PDB Chemical Component S1P

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 S1P

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C2 C1 1.523 1.530
O1 C1 1.428 1.429
C1 H1 1.100 1.089
C1 H1A 1.100 1.089
O1 P22 1.618 1.610
C3 C2 1.537 1.530
N2 C2 1.469 1.469
C2 H2 1.100 1.091
N2 HN2 1.000 1.009
N2 HN2A 1.000 1.009
C4 C3 1.516 1.508
C3 O3 1.429 1.429
C3 H3 1.100 1.090
O3 HO3 0.950 0.967
C5 C4 1.329 1.310
C4 H4 1.080 1.080
C6 C5 1.510 1.507
C5 H5 1.080 1.080
C7 C6 1.532 1.530
C6 H6 1.100 1.090
C6 H6A 1.100 1.089
C8 C7 1.508 1.530
C7 H7 1.100 1.090
C7 H7A 1.100 1.090
C8 C9 1.507 1.530
C8 H8 1.100 1.090
C8 H8A 1.100 1.090
C10 C9 1.518 1.531
C9 H9 1.100 1.089
C9 H9A 1.100 1.090
C11 C10 1.527 1.530
C10 H10 1.100 1.089
C10 H10A 1.099 1.090
C12 C11 1.531 1.530
C11 H11 1.100 1.090
C11 H11A 1.100 1.090
C12 C13 1.524 1.530
C12 H12 1.100 1.090
C12 H12A 1.100 1.089
C14 C13 1.543 1.530
C13 H13 1.100 1.090
C13 H13A 1.100 1.090
C14 C15 1.534 1.530
C14 H14 1.100 1.090
C14 H14A 1.100 1.090
C15 C16 1.529 1.530
C15 H15 1.100 1.089
C15 H15A 1.100 1.090
C16 C17 1.518 1.531
C16 H16 1.100 1.089
C16 H16A 1.100 1.090
C17 C18 1.517 1.530
C17 H17 1.100 1.090
C17 H17A 1.100 1.089
C18 H18 1.100 1.090
C18 H18A 1.100 1.089
C18 H18B 1.100 1.090
O25 P22 1.526 1.480
O24 P22 1.489 1.609
P22 O23 1.471 1.610
O23 HO23 0.950 0.967
O24 HO24 0.950 0.967

Bond Angles for S1P

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 C1 H1 109.9 109.5
C2 C1 H1A 109.9 109.5
O1 C1 H1 109.9 109.5
O1 C1 H1A 109.9 109.5
H1 C1 H1A 109.0 109.5
O1 P22 O23 107.0 109.5
C3 C2 H2 109.0 109.4
N2 C2 H2 109.0 109.5
HN2 N2 HN2A 109.5 111.0
C4 C3 H3 109.1 109.5
O3 C3 H3 111.7 109.5
C3 O3 HO3 109.5 114.0
C5 C4 H4 120.5 120.0
C6 C5 H5 120.0 120.0
C7 C6 H6 110.2 109.4
C7 C6 H6A 110.2 109.5
H6 C6 H6A 108.7 109.4
C8 C7 H7 109.9 109.5
C8 C7 H7A 109.8 109.5
H7 C7 H7A 109.1 109.4
C9 C8 H8 107.1 109.5
C9 C8 H8A 107.1 109.4
C8 C9 H9 111.2 109.5
C8 C9 H9A 111.2 109.4
H8 C8 H8A 111.8 109.5
C10 C9 H9 111.2 109.5
C10 C9 H9A 111.2 109.4
H9 C9 H9A 107.7 109.5
C11 C10 H10 107.5 109.5
C11 C10 H10A 107.5 109.5
H10 C10 H10A 111.4 109.5
C12 C11 H11 109.8 109.5
C12 C11 H11A 109.8 109.5
H11 C11 H11A 109.2 109.5
C13 C12 H12 109.8 109.4
C13 C12 H12A 109.8 109.5
C12 C13 H13 107.3 109.4
C12 C13 H13A 107.4 109.5
H12 C12 H12A 109.2 109.4
C14 C13 H13 107.4 109.5
C14 C13 H13A 107.3 109.5
H13 C13 H13A 111.5 109.4
C15 C14 H14 108.3 109.5
C15 C14 H14A 108.2 109.4
C14 C15 C16 115.1 109.4
C14 C15 H15 107.6 109.5
C14 C15 H15A 107.7 109.4
H14 C14 H14A 110.6 109.5
C16 C15 H15 107.7 109.5
C16 C15 H15A 107.7 109.4
C15 C16 C17 110.4 109.5
C15 C16 H16 109.2 109.5
C15 C16 H16A 109.2 109.5
H15 C15 H15A 111.2 109.5
C17 C16 H16 109.2 109.4
C17 C16 H16A 109.2 109.4
C16 C17 C18 112.5 109.5
C16 C17 H17 108.5 109.5
C16 C17 H17A 108.5 109.5
H16 C16 H16A 109.7 109.5
C18 C17 H17 108.5 109.5
C18 C17 H17A 108.5 109.5
C17 C18 H18 109.5 109.5
C17 C18 H18A 109.4 109.5
C17 C18 H18B 109.5 109.4
H17 C17 H17A 110.5 109.4
H18 C18 H18A 109.5 109.4
H18 C18 H18B 109.5 109.5
H18A C18 H18B 109.5 109.5
P22 O23 HO23 109.5 114.0

Torsion Angles for S1P

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O1 C1 C2 H1 240.0 120.0
O1 C1 C2 H1A 120.0 240.0
H1 C1 C2 H1A 240.0 120.0
C2 C1 O1 H1 120.0 240.0
C2 C1 O1 H1A 240.0 120.0
H1 C1 O1 H1A 120.0 240.0
C2 C1 H1 H1A 120.5 240.0
O1 C1 H1 H1A 239.4 120.0
C2 C1 H1A H1 239.5 120.0
O1 C1 H1A H1 120.6 240.0
P22 O1 C1 H1 114.9 300.0
P22 O1 C1 H1A 354.9 60.0
O1 P22 O23 HO23 115.5 60.0
C3 C2 C1 H1 59.4 55.0
C3 C2 C1 H1A 179.4 295.0
N2 C2 C3 H2 119.4 120.0
N2 C2 C1 H1 180.7 175.0
N2 C2 C1 H1A 300.7 55.0
C3 C2 N2 H2 240.6 240.0
H2 C2 C1 H1 300.1 295.1
H2 C2 C1 H1A 60.0 175.0
HN2 N2 C2 H2 61.0 56.0
HN2A N2 C2 H2 181.0 180.0
C4 C3 C2 H2 291.4 300.0
O3 C3 C4 H3 121.6 120.0
C4 C3 O3 HO3 300.3 60.0
O3 C3 C2 H2 49.8 60.0
C4 C3 O3 H3 240.0 240.0
H3 C3 C2 H2 171.4 180.0
H3 C3 O3 HO3 60.3 180.0
HO3 O3 C3 H3 60.3 180.0
C5 C4 C3 H3 358.4 245.0
H4 C4 C3 H3 178.4 65.0
C6 C5 C4 H4 359.9 0.0
H5 C5 C4 H4 179.8 180.0
C7 C6 C5 H5 308.0 305.1
H6 C6 C7 H6A 120.0 119.9
H6 C6 C5 H5 68.0 65.0
C7 C6 H6 H6A 239.1 240.0
H6A C6 C5 H5 188.0 185.0
C7 C6 H6A H6 120.9 119.9
C8 C7 C6 H6 120.9 60.0
C8 C7 C6 H6A 0.8 300.1
H7 C7 C8 H7A 120.0 120.0
H7 C7 C6 H6 240.9 180.0
H7 C7 C6 H6A 120.9 60.1
C8 C7 H7 H7A 239.6 240.0
H7A C7 C6 H6 0.9 300.0
H7A C7 C6 H6A 240.9 180.0
C8 C7 H7A H7 120.4 120.0
C9 C8 C7 H7 336.8 60.0
C9 C8 C7 H7A 216.8 300.0
H8 C8 C9 H8A 120.0 120.0
C10 C9 C8 H9 240.0 240.0
C10 C9 C8 H9A 120.0 119.9
H9 C9 C8 H9A 240.0 240.0
H8 C8 C7 H7 96.8 180.0
H8 C8 C7 H7A 336.8 60.0
C9 C8 H8 H8A 243.1 240.0
H8 C8 C9 H9 144.7 180.0
H8 C8 C9 H9A 264.8 300.0
H8A C8 C7 H7 216.8 300.0
H8A C8 C7 H7A 96.8 180.1
C9 C8 H8A H8 116.9 120.0
H8A C8 C9 H9 24.7 60.0
H8A C8 C9 H9A 144.8 180.0
C10 C9 C8 H8 24.7 59.9
C10 C9 C8 H8A 264.7 299.9
C8 C9 C10 H9 120.0 120.1
C8 C9 C10 H9A 240.0 240.1
H9 C9 C10 H9A 120.0 120.0
H9 C9 C8 H8 144.7 180.0
H9 C9 C8 H8A 24.7 60.0
C8 C9 H9 H9A 122.1 120.0
C10 C9 H9 H9A 237.9 240.0
H9A C9 C8 H8 264.8 300.0
H9A C9 C8 H8A 144.8 180.0
C8 C9 H9A H9 238.0 239.9
C10 C9 H9A H9 122.1 120.0
C11 C10 C9 H9 349.4 60.0
C11 C10 C9 H9A 229.3 300.0
H10 C10 C11 H10A 120.0 120.1
H10 C10 C9 H9 109.4 180.0
H10 C10 C9 H9A 349.4 60.0
C11 C10 H10 H10A 242.5 240.0
H10A C10 C9 H9 229.4 300.0
H10A C10 C9 H9A 109.3 180.0
C11 C10 H10A H10 117.5 120.1
C12 C11 C10 H10 69.8 60.1
C12 C11 C10 H10A 309.8 300.0
H11 C11 C12 H11A 120.0 120.0
H11 C11 C10 H10 189.8 180.0
H11 C11 C10 H10A 69.8 60.0
C12 C11 H11 H11A 239.6 240.0
H11A C11 C10 H10 309.8 300.1
H11A C11 C10 H10A 189.8 180.0
C12 C11 H11A H11 120.3 120.0
C13 C12 C11 H11 114.5 60.0
C13 C12 C11 H11A 354.5 300.0
H12 C12 C13 H12A 120.0 120.0
C14 C13 C12 H13 240.0 240.0
C14 C13 C12 H13A 120.0 120.1
H13 C13 C12 H13A 240.0 240.1
H12 C12 C11 H11 234.5 180.0
H12 C12 C11 H11A 114.5 60.0
C13 C12 H12 H12A 239.6 240.0
H12 C12 C13 H13 160.6 180.0
H12 C12 C13 H13A 280.6 299.9
H12A C12 C11 H11 354.5 300.0
H12A C12 C11 H11A 234.5 179.9
C13 C12 H12A H12 120.4 120.0
H12A C12 C13 H13 40.6 60.0
H12A C12 C13 H13A 160.6 180.0
C14 C13 C12 H12 40.6 60.0
C14 C13 C12 H12A 280.6 300.0
C12 C13 C14 H13 120.0 120.0
C12 C13 C14 H13A 240.0 240.0
H13 C13 C14 H13A 120.0 120.0
H13 C13 C12 H12 160.6 180.0
H13 C13 C12 H12A 40.6 60.0
C12 C13 H13 H13A 117.3 120.0
C14 C13 H13 H13A 242.7 240.0
H13A C13 C12 H12 280.6 299.9
H13A C13 C12 H12A 160.6 180.0
C12 C13 H13A H13 242.7 240.1
C14 C13 H13A H13 117.3 120.0
C15 C14 C13 H13 141.8 60.0
C15 C14 C13 H13A 21.8 300.0
H14 C14 C15 H14A 120.0 120.0
C16 C15 C14 H15 240.0 240.0
C16 C15 C14 H15A 120.0 119.9
C14 C15 C16 C17 177.0 180.0
C14 C15 C16 H16 297.0 300.0
C14 C15 C16 H16A 57.0 60.1
H15 C15 C14 H15A 240.0 240.0
H14 C14 C13 H13 261.9 180.0
H14 C14 C13 H13A 141.9 60.0
C15 C14 H14 H14A 241.5 240.0
H14 C14 C15 C16 181.8 60.0
H14 C14 C15 H15 301.8 180.0
H14 C14 C15 H15A 61.8 300.0
H14A C14 C13 H13 21.8 300.0
H14A C14 C13 H13A 261.8 180.0
C15 C14 H14A H14 118.5 120.1
H14A C14 C15 C16 61.9 299.9
H14A C14 C15 H15 181.9 60.0
H14A C14 C15 H15A 301.9 180.0
C16 C15 C14 H14 181.8 60.0
C16 C15 C14 H14A 61.9 299.9
C14 C15 C16 H15 120.0 120.0
C14 C15 C16 H15A 240.0 240.1
H15 C15 C16 H15A 120.0 120.0
C17 C16 C15 H16 240.0 240.0
C17 C16 C15 H16A 120.0 119.9
C15 C16 C17 C18 166.9 180.1
C15 C16 C17 H17 286.8 300.0
C15 C16 C17 H17A 46.9 60.0
H16 C16 C15 H16A 240.0 239.9
H15 C15 C14 H14 301.8 180.0
H15 C15 C14 H14A 181.9 60.0
C14 C15 H15 C16 235.4 240.0
C14 C15 H15 H15A 117.7 120.0
C16 C15 H15 H15A 242.3 240.0
H15 C15 C16 C17 57.0 60.0
H15 C15 C16 H16 177.0 180.0
H15 C15 C16 H16A 297.0 300.0
H15A C15 C14 H14 61.8 300.0
H15A C15 C14 H14A 301.9 180.0
C14 C15 H15A C16 124.6 119.9
C14 C15 H15A H15 242.3 239.9
C16 C15 H15A H15 117.7 120.0
H15A C15 C16 C17 297.0 300.0
H15A C15 C16 H16 57.0 59.9
H15A C15 C16 H16A 177.0 180.0
C17 C16 C15 H15 57.0 60.0
C17 C16 C15 H15A 297.0 300.0
C15 C16 C17 H16 120.0 120.0
C15 C16 C17 H16A 240.0 240.0
H16 C16 C17 H16A 119.9 120.0
C18 C17 C16 H17 240.0 240.0
C18 C17 C16 H17A 120.0 120.0
C16 C17 C18 H18 180.0 300.0
C16 C17 C18 H18A 300.0 60.0
C16 C17 C18 H18B 60.0 180.0
H17 C17 C16 H17A 240.0 240.0
H16 C16 C15 H15 177.0 180.0
H16 C16 C15 H15A 57.0 59.9
C15 C16 H16 C17 239.2 240.0
C15 C16 H16 H16A 119.6 120.1
C17 C16 H16 H16A 240.4 240.1
H16 C16 C17 C18 46.8 60.0
H16 C16 C17 H17 166.8 180.0
H16 C16 C17 H17A 286.9 300.0
H16A C16 C15 H15 297.0 300.0
H16A C16 C15 H15A 177.0 180.0
C15 C16 H16A C17 120.8 120.0
C15 C16 H16A H16 240.4 239.9
C17 C16 H16A H16 119.6 119.9
H16A C16 C17 C18 286.9 300.0
H16A C16 C17 H17 46.9 60.0
H16A C16 C17 H17A 166.9 180.0
C18 C17 C16 H16 46.8 60.0
C18 C17 C16 H16A 286.9 300.0
C16 C17 C18 H17 120.0 120.0
C16 C17 C18 H17A 240.0 240.0
H17 C17 C18 H17A 120.0 120.0
H18 C18 C17 H18A 240.0 240.0
H18 C18 C17 H18B 120.0 120.0
H18A C18 C17 H18B 240.0 240.0
H17 C17 C16 H16 166.8 180.0
H17 C17 C16 H16A 46.9 60.0
C16 C17 H17 C18 237.5 240.0
C16 C17 H17 H17A 118.8 120.0
C18 C17 H17 H17A 241.3 240.0
H17 C17 C18 H18 60.0 180.0
H17 C17 C18 H18A 180.0 300.0
H17 C17 C18 H18B 300.0 60.0
H17A C17 C16 H16 286.9 300.0
H17A C17 C16 H16A 166.9 180.0
C16 C17 H17A C18 122.5 120.0
C16 C17 H17A H17 241.2 240.0
C18 C17 H17A H17 118.7 120.0
H17A C17 C18 H18 300.0 60.0
H17A C17 C18 H18A 60.0 180.0
H17A C17 C18 H18B 180.0 300.0
H18 C18 C17 H17 60.0 180.0
H18 C18 C17 H17A 300.0 60.0
C17 C18 H18 H18A 120.0 120.0
C17 C18 H18 H18B 240.0 240.0
H18A C18 H18 H18B 120.0 120.0
H18A C18 C17 H17 180.0 300.0
H18A C18 C17 H17A 60.0 180.0
C17 C18 H18A H18 240.0 240.0
C17 C18 H18A H18B 120.0 120.0
H18 C18 H18A H18B 240.0 240.0
H18B C18 C17 H17 300.0 60.0
H18B C18 C17 H17A 180.0 300.0
C17 C18 H18B H18 120.0 120.0
C17 C18 H18B H18A 240.0 240.0
H18 C18 H18B H18A 120.0 120.0
O25 P22 O23 HO23 0.0 180.0
O24 P22 O23 HO23 231.2 300.0