PDB Chemical Component 2YR
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 2YR
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
S |
C8 |
1.812 |
1.814 |
C8 |
C9 |
1.520 |
1.530 |
N4 |
C9 |
1.487 |
1.465 |
N4 |
C4 |
1.335 |
1.375 |
C4 |
N3 |
1.335 |
1.327 |
C4 |
C5 |
1.427 |
1.410 |
N3 |
C2 |
1.353 |
1.333 |
C5 |
C6 |
1.341 |
1.354 |
C2 |
O2 |
1.237 |
1.220 |
C2 |
N1 |
1.402 |
1.346 |
C6 |
N1 |
1.367 |
1.362 |
N1 |
C1' |
1.476 |
1.464 |
C2' |
C3' |
1.517 |
1.547 |
C2' |
C1' |
1.528 |
1.545 |
C3' |
O3' |
1.432 |
1.429 |
C3' |
C4' |
1.522 |
1.550 |
C1' |
O4' |
1.429 |
1.438 |
O4' |
C4' |
1.446 |
1.443 |
C4' |
C5' |
1.512 |
1.530 |
C5' |
O5' |
1.438 |
1.429 |
O5' |
P |
1.590 |
1.610 |
OP2 |
P |
1.482 |
1.609 |
P |
OP1 |
1.483 |
1.480 |
OP2 |
H2 |
0.950 |
0.967 |
C5' |
H3 |
1.100 |
1.091 |
C5' |
H4 |
1.101 |
1.090 |
C4' |
H5 |
1.100 |
1.091 |
C3' |
H6 |
1.100 |
1.090 |
O3' |
H7 |
0.950 |
0.967 |
C2' |
H8 |
1.100 |
1.090 |
C2' |
H9 |
1.100 |
1.090 |
C1' |
H10 |
1.100 |
1.090 |
N4 |
H11 |
1.000 |
0.971 |
C5 |
H12 |
1.080 |
1.080 |
C6 |
H13 |
1.080 |
1.081 |
S |
H14 |
1.300 |
1.345 |
C8 |
H15 |
1.100 |
1.090 |
C8 |
H16 |
1.100 |
1.091 |
C9 |
H17 |
1.100 |
1.089 |
C9 |
H18 |
1.100 |
1.090 |
P |
OP3 |
|
1.611 |
OP3 |
H20 |
|
0.968 |
Bond Angles for 2YR
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
S |
C8 |
C9 |
108.9 |
109.5 |
C8 |
S |
H14 |
102.0 |
103.0 |
S |
C8 |
H15 |
109.6 |
109.5 |
S |
C8 |
H16 |
109.6 |
109.5 |
N4 |
C9 |
C8 |
166.8 |
109.5 |
C9 |
C8 |
H15 |
109.6 |
109.5 |
C9 |
C8 |
H16 |
109.6 |
109.5 |
C8 |
C9 |
H17 |
93.8 |
109.5 |
C8 |
C9 |
H18 |
93.8 |
109.4 |
C9 |
N4 |
H11 |
117.1 |
120.0 |
N4 |
C9 |
H17 |
93.8 |
109.5 |
N4 |
C9 |
H18 |
93.8 |
109.4 |
N4 |
C4 |
C5 |
120.2 |
120.2 |
C4 |
C5 |
C6 |
117.5 |
119.0 |
C4 |
C5 |
H12 |
121.2 |
120.5 |
C6 |
C5 |
H12 |
121.2 |
120.5 |
C5 |
C6 |
H13 |
119.5 |
120.4 |
N1 |
C1' |
H10 |
108.9 |
110.0 |
C2' |
C3' |
H6 |
109.4 |
111.0 |
C1' |
C2' |
H8 |
110.9 |
110.5 |
C1' |
C2' |
H9 |
110.9 |
110.5 |
C2' |
C1' |
H10 |
108.2 |
109.8 |
O3' |
C3' |
H6 |
110.7 |
110.8 |
C3' |
O3' |
H7 |
109.5 |
114.0 |
C3' |
C4' |
H5 |
108.6 |
110.6 |
O4' |
C4' |
H5 |
109.6 |
110.7 |
C4' |
C5' |
H3 |
109.0 |
109.5 |
C4' |
C5' |
H4 |
109.1 |
109.5 |
O5' |
P |
OP3 |
|
109.5 |
OP2 |
P |
OP3 |
|
109.5 |
OP1 |
P |
OP3 |
|
109.4 |
H3 |
C5' |
H4 |
109.5 |
109.5 |
H8 |
C2' |
H9 |
109.5 |
110.5 |
H15 |
C8 |
H16 |
109.5 |
109.4 |
H17 |
C9 |
H18 |
109.5 |
109.5 |
P |
OP3 |
H20 |
|
113.9 |
Torsion Angles for 2YR
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
N4 |
C9 |
C8 |
S |
36.1 |
180.0 |
C9 |
C8 |
S |
H15 |
240.1 |
240.0 |
C9 |
C8 |
S |
H16 |
119.9 |
120.0 |
S |
C8 |
C9 |
H17 |
161.2 |
60.0 |
S |
C8 |
C9 |
H18 |
271.0 |
300.0 |
H15 |
C8 |
S |
H16 |
239.8 |
240.1 |
C9 |
C8 |
S |
H14 |
180.0 |
180.1 |
S |
C8 |
C9 |
H15 |
119.9 |
120.0 |
S |
C8 |
C9 |
H16 |
240.1 |
240.0 |
C8 |
C9 |
N4 |
H11 |
292.8 |
360.0 |
N4 |
C9 |
C8 |
H17 |
234.9 |
120.1 |
N4 |
C9 |
C8 |
H18 |
125.1 |
240.0 |
H15 |
C8 |
C9 |
H16 |
120.2 |
120.0 |
H17 |
C9 |
C8 |
H18 |
250.2 |
120.0 |
S |
C8 |
C9 |
N4 |
36.1 |
180.0 |
N4 |
C9 |
C8 |
H15 |
276.2 |
60.0 |
N4 |
C9 |
C8 |
H16 |
156.0 |
300.1 |
C8 |
C9 |
N4 |
H17 |
125.1 |
240.0 |
C8 |
C9 |
N4 |
H18 |
234.9 |
120.0 |
C9 |
N4 |
C4 |
C5 |
284.7 |
180.0 |
H17 |
C9 |
N4 |
H18 |
109.8 |
240.0 |
N4 |
C4 |
C5 |
C6 |
179.0 |
179.6 |
N4 |
C4 |
C5 |
H12 |
359.1 |
359.9 |
C6 |
C5 |
C4 |
H12 |
180.0 |
179.8 |
C4 |
C5 |
C6 |
H13 |
180.9 |
180.0 |
C4 |
C5 |
C6 |
H12 |
180.0 |
180.2 |
C2 |
N1 |
C1' |
H10 |
305.3 |
173.9 |
C6 |
N1 |
C1' |
H10 |
125.1 |
353.7 |
N1 |
C1' |
C2' |
H8 |
343.6 |
2.8 |
N1 |
C1' |
C2' |
H9 |
221.8 |
240.1 |
C2' |
C1' |
N1 |
H10 |
121.6 |
121.0 |
O3' |
C3' |
C2' |
H6 |
235.2 |
236.4 |
C2' |
C3' |
O3' |
H7 |
180.0 |
67.3 |
C2' |
C3' |
C4' |
H5 |
82.0 |
81.6 |
N1 |
C1' |
C2' |
H10 |
238.1 |
238.9 |
C1' |
C2' |
C3' |
H6 |
275.6 |
262.6 |
H8 |
C2' |
C1' |
H9 |
121.8 |
122.6 |
C2' |
C3' |
O3' |
H6 |
124.1 |
123.7 |
O3' |
C3' |
C4' |
H5 |
319.9 |
323.4 |
O4' |
C4' |
C3' |
H5 |
243.0 |
241.4 |
C3' |
C4' |
C5' |
H3 |
257.9 |
62.9 |
C3' |
C4' |
C5' |
H4 |
17.4 |
302.8 |
C1' |
O4' |
C4' |
H5 |
269.0 |
281.4 |
C3' |
C4' |
O4' |
H5 |
116.3 |
118.5 |
O4' |
C4' |
C5' |
H3 |
140.1 |
308.7 |
O4' |
C4' |
C5' |
H4 |
259.6 |
188.6 |
H3 |
C5' |
C4' |
H4 |
240.5 |
120.1 |
C5' |
O5' |
P |
OP3 |
|
295.1 |
OP2 |
P |
O5' |
OP3 |
|
240.0 |
OP1 |
P |
O5' |
OP3 |
|
119.9 |
O5' |
P |
OP3 |
H20 |
|
300.0 |
O5' |
P |
OP2 |
OP3 |
|
120.0 |
OP1 |
P |
OP2 |
OP3 |
|
240.1 |
OP2 |
P |
OP3 |
H20 |
|
60.0 |
O5' |
P |
OP1 |
OP3 |
|
240.0 |
OP2 |
P |
OP1 |
OP3 |
|
120.0 |
OP1 |
P |
OP3 |
H20 |
|
180.0 |
H2 |
OP2 |
P |
OP3 |
|
60.0 |
C4' |
C5' |
H3 |
H4 |
119.2 |
239.9 |
C4' |
C5' |
H4 |
H3 |
240.8 |
120.0 |
H5 |
C4' |
C5' |
H3 |
19.2 |
185.7 |
H5 |
C4' |
C5' |
H4 |
138.7 |
65.6 |
H6 |
C3' |
O3' |
H7 |
55.9 |
303.5 |
H6 |
C3' |
C4' |
H5 |
198.0 |
199.9 |
H7 |
O3' |
C3' |
H6 |
55.9 |
303.5 |
H8 |
C2' |
C3' |
H6 |
34.7 |
21.4 |
C1' |
C2' |
H8 |
H9 |
237.4 |
237.4 |
H8 |
C2' |
C1' |
H10 |
105.6 |
123.9 |
H9 |
C2' |
C3' |
H6 |
156.5 |
143.9 |
C1' |
C2' |
H9 |
H8 |
122.6 |
122.6 |
H9 |
C2' |
C1' |
H10 |
343.8 |
1.3 |
H10 |
C1' |
C2' |
H8 |
105.6 |
123.9 |
H10 |
C1' |
C2' |
H9 |
343.8 |
1.3 |
H11 |
N4 |
C9 |
C8 |
292.8 |
360.0 |
H11 |
N4 |
C9 |
H17 |
167.7 |
120.0 |
H11 |
N4 |
C9 |
H18 |
57.9 |
240.0 |
H11 |
N4 |
C4 |
C5 |
104.7 |
0.1 |
C4 |
C5 |
H12 |
C6 |
180.0 |
179.8 |
H12 |
C5 |
C6 |
H13 |
0.9 |
359.8 |
H13 |
C6 |
C5 |
H12 |
0.9 |
359.8 |
H14 |
S |
C8 |
C9 |
180.0 |
180.1 |
H14 |
S |
C8 |
H15 |
299.9 |
300.1 |
H14 |
S |
C8 |
H16 |
60.1 |
60.0 |
S |
C8 |
H15 |
C9 |
240.6 |
240.0 |
H15 |
C8 |
S |
H14 |
299.9 |
300.1 |
S |
C8 |
H15 |
H16 |
120.3 |
119.9 |
C9 |
C8 |
H15 |
H16 |
239.7 |
240.0 |
H15 |
C8 |
C9 |
H17 |
41.3 |
300.0 |
H15 |
C8 |
C9 |
H18 |
151.1 |
180.0 |
S |
C8 |
H16 |
C9 |
119.4 |
120.0 |
H16 |
C8 |
S |
H14 |
60.1 |
60.0 |
S |
C8 |
H16 |
H15 |
239.7 |
240.1 |
C9 |
C8 |
H16 |
H15 |
120.3 |
120.0 |
H16 |
C8 |
C9 |
H17 |
281.1 |
180.0 |
H16 |
C8 |
C9 |
H18 |
30.9 |
60.0 |
N4 |
C9 |
H17 |
C8 |
169.2 |
239.9 |
H17 |
C9 |
C8 |
H15 |
41.3 |
300.0 |
H17 |
C9 |
C8 |
H16 |
281.1 |
180.0 |
C8 |
C9 |
H17 |
H18 |
95.4 |
240.0 |
H17 |
C9 |
N4 |
H11 |
167.7 |
120.0 |
N4 |
C9 |
H17 |
H18 |
264.6 |
120.0 |
N4 |
C9 |
H18 |
C8 |
190.8 |
120.0 |
H18 |
C9 |
C8 |
H15 |
151.1 |
180.0 |
H18 |
C9 |
C8 |
H16 |
30.9 |
60.0 |
C8 |
C9 |
H18 |
H17 |
264.6 |
120.0 |
H18 |
C9 |
N4 |
H11 |
57.9 |
240.0 |
N4 |
C9 |
H18 |
H17 |
95.4 |
240.0 |