PDB Chemical Component THM
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 THM
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.423 |
1.428 |
| O5' |
HO5' |
0.951 |
0.967 |
| C5' |
C4' |
1.505 |
1.529 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.090 |
| C4' |
O4' |
1.431 |
1.445 |
| C4' |
C3' |
1.437 |
1.549 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.403 |
1.437 |
| C3' |
O3' |
1.394 |
1.429 |
| C3' |
C2' |
1.453 |
1.548 |
| C3' |
H3' |
1.116 |
1.089 |
| O3' |
HO3' |
0.951 |
0.967 |
| C2' |
C1' |
1.489 |
1.540 |
| C2' |
H2'1 |
1.116 |
1.091 |
| C2' |
H2'2 |
1.115 |
1.089 |
| C1' |
N1 |
1.512 |
1.464 |
| C1' |
H1' |
1.114 |
1.090 |
| N1 |
C2 |
1.371 |
1.345 |
| N1 |
C6 |
1.406 |
1.369 |
| C2 |
O2 |
1.225 |
1.215 |
| C2 |
N3 |
1.338 |
1.346 |
| N3 |
C4 |
1.403 |
1.348 |
| N3 |
HN3 |
1.020 |
0.970 |
| C4 |
O4 |
1.250 |
1.218 |
| C4 |
C5 |
1.464 |
1.415 |
| C5 |
C5M |
1.583 |
1.507 |
| C5 |
C6 |
1.324 |
1.351 |
| C5M |
HM51 |
1.116 |
1.090 |
| C5M |
HM52 |
1.115 |
1.090 |
| C5M |
HM53 |
1.115 |
1.089 |
| C6 |
H6 |
1.104 |
1.079 |
Bond Angles for THM
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
HO5' |
113.8 |
106.8 |
| O5' |
C5' |
C4' |
113.8 |
109.5 |
| O5' |
C5' |
H5'1 |
110.6 |
109.5 |
| O5' |
C5' |
H5'2 |
110.6 |
109.5 |
| C4' |
C5' |
H5'1 |
110.6 |
109.4 |
| C4' |
C5' |
H5'2 |
110.7 |
109.4 |
| C5' |
C4' |
O4' |
111.7 |
110.8 |
| C5' |
C4' |
C3' |
119.2 |
110.7 |
| C5' |
C4' |
H4' |
98.9 |
110.5 |
| H5'1 |
C5' |
H5'2 |
99.6 |
109.5 |
| O4' |
C4' |
C3' |
103.2 |
103.6 |
| O4' |
C4' |
H4' |
116.2 |
110.5 |
| C4' |
O4' |
C1' |
112.5 |
106.9 |
| C3' |
C4' |
H4' |
108.2 |
110.6 |
| C4' |
C3' |
O3' |
106.9 |
110.9 |
| C4' |
C3' |
C2' |
100.6 |
102.1 |
| C4' |
C3' |
H3' |
113.9 |
110.9 |
| O4' |
C1' |
C2' |
99.7 |
107.4 |
| O4' |
C1' |
N1 |
105.3 |
109.9 |
| O4' |
C1' |
H1' |
120.4 |
109.9 |
| O3' |
C3' |
C2' |
100.8 |
110.9 |
| O3' |
C3' |
H3' |
113.8 |
110.8 |
| C3' |
O3' |
HO3' |
106.9 |
106.8 |
| C2' |
C3' |
H3' |
119.0 |
110.9 |
| C3' |
C2' |
C1' |
104.7 |
104.2 |
| C3' |
C2' |
H2'1 |
114.0 |
110.4 |
| C3' |
C2' |
H2'2 |
114.0 |
110.5 |
| C1' |
C2' |
H2'1 |
114.0 |
110.5 |
| C1' |
C2' |
H2'2 |
114.0 |
110.5 |
| C2' |
C1' |
N1 |
115.9 |
109.9 |
| C2' |
C1' |
H1' |
110.6 |
109.9 |
| H2'1 |
C2' |
H2'2 |
96.4 |
110.5 |
| N1 |
C1' |
H1' |
105.4 |
109.8 |
| C1' |
N1 |
C2 |
114.4 |
119.7 |
| C1' |
N1 |
C6 |
123.3 |
119.7 |
| C2 |
N1 |
C6 |
122.4 |
120.6 |
| N1 |
C2 |
O2 |
122.1 |
119.5 |
| N1 |
C2 |
N3 |
116.7 |
120.9 |
| N1 |
C6 |
C5 |
121.4 |
119.7 |
| N1 |
C6 |
H6 |
122.4 |
120.2 |
| O2 |
C2 |
N3 |
121.1 |
119.5 |
| C2 |
N3 |
C4 |
124.4 |
120.3 |
| C2 |
N3 |
HN3 |
115.3 |
119.9 |
| C4 |
N3 |
HN3 |
120.3 |
119.9 |
| N3 |
C4 |
O4 |
119.9 |
120.3 |
| N3 |
C4 |
C5 |
117.0 |
119.4 |
| O4 |
C4 |
C5 |
123.1 |
120.3 |
| C4 |
C5 |
C5M |
119.0 |
120.5 |
| C4 |
C5 |
C6 |
118.1 |
119.1 |
| C5M |
C5 |
C6 |
122.9 |
120.4 |
| C5 |
C5M |
HM51 |
119.0 |
109.5 |
| C5 |
C5M |
HM52 |
108.8 |
109.4 |
| C5 |
C5M |
HM53 |
108.8 |
109.5 |
| C5 |
C6 |
H6 |
116.2 |
120.2 |
| HM51 |
C5M |
HM52 |
108.7 |
109.4 |
| HM51 |
C5M |
HM53 |
108.7 |
109.6 |
| HM52 |
C5M |
HM53 |
101.3 |
109.4 |
Torsion Angles for THM
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
234.7 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
289.6 |
65.7 |
| O5' |
C5' |
C4' |
C3' |
49.9 |
180.0 |
| O5' |
C5' |
C4' |
H4' |
166.6 |
302.9 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.6 |
120.0 |
| HO5' |
O5' |
C5' |
C4' |
180.1 |
180.0 |
| HO5' |
O5' |
C5' |
H5'1 |
305.3 |
60.0 |
| HO5' |
O5' |
C5' |
H5'2 |
54.8 |
299.9 |
| C4' |
C5' |
O5' |
HO5' |
180.1 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
239.7 |
245.7 |
| O4' |
C4' |
C5' |
H4' |
123.0 |
122.8 |
| C5' |
C4' |
O4' |
C1' |
113.1 |
158.5 |
| C3' |
C4' |
C5' |
H4' |
243.2 |
237.1 |
| C5' |
C4' |
C3' |
O3' |
166.8 |
86.1 |
| C5' |
C4' |
C3' |
C2' |
271.7 |
204.3 |
| C5' |
C4' |
C3' |
H3' |
40.2 |
322.5 |
| H5'1 |
C5' |
O5' |
HO5' |
305.3 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
233.0 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
116.4 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
243.5 |
119.9 |
| H5'1 |
C5' |
C4' |
O4' |
164.3 |
185.7 |
| H5'1 |
C5' |
C4' |
C3' |
284.6 |
300.0 |
| H5'1 |
C5' |
C4' |
H4' |
41.4 |
62.9 |
| H5'2 |
C5' |
O5' |
HO5' |
54.8 |
299.9 |
| O5' |
C5' |
H5'2 |
C4' |
127.1 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
243.6 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
116.5 |
240.1 |
| H5'2 |
C5' |
C4' |
O4' |
54.9 |
305.7 |
| H5'2 |
C5' |
C4' |
C3' |
175.1 |
60.0 |
| H5'2 |
C5' |
C4' |
H4' |
291.9 |
182.9 |
| O4' |
C4' |
C5' |
H5'1 |
164.3 |
185.7 |
| O4' |
C4' |
C5' |
H5'2 |
54.9 |
305.7 |
| C5' |
C4' |
O4' |
C3' |
129.2 |
118.7 |
| C5' |
C4' |
O4' |
H4' |
247.5 |
237.2 |
| C3' |
C4' |
O4' |
H4' |
118.3 |
118.5 |
| O4' |
C4' |
C3' |
O3' |
291.3 |
204.8 |
| O4' |
C4' |
C3' |
C2' |
36.2 |
323.1 |
| O4' |
C4' |
C3' |
H3' |
164.7 |
81.3 |
| C4' |
O4' |
C1' |
C2' |
349.1 |
333.7 |
| C4' |
O4' |
C1' |
N1 |
228.7 |
214.2 |
| C4' |
O4' |
C1' |
H1' |
110.0 |
93.2 |
| C3' |
C4' |
C5' |
H5'1 |
284.6 |
300.0 |
| C3' |
C4' |
C5' |
H5'2 |
175.1 |
60.0 |
| C5' |
C4' |
C3' |
O4' |
235.5 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
111.8 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
236.3 |
241.6 |
| C3' |
C4' |
O4' |
C1' |
343.9 |
39.8 |
| O3' |
C3' |
C4' |
C2' |
255.1 |
241.7 |
| O3' |
C3' |
C4' |
H3' |
126.6 |
123.6 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
174.2 |
| C2' |
C3' |
C4' |
H3' |
231.4 |
241.8 |
| C4' |
C3' |
C2' |
C1' |
315.5 |
20.9 |
| C4' |
C3' |
C2' |
H2'1 |
80.8 |
262.2 |
| C4' |
C3' |
C2' |
H2'2 |
190.2 |
139.6 |
| H4' |
C4' |
C5' |
H5'1 |
41.4 |
62.9 |
| H4' |
C4' |
C5' |
H5'2 |
291.9 |
182.9 |
| C5' |
C4' |
H4' |
O4' |
119.7 |
123.0 |
| C5' |
C4' |
H4' |
C3' |
235.2 |
237.0 |
| O4' |
C4' |
H4' |
C3' |
115.5 |
114.1 |
| H4' |
C4' |
O4' |
C1' |
225.6 |
281.4 |
| H4' |
C4' |
C3' |
O3' |
55.0 |
323.2 |
| H4' |
C4' |
C3' |
C2' |
159.9 |
81.5 |
| H4' |
C4' |
C3' |
H3' |
288.4 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
343.9 |
39.8 |
| C1' |
O4' |
C4' |
H4' |
225.6 |
281.4 |
| C3' |
C2' |
C1' |
O4' |
34.0 |
2.0 |
| O4' |
C1' |
C2' |
H2'1 |
268.7 |
120.6 |
| O4' |
C1' |
C2' |
H2'2 |
159.3 |
243.2 |
| C2' |
C1' |
O4' |
N1 |
120.5 |
119.5 |
| C2' |
C1' |
O4' |
H1' |
239.1 |
240.5 |
| N1 |
C1' |
O4' |
H1' |
118.7 |
121.0 |
| O4' |
C1' |
N1 |
C2 |
238.5 |
58.4 |
| O4' |
C1' |
N1 |
C6 |
59.0 |
238.2 |
| O3' |
C3' |
C4' |
H4' |
55.0 |
323.2 |
| C4' |
C3' |
O3' |
C2' |
104.7 |
112.8 |
| C4' |
C3' |
O3' |
H3' |
233.3 |
236.4 |
| C2' |
C3' |
O3' |
H3' |
128.6 |
123.6 |
| O3' |
C3' |
C2' |
C1' |
65.2 |
139.1 |
| O3' |
C3' |
C2' |
H2'1 |
190.5 |
20.5 |
| O3' |
C3' |
C2' |
H2'2 |
299.9 |
257.8 |
| C2' |
C3' |
C4' |
H4' |
159.9 |
81.5 |
| C4' |
C3' |
C2' |
O3' |
250.3 |
241.7 |
| C4' |
C3' |
C2' |
H3' |
125.2 |
118.2 |
| O4' |
C1' |
C2' |
C3' |
34.0 |
2.0 |
| O3' |
C3' |
C2' |
H3' |
234.9 |
236.4 |
| C2' |
C3' |
O3' |
HO3' |
75.3 |
61.4 |
| C1' |
C2' |
C3' |
H2'1 |
234.7 |
118.7 |
| C1' |
C2' |
C3' |
H2'2 |
125.3 |
241.3 |
| C3' |
C2' |
C1' |
N1 |
146.4 |
121.5 |
| C3' |
C2' |
C1' |
H1' |
266.3 |
242.5 |
| H2'1 |
C2' |
C3' |
H2'2 |
250.6 |
122.6 |
| H3' |
C3' |
C4' |
H4' |
288.4 |
199.7 |
| C4' |
C3' |
H3' |
O3' |
122.9 |
123.6 |
| C4' |
C3' |
H3' |
C2' |
241.6 |
247.3 |
| O3' |
C3' |
H3' |
C2' |
118.6 |
123.6 |
| H3' |
C3' |
O3' |
HO3' |
306.7 |
297.8 |
| H3' |
C3' |
C2' |
C1' |
190.3 |
262.7 |
| H3' |
C3' |
C2' |
H2'1 |
315.6 |
144.0 |
| H3' |
C3' |
C2' |
H2'2 |
65.1 |
21.4 |
| HO3' |
O3' |
C3' |
C2' |
75.3 |
61.4 |
| HO3' |
O3' |
C3' |
H3' |
306.7 |
297.8 |
| O4' |
C1' |
C2' |
N1 |
247.6 |
240.5 |
| O4' |
C1' |
C2' |
H1' |
127.7 |
119.5 |
| C1' |
C2' |
C3' |
H3' |
190.3 |
262.7 |
| C3' |
C2' |
C1' |
H2'1 |
125.2 |
241.4 |
| C3' |
C2' |
C1' |
H2'2 |
234.7 |
118.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
109.5 |
237.3 |
| N1 |
C1' |
C2' |
H1' |
240.1 |
239.0 |
| C2' |
C1' |
N1 |
C2 |
129.4 |
300.4 |
| C2' |
C1' |
N1 |
C6 |
309.9 |
120.2 |
| H2'1 |
C2' |
C3' |
H3' |
315.6 |
144.0 |
| C3' |
C2' |
H2'1 |
C1' |
239.8 |
114.7 |
| C3' |
C2' |
H2'1 |
H2'2 |
119.9 |
237.4 |
| C1' |
C2' |
H2'1 |
H2'2 |
240.1 |
122.7 |
| H2'1 |
C2' |
C1' |
N1 |
21.1 |
240.1 |
| H2'1 |
C2' |
C1' |
H1' |
141.0 |
1.1 |
| H2'2 |
C2' |
C3' |
H3' |
65.1 |
21.4 |
| C3' |
C2' |
H2'2 |
C1' |
120.2 |
245.2 |
| C3' |
C2' |
H2'2 |
H2'1 |
240.1 |
122.6 |
| C1' |
C2' |
H2'2 |
H2'1 |
119.9 |
237.3 |
| H2'2 |
C2' |
C1' |
N1 |
271.7 |
2.8 |
| H2'2 |
C2' |
C1' |
H1' |
31.5 |
123.7 |
| O4' |
C1' |
N1 |
C2' |
109.1 |
118.0 |
| O4' |
C1' |
N1 |
H1' |
231.7 |
239.0 |
| N1 |
C1' |
C2' |
H2'1 |
21.1 |
240.1 |
| N1 |
C1' |
C2' |
H2'2 |
271.7 |
2.8 |
| C2' |
C1' |
N1 |
H1' |
122.6 |
121.0 |
| C2 |
N1 |
C1' |
C6 |
179.6 |
180.1 |
| C1' |
N1 |
C2 |
O2 |
357.8 |
359.9 |
| C1' |
N1 |
C2 |
N3 |
180.4 |
180.0 |
| C1' |
N1 |
C6 |
C5 |
179.9 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
359.9 |
0.1 |
| O4' |
C1' |
H1' |
C2' |
244.7 |
242.0 |
| O4' |
C1' |
H1' |
N1 |
118.6 |
121.0 |
| H1' |
C1' |
C2' |
H2'1 |
141.0 |
1.1 |
| H1' |
C1' |
C2' |
H2'2 |
31.5 |
123.7 |
| C2' |
C1' |
H1' |
N1 |
234.0 |
239.0 |
| H1' |
C1' |
N1 |
C2 |
6.8 |
179.4 |
| H1' |
C1' |
N1 |
C6 |
187.2 |
359.2 |
| C2 |
N1 |
C1' |
H1' |
6.8 |
179.4 |
| C1' |
N1 |
C2 |
C6 |
180.4 |
179.9 |
| C2 |
N1 |
C6 |
C5 |
0.3 |
359.9 |
| C2 |
N1 |
C6 |
H6 |
180.3 |
180.0 |
| O2 |
C2 |
N1 |
N3 |
177.4 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.2 |
359.7 |
| N1 |
C2 |
N3 |
HN3 |
180.2 |
179.9 |
| C6 |
N1 |
C1' |
H1' |
187.2 |
359.2 |
| C1' |
N1 |
C6 |
C2 |
179.5 |
180.1 |
| C6 |
N1 |
C2 |
O2 |
177.3 |
180.1 |
| C6 |
N1 |
C2 |
N3 |
360.0 |
0.1 |
| C4 |
C5 |
C6 |
N1 |
359.3 |
0.3 |
| C5M |
C5 |
C6 |
N1 |
178.9 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.9 |
| O2 |
C2 |
N1 |
C6 |
177.3 |
180.1 |
| N1 |
C2 |
O2 |
N3 |
182.8 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
182.8 |
179.7 |
| O2 |
C2 |
N3 |
HN3 |
2.8 |
360.0 |
| N3 |
C2 |
N1 |
C6 |
360.0 |
0.1 |
| N1 |
C2 |
N3 |
O2 |
177.4 |
180.0 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
179.8 |
| C2 |
N3 |
C4 |
O4 |
179.3 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
359.4 |
0.5 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
180.2 |
| O4 |
C4 |
N3 |
C5 |
179.9 |
179.5 |
| N3 |
C4 |
C5 |
C5M |
181.2 |
179.8 |
| N3 |
C4 |
C5 |
C6 |
0.8 |
359.5 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
179.8 |
| HN3 |
N3 |
C4 |
O4 |
359.4 |
359.8 |
| HN3 |
N3 |
C4 |
C5 |
179.4 |
180.3 |
| O4 |
C4 |
N3 |
HN3 |
359.4 |
359.8 |
| N3 |
C4 |
O4 |
C5 |
180.1 |
180.5 |
| O4 |
C4 |
C5 |
C5M |
1.2 |
0.3 |
| O4 |
C4 |
C5 |
C6 |
180.9 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
359.3 |
0.3 |
| C5 |
C4 |
N3 |
HN3 |
179.4 |
180.3 |
| N3 |
C4 |
C5 |
O4 |
179.9 |
179.5 |
| C5M |
C5 |
C4 |
C6 |
180.3 |
180.3 |
| C4 |
C5 |
C5M |
HM51 |
180.0 |
359.8 |
| C4 |
C5 |
C5M |
HM52 |
305.2 |
119.7 |
| C4 |
C5 |
C5M |
HM53 |
54.7 |
239.6 |
| C4 |
C5 |
C6 |
H6 |
179.3 |
180.2 |
| N1 |
C6 |
C5 |
C5M |
178.9 |
180.0 |
| C4 |
C5 |
C5M |
C6 |
179.6 |
179.7 |
| C5M |
C5 |
C6 |
H6 |
358.9 |
359.9 |
| HM51 |
C5M |
C5 |
HM52 |
234.8 |
240.1 |
| HM51 |
C5M |
C5 |
HM53 |
125.2 |
120.2 |
| HM52 |
C5M |
C5 |
HM53 |
250.5 |
240.1 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.1 |
| C4 |
C5 |
C6 |
C5M |
180.4 |
180.3 |
| C6 |
C5 |
C5M |
HM51 |
0.3 |
180.1 |
| C6 |
C5 |
C5M |
HM52 |
125.6 |
300.0 |
| C6 |
C5 |
C5M |
HM53 |
235.1 |
59.9 |
| HM51 |
C5M |
C5 |
C6 |
0.3 |
180.1 |
| C5 |
C5M |
HM51 |
HM52 |
125.3 |
119.9 |
| C5 |
C5M |
HM51 |
HM53 |
234.7 |
239.9 |
| HM52 |
C5M |
HM51 |
HM53 |
109.4 |
120.0 |
| HM52 |
C5M |
C5 |
C6 |
125.6 |
300.0 |
| C5 |
C5M |
HM52 |
HM51 |
229.0 |
240.1 |
| C5 |
C5M |
HM52 |
HM53 |
114.6 |
120.0 |
| HM51 |
C5M |
HM52 |
HM53 |
245.6 |
239.9 |
| HM53 |
C5M |
C5 |
C6 |
235.1 |
59.9 |
| C5 |
C5M |
HM53 |
HM51 |
131.0 |
120.1 |
| C5 |
C5M |
HM53 |
HM52 |
245.5 |
240.1 |
| HM51 |
C5M |
HM53 |
HM52 |
114.4 |
120.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.9 |