# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:57:57 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (3R)-3-hydroxy-5,5-dimethylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C[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
 GVM  GVM  '(3R)-3-hydroxy-5,5-dimethylhexanoic acid'  ligand  26  11  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GVM
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
 GVM  C1    C  C      0   0.437  5.1858   1.2169   0.8315
 GVM  O1A   O  O      0  -0.620  4.0771   1.7320   0.5164
 GVM  O1B   O  OC    -1  -0.593  6.2384   1.8437   1.0233
 GVM  C2    C  CH2    0  -0.606  5.2240  -0.3155   0.9360
 GVM  C3    C  CH1    0   0.018  3.9070  -0.9538   1.3995
 GVM  O3    O  OH1    0  -0.703  2.8556  -0.5738   0.5386
 GVM  C4    C  CH2    0  -0.399  3.6432  -0.6300   2.8721
 GVM  C5A   C  CH3    0  -0.632  1.1108  -0.8275   3.0906
 GVM  C5B   C  CH3    0  -0.635  2.5856  -1.0098   5.0761
 GVM  C5C   C  CH3    0  -0.651  2.5467  -2.8480   3.4022
 GVM  C5    C  CT     0  -0.082  2.4700  -1.3308   3.5823
 GVM  H2C1  H  HCH2   0   0.218  6.0434  -0.6264   1.5873
 GVM  H2C2  H  HCH2   0   0.242  5.4682  -0.7043  -0.0604
 GVM  H3    H  HCH1   0   0.206  4.0187  -2.0402   1.3066
 GVM  HA    H  HOH1   0   0.431  3.0242   0.3879   0.4091
 GVM  H4C1  H  HCH2   0   0.211  3.5211   0.4538   2.9873
 GVM  H4C2  H  HCH2   0   0.203  4.5569  -0.8893   3.4205
 GVM  H5A1  H  HCH3   0   0.209  1.0247   0.2547   3.2152
 GVM  H5A2  H  HCH3   0   0.205  0.3039  -1.2910   3.6640
 GVM  H5A3  H  HCH3   0   0.230  0.9504  -1.0518   2.0386
 GVM  H5B1  H  HCH3   0   0.217  2.5652   0.0688   5.2495
 GVM  H5B2  H  HCH3   0   0.217  1.7591  -1.4503   5.6393
 GVM  H5B3  H  HCH3   0   0.216  3.5186  -1.3941   5.4960
 GVM  H5C1  H  HCH3   0   0.223  2.3897  -3.1474   2.3643
 GVM  H5C2  H  HCH3   0   0.216  3.5181  -3.2395   3.7157
 GVM  H5C3  H  HCH3   0   0.221  1.7811  -3.3450   4.0026

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
 GVM  C1   O1A   deloc   1.262  0.020  1.262
 GVM  C1   O1B   deloc   1.240  0.020  1.240
 GVM  C1   C2    single  1.536  0.020  1.536
 GVM  C2   C3    single  1.535  0.020  1.535
 GVM  C3   O3    single  1.411  0.020  1.411
 GVM  C3   C4    single  1.531  0.020  1.531
 GVM  C4   C5    single  1.540  0.020  1.540
 GVM  C5A  C5    single  1.531  0.020  1.531
 GVM  C5B  C5    single  1.532  0.020  1.532
 GVM  C5C  C5    single  1.530  0.020  1.530
 GVM  C2   H2C1  single  0.970  0.020  1.090
 GVM  C2   H2C2  single  0.970  0.020  1.090
 GVM  C3   H3    single  0.970  0.020  1.090
 GVM  O3   HA    single  0.850  0.020  0.980
 GVM  C4   H4C1  single  0.970  0.020  1.090
 GVM  C4   H4C2  single  0.970  0.020  1.090
 GVM  C5A  H5A1  single  0.970  0.020  1.090
 GVM  C5A  H5A2  single  0.970  0.020  1.090
 GVM  C5A  H5A3  single  0.970  0.020  1.090
 GVM  C5B  H5B1  single  0.970  0.020  1.090
 GVM  C5B  H5B2  single  0.970  0.020  1.090
 GVM  C5B  H5B3  single  0.970  0.020  1.090
 GVM  C5C  H5C1  single  0.970  0.020  1.090
 GVM  C5C  H5C2  single  0.970  0.020  1.090
 GVM  C5C  H5C3  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
 GVM  C2    C1   O1B   118.20  3.000
 GVM  C2    C1   O1A   116.47  3.000
 GVM  O1B   C1   O1A   125.29  3.000
 GVM  H2C2  C2   H2C1  105.89  3.000
 GVM  H2C2  C2   C3    108.53  3.000
 GVM  H2C1  C2   C3    110.20  3.000
 GVM  H2C2  C2   C1    107.29  3.000
 GVM  H2C1  C2   C1    110.07  3.000
 GVM  C3    C2   C1    114.45  3.000
 GVM  H3    C3   C4    107.98  3.000
 GVM  H3    C3   O3    106.93  3.000
 GVM  C4    C3   O3    113.68  3.000
 GVM  H3    C3   C2    107.40  3.000
 GVM  C4    C3   C2    110.51  3.000
 GVM  O3    C3   C2    110.07  3.000
 GVM  HA    O3   C3    102.45  3.000
 GVM  H4C2  C4   H4C1  105.90  3.000
 GVM  H4C2  C4   C5    107.25  3.000
 GVM  H4C1  C4   C5    108.45  3.000
 GVM  H4C2  C4   C3    106.70  3.000
 GVM  H4C1  C4   C3    109.22  3.000
 GVM  C5    C4   C3    118.60  3.000
 GVM  H5A3  C5A  H5A2  108.13  3.000
 GVM  H5A3  C5A  H5A1  107.64  3.000
 GVM  H5A2  C5A  H5A1  107.58  3.000
 GVM  H5A3  C5A  C5    111.96  3.000
 GVM  H5A2  C5A  C5    110.34  3.000
 GVM  H5A1  C5A  C5    111.04  3.000
 GVM  H5B3  C5B  H5B2  107.81  3.000
 GVM  H5B3  C5B  H5B1  107.58  3.000
 GVM  H5B2  C5B  H5B1  107.58  3.000
 GVM  H5B3  C5B  C5    111.42  3.000
 GVM  H5B2  C5B  C5    111.16  3.000
 GVM  H5B1  C5B  C5    111.11  3.000
 GVM  H5C3  C5C  H5C2  107.59  3.000
 GVM  H5C3  C5C  H5C1  107.28  3.000
 GVM  H5C2  C5C  H5C1  107.60  3.000
 GVM  H5C3  C5C  C5    110.57  3.000
 GVM  H5C2  C5C  C5    111.46  3.000
 GVM  H5C1  C5C  C5    112.13  3.000
 GVM  C5C   C5   C5B   108.59  3.000
 GVM  C5C   C5   C5A   109.44  3.000
 GVM  C5B   C5   C5A   108.14  3.000
 GVM  C5C   C5   C4    111.03  3.000
 GVM  C5B   C5   C4    107.27  3.000
 GVM  C5A   C5   C4    112.25  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
 GVM  Var_01  C3    C2   C1  O1A  -31.76  30.0  3
 GVM  Var_02  C5A   C5   C4  C3   -70.76  30.0  3
 GVM  Var_03  H5A1  C5A  C5  C4   -56.72  30.0  3
 GVM  Var_04  H5B1  C5B  C5  C4    58.26  30.0  3
 GVM  Var_05  H5C1  C5C  C5  C4   -66.89  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
 GVM  chir_01  C3  C2  O3  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
 GVM  plan-1  C1   0.020
 GVM  plan-1  O1A  0.020
 GVM  plan-1  O1B  0.020
 GVM  plan-1  C2   0.020

