PDB Chemical Component 5HC
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 5HC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O4' |
C4' |
1.441 |
1.444 |
| O4' |
C1' |
1.431 |
1.443 |
| C4' |
C5' |
1.509 |
1.530 |
| C4' |
C3' |
1.526 |
1.546 |
| O2 |
C2 |
1.231 |
1.220 |
| C1' |
N1 |
1.475 |
1.465 |
| C1' |
C2' |
1.510 |
1.545 |
| C5' |
O5' |
1.434 |
1.428 |
| C2 |
N1 |
1.391 |
1.345 |
| C2 |
N3 |
1.358 |
1.332 |
| N1 |
C6 |
1.369 |
1.363 |
| N3 |
C4 |
1.326 |
1.326 |
| O5' |
P |
1.588 |
1.610 |
| C2' |
C3' |
1.499 |
1.545 |
| C6 |
C5 |
1.338 |
1.354 |
| C3' |
O3' |
1.430 |
1.429 |
| P |
OP1 |
1.484 |
1.480 |
| P |
OP2 |
1.487 |
1.609 |
| C4 |
C5 |
1.428 |
1.411 |
| C4 |
N4 |
1.342 |
1.376 |
| C5 |
C5M |
1.491 |
1.506 |
| C5M |
O5 |
1.425 |
1.430 |
| P |
OP3 |
1.607 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'' |
1.099 |
1.090 |
| C4' |
H4 |
1.100 |
1.090 |
| C3' |
H3' |
1.100 |
1.089 |
| O3' |
HO3' |
0.950 |
0.967 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'' |
1.100 |
1.090 |
| C1' |
H1' |
1.100 |
1.090 |
| N4 |
HN41 |
1.000 |
0.969 |
| N4 |
HN42 |
1.000 |
0.971 |
| C5M |
H5M2 |
1.100 |
1.090 |
| C5M |
H5M1 |
1.100 |
1.091 |
| O5 |
HO5 |
0.950 |
0.967 |
| C6 |
H6 |
1.080 |
1.081 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for 5HC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O4' |
C4' |
C3' |
105.6 |
104.8 |
| O4' |
C4' |
H4 |
109.6 |
110.5 |
| O4' |
C1' |
N1 |
105.4 |
110.4 |
| O4' |
C1' |
C2' |
107.9 |
104.8 |
| O4' |
C1' |
H1' |
110.0 |
110.4 |
| C4' |
C5' |
H5' |
109.4 |
109.5 |
| C4' |
C5' |
H5'' |
109.4 |
109.5 |
| C4' |
C3' |
O3' |
109.2 |
110.5 |
| C3' |
C4' |
H4 |
108.5 |
110.3 |
| C4' |
C3' |
H3' |
109.2 |
110.5 |
| O2 |
C2 |
N3 |
122.0 |
119.4 |
| C1' |
N1 |
C6 |
121.5 |
119.8 |
| N1 |
C1' |
H1' |
109.3 |
110.3 |
| C1' |
C2' |
H2' |
110.4 |
110.5 |
| C1' |
C2' |
H2'' |
110.4 |
110.6 |
| C2 |
N1 |
C6 |
119.8 |
120.3 |
| C2 |
N3 |
C4 |
120.4 |
120.7 |
| N1 |
C6 |
C5 |
121.5 |
119.3 |
| N1 |
C6 |
H6 |
119.3 |
120.4 |
| N3 |
C4 |
C5 |
121.6 |
119.6 |
| N3 |
C4 |
N4 |
118.3 |
120.2 |
| O5' |
P |
OP3 |
104.9 |
109.5 |
| C2' |
C3' |
H3' |
109.6 |
110.7 |
| O3' |
C3' |
H3' |
110.6 |
110.5 |
| C3' |
O3' |
HO3' |
109.5 |
113.9 |
| OP1 |
P |
OP2 |
120.4 |
109.5 |
| OP1 |
P |
OP3 |
107.6 |
109.4 |
| OP2 |
P |
OP3 |
106.7 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| N4 |
C4 |
C5 |
120.1 |
120.2 |
| C4 |
C5 |
C5M |
120.4 |
120.5 |
| C4 |
N4 |
HN41 |
120.0 |
120.0 |
| C4 |
N4 |
HN42 |
120.0 |
120.0 |
| C5 |
C5M |
O5 |
113.9 |
109.5 |
| C5 |
C5M |
H5M2 |
108.3 |
109.5 |
| C5 |
C5M |
H5M1 |
108.3 |
109.5 |
| O5 |
C5M |
H5M2 |
108.4 |
109.5 |
| O5 |
C5M |
H5M1 |
108.4 |
109.4 |
| C5M |
O5 |
HO5 |
109.5 |
114.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| H5' |
C5' |
H5'' |
109.5 |
109.4 |
| H2' |
C2' |
H2'' |
109.5 |
110.4 |
| HN41 |
N4 |
HN42 |
120.0 |
120.0 |
| H5M2 |
C5M |
H5M1 |
109.5 |
109.5 |
Torsion Angles for 5HC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O4' |
C4' |
C5' |
H5' |
68.1 |
309.6 |
| O4' |
C4' |
C5' |
H5'' |
188.0 |
189.7 |
| O4' |
C4' |
C3' |
O3' |
214.9 |
217.4 |
| C3' |
C4' |
O4' |
H4 |
116.7 |
118.9 |
| O4' |
C4' |
C3' |
H3' |
93.9 |
94.8 |
| C1' |
O4' |
C4' |
C3' |
20.7 |
40.5 |
| C1' |
O4' |
C4' |
H4 |
264.0 |
281.7 |
| O4' |
C1' |
N1 |
C6 |
34.6 |
233.5 |
| N1 |
C1' |
O4' |
H1' |
117.7 |
122.2 |
| O4' |
C1' |
C2' |
H2' |
113.5 |
265.3 |
| O4' |
C1' |
C2' |
H2'' |
234.7 |
142.7 |
| H5' |
C5' |
C4' |
H5'' |
240.1 |
119.9 |
| O4' |
C4' |
C3' |
H4 |
242.6 |
241.0 |
| C3' |
C4' |
C5' |
H5' |
186.8 |
65.0 |
| C3' |
C4' |
C5' |
H5'' |
306.7 |
305.1 |
| C2' |
C3' |
C4' |
H3' |
242.6 |
241.2 |
| O3' |
C3' |
C4' |
H3' |
121.0 |
122.6 |
| C4' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
180.1 |
180.2 |
| O2 |
C2 |
N3 |
C4 |
180.0 |
180.0 |
| O4' |
C1' |
N1 |
C2' |
118.8 |
115.4 |
| O4' |
C1' |
N1 |
H1' |
241.8 |
237.7 |
| N1 |
C1' |
C2' |
H2' |
231.0 |
24.1 |
| N1 |
C1' |
C2' |
H2'' |
352.1 |
261.5 |
| C2 |
N1 |
C1' |
C6 |
180.2 |
180.3 |
| C1' |
N1 |
C6 |
C5 |
180.0 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
0.0 |
360.0 |
| O4' |
C1' |
C2' |
N1 |
242.6 |
241.2 |
| O4' |
C1' |
C2' |
H1' |
119.3 |
119.0 |
| C1' |
C2' |
C3' |
H3' |
260.7 |
241.3 |
| H2' |
C2' |
C1' |
H2'' |
238.9 |
122.6 |
| C5' |
O5' |
P |
OP3 |
286.1 |
185.0 |
| C1' |
N1 |
C2 |
C6 |
179.8 |
179.7 |
| C2 |
N1 |
C1' |
H1' |
332.9 |
176.1 |
| C2 |
N1 |
C6 |
C5 |
359.8 |
359.5 |
| C2 |
N1 |
C6 |
H6 |
179.8 |
179.7 |
| N3 |
C2 |
N1 |
C6 |
0.1 |
0.3 |
| C2 |
N3 |
C4 |
C5 |
360.0 |
359.9 |
| C2 |
N3 |
C4 |
N4 |
180.0 |
180.0 |
| C6 |
N1 |
C1' |
H1' |
152.8 |
355.8 |
| N4 |
C4 |
N3 |
C5 |
180.0 |
180.1 |
| N3 |
C4 |
C5 |
C5M |
180.1 |
180.0 |
| N3 |
C4 |
N4 |
HN41 |
0.0 |
360.0 |
| N3 |
C4 |
N4 |
HN42 |
180.0 |
180.0 |
| OP1 |
P |
O5' |
OP3 |
114.5 |
119.9 |
| OP2 |
P |
O5' |
OP3 |
246.3 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
235.2 |
59.9 |
| O5' |
P |
OP3 |
HOP3 |
114.7 |
180.0 |
| O4' |
C1' |
C2' |
C3' |
354.1 |
24.0 |
| C2' |
C3' |
C4' |
H4 |
93.8 |
95.0 |
| C4' |
C3' |
C2' |
H3' |
117.2 |
118.7 |
| O3' |
C3' |
C2' |
H3' |
236.2 |
237.3 |
| C2' |
C3' |
O3' |
HO3' |
63.4 |
65.4 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
| C6 |
C5 |
C5M |
H5M2 |
246.0 |
120.2 |
| C6 |
C5 |
C5M |
H5M1 |
4.7 |
240.3 |
| O3' |
C3' |
C4' |
H4 |
332.3 |
336.4 |
| C4' |
C3' |
O3' |
H3' |
239.8 |
237.4 |
| C2' |
C3' |
O3' |
H3' |
123.2 |
122.8 |
| O5' |
P |
OP1 |
OP3 |
247.3 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
122.3 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
0.0 |
179.9 |
| OP1 |
P |
OP3 |
HOP3 |
360.0 |
60.0 |
| O5' |
P |
OP2 |
OP3 |
112.4 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
237.2 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
229.5 |
300.0 |
| N1 |
C6 |
C5 |
C4 |
0.1 |
0.5 |
| N3 |
C4 |
C5 |
N4 |
180.0 |
180.1 |
| C5 |
C4 |
N4 |
HN41 |
180.0 |
180.1 |
| C5 |
C4 |
N4 |
HN42 |
0.0 |
0.1 |
| C4 |
C5 |
C5M |
O5 |
305.2 |
180.0 |
| C4 |
C5 |
C5M |
H5M2 |
65.8 |
300.1 |
| C4 |
C5 |
C5M |
H5M1 |
184.5 |
60.1 |
| N3 |
C4 |
N4 |
C5 |
180.0 |
179.9 |
| N4 |
C4 |
C5 |
C5M |
0.1 |
359.9 |
| HN41 |
N4 |
C4 |
HN42 |
180.0 |
180.0 |
| N1 |
C6 |
C5 |
C5M |
179.9 |
180.3 |
| O5 |
C5M |
C5 |
H5M2 |
239.3 |
240.0 |
| O5 |
C5M |
C5 |
H5M1 |
120.7 |
119.9 |
| C5 |
C5M |
O5 |
HO5 |
180.0 |
180.0 |
| H5M2 |
C5M |
C5 |
H5M1 |
241.3 |
239.9 |
| C5 |
C5M |
O5 |
H5M2 |
120.7 |
120.1 |
| C5 |
C5M |
O5 |
H5M1 |
239.4 |
240.1 |
| H5M2 |
C5M |
O5 |
H5M1 |
118.7 |
120.0 |
| OP1 |
P |
OP3 |
OP2 |
130.4 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
122.8 |
299.9 |
| HOP2 |
OP2 |
P |
OP3 |
122.8 |
299.9 |
| C4' |
C5' |
H5' |
H5'' |
119.9 |
240.0 |
| C4' |
C5' |
H5'' |
H5' |
240.1 |
120.0 |
| O4' |
C4' |
H4 |
C3' |
114.8 |
115.5 |
| H4 |
C4' |
C5' |
H5' |
306.7 |
187.2 |
| H4 |
C4' |
C5' |
H5'' |
66.6 |
67.2 |
| H4 |
C4' |
C3' |
O3' |
332.3 |
336.4 |
| H4 |
C4' |
C3' |
H3' |
211.3 |
213.8 |
| C4' |
C3' |
H3' |
O3' |
120.2 |
122.6 |
| H3' |
C3' |
C4' |
H4 |
211.3 |
213.8 |
| H3' |
C3' |
O3' |
HO3' |
300.2 |
302.6 |
| HO3' |
O3' |
C3' |
H3' |
300.2 |
302.6 |
| C1' |
C2' |
H2' |
H2'' |
121.6 |
237.3 |
| H2' |
C2' |
C3' |
H3' |
141.2 |
0.0 |
| C1' |
C2' |
H2'' |
H2' |
238.4 |
122.7 |
| H2'' |
C2' |
C3' |
H3' |
20.1 |
122.5 |
| O4' |
C1' |
H1' |
N1 |
115.3 |
122.3 |
| O4' |
C1' |
H1' |
C2' |
242.0 |
244.5 |
| H1' |
C1' |
N1 |
C6 |
152.8 |
355.8 |
| H1' |
C1' |
C2' |
H2' |
354.2 |
146.4 |
| H1' |
C1' |
C2' |
H2'' |
115.3 |
23.8 |
| HN41 |
N4 |
C4 |
C5 |
180.0 |
180.1 |
| C4 |
N4 |
HN41 |
HN42 |
180.0 |
180.0 |
| HN42 |
N4 |
C4 |
C5 |
0.0 |
0.1 |
| C4 |
N4 |
HN42 |
HN41 |
180.0 |
180.0 |
| C5 |
C5M |
H5M2 |
O5 |
235.9 |
240.0 |
| C5 |
C5M |
H5M2 |
H5M1 |
117.9 |
120.0 |
| O5 |
C5M |
H5M2 |
H5M1 |
242.0 |
240.1 |
| H5M2 |
C5M |
O5 |
HO5 |
59.3 |
59.9 |
| C5 |
C5M |
H5M1 |
O5 |
124.1 |
119.9 |
| C5 |
C5M |
H5M1 |
H5M2 |
242.1 |
239.9 |
| O5 |
C5M |
H5M1 |
H5M2 |
118.0 |
120.0 |
| H5M1 |
C5M |
O5 |
HO5 |
300.6 |
300.0 |
| HO5 |
O5 |
C5M |
H5M2 |
59.3 |
59.9 |
| HO5 |
O5 |
C5M |
H5M1 |
300.6 |
300.0 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.8 |