PDB Chemical Component LMS
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 LMS
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1' |
N9 |
1.464 |
1.465 |
| N9 |
C8 |
1.377 |
1.363 |
| C8 |
N7 |
1.314 |
1.302 |
| N7 |
C5 |
1.388 |
1.355 |
| C5 |
C6 |
1.413 |
1.405 |
| C6 |
N6 |
1.337 |
1.383 |
| C6 |
N1 |
1.348 |
1.329 |
| N1 |
C2 |
1.339 |
1.321 |
| C2 |
N3 |
1.331 |
1.316 |
| N9 |
C4 |
1.376 |
1.372 |
| C5 |
C4 |
1.385 |
1.405 |
| N3 |
C4 |
1.344 |
1.329 |
| O5' |
S |
1.592 |
1.522 |
| O1P |
S |
1.475 |
1.422 |
| O2P |
S |
1.481 |
1.421 |
| N |
S |
1.639 |
1.656 |
| O3' |
HA |
0.950 |
0.967 |
| O2' |
HB |
0.950 |
0.967 |
| C8 |
H8 |
1.080 |
1.080 |
| C2 |
H2 |
1.080 |
1.081 |
| O5' |
C5' |
1.436 |
1.429 |
| C5' |
C4' |
1.513 |
1.530 |
| C4' |
O4' |
1.460 |
1.437 |
| C4' |
C3' |
1.533 |
1.540 |
| C3' |
O3' |
1.424 |
1.429 |
| C3' |
C2' |
1.526 |
1.548 |
| C2' |
O2' |
1.413 |
1.429 |
| O4' |
C1' |
1.411 |
1.444 |
| C2' |
C1' |
1.526 |
1.550 |
| C5' |
H5'1 |
1.099 |
1.091 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.090 |
| C3' |
H3' |
1.100 |
1.090 |
| C2' |
H2' |
1.100 |
1.090 |
| C1' |
H1' |
1.100 |
1.090 |
| N6 |
H6N1 |
1.000 |
0.969 |
| N6 |
H6N2 |
0.999 |
0.970 |
| N |
HN1 |
1.000 |
0.970 |
| N |
HN2 |
1.000 |
0.970 |
Bond Angles for LMS
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N9 |
C8 |
N7 |
113.7 |
110.0 |
| C8 |
N9 |
C4 |
105.7 |
107.4 |
| N9 |
C8 |
H8 |
123.1 |
125.0 |
| C8 |
N7 |
C5 |
104.0 |
109.4 |
| N7 |
C8 |
H8 |
123.2 |
125.0 |
| N7 |
C5 |
C6 |
132.4 |
134.6 |
| N7 |
C5 |
C4 |
110.7 |
107.2 |
| C5 |
C6 |
N6 |
124.2 |
120.8 |
| C5 |
C6 |
N1 |
117.6 |
118.4 |
| C6 |
C5 |
C4 |
116.9 |
118.2 |
| N6 |
C6 |
N1 |
118.2 |
120.7 |
| C6 |
N6 |
H6N1 |
109.5 |
120.0 |
| C6 |
N6 |
H6N2 |
109.5 |
120.0 |
| C6 |
N1 |
C2 |
118.6 |
121.2 |
| N1 |
C2 |
N3 |
129.4 |
122.5 |
| N1 |
C2 |
H2 |
115.3 |
118.7 |
| C2 |
N3 |
C4 |
110.6 |
120.6 |
| N3 |
C2 |
H2 |
115.3 |
118.7 |
| N9 |
C4 |
C5 |
105.9 |
106.0 |
| N9 |
C4 |
N3 |
127.3 |
134.9 |
| C5 |
C4 |
N3 |
126.8 |
119.1 |
| S |
N |
HN1 |
109.5 |
120.0 |
| S |
N |
HN2 |
109.5 |
120.0 |
| O5' |
C5' |
C4' |
110.4 |
109.5 |
| O5' |
C5' |
H5'1 |
109.2 |
109.5 |
| O5' |
C5' |
H5'2 |
109.0 |
109.4 |
| C5' |
C4' |
O4' |
109.5 |
109.8 |
| C5' |
C4' |
C3' |
116.2 |
109.9 |
| C4' |
C5' |
H5'1 |
109.2 |
109.5 |
| C4' |
C5' |
H5'2 |
109.0 |
109.5 |
| C5' |
C4' |
H4' |
103.7 |
109.9 |
| O4' |
C4' |
C3' |
106.1 |
107.3 |
| C4' |
O4' |
C1' |
109.1 |
106.9 |
| O4' |
C4' |
H4' |
114.3 |
109.9 |
| C4' |
C3' |
O3' |
110.2 |
110.5 |
| C4' |
C3' |
C2' |
102.6 |
104.2 |
| C3' |
C4' |
H4' |
107.2 |
110.0 |
| C4' |
C3' |
H3' |
113.3 |
110.5 |
| O3' |
C3' |
C2' |
109.2 |
110.4 |
| O3' |
C3' |
H3' |
107.2 |
110.4 |
| C3' |
C2' |
O2' |
113.2 |
111.0 |
| C3' |
C2' |
C1' |
101.1 |
102.1 |
| C2' |
C3' |
H3' |
114.2 |
110.6 |
| C3' |
C2' |
H2' |
112.7 |
110.9 |
| O2' |
C2' |
C1' |
109.8 |
110.9 |
| O2' |
C2' |
H2' |
104.4 |
110.8 |
| O4' |
C1' |
C2' |
104.7 |
103.5 |
| O4' |
C1' |
H1' |
113.9 |
110.6 |
| C1' |
C2' |
H2' |
115.9 |
110.9 |
| C2' |
C1' |
H1' |
109.9 |
110.6 |
| H5'1 |
C5' |
H5'2 |
110.2 |
109.4 |
| H6N1 |
N6 |
H6N2 |
109.4 |
120.0 |
| HN1 |
N |
HN2 |
109.5 |
120.0 |
Torsion Angles for LMS
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N9 |
C8 |
N7 |
C5 |
0.4 |
0.0 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| C8 |
N9 |
C4 |
C5 |
1.2 |
359.9 |
| C8 |
N9 |
C4 |
N3 |
180.2 |
180.0 |
| N7 |
C8 |
N9 |
C4 |
359.0 |
0.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
181.2 |
180.1 |
| C8 |
N7 |
C5 |
C4 |
0.5 |
359.9 |
| C5 |
N7 |
C8 |
H8 |
180.3 |
180.0 |
| N7 |
C5 |
C6 |
N6 |
0.9 |
359.9 |
| N7 |
C5 |
C6 |
N1 |
180.4 |
180.0 |
| C6 |
C5 |
N7 |
C4 |
180.7 |
180.1 |
| N9 |
C4 |
C5 |
N7 |
358.9 |
0.1 |
| N7 |
C5 |
C4 |
N3 |
179.9 |
180.0 |
| N7 |
C5 |
C6 |
C4 |
179.3 |
179.9 |
| N6 |
C6 |
C5 |
N1 |
180.6 |
179.9 |
| C5 |
C6 |
N6 |
H6N1 |
188.6 |
0.1 |
| C5 |
C6 |
N6 |
H6N2 |
308.6 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
359.2 |
359.9 |
| N9 |
C4 |
C5 |
C6 |
178.3 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
359.3 |
359.9 |
| C5 |
C6 |
N6 |
N1 |
179.4 |
180.1 |
| N6 |
C6 |
C5 |
C4 |
181.6 |
180.0 |
| N6 |
C6 |
N1 |
C2 |
178.6 |
180.0 |
| H6N1 |
N6 |
C6 |
H6N2 |
240.0 |
180.0 |
| C5 |
C6 |
N1 |
N6 |
180.5 |
179.9 |
| N1 |
C6 |
C5 |
C4 |
1.1 |
0.1 |
| N1 |
C6 |
N6 |
H6N1 |
9.2 |
180.0 |
| N1 |
C6 |
N6 |
H6N2 |
129.2 |
360.0 |
| C6 |
N1 |
C2 |
N3 |
0.1 |
0.1 |
| C6 |
N1 |
C2 |
H2 |
180.1 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.3 |
359.9 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
| N9 |
C4 |
N3 |
C2 |
181.2 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
360.0 |
0.1 |
| C4 |
N9 |
C8 |
N7 |
359.0 |
0.0 |
| C4 |
N9 |
C8 |
H8 |
179.0 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
358.9 |
0.1 |
| C6 |
C5 |
C4 |
N9 |
178.3 |
180.0 |
| C2 |
N3 |
C4 |
N9 |
181.2 |
180.0 |
| C5 |
C4 |
N9 |
N3 |
181.0 |
179.9 |
| N7 |
C5 |
C4 |
C6 |
180.6 |
180.1 |
| C4 |
C5 |
C6 |
N6 |
181.6 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
1.1 |
0.1 |
| C2 |
N3 |
C4 |
C5 |
360.0 |
0.1 |
| N9 |
C4 |
C5 |
N3 |
179.0 |
180.1 |
| C4 |
N3 |
C2 |
H2 |
180.3 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
181.2 |
179.9 |
| O5' |
S |
N |
HN1 |
79.6 |
360.0 |
| O5' |
S |
N |
HN2 |
199.6 |
180.0 |
| O1P |
S |
N |
HN1 |
194.5 |
113.5 |
| O1P |
S |
N |
HN2 |
314.5 |
293.6 |
| O2P |
S |
N |
HN1 |
327.6 |
246.4 |
| O2P |
S |
N |
HN2 |
87.6 |
66.5 |
| HN1 |
N |
S |
HN2 |
240.0 |
180.0 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| H8 |
C8 |
N9 |
C4 |
179.0 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
180.3 |
180.0 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.1 |
| H2 |
C2 |
N3 |
C4 |
180.3 |
180.0 |
| O5' |
C5' |
C4' |
O4' |
290.6 |
66.5 |
| O5' |
C5' |
C4' |
C3' |
50.8 |
184.3 |
| C4' |
C5' |
O5' |
H5'1 |
240.0 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
119.6 |
120.0 |
| O5' |
C5' |
C4' |
H4' |
168.2 |
305.5 |
| H5'1 |
C5' |
O5' |
H5'2 |
239.6 |
240.0 |
| O5' |
C5' |
C4' |
H5'1 |
120.0 |
120.1 |
| O5' |
C5' |
C4' |
H5'2 |
240.4 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
239.8 |
242.2 |
| C5' |
C4' |
O4' |
C1' |
132.1 |
146.0 |
| O4' |
C4' |
C5' |
H4' |
122.4 |
121.0 |
| C5' |
C4' |
C3' |
O3' |
141.2 |
119.9 |
| C5' |
C4' |
C3' |
C2' |
257.4 |
238.5 |
| C3' |
C4' |
C5' |
H4' |
242.6 |
238.8 |
| C5' |
C4' |
C3' |
H3' |
21.1 |
357.4 |
| H5'1 |
C5' |
C4' |
H5'2 |
120.4 |
120.0 |
| C5' |
C4' |
O4' |
C3' |
126.2 |
119.4 |
| O4' |
C4' |
C5' |
H5'1 |
170.6 |
306.4 |
| O4' |
C4' |
C5' |
H5'2 |
50.2 |
186.5 |
| C5' |
C4' |
O4' |
H4' |
244.2 |
239.0 |
| O4' |
C4' |
C3' |
O3' |
263.3 |
239.3 |
| O4' |
C4' |
C3' |
C2' |
19.5 |
357.9 |
| C3' |
C4' |
O4' |
H4' |
118.0 |
119.6 |
| O4' |
C4' |
C3' |
H3' |
143.1 |
116.7 |
| C4' |
O4' |
C1' |
C2' |
330.9 |
319.9 |
| C4' |
O4' |
C1' |
H1' |
91.1 |
78.4 |
| C5' |
C4' |
C3' |
O4' |
238.0 |
240.6 |
| C3' |
C4' |
C5' |
H5'1 |
290.8 |
64.3 |
| C3' |
C4' |
C5' |
H5'2 |
170.5 |
304.3 |
| C5' |
C4' |
C3' |
H4' |
115.4 |
121.1 |
| C3' |
C4' |
O4' |
C1' |
5.8 |
26.6 |
| O4' |
C4' |
C3' |
H4' |
237.5 |
240.4 |
| O3' |
C3' |
C4' |
C2' |
243.8 |
241.4 |
| O3' |
C3' |
C4' |
H3' |
120.1 |
122.6 |
| C4' |
C3' |
C2' |
O2' |
207.3 |
220.9 |
| C4' |
C3' |
C2' |
C1' |
324.6 |
339.1 |
| C2' |
C3' |
C4' |
H3' |
236.3 |
241.2 |
| C4' |
C3' |
C2' |
H2' |
89.0 |
97.3 |
| C4' |
C3' |
O3' |
C2' |
112.0 |
114.7 |
| O3' |
C3' |
C4' |
H4' |
25.8 |
358.8 |
| C4' |
C3' |
O3' |
H3' |
236.3 |
237.4 |
| O3' |
C3' |
C2' |
O2' |
324.1 |
339.6 |
| O3' |
C3' |
C2' |
C1' |
81.5 |
97.8 |
| C2' |
C3' |
O3' |
H3' |
124.2 |
122.6 |
| O3' |
C3' |
C2' |
H2' |
205.9 |
216.0 |
| C4' |
C3' |
C2' |
O3' |
243.1 |
241.3 |
| C2' |
C3' |
C4' |
H4' |
142.0 |
117.5 |
| C4' |
C3' |
C2' |
H3' |
123.1 |
118.8 |
| O3' |
C3' |
C2' |
H3' |
240.0 |
237.4 |
| O2' |
C2' |
C3' |
C1' |
242.6 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
118.2 |
123.6 |
| O4' |
C1' |
C2' |
C3' |
40.2 |
37.0 |
| C1' |
C2' |
C3' |
H2' |
235.6 |
241.8 |
| C3' |
C2' |
C1' |
H1' |
277.4 |
278.5 |
| C3' |
C2' |
O2' |
C1' |
112.1 |
112.7 |
| O2' |
C2' |
C3' |
H3' |
84.2 |
102.2 |
| C3' |
C2' |
O2' |
H2' |
237.1 |
236.3 |
| O4' |
C1' |
C2' |
O2' |
160.0 |
155.3 |
| C1' |
C2' |
O2' |
H2' |
124.9 |
123.6 |
| O2' |
C2' |
C1' |
H1' |
37.2 |
36.8 |
| C1' |
O4' |
C4' |
C3' |
5.8 |
26.6 |
| C1' |
O4' |
C4' |
H4' |
247.9 |
266.9 |
| C3' |
C2' |
C1' |
O4' |
40.2 |
37.0 |
| O2' |
C2' |
C1' |
O4' |
160.0 |
155.3 |
| O4' |
C1' |
C2' |
H2' |
278.0 |
278.8 |
| C2' |
C1' |
O4' |
H1' |
239.8 |
241.5 |
| C3' |
C2' |
C1' |
O2' |
240.2 |
241.7 |
| C1' |
C2' |
C3' |
H3' |
201.5 |
220.4 |
| C3' |
C2' |
C1' |
H2' |
122.2 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
242.0 |
236.5 |
| O4' |
C1' |
C2' |
H1' |
122.8 |
118.5 |
| O5' |
C5' |
H5'1 |
C4' |
239.3 |
239.9 |
| O5' |
C5' |
H5'1 |
H5'2 |
119.6 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
170.6 |
306.4 |
| H5'1 |
C5' |
C4' |
C3' |
290.8 |
64.3 |
| C4' |
C5' |
H5'1 |
H5'2 |
240.4 |
240.0 |
| H5'1 |
C5' |
C4' |
H4' |
48.2 |
185.4 |
| O5' |
C5' |
H5'2 |
C4' |
120.5 |
120.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
240.2 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
50.2 |
186.5 |
| H5'2 |
C5' |
C4' |
C3' |
170.5 |
304.3 |
| C4' |
C5' |
H5'2 |
H5'1 |
119.8 |
120.0 |
| H5'2 |
C5' |
C4' |
H4' |
287.8 |
65.5 |
| C5' |
C4' |
H4' |
O4' |
119.2 |
120.9 |
| C5' |
C4' |
H4' |
C3' |
236.5 |
238.9 |
| H4' |
C4' |
C5' |
H5'1 |
48.2 |
185.4 |
| H4' |
C4' |
C5' |
H5'2 |
287.8 |
65.5 |
| O4' |
C4' |
H4' |
C3' |
117.3 |
118.0 |
| H4' |
C4' |
O4' |
C1' |
247.9 |
266.9 |
| H4' |
C4' |
C3' |
O3' |
25.8 |
358.8 |
| H4' |
C4' |
C3' |
C2' |
142.0 |
117.5 |
| H4' |
C4' |
C3' |
H3' |
265.7 |
236.3 |
| C4' |
C3' |
H3' |
O3' |
121.8 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
242.9 |
245.2 |
| H3' |
C3' |
C4' |
H4' |
265.7 |
236.3 |
| O3' |
C3' |
H3' |
C2' |
121.2 |
122.6 |
| H3' |
C3' |
C2' |
O2' |
84.2 |
102.2 |
| H3' |
C3' |
C2' |
C1' |
201.5 |
220.4 |
| H3' |
C3' |
C2' |
H2' |
325.9 |
338.6 |
| C3' |
C2' |
H2' |
O2' |
123.3 |
123.7 |
| C3' |
C2' |
H2' |
C1' |
244.2 |
247.3 |
| H2' |
C2' |
C3' |
H3' |
325.9 |
338.6 |
| O2' |
C2' |
H2' |
C1' |
121.0 |
123.6 |
| H2' |
C2' |
C1' |
H1' |
155.2 |
160.3 |
| O4' |
C1' |
H1' |
C2' |
242.8 |
245.9 |
| H1' |
C1' |
C2' |
H2' |
155.2 |
160.3 |
| H6N1 |
N6 |
C6 |
N1 |
9.2 |
180.0 |
| C6 |
N6 |
H6N1 |
H6N2 |
120.0 |
180.0 |
| H6N2 |
N6 |
C6 |
N1 |
129.2 |
360.0 |
| C6 |
N6 |
H6N2 |
H6N1 |
240.0 |
180.0 |
| S |
N |
HN1 |
HN2 |
120.0 |
180.0 |
| S |
N |
HN2 |
HN1 |
240.0 |
180.0 |