PDB Chemical Component LGP
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 LGP
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP1 |
1.481 |
1.479 |
| P |
OP2 |
1.480 |
1.610 |
| P |
OP3 |
1.621 |
1.610 |
| P |
O5' |
1.622 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.968 |
| O5' |
C5' |
1.442 |
1.428 |
| C5' |
C4' |
1.544 |
1.530 |
| C5' |
H5' |
1.090 |
1.090 |
| C5' |
H5'' |
1.090 |
1.089 |
| C4' |
O4' |
1.433 |
1.430 |
| C4' |
C3' |
1.537 |
1.529 |
| C4' |
H4' |
1.086 |
1.090 |
| O4' |
C1' |
1.434 |
1.428 |
| C3' |
O3' |
1.432 |
1.428 |
| C3' |
H3'1 |
1.095 |
1.090 |
| C3' |
H3'2 |
1.113 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C1' |
N9 |
1.472 |
1.465 |
| C1' |
H1'1 |
1.078 |
1.091 |
| C1' |
H1'2 |
1.088 |
1.089 |
| N9 |
C8 |
1.350 |
1.364 |
| N9 |
C4 |
1.376 |
1.368 |
| C8 |
N7 |
1.289 |
1.301 |
| C8 |
H8 |
1.085 |
1.080 |
| N7 |
C5 |
1.399 |
1.355 |
| C5 |
C6 |
1.419 |
1.415 |
| C5 |
C4 |
1.386 |
1.398 |
| C6 |
O6 |
1.226 |
1.219 |
| C6 |
N1 |
1.387 |
1.351 |
| N1 |
C2 |
1.378 |
1.363 |
| N1 |
HN1 |
1.011 |
0.970 |
| C2 |
N2 |
1.327 |
1.372 |
| C2 |
N3 |
1.332 |
1.314 |
| N2 |
HN21 |
1.010 |
0.971 |
| N2 |
HN22 |
1.010 |
0.970 |
| N3 |
C4 |
1.352 |
1.339 |
Bond Angles for LGP
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
119.7 |
109.4 |
| OP1 |
P |
OP3 |
108.0 |
109.5 |
| OP1 |
P |
O5' |
107.9 |
109.5 |
| OP2 |
P |
OP3 |
107.9 |
109.5 |
| OP2 |
P |
O5' |
108.4 |
109.5 |
| P |
OP2 |
HOP2 |
119.6 |
106.8 |
| OP3 |
P |
O5' |
103.8 |
109.5 |
| P |
OP3 |
HOP3 |
108.1 |
106.8 |
| P |
O5' |
C5' |
121.2 |
106.8 |
| O5' |
C5' |
C4' |
112.7 |
109.5 |
| O5' |
C5' |
H5' |
108.6 |
109.4 |
| O5' |
C5' |
H5'' |
109.1 |
109.5 |
| C4' |
C5' |
H5' |
108.7 |
109.5 |
| C4' |
C5' |
H5'' |
109.0 |
109.5 |
| C5' |
C4' |
O4' |
110.5 |
109.5 |
| C5' |
C4' |
C3' |
111.3 |
109.5 |
| C5' |
C4' |
H4' |
108.4 |
109.5 |
| H5' |
C5' |
H5'' |
108.7 |
109.5 |
| O4' |
C4' |
C3' |
111.4 |
109.5 |
| O4' |
C4' |
H4' |
107.4 |
109.4 |
| C4' |
O4' |
C1' |
110.2 |
106.8 |
| C3' |
C4' |
H4' |
107.7 |
109.5 |
| C4' |
C3' |
O3' |
110.6 |
109.5 |
| C4' |
C3' |
H3'1 |
109.4 |
109.5 |
| C4' |
C3' |
H3'2 |
109.2 |
109.5 |
| O4' |
C1' |
N9 |
112.1 |
109.5 |
| O4' |
C1' |
H1'1 |
108.4 |
109.4 |
| O4' |
C1' |
H1'2 |
109.5 |
109.5 |
| O3' |
C3' |
H3'1 |
109.2 |
109.4 |
| O3' |
C3' |
H3'2 |
108.7 |
109.5 |
| C3' |
O3' |
HO3' |
110.6 |
106.8 |
| H3'1 |
C3' |
H3'2 |
109.7 |
109.5 |
| N9 |
C1' |
H1'1 |
109.0 |
109.4 |
| N9 |
C1' |
H1'2 |
108.9 |
109.5 |
| C1' |
N9 |
C8 |
129.4 |
126.3 |
| C1' |
N9 |
C4 |
126.6 |
126.3 |
| H1'1 |
C1' |
H1'2 |
108.9 |
109.5 |
| C8 |
N9 |
C4 |
103.9 |
107.5 |
| N9 |
C8 |
N7 |
117.8 |
109.8 |
| N9 |
C8 |
H8 |
121.0 |
125.1 |
| N9 |
C4 |
C5 |
106.1 |
106.2 |
| N9 |
C4 |
N3 |
126.0 |
134.2 |
| N7 |
C8 |
H8 |
121.3 |
125.1 |
| C8 |
N7 |
C5 |
101.6 |
109.3 |
| N7 |
C5 |
C6 |
130.0 |
134.1 |
| N7 |
C5 |
C4 |
110.6 |
107.3 |
| C6 |
C5 |
C4 |
119.4 |
118.6 |
| C5 |
C6 |
O6 |
128.5 |
120.9 |
| C5 |
C6 |
N1 |
111.6 |
118.4 |
| C5 |
C4 |
N3 |
127.9 |
119.7 |
| O6 |
C6 |
N1 |
119.9 |
120.8 |
| C6 |
N1 |
C2 |
125.2 |
120.3 |
| C6 |
N1 |
HN1 |
115.7 |
119.8 |
| C2 |
N1 |
HN1 |
119.0 |
119.9 |
| N1 |
C2 |
N2 |
116.3 |
119.0 |
| N1 |
C2 |
N3 |
123.7 |
121.9 |
| N2 |
C2 |
N3 |
120.0 |
119.1 |
| C2 |
N2 |
HN21 |
119.7 |
120.0 |
| C2 |
N2 |
HN22 |
120.1 |
120.0 |
| C2 |
N3 |
C4 |
112.2 |
121.1 |
| HN21 |
N2 |
HN22 |
120.2 |
120.1 |
Torsion Angles for LGP
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP1 |
OP3 |
236.1 |
120.0 |
| OP2 |
P |
OP1 |
O5' |
124.4 |
240.0 |
| OP1 |
P |
OP2 |
HOP2 |
180.0 |
300.0 |
| OP3 |
P |
OP1 |
O5' |
248.4 |
120.1 |
| OP1 |
P |
OP3 |
HOP3 |
180.0 |
180.0 |
| OP1 |
P |
O5' |
C5' |
126.6 |
60.0 |
| OP1 |
P |
OP2 |
OP3 |
124.0 |
240.0 |
| OP1 |
P |
OP2 |
O5' |
235.8 |
120.0 |
| OP3 |
P |
OP2 |
O5' |
111.8 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
310.7 |
60.1 |
| OP2 |
P |
O5' |
C5' |
355.6 |
180.0 |
| OP1 |
P |
OP3 |
OP2 |
229.3 |
119.9 |
| OP1 |
P |
OP3 |
O5' |
114.4 |
240.0 |
| OP2 |
P |
OP3 |
O5' |
245.2 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
56.0 |
59.9 |
| OP3 |
P |
O5' |
C5' |
241.1 |
300.0 |
| OP1 |
P |
O5' |
OP2 |
131.0 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
245.5 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
114.5 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
304.2 |
180.0 |
| O5' |
P |
OP3 |
HOP3 |
65.5 |
300.1 |
| P |
O5' |
C5' |
C4' |
214.1 |
180.0 |
| P |
O5' |
C5' |
H5' |
93.6 |
60.0 |
| P |
O5' |
C5' |
H5'' |
335.3 |
300.0 |
| HOP2 |
OP2 |
P |
OP3 |
56.0 |
59.9 |
| HOP2 |
OP2 |
P |
O5' |
304.2 |
180.0 |
| HOP3 |
OP3 |
P |
O5' |
65.5 |
300.1 |
| C4' |
C5' |
O5' |
H5' |
120.5 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
238.8 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
346.6 |
60.0 |
| O5' |
C5' |
C4' |
C3' |
110.9 |
180.0 |
| O5' |
C5' |
C4' |
H4' |
229.1 |
300.0 |
| H5' |
C5' |
O5' |
H5'' |
118.3 |
120.0 |
| O5' |
C5' |
C4' |
H5' |
239.5 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
121.2 |
120.0 |
| H5' |
C5' |
C4' |
H5'' |
241.7 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
235.7 |
240.0 |
| O4' |
C4' |
C5' |
H4' |
117.5 |
120.0 |
| C5' |
C4' |
O4' |
C1' |
291.2 |
210.0 |
| C3' |
C4' |
C5' |
H4' |
241.7 |
240.0 |
| C5' |
C4' |
C3' |
O3' |
22.9 |
300.0 |
| C5' |
C4' |
C3' |
H3'1 |
262.6 |
60.0 |
| C5' |
C4' |
C3' |
H3'2 |
142.5 |
180.0 |
| O5' |
C5' |
H5' |
C4' |
123.0 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
241.5 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
118.5 |
120.0 |
| H5' |
C5' |
C4' |
O4' |
107.1 |
179.9 |
| H5' |
C5' |
C4' |
C3' |
231.3 |
300.0 |
| H5' |
C5' |
C4' |
H4' |
349.6 |
60.0 |
| O5' |
C5' |
H5'' |
C4' |
236.5 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
118.2 |
119.9 |
| C4' |
C5' |
H5'' |
H5' |
241.7 |
240.0 |
| H5'' |
C5' |
C4' |
O4' |
225.4 |
299.9 |
| H5'' |
C5' |
C4' |
C3' |
349.6 |
60.0 |
| H5'' |
C5' |
C4' |
H4' |
107.9 |
180.0 |
| O4' |
C4' |
C5' |
H5' |
107.1 |
179.9 |
| O4' |
C4' |
C5' |
H5'' |
225.4 |
299.9 |
| C5' |
C4' |
O4' |
C3' |
124.2 |
120.0 |
| C5' |
C4' |
O4' |
H4' |
241.9 |
240.0 |
| C3' |
C4' |
O4' |
H4' |
117.7 |
120.0 |
| O4' |
C4' |
C3' |
O3' |
146.7 |
60.0 |
| O4' |
C4' |
C3' |
H3'1 |
26.4 |
180.0 |
| O4' |
C4' |
C3' |
H3'2 |
266.2 |
300.0 |
| C4' |
O4' |
C1' |
N9 |
188.6 |
180.0 |
| C4' |
O4' |
C1' |
H1'1 |
68.3 |
60.1 |
| C4' |
O4' |
C1' |
H1'2 |
309.6 |
300.1 |
| C3' |
C4' |
C5' |
H5' |
231.3 |
300.0 |
| C3' |
C4' |
C5' |
H5'' |
349.6 |
60.0 |
| C5' |
C4' |
C3' |
O4' |
236.2 |
240.0 |
| C5' |
C4' |
C3' |
H4' |
118.7 |
120.0 |
| O4' |
C4' |
C3' |
H4' |
242.4 |
240.0 |
| C3' |
C4' |
O4' |
C1' |
167.0 |
89.9 |
| O3' |
C3' |
C4' |
H3'1 |
120.3 |
240.0 |
| O3' |
C3' |
C4' |
H3'2 |
240.4 |
120.0 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| H3'1 |
C3' |
C4' |
H3'2 |
120.1 |
240.0 |
| H4' |
C4' |
C5' |
H5' |
349.6 |
60.0 |
| H4' |
C4' |
C5' |
H5'' |
107.9 |
180.0 |
| C5' |
C4' |
H4' |
O4' |
119.4 |
120.0 |
| C5' |
C4' |
H4' |
C3' |
239.5 |
240.0 |
| O4' |
C4' |
H4' |
C3' |
120.1 |
120.0 |
| H4' |
C4' |
O4' |
C1' |
49.3 |
329.9 |
| H4' |
C4' |
C3' |
O3' |
264.3 |
180.0 |
| H4' |
C4' |
C3' |
H3'1 |
143.9 |
300.0 |
| H4' |
C4' |
C3' |
H3'2 |
23.8 |
60.0 |
| C1' |
O4' |
C4' |
C3' |
167.0 |
89.9 |
| C1' |
O4' |
C4' |
H4' |
49.3 |
329.9 |
| N9 |
C1' |
O4' |
H1'1 |
120.4 |
119.9 |
| N9 |
C1' |
O4' |
H1'2 |
239.0 |
239.9 |
| O4' |
C1' |
N9 |
C8 |
296.8 |
0.1 |
| O4' |
C1' |
N9 |
C4 |
118.3 |
180.0 |
| H1'1 |
C1' |
O4' |
H1'2 |
118.6 |
120.0 |
| O3' |
C3' |
C4' |
H4' |
264.3 |
180.0 |
| C4' |
C3' |
O3' |
H3'1 |
239.5 |
120.0 |
| C4' |
C3' |
O3' |
H3'2 |
119.9 |
240.0 |
| H3'1 |
C3' |
O3' |
H3'2 |
240.4 |
120.0 |
| H3'1 |
C3' |
C4' |
H4' |
143.9 |
300.0 |
| C4' |
C3' |
H3'1 |
O3' |
121.2 |
240.0 |
| C4' |
C3' |
H3'1 |
H3'2 |
240.2 |
120.0 |
| O3' |
C3' |
H3'1 |
H3'2 |
119.0 |
240.0 |
| H3'1 |
C3' |
O3' |
HO3' |
300.5 |
60.0 |
| H3'2 |
C3' |
C4' |
H4' |
23.8 |
60.0 |
| C4' |
C3' |
H3'2 |
O3' |
239.2 |
120.0 |
| C4' |
C3' |
H3'2 |
H3'1 |
120.0 |
239.9 |
| O3' |
C3' |
H3'2 |
H3'1 |
240.7 |
119.9 |
| H3'2 |
C3' |
O3' |
HO3' |
60.2 |
300.0 |
| HO3' |
O3' |
C3' |
H3'1 |
300.5 |
60.0 |
| HO3' |
O3' |
C3' |
H3'2 |
60.2 |
300.0 |
| O4' |
C1' |
N9 |
H1'1 |
240.0 |
240.1 |
| O4' |
C1' |
N9 |
H1'2 |
121.3 |
120.1 |
| H1'1 |
C1' |
N9 |
H1'2 |
241.4 |
240.0 |
| C8 |
N9 |
C1' |
C4 |
178.6 |
180.1 |
| C1' |
N9 |
C8 |
N7 |
181.4 |
179.9 |
| C1' |
N9 |
C8 |
H8 |
2.6 |
359.9 |
| C1' |
N9 |
C4 |
C5 |
178.8 |
180.1 |
| C1' |
N9 |
C4 |
N3 |
358.6 |
0.1 |
| O4' |
C1' |
H1'1 |
N9 |
122.3 |
119.9 |
| O4' |
C1' |
H1'1 |
H1'2 |
241.0 |
240.0 |
| N9 |
C1' |
H1'1 |
H1'2 |
118.7 |
120.0 |
| H1'1 |
C1' |
N9 |
C8 |
56.9 |
120.1 |
| H1'1 |
C1' |
N9 |
C4 |
238.3 |
299.9 |
| O4' |
C1' |
H1'2 |
N9 |
237.1 |
239.9 |
| O4' |
C1' |
H1'2 |
H1'1 |
118.4 |
120.0 |
| N9 |
C1' |
H1'2 |
H1'1 |
241.3 |
240.1 |
| H1'2 |
C1' |
N9 |
C8 |
175.5 |
240.1 |
| H1'2 |
C1' |
N9 |
C4 |
357.0 |
59.9 |
| C8 |
N9 |
C1' |
H1'1 |
56.9 |
120.1 |
| C8 |
N9 |
C1' |
H1'2 |
175.5 |
240.1 |
| C1' |
N9 |
C8 |
C4 |
181.2 |
179.9 |
| C8 |
N9 |
C4 |
C5 |
359.9 |
360.0 |
| C8 |
N9 |
C4 |
N3 |
179.8 |
180.0 |
| N7 |
C8 |
N9 |
H8 |
178.8 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
359.8 |
0.0 |
| C4 |
N9 |
C1' |
H1'1 |
238.3 |
299.9 |
| C4 |
N9 |
C1' |
H1'2 |
357.0 |
59.9 |
| C1' |
N9 |
C4 |
C8 |
178.9 |
180.1 |
| C4 |
N9 |
C8 |
N7 |
0.2 |
0.0 |
| C4 |
N9 |
C8 |
H8 |
181.4 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
360.0 |
0.0 |
| C6 |
C5 |
C4 |
N9 |
179.8 |
180.0 |
| C5 |
C4 |
N9 |
N3 |
180.2 |
180.0 |
| C2 |
N3 |
C4 |
N9 |
180.4 |
179.9 |
| N7 |
C8 |
N9 |
C4 |
0.2 |
0.0 |
| N9 |
C8 |
N7 |
H8 |
181.2 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
180.3 |
180.0 |
| C8 |
N7 |
C5 |
C4 |
0.1 |
360.0 |
| H8 |
C8 |
N9 |
C4 |
181.4 |
180.0 |
| N9 |
C8 |
H8 |
N7 |
178.8 |
179.9 |
| H8 |
C8 |
N7 |
C5 |
178.6 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
360.0 |
0.0 |
| C5 |
N7 |
C8 |
H8 |
178.6 |
180.0 |
| C6 |
C5 |
N7 |
C4 |
180.2 |
180.0 |
| N7 |
C5 |
C6 |
O6 |
359.7 |
360.0 |
| N7 |
C5 |
C6 |
N1 |
179.6 |
179.7 |
| N7 |
C5 |
C4 |
N3 |
180.1 |
180.1 |
| N9 |
C4 |
C5 |
C6 |
179.8 |
180.0 |
| N7 |
C5 |
C6 |
C4 |
179.8 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
360.0 |
0.0 |
| O6 |
C6 |
C5 |
N1 |
180.1 |
180.2 |
| C5 |
C6 |
N1 |
C2 |
0.1 |
0.5 |
| C5 |
C6 |
N1 |
HN1 |
180.6 |
180.0 |
| N9 |
C4 |
C5 |
N3 |
179.8 |
180.0 |
| N7 |
C5 |
C4 |
C6 |
180.2 |
180.0 |
| C4 |
C5 |
C6 |
O6 |
179.9 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
359.8 |
359.8 |
| C2 |
N3 |
C4 |
C5 |
0.3 |
359.9 |
| O6 |
C6 |
C5 |
C4 |
179.9 |
180.0 |
| C5 |
C6 |
O6 |
N1 |
179.9 |
179.7 |
| O6 |
C6 |
N1 |
C2 |
180.1 |
180.3 |
| O6 |
C6 |
N1 |
HN1 |
0.5 |
359.8 |
| N1 |
C6 |
C5 |
C4 |
359.8 |
359.8 |
| C5 |
C6 |
N1 |
O6 |
180.1 |
180.2 |
| C2 |
N1 |
C6 |
HN1 |
179.6 |
180.5 |
| C6 |
N1 |
C2 |
N2 |
180.4 |
179.8 |
| C6 |
N1 |
C2 |
N3 |
0.1 |
359.4 |
| C6 |
N1 |
C2 |
HN1 |
180.4 |
179.5 |
| N2 |
C2 |
N1 |
N3 |
180.3 |
180.4 |
| N1 |
C2 |
N2 |
HN21 |
179.9 |
179.7 |
| N1 |
C2 |
N2 |
HN22 |
1.1 |
359.4 |
| N1 |
C2 |
N3 |
C4 |
359.7 |
0.4 |
| C6 |
N1 |
HN1 |
C2 |
179.6 |
180.5 |
| HN1 |
N1 |
C2 |
N2 |
359.9 |
0.3 |
| HN1 |
N1 |
C2 |
N3 |
179.6 |
179.9 |
| N2 |
C2 |
N1 |
HN1 |
359.9 |
0.3 |
| N1 |
C2 |
N2 |
N3 |
179.7 |
179.6 |
| N2 |
C2 |
N3 |
C4 |
179.4 |
180.0 |
| HN21 |
N2 |
C2 |
HN22 |
178.8 |
180.4 |
| N9 |
C4 |
N3 |
C2 |
180.4 |
179.9 |
| C5 |
C4 |
N3 |
C2 |
0.3 |
359.9 |
| N3 |
C2 |
N1 |
HN1 |
179.6 |
179.9 |
| N1 |
C2 |
N3 |
N2 |
180.3 |
180.4 |
| N3 |
C2 |
N2 |
HN21 |
0.2 |
0.1 |
| N3 |
C2 |
N2 |
HN22 |
181.4 |
179.7 |
| HN21 |
N2 |
C2 |
N3 |
0.2 |
0.1 |
| C2 |
N2 |
HN21 |
HN22 |
181.2 |
179.6 |
| HN22 |
N2 |
C2 |
N3 |
181.4 |
179.7 |
| C2 |
N2 |
HN22 |
HN21 |
178.8 |
180.4 |
| N9 |
C4 |
N3 |
C5 |
180.2 |
180.0 |