# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 00:55:36 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-oxo-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)Cc1ccccc1
#
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
 1PY  1PY  '2-oxo-3-phenylpropanoic acid'  ligand  19  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1PY
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
 1PY  O1   O  O      0  -0.576  -1.2933   0.0145   3.1334
 1PY  O2   O  OC    -1  -0.580   0.8909  -0.0142   3.6253
 1PY  O    O  O      0  -0.382   1.4025  -0.0022   0.9577
 1PY  CA   C  C      0   0.245   0.2580  -0.0038   1.3395
 1PY  CB   C  CH2    0  -0.669  -0.9116  -0.0098   0.3788
 1PY  CG   C  CR6    0   0.168  -0.4956  -0.0151  -1.0595
 1PY  CD1  C  CR16   0  -0.306  -0.2804  -1.2139  -1.7341
 1PY  CE1  C  CR16   0  -0.242   0.1319  -1.2222  -3.0600
 1PY  CZ   C  CR16   0  -0.273   0.3389  -0.0250  -3.7330
 1PY  CE2  C  CR16   0  -0.242   0.1286   1.1772  -3.0700
 1PY  CD2  C  CR16   0  -0.306  -0.2836   1.1788  -1.7440
 1PY  C    C  C      0   0.348  -0.0813  -0.0009   2.8594
 1PY  HB1  H  HCH2   0   0.282  -1.5354  -0.8775   0.6129
 1PY  HB2  H  HCH2   0   0.282  -1.5396   0.8566   0.6057
 1PY  HD1  H  HCR6   0   0.247  -0.4450  -2.1538  -1.2200
 1PY  HE1  H  HCR6   0   0.252   0.2908  -2.1647  -3.5684
 1PY  HZ   H  HCR6   0   0.252   0.6574  -0.0289  -4.7676
 1PY  HE2  H  HCR6   0   0.252   0.2846   2.1160  -3.5860
 1PY  HD2  H  HCR6   0   0.247  -0.4509   2.1224  -1.2375

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
 1PY  O1   C    deloc     1.243  0.020  1.243
 1PY  O2   C    deloc     1.238  0.020  1.238
 1PY  O    CA   double    1.206  0.020  1.206
 1PY  CA   CB   single    1.514  0.020  1.514
 1PY  CA   C    single    1.557  0.020  1.557
 1PY  CB   CG   single    1.497  0.020  1.497
 1PY  CB   HB1  single    0.970  0.020  1.090
 1PY  CB   HB2  single    0.970  0.020  1.090
 1PY  CG   CD1  aromatic  1.392  0.020  1.392
 1PY  CG   CD2  aromatic  1.392  0.020  1.392
 1PY  CD1  CE1  aromatic  1.389  0.020  1.389
 1PY  CD1  HD1  single    0.930  0.020  1.080
 1PY  CE1  CZ   aromatic  1.389  0.020  1.389
 1PY  CE1  HE1  single    0.930  0.020  1.080
 1PY  CZ   CE2  aromatic  1.389  0.020  1.389
 1PY  CZ   HZ   single    0.930  0.020  1.080
 1PY  CE2  CD2  aromatic  1.389  0.020  1.389
 1PY  CE2  HE2  single    0.930  0.020  1.080
 1PY  CD2  HD2  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
 1PY  C    CA   CB   116.81  3.000
 1PY  C    CA   O    121.03  3.000
 1PY  CB   CA   O    122.16  3.000
 1PY  HB2  CB   HB1  104.86  3.000
 1PY  HB2  CB   CG   111.19  3.000
 1PY  HB1  CB   CG   111.18  3.000
 1PY  HB2  CB   CA   107.99  3.000
 1PY  HB1  CB   CA   107.94  3.000
 1PY  CG   CB   CA   113.27  3.000
 1PY  CD2  CG   CD1  118.46  3.000
 1PY  CD2  CG   CB   120.76  3.000
 1PY  CD1  CG   CB   120.76  3.000
 1PY  HD1  CD1  CE1  119.53  3.000
 1PY  HD1  CD1  CG   119.56  3.000
 1PY  CE1  CD1  CG   120.91  3.000
 1PY  HE1  CE1  CZ   120.07  3.000
 1PY  HE1  CE1  CD1  119.81  3.000
 1PY  CZ   CE1  CD1  120.12  3.000
 1PY  HZ   CZ   CE2  120.26  3.000
 1PY  HZ   CZ   CE1  120.26  3.000
 1PY  CE2  CZ   CE1  119.48  3.000
 1PY  HE2  CE2  CD2  119.80  3.000
 1PY  HE2  CE2  CZ   120.08  3.000
 1PY  CD2  CE2  CZ   120.12  3.000
 1PY  HD2  CD2  CE2  119.54  3.000
 1PY  HD2  CD2  CG   119.55  3.000
 1PY  CE2  CD2  CG   120.91  3.000
 1PY  CA   C    O2   115.64  3.000
 1PY  CA   C    O1   115.33  3.000
 1PY  O2   C    O1   129.03  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
 1PY  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 1PY  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 1PY  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 1PY  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 1PY  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 1PY  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 1PY  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 1PY  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 1PY  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 1PY  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 1PY  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 1PY  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 1PY  CONST_13  HD1  CD1  CE1  CZ   180.00   0.0  0
 1PY  Var_01    CD1  CG   CB   CA    89.24  30.0  2
 1PY  Var_02    CG   CB   CA   O      0.06  30.0  3
 1PY  Var_03    O    CA   C    O1   179.11  30.0  3

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
 1PY  plan-1  CB   0.020
 1PY  plan-1  CG   0.020
 1PY  plan-1  CD1  0.020
 1PY  plan-1  CE1  0.020
 1PY  plan-1  CZ   0.020
 1PY  plan-1  CE2  0.020
 1PY  plan-1  CD2  0.020
 1PY  plan-1  HD1  0.020
 1PY  plan-1  HE1  0.020
 1PY  plan-1  HZ   0.020
 1PY  plan-1  HE2  0.020
 1PY  plan-1  HD2  0.020
 1PY  plan-2  O    0.020
 1PY  plan-2  CA   0.020
 1PY  plan-2  CB   0.020
 1PY  plan-2  C    0.020
 1PY  plan-3  O1   0.020
 1PY  plan-3  O2   0.020
 1PY  plan-3  CA   0.020
 1PY  plan-3  C    0.020

