# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 10:13:13 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](O)(=O)OCCN
#
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
 LPX  LPX  '(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate'  ligand  74  30  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LPX
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
 LPX  O7    O  O     0  -0.450    1.7444  -2.5080  -0.0958
 LPX  C6    C  C     0   0.607    1.7665  -1.3031  -0.1056
 LPX  O6    O  O2    0  -0.460    2.8935  -0.5962  -0.1325
 LPX  C5    C  CH2   0  -0.188    4.1279  -1.3071  -0.1597
 LPX  C4    C  CH1   0  -0.058    5.2411  -0.2736  -0.2049
 LPX  O5    O  OH1   0  -0.649    5.1617   0.5534  -1.3350
 LPX  C3    C  CH2   0  -0.182    6.5789  -0.9880  -0.1011
 LPX  O1    O  O2    0  -0.579    7.6022   0.0084  -0.0776
 LPX  P1    P  P     0   1.473    9.1376  -0.4193  -0.0589
 LPX  O3    O  OH1   0  -0.742    9.4687  -0.9438   1.4151
 LPX  O2    O  O2    0  -0.586    9.7453   1.0441  -0.1898
 LPX  C1    C  CH2   0  -0.175   11.1705   1.2306  -0.2983
 LPX  C2    C  CH2   0  -0.318   11.4715   2.6878  -0.0494
 LPX  N1    N  NH2   0  -0.798   11.1465   3.0687   1.3138
 LPX  O4    O  O     0  -0.710    9.5680  -1.4255  -1.0466
 LPX  C7    C  CH2   0  -0.584    0.5600  -0.4052  -0.0924
 LPX  C8    C  CH2   0  -0.418   -0.7626  -1.1516  -0.0339
 LPX  C9    C  CH2   0  -0.416   -1.9497  -0.1962  -0.0317
 LPX  C10   C  CH2   0  -0.413   -3.2911  -0.9159   0.0230
 LPX  C11   C  CH2   0  -0.412   -4.4803   0.0367   0.0206
 LPX  C12   C  CH2   0  -0.412   -5.8251  -0.6781   0.0650
 LPX  C13   C  CH2   0  -0.412   -7.0128   0.2766   0.0597
 LPX  C14   C  CH2   0  -0.412   -8.3593  -0.4356   0.0902
 LPX  C15   C  CH2   0  -0.412   -9.5457   0.5207   0.0833
 LPX  C16   C  CH2   0  -0.412  -10.8932  -0.1902   0.1016
 LPX  C17   C  CH2   0  -0.412  -12.0788   0.7671   0.0940
 LPX  C18   C  CH2   0  -0.412  -13.4268   0.0570   0.1040
 LPX  C19   C  CH2   0  -0.406  -14.6116   1.0150   0.0962
 LPX  C20   C  CH2   0  -0.419  -15.9613   0.3071   0.1017
 LPX  C21   C  CH3   0  -0.663  -17.1356   1.2762   0.0934
 LPX  H5    H  HCH2  0   0.245    4.2261  -1.9344   0.7298
 LPX  H5A   H  HCH2  0   0.241    4.1729  -1.9606  -1.0366
 LPX  H4    H  HCH1  0   0.255    5.1380   0.3880   0.6609
 LPX  HO5   H  HOH1  0   0.449    5.2421   0.0121  -2.1286
 LPX  H3    H  HCH2  0   0.249    6.6103  -1.5881   0.8125
 LPX  H3A   H  HCH2  0   0.244    6.7234  -1.6608  -0.9526
 LPX  HO3   H  HOH1  0   0.495    9.2353  -0.3465   2.1386
 LPX  H1    H  HCH2  0   0.233   11.6918   0.6124   0.4374
 LPX  H1A   H  HCH2  0   0.246   11.4997   0.9389  -1.2970
 LPX  H2    H  HCH2  0   0.238   12.5453   2.8142  -0.2042
 LPX  H2A   H  HCH2  0   0.212   10.9747   3.2922  -0.8209
 LPX  HN1   H  HNH2  0   0.353   11.4410   4.0232   1.4726
 LPX  HN1A  H  HNH2  0   0.344   10.1421   3.0709   1.4367
 LPX  H7    H  HCH2  0   0.274    0.6530   0.2793   0.7570
 LPX  H7A   H  HCH2  0   0.274    0.6021   0.2304  -0.9832
 LPX  H8    H  HCH2  0   0.225   -0.8452  -1.8299  -0.8872
 LPX  H8A   H  HCH2  0   0.225   -0.7979  -1.7768   0.8625
 LPX  H9    H  HCH2  0   0.212   -1.8674   0.4856   0.8219
 LPX  H9A   H  HCH2  0   0.212   -1.9119   0.4340  -0.9272
 LPX  H10   H  HCH2  0   0.209   -3.3722  -1.5991  -0.8297
 LPX  H10A  H  HCH2  0   0.209   -3.3308  -1.5448   0.9194
 LPX  H11   H  HCH2  0   0.207   -4.4013   0.7167   0.8762
 LPX  H11A  H  HCH2  0   0.207   -4.4354   0.6695  -0.8730
 LPX  H12   H  HCH2  0   0.206   -5.9034  -1.3579  -0.7909
 LPX  H12A  H  HCH2  0   0.207   -5.8720  -1.3110   0.9584
 LPX  H13   H  HCH2  0   0.206   -6.9385   0.9518   0.9197
 LPX  H13A  H  HCH2  0   0.206   -6.9602   0.9148  -0.8298
 LPX  H14   H  HCH2  0   0.206   -8.4328  -1.1097  -0.7707
 LPX  H14A  H  HCH2  0   0.206   -8.4134  -1.0745   0.9789
 LPX  H15   H  HCH2  0   0.206   -9.4760   1.1905   0.9478
 LPX  H15A  H  HCH2  0   0.206   -9.4870   1.1640  -0.8020
 LPX  H16   H  HCH2  0   0.206  -10.9626  -0.8591  -0.7636
 LPX  H16A  H  HCH2  0   0.206  -10.9528  -0.8345   0.9862
 LPX  H17   H  HCH2  0   0.206  -12.0121   1.4330   0.9618
 LPX  H17A  H  HCH2  0   0.206  -12.0159   1.4143  -0.7881
 LPX  H18   H  HCH2  0   0.206  -13.4932  -0.6083  -0.7644
 LPX  H18A  H  HCH2  0   0.206  -13.4900  -0.5909   0.9856
 LPX  H19   H  HCH2  0   0.205  -14.5472   1.6790   0.9657
 LPX  H19A  H  HCH2  0   0.205  -14.5472   1.6646  -0.7843
 LPX  H20   H  HCH2  0   0.210  -16.0254  -0.3555  -0.7674
 LPX  H20A  H  HCH2  0   0.210  -16.0258  -0.3417   0.9811
 LPX  H21   H  HCH3  0   0.225  -18.0917   0.7515   0.0960
 LPX  H21A  H  HCH3  0   0.216  -17.1134   1.9273   0.9693
 LPX  H21B  H  HCH3  0   0.215  -17.1114   1.9144  -0.7918

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
 LPX  O7   C6    double  1.205  0.020  1.205
 LPX  C6   O6    single  1.331  0.020  1.331
 LPX  C6   C7    single  1.504  0.020  1.504
 LPX  O6   C5    single  1.425  0.020  1.425
 LPX  C5   C4    single  1.520  0.020  1.520
 LPX  C4   O5    single  1.403  0.020  1.403
 LPX  C4   C3    single  1.520  0.020  1.520
 LPX  C3   O1    single  1.428  0.020  1.428
 LPX  O1   P1    single  1.594  0.020  1.594
 LPX  P1   O3    single  1.599  0.020  1.599
 LPX  P1   O2    single  1.590  0.020  1.590
 LPX  P1   O4    double  1.474  0.020  1.474
 LPX  O2   C1    single  1.441  0.020  1.441
 LPX  C1   C2    single  1.509  0.020  1.509
 LPX  C2   N1    single  1.452  0.020  1.452
 LPX  C7   C8    single  1.520  0.020  1.520
 LPX  C8   C9    single  1.524  0.020  1.524
 LPX  C9   C10   single  1.523  0.020  1.523
 LPX  C10  C11   single  1.524  0.020  1.524
 LPX  C11  C12   single  1.524  0.020  1.524
 LPX  C12  C13   single  1.524  0.020  1.524
 LPX  C13  C14   single  1.524  0.020  1.524
 LPX  C14  C15   single  1.524  0.020  1.524
 LPX  C15  C16   single  1.524  0.020  1.524
 LPX  C16  C17   single  1.524  0.020  1.524
 LPX  C17  C18   single  1.524  0.020  1.524
 LPX  C18  C19   single  1.524  0.020  1.524
 LPX  C19  C20   single  1.524  0.020  1.524
 LPX  C20  C21   single  1.523  0.020  1.523
 LPX  C5   H5    single  0.970  0.020  1.090
 LPX  C5   H5A   single  0.970  0.020  1.090
 LPX  C4   H4    single  0.970  0.020  1.090
 LPX  O5   HO5   single  0.850  0.020  0.980
 LPX  C3   H3    single  0.970  0.020  1.090
 LPX  C3   H3A   single  0.970  0.020  1.090
 LPX  O3   HO3   single  0.850  0.020  0.980
 LPX  C1   H1    single  0.970  0.020  1.090
 LPX  C1   H1A   single  0.970  0.020  1.090
 LPX  C2   H2    single  0.970  0.020  1.090
 LPX  C2   H2A   single  0.970  0.020  1.090
 LPX  N1   HN1   single  0.890  0.020  1.040
 LPX  N1   HN1A  single  0.890  0.020  1.040
 LPX  C7   H7    single  0.970  0.020  1.090
 LPX  C7   H7A   single  0.970  0.020  1.090
 LPX  C8   H8    single  0.970  0.020  1.090
 LPX  C8   H8A   single  0.970  0.020  1.090
 LPX  C9   H9    single  0.970  0.020  1.090
 LPX  C9   H9A   single  0.970  0.020  1.090
 LPX  C10  H10   single  0.970  0.020  1.090
 LPX  C10  H10A  single  0.970  0.020  1.090
 LPX  C11  H11   single  0.970  0.020  1.090
 LPX  C11  H11A  single  0.970  0.020  1.090
 LPX  C12  H12   single  0.970  0.020  1.090
 LPX  C12  H12A  single  0.970  0.020  1.090
 LPX  C13  H13   single  0.970  0.020  1.090
 LPX  C13  H13A  single  0.970  0.020  1.090
 LPX  C14  H14   single  0.970  0.020  1.090
 LPX  C14  H14A  single  0.970  0.020  1.090
 LPX  C15  H15   single  0.970  0.020  1.090
 LPX  C15  H15A  single  0.970  0.020  1.090
 LPX  C16  H16   single  0.970  0.020  1.090
 LPX  C16  H16A  single  0.970  0.020  1.090
 LPX  C17  H17   single  0.970  0.020  1.090
 LPX  C17  H17A  single  0.970  0.020  1.090
 LPX  C18  H18   single  0.970  0.020  1.090
 LPX  C18  H18A  single  0.970  0.020  1.090
 LPX  C19  H19   single  0.970  0.020  1.090
 LPX  C19  H19A  single  0.970  0.020  1.090
 LPX  C20  H20   single  0.970  0.020  1.090
 LPX  C20  H20A  single  0.970  0.020  1.090
 LPX  C21  H21   single  0.970  0.020  1.090
 LPX  C21  H21A  single  0.970  0.020  1.090
 LPX  C21  H21B  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
 LPX  C7    C6   O6    111.25  3.000
 LPX  C7    C6   O7    125.60  3.000
 LPX  O6    C6   O7    123.15  3.000
 LPX  C5    O6   C6    117.97  3.000
 LPX  H5A   C5   H5    107.80  3.000
 LPX  H5A   C5   C4    110.61  3.000
 LPX  H5    C5   C4    110.41  3.000
 LPX  H5A   C5   O6    110.42  3.000
 LPX  H5    C5   O6    110.41  3.000
 LPX  C4    C5   O6    107.21  3.000
 LPX  H4    C4   C3    108.24  3.000
 LPX  H4    C4   O5    106.00  3.000
 LPX  C3    C4   O5    112.46  3.000
 LPX  H4    C4   C5    108.57  3.000
 LPX  C3    C4   C5    108.85  3.000
 LPX  O5    C4   C5    112.55  3.000
 LPX  HO5   O5   C4    109.11  3.000
 LPX  H3A   C3   H3    107.98  3.000
 LPX  H3A   C3   O1    110.29  3.000
 LPX  H3    C3   O1    110.40  3.000
 LPX  H3A   C3   C4    110.60  3.000
 LPX  H3    C3   C4    109.89  3.000
 LPX  O1    C3   C4    107.68  3.000
 LPX  P1    O1   C3    120.20  3.000
 LPX  O4    P1   O2    117.48  3.000
 LPX  O4    P1   O3    109.46  3.000
 LPX  O2    P1   O3    107.37  3.000
 LPX  O4    P1   O1    117.17  3.000
 LPX  O2    P1   O1     96.91  3.000
 LPX  O3    P1   O1    107.35  3.000
 LPX  HO3   O3   P1    115.93  3.000
 LPX  C1    O2   P1    120.21  3.000
 LPX  H1A   C1   H1    108.71  3.000
 LPX  H1A   C1   C2    110.43  3.000
 LPX  H1    C1   C2    109.88  3.000
 LPX  H1A   C1   O2    109.42  3.000
 LPX  H1    C1   O2    110.35  3.000
 LPX  C2    C1   O2    108.05  3.000
 LPX  H2A   C2   H2    106.34  3.000
 LPX  H2A   C2   N1    114.43  3.000
 LPX  H2    C2   N1    108.83  3.000
 LPX  H2A   C2   C1    108.98  3.000
 LPX  H2    C2   C1    106.53  3.000
 LPX  N1    C2   C1    111.32  3.000
 LPX  HN1A  N1   HN1   105.54  3.000
 LPX  HN1A  N1   C2    109.68  3.000
 LPX  HN1   N1   C2    109.25  3.000
 LPX  H7A   C7   H7    105.36  3.000
 LPX  H7A   C7   C8    110.48  3.000
 LPX  H7    C7   C8    110.55  3.000
 LPX  H7A   C7   C6    107.97  3.000
 LPX  H7    C7   C6    108.17  3.000
 LPX  C8    C7   C6    113.91  3.000
 LPX  H8A   C8   H8    106.43  3.000
 LPX  H8A   C8   C9    109.40  3.000
 LPX  H8    C8   C9    109.35  3.000
 LPX  H8A   C8   C7    109.90  3.000
 LPX  H8    C8   C7    109.90  3.000
 LPX  C9    C8   C7    111.72  3.000
 LPX  H9A   C9   H9    106.03  3.000
 LPX  H9A   C9   C10   109.36  3.000
 LPX  H9    C9   C10   109.40  3.000
 LPX  H9A   C9   C8    109.43  3.000
 LPX  H9    C9   C8    109.44  3.000
 LPX  C10   C9   C8    112.95  3.000
 LPX  H10A  C10  H10   106.03  3.000
 LPX  H10A  C10  C11   109.38  3.000
 LPX  H10   C10  C11   109.32  3.000
 LPX  H10A  C10  C9    109.42  3.000
 LPX  H10   C10  C9    109.38  3.000
 LPX  C11   C10  C9    113.08  3.000
 LPX  H11A  C11  H11   105.99  3.000
 LPX  H11A  C11  C12   109.32  3.000
 LPX  H11   C11  C12   109.40  3.000
 LPX  H11A  C11  C10   109.28  3.000
 LPX  H11   C11  C10   109.29  3.000
 LPX  C12   C11  C10   113.30  3.000
 LPX  H12A  C12  H12   105.99  3.000
 LPX  H12A  C12  C13   109.35  3.000
 LPX  H12   C12  C13   109.28  3.000
 LPX  H12A  C12  C11   109.42  3.000
 LPX  H12   C12  C11   109.35  3.000
 LPX  C13   C12  C11   113.20  3.000
 LPX  H13A  C13  H13   105.96  3.000
 LPX  H13A  C13  C14   109.32  3.000
 LPX  H13   C13  C14   109.40  3.000
 LPX  H13A  C13  C12   109.28  3.000
 LPX  H13   C13  C12   109.30  3.000
 LPX  C14   C13  C12   113.32  3.000
 LPX  H14A  C14  H14   105.97  3.000
 LPX  H14A  C14  C15   109.33  3.000
 LPX  H14   C14  C15   109.28  3.000
 LPX  H14A  C14  C13   109.41  3.000
 LPX  H14   C14  C13   109.34  3.000
 LPX  C15   C14  C13   113.24  3.000
 LPX  H15A  C15  H15   105.97  3.000
 LPX  H15A  C15  C16   109.33  3.000
 LPX  H15   C15  C16   109.39  3.000
 LPX  H15A  C15  C14   109.29  3.000
 LPX  H15   C15  C14   109.30  3.000
 LPX  C16   C15  C14   113.31  3.000
 LPX  H16A  C16  H16   105.96  3.000
 LPX  H16A  C16  C17   109.33  3.000
 LPX  H16   C16  C17   109.29  3.000
 LPX  H16A  C16  C15   109.40  3.000
 LPX  H16   C16  C15   109.35  3.000
 LPX  C17   C16  C15   113.26  3.000
 LPX  H17A  C17  H17   105.96  3.000
 LPX  H17A  C17  C18   109.34  3.000
 LPX  H17   C17  C18   109.38  3.000
 LPX  H17A  C17  C16   109.29  3.000
 LPX  H17   C17  C16   109.30  3.000
 LPX  C18   C17  C16   113.30  3.000
 LPX  H18A  C18  H18   105.96  3.000
 LPX  H18A  C18  C19   109.33  3.000
 LPX  H18   C18  C19   109.30  3.000
 LPX  H18A  C18  C17   109.38  3.000
 LPX  H18   C18  C17   109.35  3.000
 LPX  C19   C18  C17   113.26  3.000
 LPX  H19A  C19  H19   105.94  3.000
 LPX  H19A  C19  C20   109.28  3.000
 LPX  H19   C19  C20   109.31  3.000
 LPX  H19A  C19  C18   109.33  3.000
 LPX  H19   C19  C18   109.34  3.000
 LPX  C20   C19  C18   113.36  3.000
 LPX  H20A  C20  H20   106.00  3.000
 LPX  H20A  C20  C21   109.64  3.000
 LPX  H20   C20  C21   109.62  3.000
 LPX  H20A  C20  C19   109.29  3.000
 LPX  H20   C20  C19   109.28  3.000
 LPX  C21   C20  C19   112.79  3.000
 LPX  H21B  C21  H21A  107.55  3.000
 LPX  H21B  C21  H21   107.61  3.000
 LPX  H21A  C21  H21   107.63  3.000
 LPX  H21B  C21  C20   111.06  3.000
 LPX  H21A  C21  C20   111.08  3.000
 LPX  H21   C21  C20   111.71  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
 LPX  Var_01  C8   C7   C6   O7      1.26  30.0  3
 LPX  Var_02  C4   C5   O6   C6    179.28  30.0  3
 LPX  Var_03  C9   C8   C7   C6   -179.64  30.0  3
 LPX  Var_04  C7   C6   O6   C5   -179.46  30.0  1
 LPX  Var_05  O3   P1   O1   C3    -74.87  30.0  3
 LPX  Var_06  C2   C1   O2   P1   -165.58  30.0  3
 LPX  Var_07  N1   C2   C1   O2     65.26  30.0  3
 LPX  Var_08  C10  C9   C8   C7    179.86  30.0  3
 LPX  Var_09  C11  C10  C9   C8   -179.81  30.0  3
 LPX  Var_10  C12  C11  C10  C9    179.58  30.0  3
 LPX  Var_11  C13  C12  C11  C10  -179.89  30.0  3
 LPX  Var_12  C14  C13  C12  C11   179.43  30.0  3
 LPX  Var_13  C15  C14  C13  C12  -179.94  30.0  3
 LPX  Var_14  C16  C15  C14  C13   179.50  30.0  3
 LPX  Var_15  C17  C16  C15  C14  -179.97  30.0  3
 LPX  Var_16  C18  C17  C16  C15   179.66  30.0  3
 LPX  Var_17  C19  C18  C17  C16  -179.99  30.0  3
 LPX  Var_18  C20  C19  C18  C17   179.82  30.0  3
 LPX  Var_19  C21  C20  C19  C18  -179.99  30.0  3
 LPX  Var_20  H3   C3   O1   P1     63.61  30.0  1
 LPX  Var_21  HN1  N1   C2   C1    174.65  30.0  3
 LPX  Var_22  H21  C21  C20  C19   179.91  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
 LPX  chir_01  C4  C5  O5  C3  positiv
 LPX  chir_02  P1  O3  O2  O4  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
 LPX  plan-1  O7  0.020
 LPX  plan-1  C6  0.020
 LPX  plan-1  O6  0.020
 LPX  plan-1  C7  0.020

