PDB Chemical Component LSH
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 LSH
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O7' |
S |
1.433 |
1.421 |
| O8' |
S |
1.446 |
1.421 |
| C6' |
S |
1.686 |
1.820 |
| C6' |
C4' |
1.542 |
1.538 |
| S |
N2' |
1.619 |
1.667 |
| C5' |
C4' |
1.516 |
1.530 |
| C5' |
O5' |
1.400 |
1.429 |
| C4' |
O4' |
1.429 |
1.435 |
| C4' |
C3' |
1.521 |
1.547 |
| N2' |
C2' |
1.472 |
1.481 |
| O4' |
C1' |
1.438 |
1.452 |
| OP1 |
P |
1.476 |
1.480 |
| O3' |
C3' |
1.420 |
1.430 |
| O5' |
P |
1.649 |
1.609 |
| C3' |
C2' |
1.507 |
1.544 |
| P |
OP2 |
1.466 |
1.610 |
| C2' |
C1' |
1.491 |
1.548 |
| C1' |
N1 |
1.465 |
1.465 |
| N1 |
C6 |
1.348 |
1.368 |
| N1 |
C2 |
1.353 |
1.346 |
| C6 |
C5 |
1.382 |
1.350 |
| O2 |
C2 |
1.255 |
1.216 |
| C2 |
N3 |
1.361 |
1.346 |
| C5 |
C7 |
1.506 |
1.507 |
| C5 |
C4 |
1.389 |
1.416 |
| N3 |
C4 |
1.359 |
1.348 |
| C4 |
O4 |
1.257 |
1.218 |
| OP2 |
H2 |
0.950 |
0.968 |
| C5' |
H3 |
1.100 |
1.090 |
| C5' |
H4 |
1.100 |
1.090 |
| C6' |
H5 |
1.100 |
1.091 |
| C6' |
H6 |
1.100 |
1.090 |
| N2' |
H7 |
1.000 |
0.970 |
| C2' |
H8 |
1.100 |
1.089 |
| C1' |
H9 |
1.100 |
1.090 |
| N3 |
H10 |
1.000 |
0.970 |
| C7 |
H11 |
1.100 |
1.090 |
| C7 |
H12 |
1.100 |
1.090 |
| C7 |
H13 |
1.100 |
1.090 |
| C6 |
H14 |
1.079 |
1.081 |
| C3' |
H15 |
1.100 |
1.090 |
| O3' |
H16 |
0.950 |
0.967 |
| P |
OP3 |
1.607 |
1.610 |
| OP3 |
H1 |
0.950 |
0.967 |
Bond Angles for LSH
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O7' |
S |
N2' |
108.2 |
104.6 |
| O8' |
S |
N2' |
109.0 |
104.5 |
| C6' |
S |
N2' |
104.7 |
103.1 |
| S |
C6' |
H5 |
108.6 |
109.6 |
| S |
C6' |
H6 |
108.7 |
109.7 |
| C6' |
C4' |
O4' |
110.5 |
108.8 |
| C6' |
C4' |
C3' |
109.8 |
108.4 |
| S |
N2' |
C2' |
120.0 |
116.5 |
| S |
N2' |
H7 |
106.8 |
121.7 |
| C5' |
C4' |
O4' |
109.7 |
111.3 |
| C5' |
C4' |
C3' |
114.5 |
111.4 |
| C4' |
C5' |
H3 |
109.9 |
109.5 |
| C4' |
C5' |
H4 |
109.9 |
109.4 |
| O4' |
C4' |
C3' |
102.8 |
105.4 |
| C4' |
O4' |
C1' |
107.5 |
109.1 |
| C4' |
C3' |
C2' |
101.0 |
101.8 |
| C4' |
C3' |
H15 |
109.7 |
111.1 |
| N2' |
C2' |
C1' |
110.0 |
106.4 |
| C2' |
N2' |
H7 |
106.8 |
121.8 |
| N2' |
C2' |
H8 |
112.5 |
113.4 |
| O4' |
C1' |
N1 |
109.2 |
109.7 |
| O4' |
C1' |
H9 |
106.5 |
109.9 |
| OP1 |
P |
OP2 |
121.7 |
109.5 |
| OP1 |
P |
OP3 |
103.3 |
109.5 |
| O3' |
C3' |
H15 |
111.1 |
110.9 |
| O5' |
P |
OP3 |
101.9 |
109.5 |
| C3' |
C2' |
H8 |
111.9 |
114.1 |
| P |
OP2 |
H2 |
109.5 |
114.0 |
| OP2 |
P |
OP3 |
108.8 |
109.5 |
| C2' |
C1' |
N1 |
120.2 |
109.8 |
| C1' |
C2' |
H8 |
112.2 |
113.5 |
| C2' |
C1' |
H9 |
105.9 |
109.8 |
| C1' |
N1 |
C6 |
119.9 |
119.7 |
| C1' |
N1 |
C2 |
118.6 |
119.7 |
| N1 |
C1' |
H9 |
106.2 |
109.8 |
| C2 |
N1 |
C6 |
121.0 |
120.7 |
| N1 |
C6 |
C5 |
121.5 |
119.7 |
| N1 |
C6 |
H14 |
119.2 |
120.2 |
| N1 |
C2 |
N3 |
117.8 |
120.9 |
| O2 |
C2 |
N3 |
121.1 |
119.6 |
| C2 |
N3 |
C4 |
123.4 |
120.3 |
| C2 |
N3 |
H10 |
118.3 |
119.9 |
| C5 |
C7 |
H11 |
109.5 |
109.5 |
| C5 |
C7 |
H12 |
109.5 |
109.5 |
| C5 |
C7 |
H13 |
109.5 |
109.5 |
| N3 |
C4 |
O4 |
119.4 |
120.3 |
| C4 |
N3 |
H10 |
118.3 |
119.9 |
| H3 |
C5' |
H4 |
109.4 |
109.5 |
| H5 |
C6' |
H6 |
109.5 |
109.7 |
| H11 |
C7 |
H12 |
109.5 |
109.4 |
| H11 |
C7 |
H13 |
109.5 |
109.4 |
| H12 |
C7 |
H13 |
109.5 |
109.5 |
| P |
OP3 |
H1 |
109.5 |
114.0 |
Torsion Angles for LSH
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O8' |
S |
O7' |
N2' |
122.3 |
117.4 |
| C6' |
S |
O7' |
N2' |
245.5 |
249.6 |
| O7' |
S |
C6' |
H5 |
273.4 |
35.3 |
| O7' |
S |
C6' |
H6 |
32.5 |
274.8 |
| O7' |
S |
N2' |
C2' |
206.7 |
198.4 |
| O7' |
S |
N2' |
H7 |
328.2 |
18.3 |
| O7' |
S |
O8' |
N2' |
238.2 |
242.6 |
| C6' |
S |
O8' |
N2' |
113.2 |
110.3 |
| O8' |
S |
C6' |
H5 |
40.8 |
172.7 |
| O8' |
S |
C6' |
H6 |
159.8 |
52.2 |
| O8' |
S |
N2' |
C2' |
80.7 |
70.0 |
| O8' |
S |
N2' |
H7 |
202.2 |
249.9 |
| O7' |
S |
C6' |
N2' |
116.6 |
111.3 |
| O8' |
S |
C6' |
N2' |
244.0 |
248.8 |
| S |
C6' |
C4' |
O4' |
51.4 |
49.9 |
| S |
C6' |
C4' |
C3' |
298.7 |
295.8 |
| C6' |
S |
N2' |
C2' |
325.4 |
314.2 |
| C6' |
S |
N2' |
H7 |
86.8 |
134.1 |
| H5 |
C6' |
S |
H6 |
241.0 |
120.5 |
| C5' |
C4' |
C6' |
O4' |
120.9 |
123.0 |
| C5' |
C4' |
C6' |
C3' |
233.6 |
237.1 |
| C6' |
C4' |
C5' |
H3 |
307.6 |
184.9 |
| C6' |
C4' |
C5' |
H4 |
68.1 |
64.9 |
| O4' |
C4' |
C6' |
C3' |
112.7 |
114.1 |
| C6' |
C4' |
O4' |
C1' |
264.9 |
266.9 |
| C6' |
C4' |
C3' |
C2' |
74.9 |
79.6 |
| C6' |
C4' |
C3' |
H15 |
190.8 |
199.2 |
| N2' |
S |
C6' |
H5 |
156.8 |
284.0 |
| N2' |
S |
C6' |
H6 |
275.8 |
163.5 |
| S |
N2' |
C2' |
C1' |
307.5 |
316.9 |
| C2' |
N2' |
S |
H7 |
238.5 |
180.1 |
| S |
N2' |
C2' |
H8 |
181.7 |
191.5 |
| C6' |
C4' |
C5' |
O4' |
238.7 |
238.5 |
| C6' |
C4' |
C5' |
C3' |
123.7 |
121.1 |
| O4' |
C4' |
C5' |
C3' |
245.0 |
242.7 |
| C5' |
C4' |
O4' |
C1' |
144.3 |
143.9 |
| C5' |
C4' |
C3' |
C2' |
198.3 |
202.4 |
| C5' |
C4' |
C3' |
H15 |
314.2 |
322.0 |
| H3 |
C5' |
C4' |
H4 |
239.5 |
120.1 |
| C5' |
O5' |
P |
OP3 |
297.4 |
185.0 |
| C6' |
C4' |
O4' |
C3' |
242.8 |
243.9 |
| C5' |
C4' |
O4' |
C3' |
122.2 |
120.9 |
| O4' |
C4' |
C5' |
H3 |
68.9 |
306.5 |
| O4' |
C4' |
C5' |
H4 |
189.4 |
186.4 |
| O4' |
C4' |
C3' |
C2' |
317.3 |
323.3 |
| O4' |
C4' |
C3' |
H15 |
73.1 |
82.9 |
| C4' |
O4' |
C1' |
N1 |
234.9 |
240.7 |
| C4' |
O4' |
C1' |
H9 |
120.6 |
119.9 |
| C6' |
C4' |
C3' |
O4' |
117.6 |
116.3 |
| C5' |
C4' |
C3' |
O4' |
241.0 |
239.1 |
| C3' |
C4' |
C5' |
H3 |
183.9 |
63.8 |
| C3' |
C4' |
C5' |
H4 |
304.4 |
303.7 |
| C3' |
C4' |
O4' |
C1' |
22.0 |
23.0 |
| O3' |
C3' |
C4' |
H15 |
123.4 |
123.9 |
| C4' |
C3' |
C2' |
H8 |
163.1 |
157.6 |
| S |
N2' |
C2' |
H7 |
121.5 |
179.9 |
| C4' |
C3' |
C2' |
N2' |
289.8 |
283.9 |
| C3' |
C2' |
N2' |
H8 |
233.6 |
233.3 |
| N2' |
C2' |
C1' |
N1 |
209.1 |
208.2 |
| C1' |
C2' |
N2' |
H8 |
125.8 |
125.4 |
| N2' |
C2' |
C1' |
H9 |
329.2 |
329.1 |
| C1' |
O4' |
C4' |
C3' |
22.0 |
23.0 |
| C2' |
C1' |
O4' |
N1 |
132.3 |
119.5 |
| O4' |
C1' |
C2' |
H8 |
209.0 |
214.2 |
| C2' |
C1' |
O4' |
H9 |
246.6 |
240.4 |
| O4' |
C1' |
N1 |
C6 |
14.9 |
24.1 |
| O4' |
C1' |
N1 |
C2 |
203.6 |
204.4 |
| N1 |
C1' |
O4' |
H9 |
114.3 |
120.8 |
| O5' |
P |
OP1 |
OP3 |
251.4 |
240.0 |
| OP1 |
P |
OP2 |
H2 |
360.0 |
180.0 |
| OP2 |
P |
OP1 |
OP3 |
122.4 |
120.0 |
| OP1 |
P |
OP3 |
H1 |
0.0 |
60.0 |
| C4' |
C3' |
O3' |
H15 |
237.5 |
236.0 |
| O3' |
C3' |
C2' |
H8 |
282.3 |
275.1 |
| OP1 |
P |
O5' |
OP3 |
109.5 |
120.0 |
| O5' |
P |
OP2 |
H2 |
229.7 |
60.0 |
| OP2 |
P |
O5' |
OP3 |
245.4 |
240.0 |
| O5' |
P |
OP3 |
H1 |
115.3 |
180.1 |
| C4' |
C3' |
C2' |
H15 |
115.8 |
118.8 |
| C3' |
C2' |
N2' |
H7 |
293.8 |
244.9 |
| N2' |
C2' |
C3' |
H8 |
126.7 |
126.3 |
| C1' |
C2' |
C3' |
H8 |
242.0 |
237.6 |
| C3' |
C2' |
C1' |
H9 |
213.0 |
217.3 |
| OP1 |
P |
OP2 |
OP3 |
240.2 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
109.9 |
120.0 |
| OP2 |
P |
OP3 |
H1 |
229.3 |
300.0 |
| C4' |
O4' |
C1' |
C2' |
7.2 |
0.2 |
| C4' |
C3' |
C2' |
C1' |
45.0 |
35.1 |
| C1' |
C2' |
N2' |
H7 |
186.0 |
137.1 |
| N2' |
C2' |
C1' |
H8 |
234.0 |
234.6 |
| O4' |
C1' |
C2' |
N1 |
233.9 |
240.5 |
| O4' |
C1' |
C2' |
H9 |
113.8 |
119.7 |
| C3' |
C2' |
C1' |
H8 |
117.8 |
122.8 |
| C2' |
C1' |
N1 |
C6 |
249.3 |
265.8 |
| C2' |
C1' |
N1 |
C2 |
78.1 |
86.1 |
| N1 |
C1' |
C2' |
H9 |
239.9 |
239.1 |
| O4' |
C1' |
N1 |
H9 |
245.5 |
239.2 |
| N1 |
C1' |
C2' |
H8 |
335.1 |
333.6 |
| C2' |
C1' |
N1 |
H9 |
119.9 |
120.9 |
| C2 |
N1 |
C1' |
C6 |
188.8 |
180.3 |
| C1' |
N1 |
C6 |
C5 |
188.9 |
179.8 |
| C1' |
N1 |
C6 |
H14 |
8.9 |
0.0 |
| C1' |
N1 |
C2 |
N3 |
171.2 |
180.0 |
| C1' |
N1 |
C6 |
C2 |
189.0 |
180.3 |
| C6 |
N1 |
C1' |
H9 |
129.4 |
144.9 |
| C6 |
N1 |
C2 |
N3 |
0.1 |
0.3 |
| C1' |
N1 |
C2 |
C6 |
171.1 |
179.7 |
| C2 |
N1 |
C1' |
H9 |
318.2 |
325.2 |
| C2 |
N1 |
C6 |
C5 |
359.9 |
359.5 |
| C2 |
N1 |
C6 |
H14 |
179.9 |
179.7 |
| O2 |
C2 |
N1 |
N3 |
178.5 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
358.6 |
359.9 |
| N1 |
C2 |
N3 |
H10 |
178.6 |
180.0 |
| N1 |
C6 |
C5 |
H14 |
180.0 |
180.2 |
| C6 |
C5 |
C7 |
H11 |
180.0 |
180.3 |
| C6 |
C5 |
C7 |
H12 |
300.0 |
300.3 |
| C6 |
C5 |
C7 |
H13 |
60.0 |
60.3 |
| O2 |
C2 |
N1 |
C6 |
178.6 |
180.3 |
| N1 |
C2 |
O2 |
N3 |
181.5 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
180.1 |
180.0 |
| O2 |
C2 |
N3 |
H10 |
0.1 |
0.1 |
| N3 |
C2 |
N1 |
C6 |
0.1 |
0.3 |
| C2 |
N3 |
C4 |
O4 |
182.8 |
180.1 |
| C4 |
N3 |
C2 |
H10 |
180.0 |
179.9 |
| N1 |
C6 |
C5 |
C7 |
179.5 |
180.3 |
| H11 |
C7 |
C5 |
H12 |
240.0 |
240.0 |
| H11 |
C7 |
C5 |
H13 |
120.0 |
120.0 |
| H12 |
C7 |
C5 |
H13 |
240.0 |
240.0 |
| N1 |
C6 |
C5 |
C4 |
1.3 |
0.5 |
| C5 |
C4 |
N3 |
H10 |
182.6 |
180.0 |
| C2 |
N3 |
C4 |
H10 |
180.0 |
180.1 |
| O4 |
C4 |
N3 |
H10 |
2.8 |
360.0 |
| H2 |
OP2 |
P |
OP3 |
119.8 |
300.0 |
| H3 |
C5' |
C4' |
O4' |
68.9 |
306.5 |
| H3 |
C5' |
C4' |
C3' |
183.9 |
63.8 |
| C4' |
C5' |
H3 |
H4 |
120.8 |
240.0 |
| H4 |
C5' |
C4' |
O4' |
189.4 |
186.4 |
| H4 |
C5' |
C4' |
C3' |
304.4 |
303.7 |
| C4' |
C5' |
H4 |
H3 |
239.2 |
120.1 |
| H5 |
C6' |
S |
N2' |
156.8 |
284.0 |
| S |
C6' |
H5 |
H6 |
118.5 |
239.5 |
| H5 |
C6' |
C4' |
O4' |
290.9 |
169.6 |
| H5 |
C6' |
C4' |
C3' |
178.2 |
55.5 |
| H6 |
C6' |
S |
N2' |
275.8 |
163.5 |
| S |
C6' |
H6 |
H5 |
241.5 |
120.5 |
| H6 |
C6' |
C4' |
O4' |
171.9 |
290.1 |
| H6 |
C6' |
C4' |
C3' |
59.2 |
176.0 |
| S |
N2' |
H7 |
C2' |
230.5 |
180.1 |
| H7 |
N2' |
C2' |
C1' |
186.0 |
137.1 |
| H7 |
N2' |
C2' |
H8 |
60.2 |
11.6 |
| N2' |
C2' |
H8 |
C1' |
124.6 |
121.5 |
| H8 |
C2' |
N2' |
H7 |
60.2 |
11.6 |
| H8 |
C2' |
C1' |
N1 |
335.1 |
333.6 |
| H8 |
C2' |
C1' |
H9 |
95.2 |
94.5 |
| O4' |
C1' |
H9 |
N1 |
116.3 |
120.7 |
| C2' |
C1' |
H9 |
N1 |
231.2 |
239.1 |
| H9 |
C1' |
C2' |
H8 |
95.2 |
94.5 |
| H9 |
C1' |
N1 |
C6 |
129.4 |
144.9 |
| H9 |
C1' |
N1 |
C2 |
318.2 |
325.2 |
| C2 |
N3 |
H10 |
C4 |
180.0 |
179.9 |
| H10 |
N3 |
C4 |
O4 |
2.8 |
360.0 |
| C5 |
C7 |
H11 |
H12 |
120.0 |
120.0 |
| C5 |
C7 |
H11 |
H13 |
240.0 |
240.0 |
| H12 |
C7 |
H11 |
H13 |
120.0 |
120.0 |
| C5 |
C7 |
H12 |
H11 |
240.0 |
240.0 |
| C5 |
C7 |
H12 |
H13 |
120.0 |
120.0 |
| H11 |
C7 |
H12 |
H13 |
240.0 |
240.1 |
| C5 |
C7 |
H13 |
H11 |
120.0 |
120.0 |
| C5 |
C7 |
H13 |
H12 |
240.0 |
240.0 |
| H11 |
C7 |
H13 |
H12 |
120.0 |
119.9 |
| N1 |
C6 |
H14 |
C5 |
180.0 |
179.8 |
| C4' |
C3' |
H15 |
C2' |
249.9 |
246.8 |
| H15 |
C3' |
C2' |
H8 |
47.3 |
38.8 |
| H16 |
O3' |
C3' |
H15 |
302.6 |
304.1 |
| OP1 |
P |
OP3 |
OP2 |
130.7 |
120.0 |
| OP3 |
P |
OP2 |
H2 |
119.8 |
300.0 |