PDB Chemical Component 0R5
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 0R5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3G |
PG |
1.507 |
1.480 |
| O2G |
PG |
1.489 |
1.610 |
| PG |
O1G |
1.515 |
1.610 |
| PG |
O3B |
1.635 |
1.610 |
| O2B |
PB |
1.503 |
1.480 |
| O1A |
PA |
1.474 |
1.480 |
| O3B |
PB |
1.625 |
1.610 |
| PB |
O1B |
1.507 |
1.610 |
| PB |
O3A |
1.618 |
1.610 |
| C5' |
O5' |
1.434 |
1.429 |
| C5' |
C4' |
1.527 |
1.530 |
| PA |
O3A |
1.620 |
1.610 |
| PA |
O5' |
1.597 |
1.611 |
| PA |
O2A |
1.516 |
1.610 |
| O3' |
C3' |
1.433 |
1.429 |
| C4' |
C3' |
1.530 |
1.545 |
| C4' |
O4' |
1.441 |
1.444 |
| C3' |
C2' |
1.524 |
1.545 |
| O4' |
C1' |
1.441 |
1.445 |
| C2' |
C1' |
1.522 |
1.545 |
| C35 |
C36 |
1.399 |
1.366 |
| C35 |
C34 |
1.392 |
1.397 |
| C1' |
N1 |
1.484 |
1.464 |
| C36 |
C31 |
1.395 |
1.399 |
| C38 |
C37 |
1.282 |
1.174 |
| C37 |
C34 |
1.287 |
1.431 |
| C34 |
C33 |
1.398 |
1.398 |
| C6 |
N1 |
1.348 |
1.364 |
| C6 |
C5 |
1.368 |
1.370 |
| N1 |
C2 |
1.416 |
1.343 |
| C31 |
C30 |
1.295 |
1.431 |
| C31 |
C32 |
1.399 |
1.400 |
| C30 |
C5M |
1.192 |
1.174 |
| C5M |
C5 |
1.300 |
1.431 |
| C5 |
C4 |
1.503 |
1.471 |
| C33 |
C32 |
1.391 |
1.366 |
| C2 |
O2 |
1.262 |
1.216 |
| C2 |
N3 |
1.348 |
1.344 |
| C4 |
N3 |
1.347 |
1.350 |
| C4 |
O4 |
1.252 |
1.218 |
| O2G |
H1 |
0.950 |
0.967 |
| O1G |
H2 |
0.950 |
0.967 |
| O1B |
H3 |
0.950 |
0.967 |
| O2A |
H4 |
0.950 |
0.966 |
| C5' |
H5 |
1.100 |
1.090 |
| C5' |
H6 |
1.100 |
1.089 |
| C4' |
H7 |
1.100 |
1.090 |
| C3' |
H8 |
1.100 |
1.090 |
| O3' |
H9 |
0.950 |
0.967 |
| C2' |
H10 |
1.100 |
1.090 |
| C2' |
H11 |
1.100 |
1.090 |
| C1' |
H12 |
1.100 |
1.090 |
| N3 |
H13 |
1.000 |
0.969 |
| C6 |
H14 |
1.080 |
1.080 |
| C36 |
H15 |
1.080 |
1.080 |
| C35 |
H16 |
1.079 |
1.080 |
| C38 |
H17 |
1.060 |
1.050 |
| C33 |
H18 |
1.080 |
1.079 |
| C32 |
H19 |
1.080 |
1.080 |
Bond Angles for 0R5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3G |
PG |
O3B |
100.7 |
109.5 |
| O2G |
PG |
O1G |
102.9 |
109.4 |
| O2G |
PG |
O3B |
114.9 |
109.5 |
| PG |
O2G |
H1 |
109.5 |
114.0 |
| O1G |
PG |
O3B |
105.7 |
109.5 |
| PG |
O1G |
H2 |
109.5 |
114.0 |
| PG |
O3B |
PB |
133.5 |
134.0 |
| O2B |
PB |
O3A |
114.3 |
109.4 |
| O1A |
PA |
O5' |
107.6 |
109.4 |
| O1A |
PA |
O2A |
113.4 |
109.5 |
| O3B |
PB |
O1B |
105.9 |
109.5 |
| O3B |
PB |
O3A |
99.7 |
109.5 |
| O1B |
PB |
O3A |
107.5 |
109.5 |
| PB |
O1B |
H3 |
109.5 |
114.0 |
| C5' |
C4' |
C3' |
110.2 |
110.4 |
| C5' |
C4' |
O4' |
112.5 |
110.4 |
| C4' |
C5' |
H5 |
110.5 |
109.5 |
| C4' |
C5' |
H6 |
110.5 |
109.5 |
| C5' |
C4' |
H7 |
109.7 |
110.3 |
| O2A |
PA |
O5' |
110.6 |
109.4 |
| PA |
O2A |
H4 |
109.5 |
114.0 |
| O3' |
C3' |
C2' |
112.9 |
110.5 |
| O3' |
C3' |
H8 |
109.6 |
110.6 |
| C3' |
C4' |
O4' |
103.7 |
104.8 |
| C4' |
C3' |
C2' |
102.8 |
104.0 |
| C3' |
C4' |
H7 |
109.7 |
110.3 |
| C4' |
C3' |
H8 |
108.3 |
110.5 |
| C4' |
O4' |
C1' |
110.1 |
105.3 |
| O4' |
C4' |
H7 |
111.0 |
110.5 |
| C3' |
C2' |
C1' |
102.4 |
104.1 |
| C2' |
C3' |
H8 |
108.4 |
110.5 |
| C3' |
C2' |
H10 |
111.2 |
110.5 |
| C3' |
C2' |
H11 |
111.2 |
110.5 |
| C2' |
C1' |
O4' |
107.2 |
104.8 |
| O4' |
C1' |
N1 |
111.5 |
110.4 |
| O4' |
C1' |
H12 |
110.7 |
110.3 |
| C2' |
C1' |
N1 |
107.7 |
110.4 |
| C1' |
C2' |
H10 |
111.2 |
110.5 |
| C1' |
C2' |
H11 |
111.2 |
110.5 |
| C2' |
C1' |
H12 |
109.6 |
110.4 |
| C35 |
C36 |
H15 |
119.4 |
120.0 |
| C35 |
C34 |
C33 |
120.2 |
120.0 |
| C34 |
C35 |
H16 |
120.5 |
119.9 |
| C1' |
N1 |
C2 |
118.1 |
119.3 |
| N1 |
C1' |
H12 |
110.1 |
110.4 |
| C36 |
C31 |
C32 |
119.3 |
119.9 |
| C37 |
C34 |
C33 |
121.8 |
120.0 |
| C34 |
C33 |
C32 |
120.4 |
120.1 |
| C34 |
C33 |
H18 |
119.8 |
119.9 |
| C5 |
C6 |
H14 |
119.3 |
120.3 |
| N1 |
C2 |
O2 |
119.4 |
119.0 |
| N1 |
C2 |
N3 |
120.7 |
122.0 |
| C31 |
C32 |
C33 |
119.9 |
120.0 |
| C31 |
C32 |
H19 |
120.0 |
120.0 |
| C32 |
C33 |
H18 |
119.8 |
120.0 |
| C33 |
C32 |
H19 |
120.1 |
120.0 |
| O2 |
C2 |
N3 |
119.8 |
119.0 |
| C2 |
N3 |
H13 |
119.4 |
119.8 |
| C4 |
N3 |
H13 |
119.4 |
119.9 |
| H5 |
C5' |
H6 |
109.5 |
109.5 |
| H10 |
C2' |
H11 |
109.5 |
110.5 |
Torsion Angles for 0R5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2G |
PG |
O3G |
O3B |
125.1 |
120.0 |
| O3G |
PG |
O2G |
H1 |
0.0 |
60.0 |
| O1G |
PG |
O3G |
O3B |
246.6 |
240.0 |
| O3G |
PG |
O1G |
H2 |
360.0 |
180.0 |
| O3G |
PG |
O3B |
PB |
106.0 |
320.0 |
| O3G |
PG |
O2G |
O3B |
242.4 |
240.0 |
| O1G |
PG |
O2G |
O3B |
114.4 |
120.0 |
| O2G |
PG |
O1G |
H2 |
128.6 |
300.0 |
| O2G |
PG |
O3B |
PB |
339.6 |
200.0 |
| O3G |
PG |
O1G |
O3B |
110.5 |
120.0 |
| O2G |
PG |
O1G |
O3B |
239.1 |
240.0 |
| O1G |
PG |
O2G |
H1 |
232.0 |
300.0 |
| O1G |
PG |
O3B |
PB |
226.9 |
80.0 |
| O2G |
PG |
O3B |
O1G |
112.7 |
120.0 |
| O3B |
PG |
O2G |
H1 |
117.6 |
180.0 |
| O3B |
PG |
O1G |
H2 |
249.5 |
59.9 |
| PG |
O3B |
PB |
O1B |
191.2 |
285.0 |
| PG |
O3B |
PB |
O3A |
79.7 |
165.0 |
| O3B |
PB |
O2B |
O3A |
116.5 |
120.0 |
| O1B |
PB |
O2B |
O3A |
238.4 |
240.0 |
| O2B |
PB |
O1B |
H3 |
0.0 |
180.0 |
| O2A |
PA |
O1A |
O5' |
122.7 |
119.9 |
| O1A |
PA |
O2A |
H4 |
0.0 |
180.0 |
| O2B |
PB |
O3B |
O3A |
235.8 |
240.0 |
| O1B |
PB |
O3B |
O3A |
111.5 |
120.0 |
| O3B |
PB |
O1B |
H3 |
128.6 |
300.0 |
| O2B |
PB |
O1B |
O3A |
125.5 |
120.0 |
| O3B |
PB |
O1B |
O3A |
254.1 |
240.0 |
| O3B |
PB |
O3A |
O1B |
110.2 |
120.0 |
| O3A |
PB |
O1B |
H3 |
234.5 |
60.0 |
| C3' |
C4' |
C5' |
O4' |
115.1 |
115.4 |
| C5' |
C4' |
C3' |
C2' |
203.3 |
217.2 |
| C3' |
C4' |
C5' |
H7 |
239.2 |
237.8 |
| C5' |
C4' |
C3' |
H8 |
317.9 |
335.8 |
| C5' |
C4' |
O4' |
C1' |
142.5 |
159.3 |
| O4' |
C4' |
C5' |
H7 |
124.1 |
122.4 |
| H5 |
C5' |
C4' |
H6 |
121.4 |
120.0 |
| O1A |
PA |
O5' |
O2A |
124.4 |
120.0 |
| O5' |
PA |
O2A |
H4 |
121.1 |
300.0 |
| O1A |
PA |
O2A |
O5' |
238.9 |
240.0 |
| O3' |
C3' |
C4' |
O4' |
201.1 |
217.4 |
| C4' |
C3' |
O3' |
C2' |
117.2 |
114.6 |
| O3' |
C3' |
C4' |
H7 |
319.6 |
336.3 |
| C4' |
C3' |
O3' |
H8 |
238.1 |
237.3 |
| O3' |
C3' |
C2' |
C1' |
158.5 |
118.6 |
| C2' |
C3' |
O3' |
H8 |
120.9 |
122.7 |
| O3' |
C3' |
C2' |
H10 |
277.4 |
237.3 |
| O3' |
C3' |
C2' |
H11 |
39.6 |
360.0 |
| C5' |
C4' |
C3' |
O4' |
239.4 |
241.2 |
| C3' |
C4' |
C5' |
H5 |
292.1 |
65.0 |
| C3' |
C4' |
C5' |
H6 |
170.7 |
305.0 |
| C5' |
C4' |
C3' |
H7 |
120.8 |
122.2 |
| O3' |
C3' |
C4' |
C2' |
237.2 |
241.4 |
| O3' |
C3' |
C4' |
H8 |
122.6 |
122.8 |
| C3' |
C4' |
O4' |
C1' |
23.5 |
40.5 |
| O4' |
C4' |
C3' |
H7 |
241.5 |
241.1 |
| C4' |
C3' |
C2' |
C1' |
34.6 |
360.0 |
| C2' |
C3' |
C4' |
H8 |
245.4 |
241.4 |
| C4' |
C3' |
C2' |
H10 |
153.5 |
118.6 |
| C4' |
C3' |
C2' |
H11 |
275.7 |
241.3 |
| C5' |
C4' |
O4' |
C3' |
119.0 |
118.8 |
| O4' |
C4' |
C5' |
H5 |
177.0 |
309.6 |
| O4' |
C4' |
C5' |
H6 |
55.6 |
189.6 |
| C5' |
C4' |
O4' |
H7 |
236.6 |
237.7 |
| O4' |
C4' |
C3' |
C2' |
323.9 |
336.1 |
| C3' |
C4' |
O4' |
H7 |
117.7 |
118.9 |
| O4' |
C4' |
C3' |
H8 |
78.5 |
94.6 |
| C2' |
C1' |
O4' |
C4' |
358.6 |
319.5 |
| C4' |
O4' |
C1' |
N1 |
241.0 |
200.7 |
| C4' |
O4' |
C1' |
H12 |
118.0 |
78.3 |
| O3' |
C3' |
C2' |
H8 |
238.4 |
237.2 |
| C2' |
C3' |
C4' |
O4' |
323.9 |
336.1 |
| C2' |
C3' |
C4' |
H7 |
82.5 |
95.0 |
| C4' |
C3' |
C2' |
H8 |
114.5 |
118.6 |
| C3' |
C2' |
C1' |
O4' |
338.7 |
24.0 |
| C3' |
C2' |
C1' |
N1 |
98.9 |
142.8 |
| C1' |
C2' |
C3' |
H10 |
241.1 |
241.3 |
| C1' |
C2' |
C3' |
H11 |
118.9 |
118.6 |
| C3' |
C2' |
C1' |
H12 |
218.6 |
265.2 |
| H10 |
C2' |
C3' |
H11 |
237.7 |
237.3 |
| C1' |
O4' |
C4' |
H7 |
265.9 |
281.6 |
| C2' |
C1' |
O4' |
N1 |
117.6 |
118.8 |
| O4' |
C1' |
C2' |
H10 |
219.9 |
265.3 |
| O4' |
C1' |
C2' |
H11 |
97.6 |
142.6 |
| C2' |
C1' |
O4' |
H12 |
240.6 |
241.2 |
| O4' |
C1' |
N1 |
C2 |
212.1 |
50.4 |
| N1 |
C1' |
O4' |
H12 |
123.0 |
122.3 |
| C4' |
O4' |
C1' |
C2' |
358.6 |
319.5 |
| C1' |
C2' |
C3' |
H8 |
280.0 |
241.4 |
| C3' |
C2' |
C1' |
H10 |
118.8 |
118.7 |
| C3' |
C2' |
C1' |
H11 |
241.2 |
241.3 |
| O4' |
C1' |
C2' |
N1 |
239.9 |
241.1 |
| O4' |
C1' |
C2' |
H12 |
120.2 |
118.7 |
| C2' |
C1' |
N1 |
C2 |
94.8 |
295.0 |
| N1 |
C1' |
C2' |
H12 |
240.3 |
237.6 |
| H10 |
C2' |
C1' |
H11 |
122.3 |
122.7 |
| C35 |
C36 |
C31 |
C32 |
358.2 |
0.3 |
| C34 |
C35 |
C36 |
H15 |
180.9 |
180.0 |
| C37 |
C34 |
C35 |
C33 |
177.2 |
180.0 |
| C35 |
C34 |
C33 |
C32 |
358.7 |
359.8 |
| C35 |
C34 |
C33 |
H18 |
178.7 |
180.0 |
| C2' |
C1' |
N1 |
O4' |
242.7 |
244.6 |
| O4' |
C1' |
N1 |
H12 |
236.7 |
237.7 |
| N1 |
C1' |
C2' |
H10 |
340.0 |
24.1 |
| N1 |
C1' |
C2' |
H11 |
217.7 |
261.5 |
| C2' |
C1' |
N1 |
H12 |
119.4 |
122.4 |
| C1' |
N1 |
C2 |
O2 |
1.3 |
0.0 |
| C1' |
N1 |
C2 |
N3 |
180.5 |
179.9 |
| C36 |
C31 |
C32 |
C33 |
1.2 |
359.5 |
| C36 |
C31 |
C32 |
H19 |
181.2 |
179.8 |
| C38 |
C37 |
C34 |
C33 |
353.3 |
7.2 |
| C35 |
C34 |
C37 |
C33 |
182.8 |
180.0 |
| C37 |
C34 |
C35 |
H16 |
357.9 |
359.9 |
| C37 |
C34 |
C33 |
C32 |
181.6 |
179.8 |
| C37 |
C34 |
C33 |
H18 |
1.6 |
360.0 |
| C33 |
C34 |
C35 |
H16 |
180.7 |
179.9 |
| C31 |
C32 |
C33 |
C34 |
0.4 |
0.5 |
| C32 |
C33 |
C34 |
H18 |
180.0 |
179.8 |
| C34 |
C33 |
C32 |
H19 |
180.3 |
180.2 |
| C6 |
N1 |
C1' |
H12 |
157.8 |
352.4 |
| C2 |
N1 |
C1' |
H12 |
335.4 |
172.6 |
| O2 |
C2 |
N1 |
N3 |
180.8 |
180.1 |
| N1 |
C2 |
N3 |
H13 |
181.0 |
180.1 |
| C34 |
C33 |
C32 |
C31 |
0.4 |
0.5 |
| C31 |
C32 |
C33 |
H18 |
180.4 |
180.3 |
| C33 |
C32 |
C31 |
H19 |
180.0 |
179.7 |
| C5M |
C5 |
C6 |
H14 |
358.2 |
359.7 |
| C5 |
C4 |
N3 |
H13 |
180.5 |
179.9 |
| C34 |
C33 |
C32 |
H18 |
180.0 |
180.2 |
| C31 |
C32 |
C33 |
H19 |
180.0 |
180.3 |
| N1 |
C2 |
O2 |
N3 |
179.2 |
179.9 |
| O2 |
C2 |
N3 |
H13 |
0.2 |
0.0 |
| N1 |
C2 |
N3 |
O2 |
180.8 |
180.1 |
| C4 |
N3 |
C2 |
H13 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
H13 |
180.0 |
180.0 |
| O4 |
C4 |
N3 |
H13 |
0.1 |
0.0 |
| H1 |
O2G |
PG |
O1G |
232.0 |
300.0 |
| H1 |
O2G |
PG |
O3B |
117.6 |
180.0 |
| H2 |
O1G |
PG |
O3B |
249.5 |
59.9 |
| H3 |
O1B |
PB |
O3A |
234.5 |
60.0 |
| H4 |
O2A |
PA |
O5' |
121.1 |
300.0 |
| H5 |
C5' |
C4' |
C3' |
292.1 |
65.0 |
| H5 |
C5' |
C4' |
O4' |
177.0 |
309.6 |
| C4' |
C5' |
H5 |
H6 |
238.0 |
240.0 |
| H5 |
C5' |
C4' |
H7 |
52.9 |
187.2 |
| H6 |
C5' |
C4' |
C3' |
170.7 |
305.0 |
| H6 |
C5' |
C4' |
O4' |
55.6 |
189.6 |
| C4' |
C5' |
H6 |
H5 |
122.0 |
120.0 |
| H6 |
C5' |
C4' |
H7 |
291.5 |
67.2 |
| C5' |
C4' |
H7 |
C3' |
238.9 |
237.8 |
| C5' |
C4' |
H7 |
O4' |
125.0 |
122.3 |
| H7 |
C4' |
C5' |
H5 |
52.9 |
187.2 |
| H7 |
C4' |
C5' |
H6 |
291.5 |
67.2 |
| C3' |
C4' |
H7 |
O4' |
246.1 |
244.6 |
| H7 |
C4' |
C3' |
C2' |
82.5 |
95.0 |
| H7 |
C4' |
C3' |
H8 |
197.1 |
213.6 |
| H7 |
C4' |
O4' |
C1' |
265.9 |
281.6 |
| O3' |
C3' |
H8 |
C2' |
123.6 |
122.7 |
| H8 |
C3' |
C4' |
O4' |
78.5 |
94.6 |
| C4' |
C3' |
H8 |
C2' |
249.1 |
245.4 |
| H8 |
C3' |
C4' |
H7 |
197.1 |
213.6 |
| H8 |
C3' |
C2' |
C1' |
280.0 |
241.4 |
| H8 |
C3' |
C2' |
H10 |
38.9 |
0.1 |
| H8 |
C3' |
C2' |
H11 |
161.2 |
122.8 |
| H9 |
O3' |
C3' |
C2' |
62.8 |
65.4 |
| H9 |
O3' |
C3' |
H8 |
301.9 |
302.7 |
| C3' |
C2' |
H10 |
C1' |
246.6 |
245.3 |
| H10 |
C2' |
C3' |
H8 |
38.9 |
0.1 |
| C3' |
C2' |
H10 |
H11 |
123.3 |
122.7 |
| H10 |
C2' |
C1' |
O4' |
219.9 |
265.3 |
| H10 |
C2' |
C1' |
N1 |
340.0 |
24.1 |
| C1' |
C2' |
H10 |
H11 |
236.7 |
237.4 |
| H10 |
C2' |
C1' |
H12 |
99.7 |
146.5 |
| C3' |
C2' |
H11 |
C1' |
113.4 |
114.7 |
| H11 |
C2' |
C3' |
H8 |
161.2 |
122.8 |
| C3' |
C2' |
H11 |
H10 |
236.7 |
237.3 |
| H11 |
C2' |
C1' |
O4' |
97.6 |
142.6 |
| H11 |
C2' |
C1' |
N1 |
217.7 |
261.5 |
| C1' |
C2' |
H11 |
H10 |
123.3 |
122.6 |
| H11 |
C2' |
C1' |
H12 |
337.4 |
23.9 |
| C2' |
C1' |
H12 |
O4' |
118.0 |
115.3 |
| O4' |
C1' |
H12 |
N1 |
123.8 |
122.3 |
| C2' |
C1' |
H12 |
N1 |
241.8 |
237.6 |
| H12 |
C1' |
C2' |
H10 |
99.7 |
146.5 |
| H12 |
C1' |
C2' |
H11 |
337.4 |
23.9 |
| H12 |
C1' |
N1 |
C2 |
335.4 |
172.6 |
| H15 |
C36 |
C31 |
C32 |
178.2 |
180.2 |
| H16 |
C35 |
C36 |
H15 |
0.9 |
0.1 |
| H16 |
C35 |
C34 |
C33 |
180.7 |
179.9 |
| C34 |
C33 |
H18 |
C32 |
180.0 |
179.8 |
| H18 |
C33 |
C32 |
H19 |
0.4 |
0.0 |
| C31 |
C32 |
H19 |
C33 |
180.0 |
179.7 |
| H19 |
C32 |
C33 |
H18 |
0.4 |
0.0 |