PDB Chemical Component SC
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 SC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.396 |
1.344 |
| N1 |
C6 |
1.374 |
1.363 |
| N1 |
C1' |
1.490 |
1.465 |
| C2 |
N3 |
1.363 |
1.331 |
| C2 |
O2 |
1.229 |
1.221 |
| N3 |
C4 |
1.342 |
1.326 |
| C4 |
C5 |
1.435 |
1.410 |
| C4 |
N4 |
1.336 |
1.376 |
| C5 |
C6 |
1.354 |
1.353 |
| C5 |
H5 |
1.080 |
1.079 |
| C6 |
H6 |
1.078 |
1.080 |
| N4 |
HN41 |
1.009 |
0.970 |
| N4 |
HN42 |
1.010 |
0.969 |
| C1' |
C2' |
1.527 |
1.540 |
| C1' |
O4' |
1.421 |
1.438 |
| C1' |
H1' |
1.091 |
1.091 |
| C2' |
C3' |
1.521 |
1.548 |
| C2' |
H2' |
1.084 |
1.089 |
| C2' |
H2'' |
1.090 |
1.090 |
| C3' |
C4' |
1.530 |
1.550 |
| C3' |
O3' |
1.418 |
1.428 |
| C3' |
H3' |
1.090 |
1.089 |
| C4' |
O4' |
1.418 |
1.445 |
| C4' |
C5' |
1.534 |
1.530 |
| C4' |
H4' |
1.092 |
1.089 |
| O3' |
HO3' |
0.950 |
0.966 |
| C5' |
O5' |
1.417 |
1.428 |
| C5' |
H5' |
1.091 |
1.090 |
| C5' |
H5'' |
1.090 |
1.090 |
| O5' |
P |
1.618 |
1.609 |
| P |
OP1 |
1.481 |
1.610 |
| P |
S2P |
2.131 |
1.863 |
| P |
OP3 |
1.622 |
1.609 |
| OP1 |
HOP1 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.966 |
Bond Angles for SC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
120.1 |
120.3 |
| C2 |
N1 |
C1' |
118.3 |
119.9 |
| N1 |
C2 |
N3 |
118.6 |
121.1 |
| N1 |
C2 |
O2 |
121.1 |
119.4 |
| C6 |
N1 |
C1' |
121.4 |
119.8 |
| N1 |
C6 |
C5 |
121.6 |
119.3 |
| N1 |
C6 |
H6 |
119.9 |
120.4 |
| N1 |
C1' |
C2' |
110.0 |
109.9 |
| N1 |
C1' |
O4' |
111.6 |
109.9 |
| N1 |
C1' |
H1' |
111.1 |
109.9 |
| N3 |
C2 |
O2 |
120.3 |
119.5 |
| C2 |
N3 |
C4 |
121.0 |
120.7 |
| N3 |
C4 |
C5 |
121.3 |
119.6 |
| N3 |
C4 |
N4 |
118.9 |
120.2 |
| C5 |
C4 |
N4 |
119.7 |
120.1 |
| C4 |
C5 |
C6 |
116.8 |
118.9 |
| C4 |
C5 |
H5 |
123.6 |
120.5 |
| C4 |
N4 |
HN41 |
120.2 |
120.0 |
| C4 |
N4 |
HN42 |
119.9 |
120.1 |
| C6 |
C5 |
H5 |
119.6 |
120.5 |
| C5 |
C6 |
H6 |
118.5 |
120.3 |
| HN41 |
N4 |
HN42 |
119.9 |
120.0 |
| C2' |
C1' |
O4' |
106.7 |
107.4 |
| C2' |
C1' |
H1' |
109.4 |
109.9 |
| C1' |
C2' |
C3' |
103.7 |
104.2 |
| C1' |
C2' |
H2' |
112.0 |
110.6 |
| C1' |
C2' |
H2'' |
109.0 |
110.5 |
| O4' |
C1' |
H1' |
107.9 |
109.8 |
| C1' |
O4' |
C4' |
108.8 |
106.9 |
| C3' |
C2' |
H2' |
111.6 |
110.5 |
| C3' |
C2' |
H2'' |
110.0 |
110.5 |
| C2' |
C3' |
C4' |
99.6 |
102.1 |
| C2' |
C3' |
O3' |
111.1 |
110.9 |
| C2' |
C3' |
H3' |
110.1 |
110.9 |
| H2' |
C2' |
H2'' |
110.4 |
110.5 |
| C4' |
C3' |
O3' |
113.2 |
111.0 |
| C4' |
C3' |
H3' |
110.0 |
110.9 |
| C3' |
C4' |
O4' |
104.9 |
103.6 |
| C3' |
C4' |
C5' |
114.3 |
110.7 |
| C3' |
C4' |
H4' |
108.9 |
110.6 |
| O3' |
C3' |
H3' |
112.2 |
110.8 |
| C3' |
O3' |
HO3' |
111.1 |
106.9 |
| O4' |
C4' |
C5' |
110.9 |
110.7 |
| O4' |
C4' |
H4' |
108.3 |
110.5 |
| C5' |
C4' |
H4' |
109.4 |
110.6 |
| C4' |
C5' |
O5' |
110.1 |
109.6 |
| C4' |
C5' |
H5' |
109.2 |
109.4 |
| C4' |
C5' |
H5'' |
108.8 |
109.4 |
| O5' |
C5' |
H5' |
110.0 |
109.5 |
| O5' |
C5' |
H5'' |
109.8 |
109.5 |
| C5' |
O5' |
P |
122.6 |
106.8 |
| H5' |
C5' |
H5'' |
109.0 |
109.5 |
| O5' |
P |
OP1 |
108.1 |
109.5 |
| O5' |
P |
S2P |
106.4 |
109.5 |
| O5' |
P |
OP3 |
105.8 |
109.5 |
| OP1 |
P |
S2P |
120.2 |
109.4 |
| OP1 |
P |
OP3 |
107.7 |
109.5 |
| P |
OP1 |
HOP1 |
108.1 |
106.8 |
| S2P |
P |
OP3 |
107.7 |
109.5 |
| P |
OP3 |
HOP3 |
105.8 |
106.8 |
Torsion Angles for SC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
176.6 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
7.1 |
359.7 |
| C2 |
N1 |
C6 |
H6 |
188.4 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
89.2 |
300.3 |
| C2 |
N1 |
C1' |
O4' |
207.4 |
58.3 |
| C2 |
N1 |
C1' |
H1' |
327.9 |
179.3 |
| N3 |
C2 |
N1 |
O2 |
180.9 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
2.9 |
0.0 |
| C2 |
N1 |
C6 |
C1' |
183.5 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
352.0 |
0.0 |
| C6 |
N1 |
C2 |
O2 |
171.1 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
272.6 |
120.3 |
| C6 |
N1 |
C1' |
O4' |
30.9 |
238.3 |
| C6 |
N1 |
C1' |
H1' |
151.4 |
359.2 |
| C4 |
C5 |
C6 |
N1 |
358.9 |
0.5 |
| N1 |
C6 |
C5 |
H5 |
179.5 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
178.7 |
179.7 |
| C2 |
N1 |
C1' |
C6 |
176.5 |
180.0 |
| C1' |
N1 |
C2 |
N3 |
175.4 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
354.5 |
360.0 |
| C1' |
N1 |
C6 |
C5 |
183.5 |
179.7 |
| C1' |
N1 |
C6 |
H6 |
4.8 |
0.1 |
| C2' |
C1' |
N1 |
O4' |
241.8 |
242.0 |
| C2' |
C1' |
N1 |
H1' |
121.2 |
121.0 |
| N1 |
C1' |
C2' |
C3' |
104.1 |
121.4 |
| N1 |
C1' |
C2' |
H2' |
343.6 |
240.1 |
| N1 |
C1' |
C2' |
H2'' |
221.2 |
2.8 |
| O4' |
C1' |
N1 |
H1' |
239.5 |
239.0 |
| N1 |
C1' |
O4' |
C4' |
230.9 |
214.2 |
| N3 |
C2 |
N1 |
C6 |
352.0 |
0.0 |
| N3 |
C2 |
N1 |
C1' |
175.4 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
179.1 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
3.1 |
0.2 |
| C2 |
N3 |
C4 |
N4 |
179.6 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
171.1 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
354.5 |
360.0 |
| N1 |
C2 |
O2 |
N3 |
180.9 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
183.9 |
180.0 |
| C4 |
N3 |
C2 |
O2 |
183.9 |
180.0 |
| C5 |
C4 |
N3 |
N4 |
183.4 |
180.2 |
| N3 |
C4 |
C5 |
C6 |
356.0 |
359.5 |
| N3 |
C4 |
C5 |
H5 |
175.4 |
180.0 |
| N3 |
C4 |
N4 |
HN41 |
180.3 |
360.0 |
| N3 |
C4 |
N4 |
HN42 |
2.3 |
179.7 |
| N1 |
C6 |
C5 |
C4 |
358.9 |
0.5 |
| N3 |
C4 |
C5 |
N4 |
176.5 |
179.8 |
| C5 |
C4 |
N4 |
HN41 |
356.9 |
179.7 |
| C5 |
C4 |
N4 |
HN42 |
178.9 |
359.5 |
| C6 |
C5 |
C4 |
H5 |
180.6 |
179.5 |
| C4 |
C5 |
C6 |
H6 |
177.6 |
180.2 |
| N3 |
C4 |
N4 |
C5 |
183.4 |
180.2 |
| N4 |
C4 |
C5 |
C6 |
179.4 |
179.7 |
| N4 |
C4 |
C5 |
H5 |
358.8 |
0.3 |
| HN41 |
N4 |
C4 |
HN42 |
178.0 |
180.3 |
| C5 |
C6 |
N1 |
C1' |
183.5 |
179.7 |
| N1 |
C6 |
C5 |
H6 |
181.3 |
180.3 |
| C6 |
C5 |
C4 |
N4 |
179.4 |
179.7 |
| C4 |
C5 |
C6 |
H5 |
179.4 |
180.5 |
| H5 |
C5 |
C4 |
N4 |
358.8 |
0.3 |
| C4 |
C5 |
H5 |
C6 |
180.6 |
179.5 |
| H5 |
C5 |
C6 |
H6 |
358.2 |
359.7 |
| H6 |
C6 |
N1 |
C1' |
4.8 |
0.1 |
| N1 |
C6 |
H6 |
C5 |
178.7 |
179.7 |
| H6 |
C6 |
C5 |
H5 |
358.2 |
359.7 |
| C4 |
N4 |
HN41 |
HN42 |
182.0 |
179.7 |
| C4 |
N4 |
HN42 |
HN41 |
178.0 |
180.3 |
| N1 |
C1' |
C2' |
O4' |
121.3 |
119.5 |
| N1 |
C1' |
C2' |
H1' |
237.7 |
239.0 |
| O4' |
C1' |
C2' |
H1' |
116.5 |
119.4 |
| C2' |
C1' |
O4' |
C4' |
351.1 |
333.7 |
| C3' |
C2' |
C1' |
H2' |
120.5 |
241.3 |
| C3' |
C2' |
C1' |
H2'' |
242.9 |
118.7 |
| C1' |
C2' |
C3' |
C4' |
33.8 |
20.9 |
| C1' |
C2' |
C3' |
O3' |
153.4 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
278.3 |
262.7 |
| H2' |
C2' |
C1' |
H2'' |
122.4 |
237.4 |
| N1 |
C1' |
O4' |
C2' |
239.8 |
240.5 |
| N1 |
C1' |
O4' |
H1' |
122.4 |
121.0 |
| C2' |
C1' |
O4' |
H1' |
242.6 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
342.9 |
1.9 |
| O4' |
C1' |
C2' |
H2' |
222.4 |
120.6 |
| O4' |
C1' |
C2' |
H2'' |
100.0 |
243.2 |
| C3' |
C4' |
O4' |
C1' |
31.5 |
39.8 |
| C1' |
O4' |
C4' |
C5' |
155.3 |
158.5 |
| C1' |
O4' |
C4' |
H4' |
275.3 |
281.4 |
| N1 |
C1' |
H1' |
C2' |
121.6 |
121.1 |
| N1 |
C1' |
H1' |
O4' |
237.3 |
239.0 |
| C2' |
C1' |
H1' |
O4' |
115.7 |
118.0 |
| H1' |
C1' |
C2' |
C3' |
226.4 |
242.5 |
| H1' |
C1' |
C2' |
H2' |
105.9 |
1.2 |
| H1' |
C1' |
C2' |
H2'' |
343.5 |
123.8 |
| H1' |
C1' |
O4' |
C4' |
108.6 |
93.2 |
| C3' |
C2' |
C1' |
O4' |
342.9 |
1.9 |
| C3' |
C2' |
C1' |
H1' |
226.4 |
242.5 |
| C1' |
C2' |
C3' |
H2' |
239.2 |
118.8 |
| C1' |
C2' |
C3' |
H2'' |
116.4 |
241.3 |
| H2' |
C2' |
C3' |
H2'' |
237.2 |
122.6 |
| C4' |
C3' |
C2' |
O3' |
240.4 |
241.8 |
| C4' |
C3' |
C2' |
H3' |
115.5 |
118.2 |
| C2' |
C3' |
C4' |
O4' |
319.7 |
323.1 |
| C2' |
C3' |
C4' |
C5' |
198.1 |
204.3 |
| C2' |
C3' |
C4' |
H4' |
75.5 |
81.5 |
| O3' |
C3' |
C2' |
H3' |
235.1 |
236.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.5 |
| H2' |
C2' |
C1' |
O4' |
222.4 |
120.6 |
| H2' |
C2' |
C1' |
H1' |
105.9 |
1.2 |
| C1' |
C2' |
H2' |
C3' |
115.8 |
245.2 |
| C1' |
C2' |
H2' |
H2'' |
238.4 |
122.6 |
| C3' |
C2' |
H2' |
H2'' |
122.6 |
237.4 |
| H2' |
C2' |
C3' |
C4' |
154.6 |
262.1 |
| H2' |
C2' |
C3' |
O3' |
274.2 |
20.4 |
| H2' |
C2' |
C3' |
H3' |
39.1 |
144.0 |
| H2'' |
C2' |
C1' |
O4' |
100.0 |
243.2 |
| H2'' |
C2' |
C1' |
H1' |
343.5 |
123.8 |
| C1' |
C2' |
H2'' |
C3' |
246.9 |
114.8 |
| C1' |
C2' |
H2'' |
H2' |
123.4 |
237.3 |
| C3' |
C2' |
H2'' |
H2' |
236.5 |
122.6 |
| H2'' |
C2' |
C3' |
C4' |
277.4 |
139.6 |
| H2'' |
C2' |
C3' |
O3' |
37.0 |
257.8 |
| H2'' |
C2' |
C3' |
H3' |
161.9 |
21.4 |
| C1' |
O4' |
C4' |
C3' |
31.5 |
39.8 |
| C4' |
C3' |
C2' |
H2' |
154.6 |
262.1 |
| C4' |
C3' |
C2' |
H2'' |
277.4 |
139.6 |
| C2' |
C3' |
C4' |
O3' |
118.0 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
244.4 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
126.3 |
123.6 |
| C4' |
C3' |
O3' |
HO3' |
291.1 |
174.2 |
| O4' |
C4' |
C3' |
C5' |
121.6 |
118.7 |
| O4' |
C4' |
C3' |
H4' |
244.2 |
241.6 |
| C5' |
C4' |
C3' |
H4' |
122.6 |
122.9 |
| C3' |
C4' |
C5' |
O5' |
57.2 |
180.0 |
| C3' |
C4' |
C5' |
H5' |
178.0 |
300.0 |
| C3' |
C4' |
C5' |
H5'' |
296.8 |
60.0 |
| O3' |
C3' |
C2' |
H2' |
274.2 |
20.4 |
| O3' |
C3' |
C2' |
H2'' |
37.0 |
257.8 |
| C2' |
C3' |
O3' |
C4' |
248.9 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
123.7 |
123.7 |
| C4' |
C3' |
O3' |
H3' |
234.8 |
236.4 |
| O3' |
C3' |
C4' |
O4' |
201.7 |
204.9 |
| O3' |
C3' |
C4' |
C5' |
80.1 |
86.1 |
| O3' |
C3' |
C4' |
H4' |
317.5 |
323.3 |
| H3' |
C3' |
C2' |
H2' |
39.1 |
144.0 |
| H3' |
C3' |
C2' |
H2'' |
161.9 |
21.4 |
| C2' |
C3' |
H3' |
C4' |
108.8 |
112.7 |
| C2' |
C3' |
H3' |
O3' |
235.7 |
236.4 |
| C4' |
C3' |
H3' |
O3' |
126.9 |
123.7 |
| H3' |
C3' |
C4' |
O4' |
75.4 |
81.3 |
| H3' |
C3' |
C4' |
C5' |
313.7 |
322.5 |
| H3' |
C3' |
C4' |
H4' |
191.1 |
199.7 |
| H3' |
C3' |
O3' |
HO3' |
56.3 |
297.8 |
| C4' |
O4' |
C1' |
H1' |
108.6 |
93.2 |
| O4' |
C4' |
C3' |
O3' |
201.7 |
204.9 |
| O4' |
C4' |
C3' |
H3' |
75.4 |
81.3 |
| C3' |
C4' |
O4' |
C5' |
236.1 |
241.3 |
| C3' |
C4' |
O4' |
H4' |
116.1 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
240.0 |
237.2 |
| O4' |
C4' |
C5' |
O5' |
298.9 |
65.7 |
| O4' |
C4' |
C5' |
H5' |
59.7 |
185.7 |
| O4' |
C4' |
C5' |
H5'' |
178.5 |
305.7 |
| C5' |
C4' |
C3' |
O3' |
80.1 |
86.1 |
| C5' |
C4' |
C3' |
H3' |
313.7 |
322.5 |
| C3' |
C4' |
C5' |
O4' |
118.3 |
114.3 |
| C3' |
C4' |
C5' |
H4' |
237.7 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
119.4 |
122.8 |
| O5' |
C5' |
C4' |
H5' |
239.2 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
120.4 |
120.0 |
| C4' |
C5' |
O5' |
P |
179.2 |
180.0 |
| H5' |
C5' |
C4' |
H5'' |
241.2 |
240.0 |
| H4' |
C4' |
C3' |
O3' |
317.5 |
323.3 |
| H4' |
C4' |
C3' |
H3' |
191.1 |
199.7 |
| C3' |
C4' |
H4' |
O4' |
246.5 |
245.9 |
| C3' |
C4' |
H4' |
C5' |
125.6 |
122.9 |
| O4' |
C4' |
H4' |
C5' |
239.1 |
237.1 |
| H4' |
C4' |
C5' |
O5' |
179.5 |
302.9 |
| H4' |
C4' |
C5' |
H5' |
300.3 |
62.9 |
| H4' |
C4' |
C5' |
H5'' |
59.1 |
182.9 |
| HO3' |
O3' |
C3' |
H3' |
56.3 |
297.8 |
| O5' |
C5' |
C4' |
H4' |
179.5 |
302.9 |
| C4' |
C5' |
O5' |
H5' |
120.3 |
119.9 |
| C4' |
C5' |
O5' |
H5'' |
240.2 |
240.0 |
| H5' |
C5' |
O5' |
H5'' |
119.9 |
120.1 |
| C5' |
O5' |
P |
OP1 |
32.3 |
180.0 |
| C5' |
O5' |
P |
S2P |
162.7 |
60.0 |
| C5' |
O5' |
P |
OP3 |
277.2 |
300.0 |
| H5' |
C5' |
C4' |
H4' |
300.3 |
62.9 |
| C4' |
C5' |
H5' |
O5' |
239.1 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
118.7 |
119.9 |
| O5' |
C5' |
H5' |
H5'' |
239.6 |
240.0 |
| H5' |
C5' |
O5' |
P |
58.9 |
60.0 |
| H5'' |
C5' |
C4' |
H4' |
59.1 |
182.9 |
| C4' |
C5' |
H5'' |
O5' |
120.6 |
120.1 |
| C4' |
C5' |
H5'' |
H5' |
241.1 |
240.1 |
| O5' |
C5' |
H5'' |
H5' |
120.5 |
120.0 |
| H5'' |
C5' |
O5' |
P |
299.0 |
300.0 |
| P |
O5' |
C5' |
H5' |
58.9 |
60.0 |
| P |
O5' |
C5' |
H5'' |
299.0 |
300.0 |
| OP1 |
P |
O5' |
S2P |
229.5 |
119.9 |
| OP1 |
P |
O5' |
OP3 |
115.1 |
240.0 |
| O5' |
P |
OP1 |
HOP1 |
180.0 |
180.0 |
| S2P |
P |
O5' |
OP3 |
245.6 |
120.1 |
| O5' |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
| O5' |
P |
OP1 |
S2P |
122.3 |
240.0 |
| O5' |
P |
OP1 |
OP3 |
246.1 |
120.0 |
| S2P |
P |
OP1 |
OP3 |
123.8 |
240.0 |
| OP1 |
P |
OP3 |
HOP3 |
64.6 |
60.0 |
| O5' |
P |
S2P |
OP1 |
236.9 |
120.0 |
| O5' |
P |
S2P |
OP3 |
113.1 |
239.9 |
| OP1 |
P |
S2P |
OP3 |
236.3 |
120.0 |
| S2P |
P |
OP1 |
HOP1 |
57.7 |
300.0 |
| S2P |
P |
OP3 |
HOP3 |
293.5 |
180.0 |
| O5' |
P |
OP3 |
OP1 |
115.4 |
240.0 |
| O5' |
P |
OP3 |
S2P |
246.5 |
120.0 |
| OP1 |
P |
OP3 |
S2P |
131.1 |
240.0 |
| OP3 |
P |
OP1 |
HOP1 |
293.9 |
60.0 |
| HOP1 |
OP1 |
P |
S2P |
57.7 |
300.0 |
| HOP1 |
OP1 |
P |
OP3 |
293.9 |
60.0 |