# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 22:13:01 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  65  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 PERFECT
;

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  -0.682  -1.5493  -2.8201   2.0660
 S9Y  C2   C  CH1   0  -0.023  -1.1244  -3.0071   0.6217
 S9Y  C1   C  CH2   0  -0.189  -2.2594  -2.8713  -0.3650
 S9Y  O3P  O  O2    0  -0.576  -2.8714  -1.5865  -0.1984
 S9Y  P    P  P     0   1.487  -4.2093  -1.2250  -0.9746
 S9Y  O2   O  O2    0  -0.469  -0.1406  -2.0284   0.2516
 S9Y  C31  C  C     0   0.611   1.1411  -2.2636   0.5244
 S9Y  O31  O  O     0  -0.450   1.5350  -3.2674   1.0624
 S9Y  C32  C  CH2   0  -0.585   2.0115  -1.1219   0.0744
 S9Y  C33  C  CH2   0  -0.418   3.4905  -1.3307   0.3554
 S9Y  C34  C  CH2   0  -0.416   4.3292  -0.1446  -0.1041
 S9Y  C35  C  CH2   0  -0.412   5.8163  -0.3318   0.1669
 S9Y  C36  C  CH2   0  -0.411   6.6620   0.8556  -0.2754
 S9Y  C37  C  CH2   0  -0.412   8.1491   0.6699  -0.0013
 S9Y  C38  C  CH2   0  -0.406   8.9949   1.8599  -0.4364
 S9Y  C39  C  CH2   0  -0.418  10.4813   1.6809  -0.1527
 S9Y  C40  C  CH3   0  -0.662  11.3146   2.8776  -0.5902
 S9Y  O1   O  OH1   0  -0.739  -3.8171  -0.8670  -2.4791
 S9Y  O4   O  O     0  -0.700  -5.2990  -2.2152  -0.9618
 S9Y  O5   O  O2    0  -0.579  -4.4919   0.1605  -0.2236
 S9Y  C4   C  CH2   0  -0.210  -5.6749   0.9020  -0.5094
 S9Y  C5   C  CH2   0  -0.351  -5.8545   2.0146   0.4918
 S9Y  N1   N  NT    1  -0.384  -4.8653   3.1499   0.4488
 S9Y  C6   C  CH3   0  -0.549  -5.4130   4.2399   1.3087
 S9Y  C7   C  CH3   0  -0.544  -3.5332   2.7517   0.9927
 S9Y  C8   C  CH3   0  -0.560  -4.6984   3.6678  -0.9369
 S9Y  H1   H  HCH3  0   0.242  -1.9116  -1.8098   2.2525
 S9Y  H2   H  HCH3  0   0.242  -2.3490  -3.5199   2.3099
 S9Y  H3   H  HCH3  0   0.250  -0.7212  -3.0194   2.7442
 S9Y  H4   H  HCH1  0   0.263  -0.7183  -4.0125   0.4816
 S9Y  H5   H  HCH2  0   0.264  -1.8874  -2.9815  -1.3866
 S9Y  H6   H  HCH2  0   0.256  -2.9829  -3.6669  -0.1760
 S9Y  H7   H  HCH2  0   0.273   1.8434  -0.9621  -0.9954
 S9Y  H8   H  HCH2  0   0.273   1.6529  -0.2104   0.5637
 S9Y  H9   H  HCH2  0   0.224   3.6454  -1.4911   1.4259
 S9Y  H10  H  HCH2  0   0.224   3.8392  -2.2377  -0.1460
 S9Y  H11  H  HCH2  0   0.212   4.1739   0.0229  -1.1756
 S9Y  H12  H  HCH2  0   0.212   3.9800   0.7647   0.3977
 S9Y  H13  H  HCH2  0   0.208   5.9690  -0.5088   1.2374
 S9Y  H14  H  HCH2  0   0.209   6.1670  -1.2368  -0.3414
 S9Y  H15  H  HCH2  0   0.207   6.5102   1.0331  -1.3460
 S9Y  H16  H  HCH2  0   0.207   6.3096   1.7602   0.2329
 S9Y  H17  H  HCH2  0   0.206   8.2993   0.4883   1.0688
 S9Y  H18  H  HCH2  0   0.206   8.5029  -0.2326  -0.5124
 S9Y  H19  H  HCH2  0   0.206   8.8504   2.0379  -1.5080
 S9Y  H20  H  HCH2  0   0.205   8.6367   2.7639   0.0694
 S9Y  H21  H  HCH2  0   0.210  10.6250   1.5033   0.9176
 S9Y  H22  H  HCH2  0   0.210  10.8404   0.7796  -0.6593
 S9Y  H23  H  HCH3  0   0.215  11.2255   3.0472  -1.6651
 S9Y  H24  H  HCH3  0   0.215  10.9882   3.7897  -0.0867
 S9Y  H25  H  HCH3  0   0.226  12.3723   2.7365  -0.3647
 S9Y  H26  H  HOH1  0   0.498  -3.0659  -0.2707  -2.6011
 S9Y  H27  H  HCH2  0   0.268  -5.6591   1.2781  -1.5344
 S9Y  H28  H  HCH2  0   0.291  -6.5605   0.2703  -0.4102
 S9Y  H29  H  HCH2  0   0.321  -6.8349   2.4520   0.3035
 S9Y  H30  H  HCH2  0   0.319  -5.8499   1.6246   1.5092
 S9Y  H31  H  HCH3  0   0.299  -6.3445   4.6011   0.8817
 S9Y  H32  H  HCH3  0   0.299  -5.5912   3.8494   2.3071
 S9Y  H33  H  HCH3  0   0.298  -4.6912   5.0501   1.3570
 S9Y  H34  H  HCH3  0   0.294  -2.8962   3.6312   1.0098
 S9Y  H35  H  HCH3  0   0.295  -3.6600   2.3716   2.0024
 S9Y  H36  H  HCH3  0   0.298  -3.0858   1.9923   0.3628
 S9Y  H37  H  HCH3  0   0.302  -5.6752   3.8815  -1.3630
 S9Y  H38  H  HCH3  0   0.306  -4.1075   4.5789  -0.9001
 S9Y  H39  H  HCH3  0   0.292  -4.1774   2.9356  -1.5468

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  1.523  0.020  1.523
 S9Y  C36  C35  single  1.523  0.020  1.523
 S9Y  C35  C34  single  1.523  0.020  1.523
 S9Y  C34  C33  single  1.524  0.020  1.524
 S9Y  C33  C32  single  1.520  0.020  1.520
 S9Y  C32  C31  single  1.505  0.020  1.505
 S9Y  C31  O31  double  1.205  0.020  1.205
 S9Y  C31  O2   single  1.331  0.020  1.331
 S9Y  C3   C2   single  1.517  0.020  1.517
 S9Y  O2   C2   single  1.436  0.020  1.436
 S9Y  C2   C1   single  1.510  0.020  1.510
 S9Y  C1   O3P  single  1.433  0.020  1.433
 S9Y  O3P  P    single  1.588  0.020  1.588
 S9Y  C6   N1   single  1.493  0.020  1.493
 S9Y  O4   P    double  1.472  0.020  1.472
 S9Y  O5   P    single  1.601  0.020  1.601
 S9Y  O5   C4   single  1.425  0.020  1.425
 S9Y  P    O1   single  1.595  0.020  1.595
 S9Y  C4   C5   single  1.507  0.020  1.507
 S9Y  N1   C8   single  1.489  0.020  1.489
 S9Y  N1   C5   single  1.506  0.020  1.506
 S9Y  N1   C7   single  1.493  0.020  1.493
 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  O1   H26  single  0.850  0.020  0.980
 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   107.52  3.000
 S9Y  H3   C3   H1   108.42  3.000
 S9Y  H2   C3   H1   108.24  3.000
 S9Y  H3   C3   C2   110.94  3.000
 S9Y  H2   C3   C2   109.84  3.000
 S9Y  H1   C3   C2   111.75  3.000
 S9Y  H4   C2   O2   109.83  3.000
 S9Y  H4   C2   C1   106.15  3.000
 S9Y  O2   C2   C1   106.57  3.000
 S9Y  H4   C2   C3   109.84  3.000
 S9Y  C1   C2   C3   113.60  3.000
 S9Y  O2   C2   C3   110.68  3.000
 S9Y  H6   C1   H5   108.29  3.000
 S9Y  H6   C1   O3P  110.50  3.000
 S9Y  H5   C1   O3P  110.15  3.000
 S9Y  H6   C1   C2   108.63  3.000
 S9Y  H5   C1   C2   110.24  3.000
 S9Y  O3P  C1   C2   109.01  3.000
 S9Y  P    O3P  C1   120.46  3.000
 S9Y  O5   P    O4   116.56  3.000
 S9Y  O5   P    O1   106.95  3.000
 S9Y  O4   P    O1   109.94  3.000
 S9Y  O1   P    O3P  107.75  3.000
 S9Y  O5   P    O3P   96.68  3.000
 S9Y  O4   P    O3P  117.78  3.000
 S9Y  C31  O2   C2   119.09  3.000
 S9Y  C32  C31  O31  125.21  3.000
 S9Y  O31  C31  O2   123.60  3.000
 S9Y  C32  C31  O2   111.19  3.000
 S9Y  H8   C32  H7   105.36  3.000
 S9Y  H8   C32  C33  110.51  3.000
 S9Y  H7   C32  C33  110.50  3.000
 S9Y  H8   C32  C31  107.98  3.000
 S9Y  H7   C32  C31  108.32  3.000
 S9Y  C33  C32  C31  113.79  3.000
 S9Y  H10  C33  H9   106.39  3.000
 S9Y  H10  C33  C34  109.38  3.000
 S9Y  H9   C33  C34  109.36  3.000
 S9Y  H10  C33  C32  109.84  3.000
 S9Y  H9   C33  C32  109.81  3.000
 S9Y  C34  C33  C32  111.90  3.000
 S9Y  H12  C34  H11  106.01  3.000
 S9Y  H12  C34  C35  109.37  3.000
 S9Y  H11  C34  C35  109.34  3.000
 S9Y  H12  C34  C33  109.42  3.000
 S9Y  H11  C34  C33  109.63  3.000
 S9Y  C35  C34  C33  112.84  3.000
 S9Y  H14  C35  H13  105.98  3.000
 S9Y  H14  C35  C36  109.35  3.000
 S9Y  H13  C35  C36  109.40  3.000
 S9Y  H14  C35  C34  109.36  3.000
 S9Y  H13  C35  C34  109.26  3.000
 S9Y  C36  C35  C34  113.24  3.000
 S9Y  H16  C36  H15  105.95  3.000
 S9Y  H16  C36  C37  109.33  3.000
 S9Y  H15  C36  C37  109.32  3.000
 S9Y  H16  C36  C35  109.28  3.000
 S9Y  H15  C36  C35  109.45  3.000
 S9Y  C37  C36  C35  113.25  3.000
 S9Y  H18  C37  H17  105.95  3.000
 S9Y  H18  C37  C38  109.32  3.000
 S9Y  H17  C37  C38  109.40  3.000
 S9Y  H18  C37  C36  109.37  3.000
 S9Y  H17  C37  C36  109.25  3.000
 S9Y  C38  C37  C36  113.29  3.000
 S9Y  H20  C38  H19  105.91  3.000
 S9Y  H20  C38  C39  109.25  3.000
 S9Y  H19  C38  C39  109.25  3.000
 S9Y  H20  C38  C37  109.33  3.000
 S9Y  H19  C38  C37  109.45  3.000
 S9Y  C39  C38  C37  113.37  3.000
 S9Y  H22  C39  H21  106.01  3.000
 S9Y  H22  C39  C40  109.56  3.000
 S9Y  H21  C39  C40  109.68  3.000
 S9Y  H22  C39  C38  109.31  3.000
 S9Y  H21  C39  C38  109.22  3.000
 S9Y  C40  C39  C38  112.84  3.000
 S9Y  H25  C40  H24  107.62  3.000
 S9Y  H25  C40  H23  107.62  3.000
 S9Y  H24  C40  H23  107.44  3.000
 S9Y  H25  C40  C39  111.70  3.000
 S9Y  H24  C40  C39  111.13  3.000
 S9Y  H23  C40  C39  111.12  3.000
 S9Y  H26  O1   P    116.64  3.000
 S9Y  C4   O5   P    120.18  3.000
 S9Y  H28  C4   H27  107.23  3.000
 S9Y  H28  C4   C5   105.66  3.000
 S9Y  H27  C4   C5   111.77  3.000
 S9Y  H28  C4   O5   110.73  3.000
 S9Y  H27  C4   O5   110.82  3.000
 S9Y  C5   C4   O5   110.47  3.000
 S9Y  H30  C5   H29  107.98  3.000
 S9Y  H30  C5   N1   107.07  3.000
 S9Y  H29  C5   N1   106.46  3.000
 S9Y  H30  C5   C4   110.82  3.000
 S9Y  H29  C5   C4   106.78  3.000
 S9Y  N1   C5   C4   117.33  3.000
 S9Y  C8   N1   C7   109.38  3.000
 S9Y  C7   N1   C6   108.20  3.000
 S9Y  C8   N1   C6   108.86  3.000
 S9Y  C7   N1   C5   112.00  3.000
 S9Y  C8   N1   C5   111.25  3.000
 S9Y  C6   N1   C5   107.04  3.000
 S9Y  H33  C6   H32  109.65  3.000
 S9Y  H33  C6   H31  109.84  3.000
 S9Y  H32  C6   H31  109.87  3.000
 S9Y  H33  C6   N1   109.06  3.000
 S9Y  H32  C6   N1   109.09  3.000
 S9Y  H31  C6   N1   109.32  3.000
 S9Y  H36  C7   H35  110.09  3.000
 S9Y  H36  C7   H34  109.55  3.000
 S9Y  H35  C7   H34  109.70  3.000
 S9Y  H36  C7   N1   110.10  3.000
 S9Y  H35  C7   N1   109.13  3.000
 S9Y  H34  C7   N1   108.24  3.000
 S9Y  H39  C8   H38  108.87  3.000
 S9Y  H39  C8   H37  110.09  3.000
 S9Y  H38  C8   H37  109.71  3.000
 S9Y  H39  C8   N1   110.00  3.000
 S9Y  H38  C8   N1   108.74  3.000
 S9Y  H37  C8   N1   109.42  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   -179.44  30.0  1
 S9Y  Var_02  O4   P    O3P  C1     46.79  30.0  3
 S9Y  Var_03  C5   C4   O5   P     169.16  30.0  3
 S9Y  Var_04  C33  C32  C31  O2   -179.88  30.0  1
 S9Y  Var_05  C34  C33  C32  C31  -179.42  30.0  1
 S9Y  Var_06  C35  C34  C33  C32  -179.97  30.0  1
 S9Y  Var_07  C36  C35  C34  C33  -179.38  30.0  1
 S9Y  Var_08  C37  C36  C35  C34   179.86  30.0  1
 S9Y  Var_09  C38  C37  C36  C35  -179.68  30.0  1
 S9Y  Var_10  C39  C38  C37  C36   179.53  30.0  1
 S9Y  Var_11  C40  C39  C38  C37  -179.92  30.0  1
 S9Y  Var_12  N1   C5   C4   O5     68.30  30.0  3
 S9Y  Var_13  C6   N1   C5   C4    168.01  30.0  3
 S9Y  Var_14  H5   C1   O3P  P      66.56  30.0  1
 S9Y  Var_15  H23  C40  C39  C38   -60.68  30.0  3
 S9Y  Var_16  H31  C6   N1   C5    -63.80  30.0  3
 S9Y  Var_17  H37  C8   N1   C5     51.15  30.0  3
 S9Y  Var_18  H34  C7   N1   C5   -175.37  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
 S9Y  chir_02  P   O4  O5  O1  both

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

