PDB Chemical Component 7DD
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 7DD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3B |
PB |
1.484 |
1.481 |
| O2A |
PA |
1.472 |
1.480 |
| O1A |
PA |
1.502 |
1.609 |
| PA |
O3A |
1.585 |
1.610 |
| PA |
O5' |
1.585 |
1.610 |
| PB |
O3A |
1.595 |
1.610 |
| PB |
O1B |
1.498 |
1.610 |
| PB |
O2B |
1.500 |
1.610 |
| N6 |
C6 |
1.342 |
1.384 |
| O5' |
C5' |
1.417 |
1.429 |
| C16 |
C8 |
1.337 |
1.343 |
| C16 |
C5 |
1.341 |
1.462 |
| C8 |
N9 |
1.339 |
1.371 |
| C5 |
C6 |
1.361 |
1.403 |
| C5 |
C4 |
1.350 |
1.407 |
| C6 |
N1 |
1.334 |
1.330 |
| C5' |
C4' |
1.525 |
1.530 |
| O4' |
C4' |
1.438 |
1.444 |
| O4' |
C1' |
1.418 |
1.445 |
| N9 |
C4 |
1.342 |
1.368 |
| N9 |
C1' |
1.473 |
1.464 |
| C4 |
N3 |
1.350 |
1.331 |
| N1 |
C2 |
1.403 |
1.321 |
| C4' |
C3' |
1.528 |
1.544 |
| C1' |
C2' |
1.541 |
1.545 |
| N3 |
C2 |
1.389 |
1.317 |
| C2' |
C3' |
1.502 |
1.545 |
| C2' |
O2' |
1.449 |
1.430 |
| C3' |
O3' |
1.445 |
1.429 |
| O1B |
H1 |
0.950 |
0.967 |
| O2B |
H2 |
0.950 |
0.967 |
| O1A |
H3 |
0.950 |
0.968 |
| C5' |
H4 |
1.100 |
1.090 |
| C5' |
H5 |
1.100 |
1.090 |
| C4' |
H6 |
1.100 |
1.090 |
| C1' |
H7 |
1.100 |
1.090 |
| C8 |
H8 |
1.080 |
1.081 |
| C16 |
H9 |
1.080 |
1.080 |
| N6 |
H10 |
1.000 |
0.970 |
| N6 |
H11 |
1.000 |
0.970 |
| C2 |
H12 |
1.080 |
1.079 |
| C2' |
H13 |
1.100 |
1.090 |
| O2' |
H14 |
0.950 |
0.968 |
| C3' |
H15 |
1.100 |
1.090 |
| O3' |
H16 |
0.951 |
0.967 |
Bond Angles for 7DD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3B |
PB |
O3A |
111.6 |
109.5 |
| O2A |
PA |
O5' |
107.6 |
109.5 |
| O1A |
PA |
O5' |
110.1 |
109.5 |
| PA |
O5' |
C5' |
118.8 |
123.0 |
| O2B |
PB |
O3A |
104.6 |
109.5 |
| PB |
O1B |
H1 |
109.5 |
114.0 |
| PB |
O2B |
H2 |
109.5 |
114.0 |
| N6 |
C6 |
N1 |
118.7 |
120.8 |
| O5' |
C5' |
C4' |
109.3 |
109.5 |
| O5' |
C5' |
H4 |
109.5 |
109.5 |
| O5' |
C5' |
H5 |
109.5 |
109.5 |
| C16 |
C8 |
H8 |
126.3 |
125.1 |
| C16 |
C5 |
C6 |
133.7 |
135.1 |
| C16 |
C5 |
C4 |
106.5 |
106.2 |
| C5 |
C16 |
H9 |
125.2 |
126.6 |
| C8 |
N9 |
C4 |
108.2 |
110.0 |
| C6 |
C5 |
C4 |
119.8 |
118.7 |
| C5 |
C6 |
N1 |
120.7 |
118.3 |
| N9 |
C4 |
C5 |
108.4 |
107.1 |
| C5 |
C4 |
N3 |
121.6 |
118.6 |
| C6 |
N1 |
C2 |
120.6 |
121.0 |
| C5' |
C4' |
C3' |
111.4 |
110.4 |
| C4' |
C5' |
H4 |
109.5 |
109.4 |
| C4' |
C5' |
H5 |
109.5 |
109.5 |
| C5' |
C4' |
H6 |
109.7 |
110.3 |
| O4' |
C4' |
C3' |
108.5 |
104.8 |
| O4' |
C4' |
H6 |
111.0 |
110.5 |
| O4' |
C1' |
C2' |
103.6 |
104.8 |
| O4' |
C1' |
H7 |
110.5 |
110.4 |
| N9 |
C4 |
N3 |
130.0 |
134.3 |
| N9 |
C1' |
C2' |
112.8 |
110.4 |
| N9 |
C1' |
H7 |
109.8 |
110.5 |
| N1 |
C2 |
H12 |
121.1 |
118.7 |
| C4' |
C3' |
C2' |
102.7 |
104.1 |
| C4' |
C3' |
O3' |
109.8 |
110.6 |
| C3' |
C4' |
H6 |
109.7 |
110.4 |
| C4' |
C3' |
H15 |
109.8 |
110.5 |
| C1' |
C2' |
C3' |
100.7 |
104.1 |
| C1' |
C2' |
O2' |
112.9 |
110.5 |
| C2' |
C1' |
H7 |
108.9 |
110.4 |
| C1' |
C2' |
H13 |
110.5 |
110.5 |
| N3 |
C2 |
H12 |
121.1 |
118.6 |
| O2' |
C2' |
C3' |
109.2 |
110.5 |
| C2' |
C3' |
O3' |
112.9 |
110.5 |
| C3' |
C2' |
H13 |
111.1 |
110.5 |
| C2' |
C3' |
H15 |
110.2 |
110.5 |
| O2' |
C2' |
H13 |
111.9 |
110.6 |
| C2' |
O2' |
H14 |
109.5 |
114.0 |
| O3' |
C3' |
H15 |
111.1 |
110.5 |
| C3' |
O3' |
H16 |
109.5 |
114.0 |
| H4 |
C5' |
H5 |
109.5 |
109.5 |
| H10 |
N6 |
H11 |
109.4 |
120.1 |
Torsion Angles for 7DD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2B |
PB |
O3B |
O3A |
243.7 |
240.0 |
| O3B |
PB |
O1B |
H1 |
0.0 |
60.0 |
| O3B |
PB |
O2B |
H2 |
0.0 |
180.0 |
| O1A |
PA |
O2A |
O5' |
123.8 |
120.0 |
| O2A |
PA |
O5' |
C5' |
185.9 |
55.1 |
| O2A |
PA |
O1A |
O5' |
237.5 |
240.0 |
| O1A |
PA |
O5' |
C5' |
58.5 |
295.0 |
| PA |
O5' |
C5' |
C4' |
186.5 |
180.0 |
| PA |
O5' |
C5' |
H4 |
306.5 |
299.9 |
| PA |
O5' |
C5' |
H5 |
66.6 |
60.0 |
| O3A |
PB |
O1B |
H1 |
121.4 |
180.0 |
| O3A |
PB |
O2B |
H2 |
239.5 |
60.0 |
| O3B |
PB |
O2B |
O3A |
120.5 |
120.0 |
| O2B |
PB |
O1B |
H1 |
232.1 |
300.0 |
| N6 |
C6 |
C5 |
C4 |
180.8 |
180.0 |
| C5 |
C6 |
N6 |
N1 |
179.1 |
180.0 |
| N6 |
C6 |
N1 |
C2 |
180.1 |
180.0 |
| O5' |
C5' |
C4' |
C3' |
177.9 |
185.0 |
| C4' |
C5' |
O5' |
H4 |
240.0 |
240.1 |
| C4' |
C5' |
O5' |
H5 |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
H6 |
299.6 |
307.2 |
| H4 |
C5' |
O5' |
H5 |
240.0 |
240.0 |
| C16 |
C8 |
N9 |
C4 |
0.3 |
360.0 |
| C5 |
C16 |
C8 |
H8 |
180.6 |
179.9 |
| C6 |
C5 |
C16 |
C4 |
182.1 |
180.0 |
| C16 |
C5 |
C6 |
N1 |
177.5 |
180.0 |
| N9 |
C4 |
C5 |
C16 |
1.5 |
0.0 |
| C16 |
C5 |
C4 |
N3 |
180.4 |
179.9 |
| C8 |
N9 |
C4 |
C5 |
358.9 |
0.0 |
| C8 |
N9 |
C4 |
N3 |
180.1 |
180.1 |
| C8 |
N9 |
C1' |
C2' |
304.8 |
268.5 |
| C8 |
N9 |
C1' |
H7 |
183.3 |
146.1 |
| N6 |
C6 |
C5 |
N1 |
181.0 |
180.0 |
| C16 |
C5 |
C6 |
C4 |
177.7 |
180.0 |
| C6 |
C5 |
C16 |
H9 |
0.8 |
0.0 |
| N9 |
C4 |
C5 |
C6 |
179.7 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
358.6 |
359.9 |
| C5 |
C6 |
N1 |
C2 |
1.0 |
0.0 |
| C16 |
C5 |
C4 |
C6 |
181.8 |
180.0 |
| C4 |
C5 |
C16 |
H9 |
178.6 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
359.8 |
0.0 |
| N9 |
C4 |
C5 |
N3 |
181.1 |
180.1 |
| N1 |
C6 |
C5 |
C4 |
359.8 |
0.0 |
| C6 |
N1 |
C2 |
H12 |
179.6 |
180.1 |
| O5' |
C5' |
C4' |
H4 |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
H5 |
240.0 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
241.8 |
244.6 |
| O4' |
C4' |
C5' |
H6 |
120.2 |
122.4 |
| C5' |
C4' |
C3' |
C2' |
252.0 |
217.2 |
| C5' |
C4' |
C3' |
O3' |
131.7 |
98.5 |
| C3' |
C4' |
C5' |
H6 |
238.4 |
237.8 |
| C5' |
C4' |
C3' |
H15 |
9.3 |
335.8 |
| H4 |
C5' |
C4' |
H5 |
120.1 |
120.0 |
| C5' |
C4' |
O4' |
C3' |
120.1 |
118.8 |
| O4' |
C4' |
C5' |
H4 |
299.8 |
309.6 |
| O4' |
C4' |
C5' |
H5 |
179.8 |
189.6 |
| C5' |
C4' |
O4' |
H6 |
240.6 |
237.7 |
| O4' |
C4' |
C3' |
C2' |
9.0 |
336.0 |
| O4' |
C4' |
C3' |
O3' |
248.7 |
217.4 |
| C3' |
C4' |
O4' |
H6 |
120.5 |
118.9 |
| O4' |
C4' |
C3' |
H15 |
126.3 |
94.7 |
| C1' |
O4' |
C4' |
C3' |
19.2 |
40.5 |
| C1' |
O4' |
C4' |
H6 |
258.6 |
281.6 |
| N9 |
C1' |
O4' |
C2' |
238.6 |
241.2 |
| N9 |
C1' |
O4' |
H7 |
122.1 |
122.4 |
| O4' |
C1' |
C2' |
C3' |
44.2 |
24.0 |
| O4' |
C1' |
C2' |
O2' |
160.5 |
142.6 |
| C2' |
C1' |
O4' |
H7 |
243.5 |
241.2 |
| O4' |
C1' |
C2' |
H13 |
286.7 |
265.3 |
| C16 |
C5 |
C4 |
N9 |
1.5 |
0.0 |
| C6 |
C5 |
C4 |
N9 |
179.7 |
180.0 |
| C5 |
C4 |
N9 |
N3 |
178.8 |
179.9 |
| C4 |
N9 |
C1' |
C2' |
120.9 |
88.2 |
| C4 |
N9 |
C1' |
H7 |
359.4 |
325.9 |
| O4' |
C1' |
N9 |
C2' |
115.8 |
115.4 |
| O4' |
C1' |
N9 |
H7 |
237.4 |
237.7 |
| N9 |
C1' |
C2' |
C3' |
164.5 |
142.8 |
| N9 |
C1' |
C2' |
O2' |
280.7 |
261.4 |
| C2' |
C1' |
N9 |
H7 |
121.6 |
122.3 |
| N9 |
C1' |
C2' |
H13 |
46.9 |
24.1 |
| N9 |
C4 |
N3 |
C5 |
178.7 |
179.9 |
| C4 |
N3 |
C2 |
H12 |
179.0 |
179.9 |
| N3 |
C2 |
N1 |
H12 |
180.0 |
179.9 |
| C3' |
C4' |
C5' |
H4 |
58.0 |
65.0 |
| C3' |
C4' |
C5' |
H5 |
297.9 |
305.0 |
| C5' |
C4' |
C3' |
H6 |
121.7 |
122.2 |
| O4' |
C4' |
C3' |
H6 |
238.7 |
241.0 |
| C1' |
C2' |
C3' |
C4' |
329.2 |
360.0 |
| O2' |
C2' |
C3' |
C4' |
210.2 |
241.4 |
| C2' |
C3' |
C4' |
O3' |
120.3 |
118.7 |
| C4' |
C3' |
C2' |
H13 |
86.3 |
118.7 |
| C2' |
C3' |
C4' |
H15 |
242.7 |
241.4 |
| O3' |
C3' |
C4' |
H15 |
122.4 |
122.7 |
| C4' |
C3' |
O3' |
H16 |
180.0 |
180.0 |
| O4' |
C1' |
C2' |
H7 |
117.7 |
118.8 |
| N9 |
C1' |
C2' |
H7 |
237.9 |
237.6 |
| C4' |
C3' |
C2' |
C1' |
329.2 |
360.0 |
| O2' |
C2' |
C1' |
C3' |
116.2 |
118.6 |
| C1' |
C2' |
C3' |
O3' |
87.3 |
118.7 |
| C3' |
C2' |
C1' |
H13 |
117.5 |
118.7 |
| C1' |
C2' |
C3' |
H15 |
212.2 |
241.3 |
| O2' |
C2' |
C1' |
H13 |
233.8 |
237.3 |
| C1' |
C2' |
O2' |
H14 |
180.0 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
2.0 |
0.0 |
| N9 |
C4 |
N3 |
C2 |
180.6 |
180.0 |
| N1 |
C2 |
N3 |
H12 |
180.0 |
180.1 |
| C4' |
C3' |
C2' |
O3' |
241.8 |
241.3 |
| C2' |
C3' |
C4' |
H6 |
130.3 |
95.0 |
| C4' |
C3' |
C2' |
H15 |
117.0 |
118.7 |
| C1' |
C2' |
C3' |
O2' |
119.0 |
118.6 |
| C3' |
C2' |
C1' |
H7 |
286.5 |
265.2 |
| C1' |
C2' |
C3' |
H13 |
242.9 |
241.3 |
| O2' |
C2' |
C3' |
H13 |
123.9 |
122.7 |
| C3' |
C2' |
O2' |
H14 |
291.1 |
294.6 |
| O3' |
C3' |
C2' |
H15 |
235.2 |
237.3 |
| C2' |
C3' |
O3' |
H16 |
66.1 |
65.3 |
| C4' |
C3' |
C2' |
O2' |
210.2 |
241.4 |
| C1' |
C2' |
O2' |
C3' |
248.9 |
245.4 |
| O2' |
C2' |
C1' |
H7 |
42.8 |
23.8 |
| C1' |
C2' |
O2' |
H13 |
125.5 |
122.7 |
| O2' |
C2' |
C3' |
O3' |
328.3 |
0.0 |
| C3' |
C2' |
O2' |
H13 |
236.6 |
237.3 |
| O2' |
C2' |
C3' |
H15 |
93.2 |
122.7 |
| C4' |
C3' |
O3' |
C2' |
113.9 |
114.7 |
| O3' |
C3' |
C4' |
H6 |
10.0 |
336.3 |
| C4' |
C3' |
O3' |
H15 |
238.3 |
237.3 |
| O3' |
C3' |
C2' |
H13 |
204.4 |
237.4 |
| C2' |
C3' |
O3' |
H15 |
124.4 |
122.6 |
| H2 |
O2B |
PB |
O3A |
239.5 |
60.0 |
| H3 |
O1A |
PA |
O5' |
122.5 |
300.0 |
| O5' |
C5' |
H4 |
C4' |
240.2 |
240.0 |
| O5' |
C5' |
H4 |
H5 |
120.1 |
120.0 |
| H4 |
C5' |
C4' |
C3' |
58.0 |
65.0 |
| C4' |
C5' |
H4 |
H5 |
239.9 |
240.0 |
| H4 |
C5' |
C4' |
H6 |
179.6 |
187.2 |
| O5' |
C5' |
H5 |
C4' |
119.8 |
120.0 |
| O5' |
C5' |
H5 |
H4 |
239.9 |
240.0 |
| H5 |
C5' |
C4' |
C3' |
297.9 |
305.0 |
| C4' |
C5' |
H5 |
H4 |
120.1 |
120.0 |
| H5 |
C5' |
C4' |
H6 |
59.6 |
67.2 |
| C5' |
C4' |
H6 |
C3' |
237.3 |
237.8 |
| H6 |
C4' |
C5' |
H4 |
179.6 |
187.2 |
| H6 |
C4' |
C5' |
H5 |
59.6 |
67.2 |
| O4' |
C4' |
H6 |
C3' |
119.8 |
115.5 |
| H6 |
C4' |
C3' |
C2' |
130.3 |
95.0 |
| H6 |
C4' |
C3' |
O3' |
10.0 |
336.3 |
| H6 |
C4' |
C3' |
H15 |
247.6 |
213.6 |
| O4' |
C1' |
H7 |
C2' |
246.8 |
244.7 |
| N9 |
C1' |
H7 |
C2' |
123.9 |
122.3 |
| H7 |
C1' |
C2' |
C3' |
286.5 |
265.2 |
| H7 |
C1' |
C2' |
O2' |
42.8 |
23.8 |
| H7 |
C1' |
C2' |
H13 |
169.0 |
146.5 |
| H8 |
C8 |
N9 |
C4 |
180.3 |
180.1 |
| H9 |
C16 |
C8 |
H8 |
0.7 |
359.9 |
| H9 |
C16 |
C5 |
C6 |
0.8 |
0.0 |
| H9 |
C16 |
C5 |
C4 |
178.6 |
180.0 |
| H10 |
N6 |
C6 |
N1 |
0.0 |
180.0 |
| H11 |
N6 |
C6 |
N1 |
120.0 |
360.0 |
| C1' |
C2' |
H13 |
C3' |
110.9 |
114.7 |
| C1' |
C2' |
H13 |
O2' |
233.2 |
237.3 |
| H13 |
C2' |
C1' |
H7 |
169.0 |
146.5 |
| O2' |
C2' |
H13 |
C3' |
237.7 |
237.3 |
| H13 |
C2' |
C3' |
O3' |
204.4 |
237.4 |
| H13 |
C2' |
C3' |
H15 |
329.3 |
0.0 |
| H13 |
C2' |
O2' |
H14 |
54.5 |
57.3 |
| H14 |
O2' |
C2' |
C3' |
291.1 |
294.6 |
| H14 |
O2' |
C2' |
H13 |
54.5 |
57.3 |
| C4' |
C3' |
H15 |
C2' |
247.6 |
245.4 |
| C4' |
C3' |
H15 |
O3' |
121.7 |
122.7 |
| H15 |
C3' |
C4' |
H6 |
247.6 |
213.6 |
| C2' |
C3' |
H15 |
O3' |
234.1 |
237.4 |
| H15 |
C3' |
C2' |
H13 |
329.3 |
0.0 |
| H15 |
C3' |
O3' |
H16 |
301.7 |
302.7 |
| H16 |
O3' |
C3' |
H15 |
301.7 |
302.7 |