PDB Chemical Component ND7
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 ND7
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2A |
PA |
1.522 |
1.480 |
| N3A |
PA |
1.698 |
1.682 |
| PA |
O5' |
1.586 |
1.610 |
| PA |
O1A |
1.502 |
1.610 |
| O5' |
C5' |
1.460 |
1.429 |
| C5' |
C4' |
1.550 |
1.530 |
| O3' |
C3' |
1.375 |
1.428 |
| C4' |
C3' |
1.566 |
1.545 |
| C4' |
O4' |
1.296 |
1.444 |
| C3' |
C2' |
1.588 |
1.545 |
| O4' |
C1' |
1.621 |
1.444 |
| C1' |
C2' |
1.340 |
1.544 |
| C1' |
N9 |
1.435 |
1.465 |
| C2' |
O2' |
1.480 |
1.429 |
| N9 |
C8 |
1.341 |
1.362 |
| N9 |
C4 |
1.362 |
1.372 |
| N3 |
C4 |
1.350 |
1.330 |
| N3 |
C2 |
1.299 |
1.316 |
| C8 |
N7 |
1.319 |
1.302 |
| C4 |
C5 |
1.349 |
1.405 |
| C2 |
N1 |
1.338 |
1.321 |
| N7 |
C5 |
1.353 |
1.355 |
| C5 |
C6 |
1.379 |
1.406 |
| N1 |
C6 |
1.306 |
1.328 |
| C6 |
N6 |
1.452 |
1.385 |
| O1A |
H1 |
0.950 |
0.967 |
| N3A |
H2 |
1.000 |
1.009 |
| N3A |
H3 |
1.000 |
1.009 |
| C5' |
H4 |
1.100 |
1.090 |
| C5' |
H5 |
1.100 |
1.090 |
| C4' |
H6 |
1.100 |
1.091 |
| C3' |
H7 |
1.100 |
1.090 |
| O3' |
H8 |
0.950 |
0.967 |
| C2' |
H9 |
1.100 |
1.090 |
| O2' |
H10 |
0.949 |
0.968 |
| C1' |
H11 |
1.100 |
1.090 |
| C8 |
H12 |
1.080 |
1.080 |
| C2 |
H13 |
1.080 |
1.080 |
| N6 |
H14 |
1.000 |
0.970 |
| N6 |
H15 |
1.000 |
0.970 |
Bond Angles for ND7
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2A |
PA |
O5' |
105.2 |
109.4 |
| N3A |
PA |
O5' |
106.6 |
109.5 |
| PA |
O5' |
C5' |
115.9 |
123.0 |
| PA |
O1A |
H1 |
109.5 |
114.0 |
| O5' |
C5' |
C4' |
105.1 |
109.5 |
| O5' |
C5' |
H4 |
110.5 |
109.5 |
| O5' |
C5' |
H5 |
110.6 |
109.5 |
| C5' |
C4' |
C3' |
108.5 |
110.4 |
| C5' |
C4' |
O4' |
106.1 |
110.4 |
| C4' |
C5' |
H4 |
110.6 |
109.5 |
| C4' |
C5' |
H5 |
110.5 |
109.5 |
| C5' |
C4' |
H6 |
109.3 |
110.3 |
| O3' |
C3' |
C2' |
117.7 |
110.5 |
| O3' |
C3' |
H7 |
110.0 |
110.6 |
| C3' |
C4' |
O4' |
110.4 |
104.8 |
| C4' |
C3' |
C2' |
101.0 |
104.0 |
| C3' |
C4' |
H6 |
109.1 |
110.3 |
| C4' |
C3' |
H7 |
107.5 |
110.4 |
| C4' |
O4' |
C1' |
107.4 |
105.3 |
| O4' |
C4' |
H6 |
113.2 |
110.5 |
| C3' |
C2' |
O2' |
110.3 |
110.5 |
| C2' |
C3' |
H7 |
107.3 |
110.6 |
| C3' |
C2' |
H9 |
109.2 |
110.5 |
| O4' |
C1' |
N9 |
104.7 |
110.4 |
| O4' |
C1' |
H11 |
107.3 |
110.5 |
| C1' |
C2' |
H9 |
113.0 |
110.6 |
| C1' |
N9 |
C8 |
127.4 |
126.3 |
| C1' |
N9 |
C4 |
125.9 |
126.3 |
| N9 |
C1' |
H11 |
109.7 |
110.3 |
| O2' |
C2' |
H9 |
110.6 |
110.5 |
| C2' |
O2' |
H10 |
109.5 |
114.0 |
| C4 |
N9 |
C8 |
106.7 |
107.4 |
| N9 |
C8 |
N7 |
110.3 |
110.0 |
| N9 |
C8 |
H12 |
124.8 |
125.1 |
| N9 |
C4 |
C5 |
107.4 |
106.0 |
| N3 |
C2 |
N1 |
121.0 |
122.5 |
| N3 |
C2 |
H13 |
119.5 |
118.7 |
| C4 |
C5 |
C6 |
117.8 |
118.2 |
| C2 |
N1 |
C6 |
121.7 |
121.2 |
| N1 |
C2 |
H13 |
119.5 |
118.8 |
| N7 |
C5 |
C6 |
133.9 |
134.7 |
| C5 |
C6 |
N1 |
119.2 |
118.5 |
| C5 |
C6 |
N6 |
120.3 |
120.7 |
| N1 |
C6 |
N6 |
120.6 |
120.8 |
| C6 |
N6 |
H14 |
109.5 |
120.0 |
| C6 |
N6 |
H15 |
109.4 |
119.9 |
| H2 |
N3A |
H3 |
109.5 |
111.0 |
| H4 |
C5' |
H5 |
109.5 |
109.4 |
| H14 |
N6 |
H15 |
109.4 |
120.1 |
Torsion Angles for ND7
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N3A |
PA |
O2A |
O5' |
114.2 |
120.0 |
| O2A |
PA |
O5' |
C5' |
178.9 |
50.1 |
| O2A |
PA |
O1A |
H1 |
0.0 |
300.0 |
| O2A |
PA |
N3A |
O5' |
246.6 |
240.0 |
| N3A |
PA |
O5' |
C5' |
62.7 |
290.0 |
| N3A |
PA |
O1A |
H1 |
121.3 |
60.0 |
| O5' |
PA |
O1A |
H1 |
236.6 |
180.0 |
| PA |
O5' |
C5' |
C4' |
156.3 |
180.0 |
| PA |
O5' |
C5' |
H4 |
275.6 |
300.0 |
| PA |
O5' |
C5' |
H5 |
37.0 |
59.9 |
| O5' |
C5' |
C4' |
C3' |
285.9 |
185.0 |
| O5' |
C5' |
C4' |
O4' |
167.1 |
69.6 |
| C4' |
C5' |
O5' |
H4 |
240.7 |
240.0 |
| C4' |
C5' |
O5' |
H5 |
119.3 |
120.1 |
| O5' |
C5' |
C4' |
H6 |
44.7 |
307.2 |
| H4 |
C5' |
O5' |
H5 |
238.6 |
240.0 |
| O5' |
C5' |
C4' |
H4 |
119.3 |
120.0 |
| O5' |
C5' |
C4' |
H5 |
240.7 |
240.0 |
| C3' |
C4' |
C5' |
O4' |
118.7 |
115.4 |
| C5' |
C4' |
C3' |
C2' |
257.6 |
217.2 |
| C3' |
C4' |
C5' |
H6 |
241.1 |
237.8 |
| C5' |
C4' |
C3' |
H7 |
9.8 |
335.8 |
| C5' |
C4' |
O4' |
C1' |
121.5 |
159.4 |
| O4' |
C4' |
C5' |
H6 |
122.4 |
122.4 |
| H4 |
C5' |
C4' |
H5 |
121.4 |
120.0 |
| O3' |
C3' |
C4' |
O4' |
247.1 |
217.4 |
| C4' |
C3' |
O3' |
C2' |
116.9 |
114.6 |
| O3' |
C3' |
C4' |
H6 |
12.2 |
336.3 |
| C4' |
C3' |
O3' |
H7 |
240.1 |
237.4 |
| O3' |
C3' |
C2' |
O2' |
337.6 |
360.0 |
| C2' |
C3' |
O3' |
H7 |
123.2 |
122.8 |
| O3' |
C3' |
C2' |
H9 |
215.8 |
237.4 |
| C5' |
C4' |
C3' |
O4' |
244.0 |
241.1 |
| C3' |
C4' |
C5' |
H4 |
166.6 |
65.0 |
| C3' |
C4' |
C5' |
H5 |
45.2 |
305.1 |
| C5' |
C4' |
C3' |
H6 |
119.0 |
122.2 |
| O3' |
C3' |
C4' |
C2' |
233.6 |
241.3 |
| O3' |
C3' |
C4' |
H7 |
121.4 |
122.7 |
| C3' |
C4' |
O4' |
C1' |
4.0 |
40.5 |
| O4' |
C4' |
C3' |
H6 |
235.0 |
241.1 |
| C4' |
C3' |
C2' |
O2' |
214.5 |
241.3 |
| C2' |
C3' |
C4' |
H7 |
247.8 |
241.4 |
| C4' |
C3' |
C2' |
H9 |
92.8 |
118.8 |
| C5' |
C4' |
O4' |
C3' |
117.5 |
118.9 |
| O4' |
C4' |
C5' |
H4 |
47.9 |
309.6 |
| O4' |
C4' |
C5' |
H5 |
286.5 |
189.6 |
| C5' |
C4' |
O4' |
H6 |
240.1 |
237.7 |
| O4' |
C4' |
C3' |
C2' |
13.5 |
336.0 |
| C3' |
C4' |
O4' |
H6 |
122.7 |
118.8 |
| O4' |
C4' |
C3' |
H7 |
125.8 |
94.7 |
| C4' |
O4' |
C1' |
N9 |
211.3 |
200.7 |
| C4' |
O4' |
C1' |
H11 |
94.8 |
78.4 |
| O3' |
C3' |
C2' |
H7 |
235.4 |
237.2 |
| C2' |
C3' |
C4' |
O4' |
13.5 |
336.0 |
| C2' |
C3' |
C4' |
H6 |
138.6 |
95.0 |
| C4' |
C3' |
C2' |
H7 |
112.4 |
118.5 |
| C1' |
C2' |
C3' |
H9 |
238.5 |
241.2 |
| O2' |
C2' |
C3' |
H9 |
121.8 |
122.5 |
| C3' |
C2' |
O2' |
H10 |
180.0 |
298.6 |
| C1' |
O4' |
C4' |
H6 |
241.4 |
281.6 |
| O4' |
C1' |
C2' |
H9 |
272.4 |
265.3 |
| O4' |
C1' |
N9 |
C8 |
64.3 |
20.3 |
| O4' |
C1' |
N9 |
C4 |
247.1 |
200.7 |
| N9 |
C1' |
O4' |
H11 |
116.5 |
122.3 |
| C4' |
O4' |
C1' |
C2' |
336.0 |
319.5 |
| C1' |
C2' |
C3' |
H7 |
218.8 |
241.4 |
| C3' |
C2' |
C1' |
H9 |
119.1 |
118.7 |
| O2' |
C2' |
C1' |
H9 |
237.0 |
237.3 |
| C1' |
C2' |
O2' |
H10 |
65.3 |
183.9 |
| O4' |
C1' |
N9 |
H11 |
245.1 |
237.6 |
| N9 |
C1' |
C2' |
H9 |
28.8 |
24.2 |
| C4 |
N9 |
C1' |
C8 |
182.9 |
180.3 |
| C1' |
N9 |
C8 |
N7 |
180.8 |
179.8 |
| C1' |
N9 |
C8 |
H12 |
0.8 |
360.0 |
| C1' |
N9 |
C4 |
C5 |
179.0 |
180.0 |
| O2' |
C2' |
C3' |
H7 |
102.2 |
122.8 |
| C3' |
C2' |
O2' |
H9 |
239.1 |
237.5 |
| C1' |
C2' |
O2' |
H9 |
124.4 |
122.8 |
| C1' |
N9 |
C8 |
C4 |
182.4 |
180.3 |
| C8 |
N9 |
C1' |
H11 |
179.1 |
142.7 |
| C8 |
N9 |
C4 |
C5 |
1.3 |
0.3 |
| C1' |
N9 |
C4 |
C8 |
177.6 |
179.7 |
| C4 |
N9 |
C1' |
H11 |
2.0 |
323.1 |
| C4 |
N9 |
C8 |
N7 |
358.4 |
359.5 |
| C4 |
N9 |
C8 |
H12 |
178.4 |
179.7 |
| N9 |
C4 |
C5 |
C6 |
179.7 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.1 |
0.0 |
| N3 |
C2 |
N1 |
C6 |
358.0 |
0.1 |
| N1 |
C2 |
N3 |
H13 |
180.0 |
179.9 |
| N9 |
C8 |
N7 |
H12 |
180.0 |
180.2 |
| C8 |
N7 |
C5 |
C6 |
179.3 |
179.7 |
| C5 |
C4 |
N9 |
C8 |
1.3 |
0.3 |
| N7 |
C5 |
C4 |
C6 |
179.7 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
359.7 |
360.0 |
| C4 |
C5 |
C6 |
N6 |
180.9 |
180.0 |
| N3 |
C2 |
N1 |
H13 |
180.0 |
180.1 |
| C5 |
C6 |
N1 |
C2 |
1.2 |
0.0 |
| C2 |
N1 |
C6 |
N6 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
1.2 |
0.5 |
| C4 |
C5 |
N7 |
C6 |
180.3 |
180.1 |
| N7 |
C5 |
C6 |
N1 |
180.0 |
180.0 |
| N7 |
C5 |
C6 |
N6 |
1.3 |
0.0 |
| C2 |
N1 |
C6 |
C5 |
1.2 |
0.0 |
| N1 |
C6 |
C5 |
N6 |
178.8 |
180.0 |
| C5 |
C6 |
N6 |
H14 |
178.7 |
0.0 |
| C5 |
C6 |
N6 |
H15 |
298.7 |
180.0 |
| C6 |
N1 |
C2 |
H13 |
178.0 |
180.0 |
| C5 |
C6 |
N1 |
N6 |
181.3 |
180.0 |
| N1 |
C6 |
N6 |
H14 |
360.0 |
180.0 |
| N1 |
C6 |
N6 |
H15 |
120.0 |
0.0 |
| C5 |
C6 |
N6 |
N1 |
178.7 |
180.0 |
| H14 |
N6 |
C6 |
H15 |
240.0 |
180.0 |
| H2 |
N3A |
PA |
O5' |
293.4 |
300.0 |
| H3 |
N3A |
PA |
O5' |
53.4 |
64.0 |
| O5' |
C5' |
H4 |
C4' |
244.1 |
240.0 |
| O5' |
C5' |
H4 |
H5 |
122.1 |
120.0 |
| H4 |
C5' |
C4' |
C3' |
166.6 |
65.0 |
| H4 |
C5' |
C4' |
O4' |
47.9 |
309.6 |
| C4' |
C5' |
H4 |
H5 |
238.0 |
240.0 |
| H4 |
C5' |
C4' |
H6 |
285.4 |
187.2 |
| O5' |
C5' |
H5 |
C4' |
115.9 |
120.0 |
| O5' |
C5' |
H5 |
H4 |
238.0 |
240.0 |
| H5 |
C5' |
C4' |
C3' |
45.2 |
305.1 |
| H5 |
C5' |
C4' |
O4' |
286.5 |
189.6 |
| C4' |
C5' |
H5 |
H4 |
122.0 |
120.0 |
| H5 |
C5' |
C4' |
H6 |
164.0 |
67.3 |
| C5' |
C4' |
H6 |
C3' |
241.5 |
237.8 |
| C5' |
C4' |
H6 |
O4' |
118.1 |
122.3 |
| H6 |
C4' |
C5' |
H4 |
285.4 |
187.2 |
| H6 |
C4' |
C5' |
H5 |
164.0 |
67.3 |
| C3' |
C4' |
H6 |
O4' |
236.6 |
244.6 |
| H6 |
C4' |
C3' |
C2' |
138.6 |
95.0 |
| H6 |
C4' |
C3' |
H7 |
250.8 |
213.6 |
| H6 |
C4' |
O4' |
C1' |
241.4 |
281.6 |
| O3' |
C3' |
H7 |
C2' |
129.1 |
122.8 |
| H7 |
C3' |
C4' |
O4' |
125.8 |
94.7 |
| C4' |
C3' |
H7 |
C2' |
252.1 |
245.4 |
| H7 |
C3' |
C4' |
H6 |
250.8 |
213.6 |
| H7 |
C3' |
C2' |
O2' |
102.2 |
122.8 |
| H7 |
C3' |
C2' |
H9 |
340.4 |
0.2 |
| H8 |
O3' |
C3' |
C2' |
63.1 |
65.4 |
| H8 |
O3' |
C3' |
H7 |
299.9 |
302.6 |
| C3' |
C2' |
H9 |
O2' |
121.5 |
122.5 |
| H9 |
C2' |
C3' |
H7 |
340.4 |
0.2 |
| H9 |
C2' |
O2' |
H10 |
300.9 |
61.1 |
| H10 |
O2' |
C2' |
H9 |
300.9 |
61.1 |
| O4' |
C1' |
H11 |
N9 |
113.2 |
122.3 |
| H11 |
C1' |
C2' |
H9 |
156.1 |
146.3 |
| H11 |
C1' |
N9 |
C8 |
179.1 |
142.7 |
| H11 |
C1' |
N9 |
C4 |
2.0 |
323.1 |
| N9 |
C8 |
H12 |
N7 |
180.0 |
179.8 |
| N3 |
C2 |
H13 |
N1 |
180.0 |
179.9 |
| H13 |
C2 |
N1 |
C6 |
178.0 |
180.0 |
| C6 |
N6 |
H14 |
H15 |
120.0 |
180.0 |
| C6 |
N6 |
H15 |
H14 |
240.0 |
180.0 |