# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:20:52 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2R)-2-hydroxy-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[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
 2RH  2RH  '(2R)-2-hydroxy-4-methylpentanoic acid'  ligand  20  9  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2RH
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
 2RH  C1   C  CH1    0  -0.091  -0.4922  -0.3110  -0.3482
 2RH  O1   O  O      0  -0.612  -2.6421  -0.7459   0.5299
 2RH  C2   C  CH2    0  -0.417   0.6425   0.2628   0.4959
 2RH  O2   O  OC    -1  -0.597  -2.0784   1.3914   0.1996
 2RH  C3   C  C      0   0.397  -1.8635   0.1697   0.1740
 2RH  O3   O  OH1    0  -0.701  -0.4636  -1.7189  -0.3577
 2RH  C4   C  CH1    0  -0.227   2.0480  -0.1640   0.0682
 2RH  C5   C  CH3    0  -0.660   2.3905   0.3083  -1.3418
 2RH  C6   C  CH3    0  -0.651   3.0776   0.3591   1.0654
 2RH  H1   H  HCH1   0   0.196  -0.3858   0.0643  -1.3771
 2RH  H2   H  HCH2   0   0.207   0.5769   1.3550   0.4676
 2RH  H2A  H  HCH2   0   0.210   0.4872  -0.0289   1.5415
 2RH  HO3  H  HOH1   0   0.424  -1.3356  -1.9430   0.0181
 2RH  H4   H  HCH1   0   0.212   2.0928  -1.2582   0.0829
 2RH  H5   H  HCH3   0   0.223   3.4018   0.0067  -1.6205
 2RH  H5A  H  HCH3   0   0.227   1.7117  -0.1000  -2.0915
 2RH  H5B  H  HCH3   0   0.209   2.3415   1.3984  -1.4101
 2RH  H6   H  HCH3   0   0.221   2.8705   0.0052   2.0773
 2RH  H6A  H  HCH3   0   0.222   4.0871   0.0375   0.8025
 2RH  H6B  H  HCH3   0   0.209   3.0746   1.4519   1.0903

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
 2RH  C3  C1   single  1.544  0.020  1.544
 2RH  C1  O3   single  1.408  0.020  1.408
 2RH  C1  C2   single  1.526  0.020  1.526
 2RH  C1  H1   single  0.970  0.020  1.090
 2RH  O1  C3   deloc   1.253  0.020  1.253
 2RH  C2  C4   single  1.530  0.020  1.530
 2RH  C2  H2   single  0.970  0.020  1.090
 2RH  C2  H2A  single  0.970  0.020  1.090
 2RH  O2  C3   deloc   1.241  0.020  1.241
 2RH  O3  HO3  single  0.850  0.020  0.980
 2RH  C4  C6   single  1.526  0.020  1.526
 2RH  C4  C5   single  1.526  0.020  1.526
 2RH  C4  H4   single  0.970  0.020  1.090
 2RH  C5  H5   single  0.970  0.020  1.090
 2RH  C5  H5A  single  0.970  0.020  1.090
 2RH  C5  H5B  single  0.970  0.020  1.090
 2RH  C6  H6   single  0.970  0.020  1.090
 2RH  C6  H6A  single  0.970  0.020  1.090
 2RH  C6  H6B  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
 2RH  H1   C1  O3   109.43  3.000
 2RH  H1   C1  C3   107.21  3.000
 2RH  O3   C1  C3   109.36  3.000
 2RH  H1   C1  C2   108.48  3.000
 2RH  O3   C1  C2   111.38  3.000
 2RH  C3   C1  C2   110.87  3.000
 2RH  H2A  C2  H2   106.36  3.000
 2RH  H2A  C2  C4   108.81  3.000
 2RH  H2   C2  C4   109.04  3.000
 2RH  H2A  C2  C1   108.78  3.000
 2RH  H2   C2  C1   108.44  3.000
 2RH  C4   C2  C1   115.06  3.000
 2RH  O2   C3  O1   127.29  3.000
 2RH  O2   C3  C1   117.86  3.000
 2RH  O1   C3  C1   114.85  3.000
 2RH  HO3  O3  C1   102.06  3.000
 2RH  H4   C4  C6   107.82  3.000
 2RH  H4   C4  C5   108.21  3.000
 2RH  C6   C4  C5   110.27  3.000
 2RH  H4   C4  C2   108.21  3.000
 2RH  C5   C4  C2   112.22  3.000
 2RH  C6   C4  C2   109.97  3.000
 2RH  H5B  C5  H5A  107.60  3.000
 2RH  H5B  C5  H5   107.52  3.000
 2RH  H5A  C5  H5   107.32  3.000
 2RH  H5B  C5  C4   110.87  3.000
 2RH  H5A  C5  C4   112.31  3.000
 2RH  H5   C5  C4   111.00  3.000
 2RH  H6B  C6  H6A  107.61  3.000
 2RH  H6B  C6  H6   107.60  3.000
 2RH  H6A  C6  H6   107.64  3.000
 2RH  H6B  C6  C4   110.84  3.000
 2RH  H6A  C6  C4   111.45  3.000
 2RH  H6   C6  C4   111.51  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
 2RH  Var_01  C6  C4  C2  C1  -174.42  30.0  3
 2RH  Var_02  H6  C6  C4  C2    57.63  30.0  3
 2RH  Var_03  H5  C5  C4  C2   179.12  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
 2RH  chir_01  C1  C3  O3  C2  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
 2RH  plan-1  C1  0.020
 2RH  plan-1  O1  0.020
 2RH  plan-1  O2  0.020
 2RH  plan-1  C3  0.020

