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