# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:13:43 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (3S)-oct-1-en-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)C=C
#
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
 3OM  3OM  '(3S)-oct-1-en-3-ol       '  ligand  25  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3OM
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
 3OM  C1   C  C2    0  -0.543   3.9995   0.4259   0.4890
 3OM  O1   O  OH1   0  -0.662   1.9181  -1.4559   0.0319
 3OM  C2   C  C1    0  -0.193   2.9205   0.7437  -0.2154
 3OM  C3   C  CH1   0  -0.004   1.7464  -0.1559  -0.4810
 3OM  C4   C  CH2   0  -0.459   0.4551   0.4979   0.0181
 3OM  C5   C  CH2   0  -0.412  -0.8062  -0.2722  -0.3507
 3OM  C6   C  CH2   0  -0.407  -2.0749   0.3847   0.1782
 3OM  C7   C  CH2   0  -0.418  -3.3418  -0.3778  -0.1897
 3OM  C8   C  CH3   0  -0.661  -4.6074   0.2741   0.3495
 3OM  H1   H  H     0   0.237   4.7941   1.1432   0.6467
 3OM  H1A  H  H     0   0.232   4.1387  -0.5520   0.9330
 3OM  H2   H  H     0   0.246   2.8389   1.7386  -0.6450
 3OM  H3   H  HCH1  0   0.235   1.6609  -0.2790  -1.5681
 3OM  H4   H  HCH2  0   0.223   0.5183   0.6187   1.1065
 3OM  H4A  H  HCH2  0   0.226   0.3948   1.5105  -0.3924
 3OM  H5   H  HCH2  0   0.211  -0.8700  -0.3587  -1.4410
 3OM  H5A  H  HCH2  0   0.214  -0.7416  -1.2941   0.0332
 3OM  H6   H  HCH2  0   0.207  -2.0099   0.4725   1.2683
 3OM  H6A  H  HCH2  0   0.207  -2.1455   1.4094  -0.2033
 3OM  H7   H  HCH2  0   0.210  -3.4106  -0.4607  -1.2787
 3OM  H7A  H  HCH2  0   0.210  -3.2674  -1.4027   0.1865
 3OM  H8   H  HCH3  0   0.225  -5.4972  -0.2959   0.0788
 3OM  H8A  H  HCH3  0   0.215  -4.5818   0.3482   1.4383
 3OM  H8B  H  HCH3  0   0.215  -4.7316   1.2844  -0.0452
 3OM  HO1  H  HOH1  0   0.444   1.8974  -1.4060   0.9942

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
 3OM  C1  C2   double  1.327  0.020  1.327
 3OM  O1  C3   single  1.408  0.020  1.408
 3OM  C2  C3   single  1.503  0.020  1.503
 3OM  C3  C4   single  1.531  0.020  1.531
 3OM  C4  C5   single  1.523  0.020  1.523
 3OM  C5  C6   single  1.523  0.020  1.523
 3OM  C6  C7   single  1.524  0.020  1.524
 3OM  C7  C8   single  1.522  0.020  1.522
 3OM  C1  H1   single  0.930  0.020  1.080
 3OM  C1  H1A  single  0.930  0.020  1.080
 3OM  O1  HO1  single  0.850  0.020  0.980
 3OM  C2  H2   single  0.930  0.020  1.080
 3OM  C3  H3   single  0.970  0.020  1.090
 3OM  C4  H4   single  0.970  0.020  1.090
 3OM  C4  H4A  single  0.970  0.020  1.090
 3OM  C5  H5   single  0.970  0.020  1.090
 3OM  C5  H5A  single  0.970  0.020  1.090
 3OM  C6  H6   single  0.970  0.020  1.090
 3OM  C6  H6A  single  0.970  0.020  1.090
 3OM  C7  H7   single  0.970  0.020  1.090
 3OM  C7  H7A  single  0.970  0.020  1.090
 3OM  C8  H8   single  0.970  0.020  1.090
 3OM  C8  H8A  single  0.970  0.020  1.090
 3OM  C8  H8B  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
 3OM  H1A  C1  H1   116.39  3.000
 3OM  H1A  C1  C2   122.57  3.000
 3OM  H1   C1  C2   121.04  3.000
 3OM  HO1  O1  C3   108.26  3.000
 3OM  H2   C2  C3   114.81  3.000
 3OM  H2   C2  C1   119.34  3.000
 3OM  C3   C2  C1   125.85  3.000
 3OM  H3   C3  C4   107.77  3.000
 3OM  H3   C3  C2   107.65  3.000
 3OM  C4   C3  C2   110.22  3.000
 3OM  H3   C3  O1   105.48  3.000
 3OM  C4   C3  O1   112.23  3.000
 3OM  C2   C3  O1   113.14  3.000
 3OM  H4A  C4  H4   105.87  3.000
 3OM  H4A  C4  C5   109.35  3.000
 3OM  H4   C4  C5   110.09  3.000
 3OM  H4A  C4  C3   108.62  3.000
 3OM  H4   C4  C3   108.78  3.000
 3OM  C5   C4  C3   113.80  3.000
 3OM  H5A  C5  H5   106.21  3.000
 3OM  H5A  C5  C6   109.29  3.000
 3OM  H5   C5  C6   109.33  3.000
 3OM  H5A  C5  C4   109.79  3.000
 3OM  H5   C5  C4   109.21  3.000
 3OM  C6   C5  C4   112.80  3.000
 3OM  H6A  C6  H6   105.98  3.000
 3OM  H6A  C6  C7   109.29  3.000
 3OM  H6   C6  C7   109.25  3.000
 3OM  H6A  C6  C5   109.63  3.000
 3OM  H6   C6  C5   109.30  3.000
 3OM  C7   C6  C5   113.13  3.000
 3OM  H7A  C7  H7   105.98  3.000
 3OM  H7A  C7  C8   109.62  3.000
 3OM  H7   C7  C8   109.43  3.000
 3OM  H7A  C7  C6   109.22  3.000
 3OM  H7   C7  C6   109.29  3.000
 3OM  C8   C7  C6   113.05  3.000
 3OM  H8B  C8  H8A  107.48  3.000
 3OM  H8B  C8  H8   107.52  3.000
 3OM  H8A  C8  H8   107.59  3.000
 3OM  H8B  C8  C7   111.27  3.000
 3OM  H8A  C8  C7   111.27  3.000
 3OM  H8   C8  C7   111.50  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
 3OM  Var_01  C6  C5  C4  C3   178.97  30.0  3
 3OM  Var_02  C7  C6  C5  C4   179.85  30.0  3
 3OM  Var_03  C8  C7  C6  C5   179.52  30.0  3
 3OM  Var_04  H1  C1  C2  C3  -178.90   0.0  2
 3OM  Var_05  H8  C8  C7  C6  -179.54  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
 3OM  chir_01  C3  O1  C2  C4  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
 3OM  plan-1  C1   0.020
 3OM  plan-1  C2   0.020
 3OM  plan-1  C3   0.020
 3OM  plan-1  H1   0.020
 3OM  plan-1  H1A  0.020
 3OM  plan-1  H2   0.020

