PDB Chemical Component R5I
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 R5I
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O1D |
C1D |
1.305 |
1.429 |
| O1B |
PB |
1.488 |
1.480 |
| O2D |
C2D |
1.424 |
1.428 |
| C1D |
C2D |
1.520 |
1.549 |
| C1D |
O4D |
1.421 |
1.444 |
| C2D |
C3D |
1.527 |
1.551 |
| O4D |
C4D |
1.455 |
1.437 |
| O3A |
PB |
1.606 |
1.610 |
| O3A |
PA |
1.603 |
1.610 |
| PB |
O5D |
1.583 |
1.609 |
| PB |
O2B |
1.482 |
1.611 |
| O2A |
PA |
1.494 |
1.480 |
| C5D |
O5D |
1.413 |
1.429 |
| C5D |
C4D |
1.504 |
1.530 |
| C3D |
C4D |
1.526 |
1.541 |
| C3D |
O3D |
1.430 |
1.430 |
| PA |
O1A |
1.523 |
1.610 |
| PA |
O5' |
1.601 |
1.610 |
| O3' |
C3' |
1.428 |
1.428 |
| O5' |
C5' |
1.447 |
1.429 |
| C5' |
C4' |
1.507 |
1.530 |
| C3' |
C4' |
1.527 |
1.544 |
| C3' |
C2' |
1.531 |
1.548 |
| C4' |
O4' |
1.442 |
1.445 |
| C2' |
O2' |
1.409 |
1.429 |
| C2' |
C1' |
1.522 |
1.544 |
| O4' |
C1' |
1.410 |
1.444 |
| C8 |
N9 |
1.385 |
1.362 |
| C8 |
N7 |
1.319 |
1.302 |
| C1' |
N9 |
1.450 |
1.465 |
| N9 |
C4 |
1.367 |
1.368 |
| N7 |
C5 |
1.387 |
1.354 |
| C4 |
C5 |
1.379 |
1.398 |
| C4 |
N3 |
1.364 |
1.340 |
| C5 |
C6 |
1.422 |
1.417 |
| N3 |
C2 |
1.310 |
1.304 |
| C6 |
O1 |
1.245 |
1.219 |
| C6 |
N1 |
1.403 |
1.353 |
| C2 |
N1 |
1.348 |
1.357 |
| N1 |
H1 |
1.000 |
0.970 |
| C2 |
H2 |
1.080 |
1.080 |
| C8 |
H3 |
1.080 |
1.081 |
| C1' |
H4 |
1.100 |
1.090 |
| C4' |
H5 |
1.100 |
1.090 |
| C5' |
H6 |
1.100 |
1.090 |
| C5' |
H7 |
1.101 |
1.089 |
| O1A |
H8 |
0.950 |
0.967 |
| O2B |
H9 |
0.950 |
0.966 |
| C5D |
H10 |
1.100 |
1.090 |
| C5D |
H11 |
1.100 |
1.089 |
| C4D |
H12 |
1.100 |
1.090 |
| C1D |
H13 |
1.100 |
1.090 |
| O1D |
H14 |
0.950 |
0.967 |
| C2D |
H15 |
1.099 |
1.091 |
| O2D |
H16 |
0.950 |
0.968 |
| C3D |
H17 |
1.100 |
1.090 |
| O3D |
H18 |
0.951 |
0.967 |
| C3' |
H19 |
1.100 |
1.090 |
| O3' |
H20 |
0.950 |
0.967 |
| C2' |
H21 |
1.100 |
1.090 |
| O2' |
H22 |
0.950 |
0.967 |
Bond Angles for R5I
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1D |
C1D |
C2D |
101.8 |
110.6 |
| O1D |
C1D |
H13 |
114.1 |
110.7 |
| O1B |
PB |
O5D |
107.7 |
109.5 |
| O2D |
C2D |
C3D |
114.2 |
110.8 |
| O2D |
C2D |
H15 |
110.5 |
110.8 |
| C1D |
C2D |
C3D |
98.8 |
102.1 |
| C2D |
C1D |
H13 |
110.5 |
110.6 |
| C1D |
C2D |
H15 |
109.1 |
110.9 |
| C2D |
C3D |
O3D |
113.3 |
110.5 |
| C3D |
C2D |
H15 |
109.1 |
111.0 |
| C2D |
C3D |
H17 |
110.1 |
110.5 |
| O4D |
C4D |
H12 |
109.6 |
109.9 |
| O3A |
PB |
O5D |
98.4 |
109.5 |
| O3A |
PB |
O2B |
109.7 |
109.5 |
| O2B |
PB |
O5D |
108.8 |
109.5 |
| PB |
O2B |
H9 |
109.5 |
114.0 |
| O2A |
PA |
O1A |
119.0 |
109.5 |
| C4D |
C5D |
H10 |
110.7 |
109.5 |
| C4D |
C5D |
H11 |
110.7 |
109.5 |
| C5D |
C4D |
H12 |
109.0 |
109.8 |
| C3D |
C4D |
H12 |
108.7 |
109.9 |
| O3D |
C3D |
H17 |
111.6 |
110.6 |
| C3D |
O3D |
H18 |
109.5 |
114.0 |
| PA |
O1A |
H8 |
109.5 |
114.0 |
| O3' |
C3' |
C2' |
112.6 |
110.4 |
| O3' |
C3' |
H19 |
110.9 |
110.6 |
| O5' |
C5' |
H6 |
109.4 |
109.5 |
| O5' |
C5' |
H7 |
109.4 |
109.5 |
| C5' |
C4' |
H5 |
108.4 |
110.4 |
| C3' |
C4' |
H5 |
108.2 |
110.4 |
| C3' |
C2' |
O2' |
112.7 |
110.5 |
| C2' |
C3' |
H19 |
109.5 |
110.5 |
| C3' |
C2' |
H21 |
110.6 |
110.5 |
| O2' |
C2' |
H21 |
112.5 |
110.5 |
| C2' |
O2' |
H22 |
109.5 |
114.0 |
| C2' |
C1' |
H4 |
107.8 |
110.4 |
| O4' |
C1' |
H4 |
109.3 |
110.3 |
| N9 |
C8 |
H3 |
123.9 |
125.1 |
| N3 |
C2 |
H2 |
117.8 |
118.9 |
| C6 |
N1 |
H1 |
116.9 |
119.8 |
| C2 |
N1 |
H1 |
116.9 |
119.9 |
| H6 |
C5' |
H7 |
109.5 |
109.4 |
| H10 |
C5D |
H11 |
109.5 |
109.5 |
Torsion Angles for R5I
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1D |
C1D |
C2D |
C3D |
159.4 |
155.5 |
| C2D |
C1D |
O1D |
H13 |
119.1 |
123.0 |
| O1D |
C1D |
C2D |
H15 |
45.6 |
37.2 |
| O3A |
PB |
O1B |
O5D |
254.9 |
240.0 |
| O2B |
PB |
O1B |
O5D |
126.9 |
120.0 |
| O1B |
PB |
O2B |
H9 |
360.0 |
179.9 |
| C1D |
C2D |
O2D |
C3D |
247.1 |
247.3 |
| O2D |
C2D |
C1D |
H13 |
42.8 |
36.6 |
| C1D |
C2D |
O2D |
H15 |
123.7 |
123.7 |
| O2D |
C2D |
C3D |
O3D |
316.4 |
339.6 |
| C3D |
C2D |
O2D |
H15 |
236.6 |
236.4 |
| O2D |
C2D |
C3D |
H17 |
82.1 |
102.3 |
| O1D |
C1D |
C2D |
H13 |
238.4 |
237.0 |
| O2D |
C2D |
C1D |
C3D |
121.8 |
118.1 |
| O2D |
C2D |
C1D |
H15 |
235.6 |
236.4 |
| C1D |
C2D |
C3D |
O3D |
78.3 |
97.8 |
| C3D |
C2D |
C1D |
H15 |
113.8 |
118.3 |
| C1D |
C2D |
C3D |
H17 |
204.1 |
220.5 |
| C1D |
O4D |
C4D |
H12 |
244.8 |
266.9 |
| O2D |
C2D |
C3D |
H15 |
124.2 |
123.5 |
| C3D |
C2D |
C1D |
H13 |
281.1 |
278.5 |
| C1D |
C2D |
C3D |
H15 |
246.1 |
241.7 |
| C2D |
C3D |
C4D |
H12 |
142.5 |
117.6 |
| O3D |
C3D |
C2D |
H17 |
234.3 |
237.3 |
| C2D |
C3D |
O3D |
H18 |
180.0 |
61.5 |
| O4D |
C4D |
C5D |
H10 |
298.5 |
306.7 |
| O4D |
C4D |
C5D |
H11 |
176.9 |
186.7 |
| C5D |
C4D |
O4D |
H12 |
242.1 |
239.0 |
| C3D |
C4D |
O4D |
H12 |
117.8 |
119.5 |
| O1B |
PB |
O3A |
O5D |
111.7 |
120.0 |
| O2B |
PB |
O3A |
O5D |
246.5 |
240.0 |
| O3A |
PB |
O2B |
H9 |
233.0 |
60.0 |
| O3A |
PA |
O1A |
H8 |
120.6 |
300.0 |
| O3A |
PB |
O5D |
O2B |
245.8 |
240.0 |
| O5D |
PB |
O2B |
H9 |
126.4 |
299.9 |
| O1B |
PB |
O2B |
O5D |
233.6 |
240.0 |
| O3A |
PB |
O2B |
O5D |
106.6 |
120.0 |
| O2A |
PA |
O1A |
H8 |
0.0 |
180.0 |
| O4D |
C4D |
C5D |
H12 |
118.3 |
121.0 |
| C3D |
C4D |
C5D |
H12 |
237.3 |
239.0 |
| H10 |
C5D |
C4D |
H11 |
121.6 |
120.0 |
| O4D |
C4D |
C3D |
H12 |
241.6 |
240.5 |
| C3D |
C4D |
C5D |
H10 |
57.5 |
64.7 |
| C3D |
C4D |
C5D |
H11 |
295.9 |
304.7 |
| C5D |
C4D |
C3D |
H12 |
122.9 |
120.9 |
| O3D |
C3D |
C2D |
H15 |
192.2 |
216.0 |
| C2D |
C3D |
O3D |
H17 |
124.9 |
122.7 |
| O3D |
C3D |
C4D |
H12 |
22.3 |
359.0 |
| PA |
O5' |
C5' |
H6 |
358.0 |
60.0 |
| PA |
O5' |
C5' |
H7 |
118.0 |
300.0 |
| O3' |
C3' |
C4' |
H5 |
317.6 |
336.2 |
| O3' |
C3' |
C2' |
O2' |
43.4 |
0.0 |
| C2' |
C3' |
O3' |
H19 |
123.1 |
122.7 |
| O3' |
C3' |
C2' |
H21 |
276.6 |
237.4 |
| O5' |
C5' |
C4' |
H5 |
176.6 |
304.3 |
| H6 |
C5' |
O5' |
H7 |
240.0 |
120.0 |
| C3' |
C4' |
C5' |
H5 |
237.2 |
237.6 |
| C5' |
C4' |
C3' |
H5 |
123.0 |
122.4 |
| O3' |
C3' |
C2' |
H19 |
236.1 |
237.3 |
| C2' |
C3' |
C4' |
H5 |
77.9 |
94.7 |
| O2' |
C2' |
C3' |
H21 |
126.8 |
122.6 |
| C3' |
C2' |
O2' |
H22 |
180.0 |
298.5 |
| C3' |
C2' |
C1' |
H4 |
217.1 |
265.0 |
| C4' |
O4' |
C1' |
H4 |
117.7 |
78.5 |
| O2' |
C2' |
C3' |
H19 |
167.3 |
122.7 |
| C3' |
C2' |
O2' |
H21 |
234.2 |
237.4 |
| O2' |
C2' |
C1' |
H4 |
335.9 |
23.6 |
| O4' |
C1' |
C2' |
H4 |
117.6 |
118.9 |
| C2' |
C1' |
O4' |
H4 |
243.4 |
241.1 |
| C1' |
N9 |
C8 |
H3 |
2.0 |
0.9 |
| C4 |
N3 |
C2 |
H2 |
179.4 |
180.0 |
| C5 |
C6 |
N1 |
H1 |
179.8 |
180.3 |
| N3 |
C2 |
N1 |
H1 |
180.9 |
180.0 |
| C2 |
N1 |
C6 |
H1 |
180.0 |
180.1 |
| C6 |
N1 |
C2 |
H1 |
180.0 |
179.9 |
| H2 |
C2 |
N1 |
H1 |
0.8 |
0.1 |
| O5' |
C5' |
H6 |
H7 |
119.9 |
240.0 |
| H6 |
C5' |
C4' |
H5 |
56.6 |
64.2 |
| O5' |
C5' |
H7 |
H6 |
240.1 |
120.0 |
| H7 |
C5' |
C4' |
H5 |
296.6 |
184.2 |
| H9 |
O2B |
PB |
O5D |
126.4 |
299.9 |
| C4D |
C5D |
H10 |
H11 |
237.7 |
239.9 |
| H10 |
C5D |
C4D |
H12 |
180.2 |
185.7 |
| C4D |
C5D |
H11 |
H10 |
122.3 |
120.0 |
| H11 |
C5D |
C4D |
H12 |
58.6 |
65.6 |
| H12 |
C4D |
C5D |
H10 |
180.2 |
185.7 |
| H12 |
C4D |
C5D |
H11 |
58.6 |
65.6 |
| O1D |
C1D |
H13 |
C2D |
114.0 |
123.0 |
| H13 |
C1D |
C2D |
C3D |
281.1 |
278.5 |
| H13 |
C1D |
C2D |
H15 |
167.3 |
160.2 |
| H14 |
O1D |
C1D |
C2D |
180.0 |
180.0 |
| H14 |
O1D |
C1D |
H13 |
60.9 |
57.0 |
| O2D |
C2D |
H15 |
C3D |
233.7 |
236.5 |
| C1D |
C2D |
H15 |
C3D |
106.9 |
112.8 |
| H15 |
C2D |
C1D |
H13 |
167.3 |
160.2 |
| H15 |
C2D |
C3D |
O3D |
192.2 |
216.0 |
| H15 |
C2D |
C3D |
H17 |
317.9 |
338.7 |
| H16 |
O2D |
C2D |
C3D |
292.9 |
174.1 |
| H16 |
O2D |
C2D |
H15 |
56.3 |
297.8 |
| C2D |
C3D |
H17 |
O3D |
233.3 |
237.4 |
| H17 |
C3D |
C2D |
H15 |
317.9 |
338.7 |
| H17 |
C3D |
C4D |
H12 |
259.4 |
236.2 |
| H17 |
C3D |
O3D |
H18 |
55.1 |
298.8 |
| H18 |
O3D |
C3D |
H17 |
55.1 |
298.8 |
| O3' |
C3' |
H19 |
C2' |
124.8 |
122.6 |
| H19 |
C3' |
C4' |
H5 |
193.0 |
213.5 |
| H19 |
C3' |
C2' |
O2' |
167.3 |
122.7 |
| H19 |
C3' |
C2' |
H21 |
40.4 |
0.1 |
| H20 |
O3' |
C3' |
C2' |
66.8 |
65.4 |
| H20 |
O3' |
C3' |
H19 |
303.8 |
302.7 |
| C3' |
C2' |
H21 |
O2' |
127.0 |
122.6 |
| H21 |
C2' |
C3' |
H19 |
40.4 |
0.1 |
| H21 |
C2' |
O2' |
H22 |
305.8 |
61.1 |
| H21 |
C2' |
C1' |
H4 |
99.5 |
146.4 |
| H22 |
O2' |
C2' |
H21 |
305.8 |
61.1 |