# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 17:07:23 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (2R)-octane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[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
 7F2  7F2  '(2R)-octane-1,2-diol     '  ligand  28  10  .  2022-07-23  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_7F2
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
 7F2  C1   C  CH3   0  -0.662   5.3912  -0.2694  -0.2008
 7F2  C2   C  CH2   0  -0.419   4.1309   0.4169   0.3075
 7F2  CE   C  CH2   0  -0.406   2.8522  -0.2146  -0.2285
 7F2  CD   C  CH2   0  -0.412   1.5863   0.4816   0.2551
 7F2  CG   C  CH2   0  -0.409   0.3089  -0.1915  -0.2308
 7F2  CB   C  CH2   0  -0.456  -0.9506   0.5559   0.1892
 7F2  CA   C  CH1   0  -0.001  -2.2438  -0.1515  -0.2048
 7F2  C    C  CH2   0  -0.152  -3.4482   0.7234   0.1004
 7F2  O    O  OH1   0  -0.672  -4.6179   0.0876  -0.3589
 7F2  O1   O  OH1   0  -0.665  -2.3563  -1.4271   0.3940
 7F2  H1   H  HCH3  0   0.215   5.4098  -1.3229   0.0846
 7F2  H2   H  HCH3  0   0.215   5.4530  -0.2248  -1.2900
 7F2  H3   H  HCH3  0   0.226   6.2917   0.1972   0.1999
 7F2  H4   H  HCH2  0   0.210   4.1156   0.3894   1.4014
 7F2  H5   H  HCH2  0   0.210   4.1548   1.4760   0.0328
 7F2  H6   H  HCH2  0   0.206   2.8745  -0.2047  -1.3239
 7F2  H7   H  HCH2  0   0.206   2.8203  -1.2711   0.0619
 7F2  H8   H  HCH2  0   0.207   1.5834   0.5116   1.3502
 7F2  H9   H  HCH2  0   0.207   1.6001   1.5264  -0.0743
 7F2  H10  H  HCH2  0   0.209   0.3315  -0.2700  -1.3232
 7F2  H11  H  HCH2  0   0.213   0.2754  -1.2168   0.1474
 7F2  H12  H  HCH2  0   0.216  -0.9436   0.7139   1.2750
 7F2  H13  H  HCH2  0   0.221  -0.9426   1.5538  -0.2596
 7F2  H14  H  HCH1  0   0.218  -2.2236  -0.3392  -1.2846
 7F2  H15  H  HCH2  0   0.187  -3.4887   0.9138   1.1837
 7F2  H16  H  HCH2  0   0.195  -3.3005   1.6976  -0.3844
 7F2  H17  H  HOH1  0   0.453  -5.3631   0.6643  -0.1695
 7F2  H18  H  HOH1  0   0.439  -2.3307  -1.3096   1.3501

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
 7F2  O   C    single  1.408  0.020  1.408
 7F2  CB  CA   single  1.526  0.020  1.526
 7F2  CB  CG   single  1.524  0.020  1.524
 7F2  CA  C    single  1.520  0.020  1.520
 7F2  CD  CG   single  1.523  0.020  1.523
 7F2  CD  CE   single  1.523  0.020  1.523
 7F2  CE  C2   single  1.524  0.020  1.524
 7F2  C2  C1   single  1.522  0.020  1.522
 7F2  CA  O1   single  1.414  0.020  1.414
 7F2  C1  H1   single  0.970  0.020  1.090
 7F2  C1  H2   single  0.970  0.020  1.090
 7F2  C1  H3   single  0.970  0.020  1.090
 7F2  C2  H4   single  0.970  0.020  1.090
 7F2  C2  H5   single  0.970  0.020  1.090
 7F2  CE  H6   single  0.970  0.020  1.090
 7F2  CE  H7   single  0.970  0.020  1.090
 7F2  CD  H8   single  0.970  0.020  1.090
 7F2  CD  H9   single  0.970  0.020  1.090
 7F2  CG  H10  single  0.970  0.020  1.090
 7F2  CG  H11  single  0.970  0.020  1.090
 7F2  CB  H12  single  0.970  0.020  1.090
 7F2  CB  H13  single  0.970  0.020  1.090
 7F2  CA  H14  single  0.970  0.020  1.090
 7F2  C   H15  single  0.970  0.020  1.090
 7F2  C   H16  single  0.970  0.020  1.090
 7F2  O   H17  single  0.850  0.020  0.980
 7F2  O1  H18  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
 7F2  H3   C1  H2   107.60  3.000
 7F2  H3   C1  H1   107.62  3.000
 7F2  H2   C1  H1   107.42  3.000
 7F2  H3   C1  C2   111.59  3.000
 7F2  H2   C1  C2   111.19  3.000
 7F2  H1   C1  C2   111.22  3.000
 7F2  H5   C2  H4   105.99  3.000
 7F2  H5   C2  CE   109.34  3.000
 7F2  H4   C2  CE   109.24  3.000
 7F2  H5   C2  C1   109.54  3.000
 7F2  H4   C2  C1   109.51  3.000
 7F2  CE   C2  C1   112.98  3.000
 7F2  H7   CE  H6   105.91  3.000
 7F2  H7   CE  CD   109.40  3.000
 7F2  H6   CE  CD   109.28  3.000
 7F2  H7   CE  C2   109.31  3.000
 7F2  H6   CE  C2   109.32  3.000
 7F2  CD   CE  C2   113.35  3.000
 7F2  H9   CD  H8   105.93  3.000
 7F2  H9   CD  CG   109.64  3.000
 7F2  H8   CD  CG   109.19  3.000
 7F2  H9   CD  CE   109.26  3.000
 7F2  H8   CD  CE   109.39  3.000
 7F2  CG   CD  CE   113.18  3.000
 7F2  H11  CG  H10  106.17  3.000
 7F2  H11  CG  CB   109.84  3.000
 7F2  H10  CG  CB   109.09  3.000
 7F2  H11  CG  CD   109.25  3.000
 7F2  H10  CG  CD   109.41  3.000
 7F2  CB   CG  CD   112.86  3.000
 7F2  H13  CB  H12  105.93  3.000
 7F2  H13  CB  CA   108.85  3.000
 7F2  H12  CB  CA   109.13  3.000
 7F2  H13  CB  CG   109.16  3.000
 7F2  H12  CB  CG   109.77  3.000
 7F2  CA   CB  CG   113.71  3.000
 7F2  H14  CA  O1   105.32  3.000
 7F2  H14  CA  C    108.12  3.000
 7F2  O1   CA  C    111.80  3.000
 7F2  H14  CA  CB   108.55  3.000
 7F2  O1   CA  CB   112.11  3.000
 7F2  C    CA  CB   110.67  3.000
 7F2  H16  C   H15  106.62  3.000
 7F2  H16  C   O    111.60  3.000
 7F2  H15  C   O    111.62  3.000
 7F2  H16  C   CA   108.39  3.000
 7F2  H15  C   CA   109.06  3.000
 7F2  O    C   CA   109.44  3.000
 7F2  H17  O   C    107.99  3.000
 7F2  H18  O1  CA   107.95  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
 7F2  Var_01  CD  CE  C2  C1  -178.96  30.0  1
 7F2  Var_02  CG  CD  CE  C2  -177.34  30.0  1
 7F2  Var_03  CB  CG  CD  CE  -176.67  30.0  3
 7F2  Var_04  CA  CB  CG  CD  -176.04  30.0  1
 7F2  Var_05  H1  C1  C2  CE   -59.55  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
 7F2  chir_01  CA  CB  C  O1  positiv

