PDB Chemical Component 7DT
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 7DT
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2B |
PB |
1.516 |
1.480 |
| O2A |
PA |
1.489 |
1.479 |
| O1A |
PA |
1.498 |
1.610 |
| PA |
O3A |
1.582 |
1.610 |
| PA |
O5' |
1.572 |
1.611 |
| PB |
O3A |
1.615 |
1.610 |
| PB |
O1B |
1.538 |
1.610 |
| PB |
O3B |
1.527 |
1.610 |
| O3B |
PG |
1.629 |
1.610 |
| O2G |
PG |
1.496 |
1.480 |
| O5' |
C5' |
1.452 |
1.428 |
| C20 |
C8 |
1.375 |
1.344 |
| C20 |
C5 |
1.369 |
1.462 |
| N6 |
C6 |
1.375 |
1.384 |
| C8 |
N9 |
1.353 |
1.371 |
| PG |
O1G |
1.489 |
1.610 |
| PG |
O3G |
1.536 |
1.609 |
| C5 |
C6 |
1.407 |
1.403 |
| C5 |
C4 |
1.375 |
1.408 |
| C6 |
N1 |
1.301 |
1.330 |
| C5' |
C4' |
1.512 |
1.529 |
| O4' |
C4' |
1.432 |
1.444 |
| O4' |
C1' |
1.409 |
1.445 |
| N9 |
C4 |
1.372 |
1.368 |
| N9 |
C1' |
1.483 |
1.465 |
| C4 |
N3 |
1.333 |
1.331 |
| N1 |
C2 |
1.352 |
1.321 |
| C4' |
C3' |
1.540 |
1.544 |
| C1' |
C2' |
1.564 |
1.545 |
| N3 |
C2 |
1.360 |
1.315 |
| C2' |
C3' |
1.558 |
1.545 |
| C2' |
O2' |
1.410 |
1.428 |
| C3' |
O3' |
1.369 |
1.429 |
| O3G |
H1 |
0.951 |
0.967 |
| O1G |
H2 |
0.950 |
0.967 |
| O1B |
H3 |
0.950 |
0.968 |
| O1A |
H4 |
0.950 |
0.968 |
| C5' |
H5 |
1.099 |
1.090 |
| C5' |
H6 |
1.100 |
1.091 |
| C4' |
H7 |
1.100 |
1.090 |
| C1' |
H8 |
1.100 |
1.090 |
| C8 |
H9 |
1.080 |
1.080 |
| C20 |
H10 |
1.080 |
1.079 |
| N6 |
H11 |
1.000 |
0.970 |
| N6 |
H12 |
1.000 |
0.970 |
| C2 |
H13 |
1.080 |
1.080 |
| C2' |
H14 |
1.100 |
1.090 |
| O2' |
H15 |
0.950 |
0.967 |
| C3' |
H16 |
1.100 |
1.090 |
| O3' |
H17 |
0.950 |
0.968 |
Bond Angles for 7DT
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2B |
PB |
O3A |
106.9 |
109.5 |
| O2B |
PB |
O1B |
117.1 |
109.5 |
| O2A |
PA |
O5' |
108.4 |
109.4 |
| O1A |
PA |
O5' |
109.1 |
109.5 |
| PA |
O5' |
C5' |
122.8 |
123.0 |
| O1B |
PB |
O3A |
104.0 |
109.5 |
| PB |
O1B |
H3 |
109.5 |
114.0 |
| O2G |
PG |
O1G |
118.2 |
109.5 |
| O5' |
C5' |
C4' |
110.1 |
109.5 |
| O5' |
C5' |
H5 |
109.3 |
109.4 |
| O5' |
C5' |
H6 |
109.3 |
109.5 |
| C20 |
C8 |
H9 |
125.9 |
125.1 |
| C20 |
C5 |
C6 |
133.3 |
135.1 |
| C20 |
C5 |
C4 |
106.3 |
106.2 |
| C5 |
C20 |
H10 |
125.6 |
126.6 |
| N6 |
C6 |
N1 |
121.9 |
120.8 |
| C8 |
N9 |
C4 |
107.6 |
110.1 |
| PG |
O1G |
H2 |
109.5 |
114.0 |
| PG |
O3G |
H1 |
109.5 |
114.0 |
| C6 |
C5 |
C4 |
120.4 |
118.6 |
| C5 |
C6 |
N1 |
118.1 |
118.3 |
| N9 |
C4 |
C5 |
109.1 |
107.1 |
| C5 |
C4 |
N3 |
118.1 |
118.6 |
| C6 |
N1 |
C2 |
122.7 |
121.0 |
| C5' |
C4' |
C3' |
110.0 |
110.4 |
| C4' |
C5' |
H5 |
109.3 |
109.5 |
| C4' |
C5' |
H6 |
109.3 |
109.5 |
| C5' |
C4' |
H7 |
111.2 |
110.3 |
| O4' |
C4' |
C3' |
107.7 |
104.8 |
| O4' |
C4' |
H7 |
112.5 |
110.4 |
| O4' |
C1' |
C2' |
104.5 |
104.8 |
| O4' |
C1' |
H8 |
111.8 |
110.4 |
| N9 |
C4 |
N3 |
132.7 |
134.3 |
| N9 |
C1' |
C2' |
108.4 |
110.4 |
| N9 |
C1' |
H8 |
110.7 |
110.4 |
| N1 |
C2 |
H13 |
120.5 |
118.6 |
| C4' |
C3' |
C2' |
103.2 |
104.1 |
| C4' |
C3' |
O3' |
107.6 |
110.5 |
| C3' |
C4' |
H7 |
110.8 |
110.4 |
| C4' |
C3' |
H16 |
110.5 |
110.5 |
| C1' |
C2' |
C3' |
97.5 |
104.0 |
| C1' |
C2' |
O2' |
113.4 |
110.5 |
| C2' |
C1' |
H8 |
109.5 |
110.4 |
| C1' |
C2' |
H14 |
111.3 |
110.5 |
| N3 |
C2 |
H13 |
120.5 |
118.7 |
| O2' |
C2' |
C3' |
108.5 |
110.6 |
| C2' |
C3' |
O3' |
111.5 |
110.5 |
| C3' |
C2' |
H14 |
111.3 |
110.5 |
| C2' |
C3' |
H16 |
110.3 |
110.5 |
| O2' |
C2' |
H14 |
113.7 |
110.6 |
| C2' |
O2' |
H15 |
109.5 |
114.0 |
| O3' |
C3' |
H16 |
113.2 |
110.5 |
| C3' |
O3' |
H17 |
109.5 |
114.0 |
| H5 |
C5' |
H6 |
109.5 |
109.4 |
| H11 |
N6 |
H12 |
109.4 |
120.0 |
Torsion Angles for 7DT
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1B |
PB |
O2B |
O3A |
116.1 |
120.0 |
| O2B |
PB |
O1B |
H3 |
0.0 |
180.0 |
| O1A |
PA |
O2A |
O5' |
122.4 |
120.0 |
| O2A |
PA |
O5' |
C5' |
178.3 |
55.0 |
| O2A |
PA |
O1A |
O5' |
237.9 |
240.0 |
| O1A |
PA |
O5' |
C5' |
52.3 |
295.1 |
| PA |
O5' |
C5' |
C4' |
184.3 |
180.0 |
| PA |
O5' |
C5' |
H5 |
304.4 |
300.0 |
| PA |
O5' |
C5' |
H6 |
64.2 |
59.9 |
| O2B |
PB |
O3A |
O1B |
124.5 |
120.0 |
| O3A |
PB |
O1B |
H3 |
117.7 |
300.0 |
| O2B |
PB |
O1B |
O3A |
242.3 |
240.0 |
| O3B |
PG |
O1G |
H2 |
245.3 |
180.0 |
| O3B |
PG |
O3G |
H1 |
111.8 |
60.0 |
| O2G |
PG |
O1G |
H2 |
0.0 |
60.0 |
| O2G |
PG |
O3G |
H1 |
0.0 |
180.0 |
| O5' |
C5' |
C4' |
C3' |
178.9 |
185.0 |
| C4' |
C5' |
O5' |
H5 |
239.9 |
240.0 |
| C4' |
C5' |
O5' |
H6 |
120.1 |
120.1 |
| O5' |
C5' |
C4' |
H7 |
302.1 |
307.2 |
| H5 |
C5' |
O5' |
H6 |
240.2 |
240.1 |
| C20 |
C8 |
N9 |
C4 |
358.2 |
360.0 |
| C5 |
C20 |
C8 |
H9 |
181.5 |
180.0 |
| C6 |
C5 |
C20 |
C4 |
180.7 |
179.9 |
| C20 |
C5 |
C6 |
N1 |
179.4 |
180.0 |
| N9 |
C4 |
C5 |
C20 |
359.6 |
360.0 |
| C20 |
C5 |
C4 |
N3 |
179.7 |
179.9 |
| N6 |
C6 |
C5 |
C4 |
180.4 |
180.0 |
| C5 |
C6 |
N6 |
N1 |
179.7 |
180.0 |
| N6 |
C6 |
N1 |
C2 |
180.2 |
180.0 |
| C8 |
N9 |
C4 |
C5 |
1.4 |
0.0 |
| C8 |
N9 |
C4 |
N3 |
181.2 |
180.1 |
| C8 |
N9 |
C1' |
C2' |
299.4 |
268.4 |
| C8 |
N9 |
C1' |
H8 |
179.3 |
146.1 |
| O1G |
PG |
O3G |
H1 |
223.7 |
299.9 |
| C20 |
C5 |
C6 |
C4 |
179.2 |
180.1 |
| C6 |
C5 |
C20 |
H10 |
0.0 |
360.0 |
| N6 |
C6 |
C5 |
N1 |
180.3 |
180.0 |
| N9 |
C4 |
C5 |
C6 |
179.0 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
359.1 |
360.0 |
| C5 |
C6 |
N1 |
C2 |
0.5 |
0.0 |
| C20 |
C5 |
C4 |
C6 |
180.6 |
180.0 |
| C4 |
C5 |
C20 |
H10 |
179.3 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
0.2 |
360.0 |
| N9 |
C4 |
C5 |
N3 |
179.9 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
0.2 |
360.0 |
| C6 |
N1 |
C2 |
H13 |
179.6 |
180.0 |
| O5' |
C5' |
C4' |
H5 |
120.1 |
120.0 |
| O5' |
C5' |
C4' |
H6 |
239.9 |
239.9 |
| O4' |
C4' |
C5' |
C3' |
244.7 |
244.6 |
| O4' |
C4' |
C5' |
H7 |
121.5 |
122.3 |
| C5' |
C4' |
C3' |
C2' |
257.2 |
217.2 |
| C5' |
C4' |
C3' |
O3' |
139.2 |
98.5 |
| C3' |
C4' |
C5' |
H7 |
236.8 |
237.7 |
| C5' |
C4' |
C3' |
H16 |
15.1 |
335.8 |
| H5 |
C5' |
C4' |
H6 |
119.8 |
119.9 |
| C5' |
C4' |
O4' |
C3' |
116.9 |
118.9 |
| O4' |
C4' |
C5' |
H5 |
303.5 |
309.6 |
| O4' |
C4' |
C5' |
H6 |
183.7 |
189.6 |
| C5' |
C4' |
O4' |
H7 |
239.3 |
237.8 |
| O4' |
C4' |
C3' |
C2' |
10.3 |
336.0 |
| O4' |
C4' |
C3' |
O3' |
252.3 |
217.4 |
| C3' |
C4' |
O4' |
H7 |
122.5 |
118.9 |
| O4' |
C4' |
C3' |
H16 |
128.2 |
94.7 |
| C1' |
O4' |
C4' |
C3' |
19.0 |
40.5 |
| C1' |
O4' |
C4' |
H7 |
256.5 |
281.6 |
| N9 |
C1' |
O4' |
C2' |
243.0 |
241.2 |
| N9 |
C1' |
O4' |
H8 |
124.7 |
122.4 |
| O4' |
C1' |
C2' |
C3' |
45.0 |
24.0 |
| O4' |
C1' |
C2' |
O2' |
158.9 |
142.6 |
| C2' |
C1' |
O4' |
H8 |
241.7 |
241.2 |
| O4' |
C1' |
C2' |
H14 |
288.6 |
265.3 |
| C20 |
C5 |
C4 |
N9 |
359.6 |
360.0 |
| C6 |
C5 |
C4 |
N9 |
179.0 |
180.0 |
| C5 |
C4 |
N9 |
N3 |
180.1 |
180.0 |
| C4 |
N9 |
C1' |
C2' |
121.0 |
88.2 |
| C4 |
N9 |
C1' |
H8 |
0.9 |
325.9 |
| O4' |
C1' |
N9 |
C2' |
114.6 |
115.4 |
| O4' |
C1' |
N9 |
H8 |
234.7 |
237.7 |
| N9 |
C1' |
C2' |
C3' |
164.3 |
142.8 |
| N9 |
C1' |
C2' |
O2' |
278.2 |
261.5 |
| C2' |
C1' |
N9 |
H8 |
120.1 |
122.3 |
| N9 |
C1' |
C2' |
H14 |
47.9 |
24.2 |
| N9 |
C4 |
N3 |
C5 |
180.1 |
179.9 |
| C4 |
N3 |
C2 |
H13 |
179.6 |
180.0 |
| N3 |
C2 |
N1 |
H13 |
180.0 |
180.0 |
| C3' |
C4' |
C5' |
H5 |
58.8 |
65.0 |
| C3' |
C4' |
C5' |
H6 |
299.0 |
305.0 |
| C5' |
C4' |
C3' |
H7 |
123.4 |
122.2 |
| O4' |
C4' |
C3' |
H7 |
236.5 |
241.1 |
| C1' |
C2' |
C3' |
C4' |
328.3 |
0.0 |
| O2' |
C2' |
C3' |
C4' |
210.5 |
241.4 |
| C2' |
C3' |
C4' |
O3' |
118.0 |
118.6 |
| C4' |
C3' |
C2' |
H14 |
84.6 |
118.6 |
| C2' |
C3' |
C4' |
H16 |
242.1 |
241.3 |
| O3' |
C3' |
C4' |
H16 |
124.1 |
122.7 |
| C4' |
C3' |
O3' |
H17 |
180.0 |
180.0 |
| O4' |
C1' |
C2' |
H8 |
119.8 |
118.8 |
| N9 |
C1' |
C2' |
H8 |
239.2 |
237.7 |
| C4' |
C3' |
C2' |
C1' |
328.3 |
0.0 |
| O2' |
C2' |
C1' |
C3' |
113.9 |
118.7 |
| C1' |
C2' |
C3' |
O3' |
83.6 |
118.7 |
| C3' |
C2' |
C1' |
H14 |
116.4 |
118.6 |
| C1' |
C2' |
C3' |
H16 |
210.2 |
241.3 |
| O2' |
C2' |
C1' |
H14 |
230.3 |
237.3 |
| C1' |
C2' |
O2' |
H15 |
180.0 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
1.0 |
0.1 |
| N9 |
C4 |
N3 |
C2 |
181.2 |
180.0 |
| N1 |
C2 |
N3 |
H13 |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
O3' |
244.7 |
241.3 |
| C2' |
C3' |
C4' |
H7 |
133.8 |
94.9 |
| C4' |
C3' |
C2' |
H16 |
118.1 |
118.7 |
| C1' |
C2' |
C3' |
O2' |
117.8 |
118.6 |
| C3' |
C2' |
C1' |
H8 |
285.2 |
265.1 |
| C1' |
C2' |
C3' |
H14 |
243.6 |
241.4 |
| O2' |
C2' |
C3' |
H14 |
125.8 |
122.8 |
| C3' |
C2' |
O2' |
H15 |
287.2 |
294.6 |
| O3' |
C3' |
C2' |
H16 |
233.4 |
237.3 |
| C2' |
C3' |
O3' |
H17 |
67.4 |
65.3 |
| C4' |
C3' |
C2' |
O2' |
210.5 |
241.4 |
| C1' |
C2' |
O2' |
C3' |
252.8 |
245.4 |
| O2' |
C2' |
C1' |
H8 |
39.1 |
23.8 |
| C1' |
C2' |
O2' |
H14 |
128.4 |
122.6 |
| O2' |
C2' |
C3' |
O3' |
325.7 |
0.1 |
| C3' |
C2' |
O2' |
H14 |
235.6 |
237.2 |
| O2' |
C2' |
C3' |
H16 |
92.4 |
122.7 |
| C4' |
C3' |
O3' |
C2' |
112.5 |
114.7 |
| O3' |
C3' |
C4' |
H7 |
15.8 |
336.3 |
| C4' |
C3' |
O3' |
H16 |
237.6 |
237.3 |
| O3' |
C3' |
C2' |
H14 |
199.9 |
237.3 |
| C2' |
C3' |
O3' |
H16 |
125.0 |
122.6 |
| H3 |
O1B |
PB |
O3A |
117.7 |
300.0 |
| H4 |
O1A |
PA |
O5' |
122.1 |
299.9 |
| O5' |
C5' |
H5 |
C4' |
239.4 |
239.9 |
| O5' |
C5' |
H5 |
H6 |
119.7 |
120.0 |
| H5 |
C5' |
C4' |
C3' |
58.8 |
65.0 |
| C4' |
C5' |
H5 |
H6 |
240.3 |
240.0 |
| H5 |
C5' |
C4' |
H7 |
182.0 |
187.2 |
| O5' |
C5' |
H6 |
C4' |
120.6 |
120.1 |
| O5' |
C5' |
H6 |
H5 |
240.3 |
240.1 |
| H6 |
C5' |
C4' |
C3' |
299.0 |
305.0 |
| C4' |
C5' |
H6 |
H5 |
119.7 |
120.0 |
| H6 |
C5' |
C4' |
H7 |
62.2 |
67.3 |
| C5' |
C4' |
H7 |
C3' |
237.3 |
237.7 |
| H7 |
C4' |
C5' |
H5 |
182.0 |
187.2 |
| H7 |
C4' |
C5' |
H6 |
62.2 |
67.3 |
| O4' |
C4' |
H7 |
C3' |
120.7 |
115.4 |
| H7 |
C4' |
C3' |
C2' |
133.8 |
94.9 |
| H7 |
C4' |
C3' |
O3' |
15.8 |
336.3 |
| H7 |
C4' |
C3' |
H16 |
251.7 |
213.6 |
| O4' |
C1' |
H8 |
C2' |
244.7 |
244.6 |
| N9 |
C1' |
H8 |
C2' |
119.5 |
122.3 |
| H8 |
C1' |
C2' |
C3' |
285.2 |
265.1 |
| H8 |
C1' |
C2' |
O2' |
39.1 |
23.8 |
| H8 |
C1' |
C2' |
H14 |
168.8 |
146.5 |
| H9 |
C8 |
N9 |
C4 |
178.2 |
180.0 |
| H10 |
C20 |
C8 |
H9 |
1.5 |
359.9 |
| H10 |
C20 |
C5 |
C6 |
0.0 |
360.0 |
| H10 |
C20 |
C5 |
C4 |
179.3 |
180.0 |
| H11 |
N6 |
C6 |
N1 |
360.0 |
180.0 |
| H12 |
N6 |
C6 |
N1 |
120.0 |
360.0 |
| C1' |
C2' |
H14 |
C3' |
107.6 |
114.6 |
| C1' |
C2' |
H14 |
O2' |
230.5 |
237.4 |
| H14 |
C2' |
C1' |
H8 |
168.8 |
146.5 |
| O2' |
C2' |
H14 |
C3' |
237.1 |
237.2 |
| H14 |
C2' |
C3' |
O3' |
199.9 |
237.3 |
| H14 |
C2' |
C3' |
H16 |
326.6 |
359.9 |
| H14 |
C2' |
O2' |
H15 |
51.6 |
57.4 |
| H15 |
O2' |
C2' |
C3' |
287.2 |
294.6 |
| H15 |
O2' |
C2' |
H14 |
51.6 |
57.4 |
| C4' |
C3' |
H16 |
C2' |
246.5 |
245.3 |
| C4' |
C3' |
H16 |
O3' |
120.8 |
122.7 |
| H16 |
C3' |
C4' |
H7 |
251.7 |
213.6 |
| C2' |
C3' |
H16 |
O3' |
234.3 |
237.4 |
| H16 |
C3' |
C2' |
H14 |
326.6 |
359.9 |
| H16 |
C3' |
O3' |
H17 |
302.4 |
302.6 |
| H17 |
O3' |
C3' |
H16 |
302.4 |
302.6 |