PDB Chemical Component Y2F

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 Y2F

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C02 N01 1.356 1.324
C06 N01 1.359 1.320
C03 C02 1.397 1.392
C02 N02 1.358 1.390
N02 HN02 1.000 0.970
N02 HN0A 1.000 0.970
C04 C03 1.398 1.383
C03 H03 1.080 1.080
C07 C04 1.511 1.507
C04 C05 1.404 1.389
C05 C06 1.395 1.380
C05 H05 1.080 1.080
C06 C08 1.526 1.507
C07 H07 1.100 1.089
C07 H07A 1.100 1.089
C07 H07B 1.100 1.090
C4' C08 1.537 1.530
C08 H08 1.100 1.089
C08 H08A 1.099 1.090
C3' O09 1.427 1.430
O09 C10 1.426 1.429
N1' C5' 1.470 1.486
N1' C2' 1.450 1.486
N1' HN1' 1.000 1.009
C10 C11 1.529 1.529
C10 H10 1.101 1.091
C10 H10A 1.100 1.091
N12 C11 1.451 1.470
C11 H11 1.100 1.090
C11 H11A 1.100 1.090
N12 C13 1.461 1.469
N12 HN12 1.000 1.008
C13 C15 1.533 1.529
C13 C14 1.525 1.530
C13 H13 1.100 1.090
C14 H14 1.100 1.090
C14 H14A 1.100 1.090
C14 H14B 1.100 1.090
C15 C21 1.527 1.507
C15 H15 1.100 1.091
C15 H15A 1.100 1.090
C2' C3' 1.532 1.544
C2' H2' 1.100 1.090
C2' H2'A 1.100 1.089
C22 C21 1.400 1.382
C21 C26 1.382 1.382
C22 C23 1.402 1.382
C22 H22 1.080 1.081
C23 C24 1.398 1.382
C23 H23 1.080 1.080
C24 C25 1.389 1.385
C24 H24 1.080 1.079
C26 C25 1.387 1.385
C25 F25 1.348 1.351
C26 H26 1.080 1.080
C4' C3' 1.520 1.543
C3' H3' 1.100 1.090
C5' C4' 1.544 1.543
C4' H4' 1.100 1.089
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.089

Bond Angles for Y2F

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C02 N02 HN02 109.5 119.9
C02 N02 HN0A 109.5 120.0
HN02 N02 HN0A 109.5 120.0
C04 C03 H03 120.1 120.4
C04 C05 C06 119.0 119.3
C04 C05 H05 120.5 120.4
C06 C05 H05 120.5 120.3
C05 C06 C08 120.8 119.6
C06 C08 H08 109.3 109.5
C06 C08 H08A 109.3 109.4
H07 C07 H07A 109.4 109.5
H07 C07 H07B 109.5 109.5
H07A C07 H07B 109.5 109.4
C4' C08 H08 109.3 109.5
C4' C08 H08A 109.3 109.4
H08 C08 H08A 109.6 109.6
O09 C10 C11 107.8 109.5
O09 C10 H10 110.0 109.5
O09 C10 H10A 110.1 109.4
C2' N1' C5' 111.9 104.2
C5' N1' HN1' 108.7 111.0
N1' C5' C4' 103.9 104.6
N1' C5' H5' 111.4 110.4
N1' C5' H5'A 111.4 110.5
C2' N1' HN1' 108.7 111.0
N1' C2' C3' 102.9 104.6
N1' C2' H2' 111.7 110.4
N1' C2' H2'A 111.7 110.4
C11 C10 H10 110.0 109.5
C11 C10 H10A 110.0 109.5
C10 C11 H11 107.9 109.5
C10 C11 H11A 107.8 109.5
H10 C10 H10A 108.9 109.5
N12 C11 H11 107.9 109.5
N12 C11 H11A 107.9 109.4
H11 C11 H11A 111.1 109.5
C13 N12 HN12 105.7 111.0
N12 C13 C15 111.2 109.5
N12 C13 C14 112.7 109.5
N12 C13 H13 106.1 109.5
C14 C13 C15 110.0 109.5
C15 C13 H13 109.1 109.5
C13 C15 C21 112.6 109.5
C13 C15 H15 108.5 109.5
C13 C15 H15A 108.4 109.5
C14 C13 H13 107.5 109.4
C13 C14 H14 109.5 109.5
C13 C14 H14A 109.5 109.5
C13 C14 H14B 109.5 109.5
H14 C14 H14A 109.5 109.4
H14 C14 H14B 109.4 109.5
H14A C14 H14B 109.5 109.4
C21 C15 H15 108.4 109.4
C21 C15 H15A 108.5 109.5
C15 C21 C26 118.1 120.0
H15 C15 H15A 110.5 109.4
C3' C2' H2' 111.7 110.4
C3' C2' H2'A 111.7 110.4
C2' C3' H3' 113.2 110.3
H2' C2' H2'A 107.2 110.4
C22 C21 C26 118.3 120.0
C21 C26 C25 120.9 120.0
C21 C26 H26 119.5 120.1
C23 C22 H22 119.3 120.0
C22 C23 C24 119.3 120.0
C22 C23 H23 120.3 120.0
C24 C23 H23 120.4 119.9
C23 C24 C25 119.0 120.0
C23 C24 H24 120.5 120.0
C25 C24 H24 120.5 120.0
C24 C25 F25 122.6 120.0
C4' C3' H3' 114.7 110.4
C5' C4' H4' 112.6 110.5
H5' C5' H5'A 107.5 110.5

Torsion Angles for Y2F

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C03 C02 N02 HN02 180.6 180.0
C03 C02 N02 HN0A 300.7 0.0
HN02 N02 C02 HN0A 240.0 180.0
C02 N02 HN02 HN0A 120.0 180.0
C02 N02 HN0A HN02 239.9 180.0
C07 C04 C03 H03 359.7 0.1
C07 C04 C05 H05 0.6 0.0
C05 C04 C03 H03 180.0 180.1
C06 C05 C04 H05 180.0 180.0
C04 C05 C06 C08 179.3 180.0
C04 C05 C06 H05 180.0 180.0
C05 C06 C08 H08 51.8 245.0
C05 C06 C08 H08A 171.8 5.1
C04 C05 H05 C06 180.0 180.0
H05 C05 C06 C08 359.3 359.9
C08 C06 C05 H05 359.3 359.9
C4' C08 C06 H08 240.0 240.0
C4' C08 C06 H08A 120.0 119.9
H08 C08 C06 H08A 240.0 239.9
H07A C07 H07 H07B 120.0 120.0
H07 C07 H07A H07B 240.0 240.0
H07 C07 H07B H07A 120.0 120.0
C06 C08 C4' H08 120.0 120.0
C06 C08 C4' H08A 240.0 240.1
H08 C08 C4' H08A 120.0 120.1
C06 C08 H08 H08A 119.8 120.0
C4' C08 H08 H08A 240.2 240.0
C06 C08 H08A H08 240.2 240.0
C4' C08 H08A H08 119.9 120.1
C3' O09 C10 H10 296.0 300.0
C3' O09 C10 H10A 56.0 60.0
C11 C10 O09 H10 240.0 239.9
C11 C10 O09 H10A 120.0 120.0
O09 C10 C11 H11 189.7 185.0
O09 C10 C11 H11A 309.8 305.1
H10 C10 O09 H10A 240.0 240.0
C2' N1' C5' HN1' 240.0 240.5
C5' N1' C2' C3' 16.9 320.5
C5' N1' C2' H2' 136.9 79.3
C5' N1' C2' H2'A 256.9 201.7
N1' C5' C4' H4' 92.2 95.1
H5' C5' N1' H5'A 240.0 237.6
C5' N1' C2' HN1' 120.0 119.5
C2' N1' C5' C4' 7.9 39.5
C2' N1' C5' H5' 127.9 158.2
C2' N1' C5' H5'A 247.9 280.7
C3' C2' N1' H2' 240.0 241.2
C3' C2' N1' H2'A 120.0 118.8
N1' C2' C3' H3' 200.2 264.8
H2' C2' N1' H2'A 240.0 237.6
C2' N1' HN1' C5' 122.0 115.4
HN1' N1' C5' C4' 127.9 159.0
HN1' N1' C5' H5' 247.9 277.7
HN1' N1' C5' H5'A 7.9 40.2
HN1' N1' C2' C3' 256.9 201.0
HN1' N1' C2' H2' 16.9 319.8
HN1' N1' C2' H2'A 136.9 82.2
O09 C10 C11 H10 120.0 120.0
O09 C10 C11 H10A 240.0 240.0
H10 C10 C11 H10A 120.0 120.0
N12 C11 C10 H11 240.0 240.0
N12 C11 C10 H11A 120.0 120.0
H11 C11 C10 H11A 240.0 240.0
O09 C10 H10 C11 241.4 240.0
O09 C10 H10 H10A 120.7 120.0
C11 C10 H10 H10A 239.3 240.0
H10 C10 C11 H11 69.7 65.0
H10 C10 C11 H11A 189.8 185.0
O09 C10 H10A C11 118.6 120.0
O09 C10 H10A H10 239.3 240.0
C11 C10 H10A H10 120.7 120.0
H10A C10 C11 H11 309.8 305.0
H10A C10 C11 H11A 69.8 65.0
N12 C11 C10 H10 309.7 305.0
N12 C11 C10 H10A 189.8 185.0
C10 C11 N12 H11 120.0 120.0
C10 C11 N12 H11A 240.0 240.0
H11 C11 N12 H11A 120.0 120.0
H11 C11 C10 H10 69.7 65.0
H11 C11 C10 H10A 309.8 305.0
C10 C11 H11 H11A 118.0 120.1
N12 C11 H11 H11A 242.0 240.1
H11A C11 C10 H10 189.8 185.0
H11A C11 C10 H10A 69.8 65.0
C10 C11 H11A H11 242.0 239.9
N12 C11 H11A H11 118.0 120.0
C13 N12 C11 H11 23.0 60.0
C13 N12 C11 H11A 262.9 300.0
C14 C13 N12 C15 235.9 240.0
C15 C13 N12 H13 241.5 240.0
N12 C13 C15 C21 175.9 65.0
N12 C13 C15 H15 295.9 185.0
N12 C13 C15 H15A 55.9 305.0
C14 C13 N12 H13 117.4 119.9
N12 C13 C14 H14 180.0 300.0
N12 C13 C14 H14A 300.0 60.0
N12 C13 C14 H14B 60.0 180.0
HN12 N12 C11 H11 143.0 183.9
HN12 N12 C11 H11A 22.9 63.9
HN12 N12 C13 C15 13.5 81.1
HN12 N12 C13 C14 249.4 321.0
HN12 N12 C13 H13 132.0 201.1
C15 C13 N12 HN12 13.5 81.1
N12 C13 C15 C14 234.3 240.0
N12 C13 C15 H13 116.7 120.0
C14 C13 C15 H13 242.4 240.0
C15 C13 C14 H14 55.2 180.0
C15 C13 C14 H14A 175.2 300.0
C15 C13 C14 H14B 295.2 60.0
C21 C15 C13 H15 240.0 240.0
C21 C15 C13 H15A 120.0 120.1
C13 C15 C21 C26 124.6 89.9
H15 C15 C13 H15A 240.0 240.1
C14 C13 N12 HN12 249.4 321.0
N12 C13 C14 C15 124.8 120.0
N12 C13 C14 H13 243.4 240.0
C15 C13 C14 H13 118.6 120.0
C14 C13 C15 C21 301.6 185.0
C14 C13 C15 H15 61.6 305.0
C14 C13 C15 H15A 181.6 65.0
H14 C14 C13 H14A 240.0 240.0
H14 C14 C13 H14B 120.0 120.1
H14A C14 C13 H14B 240.0 240.0
H13 C13 N12 HN12 132.0 201.1
N12 C13 H13 C15 240.1 240.0
N12 C13 H13 C14 120.9 120.0
C14 C13 H13 C15 119.2 120.0
H13 C13 C15 C21 59.2 305.0
H13 C13 C15 H15 179.2 65.0
H13 C13 C15 H15A 299.2 184.9
H13 C13 C14 H14 296.6 60.0
H13 C13 C14 H14A 56.6 180.0
H13 C13 C14 H14B 176.6 300.0
H14 C14 C13 C15 55.2 180.0
H14 C14 C13 H13 296.6 60.0
C13 C14 H14 H14A 120.0 120.0
C13 C14 H14 H14B 240.0 239.9
H14A C14 H14 H14B 120.0 119.9
H14A C14 C13 C15 175.2 300.0
H14A C14 C13 H13 56.6 180.0
C13 C14 H14A H14 240.0 239.9
C13 C14 H14A H14B 120.0 120.0
H14 C14 H14A H14B 240.0 240.1
H14B C14 C13 C15 295.2 60.0
H14B C14 C13 H13 176.6 300.0
C13 C14 H14B H14 120.0 120.1
C13 C14 H14B H14A 240.0 240.0
H14 C14 H14B H14A 120.0 119.9
C21 C15 C13 H13 59.2 305.0
C13 C15 C21 H15 120.0 120.0
C13 C15 C21 H15A 240.0 239.9
H15 C15 C21 H15A 120.0 119.9
C22 C21 C15 C26 179.6 180.4
C15 C21 C26 C25 179.1 179.8
C15 C21 C26 H26 359.1 0.1
H15 C15 C13 H13 179.2 65.0
C13 C15 H15 C21 237.5 239.9
C13 C15 H15 H15A 118.7 120.0
C21 C15 H15 H15A 241.3 240.1
H15 C15 C21 C26 4.6 329.9
H15A C15 C13 H13 299.2 184.9
C13 C15 H15A C21 122.5 120.1
C13 C15 H15A H15 241.3 240.0
C21 C15 H15A H15 118.7 119.9
H15A C15 C21 C26 244.6 210.0
C3' C2' N1' C5' 16.9 320.5
C3' C2' N1' HN1' 256.9 201.0
N1' C2' C3' H2' 120.0 118.8
N1' C2' C3' H2'A 240.0 241.2
H2' C2' C3' H2'A 120.0 122.4
C4' C3' C2' H3' 124.6 119.0
H2' C2' N1' C5' 136.9 79.3
H2' C2' N1' HN1' 16.9 319.8
N1' C2' H2' C3' 245.3 244.8
N1' C2' H2' H2'A 122.7 122.4
C3' C2' H2' H2'A 237.4 237.6
H2' C2' C3' H3' 80.3 146.1
H2'A C2' N1' C5' 256.9 201.7
H2'A C2' N1' HN1' 136.9 82.2
N1' C2' H2'A C3' 114.7 115.2
N1' C2' H2'A H2' 237.4 237.6
C3' C2' H2'A H2' 122.6 122.4
H2'A C2' C3' H3' 320.2 23.6
C22 C21 C15 H15 184.2 150.3
C22 C21 C15 H15A 64.2 30.4
C15 C21 C22 C26 180.4 179.6
C22 C21 C26 C25 359.4 359.4
C22 C21 C26 H26 179.4 179.7
C26 C21 C15 H15 4.6 329.9
C26 C21 C15 H15A 244.6 210.0
C23 C22 C21 C26 0.6 0.4
C24 C23 C22 H23 180.0 180.0
C22 C23 C24 C25 0.7 0.0
C22 C23 C24 H24 180.7 180.0
H22 C22 C21 C26 180.6 180.2
H22 C22 C23 C24 179.3 180.1
H22 C22 C23 H23 359.3 0.0
C24 C23 C22 H22 179.3 180.1
C22 C23 C24 H23 180.0 180.0
C25 C24 C23 H24 180.0 180.0
C23 C24 C25 F25 179.2 180.0
H23 C23 C22 H22 359.3 0.0
C22 C23 H23 C24 180.0 180.0
H23 C23 C24 C25 180.7 180.1
H23 C23 C24 H24 0.7 0.0
C21 C26 C25 C24 0.6 0.6
C25 C24 C23 H23 180.7 180.1
C23 C24 C25 H24 180.0 180.0
H24 C24 C23 H23 0.7 0.0
C23 C24 H24 C25 180.0 180.0
H24 C24 C25 F25 359.2 360.0
C21 C26 C25 H26 180.0 180.3
C26 C25 C24 H24 179.4 179.8
C21 C26 C25 F25 180.8 180.3
F25 C25 C24 H24 359.2 360.0
C21 C26 H26 C25 180.0 179.7
C3' C4' C08 H08 51.3 55.0
C3' C4' C08 H08A 291.2 294.9
N1' C5' C4' C3' 330.6 336.1
C4' C3' C2' H2' 204.8 265.1
C4' C3' C2' H2'A 84.8 142.6
C2' C3' C4' H3' 236.4 241.1
H3' C3' C2' H2' 80.3 146.1
H3' C3' C2' H2'A 320.2 23.6
C5' C4' C08 H08 170.2 170.6
C5' C4' C08 H08A 50.2 50.5
C4' C5' N1' HN1' 127.9 159.0
N1' C5' C4' H5' 120.0 118.7
N1' C5' C4' H5'A 240.0 241.2
C5' C4' C3' H3' 163.4 118.9
H4' C4' C08 H08 290.5 292.9
H4' C4' C08 H08A 170.5 172.8
H4' C4' C3' H3' 42.2 359.9
H5' C5' N1' HN1' 247.9 277.7
N1' C5' H5' C4' 244.5 244.8
N1' C5' H5' H5'A 122.3 122.4
H5' C5' C4' H4' 332.2 336.3
H5'A C5' N1' HN1' 7.9 40.2
N1' C5' H5'A C4' 115.5 115.2
N1' C5' H5'A H5' 237.7 237.6
H5'A C5' C4' H4' 212.3 213.9