PDB Chemical Component C1Y
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 C1Y
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C8 |
N7 |
1.366 |
1.364 |
| C8 |
C9 |
1.386 |
1.346 |
| N7 |
C5 |
1.335 |
1.374 |
| C9 |
C10 |
1.509 |
1.507 |
| C9 |
C4 |
1.465 |
1.459 |
| C10 |
N1' |
1.462 |
1.469 |
| C5 |
C4 |
1.453 |
1.406 |
| C5 |
C6 |
1.470 |
1.400 |
| N6 |
C6 |
1.349 |
1.385 |
| C4 |
N3 |
1.356 |
1.336 |
| C6 |
N1 |
1.357 |
1.330 |
| N1' |
C1' |
1.489 |
1.485 |
| N1' |
C2' |
1.477 |
1.479 |
| C1' |
C4' |
1.529 |
1.552 |
| N3 |
C2 |
1.340 |
1.315 |
| N1 |
C2 |
1.350 |
1.321 |
| C2' |
C3' |
1.508 |
1.540 |
| C4' |
C20 |
1.542 |
1.530 |
| C4' |
C3' |
1.524 |
1.546 |
| C21 |
C20 |
1.543 |
1.530 |
| C21 |
C22 |
1.521 |
1.530 |
| O3' |
C3' |
1.435 |
1.429 |
| C10 |
H1 |
1.100 |
1.091 |
| C10 |
H2 |
1.100 |
1.090 |
| C20 |
H3 |
1.100 |
1.091 |
| C20 |
H4 |
1.100 |
1.090 |
| C21 |
H5 |
1.100 |
1.090 |
| C21 |
H6 |
1.100 |
1.090 |
| C8 |
H7 |
1.081 |
1.080 |
| C22 |
H8 |
1.101 |
1.090 |
| C22 |
H9 |
1.100 |
1.091 |
| C22 |
H10 |
1.100 |
1.090 |
| O3' |
H11 |
0.951 |
0.967 |
| C3' |
H12 |
1.100 |
1.090 |
| C2' |
H13 |
1.100 |
1.091 |
| C2' |
H14 |
1.100 |
1.090 |
| C1' |
H16 |
1.100 |
1.090 |
| C1' |
H17 |
1.100 |
1.089 |
| C4' |
H18 |
1.100 |
1.090 |
| N7 |
H19 |
1.000 |
0.970 |
| N6 |
H20 |
1.000 |
0.970 |
| N6 |
H21 |
1.000 |
0.970 |
| C2 |
H22 |
1.080 |
1.080 |
Bond Angles for C1Y
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C9 |
C8 |
N7 |
111.3 |
109.9 |
| N7 |
C8 |
H7 |
124.4 |
125.1 |
| C8 |
N7 |
H19 |
124.8 |
125.1 |
| C9 |
C8 |
H7 |
124.4 |
125.1 |
| C9 |
C10 |
H1 |
107.4 |
109.5 |
| C9 |
C10 |
H2 |
107.3 |
109.5 |
| C9 |
C4 |
N3 |
131.8 |
134.9 |
| C10 |
N1' |
C1' |
116.9 |
111.0 |
| C10 |
N1' |
C2' |
114.3 |
111.0 |
| N1' |
C10 |
H1 |
107.4 |
109.4 |
| N1' |
C10 |
H2 |
107.4 |
109.5 |
| C5 |
C4 |
N3 |
122.0 |
119.1 |
| C5 |
C6 |
N1 |
118.0 |
118.6 |
| N6 |
C6 |
N1 |
121.8 |
120.7 |
| C4 |
N3 |
C2 |
118.9 |
120.4 |
| C6 |
N1 |
C2 |
122.3 |
121.4 |
| N1' |
C1' |
C4' |
105.6 |
103.3 |
| N1' |
C1' |
H16 |
110.4 |
110.7 |
| N1' |
C1' |
H17 |
110.4 |
110.7 |
| N1' |
C2' |
H13 |
111.6 |
109.9 |
| N1' |
C2' |
H14 |
111.5 |
110.1 |
| C4' |
C1' |
H16 |
110.4 |
110.6 |
| C4' |
C1' |
H17 |
110.4 |
110.7 |
| C1' |
C4' |
H18 |
108.8 |
110.7 |
| N3 |
C2 |
N1 |
123.3 |
122.4 |
| N3 |
C2 |
H22 |
118.4 |
118.8 |
| N1 |
C2 |
H22 |
118.4 |
118.8 |
| C2' |
C3' |
H12 |
110.2 |
110.3 |
| C4' |
C20 |
H3 |
108.4 |
109.5 |
| C4' |
C20 |
H4 |
108.4 |
109.5 |
| C4' |
C3' |
H12 |
110.0 |
110.3 |
| C21 |
C20 |
H3 |
108.4 |
109.5 |
| C21 |
C20 |
H4 |
108.4 |
109.5 |
| C22 |
C21 |
H5 |
108.0 |
109.5 |
| C22 |
C21 |
H6 |
108.0 |
109.5 |
| C21 |
C22 |
H8 |
109.5 |
109.5 |
| C21 |
C22 |
H9 |
109.5 |
109.5 |
| C21 |
C22 |
H10 |
109.5 |
109.5 |
| C3' |
O3' |
H11 |
109.5 |
114.0 |
| O3' |
C3' |
H12 |
111.3 |
110.2 |
| H1 |
C10 |
H2 |
109.4 |
109.5 |
| H3 |
C20 |
H4 |
109.5 |
109.5 |
| H5 |
C21 |
H6 |
109.5 |
109.5 |
| H8 |
C22 |
H9 |
109.5 |
109.5 |
| H8 |
C22 |
H10 |
109.4 |
109.5 |
| H9 |
C22 |
H10 |
109.5 |
109.5 |
| H13 |
C2' |
H14 |
109.5 |
109.9 |
| H16 |
C1' |
H17 |
109.5 |
110.7 |
| H20 |
N6 |
H21 |
109.4 |
120.0 |
Torsion Angles for C1Y
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C9 |
C8 |
N7 |
H7 |
180.0 |
180.1 |
| N7 |
C8 |
C9 |
H7 |
180.0 |
179.9 |
| C9 |
C8 |
N7 |
H19 |
181.3 |
180.0 |
| C8 |
C9 |
C10 |
H1 |
10.8 |
140.0 |
| C8 |
C9 |
C10 |
H2 |
128.4 |
20.0 |
| C8 |
C9 |
C4 |
N3 |
180.4 |
180.0 |
| N7 |
C5 |
C6 |
N1 |
179.3 |
180.0 |
| C10 |
C9 |
C4 |
N3 |
357.8 |
359.8 |
| N1' |
C10 |
C9 |
H1 |
238.8 |
119.9 |
| N1' |
C10 |
C9 |
H2 |
121.2 |
240.0 |
| H1 |
C10 |
C9 |
H2 |
242.4 |
120.1 |
| C5 |
C4 |
C9 |
N3 |
180.4 |
180.3 |
| C9 |
C4 |
N3 |
C2 |
180.3 |
180.3 |
| C9 |
C10 |
N1' |
H1 |
121.2 |
240.0 |
| C9 |
C10 |
N1' |
H2 |
238.8 |
120.0 |
| C10 |
N1' |
C1' |
C4' |
209.6 |
200.3 |
| C10 |
N1' |
C1' |
H16 |
329.0 |
318.7 |
| C10 |
N1' |
C1' |
H17 |
90.2 |
81.8 |
| C10 |
N1' |
C2' |
H13 |
288.2 |
26.4 |
| C10 |
N1' |
C2' |
H14 |
51.0 |
265.3 |
| H1 |
C10 |
N1' |
H2 |
117.6 |
240.0 |
| C9 |
C4 |
C5 |
N3 |
179.6 |
179.8 |
| C5 |
C4 |
N3 |
C2 |
359.8 |
0.0 |
| C6 |
C5 |
C4 |
N3 |
0.2 |
360.0 |
| N6 |
C6 |
C5 |
N1 |
180.4 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
1.0 |
359.9 |
| C5 |
C6 |
N6 |
N1 |
179.5 |
180.0 |
| N6 |
C6 |
N1 |
C2 |
180.6 |
179.9 |
| C4 |
N3 |
C2 |
N1 |
0.5 |
359.9 |
| C4 |
N3 |
C2 |
H22 |
180.5 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
359.1 |
0.1 |
| C6 |
N1 |
C2 |
H22 |
179.0 |
180.0 |
| C10 |
N1' |
C1' |
C2' |
230.0 |
239.5 |
| C1' |
N1' |
C10 |
H1 |
286.3 |
310.0 |
| C1' |
N1' |
C10 |
H2 |
168.7 |
70.0 |
| C1' |
N1' |
C2' |
H13 |
156.8 |
265.9 |
| C1' |
N1' |
C2' |
H14 |
279.6 |
144.8 |
| C4' |
C1' |
N1' |
H16 |
240.6 |
241.6 |
| C4' |
C1' |
N1' |
H17 |
119.4 |
118.5 |
| N1' |
C1' |
C4' |
H18 |
238.4 |
278.9 |
| H16 |
C1' |
N1' |
H17 |
238.8 |
236.9 |
| C10 |
N1' |
C2' |
C1' |
131.4 |
120.5 |
| C2' |
N1' |
C10 |
H1 |
159.7 |
192.6 |
| C2' |
N1' |
C10 |
H2 |
42.1 |
312.6 |
| N1' |
C2' |
C3' |
H12 |
200.5 |
239.7 |
| H13 |
C2' |
N1' |
H14 |
237.2 |
121.1 |
| N1' |
C1' |
C4' |
H16 |
119.4 |
118.5 |
| N1' |
C1' |
C4' |
H17 |
240.6 |
241.5 |
| C1' |
C4' |
C20 |
H3 |
209.8 |
306.4 |
| C1' |
C4' |
C20 |
H4 |
328.5 |
186.5 |
| C1' |
C4' |
C3' |
H12 |
147.6 |
97.1 |
| H16 |
C1' |
C4' |
H17 |
121.2 |
123.0 |
| C6 |
N1 |
C2 |
N3 |
359.1 |
0.1 |
| N1 |
C2 |
N3 |
H22 |
180.0 |
179.9 |
| N3 |
C2 |
N1 |
H22 |
180.0 |
180.1 |
| C10 |
N1' |
C2' |
C3' |
169.6 |
145.8 |
| C4' |
C3' |
C2' |
H12 |
118.2 |
119.0 |
| C2' |
C3' |
O3' |
H11 |
180.0 |
62.7 |
| O3' |
C3' |
C2' |
H12 |
238.2 |
238.0 |
| C21 |
C20 |
C4' |
H3 |
239.4 |
120.0 |
| C21 |
C20 |
C4' |
H4 |
120.7 |
240.0 |
| H3 |
C20 |
C4' |
H4 |
241.3 |
120.0 |
| C2' |
C3' |
C4' |
H12 |
241.6 |
241.0 |
| C3' |
C4' |
C20 |
H3 |
327.8 |
59.9 |
| C3' |
C4' |
C20 |
H4 |
86.5 |
299.9 |
| C4' |
C3' |
O3' |
H11 |
294.9 |
178.6 |
| O3' |
C3' |
C4' |
H12 |
124.7 |
122.0 |
| C4' |
C20 |
C21 |
H3 |
120.7 |
240.0 |
| C4' |
C20 |
C21 |
H4 |
239.3 |
120.0 |
| H3 |
C20 |
C21 |
H4 |
118.7 |
240.0 |
| C22 |
C21 |
C20 |
H3 |
352.0 |
300.0 |
| C22 |
C21 |
C20 |
H4 |
233.3 |
60.0 |
| H5 |
C21 |
C22 |
H6 |
118.3 |
120.0 |
| H8 |
C22 |
C21 |
H9 |
240.0 |
240.0 |
| H8 |
C22 |
C21 |
H10 |
120.0 |
120.0 |
| H9 |
C22 |
C21 |
H10 |
240.0 |
240.0 |
| C2' |
C3' |
O3' |
H12 |
121.1 |
122.1 |
| C4' |
C3' |
O3' |
H12 |
236.0 |
237.9 |
| C9 |
C10 |
H1 |
H2 |
116.2 |
240.0 |
| H1 |
C10 |
N1' |
C1' |
286.3 |
310.0 |
| H1 |
C10 |
N1' |
C2' |
159.7 |
192.6 |
| N1' |
C10 |
H1 |
H2 |
243.7 |
120.0 |
| C9 |
C10 |
H2 |
H1 |
243.8 |
120.0 |
| H2 |
C10 |
N1' |
C1' |
168.7 |
70.0 |
| H2 |
C10 |
N1' |
C2' |
42.1 |
312.6 |
| N1' |
C10 |
H2 |
H1 |
116.3 |
240.0 |
| C4' |
C20 |
H3 |
H4 |
118.0 |
240.0 |
| C21 |
C20 |
H3 |
H4 |
242.0 |
120.0 |
| C4' |
C20 |
H4 |
H3 |
242.0 |
120.0 |
| C21 |
C20 |
H4 |
H3 |
118.0 |
240.0 |
| H5 |
C21 |
C20 |
H3 |
112.9 |
60.0 |
| H5 |
C21 |
C20 |
H4 |
354.2 |
180.0 |
| C22 |
C21 |
H5 |
H6 |
242.6 |
240.0 |
| H5 |
C21 |
C22 |
H8 |
59.1 |
180.0 |
| H5 |
C21 |
C22 |
H9 |
179.1 |
300.0 |
| H5 |
C21 |
C22 |
H10 |
299.1 |
60.0 |
| H6 |
C21 |
C20 |
H3 |
231.2 |
180.0 |
| H6 |
C21 |
C20 |
H4 |
112.5 |
300.0 |
| C22 |
C21 |
H6 |
H5 |
117.4 |
120.0 |
| H6 |
C21 |
C22 |
H8 |
300.8 |
60.0 |
| H6 |
C21 |
C22 |
H9 |
60.8 |
180.0 |
| H6 |
C21 |
C22 |
H10 |
180.8 |
300.0 |
| C9 |
C8 |
H7 |
N7 |
180.0 |
179.8 |
| H7 |
C8 |
N7 |
H19 |
1.3 |
359.9 |
| H8 |
C22 |
C21 |
H5 |
59.1 |
180.0 |
| H8 |
C22 |
C21 |
H6 |
300.8 |
60.0 |
| C21 |
C22 |
H8 |
H9 |
120.0 |
120.0 |
| C21 |
C22 |
H8 |
H10 |
240.0 |
240.0 |
| H9 |
C22 |
H8 |
H10 |
120.0 |
120.0 |
| H9 |
C22 |
C21 |
H5 |
179.1 |
300.0 |
| H9 |
C22 |
C21 |
H6 |
60.8 |
180.0 |
| C21 |
C22 |
H9 |
H8 |
240.0 |
240.0 |
| C21 |
C22 |
H9 |
H10 |
120.0 |
120.0 |
| H8 |
C22 |
H9 |
H10 |
240.0 |
240.0 |
| H10 |
C22 |
C21 |
H5 |
299.1 |
60.0 |
| H10 |
C22 |
C21 |
H6 |
180.8 |
300.0 |
| C21 |
C22 |
H10 |
H8 |
120.0 |
120.0 |
| C21 |
C22 |
H10 |
H9 |
240.0 |
240.0 |
| H8 |
C22 |
H10 |
H9 |
120.0 |
120.0 |
| H11 |
O3' |
C3' |
H12 |
58.9 |
300.7 |
| H12 |
C3' |
O3' |
H11 |
58.9 |
300.7 |
| N1' |
C2' |
H13 |
H14 |
123.9 |
238.7 |
| H13 |
C2' |
C3' |
H12 |
81.9 |
359.1 |
| N1' |
C2' |
H14 |
H13 |
236.0 |
121.2 |
| H14 |
C2' |
C3' |
H12 |
319.1 |
120.2 |
| N1' |
C1' |
H16 |
C4' |
243.6 |
246.1 |
| N1' |
C1' |
H16 |
H17 |
121.7 |
123.1 |
| C4' |
C1' |
H16 |
H17 |
238.2 |
237.0 |
| H16 |
C1' |
C4' |
H18 |
119.0 |
160.4 |
| N1' |
C1' |
H17 |
C4' |
116.4 |
113.9 |
| N1' |
C1' |
H17 |
H16 |
238.2 |
236.9 |
| C4' |
C1' |
H17 |
H16 |
121.8 |
123.0 |
| H17 |
C1' |
C4' |
H18 |
357.8 |
37.4 |
| H18 |
C4' |
C1' |
H16 |
119.0 |
160.4 |
| H18 |
C4' |
C1' |
H17 |
357.8 |
37.4 |
| H18 |
C4' |
C20 |
H3 |
89.0 |
183.3 |
| H18 |
C4' |
C20 |
H4 |
207.7 |
63.3 |
| H18 |
C4' |
C3' |
H12 |
263.4 |
215.5 |
| H19 |
N7 |
C8 |
H7 |
1.3 |
359.9 |
| H20 |
N6 |
C6 |
N1 |
0.0 |
180.0 |
| H21 |
N6 |
C6 |
N1 |
120.0 |
0.0 |
| N3 |
C2 |
H22 |
N1 |
180.0 |
179.9 |