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