# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:26:49 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 2-[[(2~{S})-2-decanoyloxypropoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)O[C@@H](C)CO[P](O)(=O)OCC[N+](C)(C)C
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 S9Y  S9Y  2-[[(2~{S})-2-decanoyloxypropoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium  ligand  64  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S9Y
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 S9Y  C3   C  CH3    0  -0.683  -1.9592  -3.2884   2.0197
 S9Y  C2   C  CH1    0  -0.015  -1.7812  -3.2002   0.5155
 S9Y  C1   C  CH2    0  -0.165  -3.0690  -2.9257  -0.2297
 S9Y  O3P  O  O2     0  -0.610  -3.6551  -1.7397   0.2600
 S9Y  P    P  P      0   1.362  -4.9075  -1.0721  -0.5649
 S9Y  O2   O  O2     0  -0.463  -0.8760  -2.1337   0.1783
 S9Y  C31  C  C      0   0.611   0.4330  -2.3443   0.2462
 S9Y  O31  O  O      0  -0.454   0.9282  -3.3971   0.5641
 S9Y  C32  C  CH2    0  -0.587   1.2051  -1.1084  -0.1327
 S9Y  C33  C  CH2    0  -0.416   2.6958  -1.2035   0.1496
 S9Y  C34  C  CH2    0  -0.416   3.4244   0.0861  -0.2060
 S9Y  C35  C  CH2    0  -0.413   4.9174   0.0213   0.0891
 S9Y  C36  C  CH2    0  -0.412   5.6536   1.3118  -0.2466
 S9Y  C37  C  CH2    0  -0.412   7.1455   1.2482   0.0564
 S9Y  C38  C  CH2    0  -0.407   7.8835   2.5389  -0.2741
 S9Y  C39  C  CH2    0  -0.418   9.3749   2.4768   0.0327
 S9Y  C40  C  CH3    0  -0.662  10.1028   3.7707  -0.3040
 S9Y  O1   O  OP    -1  -0.787  -4.4633  -0.6684  -1.9388
 S9Y  O4   O  O      0  -0.774  -6.1319  -1.9057  -0.3707
 S9Y  O5   O  O2     0  -0.612  -4.9986   0.2534   0.4102
 S9Y  C4   C  CH2    0  -0.183  -5.0871   1.5577  -0.1077
 S9Y  C5   C  CH2    0  -0.339  -4.1251   2.5205   0.5525
 S9Y  N1   N  NT     1  -0.379  -2.6495   2.3302   0.2924
 S9Y  C6   C  CH3    0  -0.547  -1.9625   3.5783   0.7352
 S9Y  C7   C  CH3    0  -0.568  -2.0871   1.1944   1.0796
 S9Y  C8   C  CH3    0  -0.569  -2.3731   2.1132  -1.1542
 S9Y  H1   H  HCH3   0   0.238  -2.2856  -2.3386   2.4411
 S9Y  H2   H  HCH3   0   0.238  -2.7112  -4.0412   2.2578
 S9Y  H3   H  HCH3   0   0.244  -1.0319  -3.5816   2.5097
 S9Y  H4   H  HCH1   0   0.250  -1.3901  -4.1480   0.1353
 S9Y  H5   H  HCH2   0   0.230  -2.8589  -2.8542  -1.3026
 S9Y  H6   H  HCH2   0   0.222  -3.7327  -3.7849  -0.0827
 S9Y  H7   H  HCH2   0   0.277   1.0295  -0.9136  -1.1962
 S9Y  H8   H  HCH2   0   0.261   0.7721  -0.2534   0.3946
 S9Y  H9   H  HCH2   0   0.224   2.8557  -1.4294   1.2077
 S9Y  H10  H  HCH2   0   0.225   3.1301  -2.0341  -0.4128
 S9Y  H11  H  HCH2   0   0.213   3.2730   0.3141  -1.2667
 S9Y  H12  H  HCH2   0   0.211   2.9804   0.9206   0.3482
 S9Y  H13  H  HCH2   0   0.208   5.0653  -0.2161   1.1485
 S9Y  H14  H  HCH2   0   0.209   5.3632  -0.8083  -0.4709
 S9Y  H15  H  HCH2   0   0.207   5.5093   1.5490  -1.3066
 S9Y  H16  H  HCH2   0   0.207   5.2047   2.1413   0.3113
 S9Y  H17  H  HCH2   0   0.206   7.2887   1.0086   1.1160
 S9Y  H18  H  HCH2   0   0.206   7.5946   0.4197  -0.5028
 S9Y  H19  H  HCH2   0   0.206   7.7430   2.7779  -1.3344
 S9Y  H20  H  HCH2   0   0.206   7.4332   3.3684   0.2829
 S9Y  H21  H  HCH2   0   0.210   9.5152   2.2408   1.0921
 S9Y  H22  H  HCH2   0   0.210   9.8232   1.6471  -0.5230
 S9Y  H23  H  HCH3   0   0.215  10.0157   4.0066  -1.3665
 S9Y  H24  H  HCH3   0   0.215   9.6871   4.6125   0.2534
 S9Y  H25  H  HCH3   0   0.226  11.1653   3.7090  -0.0656
 S9Y  H27  H  HCH2   0   0.243  -4.9749   1.5813  -1.1932
 S9Y  H28  H  HCH2   0   0.258  -6.0785   1.9687   0.1079
 S9Y  H29  H  HCH2   0   0.302  -4.3692   3.5174   0.1852
 S9Y  H30  H  HCH2   0   0.302  -4.2476   2.5225   1.6352
 S9Y  H31  H  HCH3   0   0.295  -2.3407   4.4206   0.1620
 S9Y  H32  H  HCH3   0   0.296  -2.1576   3.7341   1.7931
 S9Y  H33  H  HCH3   0   0.293  -0.8937   3.4713   0.5720
 S9Y  H34  H  HCH3   0   0.275  -1.0047   1.2152   0.9792
 S9Y  H35  H  HCH3   0   0.291  -2.3529   1.3239   2.1252
 S9Y  H36  H  HCH3   0   0.315  -2.4633   0.2475   0.7144
 S9Y  H37  H  HCH3   0   0.295  -2.7909   2.9379  -1.7270
 S9Y  H38  H  HCH3   0   0.290  -1.2963   2.0785  -1.2984
 S9Y  H39  H  HCH3   0   0.297  -2.8155   1.1747  -1.4786

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 S9Y  C40  C39  single  1.522  0.020  1.522
 S9Y  C39  C38  single  1.524  0.020  1.524
 S9Y  C38  C37  single  1.523  0.020  1.523
 S9Y  C37  C36  single  1.524  0.020  1.524
 S9Y  C36  C35  single  1.523  0.020  1.523
 S9Y  C35  C34  single  1.523  0.020  1.523
 S9Y  C34  C33  single  1.523  0.020  1.523
 S9Y  C33  C32  single  1.520  0.020  1.520
 S9Y  C32  C31  single  1.506  0.020  1.506
 S9Y  C31  O31  double  1.206  0.020  1.206
 S9Y  C31  O2   single  1.328  0.020  1.328
 S9Y  C3   C2   single  1.517  0.020  1.517
 S9Y  O2   C2   single  1.439  0.020  1.439
 S9Y  C2   C1   single  1.513  0.020  1.513
 S9Y  C1   O3P  single  1.411  0.020  1.411
 S9Y  O3P  P    single  1.642  0.020  1.642
 S9Y  C6   N1   single  1.492  0.020  1.492
 S9Y  O4   P    deloc   1.494  0.020  1.494
 S9Y  O5   P    single  1.648  0.020  1.648
 S9Y  O5   C4   single  1.406  0.020  1.406
 S9Y  P    O1   deloc   1.499  0.020  1.499
 S9Y  C4   C5   single  1.513  0.020  1.513
 S9Y  N1   C8   single  1.489  0.020  1.489
 S9Y  N1   C5   single  1.510  0.020  1.510
 S9Y  N1   C7   single  1.492  0.020  1.492
 S9Y  C3   H1   single  0.970  0.020  1.090
 S9Y  C3   H2   single  0.970  0.020  1.090
 S9Y  C3   H3   single  0.970  0.020  1.090
 S9Y  C2   H4   single  0.970  0.020  1.090
 S9Y  C1   H5   single  0.970  0.020  1.090
 S9Y  C1   H6   single  0.970  0.020  1.090
 S9Y  C32  H7   single  0.970  0.020  1.090
 S9Y  C32  H8   single  0.970  0.020  1.090
 S9Y  C33  H9   single  0.970  0.020  1.090
 S9Y  C33  H10  single  0.970  0.020  1.090
 S9Y  C34  H11  single  0.970  0.020  1.090
 S9Y  C34  H12  single  0.970  0.020  1.090
 S9Y  C35  H13  single  0.970  0.020  1.090
 S9Y  C35  H14  single  0.970  0.020  1.090
 S9Y  C36  H15  single  0.970  0.020  1.090
 S9Y  C36  H16  single  0.970  0.020  1.090
 S9Y  C37  H17  single  0.970  0.020  1.090
 S9Y  C37  H18  single  0.970  0.020  1.090
 S9Y  C38  H19  single  0.970  0.020  1.090
 S9Y  C38  H20  single  0.970  0.020  1.090
 S9Y  C39  H21  single  0.970  0.020  1.090
 S9Y  C39  H22  single  0.970  0.020  1.090
 S9Y  C40  H23  single  0.970  0.020  1.090
 S9Y  C40  H24  single  0.970  0.020  1.090
 S9Y  C40  H25  single  0.970  0.020  1.090
 S9Y  C4   H27  single  0.970  0.020  1.090
 S9Y  C4   H28  single  0.970  0.020  1.090
 S9Y  C5   H29  single  0.970  0.020  1.090
 S9Y  C5   H30  single  0.970  0.020  1.090
 S9Y  C6   H31  single  0.970  0.020  1.090
 S9Y  C6   H32  single  0.970  0.020  1.090
 S9Y  C6   H33  single  0.970  0.020  1.090
 S9Y  C7   H34  single  0.970  0.020  1.090
 S9Y  C7   H35  single  0.970  0.020  1.090
 S9Y  C7   H36  single  0.970  0.020  1.090
 S9Y  C8   H37  single  0.970  0.020  1.090
 S9Y  C8   H38  single  0.970  0.020  1.090
 S9Y  C8   H39  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 S9Y  H3   C3   H2   107.64  3.000
 S9Y  H3   C3   H1   108.42  3.000
 S9Y  H2   C3   H1   108.11  3.000
 S9Y  H3   C3   C2   111.21  3.000
 S9Y  H2   C3   C2   109.73  3.000
 S9Y  H1   C3   C2   111.60  3.000
 S9Y  H4   C2   O2   109.63  3.000
 S9Y  H4   C2   C1   106.88  3.000
 S9Y  O2   C2   C1   106.59  3.000
 S9Y  H4   C2   C3   109.64  3.000
 S9Y  C1   C2   C3   113.51  3.000
 S9Y  O2   C2   C3   110.44  3.000
 S9Y  H6   C1   H5   107.38  3.000
 S9Y  H6   C1   O3P  111.16  3.000
 S9Y  H5   C1   O3P  111.39  3.000
 S9Y  H6   C1   C2   107.90  3.000
 S9Y  H5   C1   C2   109.33  3.000
 S9Y  O3P  C1   C2   109.59  3.000
 S9Y  P    O3P  C1   118.98  3.000
 S9Y  O5   P    O4   109.06  3.000
 S9Y  O5   P    O1   110.00  3.000
 S9Y  O4   P    O1   120.81  3.000
 S9Y  O1   P    O3P  110.12  3.000
 S9Y  O5   P    O3P   94.12  3.000
 S9Y  O4   P    O3P  109.45  3.000
 S9Y  C31  O2   C2   119.39  3.000
 S9Y  C32  C31  O31  124.91  3.000
 S9Y  O31  C31  O2   123.83  3.000
 S9Y  C32  C31  O2   111.26  3.000
 S9Y  H8   C32  H7   105.40  3.000
 S9Y  H8   C32  C33  110.34  3.000
 S9Y  H7   C32  C33  110.40  3.000
 S9Y  H8   C32  C31  108.50  3.000
 S9Y  H7   C32  C31  107.95  3.000
 S9Y  C33  C32  C31  113.88  3.000
 S9Y  H10  C33  H9   106.43  3.000
 S9Y  H10  C33  C34  109.46  3.000
 S9Y  H9   C33  C34  109.31  3.000
 S9Y  H10  C33  C32  109.98  3.000
 S9Y  H9   C33  C32  109.62  3.000
 S9Y  C34  C33  C32  111.88  3.000
 S9Y  H12  C34  H11  105.98  3.000
 S9Y  H12  C34  C35  109.36  3.000
 S9Y  H11  C34  C35  109.38  3.000
 S9Y  H12  C34  C33  109.44  3.000
 S9Y  H11  C34  C33  109.64  3.000
 S9Y  C35  C34  C33  112.80  3.000
 S9Y  H14  C35  H13  105.97  3.000
 S9Y  H14  C35  C36  109.40  3.000
 S9Y  H13  C35  C36  109.36  3.000
 S9Y  H14  C35  C34  109.39  3.000
 S9Y  H13  C35  C34  109.19  3.000
 S9Y  C36  C35  C34  113.27  3.000
 S9Y  H16  C36  H15  105.94  3.000
 S9Y  H16  C36  C37  109.36  3.000
 S9Y  H15  C36  C37  109.29  3.000
 S9Y  H16  C36  C35  109.33  3.000
 S9Y  H15  C36  C35  109.45  3.000
 S9Y  C37  C36  C35  113.21  3.000
 S9Y  H18  C37  H17  105.94  3.000
 S9Y  H18  C37  C38  109.35  3.000
 S9Y  H17  C37  C38  109.38  3.000
 S9Y  H18  C37  C36  109.35  3.000
 S9Y  H17  C37  C36  109.23  3.000
 S9Y  C38  C37  C36  113.33  3.000
 S9Y  H20  C38  H19  105.91  3.000
 S9Y  H20  C38  C39  109.31  3.000
 S9Y  H19  C38  C39  109.22  3.000
 S9Y  H20  C38  C37  109.39  3.000
 S9Y  H19  C38  C37  109.43  3.000
 S9Y  C39  C38  C37  113.33  3.000
 S9Y  H22  C39  H21  105.99  3.000
 S9Y  H22  C39  C40  109.64  3.000
 S9Y  H21  C39  C40  109.64  3.000
 S9Y  H22  C39  C38  109.24  3.000
 S9Y  H21  C39  C38  109.22  3.000
 S9Y  C40  C39  C38  112.88  3.000
 S9Y  H25  C40  H24  107.64  3.000
 S9Y  H25  C40  H23  107.61  3.000
 S9Y  H24  C40  H23  107.44  3.000
 S9Y  H25  C40  C39  111.68  3.000
 S9Y  H24  C40  C39  111.12  3.000
 S9Y  H23  C40  C39  111.14  3.000
 S9Y  C4   O5   P    122.11  3.000
 S9Y  H28  C4   H27  106.31  3.000
 S9Y  H28  C4   C5   104.54  3.000
 S9Y  H27  C4   C5   110.79  3.000
 S9Y  H28  C4   O5   109.44  3.000
 S9Y  H27  C4   O5   112.32  3.000
 S9Y  C5   C4   O5   112.93  3.000
 S9Y  H30  C5   H29  107.94  3.000
 S9Y  H30  C5   N1   106.34  3.000
 S9Y  H29  C5   N1   106.02  3.000
 S9Y  H30  C5   C4   111.30  3.000
 S9Y  H29  C5   C4   107.01  3.000
 S9Y  N1   C5   C4   117.77  3.000
 S9Y  C8   N1   C7   109.37  3.000
 S9Y  C7   N1   C6   107.86  3.000
 S9Y  C8   N1   C6   108.96  3.000
 S9Y  C7   N1   C5   111.92  3.000
 S9Y  C8   N1   C5   111.54  3.000
 S9Y  C6   N1   C5   107.06  3.000
 S9Y  H33  C6   H32  109.68  3.000
 S9Y  H33  C6   H31  109.84  3.000
 S9Y  H32  C6   H31  109.87  3.000
 S9Y  H33  C6   N1   109.03  3.000
 S9Y  H32  C6   N1   109.03  3.000
 S9Y  H31  C6   N1   109.37  3.000
 S9Y  H36  C7   H35  110.11  3.000
 S9Y  H36  C7   H34  109.37  3.000
 S9Y  H35  C7   H34  109.27  3.000
 S9Y  H36  C7   N1   110.91  3.000
 S9Y  H35  C7   N1   108.95  3.000
 S9Y  H34  C7   N1   108.18  3.000
 S9Y  H39  C8   H38  109.64  3.000
 S9Y  H39  C8   H37  109.95  3.000
 S9Y  H38  C8   H37  109.56  3.000
 S9Y  H39  C8   N1   109.89  3.000
 S9Y  H38  C8   N1   108.51  3.000
 S9Y  H37  C8   N1   109.26  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 S9Y  Var_01  C32  C31  O2   C2   -179.53  30.0  2
 S9Y  Var_02  O4   P    O3P  C1     72.74  30.0  3
 S9Y  Var_03  C5   C4   O5   P    -132.58  30.0  3
 S9Y  Var_04  C33  C32  C31  O2    170.12  30.0  1
 S9Y  Var_05  C34  C33  C32  C31  -178.05  30.0  2
 S9Y  Var_06  C35  C34  C33  C32   179.11  30.0  1
 S9Y  Var_07  C36  C35  C34  C33  -179.29  30.0  1
 S9Y  Var_08  C37  C36  C35  C34   179.68  30.0  1
 S9Y  Var_09  C38  C37  C36  C35  -179.81  30.0  1
 S9Y  Var_10  C39  C38  C37  C36   179.83  30.0  1
 S9Y  Var_11  C40  C39  C38  C37   179.88  30.0  1
 S9Y  Var_12  N1   C5   C4   O5     68.67  30.0  3
 S9Y  Var_13  C6   N1   C5   C4    165.29  30.0  3
 S9Y  Var_14  H5   C1   O3P  P      47.61  30.0  1
 S9Y  Var_15  H23  C40  C39  C38   -60.50  30.0  3
 S9Y  Var_16  H31  C6   N1   C5    -60.51  30.0  3
 S9Y  Var_17  H37  C8   N1   C5     55.19  30.0  3
 S9Y  Var_18  H34  C7   N1   C5   -170.63  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 S9Y  chir_01  C2  C3  O2  C1  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 S9Y  plan-1  O2   0.020
 S9Y  plan-1  C31  0.020
 S9Y  plan-1  O31  0.020
 S9Y  plan-1  C32  0.020

