PDB Chemical Component 5HM
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 5HM
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N4 |
C4 |
1.361 |
1.375 |
| C4 |
N3 |
1.360 |
1.327 |
| C4 |
C5 |
1.495 |
1.410 |
| N3 |
C2 |
1.349 |
1.332 |
| CM5 |
OM5 |
1.439 |
1.430 |
| CM5 |
C5 |
1.503 |
1.507 |
| C5 |
C6 |
1.374 |
1.354 |
| C2 |
O2 |
1.354 |
1.219 |
| C2 |
N1 |
1.336 |
1.345 |
| C6 |
N1 |
1.358 |
1.363 |
| N1 |
C1' |
1.490 |
1.465 |
| OP1 |
P |
1.535 |
1.480 |
| C1' |
O4' |
1.440 |
1.445 |
| C1' |
C2' |
1.521 |
1.545 |
| OP2 |
P |
1.512 |
1.610 |
| O4' |
C4' |
1.440 |
1.444 |
| C2' |
O2' |
1.422 |
1.429 |
| C2' |
C3' |
1.514 |
1.546 |
| P |
O5' |
1.598 |
1.609 |
| P |
OP3 |
1.535 |
1.610 |
| O5' |
C5' |
1.423 |
1.429 |
| C5' |
C4' |
1.511 |
1.530 |
| C4' |
C3' |
1.516 |
1.545 |
| C3' |
O3' |
1.443 |
1.429 |
| OP3 |
H1 |
0.950 |
0.966 |
| OP2 |
H2 |
0.950 |
0.967 |
| C5' |
H3 |
1.100 |
1.091 |
| C5' |
H4 |
1.100 |
1.090 |
| C4' |
H5 |
1.100 |
1.090 |
| C3' |
H6 |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C2' |
H8 |
1.100 |
1.090 |
| O2' |
H9 |
0.950 |
0.967 |
| C1' |
H10 |
1.100 |
1.090 |
| C6 |
H11 |
1.080 |
1.080 |
| CM5 |
H12 |
1.099 |
1.090 |
| CM5 |
H13 |
1.100 |
1.089 |
| OM5 |
H14 |
0.950 |
0.967 |
| N4 |
H15 |
1.000 |
0.970 |
| N4 |
H16 |
1.000 |
0.970 |
Bond Angles for 5HM
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OM5 |
CM5 |
H12 |
110.0 |
109.4 |
| OM5 |
CM5 |
H13 |
110.0 |
109.5 |
| CM5 |
OM5 |
H14 |
109.5 |
114.0 |
| C5 |
C6 |
H11 |
119.2 |
120.4 |
| N1 |
C1' |
H10 |
109.9 |
110.4 |
| OP1 |
P |
O5' |
104.2 |
109.5 |
| C1' |
C2' |
H8 |
108.5 |
110.6 |
| OP2 |
P |
O5' |
100.8 |
109.5 |
| O4' |
C4' |
C3' |
109.8 |
104.8 |
| O4' |
C4' |
H5 |
109.7 |
110.5 |
| O2' |
C2' |
H8 |
109.8 |
110.5 |
| C2' |
O2' |
H9 |
109.5 |
114.0 |
| C2' |
C3' |
H6 |
108.9 |
110.6 |
| P |
O5' |
C5' |
115.0 |
123.1 |
| P |
OP3 |
H1 |
109.5 |
114.0 |
| O5' |
C5' |
C4' |
108.0 |
109.5 |
| O5' |
C5' |
H3 |
109.9 |
109.4 |
| O5' |
C5' |
H4 |
109.8 |
109.5 |
| C5' |
C4' |
C3' |
109.5 |
110.4 |
| C4' |
C5' |
H3 |
109.8 |
109.5 |
| C4' |
C5' |
H4 |
109.8 |
109.5 |
| C5' |
C4' |
H5 |
108.7 |
110.3 |
| C4' |
C3' |
O3' |
112.6 |
110.6 |
| C3' |
C4' |
H5 |
108.6 |
110.3 |
| C4' |
C3' |
H6 |
108.9 |
110.5 |
| O3' |
C3' |
H6 |
109.9 |
110.4 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| H3 |
C5' |
H4 |
109.5 |
109.4 |
| H12 |
CM5 |
H13 |
109.5 |
109.5 |
| H15 |
N4 |
H16 |
120.0 |
120.0 |
Torsion Angles for 5HM
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4 |
C5 |
C6 |
H11 |
180.7 |
180.0 |
| H12 |
CM5 |
OM5 |
H13 |
239.3 |
120.0 |
| CM5 |
C5 |
C6 |
H11 |
359.3 |
0.0 |
| C2 |
N1 |
C1' |
H10 |
313.0 |
175.8 |
| C6 |
N1 |
C1' |
H10 |
132.7 |
355.5 |
| N1 |
C1' |
C2' |
H8 |
350.3 |
24.1 |
| OP2 |
P |
OP1 |
O5' |
250.4 |
120.0 |
| OP1 |
P |
O5' |
C5' |
50.9 |
55.0 |
| OP1 |
P |
OP3 |
H1 |
0.0 |
300.0 |
| C1' |
O4' |
C4' |
H5 |
233.6 |
281.6 |
| O2' |
C2' |
C1' |
H8 |
238.5 |
237.4 |
| C1' |
C2' |
O2' |
H9 |
180.0 |
183.9 |
| C1' |
C2' |
C3' |
H6 |
252.2 |
241.3 |
| OP1 |
P |
OP2 |
O5' |
111.7 |
240.0 |
| OP2 |
P |
O5' |
C5' |
171.2 |
295.0 |
| OP2 |
P |
OP3 |
H1 |
222.5 |
60.0 |
| C5' |
C4' |
O4' |
C3' |
120.9 |
118.9 |
| O4' |
C4' |
C5' |
H3 |
297.4 |
309.6 |
| O4' |
C4' |
C5' |
H4 |
177.0 |
189.6 |
| C5' |
C4' |
O4' |
H5 |
240.2 |
237.7 |
| O4' |
C4' |
C3' |
O3' |
237.1 |
217.4 |
| C3' |
C4' |
O4' |
H5 |
119.3 |
118.8 |
| O4' |
C4' |
C3' |
H6 |
115.0 |
94.8 |
| C1' |
C2' |
O2' |
H8 |
120.7 |
122.7 |
| O2' |
C2' |
C3' |
H6 |
129.7 |
122.7 |
| C2' |
C3' |
C4' |
H5 |
119.0 |
95.0 |
| C4' |
C3' |
C2' |
H6 |
115.9 |
118.6 |
| O3' |
C3' |
C2' |
H6 |
238.0 |
237.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
65.3 |
| O5' |
P |
OP3 |
H1 |
112.6 |
180.0 |
| P |
O5' |
C5' |
C4' |
192.4 |
180.0 |
| P |
O5' |
C5' |
H3 |
312.2 |
300.0 |
| P |
O5' |
C5' |
H4 |
72.6 |
59.9 |
| O5' |
C5' |
C4' |
C3' |
178.3 |
185.0 |
| C4' |
C5' |
O5' |
H3 |
240.2 |
240.0 |
| C4' |
C5' |
O5' |
H4 |
119.7 |
120.1 |
| O5' |
C5' |
C4' |
H5 |
296.8 |
307.2 |
| H3 |
C5' |
O5' |
H4 |
239.5 |
240.1 |
| O4' |
C4' |
C5' |
C3' |
238.9 |
244.5 |
| O4' |
C4' |
C5' |
H5 |
120.4 |
122.4 |
| O5' |
C5' |
C4' |
H3 |
119.8 |
120.0 |
| O5' |
C5' |
C4' |
H4 |
240.3 |
240.0 |
| C5' |
C4' |
C3' |
O3' |
115.7 |
98.5 |
| C3' |
C4' |
C5' |
H5 |
241.5 |
237.8 |
| C5' |
C4' |
C3' |
H6 |
353.5 |
335.9 |
| H3 |
C5' |
C4' |
H4 |
120.5 |
120.0 |
| O4' |
C4' |
C3' |
H5 |
240.0 |
241.1 |
| C2' |
C3' |
C4' |
H6 |
244.1 |
241.3 |
| C3' |
C4' |
C5' |
H3 |
58.5 |
65.1 |
| C3' |
C4' |
C5' |
H4 |
298.1 |
305.1 |
| C5' |
C4' |
C3' |
H5 |
118.6 |
122.2 |
| O3' |
C3' |
C4' |
H6 |
122.1 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
296.9 |
180.0 |
| C2' |
C3' |
O3' |
H6 |
121.5 |
122.7 |
| O3' |
C3' |
C4' |
H5 |
357.1 |
336.3 |
| C4' |
C3' |
O3' |
H6 |
238.4 |
237.4 |
| H2 |
OP2 |
P |
O5' |
248.3 |
300.0 |
| O5' |
C5' |
H3 |
C4' |
241.4 |
240.0 |
| O5' |
C5' |
H3 |
H4 |
120.7 |
119.9 |
| H3 |
C5' |
C4' |
C3' |
58.5 |
65.1 |
| C4' |
C5' |
H3 |
H4 |
239.3 |
240.0 |
| H3 |
C5' |
C4' |
H5 |
177.0 |
187.2 |
| O5' |
C5' |
H4 |
C4' |
118.6 |
120.1 |
| O5' |
C5' |
H4 |
H3 |
239.3 |
240.1 |
| H4 |
C5' |
C4' |
C3' |
298.1 |
305.1 |
| C4' |
C5' |
H4 |
H3 |
120.7 |
120.0 |
| H4 |
C5' |
C4' |
H5 |
56.6 |
67.3 |
| O4' |
C4' |
H5 |
C3' |
120.1 |
115.4 |
| C5' |
C4' |
H5 |
C3' |
240.9 |
237.8 |
| H5 |
C4' |
C5' |
H3 |
177.0 |
187.2 |
| H5 |
C4' |
C5' |
H4 |
56.6 |
67.3 |
| H5 |
C4' |
C3' |
O3' |
357.1 |
336.3 |
| H5 |
C4' |
C3' |
H6 |
235.0 |
213.7 |
| C4' |
C3' |
H6 |
O3' |
123.8 |
122.6 |
| H6 |
C3' |
C4' |
H5 |
235.0 |
213.7 |
| H6 |
C3' |
O3' |
HO3' |
58.5 |
302.6 |
| HO3' |
O3' |
C3' |
H6 |
58.5 |
302.6 |
| H8 |
C2' |
O2' |
H9 |
59.3 |
61.2 |
| H8 |
C2' |
C3' |
H6 |
9.8 |
0.1 |
| H9 |
O2' |
C2' |
H8 |
59.3 |
61.2 |
| H10 |
C1' |
C2' |
H8 |
110.4 |
146.5 |
| OM5 |
CM5 |
H12 |
H13 |
121.0 |
240.0 |
| H12 |
CM5 |
OM5 |
H14 |
219.0 |
60.0 |
| OM5 |
CM5 |
H13 |
H12 |
239.0 |
120.0 |
| H13 |
CM5 |
OM5 |
H14 |
339.7 |
300.0 |
| H14 |
OM5 |
CM5 |
H12 |
219.0 |
60.0 |
| H14 |
OM5 |
CM5 |
H13 |
339.7 |
300.0 |