# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 15:09:03 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2S,3R)-2-hexyl-3-hydroxynonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@@H](O)[C@H](CCCCCC)C(O)=O
#
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
 KKJ  KKJ  '(2S,3R)-2-hexyl-3-hydroxynonanoic acid'  ligand  47  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KKJ
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
 KKJ  O1    O  OH1    0  -0.673   0.6905   1.9846   0.0961
 KKJ  C2    C  CH1    0   0.069   0.7097   0.5772   0.2806
 KKJ  C3    C  CH1    0  -0.358  -0.5663  -0.0905  -0.2515
 KKJ  C4    C  C      0   0.406  -0.5492  -1.5980   0.0758
 KKJ  O5    O  OC    -1  -0.618  -0.5601  -2.4038  -0.8761
 KKJ  O6    O  O      0  -0.618  -0.5291  -1.8945   1.2899
 KKJ  C7    C  CH2    0  -0.453   1.9725  -0.0311  -0.3261
 KKJ  C8    C  CH2    0  -0.409   3.2706   0.5598   0.2097
 KKJ  C9    C  CH2    0  -0.412   4.5049  -0.0958  -0.3973
 KKJ  C10   C  CH2    0  -0.406   5.8152   0.4657   0.1386
 KKJ  C11   C  CH2    0  -0.419   7.0461  -0.1863  -0.4791
 KKJ  C12   C  CH3    0  -0.662   8.3530   0.3770   0.0611
 KKJ  C13   C  CH2    0  -0.398  -1.8299   0.5548   0.3188
 KKJ  C14   C  CH2    0  -0.418  -3.1208  -0.0190  -0.2540
 KKJ  C15   C  CH2    0  -0.410  -4.3667   0.6639   0.2965
 KKJ  C16   C  CH2    0  -0.406  -5.6639   0.1123  -0.2806
 KKJ  C17   C  CH2    0  -0.419  -6.9100   0.7780   0.2902
 KKJ  C18   C  CH3    0  -0.662  -8.2018   0.2205  -0.2910
 KKJ  HO1   H  HOH1   0   0.435   0.6623   2.1571  -0.8513
 KKJ  H2    H  HCH1   0   0.198   0.7405   0.4342   1.3659
 KKJ  H3    H  HCH1   0   0.184  -0.5785   0.0284  -1.3440
 KKJ  H7    H  HCH2   0   0.225   1.9767  -1.1090  -0.1409
 KKJ  H7A   H  HCH2   0   0.206   1.9374   0.0821  -1.4174
 KKJ  H8    H  HCH2   0   0.210   3.3020   1.6357   0.0177
 KKJ  H8A   H  HCH2   0   0.204   3.2991   0.4440   1.2993
 KKJ  H9    H  HCH2   0   0.206   4.4707  -1.1756  -0.2135
 KKJ  H9A   H  HCH2   0   0.206   4.4786   0.0232  -1.4865
 KKJ  H10   H  HCH2   0   0.205   5.8494   1.5462  -0.0406
 KKJ  H10A  H  HCH2   0   0.205   5.8469   0.3407   1.2269
 KKJ  H11   H  HCH2   0   0.210   7.0103  -1.2656  -0.3007
 KKJ  H11A  H  HCH2   0   0.210   7.0139  -0.0598  -1.5659
 KKJ  H12   H  HCH3   0   0.215   8.4312   1.4485  -0.1328
 KKJ  H12A  H  HCH3   0   0.215   8.4279   0.2343   1.1410
 KKJ  H12B  H  HCH3   0   0.225   9.2177  -0.1052  -0.3962
 KKJ  H13   H  HCH2   0   0.198  -1.8307   0.4365   1.4072
 KKJ  H13A  H  HCH2   0   0.207  -1.8131   1.6313   0.1282
 KKJ  H14   H  HCH2   0   0.201  -3.1072   0.0768  -1.3458
 KKJ  H14A  H  HCH2   0   0.211  -3.1838  -1.0923  -0.0470
 KKJ  H15   H  HCH2   0   0.204  -4.3831   0.5599   1.3875
 KKJ  H15A  H  HCH2   0   0.204  -4.3093   1.7403   0.0989
 KKJ  H16   H  HCH2   0   0.205  -5.6565   0.2298  -1.3701
 KKJ  H16A  H  HCH2   0   0.205  -5.7142  -0.9668  -0.0958
 KKJ  H17   H  HCH2   0   0.209  -6.9161   0.6571   1.3780
 KKJ  H17A  H  HCH2   0   0.209  -6.8601   1.8560   0.1071
 KKJ  H18   H  HCH3   0   0.215  -8.2408   0.3595  -1.3732
 KKJ  H18A  H  HCH3   0   0.215  -8.2924  -0.8498  -0.0959
 KKJ  H18B  H  HCH3   0   0.225  -9.0783   0.7093   0.1361

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
 KKJ  O1   C2    single  1.420  0.020  1.420
 KKJ  C2   C3    single  1.535  0.020  1.535
 KKJ  C2   C7    single  1.527  0.020  1.527
 KKJ  C3   C4    single  1.543  0.020  1.543
 KKJ  C3   C13   single  1.529  0.020  1.529
 KKJ  C4   O5    deloc   1.247  0.020  1.247
 KKJ  C4   O6    deloc   1.250  0.020  1.250
 KKJ  C7   C8    single  1.524  0.020  1.524
 KKJ  C8   C9    single  1.524  0.020  1.524
 KKJ  C9   C10   single  1.523  0.020  1.523
 KKJ  C10  C11   single  1.524  0.020  1.524
 KKJ  C11  C12   single  1.522  0.020  1.522
 KKJ  C13  C14   single  1.524  0.020  1.524
 KKJ  C14  C15   single  1.524  0.020  1.524
 KKJ  C15  C16   single  1.523  0.020  1.523
 KKJ  C16  C17   single  1.524  0.020  1.524
 KKJ  C17  C18   single  1.522  0.020  1.522
 KKJ  O1   HO1   single  0.850  0.020  0.980
 KKJ  C2   H2    single  0.970  0.020  1.090
 KKJ  C3   H3    single  0.970  0.020  1.090
 KKJ  C7   H7    single  0.970  0.020  1.090
 KKJ  C7   H7A   single  0.970  0.020  1.090
 KKJ  C8   H8    single  0.970  0.020  1.090
 KKJ  C8   H8A   single  0.970  0.020  1.090
 KKJ  C9   H9    single  0.970  0.020  1.090
 KKJ  C9   H9A   single  0.970  0.020  1.090
 KKJ  C10  H10   single  0.970  0.020  1.090
 KKJ  C10  H10A  single  0.970  0.020  1.090
 KKJ  C11  H11   single  0.970  0.020  1.090
 KKJ  C11  H11A  single  0.970  0.020  1.090
 KKJ  C12  H12   single  0.970  0.020  1.090
 KKJ  C12  H12A  single  0.970  0.020  1.090
 KKJ  C12  H12B  single  0.970  0.020  1.090
 KKJ  C13  H13   single  0.970  0.020  1.090
 KKJ  C13  H13A  single  0.970  0.020  1.090
 KKJ  C14  H14   single  0.970  0.020  1.090
 KKJ  C14  H14A  single  0.970  0.020  1.090
 KKJ  C15  H15   single  0.970  0.020  1.090
 KKJ  C15  H15A  single  0.970  0.020  1.090
 KKJ  C16  H16   single  0.970  0.020  1.090
 KKJ  C16  H16A  single  0.970  0.020  1.090
 KKJ  C17  H17   single  0.970  0.020  1.090
 KKJ  C17  H17A  single  0.970  0.020  1.090
 KKJ  C18  H18   single  0.970  0.020  1.090
 KKJ  C18  H18A  single  0.970  0.020  1.090
 KKJ  C18  H18B  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
 KKJ  HO1   O1   C2    107.80  3.000
 KKJ  H2    C2   C7    108.57  3.000
 KKJ  H2    C2   C3    108.06  3.000
 KKJ  C7    C2   C3    112.10  3.000
 KKJ  H2    C2   O1    104.99  3.000
 KKJ  C7    C2   O1    110.76  3.000
 KKJ  C3    C2   O1    112.02  3.000
 KKJ  H3    C3   C13   108.41  3.000
 KKJ  H3    C3   C4    108.46  3.000
 KKJ  C13   C3   C4    110.02  3.000
 KKJ  H3    C3   C2    107.86  3.000
 KKJ  C13   C3   C2    111.97  3.000
 KKJ  C4    C3   C2    110.02  3.000
 KKJ  O6    C4   O5    126.04  3.000
 KKJ  O6    C4   C3    115.97  3.000
 KKJ  O5    C4   C3    117.99  3.000
 KKJ  H7A   C7   H7    105.67  3.000
 KKJ  H7A   C7   C8    109.69  3.000
 KKJ  H7    C7   C8    108.63  3.000
 KKJ  H7A   C7   C2    109.11  3.000
 KKJ  H7    C7   C2    109.17  3.000
 KKJ  C8    C7   C2    114.22  3.000
 KKJ  H8A   C8   H8    106.13  3.000
 KKJ  H8A   C8   C9    109.24  3.000
 KKJ  H8    C8   C9    109.28  3.000
 KKJ  H8A   C8   C7    109.32  3.000
 KKJ  H8    C8   C7    110.15  3.000
 KKJ  C9    C8   C7    112.53  3.000
 KKJ  H9A   C9   H9    105.83  3.000
 KKJ  H9A   C9   C10   109.29  3.000
 KKJ  H9    C9   C10   109.33  3.000
 KKJ  H9A   C9   C8    109.26  3.000
 KKJ  H9    C9   C8    109.38  3.000
 KKJ  C10   C9   C8    113.46  3.000
 KKJ  H10A  C10  H10   105.90  3.000
 KKJ  H10A  C10  C11   109.30  3.000
 KKJ  H10   C10  C11   109.29  3.000
 KKJ  H10A  C10  C9    109.41  3.000
 KKJ  H10   C10  C9    109.44  3.000
 KKJ  C11   C10  C9    113.24  3.000
 KKJ  H11A  C11  H11   105.95  3.000
 KKJ  H11A  C11  C12   109.56  3.000
 KKJ  H11   C11  C12   109.58  3.000
 KKJ  H11A  C11  C10   109.23  3.000
 KKJ  H11   C11  C10   109.23  3.000
 KKJ  C12   C11  C10   113.04  3.000
 KKJ  H12B  C12  H12A  107.61  3.000
 KKJ  H12B  C12  H12   107.61  3.000
 KKJ  H12A  C12  H12   107.40  3.000
 KKJ  H12B  C12  C11   111.61  3.000
 KKJ  H12A  C12  C11   111.20  3.000
 KKJ  H12   C12  C11   111.21  3.000
 KKJ  H13A  C13  H13   106.24  3.000
 KKJ  H13A  C13  C14   108.55  3.000
 KKJ  H13   C13  C14   109.41  3.000
 KKJ  H13A  C13  C3    109.74  3.000
 KKJ  H13   C13  C3    109.01  3.000
 KKJ  C14   C13  C3    113.63  3.000
 KKJ  H14A  C14  H14   105.95  3.000
 KKJ  H14A  C14  C15   108.90  3.000
 KKJ  H14   C14  C15   109.32  3.000
 KKJ  H14A  C14  C13   110.28  3.000
 KKJ  H14   C14  C13   109.32  3.000
 KKJ  C15   C14  C13   112.83  3.000
 KKJ  H15A  C15  H15   105.87  3.000
 KKJ  H15A  C15  C16   109.39  3.000
 KKJ  H15   C15  C16   109.27  3.000
 KKJ  H15A  C15  C14   109.40  3.000
 KKJ  H15   C15  C14   109.23  3.000
 KKJ  C16   C15  C14   113.40  3.000
 KKJ  H16A  C16  H16   105.88  3.000
 KKJ  H16A  C16  C17   109.24  3.000
 KKJ  H16   C16  C17   109.33  3.000
 KKJ  H16A  C16  C15   109.38  3.000
 KKJ  H16   C16  C15   109.39  3.000
 KKJ  C17   C16  C15   113.35  3.000
 KKJ  H17A  C17  H17   105.98  3.000
 KKJ  H17A  C17  C18   109.60  3.000
 KKJ  H17   C17  C18   109.53  3.000
 KKJ  H17A  C17  C16   109.30  3.000
 KKJ  H17   C17  C16   109.18  3.000
 KKJ  C18   C17  C16   113.01  3.000
 KKJ  H18B  C18  H18A  107.62  3.000
 KKJ  H18B  C18  H18   107.60  3.000
 KKJ  H18A  C18  H18   107.40  3.000
 KKJ  H18B  C18  C17   111.62  3.000
 KKJ  H18A  C18  C17   111.17  3.000
 KKJ  H18   C18  C17   111.23  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
 KKJ  Var_01  C9   C8   C7   C2    178.70  30.0  3
 KKJ  Var_02  C15  C14  C13  C3   -178.35  30.0  3
 KKJ  Var_03  C10  C9   C8   C7   -179.18  30.0  3
 KKJ  Var_04  C11  C10  C9   C8   -179.58  30.0  3
 KKJ  Var_05  C12  C11  C10  C9   -179.92  30.0  3
 KKJ  Var_06  C16  C15  C14  C13   179.27  30.0  3
 KKJ  Var_07  C17  C16  C15  C14   178.92  30.0  3
 KKJ  Var_08  C18  C17  C16  C15  -179.97  30.0  3
 KKJ  Var_09  H12  C12  C11  C10   -59.80  30.0  3
 KKJ  Var_10  H18  C18  C17  C16   -60.07  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
 KKJ  chir_01  C2  O1  C3  C7   negativ
 KKJ  chir_02  C3  C2  C4  C13  negativ

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
 KKJ  plan-1  C3  0.020
 KKJ  plan-1  C4  0.020
 KKJ  plan-1  O5  0.020
 KKJ  plan-1  O6  0.020

