# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:42:07 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-(4-methylphenyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CCC(O)=O)cc1
#
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
 PPT  PPT  '3-(4-methylphenyl)propanoic acid'  ligand  23  12  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PPT
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
 PPT  CA   C  CH2    0  -0.575   0.0779  -0.4322  -1.8547
 PPT  C    C  C      0   0.412   0.0582  -0.2046  -3.3769
 PPT  OT1  O  O      0  -0.607  -0.2069   0.9408  -3.7912
 PPT  OT2  O  OC    -1  -0.630   0.3035  -1.2082  -4.0784
 PPT  CB   C  CH2    0  -0.497  -0.0964   0.8194  -0.9984
 PPT  CG   C  CR6    0   0.120  -0.0661   0.5003   0.4706
 PPT  CD1  C  CR16   0  -0.294   1.1425   0.2684   1.1281
 PPT  CD2  C  CR16   0  -0.306  -1.2363   0.3775   1.2125
 PPT  CE1  C  CR16   0  -0.281   1.1769  -0.0736   2.4709
 PPT  CE2  C  CR16   0  -0.288  -1.2033   0.0347   2.5596
 PPT  CZ   C  CR6    0   0.078   0.0024  -0.1966   3.2136
 PPT  CH   C  CH3    0  -0.723   0.0472  -0.5460   4.6736
 PPT  HA1  H  HCH2   0   0.225   1.0152  -0.9322  -1.5898
 PPT  HA2  H  HCH2   0   0.229  -0.7093  -1.1542  -1.6080
 PPT  HB1  H  HCH2   0   0.226  -1.0410   1.3047  -1.2506
 PPT  HB2  H  HCH2   0   0.226   0.6932   1.5371  -1.2350
 PPT  HD1  H  HCR6   0   0.239   2.0734   0.3580   0.5788
 PPT  HD2  H  HCR6   0   0.239  -2.1929   0.5535   0.7333
 PPT  HE1  H  HCR6   0   0.240   2.1333  -0.2488   2.9508
 PPT  HE2  H  HCR6   0   0.240  -2.1340  -0.0555   3.1083
 PPT  HH1  H  HCH3   0   0.244   0.3888   0.3013   5.2720
 PPT  HH2  H  HCH3   0   0.241  -0.9353  -0.8334   5.0467
 PPT  HH3  H  HCH3   0   0.241   0.7342  -1.3706   4.8673

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
 PPT  CA   C    single    1.539  0.020  1.539
 PPT  CA   CB   single    1.526  0.020  1.526
 PPT  CA   HA1  single    0.970  0.020  1.090
 PPT  CA   HA2  single    0.970  0.020  1.090
 PPT  C    OT1  deloc     1.247  0.020  1.247
 PPT  C    OT2  deloc     1.249  0.020  1.249
 PPT  CB   CG   single    1.504  0.020  1.504
 PPT  CB   HB1  single    0.970  0.020  1.090
 PPT  CB   HB2  single    0.970  0.020  1.090
 PPT  CG   CD1  aromatic  1.395  0.020  1.395
 PPT  CG   CD2  aromatic  1.391  0.020  1.391
 PPT  CD1  CE1  aromatic  1.386  0.020  1.386
 PPT  CD1  HD1  single    0.930  0.020  1.080
 PPT  CD2  CE2  aromatic  1.390  0.020  1.390
 PPT  CD2  HD2  single    0.930  0.020  1.080
 PPT  CE1  CZ   aromatic  1.395  0.020  1.395
 PPT  CE1  HE1  single    0.930  0.020  1.080
 PPT  CE2  CZ   aromatic  1.391  0.020  1.391
 PPT  CE2  HE2  single    0.930  0.020  1.080
 PPT  CZ   CH   single    1.502  0.020  1.502
 PPT  CH   HH1  single    0.970  0.020  1.090
 PPT  CH   HH2  single    0.970  0.020  1.090
 PPT  CH   HH3  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
 PPT  HA2  CA   HA1  105.04  3.000
 PPT  HA2  CA   CB   109.37  3.000
 PPT  HA1  CA   CB   109.66  3.000
 PPT  HA2  CA   C    108.11  3.000
 PPT  HA1  CA   C    108.53  3.000
 PPT  CB   CA   C    115.60  3.000
 PPT  OT2  C    OT1  126.41  3.000
 PPT  OT2  C    CA   115.73  3.000
 PPT  OT1  C    CA   117.86  3.000
 PPT  HB2  CB   HB1  106.46  3.000
 PPT  HB2  CB   CG   109.65  3.000
 PPT  HB1  CB   CG   109.73  3.000
 PPT  HB2  CB   CA   109.54  3.000
 PPT  HB1  CB   CA   109.50  3.000
 PPT  CG   CB   CA   111.82  3.000
 PPT  CD2  CG   CD1  117.56  3.000
 PPT  CD2  CG   CB   121.52  3.000
 PPT  CD1  CG   CB   120.88  3.000
 PPT  HD1  CD1  CE1  119.33  3.000
 PPT  HD1  CD1  CG   119.40  3.000
 PPT  CE1  CD1  CG   121.27  3.000
 PPT  HD2  CD2  CE2  119.28  3.000
 PPT  HD2  CD2  CG   119.48  3.000
 PPT  CE2  CD2  CG   121.23  3.000
 PPT  HE1  CE1  CZ   119.52  3.000
 PPT  HE1  CE1  CD1  119.38  3.000
 PPT  CZ   CE1  CD1  121.11  3.000
 PPT  HE2  CE2  CZ   119.49  3.000
 PPT  HE2  CE2  CD2  119.38  3.000
 PPT  CZ   CE2  CD2  121.14  3.000
 PPT  CH   CZ   CE2  121.44  3.000
 PPT  CH   CZ   CE1  120.86  3.000
 PPT  CE2  CZ   CE1  117.69  3.000
 PPT  HH3  CH   HH2  107.92  3.000
 PPT  HH3  CH   HH1  106.99  3.000
 PPT  HH2  CH   HH1  107.40  3.000
 PPT  HH3  CH   CZ   111.55  3.000
 PPT  HH2  CH   CZ   111.56  3.000
 PPT  HH1  CH   CZ   111.19  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
 PPT  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PPT  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PPT  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PPT  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PPT  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PPT  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PPT  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PPT  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PPT  CONST_09  CH   CZ   CE1  CD1  180.00   0.0  0
 PPT  CONST_10  CH   CZ   CE2  CD2  180.00   0.0  0
 PPT  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 PPT  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 PPT  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 PPT  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 PPT  Var_01    CD1  CG   CB   CA    78.30  30.0  2
 PPT  Var_02    HH1  CH   CZ   CE1   73.63  30.0  2
 PPT  Var_03    CG   CB   CA   C    179.92  30.0  3
 PPT  Var_04    CB   CA   C    OT1   -5.89  30.0  2

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
 PPT  plan-1  CB   0.020
 PPT  plan-1  CG   0.020
 PPT  plan-1  CD1  0.020
 PPT  plan-1  CD2  0.020
 PPT  plan-1  CE1  0.020
 PPT  plan-1  CE2  0.020
 PPT  plan-1  CZ   0.020
 PPT  plan-1  CH   0.020
 PPT  plan-1  HD1  0.020
 PPT  plan-1  HD2  0.020
 PPT  plan-1  HE1  0.020
 PPT  plan-1  HE2  0.020
 PPT  plan-2  CA   0.020
 PPT  plan-2  C    0.020
 PPT  plan-2  OT1  0.020
 PPT  plan-2  OT2  0.020

