# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:28:07 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S)-2-hydroxyoctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@H](O)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
 HOC  HOC  '(2S)-2-hydroxyoctanoic acid'  ligand  26  11  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HOC
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
 HOC  C8   C  CH3    0  -0.662   5.7297   0.0773  -0.0954
 HOC  C7   C  CH2    0  -0.419   4.4154  -0.5103   0.3992
 HOC  OH   O  OH1    0  -0.702  -1.9432   1.7243  -0.0215
 HOC  C1   C  C      0   0.394  -3.1905  -0.3314   0.0770
 HOC  C2   C  CH1    0  -0.082  -1.8959   0.3675  -0.3948
 HOC  C3   C  CH2    0  -0.430  -0.6605  -0.3249   0.1735
 HOC  C4   C  CH2    0  -0.411   0.6521   0.2791  -0.3076
 HOC  C5   C  CH2    0  -0.411   1.8743  -0.4105   0.2857
 HOC  C6   C  CH2    0  -0.405   3.1937   0.1715  -0.2044
 HOC  H81  H  HCH3   0   0.215   5.8064   1.1377   0.1526
 HOC  H82  H  HCH3   0   0.225   6.5883  -0.4280   0.3485
 HOC  H83  H  HCH3   0   0.215   5.8186  -0.0116  -1.1799
 HOC  H71  H  HCH2   0   0.210   4.3819  -1.5798   0.1694
 HOC  H72  H  HCH2   0   0.209   4.3685  -0.4354   1.4901
 HOC  HOH  H  HOH1   0   0.424  -2.7757   1.7597   0.4876
 HOC  H2   H  HCH1   0   0.190  -1.8527   0.2886  -1.4928
 HOC  H31  H  HCH2   0   0.212  -0.6970  -1.3817  -0.1033
 HOC  H32  H  HCH2   0   0.205  -0.7008  -0.2907   1.2690
 HOC  H41  H  HCH2   0   0.211   0.6840   1.3440  -0.0592
 HOC  H42  H  HCH2   0   0.203   0.6981   0.2203  -1.4014
 HOC  H51  H  HCH2   0   0.205   1.8391  -1.4802   0.0505
 HOC  H52  H  HCH2   0   0.205   1.8320  -0.3426   1.3787
 HOC  H61  H  HCH2   0   0.205   3.2271   1.2426   0.0250
 HOC  H62  H  HCH2   0   0.205   3.2407   0.0973  -1.2968
 HOC  O1A  O  OC    -1  -0.596  -3.3514  -1.5234  -0.2260
 HOC  O1B  O  O      0  -0.612  -3.9656   0.3951   0.7429

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
 HOC  C8  C7   single  1.522  0.020  1.522
 HOC  C8  H81  single  0.970  0.020  1.090
 HOC  C8  H82  single  0.970  0.020  1.090
 HOC  C8  H83  single  0.970  0.020  1.090
 HOC  C7  C6   single  1.524  0.020  1.524
 HOC  C7  H71  single  0.970  0.020  1.090
 HOC  C7  H72  single  0.970  0.020  1.090
 HOC  OH  C2   single  1.408  0.020  1.408
 HOC  OH  HOH  single  0.850  0.020  0.980
 HOC  C1  C2   single  1.545  0.020  1.545
 HOC  C1  O1A  deloc   1.240  0.020  1.240
 HOC  C1  O1B  deloc   1.254  0.020  1.254
 HOC  C2  C3   single  1.526  0.020  1.526
 HOC  C2  H2   single  0.970  0.020  1.090
 HOC  C3  C4   single  1.523  0.020  1.523
 HOC  C3  H31  single  0.970  0.020  1.090
 HOC  C3  H32  single  0.970  0.020  1.090
 HOC  C4  C5   single  1.524  0.020  1.524
 HOC  C4  H41  single  0.970  0.020  1.090
 HOC  C4  H42  single  0.970  0.020  1.090
 HOC  C5  C6   single  1.523  0.020  1.523
 HOC  C5  H51  single  0.970  0.020  1.090
 HOC  C5  H52  single  0.970  0.020  1.090
 HOC  C6  H61  single  0.970  0.020  1.090
 HOC  C6  H62  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
 HOC  H83  C8  H82  107.61  3.000
 HOC  H83  C8  H81  107.40  3.000
 HOC  H82  C8  H81  107.59  3.000
 HOC  H83  C8  C7   111.20  3.000
 HOC  H82  C8  C7   111.63  3.000
 HOC  H81  C8  C7   111.21  3.000
 HOC  H72  C7  H71  105.95  3.000
 HOC  H72  C7  C6   109.26  3.000
 HOC  H71  C7  C6   109.24  3.000
 HOC  H72  C7  C8   109.54  3.000
 HOC  H71  C7  C8   109.60  3.000
 HOC  C6   C7  C8   113.00  3.000
 HOC  HOH  OH  C2   101.64  3.000
 HOC  O1B  C1  O1A  127.33  3.000
 HOC  O1B  C1  C2   114.71  3.000
 HOC  O1A  C1  C2   117.96  3.000
 HOC  H2   C2  C3   107.87  3.000
 HOC  H2   C2  C1   107.75  3.000
 HOC  C3   C2  C1   111.06  3.000
 HOC  H2   C2  OH   109.55  3.000
 HOC  C3   C2  OH   111.45  3.000
 HOC  C1   C2  OH   109.08  3.000
 HOC  H32  C3  H31  106.37  3.000
 HOC  H32  C3  C4   109.57  3.000
 HOC  H31  C3  C4   109.40  3.000
 HOC  H32  C3  C2   109.15  3.000
 HOC  H31  C3  C2   108.50  3.000
 HOC  C4   C3  C2   113.59  3.000
 HOC  H42  C4  H41  106.12  3.000
 HOC  H42  C4  C5   109.31  3.000
 HOC  H41  C4  C5   109.19  3.000
 HOC  H42  C4  C3   109.28  3.000
 HOC  H41  C4  C3   109.84  3.000
 HOC  C5   C4  C3   112.88  3.000
 HOC  H52  C5  H51  105.86  3.000
 HOC  H52  C5  C6   109.31  3.000
 HOC  H51  C5  C6   109.38  3.000
 HOC  H52  C5  C4   109.23  3.000
 HOC  H51  C5  C4   109.42  3.000
 HOC  C6   C5  C4   113.37  3.000
 HOC  H62  C6  H61  105.88  3.000
 HOC  H62  C6  C5   109.39  3.000
 HOC  H61  C6  C5   109.42  3.000
 HOC  H62  C6  C7   109.28  3.000
 HOC  H61  C6  C7   109.27  3.000
 HOC  C5   C6  C7   113.33  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
 HOC  Var_01  C5   C6  C7  C8  -179.99  30.0  3
 HOC  Var_02  C4   C5  C6  C7   179.47  30.0  1
 HOC  Var_03  C5   C4  C3  C2   179.13  30.0  3
 HOC  Var_04  C6   C5  C4  C3   179.14  30.0  3
 HOC  Var_05  H81  C8  C7  C6    59.95  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
 HOC  chir_01  C2  OH  C1  C3  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
 HOC  plan-1  C1   0.020
 HOC  plan-1  C2   0.020
 HOC  plan-1  O1A  0.020
 HOC  plan-1  O1B  0.020

