PDB Chemical Component CTD
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 CTD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.368 |
1.346 |
| N1 |
C6 |
1.364 |
1.359 |
| N1 |
C1' |
1.615 |
1.464 |
| C2 |
C3 |
1.421 |
1.398 |
| C2 |
O2 |
1.232 |
1.221 |
| C3 |
C4 |
1.340 |
1.385 |
| C3 |
H3 |
1.104 |
1.080 |
| C4 |
C5 |
1.429 |
1.411 |
| C4 |
N4 |
1.324 |
1.383 |
| C5 |
C6 |
1.344 |
1.349 |
| C5 |
H5 |
1.104 |
1.080 |
| C6 |
H6 |
1.103 |
1.079 |
| N4 |
HN41 |
1.021 |
0.970 |
| N4 |
HN42 |
1.020 |
0.970 |
| C1' |
C2' |
1.483 |
1.544 |
| C1' |
O4' |
1.429 |
1.443 |
| C1' |
H1' |
1.115 |
1.090 |
| C2' |
O2' |
1.453 |
1.429 |
| C2' |
C3' |
1.455 |
1.547 |
| C2' |
H2' |
1.115 |
1.091 |
| O2' |
HO2' |
0.950 |
0.967 |
| C3' |
C4' |
1.528 |
1.544 |
| C3' |
O3' |
1.403 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| C4' |
O4' |
1.418 |
1.444 |
| C4' |
C5' |
1.473 |
1.530 |
| C4' |
H4' |
1.114 |
1.089 |
| O3' |
HO3' |
0.949 |
0.966 |
| C5' |
O5' |
1.421 |
1.428 |
| C5' |
H5'1 |
1.115 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.091 |
| O5' |
HO5' |
0.950 |
0.967 |
Bond Angles for CTD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
123.6 |
121.1 |
| C2 |
N1 |
C1' |
117.5 |
119.4 |
| N1 |
C2 |
C3 |
116.6 |
120.2 |
| N1 |
C2 |
O2 |
123.3 |
119.9 |
| C6 |
N1 |
C1' |
118.8 |
119.4 |
| N1 |
C6 |
C5 |
118.9 |
120.9 |
| N1 |
C6 |
H6 |
121.3 |
119.6 |
| N1 |
C1' |
C2' |
137.4 |
110.4 |
| N1 |
C1' |
O4' |
100.1 |
110.4 |
| N1 |
C1' |
H1' |
98.9 |
110.4 |
| C3 |
C2 |
O2 |
119.9 |
119.9 |
| C2 |
C3 |
C4 |
120.7 |
119.1 |
| C2 |
C3 |
H3 |
122.6 |
120.5 |
| C4 |
C3 |
H3 |
116.7 |
120.4 |
| C3 |
C4 |
C5 |
119.3 |
118.9 |
| C3 |
C4 |
N4 |
119.8 |
120.6 |
| C5 |
C4 |
N4 |
120.8 |
120.6 |
| C4 |
C5 |
C6 |
120.3 |
119.8 |
| C4 |
C5 |
H5 |
122.9 |
120.1 |
| C4 |
N4 |
HN41 |
119.9 |
120.0 |
| C4 |
N4 |
HN42 |
108.5 |
120.0 |
| C6 |
C5 |
H5 |
116.8 |
120.1 |
| C5 |
C6 |
H6 |
119.8 |
119.6 |
| HN41 |
N4 |
HN42 |
108.4 |
120.0 |
| C2' |
C1' |
O4' |
115.3 |
104.9 |
| C2' |
C1' |
H1' |
73.3 |
110.3 |
| C1' |
C2' |
O2' |
110.1 |
110.8 |
| C1' |
C2' |
C3' |
100.4 |
104.0 |
| C1' |
C2' |
H2' |
117.5 |
110.4 |
| O4' |
C1' |
H1' |
134.5 |
110.3 |
| C1' |
O4' |
C4' |
101.2 |
105.3 |
| O2' |
C2' |
C3' |
116.5 |
110.5 |
| O2' |
C2' |
H2' |
101.8 |
110.5 |
| C2' |
O2' |
HO2' |
110.2 |
106.8 |
| C3' |
C2' |
H2' |
111.4 |
110.5 |
| C2' |
C3' |
C4' |
103.2 |
104.1 |
| C2' |
C3' |
O3' |
110.7 |
110.6 |
| C2' |
C3' |
H3' |
112.4 |
110.6 |
| C4' |
C3' |
O3' |
108.6 |
110.5 |
| C4' |
C3' |
H3' |
114.4 |
110.5 |
| C3' |
C4' |
O4' |
108.8 |
104.8 |
| C3' |
C4' |
C5' |
115.8 |
110.5 |
| C3' |
C4' |
H4' |
107.0 |
110.4 |
| O3' |
C3' |
H3' |
107.5 |
110.5 |
| C3' |
O3' |
HO3' |
110.7 |
106.8 |
| O4' |
C4' |
C5' |
113.6 |
110.4 |
| O4' |
C4' |
H4' |
109.6 |
110.4 |
| C5' |
C4' |
H4' |
101.5 |
110.3 |
| C4' |
C5' |
O5' |
107.3 |
109.5 |
| C4' |
C5' |
H5'1 |
113.0 |
109.5 |
| C4' |
C5' |
H5'2 |
113.0 |
109.4 |
| O5' |
C5' |
H5'1 |
113.0 |
109.5 |
| O5' |
C5' |
H5'2 |
113.0 |
109.4 |
| C5' |
O5' |
HO5' |
107.3 |
106.8 |
| H5'1 |
C5' |
H5'2 |
97.4 |
109.4 |
Torsion Angles for CTD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
179.9 |
179.9 |
| C2 |
N1 |
C6 |
C5 |
359.7 |
359.8 |
| C2 |
N1 |
C6 |
H6 |
179.7 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
95.0 |
121.5 |
| C2 |
N1 |
C1' |
O4' |
241.6 |
237.0 |
| C2 |
N1 |
C1' |
H1' |
20.1 |
359.2 |
| C3 |
C2 |
N1 |
O2 |
185.7 |
179.9 |
| N1 |
C2 |
C3 |
C4 |
8.9 |
0.1 |
| N1 |
C2 |
C3 |
H3 |
188.8 |
180.1 |
| C2 |
N1 |
C6 |
C1' |
180.1 |
180.1 |
| C6 |
N1 |
C2 |
C3 |
355.7 |
359.9 |
| C6 |
N1 |
C2 |
O2 |
170.0 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
275.1 |
301.6 |
| C6 |
N1 |
C1' |
O4' |
61.7 |
57.1 |
| C6 |
N1 |
C1' |
H1' |
200.1 |
179.3 |
| C4 |
C5 |
C6 |
N1 |
0.8 |
0.5 |
| N1 |
C6 |
C5 |
H5 |
180.8 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.8 |
| C2 |
N1 |
C1' |
C6 |
179.9 |
179.9 |
| C1' |
N1 |
C2 |
C3 |
175.8 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
350.1 |
0.1 |
| C1' |
N1 |
C6 |
C5 |
179.6 |
179.7 |
| C1' |
N1 |
C6 |
H6 |
359.6 |
359.9 |
| C2' |
C1' |
N1 |
O4' |
213.4 |
244.5 |
| C2' |
C1' |
N1 |
H1' |
75.0 |
122.3 |
| N1 |
C1' |
C2' |
O2' |
284.2 |
261.5 |
| N1 |
C1' |
C2' |
C3' |
160.9 |
142.7 |
| N1 |
C1' |
C2' |
H2' |
40.1 |
24.2 |
| O4' |
C1' |
N1 |
H1' |
221.6 |
237.8 |
| N1 |
C1' |
O4' |
C4' |
207.5 |
200.6 |
| C3 |
C2 |
N1 |
C6 |
355.7 |
359.9 |
| C3 |
C2 |
N1 |
C1' |
175.8 |
180.0 |
| N1 |
C2 |
C3 |
O2 |
174.5 |
180.1 |
| C4 |
C3 |
C2 |
H3 |
180.0 |
180.0 |
| C2 |
C3 |
C4 |
C5 |
351.4 |
0.2 |
| C2 |
C3 |
C4 |
N4 |
171.6 |
179.9 |
| O2 |
C2 |
N1 |
C6 |
170.0 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
350.1 |
0.1 |
| N1 |
C2 |
O2 |
C3 |
185.9 |
179.9 |
| O2 |
C2 |
C3 |
C4 |
194.3 |
180.0 |
| O2 |
C2 |
C3 |
H3 |
14.3 |
0.0 |
| C4 |
C3 |
C2 |
O2 |
194.3 |
180.0 |
| C2 |
C3 |
C4 |
H3 |
180.0 |
180.0 |
| C5 |
C4 |
C3 |
N4 |
179.7 |
180.3 |
| C3 |
C4 |
C5 |
C6 |
3.8 |
359.5 |
| C3 |
C4 |
C5 |
H5 |
183.7 |
180.0 |
| C3 |
C4 |
N4 |
HN41 |
180.0 |
180.0 |
| C3 |
C4 |
N4 |
HN42 |
54.7 |
359.8 |
| H3 |
C3 |
C2 |
O2 |
14.3 |
0.0 |
| C2 |
C3 |
H3 |
C4 |
180.0 |
180.0 |
| H3 |
C3 |
C4 |
C5 |
171.4 |
180.2 |
| H3 |
C3 |
C4 |
N4 |
351.7 |
359.9 |
| N1 |
C6 |
C5 |
C4 |
0.8 |
0.5 |
| C5 |
C4 |
C3 |
H3 |
171.4 |
180.2 |
| C3 |
C4 |
C5 |
N4 |
180.3 |
179.7 |
| C5 |
C4 |
N4 |
HN41 |
0.3 |
359.7 |
| C5 |
C4 |
N4 |
HN42 |
235.0 |
179.4 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.5 |
| C4 |
C5 |
C6 |
H6 |
180.8 |
180.3 |
| N4 |
C4 |
C3 |
H3 |
351.7 |
359.9 |
| C3 |
C4 |
N4 |
C5 |
179.7 |
180.3 |
| N4 |
C4 |
C5 |
C6 |
183.5 |
179.8 |
| N4 |
C4 |
C5 |
H5 |
3.5 |
0.3 |
| HN41 |
N4 |
C4 |
HN42 |
125.3 |
180.3 |
| C5 |
C6 |
N1 |
C1' |
179.6 |
179.7 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
| C6 |
C5 |
C4 |
N4 |
183.5 |
179.8 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.5 |
| H5 |
C5 |
C4 |
N4 |
3.5 |
0.3 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.5 |
| H5 |
C5 |
C6 |
H6 |
0.8 |
359.8 |
| H6 |
C6 |
N1 |
C1' |
359.6 |
359.9 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.8 |
| H6 |
C6 |
C5 |
H5 |
0.8 |
359.8 |
| C4 |
N4 |
HN41 |
HN42 |
234.7 |
179.7 |
| C4 |
N4 |
HN42 |
HN41 |
131.8 |
180.3 |
| N1 |
C1' |
C2' |
O4' |
143.2 |
118.9 |
| N1 |
C1' |
C2' |
H1' |
275.0 |
237.7 |
| O4' |
C1' |
C2' |
H1' |
131.8 |
118.8 |
| C2' |
C1' |
O4' |
C4' |
3.1 |
319.6 |
| O2' |
C2' |
C1' |
C3' |
123.3 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
244.2 |
237.3 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
183.8 |
| C3' |
C2' |
C1' |
H2' |
120.8 |
118.6 |
| C1' |
C2' |
C3' |
C4' |
330.9 |
0.2 |
| C1' |
C2' |
C3' |
O3' |
87.0 |
118.8 |
| C1' |
C2' |
C3' |
H3' |
207.1 |
241.5 |
| N1 |
C1' |
O4' |
C2' |
204.3 |
241.1 |
| N1 |
C1' |
O4' |
H1' |
113.3 |
122.2 |
| C2' |
C1' |
O4' |
H1' |
269.0 |
241.2 |
| O4' |
C1' |
C2' |
O2' |
141.1 |
142.6 |
| O4' |
C1' |
C2' |
C3' |
17.7 |
23.8 |
| O4' |
C1' |
C2' |
H2' |
256.9 |
265.3 |
| C3' |
C4' |
O4' |
C1' |
337.5 |
40.5 |
| C1' |
O4' |
C4' |
C5' |
108.0 |
159.5 |
| C1' |
O4' |
C4' |
H4' |
220.8 |
281.7 |
| N1 |
C1' |
H1' |
C2' |
137.0 |
122.3 |
| N1 |
C1' |
H1' |
O4' |
246.3 |
237.7 |
| C2' |
C1' |
H1' |
O4' |
109.3 |
115.4 |
| H1' |
C1' |
C2' |
O2' |
9.2 |
23.7 |
| H1' |
C1' |
C2' |
C3' |
245.9 |
265.0 |
| H1' |
C1' |
C2' |
H2' |
125.1 |
146.4 |
| H1' |
C1' |
O4' |
C4' |
94.2 |
78.4 |
| O2' |
C2' |
C1' |
O4' |
141.1 |
142.6 |
| O2' |
C2' |
C1' |
H1' |
9.2 |
23.7 |
| C1' |
C2' |
O2' |
C3' |
246.6 |
245.3 |
| C1' |
C2' |
O2' |
H2' |
125.4 |
122.7 |
| C3' |
C2' |
O2' |
H2' |
238.7 |
237.4 |
| O2' |
C2' |
C3' |
C4' |
212.1 |
241.2 |
| O2' |
C2' |
C3' |
O3' |
328.1 |
359.9 |
| O2' |
C2' |
C3' |
H3' |
88.3 |
122.5 |
| C3' |
C2' |
C1' |
O4' |
17.7 |
23.8 |
| C3' |
C2' |
C1' |
H1' |
245.9 |
265.0 |
| C1' |
C2' |
C3' |
O2' |
118.8 |
119.0 |
| C1' |
C2' |
C3' |
H2' |
234.9 |
241.5 |
| O2' |
C2' |
C3' |
H2' |
116.0 |
122.6 |
| C3' |
C2' |
O2' |
HO2' |
293.3 |
298.5 |
| C4' |
C3' |
C2' |
O3' |
244.0 |
241.3 |
| C4' |
C3' |
C2' |
H3' |
123.8 |
118.7 |
| C2' |
C3' |
C4' |
O4' |
34.7 |
335.9 |
| C2' |
C3' |
C4' |
C5' |
265.4 |
217.0 |
| C2' |
C3' |
C4' |
H4' |
153.1 |
94.8 |
| O3' |
C3' |
C2' |
H3' |
239.8 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
183.9 |
| H2' |
C2' |
C1' |
O4' |
256.9 |
265.3 |
| H2' |
C2' |
C1' |
H1' |
125.1 |
146.4 |
| C1' |
C2' |
H2' |
O2' |
239.7 |
237.1 |
| C1' |
C2' |
H2' |
C3' |
114.9 |
114.5 |
| O2' |
C2' |
H2' |
C3' |
235.2 |
237.4 |
| H2' |
C2' |
O2' |
HO2' |
54.6 |
61.1 |
| H2' |
C2' |
C3' |
C4' |
96.1 |
118.7 |
| H2' |
C2' |
C3' |
O3' |
212.1 |
237.3 |
| H2' |
C2' |
C3' |
H3' |
332.3 |
360.0 |
| HO2' |
O2' |
C2' |
C3' |
293.3 |
298.5 |
| HO2' |
O2' |
C2' |
H2' |
54.6 |
61.1 |
| C1' |
O4' |
C4' |
C3' |
337.5 |
40.5 |
| C4' |
C3' |
C2' |
H2' |
96.1 |
118.7 |
| C2' |
C3' |
C4' |
O3' |
117.5 |
118.7 |
| C2' |
C3' |
C4' |
H3' |
237.6 |
241.3 |
| O3' |
C3' |
C4' |
H3' |
120.0 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
292.6 |
298.6 |
| O4' |
C4' |
C3' |
C5' |
129.3 |
118.9 |
| O4' |
C4' |
C3' |
H4' |
241.6 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
112.3 |
122.3 |
| C3' |
C4' |
C5' |
O5' |
61.4 |
176.8 |
| C3' |
C4' |
C5' |
H5'1 |
186.7 |
296.9 |
| C3' |
C4' |
C5' |
H5'2 |
296.2 |
56.9 |
| O3' |
C3' |
C2' |
H2' |
212.1 |
237.3 |
| C2' |
C3' |
O3' |
C4' |
247.4 |
245.3 |
| C2' |
C3' |
O3' |
H3' |
123.1 |
122.7 |
| C4' |
C3' |
O3' |
H3' |
235.7 |
237.4 |
| O3' |
C3' |
C4' |
O4' |
277.1 |
217.2 |
| O3' |
C3' |
C4' |
C5' |
147.8 |
98.3 |
| O3' |
C3' |
C4' |
H4' |
35.5 |
336.1 |
| H3' |
C3' |
C2' |
H2' |
332.3 |
360.0 |
| C2' |
C3' |
H3' |
C4' |
117.3 |
114.7 |
| C2' |
C3' |
H3' |
O3' |
237.9 |
237.3 |
| C4' |
C3' |
H3' |
O3' |
120.6 |
122.6 |
| H3' |
C3' |
C4' |
O4' |
157.1 |
94.6 |
| H3' |
C3' |
C4' |
C5' |
27.8 |
335.7 |
| H3' |
C3' |
C4' |
H4' |
275.5 |
213.5 |
| H3' |
C3' |
O3' |
HO3' |
56.9 |
61.2 |
| C4' |
O4' |
C1' |
H1' |
94.2 |
78.4 |
| O4' |
C4' |
C3' |
O3' |
277.1 |
217.2 |
| O4' |
C4' |
C3' |
H3' |
157.1 |
94.6 |
| C3' |
C4' |
O4' |
C5' |
229.4 |
241.0 |
| C3' |
C4' |
O4' |
H4' |
116.7 |
118.8 |
| C5' |
C4' |
O4' |
H4' |
247.3 |
237.8 |
| O4' |
C4' |
C5' |
O5' |
294.5 |
61.4 |
| O4' |
C4' |
C5' |
H5'1 |
59.7 |
181.5 |
| O4' |
C4' |
C5' |
H5'2 |
169.2 |
301.5 |
| C5' |
C4' |
C3' |
O3' |
147.8 |
98.3 |
| C5' |
C4' |
C3' |
H3' |
27.8 |
335.7 |
| C3' |
C4' |
C5' |
O4' |
127.0 |
115.4 |
| C3' |
C4' |
C5' |
H4' |
244.5 |
237.7 |
| O4' |
C4' |
C5' |
H4' |
117.6 |
122.3 |
| O5' |
C5' |
C4' |
H5'1 |
234.8 |
239.9 |
| O5' |
C5' |
C4' |
H5'2 |
125.2 |
120.0 |
| C4' |
C5' |
O5' |
HO5' |
179.9 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
240.0 |
| H4' |
C4' |
C3' |
O3' |
35.5 |
336.1 |
| H4' |
C4' |
C3' |
H3' |
275.5 |
213.5 |
| C3' |
C4' |
H4' |
O4' |
242.2 |
244.6 |
| C3' |
C4' |
H4' |
C5' |
121.8 |
122.4 |
| O4' |
C4' |
H4' |
C5' |
239.6 |
237.7 |
| H4' |
C4' |
C5' |
O5' |
176.9 |
299.2 |
| H4' |
C4' |
C5' |
H5'1 |
302.2 |
59.2 |
| H4' |
C4' |
C5' |
H5'2 |
51.7 |
179.2 |
| HO3' |
O3' |
C3' |
H3' |
56.9 |
61.2 |
| O5' |
C5' |
C4' |
H4' |
176.9 |
299.2 |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
120.1 |
| C4' |
C5' |
O5' |
H5'2 |
234.7 |
240.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
119.9 |
| H5'1 |
C5' |
C4' |
H4' |
302.2 |
59.2 |
| C4' |
C5' |
H5'1 |
O5' |
237.9 |
239.9 |
| C4' |
C5' |
H5'1 |
H5'2 |
119.0 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
241.1 |
240.1 |
| H5'1 |
C5' |
O5' |
HO5' |
54.7 |
59.9 |
| H5'2 |
C5' |
C4' |
H4' |
51.7 |
179.2 |
| C4' |
C5' |
H5'2 |
O5' |
122.1 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
241.0 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
118.9 |
120.0 |
| H5'2 |
C5' |
O5' |
HO5' |
305.2 |
300.0 |
| HO5' |
O5' |
C5' |
H5'1 |
54.7 |
59.9 |
| HO5' |
O5' |
C5' |
H5'2 |
305.2 |
300.0 |