# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:01:01 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3R)-2-oxo-3-phenylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](c1ccccc1)C(=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
 56D  56D  '(3R)-2-oxo-3-phenylbutanoic acid'  ligand  23  13  .  2021-08-04  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_56D
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
 56D  OAL  O  OH1   0  -0.568  -3.5445  -0.9175   0.5825
 56D  CAI  C  C     0   0.483  -2.7487   0.1113   0.3980
 56D  OAM  O  O     0  -0.402  -3.0714   1.2681   0.4441
 56D  CAH  C  C     0   0.324  -1.3013  -0.3413   0.1273
 56D  OAK  O  O     0  -0.328  -1.0088  -1.4936   0.2913
 56D  CAG  C  CH1   0  -0.497  -0.3541   0.7305  -0.3554
 56D  CAJ  C  CH3   0  -0.655  -0.6481   1.0079  -1.8393
 56D  CAD  C  CR6   0   0.191   1.0779   0.3476  -0.0870
 56D  CAC  C  CR16  0  -0.306   1.7499  -0.5843  -0.8748
 56D  CAB  C  CR16  0  -0.242   3.0634  -0.9328  -0.5936
 56D  CAA  C  CR16  0  -0.269   3.7251  -0.3574   0.4838
 56D  CAF  C  CR16  0  -0.240   3.0638   0.5698   1.2767
 56D  CAE  C  CR16  0  -0.306   1.7489   0.9155   0.9923
 56D  H1   H  HOH1  0   0.494  -4.4488  -0.6179   0.7663
 56D  H2   H  HCH1  0   0.297  -0.5830   1.6479   0.1927
 56D  H3   H  HCH3  0   0.241  -0.4927   0.1253  -2.4585
 56D  H4   H  HCH3  0   0.253  -1.6740   1.3428  -1.9865
 56D  H5   H  HCH3  0   0.261   0.0122   1.7966  -2.1966
 56D  H6   H  HCR6  0   0.249   1.2550  -1.0438  -1.7209
 56D  H7   H  HCR6  0   0.256   3.5712  -1.6577  -1.2168
 56D  H8   H  HCR6  0   0.256   4.7502  -0.6283   0.7006
 56D  H9   H  HCR6  0   0.256   3.5707   1.0268   2.1168
 56D  H10  H  HCR6  0   0.253   1.2399   1.6411   1.6162

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
 56D  OAM  CAI  double    1.202  0.020  1.202
 56D  CAI  OAL  single    1.314  0.020  1.314
 56D  CAI  CAH  single    1.540  0.020  1.540
 56D  CAG  CAJ  single    1.538  0.020  1.538
 56D  CAG  CAH  single    1.510  0.020  1.510
 56D  CAG  CAD  single    1.506  0.020  1.506
 56D  CAC  CAB  aromatic  1.388  0.020  1.388
 56D  CAC  CAD  aromatic  1.393  0.020  1.393
 56D  CAH  OAK  double    1.200  0.020  1.200
 56D  CAB  CAA  aromatic  1.389  0.020  1.389
 56D  CAD  CAE  aromatic  1.392  0.020  1.392
 56D  CAA  CAF  aromatic  1.388  0.020  1.388
 56D  CAE  CAF  aromatic  1.389  0.020  1.389
 56D  OAL  H1   single    0.850  0.020  0.980
 56D  CAG  H2   single    0.970  0.020  1.090
 56D  CAJ  H3   single    0.970  0.020  1.090
 56D  CAJ  H4   single    0.970  0.020  1.090
 56D  CAJ  H5   single    0.970  0.020  1.090
 56D  CAC  H6   single    0.930  0.020  1.080
 56D  CAB  H7   single    0.930  0.020  1.080
 56D  CAA  H8   single    0.930  0.020  1.080
 56D  CAF  H9   single    0.930  0.020  1.080
 56D  CAE  H10  single    0.930  0.020  1.080

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
 56D  H1   OAL  CAI  110.45  3.000
 56D  CAH  CAI  OAM  122.81  3.000
 56D  CAH  CAI  OAL  111.33  3.000
 56D  OAM  CAI  OAL  125.86  3.000
 56D  CAG  CAH  OAK  124.92  3.000
 56D  OAK  CAH  CAI  119.15  3.000
 56D  CAG  CAH  CAI  115.92  3.000
 56D  H2   CAG  CAD  108.85  3.000
 56D  H2   CAG  CAJ  107.00  3.000
 56D  CAD  CAG  CAJ  113.54  3.000
 56D  H2   CAG  CAH  107.71  3.000
 56D  CAD  CAG  CAH  111.04  3.000
 56D  CAJ  CAG  CAH  108.46  3.000
 56D  H5   CAJ  H4   107.70  3.000
 56D  H5   CAJ  H3   108.29  3.000
 56D  H4   CAJ  H3   107.86  3.000
 56D  H5   CAJ  CAG  109.35  3.000
 56D  H4   CAJ  CAG  111.46  3.000
 56D  H3   CAJ  CAG  112.03  3.000
 56D  CAE  CAD  CAC  118.61  3.000
 56D  CAE  CAD  CAG  119.52  3.000
 56D  CAC  CAD  CAG  121.86  3.000
 56D  H6   CAC  CAB  118.98  3.000
 56D  H6   CAC  CAD  120.36  3.000
 56D  CAB  CAC  CAD  120.66  3.000
 56D  H7   CAB  CAA  120.02  3.000
 56D  H7   CAB  CAC  119.71  3.000
 56D  CAA  CAB  CAC  120.26  3.000
 56D  H8   CAA  CAF  120.28  3.000
 56D  H8   CAA  CAB  120.19  3.000
 56D  CAF  CAA  CAB  119.53  3.000
 56D  H9   CAF  CAE  119.82  3.000
 56D  H9   CAF  CAA  120.16  3.000
 56D  CAE  CAF  CAA  120.03  3.000
 56D  H10  CAE  CAF  119.55  3.000
 56D  H10  CAE  CAD  119.54  3.000
 56D  CAF  CAE  CAD  120.90  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
 56D  CONST_01  CAA  CAB  CAC  CAD    0.00   0.0  0
 56D  CONST_02  CAA  CAF  CAE  CAD    0.00   0.0  0
 56D  CONST_03  CAF  CAA  CAB  CAC    0.00   0.0  0
 56D  CONST_04  CAF  CAE  CAD  CAC    0.00   0.0  0
 56D  CONST_05  CAE  CAD  CAC  CAB    0.00   0.0  0
 56D  CONST_06  CAE  CAF  CAA  CAB    0.00   0.0  0
 56D  CONST_07  CAB  CAC  CAD  CAG  180.00   0.0  0
 56D  CONST_08  CAF  CAE  CAD  CAG  180.00   0.0  0
 56D  CONST_09  H7   CAB  CAC  CAD  180.00   0.0  0
 56D  CONST_10  H9   CAF  CAE  CAD  180.00   0.0  0
 56D  CONST_11  H8   CAA  CAB  CAC  180.00   0.0  0
 56D  CONST_12  H10  CAE  CAD  CAC  180.00   0.0  0
 56D  CONST_13  H6   CAC  CAB  CAA  180.00   0.0  0
 56D  CONST_14  H1   OAL  CAI  OAM    0.00   0.0  0
 56D  Var_01    CAG  CAH  CAI  OAL  168.86  30.0  2

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
 56D  chir_01  CAG  CAJ  CAH  CAD  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
 56D  plan-1  CAG  0.020
 56D  plan-1  CAD  0.020
 56D  plan-1  CAC  0.020
 56D  plan-1  CAB  0.020
 56D  plan-1  CAA  0.020
 56D  plan-1  CAF  0.020
 56D  plan-1  CAE  0.020
 56D  plan-1  H6   0.020
 56D  plan-1  H7   0.020
 56D  plan-1  H8   0.020
 56D  plan-1  H9   0.020
 56D  plan-1  H10  0.020
 56D  plan-2  CAI  0.020
 56D  plan-2  CAH  0.020
 56D  plan-2  OAK  0.020
 56D  plan-2  CAG  0.020
 56D  plan-3  OAL  0.020
 56D  plan-3  CAI  0.020
 56D  plan-3  OAM  0.020
 56D  plan-3  CAH  0.020
 56D  plan-3  H1   0.020

