# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:11:14 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (3S)-3-hydroxyoctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)CC(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
 3HO  3HO  '(3S)-3-hydroxyoctanoic acid'  ligand  27  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3HO
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
 3HO  O1   O  O     0  -0.448   3.5183  -0.5142  -1.1866
 3HO  C1   C  C     0   0.549   3.3170   0.1749  -0.2172
 3HO  O2   O  OH1   0  -0.592   4.2724   0.5075   0.6440
 3HO  C2   C  CH2   0  -0.594   1.9884   0.7860   0.1358
 3HO  C3   C  CH1   0   0.040   0.8181  -0.1467  -0.1628
 3HO  O3   O  OH1   0  -0.666   0.9559  -1.3620   0.5445
 3HO  C4   C  CH2   0  -0.451  -0.5078   0.5520   0.1166
 3HO  C5   C  CH2   0  -0.409  -1.7333  -0.3144  -0.1437
 3HO  C6   C  CH2   0  -0.407  -3.0371   0.4481   0.0571
 3HO  C7   C  CH2   0  -0.418  -4.2774  -0.4092  -0.1607
 3HO  C8   C  CH3   0  -0.662  -5.5731   0.3620   0.0491
 3HO  HO2  H  HOH1  0   0.478   5.1194   0.1318   0.3593
 3HO  H2   H  HCH2  0   0.264   1.9753   1.0939   1.1841
 3HO  H2A  H  HCH2  0   0.287   1.8896   1.7024  -0.4560
 3HO  H3   H  HCH1  0   0.231   0.8491  -0.4211  -1.2210
 3HO  HO3  H  HOH1  0   0.443   0.8339  -1.1828   1.4833
 3HO  H4   H  HCH2  0   0.219  -0.5225   0.9085   1.1539
 3HO  H4A  H  HCH2  0   0.226  -0.5556   1.4472  -0.5111
 3HO  H5   H  HCH2  0   0.210  -1.6950  -0.7066  -1.1660
 3HO  H5A  H  HCH2  0   0.213  -1.7204  -1.1842   0.5191
 3HO  H6   H  HCH2  0   0.207  -3.0601   0.8661   1.0698
 3HO  H6A  H  HCH2  0   0.207  -3.0656   1.3058  -0.6241
 3HO  H7   H  HCH2  0   0.210  -4.2574  -0.8257  -1.1727
 3HO  H7A  H  HCH2  0   0.210  -4.2491  -1.2661   0.5197
 3HO  H8   H  HCH3  0   0.215  -5.6279   0.7704   1.0601
 3HO  H8A  H  HCH3  0   0.216  -5.6531   1.1985  -0.6476
 3HO  H8B  H  HCH3  0   0.226  -6.4470  -0.2742  -0.0972

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
 3HO  O1  C1   double  1.206  0.020  1.206
 3HO  C2  C1   single  1.504  0.020  1.504
 3HO  C1  O2   single  1.329  0.020  1.329
 3HO  O2  HO2  single  0.850  0.020  0.980
 3HO  C2  C3   single  1.526  0.020  1.526
 3HO  C2  H2   single  0.970  0.020  1.090
 3HO  C2  H2A  single  0.970  0.020  1.090
 3HO  O3  C3   single  1.413  0.020  1.413
 3HO  C4  C3   single  1.525  0.020  1.525
 3HO  C3  H3   single  0.970  0.020  1.090
 3HO  O3  HO3  single  0.850  0.020  0.980
 3HO  C4  C5   single  1.523  0.020  1.523
 3HO  C4  H4   single  0.970  0.020  1.090
 3HO  C4  H4A  single  0.970  0.020  1.090
 3HO  C6  C5   single  1.524  0.020  1.524
 3HO  C5  H5   single  0.970  0.020  1.090
 3HO  C5  H5A  single  0.970  0.020  1.090
 3HO  C6  C7   single  1.523  0.020  1.523
 3HO  C6  H6   single  0.970  0.020  1.090
 3HO  C6  H6A  single  0.970  0.020  1.090
 3HO  C8  C7   single  1.522  0.020  1.522
 3HO  C7  H7   single  0.970  0.020  1.090
 3HO  C7  H7A  single  0.970  0.020  1.090
 3HO  C8  H8   single  0.970  0.020  1.090
 3HO  C8  H8A  single  0.970  0.020  1.090
 3HO  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
 3HO  C2   C1  O2   112.41  3.000
 3HO  O2   C1  O1   122.96  3.000
 3HO  C2   C1  O1   124.61  3.000
 3HO  HO2  O2  C1   109.93  3.000
 3HO  H2A  C2  H2   106.35  3.000
 3HO  H2A  C2  C3   109.66  3.000
 3HO  H2   C2  C3   110.53  3.000
 3HO  H2A  C2  C1   107.03  3.000
 3HO  H2   C2  C1   110.50  3.000
 3HO  C3   C2  C1   112.52  3.000
 3HO  H3   C3  C4   108.48  3.000
 3HO  H3   C3  O3   105.41  3.000
 3HO  C4   C3  O3   112.78  3.000
 3HO  H3   C3  C2   108.72  3.000
 3HO  C4   C3  C2   110.55  3.000
 3HO  O3   C3  C2   110.67  3.000
 3HO  HO3  O3  C3   108.38  3.000
 3HO  H4A  C4  H4   106.02  3.000
 3HO  H4A  C4  C5   109.39  3.000
 3HO  H4   C4  C5   109.61  3.000
 3HO  H4A  C4  C3   107.92  3.000
 3HO  H4   C4  C3   109.51  3.000
 3HO  C5   C4  C3   114.06  3.000
 3HO  H5A  C5  H5   106.28  3.000
 3HO  H5A  C5  C6   109.16  3.000
 3HO  H5   C5  C6   109.39  3.000
 3HO  H5A  C5  C4   109.83  3.000
 3HO  H5   C5  C4   109.57  3.000
 3HO  C6   C5  C4   112.41  3.000
 3HO  H6A  C6  H6   105.98  3.000
 3HO  H6A  C6  C7   109.30  3.000
 3HO  H6   C6  C7   109.25  3.000
 3HO  H6A  C6  C5   109.40  3.000
 3HO  H6   C6  C5   109.31  3.000
 3HO  C7   C6  C5   113.34  3.000
 3HO  H7A  C7  H7   106.04  3.000
 3HO  H7A  C7  C8   109.45  3.000
 3HO  H7   C7  C8   109.62  3.000
 3HO  H7A  C7  C6   109.31  3.000
 3HO  H7   C7  C6   109.36  3.000
 3HO  C8   C7  C6   112.84  3.000
 3HO  H8B  C8  H8A  107.61  3.000
 3HO  H8B  C8  H8   107.59  3.000
 3HO  H8A  C8  H8   107.50  3.000
 3HO  H8B  C8  C7   111.59  3.000
 3HO  H8A  C8  C7   111.26  3.000
 3HO  H8   C8  C7   111.09  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
 3HO  CONST_01  HO2  O2  C1  O1     0.00   0.0  0
 3HO  Var_01    C3   C2  C1  O1    38.38  30.0  2
 3HO  Var_02    C6   C5  C4  C3  -176.16  30.0  3
 3HO  Var_03    C7   C6  C5  C4  -178.41  30.0  1
 3HO  Var_04    C8   C7  C6  C5   179.73  30.0  3
 3HO  Var_05    H8   C8  C7  C6   -59.09  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
 3HO  chir_01  C3  C2  O3  C4  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
 3HO  plan-1  O1   0.020
 3HO  plan-1  C1   0.020
 3HO  plan-1  O2   0.020
 3HO  plan-1  C2   0.020
 3HO  plan-1  HO2  0.020

