PDB Chemical Component SDH
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 SDH
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.479 |
1.720 |
| P |
O5' |
1.622 |
1.720 |
| P |
OP1 |
1.590 |
1.720 |
| O5' |
C5' |
1.394 |
1.429 |
| C5' |
C4' |
1.547 |
1.530 |
| O3' |
C3' |
1.390 |
1.429 |
| C4' |
C3' |
1.554 |
1.544 |
| C4' |
O4' |
1.411 |
1.444 |
| C3' |
C2' |
1.534 |
1.545 |
| O4' |
C1' |
1.404 |
1.445 |
| C2' |
C1' |
1.532 |
1.545 |
| C1' |
N9 |
1.477 |
1.465 |
| O6 |
C6 |
1.204 |
1.217 |
| C6 |
N1 |
1.422 |
1.333 |
| C6 |
C4 |
1.575 |
1.505 |
| N9 |
C4 |
1.474 |
1.462 |
| N9 |
C8 |
1.414 |
1.348 |
| N1 |
C2 |
1.368 |
1.318 |
| O8 |
C8 |
1.217 |
1.216 |
| C2 |
N2 |
1.362 |
1.363 |
| C2 |
N3 |
1.431 |
1.365 |
| C4 |
N3 |
1.478 |
1.464 |
| C4 |
C5 |
1.548 |
1.506 |
| C8 |
N7 |
1.435 |
1.341 |
| C5 |
N7 |
1.389 |
1.352 |
| C5 |
O5 |
1.213 |
1.213 |
| OP1 |
H1 |
0.950 |
0.966 |
| OP2 |
H2 |
0.950 |
0.968 |
| N7 |
H3 |
1.000 |
0.970 |
| N2 |
H4 |
1.000 |
0.970 |
| N2 |
H5 |
1.000 |
0.970 |
| N3 |
H6 |
1.000 |
0.969 |
| C2' |
H7 |
1.100 |
1.090 |
| C2' |
H8 |
1.100 |
1.091 |
| C5' |
H9 |
1.100 |
1.090 |
| C5' |
H10 |
1.100 |
1.090 |
| C4' |
H11 |
1.100 |
1.091 |
| C1' |
H12 |
1.100 |
1.090 |
| C3' |
H13 |
1.100 |
1.090 |
| O3' |
H14 |
0.950 |
0.968 |
| P |
OP3 |
|
1.720 |
| P |
H15 |
|
1.470 |
| OP3 |
H16 |
|
0.967 |
Bond Angles for SDH
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
O5' |
115.2 |
90.0 |
| OP2 |
P |
OP3 |
|
120.0 |
| OP2 |
P |
H15 |
|
120.0 |
| OP1 |
P |
O5' |
105.5 |
179.9 |
| P |
O5' |
C5' |
121.8 |
114.0 |
| O5' |
P |
OP3 |
|
90.0 |
| O5' |
P |
H15 |
|
90.0 |
| P |
OP1 |
H1 |
109.5 |
114.0 |
| OP1 |
P |
OP3 |
|
90.0 |
| OP1 |
P |
H15 |
|
90.0 |
| O5' |
C5' |
C4' |
109.8 |
109.5 |
| O5' |
C5' |
H9 |
109.4 |
109.5 |
| O5' |
C5' |
H10 |
109.4 |
109.5 |
| C5' |
C4' |
C3' |
112.2 |
110.4 |
| C5' |
C4' |
O4' |
110.8 |
110.4 |
| C4' |
C5' |
H9 |
109.4 |
109.4 |
| C4' |
C5' |
H10 |
109.4 |
109.5 |
| C5' |
C4' |
H11 |
108.7 |
110.3 |
| O3' |
C3' |
H13 |
114.5 |
110.5 |
| O4' |
C4' |
C3' |
105.8 |
104.8 |
| C3' |
C4' |
H11 |
108.6 |
110.4 |
| C4' |
C3' |
H13 |
111.7 |
110.5 |
| C4' |
O4' |
C1' |
111.8 |
105.3 |
| O4' |
C4' |
H11 |
110.6 |
110.5 |
| C3' |
C2' |
H7 |
111.5 |
110.5 |
| C3' |
C2' |
H8 |
111.5 |
110.6 |
| C2' |
C1' |
O4' |
107.3 |
104.8 |
| O4' |
C1' |
H12 |
107.1 |
110.4 |
| C1' |
C2' |
H7 |
111.5 |
110.6 |
| C1' |
C2' |
H8 |
111.5 |
110.5 |
| C2' |
C1' |
H12 |
105.6 |
110.3 |
| O6 |
C6 |
N1 |
129.0 |
127.2 |
| C6 |
N1 |
C2 |
106.4 |
112.4 |
| C6 |
C4 |
N3 |
103.6 |
104.3 |
| C8 |
N9 |
C4 |
108.4 |
106.1 |
| N9 |
C4 |
N3 |
117.7 |
112.1 |
| N9 |
C4 |
C5 |
105.0 |
104.7 |
| N9 |
C8 |
N7 |
109.4 |
112.4 |
| N1 |
C2 |
N2 |
122.8 |
123.9 |
| N1 |
C2 |
N3 |
116.1 |
112.3 |
| O8 |
C8 |
N7 |
123.3 |
123.8 |
| N2 |
C2 |
N3 |
121.1 |
123.8 |
| C2 |
N2 |
H4 |
120.0 |
120.0 |
| C2 |
N2 |
H5 |
120.0 |
120.0 |
| C4 |
N3 |
C2 |
105.5 |
105.4 |
| C2 |
N3 |
H6 |
127.3 |
127.3 |
| C4 |
N3 |
H6 |
127.3 |
127.3 |
| C8 |
N7 |
H3 |
124.6 |
124.2 |
| C5 |
N7 |
H3 |
124.6 |
124.3 |
| H4 |
N2 |
H5 |
120.0 |
120.0 |
| H7 |
C2' |
H8 |
109.5 |
110.4 |
| H9 |
C5' |
H10 |
109.5 |
109.5 |
| OP3 |
P |
H15 |
|
120.0 |
| P |
OP3 |
H16 |
|
114.0 |
Torsion Angles for SDH
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
O5' |
120.8 |
180.0 |
| OP2 |
P |
O5' |
C5' |
188.7 |
60.0 |
| O5' |
P |
OP2 |
OP3 |
|
89.9 |
| O5' |
P |
OP2 |
H15 |
|
270.0 |
| OP2 |
P |
OP1 |
H1 |
180.0 |
299.9 |
| OP1 |
P |
OP2 |
OP3 |
|
270.0 |
| OP1 |
P |
OP2 |
H15 |
|
90.0 |
| OP3 |
P |
OP2 |
H15 |
|
180.1 |
| OP2 |
P |
OP3 |
H16 |
|
180.0 |
| OP2 |
P |
O5' |
OP3 |
|
240.0 |
| OP2 |
P |
O5' |
H15 |
|
120.0 |
| O5' |
P |
OP1 |
H1 |
306.2 |
274.9 |
| OP1 |
P |
O5' |
OP3 |
|
265.1 |
| OP1 |
P |
O5' |
H15 |
|
145.0 |
| P |
O5' |
C5' |
C4' |
182.7 |
180.0 |
| P |
O5' |
C5' |
H9 |
302.7 |
300.0 |
| P |
O5' |
C5' |
H10 |
62.6 |
60.0 |
| OP3 |
P |
O5' |
H15 |
|
240.0 |
| O5' |
P |
OP3 |
H16 |
|
90.0 |
| OP2 |
P |
OP1 |
O5' |
233.8 |
25.0 |
| OP2 |
P |
OP1 |
OP3 |
|
120.0 |
| OP2 |
P |
OP1 |
H15 |
|
240.0 |
| OP1 |
P |
O5' |
C5' |
64.3 |
85.1 |
| O5' |
P |
OP1 |
OP3 |
|
94.9 |
| O5' |
P |
OP1 |
H15 |
|
215.0 |
| OP3 |
P |
OP1 |
H15 |
|
120.0 |
| OP1 |
P |
OP3 |
H16 |
|
270.0 |
| C5' |
O5' |
P |
OP3 |
|
180.0 |
| C5' |
O5' |
P |
H15 |
|
300.0 |
| O5' |
C5' |
C4' |
C3' |
251.7 |
185.0 |
| O5' |
C5' |
C4' |
O4' |
133.7 |
69.6 |
| C4' |
C5' |
O5' |
H9 |
240.0 |
240.0 |
| C4' |
C5' |
O5' |
H10 |
120.1 |
120.0 |
| O5' |
C5' |
C4' |
H11 |
11.9 |
307.2 |
| H9 |
C5' |
O5' |
H10 |
240.1 |
240.0 |
| O5' |
C5' |
C4' |
H9 |
120.1 |
120.0 |
| O5' |
C5' |
C4' |
H10 |
239.9 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
242.0 |
244.6 |
| C3' |
C4' |
C5' |
H11 |
239.8 |
237.7 |
| C5' |
C4' |
C3' |
H13 |
25.7 |
335.8 |
| C5' |
C4' |
O4' |
C1' |
113.3 |
159.4 |
| O4' |
C4' |
C5' |
H11 |
121.8 |
122.3 |
| H9 |
C5' |
C4' |
H10 |
119.9 |
120.0 |
| O3' |
C3' |
C4' |
H11 |
31.6 |
336.3 |
| C4' |
C3' |
O3' |
H13 |
235.5 |
237.3 |
| O3' |
C3' |
C2' |
H7 |
198.9 |
359.9 |
| O3' |
C3' |
C2' |
H8 |
321.6 |
237.4 |
| C5' |
C4' |
C3' |
O4' |
239.0 |
241.2 |
| C3' |
C4' |
C5' |
H9 |
131.6 |
65.0 |
| C3' |
C4' |
C5' |
H10 |
11.7 |
305.0 |
| C5' |
C4' |
C3' |
H11 |
120.3 |
122.2 |
| O3' |
C3' |
C4' |
H13 |
126.2 |
122.7 |
| C3' |
C4' |
O4' |
C1' |
351.4 |
40.5 |
| O4' |
C4' |
C3' |
H11 |
241.2 |
241.0 |
| C4' |
C3' |
C2' |
H7 |
85.9 |
241.3 |
| C4' |
C3' |
C2' |
H8 |
208.5 |
118.7 |
| C5' |
C4' |
O4' |
C3' |
121.9 |
118.9 |
| O4' |
C4' |
C5' |
H9 |
13.6 |
309.6 |
| O4' |
C4' |
C5' |
H10 |
253.7 |
189.6 |
| C5' |
C4' |
O4' |
H11 |
239.3 |
237.8 |
| C3' |
C4' |
O4' |
H11 |
117.5 |
118.9 |
| O4' |
C4' |
C3' |
H13 |
146.7 |
94.7 |
| C2' |
C1' |
O4' |
C4' |
346.7 |
319.5 |
| C4' |
O4' |
C1' |
H12 |
99.7 |
78.3 |
| C1' |
C2' |
C3' |
H7 |
241.3 |
118.7 |
| C1' |
C2' |
C3' |
H8 |
118.7 |
241.3 |
| C3' |
C2' |
C1' |
H12 |
275.3 |
265.1 |
| H7 |
C2' |
C3' |
H8 |
237.3 |
122.6 |
| C1' |
O4' |
C4' |
C3' |
351.4 |
40.5 |
| C1' |
O4' |
C4' |
H11 |
234.0 |
281.6 |
| O4' |
C1' |
C2' |
H7 |
270.6 |
142.6 |
| O4' |
C1' |
C2' |
H8 |
148.0 |
265.2 |
| C2' |
C1' |
O4' |
H12 |
247.0 |
241.2 |
| C4' |
O4' |
C1' |
C2' |
346.7 |
319.5 |
| C3' |
C2' |
C1' |
H7 |
118.7 |
241.3 |
| C3' |
C2' |
C1' |
H8 |
241.3 |
118.8 |
| O4' |
C1' |
C2' |
H12 |
114.0 |
118.8 |
| H7 |
C2' |
C1' |
H8 |
122.7 |
237.4 |
| O6 |
C6 |
N1 |
C2 |
179.9 |
180.0 |
| O6 |
C6 |
C4 |
N3 |
180.4 |
180.0 |
| N1 |
C6 |
C4 |
N3 |
0.4 |
359.9 |
| C6 |
N1 |
C2 |
N2 |
180.0 |
180.1 |
| C6 |
N1 |
C2 |
N3 |
359.6 |
0.0 |
| N9 |
C4 |
C6 |
N3 |
133.1 |
121.6 |
| C6 |
C4 |
N3 |
C2 |
359.5 |
0.1 |
| C6 |
C4 |
N3 |
H6 |
179.5 |
180.0 |
| C6 |
C4 |
N9 |
N3 |
233.3 |
243.0 |
| C4 |
N9 |
C8 |
N7 |
0.7 |
0.0 |
| N9 |
C4 |
N3 |
C2 |
225.5 |
238.6 |
| N9 |
C4 |
N3 |
H6 |
45.5 |
58.5 |
| C8 |
N9 |
C4 |
N3 |
239.8 |
238.4 |
| C8 |
N9 |
C4 |
C5 |
359.6 |
360.0 |
| O8 |
C8 |
N9 |
N7 |
179.3 |
180.0 |
| N9 |
C8 |
N7 |
H3 |
179.2 |
179.9 |
| N2 |
C2 |
N1 |
N3 |
180.4 |
180.0 |
| N1 |
C2 |
N2 |
H4 |
0.0 |
359.9 |
| N1 |
C2 |
N2 |
H5 |
180.0 |
180.0 |
| C4 |
N3 |
C2 |
N1 |
0.6 |
360.0 |
| N1 |
C2 |
N3 |
H6 |
180.6 |
180.0 |
| O8 |
C8 |
N9 |
C4 |
180.0 |
180.0 |
| N9 |
C8 |
O8 |
N7 |
180.8 |
180.0 |
| O8 |
C8 |
N7 |
H3 |
359.8 |
359.9 |
| N1 |
C2 |
N2 |
N3 |
179.6 |
179.9 |
| C4 |
N3 |
C2 |
N2 |
180.2 |
179.9 |
| N2 |
C2 |
N3 |
H6 |
0.2 |
360.0 |
| H4 |
N2 |
C2 |
H5 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
N2 |
180.4 |
180.0 |
| N3 |
C2 |
N2 |
H4 |
180.4 |
180.0 |
| N3 |
C2 |
N2 |
H5 |
0.4 |
0.0 |
| C4 |
N3 |
C2 |
H6 |
180.0 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
118.3 |
117.4 |
| N1 |
C2 |
N3 |
C4 |
0.6 |
360.0 |
| N2 |
C2 |
N3 |
C4 |
180.2 |
179.9 |
| C2 |
N3 |
C4 |
H6 |
180.0 |
180.0 |
| N9 |
C4 |
C5 |
N3 |
233.8 |
238.2 |
| C4 |
C5 |
N7 |
H3 |
180.5 |
180.1 |
| N7 |
C8 |
N9 |
C4 |
0.7 |
0.0 |
| C5 |
N7 |
C8 |
H3 |
180.0 |
180.1 |
| N9 |
C4 |
C5 |
N7 |
359.9 |
0.0 |
| C8 |
N7 |
C5 |
H3 |
180.0 |
179.9 |
| N9 |
C4 |
C5 |
O5 |
180.8 |
180.0 |
| O5 |
C5 |
N7 |
H3 |
359.7 |
0.1 |
| H1 |
OP1 |
P |
O5' |
306.2 |
274.9 |
| H1 |
OP1 |
P |
OP3 |
|
180.0 |
| H1 |
OP1 |
P |
H15 |
|
59.9 |
| H2 |
OP2 |
P |
O5' |
180.0 |
269.9 |
| H2 |
OP2 |
P |
OP3 |
|
180.0 |
| H2 |
OP2 |
P |
H15 |
|
359.9 |
| H4 |
N2 |
C2 |
N3 |
180.4 |
180.0 |
| C2 |
N2 |
H4 |
H5 |
180.0 |
180.0 |
| H5 |
N2 |
C2 |
N3 |
0.4 |
0.0 |
| C2 |
N2 |
H5 |
H4 |
180.0 |
180.0 |
| C4 |
N3 |
H6 |
C2 |
180.0 |
180.1 |
| C3' |
C2' |
H7 |
H8 |
123.8 |
237.3 |
| H7 |
C2' |
C1' |
O4' |
270.6 |
142.6 |
| C1' |
C2' |
H7 |
H8 |
236.2 |
122.6 |
| H7 |
C2' |
C1' |
H12 |
156.6 |
23.8 |
| C3' |
C2' |
H8 |
H7 |
236.2 |
122.6 |
| H8 |
C2' |
C1' |
O4' |
148.0 |
265.2 |
| C1' |
C2' |
H8 |
H7 |
123.8 |
237.4 |
| H8 |
C2' |
C1' |
H12 |
33.9 |
146.3 |
| O5' |
C5' |
H9 |
C4' |
239.7 |
240.0 |
| O5' |
C5' |
H9 |
H10 |
119.9 |
120.0 |
| H9 |
C5' |
C4' |
C3' |
131.6 |
65.0 |
| H9 |
C5' |
C4' |
O4' |
13.6 |
309.6 |
| C4' |
C5' |
H9 |
H10 |
240.2 |
240.0 |
| H9 |
C5' |
C4' |
H11 |
251.8 |
187.3 |
| O5' |
C5' |
H10 |
C4' |
120.3 |
120.0 |
| O5' |
C5' |
H10 |
H9 |
240.1 |
240.0 |
| H10 |
C5' |
C4' |
C3' |
11.7 |
305.0 |
| H10 |
C5' |
C4' |
O4' |
253.7 |
189.6 |
| C4' |
C5' |
H10 |
H9 |
119.8 |
120.0 |
| H10 |
C5' |
C4' |
H11 |
131.9 |
67.3 |
| C5' |
C4' |
H11 |
C3' |
237.6 |
237.7 |
| C5' |
C4' |
H11 |
O4' |
121.9 |
122.3 |
| H11 |
C4' |
C5' |
H9 |
251.8 |
187.3 |
| H11 |
C4' |
C5' |
H10 |
131.9 |
67.3 |
| O4' |
C4' |
H11 |
C3' |
115.7 |
115.5 |
| H11 |
C4' |
C3' |
H13 |
265.4 |
213.6 |
| H11 |
C4' |
O4' |
C1' |
234.0 |
281.6 |
| C2' |
C1' |
H12 |
O4' |
114.1 |
115.4 |
| H12 |
C1' |
C2' |
H7 |
156.6 |
23.8 |
| H12 |
C1' |
C2' |
H8 |
33.9 |
146.3 |
| H13 |
C3' |
C4' |
H11 |
265.4 |
213.6 |
| H13 |
C3' |
C2' |
H7 |
325.9 |
122.6 |
| H13 |
C3' |
C2' |
H8 |
88.6 |
0.1 |
| H14 |
O3' |
C3' |
H13 |
304.6 |
302.6 |
| OP2 |
P |
OP3 |
O5' |
|
89.9 |
| OP2 |
P |
OP3 |
H15 |
|
179.9 |
| OP1 |
P |
OP3 |
O5' |
|
179.9 |
| OP3 |
P |
O5' |
C5' |
|
180.0 |
| O5' |
P |
OP3 |
H15 |
|
90.0 |
| OP3 |
P |
OP1 |
H1 |
|
180.0 |
| OP1 |
P |
OP3 |
H15 |
|
269.9 |
| OP2 |
P |
H15 |
O5' |
|
270.0 |
| OP2 |
P |
H15 |
OP3 |
|
180.1 |
| OP1 |
P |
H15 |
O5' |
|
180.0 |
| H15 |
P |
O5' |
C5' |
|
300.0 |
| O5' |
P |
H15 |
OP3 |
|
270.0 |
| H15 |
P |
OP1 |
H1 |
|
59.9 |
| OP1 |
P |
H15 |
OP3 |
|
90.1 |
| H15 |
P |
OP3 |
H16 |
|
0.0 |
| H16 |
OP3 |
P |
H15 |
|
0.0 |