PDB Chemical Component D33
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 D33
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C4 |
H44 |
1.080 |
1.080 |
| C5 |
C4 |
1.375 |
1.346 |
| C2 |
N3 |
1.323 |
1.306 |
| N1 |
C5 |
1.383 |
1.369 |
| N1 |
C2 |
1.371 |
1.350 |
| P |
O5' |
1.609 |
1.611 |
| P |
OP2 |
1.479 |
1.609 |
| OP1 |
P |
1.480 |
1.479 |
| OP2 |
HOP2 |
0.950 |
0.968 |
| C5' |
O5' |
1.428 |
1.428 |
| C5' |
C4' |
1.528 |
1.530 |
| C5' |
H25' |
1.100 |
1.091 |
| C4' |
O4' |
1.430 |
1.444 |
| C4' |
C3' |
1.527 |
1.550 |
| O4' |
C1' |
1.433 |
1.437 |
| C1' |
N1 |
1.478 |
1.465 |
| C1' |
C2' |
1.530 |
1.541 |
| N3 |
C4 |
1.378 |
1.342 |
| C2' |
H22' |
1.100 |
1.091 |
| C2' |
H12' |
1.100 |
1.090 |
| C3' |
C2' |
1.527 |
1.548 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
C3' |
1.434 |
1.429 |
| O3' |
HO3' |
0.950 |
0.967 |
| H15' |
C5' |
1.100 |
1.090 |
| H4' |
C4' |
1.100 |
1.090 |
| H1' |
C1' |
1.100 |
1.090 |
| H55 |
C5 |
1.080 |
1.080 |
| H22 |
C2 |
1.080 |
1.080 |
| P |
OP3 |
1.720 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for D33
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5 |
C4 |
H44 |
124.9 |
126.0 |
| N3 |
C4 |
H44 |
124.9 |
126.0 |
| N1 |
C2 |
N3 |
112.2 |
108.7 |
| OP2 |
P |
O5' |
108.3 |
109.5 |
| OP1 |
P |
O5' |
108.1 |
109.4 |
| O5' |
P |
OP3 |
101.5 |
109.5 |
| OP1 |
P |
OP2 |
120.0 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| OP2 |
P |
OP3 |
93.9 |
109.5 |
| OP1 |
P |
OP3 |
122.9 |
109.5 |
| C4' |
C5' |
H25' |
108.7 |
109.4 |
| C5' |
C4' |
O4' |
109.6 |
110.6 |
| C5' |
C4' |
C3' |
109.0 |
110.6 |
| H15' |
C5' |
H25' |
111.2 |
109.5 |
| O4' |
C4' |
C3' |
108.0 |
103.5 |
| C4' |
O4' |
C1' |
110.5 |
107.0 |
| C4' |
C3' |
C2' |
105.7 |
102.1 |
| C4' |
C3' |
H3' |
112.5 |
110.9 |
| O4' |
C1' |
C2' |
107.1 |
107.3 |
| C1' |
C2' |
H22' |
110.8 |
110.5 |
| C1' |
C2' |
H12' |
111.7 |
110.5 |
| H22' |
C2' |
H12' |
106.4 |
110.4 |
| C3' |
C2' |
H22' |
110.9 |
110.5 |
| C3' |
C2' |
H12' |
111.7 |
110.7 |
| O3' |
C3' |
H3' |
108.6 |
110.8 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
Torsion Angles for D33
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N3 |
C4 |
C5 |
H44 |
180.0 |
180.2 |
| C2 |
N3 |
C4 |
H44 |
180.2 |
179.8 |
| N1 |
C5 |
C4 |
H44 |
179.5 |
180.0 |
| OP1 |
P |
O5' |
OP2 |
228.6 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
143.0 |
60.0 |
| OP2 |
P |
O5' |
OP3 |
262.0 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
130.6 |
120.0 |
| O5' |
P |
OP3 |
HOP3 |
76.3 |
180.0 |
| OP1 |
P |
OP2 |
O5' |
124.6 |
120.0 |
| O5' |
P |
OP2 |
OP3 |
103.5 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
228.1 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
185.8 |
300.0 |
| OP2 |
P |
OP1 |
O5' |
235.3 |
240.0 |
| O5' |
P |
OP1 |
OP3 |
242.4 |
240.0 |
| OP1 |
P |
OP2 |
HOP2 |
267.6 |
180.0 |
| OP2 |
P |
OP1 |
OP3 |
117.8 |
120.0 |
| OP1 |
P |
OP3 |
HOP3 |
315.6 |
60.1 |
| HOP2 |
OP2 |
P |
O5' |
143.0 |
60.0 |
| HOP2 |
OP2 |
P |
OP3 |
39.5 |
300.0 |
| C5' |
O5' |
P |
OP3 |
275.5 |
185.0 |
| H15' |
C5' |
C4' |
H25' |
239.1 |
120.0 |
| O4' |
C4' |
C5' |
C3' |
242.1 |
246.0 |
| C5' |
C4' |
O4' |
C1' |
133.0 |
158.5 |
| C5' |
C4' |
C3' |
C2' |
237.4 |
204.5 |
| C5' |
C4' |
C3' |
H3' |
359.4 |
322.7 |
| H25' |
C5' |
C4' |
O4' |
207.0 |
186.5 |
| H25' |
C5' |
C4' |
C3' |
324.9 |
300.5 |
| O4' |
C4' |
C5' |
H25' |
207.0 |
186.5 |
| C5' |
C4' |
O4' |
C3' |
118.6 |
118.5 |
| O4' |
C4' |
C3' |
C2' |
356.4 |
323.0 |
| O4' |
C4' |
C3' |
H3' |
118.3 |
81.2 |
| C4' |
O4' |
C1' |
C2' |
340.7 |
333.5 |
| C3' |
C4' |
C5' |
H25' |
324.9 |
300.5 |
| C5' |
C4' |
C3' |
O4' |
241.0 |
241.5 |
| C3' |
C4' |
O4' |
C1' |
14.4 |
40.1 |
| C4' |
C3' |
C2' |
H22' |
232.5 |
262.2 |
| C4' |
C3' |
C2' |
H12' |
114.1 |
139.6 |
| O3' |
C3' |
C4' |
H3' |
120.3 |
123.6 |
| C1' |
O4' |
C4' |
C3' |
14.4 |
40.1 |
| O4' |
C1' |
C2' |
H22' |
136.1 |
120.7 |
| O4' |
C1' |
C2' |
H12' |
254.6 |
243.2 |
| C1' |
N1 |
C2 |
N3 |
176.6 |
179.8 |
| C4' |
C3' |
C2' |
C1' |
352.5 |
20.9 |
| H22' |
C2' |
C1' |
H12' |
241.6 |
237.5 |
| C3' |
C2' |
C1' |
H22' |
240.0 |
241.3 |
| C3' |
C2' |
C1' |
H12' |
121.6 |
118.9 |
| C5 |
C4 |
N3 |
H44 |
180.0 |
179.8 |
| C1' |
C2' |
H22' |
H12' |
121.7 |
122.5 |
| C3' |
C2' |
H22' |
H12' |
238.3 |
237.3 |
| C1' |
C2' |
H12' |
H22' |
238.9 |
237.5 |
| C3' |
C2' |
H12' |
H22' |
121.1 |
122.6 |
| C4' |
C3' |
C2' |
H3' |
122.5 |
118.2 |
| C1' |
C2' |
C3' |
H22' |
120.0 |
118.7 |
| C1' |
C2' |
C3' |
H12' |
238.4 |
241.3 |
| H22' |
C2' |
C3' |
H12' |
118.5 |
122.6 |
| C4' |
C3' |
H3' |
C2' |
241.5 |
247.3 |
| H3' |
C3' |
C2' |
H22' |
110.0 |
144.0 |
| H3' |
C3' |
C2' |
H12' |
351.5 |
21.4 |
| C4' |
C3' |
O3' |
H3' |
237.3 |
236.3 |
| O3' |
C3' |
C2' |
H22' |
349.6 |
20.4 |
| O3' |
C3' |
C2' |
H12' |
231.2 |
257.8 |
| HO3' |
O3' |
C3' |
H3' |
301.5 |
303.7 |
| C4' |
C5' |
H15' |
H25' |
119.4 |
240.0 |
| H4' |
C4' |
C3' |
H3' |
239.1 |
199.7 |
| H1' |
C1' |
C2' |
H22' |
15.3 |
1.2 |
| H1' |
C1' |
C2' |
H12' |
133.7 |
123.7 |
| H55 |
C5 |
C4 |
H44 |
359.5 |
0.1 |
| OP2 |
P |
OP3 |
O5' |
109.5 |
120.0 |
| OP1 |
P |
OP3 |
O5' |
239.3 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
129.8 |
120.1 |
| OP3 |
P |
OP2 |
HOP2 |
39.5 |
300.0 |