PDB Chemical Component YCO
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 YCO
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP2 |
1.839 |
1.611 |
P |
OP3 |
1.720 |
1.610 |
N1 |
C1' |
1.495 |
1.465 |
N1 |
C6 |
1.418 |
1.383 |
C2 |
N1 |
1.412 |
1.342 |
O2 |
C2 |
1.349 |
1.217 |
N3 |
C2 |
1.355 |
1.348 |
N3 |
C4 |
1.346 |
1.382 |
N3 |
HN3 |
1.000 |
0.970 |
C4 |
C5 |
1.487 |
1.467 |
C5 |
C6 |
1.390 |
1.346 |
C5 |
O14 |
1.373 |
1.359 |
C6 |
H6 |
1.080 |
1.080 |
N7 |
C4 |
1.347 |
1.312 |
N7 |
C8 |
1.360 |
1.368 |
C8 |
C13 |
1.406 |
1.400 |
C9 |
C8 |
1.399 |
1.396 |
C9 |
C10 |
1.397 |
1.381 |
C9 |
H9 |
1.080 |
1.079 |
C1' |
C2' |
1.515 |
1.541 |
C1' |
O4' |
1.441 |
1.437 |
C1' |
H1' |
1.100 |
1.089 |
C10 |
C11 |
1.399 |
1.383 |
C10 |
H10 |
1.080 |
1.080 |
C11 |
C12 |
1.397 |
1.384 |
C11 |
H11 |
1.080 |
1.080 |
C12 |
H12 |
1.079 |
1.081 |
C13 |
C12 |
1.400 |
1.384 |
C13 |
O14 |
1.381 |
1.361 |
C2' |
C3' |
1.508 |
1.547 |
C2' |
H2' |
1.100 |
1.090 |
C2' |
H2'A |
1.099 |
1.090 |
C3' |
O3' |
1.425 |
1.430 |
C3' |
C4' |
1.509 |
1.550 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.967 |
C4' |
C5' |
1.515 |
1.530 |
C4' |
H4' |
1.100 |
1.091 |
O4' |
C4' |
1.429 |
1.443 |
C5' |
O5' |
1.409 |
1.429 |
C5' |
H5' |
1.100 |
1.089 |
C5' |
H5'A |
1.100 |
1.090 |
O5' |
P |
1.708 |
1.610 |
OP1 |
P |
1.801 |
1.480 |
OP2 |
HOP2 |
0.950 |
0.967 |
OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for YCO
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP3 |
92.2 |
109.4 |
O5' |
P |
OP2 |
119.3 |
109.5 |
OP1 |
P |
OP2 |
120.0 |
109.5 |
P |
OP2 |
HOP2 |
109.5 |
114.0 |
O5' |
P |
OP3 |
97.6 |
109.5 |
OP1 |
P |
OP3 |
95.2 |
109.5 |
P |
OP3 |
HOP3 |
109.5 |
114.0 |
C6 |
N1 |
C1' |
120.4 |
119.2 |
C2 |
N1 |
C1' |
118.1 |
119.2 |
N1 |
C1' |
C2' |
113.9 |
109.9 |
N1 |
C1' |
O4' |
109.2 |
109.9 |
N1 |
C1' |
H1' |
106.3 |
109.9 |
C2 |
N1 |
C6 |
118.1 |
121.7 |
N1 |
C6 |
C5 |
119.4 |
119.5 |
N1 |
C6 |
H6 |
120.3 |
120.2 |
C4 |
N3 |
HN3 |
119.4 |
120.3 |
N3 |
C4 |
C5 |
119.3 |
118.7 |
C4 |
C5 |
C6 |
118.8 |
118.8 |
C4 |
C5 |
O14 |
118.7 |
119.5 |
C6 |
C5 |
O14 |
122.5 |
121.7 |
C5 |
C6 |
H6 |
120.3 |
120.3 |
C5 |
O14 |
C13 |
119.5 |
119.2 |
N7 |
C8 |
C13 |
120.8 |
120.8 |
C9 |
C8 |
C13 |
119.9 |
119.6 |
C8 |
C13 |
C12 |
119.7 |
119.8 |
C8 |
C13 |
O14 |
120.7 |
120.4 |
C10 |
C9 |
H9 |
119.9 |
120.1 |
C9 |
C10 |
C11 |
120.1 |
120.3 |
C9 |
C10 |
H10 |
120.0 |
119.8 |
C2' |
C1' |
O4' |
108.4 |
107.3 |
C2' |
C1' |
H1' |
107.1 |
109.9 |
C1' |
C2' |
C3' |
102.0 |
104.2 |
C1' |
C2' |
H2' |
112.1 |
110.5 |
C1' |
C2' |
H2'A |
112.1 |
110.5 |
O4' |
C1' |
H1' |
112.0 |
110.0 |
C1' |
O4' |
C4' |
108.8 |
107.0 |
C11 |
C10 |
H10 |
120.0 |
119.9 |
C10 |
C11 |
C12 |
119.9 |
120.3 |
C10 |
C11 |
H11 |
120.0 |
119.9 |
C12 |
C11 |
H11 |
120.0 |
119.8 |
C11 |
C12 |
H12 |
119.9 |
120.0 |
C13 |
C12 |
H12 |
119.9 |
119.9 |
C3' |
C2' |
H2' |
112.0 |
110.5 |
C3' |
C2' |
H2'A |
112.0 |
110.5 |
C2' |
C3' |
O3' |
112.0 |
110.9 |
C2' |
C3' |
C4' |
104.2 |
102.1 |
C2' |
C3' |
H3' |
111.7 |
110.9 |
H2' |
C2' |
H2'A |
106.8 |
110.5 |
O3' |
C3' |
C4' |
110.6 |
110.9 |
O3' |
C3' |
H3' |
105.4 |
110.8 |
C3' |
O3' |
HO3' |
109.5 |
114.0 |
C4' |
C3' |
H3' |
113.1 |
111.0 |
C3' |
C4' |
C5' |
108.0 |
110.6 |
C3' |
C4' |
H4' |
113.3 |
110.6 |
C5' |
C4' |
H4' |
108.4 |
110.5 |
O4' |
C4' |
C5' |
110.8 |
110.7 |
C4' |
C5' |
O5' |
108.4 |
109.4 |
C4' |
C5' |
H5' |
109.9 |
109.5 |
C4' |
C5' |
H5'A |
109.9 |
109.4 |
O4' |
C4' |
H4' |
110.6 |
110.8 |
O5' |
C5' |
H5' |
109.8 |
109.5 |
O5' |
C5' |
H5'A |
109.8 |
109.4 |
H5' |
C5' |
H5'A |
109.1 |
109.5 |
Torsion Angles for YCO
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O5' |
P |
OP2 |
OP3 |
100.0 |
120.0 |
OP1 |
P |
OP2 |
OP3 |
262.7 |
240.0 |
OP2 |
P |
OP3 |
HOP3 |
239.6 |
60.0 |
O5' |
P |
OP3 |
OP2 |
240.0 |
240.0 |
OP1 |
P |
OP3 |
OP2 |
120.4 |
120.0 |
OP3 |
P |
OP2 |
HOP2 |
180.0 |
60.0 |
C2 |
N1 |
C1' |
C6 |
158.9 |
180.2 |
C1' |
N1 |
C6 |
C5 |
169.5 |
179.7 |
C1' |
N1 |
C6 |
H6 |
349.5 |
360.0 |
C2' |
C1' |
N1 |
O4' |
238.7 |
242.2 |
C2' |
C1' |
N1 |
H1' |
117.7 |
121.0 |
N1 |
C1' |
C2' |
C3' |
101.2 |
121.4 |
N1 |
C1' |
C2' |
H2' |
221.1 |
240.1 |
N1 |
C1' |
C2' |
H2'A |
341.2 |
2.8 |
O4' |
C1' |
N1 |
H1' |
239.0 |
238.8 |
N1 |
C1' |
O4' |
C4' |
236.3 |
214.1 |
C2 |
N1 |
C6 |
C1' |
201.1 |
179.8 |
C6 |
N1 |
C1' |
C2' |
263.9 |
115.1 |
C6 |
N1 |
C1' |
O4' |
25.3 |
232.9 |
C6 |
N1 |
C1' |
H1' |
146.3 |
354.0 |
C4 |
C5 |
C6 |
N1 |
354.4 |
0.4 |
N1 |
C6 |
C5 |
O14 |
175.2 |
180.2 |
C5 |
C6 |
N1 |
H6 |
180.0 |
179.8 |
C6 |
N1 |
C2 |
C1' |
159.4 |
180.2 |
C2 |
N1 |
C1' |
C2' |
62.9 |
295.3 |
C2 |
N1 |
C1' |
O4' |
184.2 |
53.1 |
C2 |
N1 |
C1' |
H1' |
305.2 |
174.2 |
C2 |
N1 |
C6 |
C5 |
10.6 |
359.5 |
C2 |
N1 |
C6 |
H6 |
190.6 |
179.7 |
O2 |
C2 |
N1 |
C1' |
17.5 |
0.0 |
O2 |
C2 |
N1 |
C6 |
176.9 |
180.2 |
N3 |
C2 |
N1 |
C1' |
189.5 |
180.0 |
N3 |
C2 |
N1 |
C6 |
348.9 |
0.2 |
N3 |
C4 |
C5 |
C6 |
0.7 |
359.8 |
N3 |
C4 |
C5 |
O14 |
179.9 |
180.0 |
HN3 |
N3 |
C4 |
C5 |
179.1 |
180.0 |
N1 |
C6 |
C5 |
C4 |
354.4 |
0.4 |
C5 |
C4 |
N3 |
HN3 |
179.1 |
180.0 |
C6 |
C5 |
C4 |
O14 |
180.8 |
179.8 |
C4 |
C5 |
C6 |
H6 |
174.3 |
180.2 |
C4 |
C5 |
O14 |
C13 |
0.2 |
0.1 |
C5 |
C6 |
N1 |
C1' |
169.5 |
179.7 |
N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
C4 |
C5 |
C6 |
O14 |
179.1 |
180.2 |
C6 |
C5 |
O14 |
C13 |
179.3 |
180.3 |
C4 |
C5 |
O14 |
C6 |
180.9 |
179.8 |
O14 |
C5 |
C6 |
H6 |
355.2 |
0.0 |
C8 |
C13 |
O14 |
C5 |
359.6 |
359.9 |
H6 |
C6 |
N1 |
C1' |
349.5 |
360.0 |
N1 |
C6 |
H6 |
C5 |
180.0 |
179.8 |
H6 |
C6 |
C5 |
O14 |
355.2 |
0.0 |
N7 |
C4 |
N3 |
HN3 |
358.3 |
0.1 |
N7 |
C4 |
C5 |
O14 |
0.6 |
359.9 |
C9 |
C8 |
N7 |
C13 |
179.8 |
180.0 |
N7 |
C8 |
C13 |
C12 |
179.8 |
180.1 |
N7 |
C8 |
C13 |
O14 |
359.9 |
0.1 |
C5 |
O14 |
C13 |
C8 |
359.6 |
359.9 |
C8 |
C13 |
C12 |
H12 |
179.8 |
180.0 |
N7 |
C8 |
C9 |
C13 |
180.2 |
180.0 |
C9 |
C8 |
C13 |
C12 |
0.1 |
0.0 |
C9 |
C8 |
C13 |
O14 |
180.1 |
180.0 |
C10 |
C9 |
C8 |
C13 |
0.3 |
360.0 |
C11 |
C10 |
C9 |
H10 |
180.0 |
180.1 |
C9 |
C10 |
C11 |
C12 |
0.4 |
360.0 |
C9 |
C10 |
C11 |
H11 |
180.5 |
180.0 |
H9 |
C9 |
C8 |
C13 |
180.3 |
180.0 |
H9 |
C9 |
C10 |
C11 |
179.5 |
180.0 |
H9 |
C9 |
C10 |
H10 |
359.5 |
360.0 |
N1 |
C1' |
C2' |
O4' |
121.8 |
119.5 |
N1 |
C1' |
C2' |
H1' |
242.8 |
239.0 |
O4' |
C1' |
C2' |
H1' |
121.0 |
119.5 |
C2' |
C1' |
O4' |
C4' |
1.0 |
333.5 |
C3' |
C2' |
C1' |
H2' |
240.0 |
241.3 |
C3' |
C2' |
C1' |
H2'A |
120.0 |
118.7 |
C1' |
C2' |
C3' |
O3' |
151.0 |
139.1 |
C1' |
C2' |
C3' |
C4' |
31.4 |
20.9 |
C1' |
C2' |
C3' |
H3' |
269.0 |
262.6 |
H2' |
C2' |
C1' |
H2'A |
240.0 |
237.4 |
N1 |
C1' |
O4' |
C2' |
235.4 |
240.6 |
N1 |
C1' |
O4' |
H1' |
117.5 |
121.1 |
C2' |
C1' |
O4' |
H1' |
242.1 |
240.5 |
O4' |
C1' |
C2' |
C3' |
339.4 |
2.0 |
O4' |
C1' |
C2' |
H2' |
99.4 |
120.7 |
O4' |
C1' |
C2' |
H2'A |
219.4 |
243.3 |
C1' |
O4' |
C4' |
C5' |
136.1 |
158.5 |
C1' |
O4' |
C4' |
H4' |
256.4 |
281.5 |
N1 |
C1' |
H1' |
C2' |
122.1 |
121.0 |
N1 |
C1' |
H1' |
O4' |
240.8 |
238.9 |
C2' |
C1' |
H1' |
O4' |
118.7 |
117.9 |
H1' |
C1' |
C2' |
C3' |
218.4 |
242.5 |
H1' |
C1' |
C2' |
H2' |
338.4 |
1.2 |
H1' |
C1' |
C2' |
H2'A |
98.4 |
123.8 |
H1' |
C1' |
O4' |
C4' |
118.9 |
93.0 |
C11 |
C10 |
C9 |
H9 |
179.5 |
180.0 |
C9 |
C10 |
C11 |
H10 |
180.0 |
179.9 |
C12 |
C11 |
C10 |
H11 |
180.0 |
180.0 |
C10 |
C11 |
C12 |
H12 |
179.9 |
180.0 |
H10 |
C10 |
C9 |
H9 |
359.5 |
360.0 |
C9 |
C10 |
H10 |
C11 |
180.0 |
180.1 |
H10 |
C10 |
C11 |
C12 |
180.4 |
180.0 |
H10 |
C10 |
C11 |
H11 |
0.4 |
0.1 |
C8 |
C13 |
C12 |
C11 |
359.9 |
360.0 |
C12 |
C11 |
C10 |
H10 |
180.4 |
180.0 |
C10 |
C11 |
C12 |
H11 |
180.0 |
180.0 |
C13 |
C12 |
C11 |
H12 |
180.0 |
180.0 |
H11 |
C11 |
C10 |
H10 |
0.4 |
0.1 |
C10 |
C11 |
H11 |
C12 |
180.0 |
180.0 |
H11 |
C11 |
C12 |
H12 |
359.9 |
359.9 |
H12 |
C12 |
C11 |
H11 |
359.9 |
359.9 |
C5 |
O14 |
C13 |
C12 |
179.7 |
179.9 |
C8 |
C13 |
C12 |
O14 |
180.1 |
180.0 |
C13 |
C12 |
C11 |
H11 |
179.9 |
180.0 |
C11 |
C12 |
C13 |
H12 |
180.0 |
180.0 |
C8 |
C13 |
O14 |
C12 |
179.9 |
180.0 |
O14 |
C13 |
C12 |
H12 |
359.8 |
0.0 |
C3' |
C2' |
C1' |
O4' |
339.4 |
2.0 |
C3' |
C2' |
C1' |
H1' |
218.4 |
242.5 |
C1' |
C2' |
C3' |
H2' |
120.0 |
118.7 |
C1' |
C2' |
C3' |
H2'A |
240.0 |
241.3 |
H2' |
C2' |
C3' |
H2'A |
120.0 |
122.6 |
O3' |
C3' |
C2' |
C4' |
119.6 |
118.2 |
O3' |
C3' |
C2' |
H3' |
241.9 |
236.4 |
C2' |
C3' |
O3' |
HO3' |
180.0 |
61.5 |
C4' |
C3' |
C2' |
H3' |
122.4 |
118.2 |
C2' |
C3' |
C4' |
C5' |
209.3 |
204.4 |
C2' |
C3' |
C4' |
H4' |
89.1 |
81.7 |
H2' |
C2' |
C1' |
O4' |
99.4 |
120.7 |
H2' |
C2' |
C1' |
H1' |
338.4 |
1.2 |
C1' |
C2' |
H2' |
C3' |
246.1 |
245.2 |
C1' |
C2' |
H2' |
H2'A |
123.1 |
122.6 |
C3' |
C2' |
H2' |
H2'A |
237.0 |
237.4 |
H2' |
C2' |
C3' |
O3' |
31.0 |
20.3 |
H2' |
C2' |
C3' |
C4' |
271.4 |
262.2 |
H2' |
C2' |
C3' |
H3' |
149.0 |
143.9 |
H2'A |
C2' |
C1' |
O4' |
219.4 |
243.3 |
H2'A |
C2' |
C1' |
H1' |
98.4 |
123.8 |
C1' |
C2' |
H2'A |
C3' |
113.9 |
114.8 |
C1' |
C2' |
H2'A |
H2' |
236.9 |
237.4 |
C3' |
C2' |
H2'A |
H2' |
123.0 |
122.6 |
H2'A |
C2' |
C3' |
O3' |
271.0 |
257.7 |
H2'A |
C2' |
C3' |
C4' |
151.4 |
139.6 |
H2'A |
C2' |
C3' |
H3' |
29.0 |
21.3 |
O3' |
C3' |
C2' |
H2' |
31.0 |
20.3 |
O3' |
C3' |
C2' |
H2'A |
271.0 |
257.7 |
C2' |
C3' |
O3' |
C4' |
244.3 |
247.3 |
C2' |
C3' |
O3' |
H3' |
121.7 |
123.7 |
C4' |
C3' |
O3' |
H3' |
237.4 |
236.3 |
O3' |
C3' |
C4' |
C5' |
88.7 |
86.2 |
O3' |
C3' |
C4' |
H4' |
328.6 |
323.5 |
C1' |
O4' |
C4' |
C3' |
19.4 |
40.0 |
C4' |
C3' |
C2' |
H2' |
271.4 |
262.2 |
C4' |
C3' |
C2' |
H2'A |
151.4 |
139.6 |
C2' |
C3' |
C4' |
O3' |
120.5 |
118.2 |
C2' |
C3' |
C4' |
H3' |
238.5 |
241.8 |
O3' |
C3' |
C4' |
H3' |
118.0 |
123.6 |
C4' |
C3' |
O3' |
HO3' |
295.7 |
174.1 |
C5' |
C4' |
C3' |
H4' |
120.1 |
122.8 |
O4' |
C4' |
C3' |
C5' |
118.6 |
118.5 |
C3' |
C4' |
C5' |
O5' |
163.8 |
185.0 |
C3' |
C4' |
C5' |
H5' |
283.7 |
305.0 |
C3' |
C4' |
C5' |
H5'A |
43.8 |
65.1 |
O4' |
C4' |
C3' |
H4' |
238.7 |
241.3 |
H3' |
C3' |
C2' |
H2' |
149.0 |
143.9 |
H3' |
C3' |
C2' |
H2'A |
29.0 |
21.3 |
C2' |
C3' |
H3' |
O3' |
238.1 |
236.3 |
C2' |
C3' |
H3' |
C4' |
117.1 |
112.7 |
O3' |
C3' |
H3' |
C4' |
239.0 |
236.4 |
H3' |
C3' |
O3' |
HO3' |
58.3 |
297.8 |
H3' |
C3' |
C4' |
C5' |
330.8 |
322.7 |
H3' |
C3' |
C4' |
H4' |
210.6 |
199.9 |
HO3' |
O3' |
C3' |
C4' |
295.7 |
174.1 |
HO3' |
O3' |
C3' |
H3' |
58.3 |
297.8 |
C5' |
C4' |
C3' |
H3' |
330.8 |
322.7 |
C3' |
C4' |
C5' |
H4' |
236.8 |
237.2 |
O4' |
C4' |
C5' |
H4' |
121.6 |
123.1 |
O5' |
C5' |
C4' |
H5' |
240.0 |
240.0 |
O5' |
C5' |
C4' |
H5'A |
120.0 |
119.9 |
H5' |
C5' |
C4' |
H5'A |
240.0 |
239.9 |
H4' |
C4' |
C3' |
H3' |
210.6 |
199.9 |
C3' |
C4' |
H4' |
C5' |
119.9 |
122.8 |
O4' |
C4' |
H4' |
C5' |
238.3 |
237.0 |
H4' |
C4' |
C5' |
O5' |
286.9 |
307.8 |
H4' |
C4' |
C5' |
H5' |
46.9 |
67.8 |
H4' |
C4' |
C5' |
H5'A |
166.9 |
187.9 |
C4' |
O4' |
C1' |
H1' |
118.9 |
93.0 |
O4' |
C4' |
C3' |
H3' |
89.3 |
81.2 |
C3' |
C4' |
O4' |
C5' |
243.3 |
241.5 |
C3' |
C4' |
O4' |
H4' |
123.0 |
118.6 |
C5' |
C4' |
O4' |
H4' |
239.7 |
237.0 |
O4' |
C4' |
C5' |
O5' |
48.5 |
70.9 |
O4' |
C4' |
C5' |
H5' |
168.5 |
190.9 |
O4' |
C4' |
C5' |
H5'A |
288.5 |
311.0 |
C5' |
O5' |
P |
OP2 |
1.2 |
175.1 |
C5' |
O5' |
P |
OP3 |
98.1 |
295.0 |
O5' |
C5' |
C4' |
H4' |
286.9 |
307.8 |
C4' |
C5' |
O5' |
H5' |
120.0 |
120.1 |
C4' |
C5' |
O5' |
H5'A |
240.0 |
240.1 |
H5' |
C5' |
O5' |
H5'A |
120.0 |
120.1 |
H5' |
C5' |
C4' |
H4' |
46.9 |
67.8 |
C4' |
C5' |
H5' |
O5' |
240.9 |
240.0 |
C4' |
C5' |
H5' |
H5'A |
120.5 |
120.0 |
O5' |
C5' |
H5' |
H5'A |
239.6 |
240.0 |
H5'A |
C5' |
C4' |
H4' |
166.9 |
187.9 |
C4' |
C5' |
H5'A |
O5' |
119.1 |
119.9 |
C4' |
C5' |
H5'A |
H5' |
239.5 |
239.9 |
O5' |
C5' |
H5'A |
H5' |
120.4 |
120.0 |
OP2 |
P |
O5' |
OP3 |
263.1 |
240.0 |
OP1 |
P |
O5' |
OP2 |
197.1 |
240.0 |
O5' |
P |
OP2 |
HOP2 |
280.0 |
180.0 |
OP1 |
P |
O5' |
OP3 |
100.2 |
120.0 |
O5' |
P |
OP3 |
HOP3 |
119.6 |
300.0 |
OP2 |
P |
OP1 |
OP3 |
95.6 |
120.0 |
O5' |
P |
OP1 |
OP2 |
162.8 |
120.0 |
OP1 |
P |
OP2 |
HOP2 |
82.7 |
300.0 |
O5' |
P |
OP1 |
OP3 |
258.4 |
239.9 |
OP1 |
P |
OP3 |
HOP3 |
360.0 |
180.0 |
HOP2 |
OP2 |
P |
OP3 |
180.0 |
60.0 |