# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:48:43 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (2R)-2,3-dihydroxypropyl hexadecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO
#
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
 EKG  EKG  '(2R)-2,3-dihydroxypropyl hexadecanoate'  ligand  61  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EKG
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
 EKG  C19  C  CH3   0  -0.662   13.4976  -0.4755   0.1860
 EKG  C8   C  CH2   0  -0.412    3.3237  -0.3674   0.0510
 EKG  C7   C  CH2   0  -0.412    2.0652   0.4743  -0.1169
 EKG  C15  C  CH2   0  -0.418   12.2426   0.3698   0.0189
 EKG  C9   C  CH2   0  -0.411    4.6084   0.4393  -0.0887
 EKG  C6   C  CH2   0  -0.412    0.7776  -0.3274   0.0246
 EKG  C21  C  CH2   0  -0.184   -7.8967   0.5445  -0.0539
 EKG  C14  C  CH2   0  -0.406   10.9603  -0.4440   0.1414
 EKG  C10  C  CH2   0  -0.412    5.8697  -0.3984   0.0786
 EKG  C5   C  CH2   0  -0.412   -0.4765   0.5205  -0.1434
 EKG  C13  C  CH2   0  -0.411    9.6967   0.3904  -0.0237
 EKG  C11  C  CH2   0  -0.411    7.1523   0.4122  -0.0579
 EKG  C4   C  CH2   0  -0.416   -1.7675  -0.2742   0.0030
 EKG  C12  C  CH2   0  -0.411    8.4153  -0.4229   0.1090
 EKG  C3   C  CH2   0  -0.417   -3.0107   0.5890  -0.1689
 EKG  C2   C  CH2   0  -0.584   -4.2917  -0.2131  -0.0072
 EKG  C24  C  CH2   0  -0.165  -10.3271   0.2377   0.3210
 EKG  C22  C  CH1   0  -0.049   -8.9740  -0.4569   0.3255
 EKG  O19  O  O     0  -0.453   -5.5729   1.7682  -0.5039
 EKG  C1   C  C     0   0.607   -5.5410   0.6076  -0.1781
 EKG  O20  O  O2    0  -0.460   -6.6334  -0.1076   0.0713
 EKG  O23  O  OH1   0  -0.656   -8.9485  -1.5991  -0.4951
 EKG  H1   H  HCH3  0   0.225   14.4031   0.1278   0.1103
 EKG  H2   H  HCH3  0   0.215   13.5117  -0.9698   1.1595
 EKG  H3   H  HCH3  0   0.215   13.5545  -1.2541  -0.5772
 EKG  H4   H  HCH2  0   0.206    3.3067  -0.8551   1.0323
 EKG  H5   H  HCH2  0   0.206    3.3210  -1.1765  -0.6880
 EKG  H6   H  HCH2  0   0.206    2.0699   1.2841   0.6214
 EKG  H7   H  HCH2  0   0.206    2.0825   0.9613  -1.0985
 EKG  H8   H  HCH2  0   0.209   12.2369   1.1684   0.7674
 EKG  H9   H  HCH2  0   0.210   12.2625   0.8693  -0.9550
 EKG  H10  H  HCH2  0   0.206    4.6245   0.9275  -1.0698
 EKG  H11  H  HCH2  0   0.206    4.6101   1.2484   0.6505
 EKG  H12  H  HCH2  0   0.207    0.7708  -1.1372  -0.7137
 EKG  H13  H  HCH2  0   0.207    0.7592  -0.8138   1.0065
 EKG  H14  H  HCH2  0   0.236   -8.0403   0.8954  -1.0809
 EKG  H15  H  HCH2  0   0.239   -7.9382   1.4137   0.6069
 EKG  H16  H  HCH2  0   0.205   10.9675  -1.2451  -0.6065
 EKG  H17  H  HCH2  0   0.205   10.9416  -0.9432   1.1170
 EKG  H18  H  HCH2  0   0.206    5.8533  -0.8885   1.0587
 EKG  H19  H  HCH2  0   0.206    5.8703  -1.2059  -0.6623
 EKG  H20  H  HCH2  0   0.208   -0.4664   1.3321   0.5928
 EKG  H21  H  HCH2  0   0.208   -0.4588   1.0045  -1.1263
 EKG  H22  H  HCH2  0   0.206    9.6936   1.1948   0.7207
 EKG  H23  H  HCH2  0   0.206    9.7128   0.8848  -1.0017
 EKG  H24  H  HCH2  0   0.206    7.1682   0.9028  -1.0378
 EKG  H25  H  HCH2  0   0.206    7.1510   1.2195   0.6833
 EKG  H26  H  HCH2  0   0.212   -1.7806  -1.0859  -0.7329
 EKG  H27  H  HCH2  0   0.212   -1.7878  -0.7566   0.9865
 EKG  H28  H  HCH2  0   0.206    8.4185  -1.2288  -0.6337
 EKG  H29  H  HCH2  0   0.206    8.3985  -0.9152   1.0880
 EKG  H30  H  HCH2  0   0.224   -2.9907   1.4024   0.5618
 EKG  H31  H  HCH2  0   0.224   -2.9912   1.0603  -1.1550
 EKG  H32  H  HCH2  0   0.274   -4.3253  -1.0319  -0.7341
 EKG  H33  H  HCH2  0   0.271   -4.3244  -0.6946   0.9750
 EKG  H34  H  HCH2  0   0.204  -10.2696   1.1241   0.9661
 EKG  H35  H  HCH2  0   0.198  -10.5447   0.5996  -0.6949
 EKG  H36  H  HCH1  0   0.240   -8.7732  -0.8134   1.3413
 EKG  H37  H  HOH1  0   0.445   -9.1957  -1.3416  -1.3904
 EKG  H38  H  HOH1  0   0.457  -12.1563  -0.2289   0.7344
 EKG  O25  O  OH1   0  -0.667  -11.3029  -0.6699   0.7687

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
 EKG  O25  C24  single  1.406  0.020  1.406
 EKG  C24  C22  single  1.521  0.020  1.521
 EKG  C22  C21  single  1.519  0.020  1.519
 EKG  C22  O23  single  1.407  0.020  1.407
 EKG  C21  O20  single  1.427  0.020  1.427
 EKG  O20  C1   single  1.329  0.020  1.329
 EKG  C1   O19  double  1.206  0.020  1.206
 EKG  C1   C2   single  1.505  0.020  1.505
 EKG  C2   C3   single  1.520  0.020  1.520
 EKG  C3   C4   single  1.523  0.020  1.523
 EKG  C19  C15  single  1.522  0.020  1.522
 EKG  C4   C5   single  1.523  0.020  1.523
 EKG  C15  C14  single  1.524  0.020  1.524
 EKG  C5   C6   single  1.523  0.020  1.523
 EKG  C14  C13  single  1.523  0.020  1.523
 EKG  C6   C7   single  1.523  0.020  1.523
 EKG  C13  C12  single  1.523  0.020  1.523
 EKG  C11  C12  single  1.523  0.020  1.523
 EKG  C11  C10  single  1.523  0.020  1.523
 EKG  C8   C7   single  1.523  0.020  1.523
 EKG  C8   C9   single  1.523  0.020  1.523
 EKG  C9   C10  single  1.523  0.020  1.523
 EKG  C19  H1   single  0.970  0.020  1.090
 EKG  C19  H2   single  0.970  0.020  1.090
 EKG  C19  H3   single  0.970  0.020  1.090
 EKG  C8   H4   single  0.970  0.020  1.090
 EKG  C8   H5   single  0.970  0.020  1.090
 EKG  C7   H6   single  0.970  0.020  1.090
 EKG  C7   H7   single  0.970  0.020  1.090
 EKG  C15  H8   single  0.970  0.020  1.090
 EKG  C15  H9   single  0.970  0.020  1.090
 EKG  C9   H10  single  0.970  0.020  1.090
 EKG  C9   H11  single  0.970  0.020  1.090
 EKG  C6   H12  single  0.970  0.020  1.090
 EKG  C6   H13  single  0.970  0.020  1.090
 EKG  C21  H14  single  0.970  0.020  1.090
 EKG  C21  H15  single  0.970  0.020  1.090
 EKG  C14  H16  single  0.970  0.020  1.090
 EKG  C14  H17  single  0.970  0.020  1.090
 EKG  C10  H18  single  0.970  0.020  1.090
 EKG  C10  H19  single  0.970  0.020  1.090
 EKG  C5   H20  single  0.970  0.020  1.090
 EKG  C5   H21  single  0.970  0.020  1.090
 EKG  C13  H22  single  0.970  0.020  1.090
 EKG  C13  H23  single  0.970  0.020  1.090
 EKG  C11  H24  single  0.970  0.020  1.090
 EKG  C11  H25  single  0.970  0.020  1.090
 EKG  C4   H26  single  0.970  0.020  1.090
 EKG  C4   H27  single  0.970  0.020  1.090
 EKG  C12  H28  single  0.970  0.020  1.090
 EKG  C12  H29  single  0.970  0.020  1.090
 EKG  C3   H30  single  0.970  0.020  1.090
 EKG  C3   H31  single  0.970  0.020  1.090
 EKG  C2   H32  single  0.970  0.020  1.090
 EKG  C2   H33  single  0.970  0.020  1.090
 EKG  C24  H34  single  0.970  0.020  1.090
 EKG  C24  H35  single  0.970  0.020  1.090
 EKG  C22  H36  single  0.970  0.020  1.090
 EKG  O23  H37  single  0.850  0.020  0.980
 EKG  O25  H38  single  0.850  0.020  0.980

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
 EKG  H3   C19  H2   107.44  3.000
 EKG  H3   C19  H1   107.62  3.000
 EKG  H2   C19  H1   107.55  3.000
 EKG  H3   C19  C15  111.23  3.000
 EKG  H2   C19  C15  111.10  3.000
 EKG  H1   C19  C15  111.69  3.000
 EKG  H5   C8   H4   105.98  3.000
 EKG  H5   C8   C9   109.34  3.000
 EKG  H4   C8   C9   109.32  3.000
 EKG  H5   C8   C7   109.36  3.000
 EKG  H4   C8   C7   109.38  3.000
 EKG  C9   C8   C7   113.21  3.000
 EKG  H7   C7   H6   105.96  3.000
 EKG  H7   C7   C6   109.30  3.000
 EKG  H6   C7   C6   109.26  3.000
 EKG  H7   C7   C8   109.35  3.000
 EKG  H6   C7   C8   109.30  3.000
 EKG  C6   C7   C8   113.41  3.000
 EKG  H9   C15  H8   105.99  3.000
 EKG  H9   C15  C14  109.30  3.000
 EKG  H8   C15  C14  109.29  3.000
 EKG  H9   C15  C19  109.64  3.000
 EKG  H8   C15  C19  109.53  3.000
 EKG  C14  C15  C19  112.85  3.000
 EKG  H11  C9   H10  105.95  3.000
 EKG  H11  C9   C10  109.30  3.000
 EKG  H10  C9   C10  109.34  3.000
 EKG  H11  C9   C8   109.29  3.000
 EKG  H10  C9   C8   109.29  3.000
 EKG  C10  C9   C8   113.39  3.000
 EKG  H13  C6   H12  106.00  3.000
 EKG  H13  C6   C5   109.39  3.000
 EKG  H12  C6   C5   109.39  3.000
 EKG  H13  C6   C7   109.33  3.000
 EKG  H12  C6   C7   109.36  3.000
 EKG  C5   C6   C7   113.12  3.000
 EKG  H15  C21  H14  107.90  3.000
 EKG  H15  C21  O20  110.12  3.000
 EKG  H14  C21  O20  110.18  3.000
 EKG  H15  C21  C22  110.27  3.000
 EKG  H14  C21  C22  110.65  3.000
 EKG  O20  C21  C22  107.74  3.000
 EKG  H17  C14  H16  105.94  3.000
 EKG  H17  C14  C13  109.38  3.000
 EKG  H16  C14  C13  109.38  3.000
 EKG  H17  C14  C15  109.22  3.000
 EKG  H16  C14  C15  109.27  3.000
 EKG  C13  C14  C15  113.38  3.000
 EKG  H19  C10  H18  105.97  3.000
 EKG  H19  C10  C11  109.33  3.000
 EKG  H18  C10  C11  109.32  3.000
 EKG  H19  C10  C9   109.35  3.000
 EKG  H18  C10  C9   109.37  3.000
 EKG  C11  C10  C9   113.24  3.000
 EKG  H21  C5   H20  105.99  3.000
 EKG  H21  C5   C4   109.29  3.000
 EKG  H20  C5   C4   109.25  3.000
 EKG  H21  C5   C6   109.36  3.000
 EKG  H20  C5   C6   109.31  3.000
 EKG  C4   C5   C6   113.38  3.000
 EKG  H23  C13  H22  105.96  3.000
 EKG  H23  C13  C12  109.33  3.000
 EKG  H22  C13  C12  109.29  3.000
 EKG  H23  C13  C14  109.37  3.000
 EKG  H22  C13  C14  109.32  3.000
 EKG  C12  C13  C14  113.32  3.000
 EKG  H25  C11  H24  105.97  3.000
 EKG  H25  C11  C12  109.31  3.000
 EKG  H24  C11  C12  109.35  3.000
 EKG  H25  C11  C10  109.29  3.000
 EKG  H24  C11  C10  109.30  3.000
 EKG  C12  C11  C10  113.36  3.000
 EKG  H27  C4   H26  106.06  3.000
 EKG  H27  C4   C3   109.61  3.000
 EKG  H26  C4   C3   109.52  3.000
 EKG  H27  C4   C5   109.37  3.000
 EKG  H26  C4   C5   109.40  3.000
 EKG  C3   C4   C5   112.66  3.000
 EKG  H29  C12  H28  105.97  3.000
 EKG  H29  C12  C11  109.36  3.000
 EKG  H28  C12  C11  109.35  3.000
 EKG  H29  C12  C13  109.30  3.000
 EKG  H28  C12  C13  109.34  3.000
 EKG  C11  C12  C13  113.27  3.000
 EKG  H31  C3   H30  106.36  3.000
 EKG  H31  C3   C2   109.79  3.000
 EKG  H30  C3   C2   109.69  3.000
 EKG  H31  C3   C4   109.36  3.000
 EKG  H30  C3   C4   109.34  3.000
 EKG  C2   C3   C4   112.13  3.000
 EKG  H33  C2   H32  105.41  3.000
 EKG  H33  C2   C1   108.49  3.000
 EKG  H32  C2   C1   107.87  3.000
 EKG  H33  C2   C3   110.66  3.000
 EKG  H32  C2   C3   110.47  3.000
 EKG  C1   C2   C3   113.57  3.000
 EKG  H35  C24  H34  106.70  3.000
 EKG  H35  C24  O25  111.66  3.000
 EKG  H34  C24  O25  111.74  3.000
 EKG  H35  C24  C22  109.21  3.000
 EKG  H34  C24  C22  108.69  3.000
 EKG  O25  C24  C22  108.77  3.000
 EKG  H36  C22  O23  105.87  3.000
 EKG  H36  C22  C24  108.34  3.000
 EKG  O23  C22  C24  112.66  3.000
 EKG  H36  C22  C21  108.43  3.000
 EKG  O23  C22  C21  112.13  3.000
 EKG  C24  C22  C21  109.22  3.000
 EKG  O20  C1   O19  123.15  3.000
 EKG  O19  C1   C2   125.29  3.000
 EKG  O20  C1   C2   111.56  3.000
 EKG  C1   O20  C21  117.72  3.000
 EKG  H37  O23  C22  108.68  3.000
 EKG  H38  O25  C24  107.98  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
 EKG  Var_01  C13  C14  C15  C19   179.99  30.0  3
 EKG  Var_02  C5   C6   C7   C8    179.95  30.0  1
 EKG  Var_03  C11  C10  C9   C8   -179.84  30.0  3
 EKG  Var_04  C4   C5   C6   C7   -179.75  30.0  1
 EKG  Var_05  C10  C9   C8   C7    180.00  30.0  3
 EKG  Var_06  C12  C13  C14  C15  -179.59  30.0  3
 EKG  Var_07  C6   C7   C8   C9   -179.89  30.0  3
 EKG  Var_08  C12  C11  C10  C9    180.00  30.0  1
 EKG  Var_09  C3   C4   C5   C6   -179.96  30.0  1
 EKG  Var_10  O19  C1   O20  C21    -0.15  30.0  3
 EKG  Var_11  C11  C12  C13  C14  -179.93  30.0  3
 EKG  Var_12  C13  C12  C11  C10  -179.82  30.0  3
 EKG  Var_13  C2   C3   C4   C5   -179.45  30.0  1
 EKG  Var_14  C1   C2   C3   C4   -179.69  30.0  1
 EKG  Var_15  O20  C1   C2   C3   -175.22  30.0  1
 EKG  Var_16  H1   C19  C15  C14  -179.12  30.0  3
 EKG  Var_17  H14  C21  O20  C1     61.14  30.0  1

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
 EKG  chir_01  C22  C24  C21  O23  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
 EKG  plan-1  C2   0.020
 EKG  plan-1  O19  0.020
 EKG  plan-1  C1   0.020
 EKG  plan-1  O20  0.020

