PDB Chemical Component SDG
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 SDG
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O3P |
1.608 |
1.610 |
| O3P |
HO3P |
0.950 |
0.967 |
| N3 |
C2 |
1.336 |
1.323 |
| N2 |
C2 |
1.347 |
1.386 |
| C2 |
N1 |
1.380 |
1.328 |
| O1P |
P |
1.494 |
1.480 |
| P |
O5' |
1.584 |
1.610 |
| P |
O2P |
1.504 |
1.611 |
| O2P |
HO2P |
0.950 |
0.967 |
| O5' |
C5' |
1.421 |
1.428 |
| C1' |
N9 |
1.472 |
1.465 |
| N9 |
C4 |
1.388 |
1.372 |
| N9 |
C8 |
1.383 |
1.364 |
| N3 |
C4 |
1.353 |
1.327 |
| C4 |
C5 |
1.384 |
1.408 |
| N2 |
HN2 |
1.000 |
0.970 |
| N2 |
HN2A |
1.000 |
0.970 |
| N1 |
C6 |
1.390 |
1.321 |
| C5 |
C6 |
1.475 |
1.396 |
| C6 |
SE |
1.811 |
1.959 |
| C5 |
N7 |
1.391 |
1.357 |
| C8 |
N7 |
1.316 |
1.300 |
| C8 |
H8 |
1.080 |
1.080 |
| C3' |
C2' |
1.527 |
1.545 |
| C2' |
C1' |
1.522 |
1.545 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| C5' |
C4' |
1.508 |
1.530 |
| C5' |
H5' |
1.100 |
1.091 |
| C5' |
H5'A |
1.100 |
1.090 |
| C4' |
C3' |
1.529 |
1.545 |
| C4' |
O4' |
1.457 |
1.444 |
| C4' |
H4' |
1.100 |
1.090 |
| O4' |
C1' |
1.421 |
1.444 |
| C1' |
H1' |
1.100 |
1.090 |
| O3' |
C3' |
1.431 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.966 |
| SE |
HSE |
1.500 |
1.560 |
Bond Angles for SDG
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
O3P |
HO3P |
109.5 |
114.0 |
| N3 |
C2 |
N1 |
124.5 |
122.2 |
| N2 |
C2 |
N1 |
115.5 |
118.9 |
| C2 |
N1 |
C6 |
124.7 |
121.2 |
| O1P |
P |
O5' |
108.6 |
109.5 |
| O1P |
P |
O2P |
120.1 |
109.5 |
| O2P |
P |
O5' |
108.9 |
109.5 |
| P |
O5' |
C5' |
122.3 |
123.0 |
| P |
O2P |
HO2P |
109.5 |
114.0 |
| O5' |
C5' |
C4' |
108.5 |
109.5 |
| O5' |
C5' |
H5' |
109.8 |
109.5 |
| O5' |
C5' |
H5'A |
110.0 |
109.5 |
| C4 |
N9 |
C8 |
105.9 |
107.4 |
| N9 |
C4 |
C5 |
105.5 |
106.0 |
| N9 |
C8 |
N7 |
113.1 |
110.1 |
| N9 |
C8 |
H8 |
123.5 |
125.0 |
| N3 |
C4 |
C5 |
128.4 |
119.1 |
| C4 |
C5 |
C6 |
118.1 |
118.4 |
| C4 |
C5 |
N7 |
110.8 |
107.0 |
| HN2 |
N2 |
HN2A |
109.4 |
120.0 |
| N1 |
C6 |
SE |
120.8 |
120.6 |
| C6 |
SE |
HSE |
109.5 |
101.0 |
| C3' |
C2' |
H2' |
111.1 |
110.5 |
| C3' |
C2' |
H2'A |
112.1 |
110.6 |
| C1' |
C2' |
H2' |
111.0 |
110.5 |
| C1' |
C2' |
H2'A |
112.1 |
110.5 |
| C2' |
C1' |
O4' |
103.9 |
104.8 |
| C2' |
C1' |
H1' |
111.1 |
110.3 |
| H2' |
C2' |
H2'A |
105.9 |
110.4 |
| C4' |
C5' |
H5' |
109.8 |
109.5 |
| C4' |
C5' |
H5'A |
110.0 |
109.4 |
| C5' |
C4' |
C3' |
115.7 |
110.4 |
| C5' |
C4' |
O4' |
110.6 |
110.4 |
| C5' |
C4' |
H4' |
103.3 |
110.3 |
| H5' |
C5' |
H5'A |
108.8 |
109.4 |
| O4' |
C4' |
C3' |
106.4 |
104.8 |
| C3' |
C4' |
H4' |
107.8 |
110.4 |
| C4' |
C3' |
H3' |
114.0 |
110.5 |
| O4' |
C4' |
H4' |
113.1 |
110.4 |
| C4' |
O4' |
C1' |
107.4 |
105.3 |
| O4' |
C1' |
H1' |
117.7 |
110.4 |
| O3' |
C3' |
H3' |
107.4 |
110.6 |
Torsion Angles for SDG
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N2 |
C2 |
N3 |
N1 |
179.8 |
180.2 |
| N3 |
C2 |
N1 |
C6 |
359.7 |
359.9 |
| N3 |
C2 |
N2 |
N1 |
180.2 |
179.8 |
| N2 |
C2 |
N1 |
C6 |
179.9 |
179.7 |
| C2 |
N1 |
C6 |
SE |
177.5 |
180.0 |
| O1P |
P |
O3P |
HO3P |
357.1 |
300.1 |
| O2P |
P |
O1P |
O5' |
233.8 |
120.0 |
| O1P |
P |
O5' |
C5' |
218.4 |
55.0 |
| O1P |
P |
O2P |
HO2P |
0.8 |
180.0 |
| O5' |
P |
O3P |
HO3P |
110.6 |
180.1 |
| O1P |
P |
O5' |
O2P |
227.6 |
120.0 |
| O5' |
P |
O2P |
HO2P |
234.8 |
300.0 |
| P |
O5' |
C5' |
C4' |
187.2 |
180.0 |
| P |
O5' |
C5' |
H5' |
307.2 |
300.1 |
| P |
O5' |
C5' |
H5'A |
66.8 |
60.0 |
| O2P |
P |
O3P |
HO3P |
226.4 |
60.1 |
| O1P |
P |
O2P |
O5' |
126.0 |
240.0 |
| O2P |
P |
O5' |
C5' |
350.8 |
295.0 |
| HO2P |
O2P |
P |
O5' |
234.8 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
240.0 |
239.9 |
| C4' |
C5' |
O5' |
H5'A |
120.4 |
120.0 |
| O5' |
C5' |
C4' |
C3' |
206.5 |
185.0 |
| O5' |
C5' |
C4' |
O4' |
85.4 |
69.6 |
| O5' |
C5' |
C4' |
H4' |
324.1 |
307.3 |
| H5' |
C5' |
O5' |
H5'A |
240.4 |
240.1 |
| C1' |
N9 |
C8 |
H8 |
350.7 |
0.1 |
| C4 |
N9 |
C8 |
N7 |
355.6 |
360.0 |
| C4 |
N9 |
C8 |
H8 |
175.6 |
180.0 |
| N3 |
C4 |
N9 |
C5 |
176.9 |
180.0 |
| N9 |
C4 |
C5 |
C6 |
174.4 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
355.9 |
360.0 |
| C8 |
N9 |
C4 |
C5 |
5.0 |
0.0 |
| C4 |
N3 |
C2 |
N1 |
0.4 |
0.0 |
| N3 |
C4 |
N9 |
C8 |
181.9 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
183.8 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
357.6 |
0.0 |
| N3 |
C4 |
C5 |
N7 |
179.1 |
180.0 |
| C5 |
C4 |
N9 |
C8 |
5.0 |
0.0 |
| HN2 |
N2 |
C2 |
N1 |
4.8 |
360.0 |
| HN2A |
N2 |
C2 |
N1 |
124.8 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
2.1 |
360.0 |
| N1 |
C6 |
SE |
HSE |
181.3 |
90.0 |
| C4 |
C5 |
C6 |
N7 |
181.8 |
180.0 |
| C5 |
C6 |
SE |
HSE |
359.6 |
270.0 |
| C4 |
C5 |
C6 |
SE |
183.8 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
1.9 |
0.0 |
| C4 |
C5 |
N7 |
C6 |
178.3 |
180.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.1 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
179.9 |
| C1' |
C2' |
C3' |
H2' |
240.0 |
118.7 |
| C1' |
C2' |
C3' |
H2'A |
121.8 |
241.3 |
| C3' |
C2' |
C1' |
H1' |
265.0 |
265.1 |
| H2' |
C2' |
C3' |
H2'A |
241.8 |
122.6 |
| C3' |
C2' |
C1' |
H2' |
120.0 |
241.4 |
| C3' |
C2' |
C1' |
H2'A |
238.2 |
118.8 |
| H2' |
C2' |
C1' |
H2'A |
118.2 |
237.4 |
| C4' |
O4' |
C1' |
C2' |
322.3 |
319.5 |
| O4' |
C1' |
C2' |
H1' |
127.4 |
118.8 |
| C3' |
C2' |
H2' |
H2'A |
121.9 |
237.3 |
| C1' |
C2' |
H2' |
H2'A |
238.1 |
122.6 |
| H2' |
C2' |
C1' |
O4' |
272.4 |
142.6 |
| H2' |
C2' |
C1' |
H1' |
145.0 |
23.8 |
| C3' |
C2' |
H2'A |
H2' |
238.7 |
122.6 |
| C1' |
C2' |
H2'A |
H2' |
121.2 |
237.4 |
| H2'A |
C2' |
C1' |
O4' |
154.2 |
265.2 |
| H2'A |
C2' |
C1' |
H1' |
26.8 |
146.4 |
| O5' |
C5' |
C4' |
H5' |
120.0 |
120.0 |
| O5' |
C5' |
C4' |
H5'A |
239.6 |
240.0 |
| H5' |
C5' |
C4' |
H5'A |
119.6 |
119.9 |
| O4' |
C4' |
C5' |
C3' |
238.9 |
244.6 |
| C3' |
C4' |
C5' |
H4' |
242.5 |
237.7 |
| C5' |
C4' |
C3' |
H3' |
352.1 |
335.9 |
| O4' |
C4' |
C5' |
H4' |
121.3 |
122.3 |
| C5' |
C4' |
O4' |
C1' |
154.5 |
159.4 |
| O5' |
C5' |
H5' |
C4' |
240.8 |
239.9 |
| O5' |
C5' |
H5' |
H5'A |
120.4 |
119.9 |
| C4' |
C5' |
H5' |
H5'A |
239.6 |
240.0 |
| H5' |
C5' |
C4' |
C3' |
86.6 |
65.0 |
| H5' |
C5' |
C4' |
O4' |
325.4 |
309.6 |
| H5' |
C5' |
C4' |
H4' |
204.1 |
187.3 |
| O5' |
C5' |
H5'A |
C4' |
119.5 |
120.1 |
| O5' |
C5' |
H5'A |
H5' |
239.7 |
240.1 |
| C4' |
C5' |
H5'A |
H5' |
120.3 |
120.0 |
| H5'A |
C5' |
C4' |
C3' |
326.9 |
305.0 |
| H5'A |
C5' |
C4' |
O4' |
205.8 |
189.6 |
| H5'A |
C5' |
C4' |
H4' |
84.5 |
67.3 |
| C4' |
C3' |
C2' |
H2' |
104.7 |
241.4 |
| C4' |
C3' |
C2' |
H2'A |
222.9 |
118.7 |
| C3' |
C4' |
C5' |
H5' |
86.6 |
65.0 |
| C3' |
C4' |
C5' |
H5'A |
326.9 |
305.0 |
| C5' |
C4' |
C3' |
O4' |
236.7 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
115.0 |
122.2 |
| O4' |
C4' |
C3' |
H4' |
238.4 |
241.1 |
| C3' |
C4' |
O4' |
C1' |
28.1 |
40.5 |
| O3' |
C3' |
C4' |
H3' |
119.8 |
122.7 |
| C2' |
C1' |
O4' |
C4' |
322.3 |
319.5 |
| O4' |
C4' |
C5' |
H5' |
325.4 |
309.6 |
| O4' |
C4' |
C5' |
H5'A |
205.8 |
189.6 |
| C5' |
C4' |
O4' |
C3' |
126.5 |
118.9 |
| C5' |
C4' |
O4' |
H4' |
244.6 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
118.2 |
118.9 |
| O4' |
C4' |
C3' |
H3' |
115.5 |
94.7 |
| C4' |
O4' |
C1' |
H1' |
85.6 |
78.3 |
| H4' |
C4' |
C5' |
H5' |
204.1 |
187.3 |
| H4' |
C4' |
C5' |
H5'A |
84.5 |
67.3 |
| C5' |
C4' |
H4' |
C3' |
237.0 |
237.7 |
| C5' |
C4' |
H4' |
O4' |
119.7 |
122.3 |
| O4' |
C4' |
H4' |
C3' |
117.4 |
115.4 |
| H4' |
C4' |
C3' |
H3' |
237.1 |
213.6 |
| H4' |
C4' |
O4' |
C1' |
269.9 |
281.6 |
| O4' |
C1' |
C2' |
H2' |
272.4 |
142.6 |
| O4' |
C1' |
C2' |
H2'A |
154.2 |
265.2 |
| C2' |
C1' |
O4' |
H1' |
236.8 |
241.2 |
| C1' |
O4' |
C4' |
C3' |
28.1 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
269.9 |
281.6 |
| H1' |
C1' |
C2' |
H2' |
145.0 |
23.8 |
| H1' |
C1' |
C2' |
H2'A |
26.8 |
146.4 |
| C2' |
C1' |
H1' |
O4' |
119.5 |
115.3 |
| O3' |
C3' |
C2' |
H2' |
221.3 |
360.0 |
| O3' |
C3' |
C2' |
H2'A |
339.5 |
237.4 |
| O3' |
C3' |
C4' |
H4' |
356.8 |
336.3 |
| C4' |
C3' |
O3' |
H3' |
236.2 |
237.3 |
| H3' |
C3' |
C2' |
H2' |
341.2 |
122.7 |
| H3' |
C3' |
C2' |
H2'A |
99.5 |
0.1 |
| H3' |
C3' |
C4' |
H4' |
237.1 |
213.6 |
| HO3' |
O3' |
C3' |
H3' |
232.4 |
302.6 |