296.9 |
| C2 |
N1 |
C1' |
O4' |
227.5 |
181.2 |
| C2 |
N1 |
C1' |
H1' |
46.9 |
59.0 |
| O2 |
C2 |
N1 |
N3 |
180.5 |
180.5 |
| N1 |
C2 |
N3 |
C4 |
0.3 |
12.6 |
| N1 |
C2 |
N3 |
HN3 |
180.3 |
192.3 |
| C2 |
N1 |
C6 |
C1' |
226.7 |
180.3 |
| C6 |
N1 |
C2 |
O2 |
157.1 |
185.7 |
| C6 |
N1 |
C2 |
N3 |
336.6 |
5.1 |
| C6 |
N1 |
C1' |
C2' |
270.0 |
117.2 |
| C6 |
N1 |
C1' |
O4' |
89.6 |
1.5 |
| C6 |
N1 |
C1' |
H1' |
268.9 |
239.3 |
| C4 |
C5 |
C6 |
N1 |
310.2 |
46.7 |
| N1 |
C6 |
C5 |
H51 |
190.2 |
166.6 |
| N1 |
C6 |
C5 |
H52 |
70.2 |
286.8 |
| C5 |
C6 |
N1 |
H61 |
240.0 |
240.0 |
| C5 |
C6 |
N1 |
H62 |
120.0 |
120.0 |
| H61 |
C6 |
N1 |
H62 |
240.0 |
240.0 |
| C2 |
N1 |
C1' |
C6 |
137.9 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
27.5 |
6.0 |
| C1' |
N1 |
C2 |
N3 |
206.9 |
185.4 |
| C1' |
N1 |
C6 |
C5 |
182.4 |
144.1 |
| C1' |
N1 |
C6 |
H61 |
302.4 |
264.1 |
| C1' |
N1 |
C6 |
H62 |
62.5 |
24.1 |
| C2' |
C1' |
N1 |
O4' |
180.4 |
115.7 |
| C2' |
C1' |
N1 |
H1' |
1.0 |
237.9 |
| N1 |
C1' |
C2' |
C3' |
179.8 |
204.6 |
| N1 |
C1' |
C2' |
H2'1 |
299.8 |
322.5 |
| N1 |
C1' |
C2' |
H2'2 |
56.5 |
86.7 |
| O4' |
C1' |
N1 |
H1' |
180.6 |
122.2 |
| N1 |
C1' |
O4' |
C4' |
186.9 |
143.4 |
| O2 |
C2 |
N1 |
C6 |
157.1 |
185.7 |
| O2 |
C2 |
N1 |
C1' |
27.5 |
6.0 |
| N1 |
C2 |
O2 |
N3 |
179.5 |
179.5 |
| O2 |
C2 |
N3 |
C4 |
179.8 |
192.1 |
| O2 |
C2 |
N3 |
HN3 |
359.8 |
11.7 |
| N3 |
C2 |
N1 |
C6 |
336.6 |
5.1 |
| N3 |
C2 |
N1 |
C1' |
206.9 |
185.4 |
| N1 |
C2 |
N3 |
O2 |
180.5 |
180.5 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.3 |
| C2 |
N3 |
C4 |
O4 |
116.6 |
184.2 |
| C2 |
N3 |
C4 |
C5 |
352.7 |
4.1 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.7 |
| O4 |
C4 |
N3 |
C5 |
123.9 |
180.1 |
| N3 |
C4 |
C5 |
C6 |
31.8 |
325.8 |
| N3 |
C4 |
C5 |
H51 |
151.8 |
205.9 |
| N3 |
C4 |
C5 |
H52 |
271.8 |
85.8 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.3 |
| HN3 |
N3 |
C4 |
O4 |
296.6 |
4.5 |
| HN3 |
N3 |
C4 |
C5 |
172.7 |
184.4 |
| O4 |
C4 |
N3 |
HN3 |
296.6 |
4.5 |
| N3 |
C4 |
O4 |
C5 |
231.5 |
179.9 |
| O4 |
C4 |
C5 |
C6 |
264.3 |
145.7 |
| O4 |
C4 |
C5 |
H51 |
24.3 |
25.8 |
| O4 |
C4 |
C5 |
H52 |
144.3 |
265.7 |
| N1 |
C6 |
C5 |
C4 |
310.2 |
46.7 |
| C5 |
C4 |
N3 |
HN3 |
172.7 |
184.4 |
| N3 |
C4 |
C5 |
O4 |
127.4 |
180.1 |
| C6 |
C5 |
C4 |
H51 |
240.0 |
119.9 |
| C6 |
C5 |
C4 |
H52 |
120.0 |
240.0 |
| C4 |
C5 |
C6 |
H61 |
190.2 |
286.7 |
| C4 |
C5 |
C6 |
H62 |
70.2 |
166.7 |
| H51 |
C5 |
C4 |
H52 |
240.0 |
120.1 |
| C5 |
C6 |
N1 |
C1' |
182.4 |
144.1 |
| N1 |
C6 |
C5 |
H61 |
120.0 |
120.0 |
| N1 |
C6 |
C5 |
H62 |
240.0 |
240.0 |
| C4 |
C5 |
C6 |
H51 |
120.0 |
240.1 |
| C4 |
C5 |
C6 |
H52 |
240.0 |
119.9 |
| H51 |
C5 |
C6 |
H52 |
120.0 |
239.8 |
| H61 |
C6 |
C5 |
H62 |
120.0 |
120.0 |
| C4 |
C5 |
H51 |
C6 |
240.0 |
119.7 |
| C4 |
C5 |
H51 |
H52 |
120.0 |
239.9 |
| C6 |
C5 |
H51 |
H52 |
240.0 |
120.2 |
| H51 |
C5 |
C6 |
H61 |
70.2 |
46.6 |
| H51 |
C5 |
C6 |
H62 |
310.2 |
286.6 |
| C4 |
C5 |
H52 |
C6 |
120.0 |
240.3 |
| C4 |
C5 |
H52 |
H51 |
240.0 |
120.1 |
| C6 |
C5 |
H52 |
H51 |
120.0 |
239.8 |
| H52 |
C5 |
C6 |
H61 |
310.2 |
166.8 |
| H52 |
C5 |
C6 |
H62 |
190.2 |
46.8 |
| H61 |
C6 |
N1 |
C1' |
302.4 |
264.1 |
| N1 |
C6 |
H61 |
C5 |
240.0 |
240.0 |
| N1 |
C6 |
H61 |
H62 |
120.0 |
120.0 |
| H61 |
C6 |
C5 |
H51 |
70.2 |
46.6 |
| H61 |
C6 |
C5 |
H52 |
310.2 |
166.8 |
| C5 |
C6 |
H61 |
H62 |
240.0 |
240.0 |
| H62 |
C6 |
N1 |
C1' |
62.5 |
24.1 |
| N1 |
C6 |
H62 |
C5 |
120.0 |
120.0 |
| N1 |
C6 |
H62 |
H61 |
240.0 |
240.0 |
| H62 |
C6 |
C5 |
H51 |
310.2 |
286.6 |
| H62 |
C6 |
C5 |
H52 |
190.2 |
46.8 |
| C5 |
C6 |
H62 |
H61 |
120.0 |
120.0 |
| N1 |
C1' |
C2' |
O4' |
179.5 |
241.1 |
| N1 |
C1' |
C2' |
H1' |
358.6 |
122.1 |
| O4' |
C1' |
C2' |
H1' |
179.1 |
241.1 |
| C2' |
C1' |
O4' |
C4' |
6.6 |
24.5 |
| C3' |
C2' |
C1' |
H2'1 |
240.0 |
242.1 |
| C3' |
C2' |
C1' |
H2'2 |
123.3 |
117.9 |
| C1' |
C2' |
C3' |
O3' |
115.5 |
275.9 |
| C1' |
C2' |
C3' |
C4' |
353.4 |
34.1 |
| C1' |
C2' |
C3' |
H3' |
233.3 |
152.3 |
| H2'1 |
C2' |
C1' |
H2'2 |
243.3 |
235.8 |
| N1 |
C1' |
O4' |
C2' |
180.3 |
118.9 |
| N1 |
C1' |
O4' |
H1' |
177.5 |
237.8 |
| C2' |
C1' |
O4' |
H1' |
357.3 |
118.9 |
| O4' |
C1' |
C2' |
C3' |
0.2 |
323.5 |
| O4' |
C1' |
C2' |
H2'1 |
120.2 |
81.5 |
| O4' |
C1' |
C2' |
H2'2 |
236.9 |
205.6 |
| C3' |
C4' |
O4' |
C1' |
349.6 |
358.2 |
| C1' |
O4' |
C4' |
C5' |
117.3 |
117.8 |
| C1' |
O4' |
C4' |
H4' |
232.2 |
238.7 |
| N1 |
C1' |
H1' |
C2' |
179.2 |
237.9 |
| N1 |
C1' |
H1' |
O4' |
182.4 |
122.2 |
| C2' |
C1' |
H1' |
O4' |
3.3 |
244.3 |
| H1' |
C1' |
C2' |
C3' |
181.2 |
82.5 |
| H1' |
C1' |
C2' |
H2'1 |
301.2 |
200.4 |
| H1' |
C1' |
C2' |
H2'2 |
57.8 |
324.6 |
| H1' |
C1' |
O4' |
C4' |
9.3 |
265.5 |
| C3' |
C2' |
C1' |
O4' |
0.2 |
323.5 |
| C3' |
C2' |
C1' |
H1' |
181.2 |
82.5 |
| C1' |
C2' |
C3' |
H2'1 |
120.0 |
117.9 |
| C1' |
C2' |
C3' |
H2'2 |
236.7 |
242.1 |
| H2'1 |
C2' |
C3' |
H2'2 |
116.7 |
124.2 |
| O3' |
C3' |
C2' |
C4' |
122.1 |
241.8 |
| O3' |
C3' |
C2' |
H3' |
242.1 |
123.6 |
| C2' |
C3' |
O3' |
HO3' |
125.0 |
298.5 |
| C4' |
C3' |
C2' |
H3' |
120.0 |
241.8 |
| C2' |
C3' |
C4' |
O4' |
11.4 |
338.7 |
| C2' |
C3' |
C4' |
C5' |
244.5 |
219.1 |
| C2' |
C3' |
C4' |
H4' |
129.8 |
98.2 |
| H2'1 |
C2' |
C1' |
O4' |
120.2 |
81.5 |
| H2'1 |
C2' |
C1' |
H1' |
301.2 |
200.4 |
| C1' |
C2' |
H2'1 |
C3' |
247.8 |
248.5 |
| C1' |
C2' |
H2'1 |
H2'2 |
123.9 |
124.2 |
| C3' |
C2' |
H2'1 |
H2'2 |
236.1 |
235.8 |
| H2'1 |
C2' |
C3' |
O3' |
355.5 |
158.0 |
| H2'1 |
C2' |
C3' |
C4' |
233.3 |
276.2 |
| H2'1 |
C2' |
C3' |
H3' |
113.3 |
34.4 |
| H2'2 |
C2' |
C1' |
O4' |
236.9 |
205.6 |
| H2'2 |
C2' |
C1' |
H1' |
57.8 |
324.6 |
| C1' |
C2' |
H2'2 |
C3' |
114.9 |
111.5 |
| C1' |
C2' |
H2'2 |
H2'1 |
237.4 |
235.8 |
| C3' |
C2' |
H2'2 |
H2'1 |
122.6 |
124.2 |
| H2'2 |
C2' |
C3' |
O3' |
238.8 |
33.8 |
| H2'2 |
C2' |
C3' |
C4' |
116.7 |
152.0 |
| H2'2 |
C2' |
C3' |
H3' |
356.6 |
270.2 |
| O3' |
C3' |
C2' |
H2'1 |
355.5 |
158.0 |
| O3' |
C3' |
C2' |
H2'2 |
238.8 |
33.8 |
| C2' |
C3' |
O3' |
C4' |
238.8 |
112.8 |
| C2' |
C3' |
O3' |
H3' |
118.9 |
236.5 |
| C4' |
C3' |
O3' |
H3' |
240.1 |
123.7 |
| O3' |
C3' |
C4' |
O4' |
248.3 |
96.8 |
| O3' |
C3' |
C4' |
C5' |
121.5 |
337.2 |
| O3' |
C3' |
C4' |
H4' |
6.7 |
216.3 |
| C1' |
O4' |
C4' |
C3' |
349.6 |
358.2 |
| C4' |
C3' |
C2' |
H2'1 |
233.3 |
276.2 |
| C4' |
C3' |
C2' |
H2'2 |
116.7 |
152.0 |
| C2' |
C3' |
C4' |
O3' |
123.1 |
241.9 |
| C2' |
C3' |
C4' |
H3' |
241.0 |
118.2 |
| O3' |
C3' |
C4' |
H3' |
117.9 |
236.3 |
| C4' |
C3' |
O3' |
HO3' |
246.1 |
185.7 |
| O4' |
C4' |
C3' |
C5' |
126.8 |
119.6 |
| O4' |
C4' |
C3' |
H4' |
241.6 |
240.5 |
| C5' |
C4' |
C3' |
H4' |
114.8 |
120.9 |
| C3' |
C4' |
C5' |
O5' |
57.7 |
184.6 |
| C3' |
C4' |
C5' |
H5'1 |
177.7 |
64.7 |
| C3' |
C4' |
C5' |
H5'2 |
296.6 |
304.6 |
| H3' |
C3' |
C2' |
H2'1 |
113.3 |
34.4 |
| H3' |
C3' |
C2' |
H2'2 |
356.6 |
270.2 |
| C2' |
C3' |
H3' |
O3' |
239.0 |
123.5 |
| C2' |
C3' |
H3' |
C4' |
119.0 |
247.2 |
| O3' |
C3' |
H3' |
C4' |
240.0 |
123.6 |
| H3' |
C3' |
O3' |
HO3' |
6.1 |
62.1 |
| H3' |
C3' |
C4' |
O4' |
130.4 |
220.5 |
| H3' |
C3' |
C4' |
C5' |
3.6 |
101.0 |
| H3' |
C3' |
C4' |
H4' |
248.8 |
340.0 |
| HO3' |
O3' |
C3' |
C4' |
246.1 |
185.7 |
| HO3' |
O3' |
C3' |
H3' |
6.1 |
62.1 |
| C4' |
O4' |
C1' |
H1' |
9.3 |
265.5 |
| O4' |
C4' |
C3' |
H3' |
130.4 |
220.5 |
| C3' |
C4' |
O4' |
C5' |
232.3 |
240.5 |
| C3' |
C4' |
O4' |
H4' |
117.3 |
119.6 |
| C5' |
C4' |
O4' |
H4' |
245.1 |
239.1 |
| O4' |
C4' |
C5' |
O5' |
292.4 |
66.4 |
| O4' |
C4' |
C5' |
H5'1 |
52.4 |
306.5 |
| O4' |
C4' |
C5' |
H5'2 |
171.3 |
186.4 |
| C5' |
C4' |
C3' |
H3' |
3.6 |
101.0 |
| C3' |
C4' |
C5' |
O4' |
125.2 |
118.2 |
| C3' |
C4' |
C5' |
H4' |
243.2 |
239.1 |
| O4' |
C4' |
C5' |
H4' |
118.0 |
120.9 |
| O5' |
C5' |
C4' |
H5'1 |
240.0 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
121.1 |
240.0 |
| C4' |
C5' |
O5' |
HO5' |
105.6 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
241.1 |
120.0 |
| H4' |
C4' |
C3' |
H3' |
248.8 |
340.0 |
| C3' |
C4' |
H4' |
O4' |
241.5 |
241.8 |
| C3' |
C4' |
H4' |
C5' |
121.2 |
120.9 |
| O4' |
C4' |
H4' |
C5' |
239.8 |
239.1 |
| H4' |
C4' |
C5' |
O5' |
174.4 |
305.6 |
| H4' |
C4' |
C5' |
H5'1 |
294.4 |
185.6 |
| H4' |
C4' |
C5' |
H5'2 |
53.3 |
65.6 |
| O5' |
C5' |
C4' |
H4' |
174.4 |
305.6 |
| C4' |
C5' |
O5' |
H5'1 |
120.0 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
238.9 |
120.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
118.9 |
240.0 |
| H5'1 |
C5' |
C4' |
H4' |
294.4 |
185.6 |
| C4' |
C5' |
H5'1 |
O5' |
242.3 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
121.2 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
238.8 |
120.0 |
| H5'1 |
C5' |
O5' |
HO5' |
345.6 |
300.0 |
| H5'2 |
C5' |
C4' |
H4' |
53.3 |
65.6 |
| C4' |
C5' |
H5'2 |
O5' |
118.5 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
239.2 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
120.8 |
240.0 |
| H5'2 |
C5' |
O5' |
HO5' |
226.7 |
60.0 |
| HO5' |
O5' |
C5' |
H5'1 |
345.6 |
300.0 |
| HO5' |
O5' |
C5' |
H5'2 |
226.7 |
60.0 |