# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:14:25 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S)-2-methyl-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Cc1ccccc1)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
 DPH  DPH  '(2S)-2-methyl-3-phenylpropanoic acid'  ligand  23  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DPH
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
 DPH  CM   C  CH3    0  -0.652   1.5837   0.6252   1.1905
 DPH  CA   C  CH1    0  -0.371   0.0910   0.3349   1.3238
 DPH  CB   C  CH2    0  -0.493  -0.3555  -0.7810   0.3726
 DPH  CG   C  CR6    0   0.141  -0.2036  -0.4172  -1.0781
 DPH  CD1  C  CR16   0  -0.314   0.8499  -0.9028  -1.8495
 DPH  CD2  C  CR16   0  -0.310  -1.1186   0.4433  -1.6861
 DPH  CE1  C  CR16   0  -0.242   0.9893  -0.5413  -3.1844
 DPH  CE2  C  CR16   0  -0.241  -0.9856   0.8090  -3.0181
 DPH  CZ   C  CR16   0  -0.278   0.0721   0.3177  -3.7742
 DPH  C    C  C      0   0.427  -0.2764   0.0480   2.7998
 DPH  O    O  O      0  -0.603  -0.9122  -0.9942   3.0549
 DPH  OXT  O  OC    -1  -0.621   0.0939   0.9032   3.6309
 DPH  HM1  H  HCH3   0   0.225   1.8825   1.4455   1.8408
 DPH  HM2  H  HCH3   0   0.207   2.1784  -0.2506   1.4630
 DPH  HM3  H  HCH3   0   0.219   1.8520   0.8950   0.1681
 DPH  HA   H  HCH1   0   0.221  -0.4479   1.2495   1.0403
 DPH  HB1  H  HCH2   0   0.222   0.2126  -1.6905   0.5889
 DPH  HB2  H  HCH2   0   0.233  -1.4018  -1.0180   0.5735
 DPH  HD1  H  HCR6   0   0.241   1.5715  -1.5756  -1.4001
 DPH  HD2  H  HCR6   0   0.241  -1.9503   0.8301  -1.1073
 DPH  HE1  H  HCR6   0   0.249   1.8148  -0.9348  -3.7644
 DPH  HE2  H  HCR6   0   0.249  -1.7108   1.4748  -3.4690
 DPH  HZ   H  HCR6   0   0.249   0.1776   0.5998  -4.8138

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
 DPH  CM   CA   single    1.526  0.020  1.526
 DPH  CM   HM1  single    0.970  0.020  1.090
 DPH  CM   HM2  single    0.970  0.020  1.090
 DPH  CM   HM3  single    0.970  0.020  1.090
 DPH  CA   CB   single    1.533  0.020  1.533
 DPH  CA   C    single    1.548  0.020  1.548
 DPH  CA   HA   single    0.970  0.020  1.090
 DPH  CB   CG   single    1.503  0.020  1.503
 DPH  CB   HB1  single    0.970  0.020  1.090
 DPH  CB   HB2  single    0.970  0.020  1.090
 DPH  CG   CD1  aromatic  1.393  0.020  1.393
 DPH  CG   CD2  aromatic  1.396  0.020  1.396
 DPH  CD1  CE1  aromatic  1.390  0.020  1.390
 DPH  CD1  HD1  single    0.930  0.020  1.080
 DPH  CD2  CE2  aromatic  1.388  0.020  1.388
 DPH  CD2  HD2  single    0.930  0.020  1.080
 DPH  CE1  CZ   aromatic  1.388  0.020  1.388
 DPH  CE1  HE1  single    0.930  0.020  1.080
 DPH  CE2  CZ   aromatic  1.390  0.020  1.390
 DPH  CE2  HE2  single    0.930  0.020  1.080
 DPH  CZ   HZ   single    0.930  0.020  1.080
 DPH  C    O    deloc     1.247  0.020  1.247
 DPH  C    OXT  deloc     1.249  0.020  1.249

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
 DPH  HM3  CM   HM2  107.34  3.000
 DPH  HM3  CM   HM1  107.82  3.000
 DPH  HM2  CM   HM1  107.79  3.000
 DPH  HM3  CM   CA   111.68  3.000
 DPH  HM2  CM   CA   110.97  3.000
 DPH  HM1  CM   CA   111.07  3.000
 DPH  HA   CA   C    106.49  3.000
 DPH  HA   CA   CB   107.64  3.000
 DPH  C    CA   CB   112.81  3.000
 DPH  HA   CA   CM   107.38  3.000
 DPH  C    CA   CM   110.53  3.000
 DPH  CB   CA   CM   111.66  3.000
 DPH  HB2  CB   HB1  106.32  3.000
 DPH  HB2  CB   CG   109.08  3.000
 DPH  HB1  CB   CG   109.85  3.000
 DPH  HB2  CB   CA   108.85  3.000
 DPH  HB1  CB   CA   109.35  3.000
 DPH  CG   CB   CA   113.16  3.000
 DPH  CD2  CG   CD1  118.00  3.000
 DPH  CD2  CG   CB   120.23  3.000
 DPH  CD1  CG   CB   121.76  3.000
 DPH  HD1  CD1  CE1  119.52  3.000
 DPH  HD1  CD1  CG   119.35  3.000
 DPH  CE1  CD1  CG   121.13  3.000
 DPH  HD2  CD2  CE2  119.46  3.000
 DPH  HD2  CD2  CG   119.35  3.000
 DPH  CE2  CD2  CG   121.19  3.000
 DPH  HE1  CE1  CZ   120.06  3.000
 DPH  HE1  CE1  CD1  119.76  3.000
 DPH  CZ   CE1  CD1  120.18  3.000
 DPH  HE2  CE2  CZ   120.03  3.000
 DPH  HE2  CE2  CD2  119.84  3.000
 DPH  CZ   CE2  CD2  120.13  3.000
 DPH  HZ   CZ   CE2  120.30  3.000
 DPH  HZ   CZ   CE1  120.33  3.000
 DPH  CE2  CZ   CE1  119.37  3.000
 DPH  OXT  C    O    125.97  3.000
 DPH  OXT  C    CA   115.93  3.000
 DPH  O    C    CA   118.09  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
 DPH  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 DPH  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 DPH  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 DPH  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 DPH  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 DPH  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 DPH  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 DPH  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 DPH  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 DPH  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 DPH  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 DPH  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 DPH  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 DPH  Var_01    CD1  CG   CB   CA   102.57  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
 DPH  chir_01  CA  CM  CB  C  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
 DPH  plan-1  CB   0.020
 DPH  plan-1  CG   0.020
 DPH  plan-1  CD1  0.020
 DPH  plan-1  CD2  0.020
 DPH  plan-1  CE1  0.020
 DPH  plan-1  CE2  0.020
 DPH  plan-1  CZ   0.020
 DPH  plan-1  HD1  0.020
 DPH  plan-1  HD2  0.020
 DPH  plan-1  HE1  0.020
 DPH  plan-1  HE2  0.020
 DPH  plan-1  HZ   0.020
 DPH  plan-2  CA   0.020
 DPH  plan-2  C    0.020
 DPH  plan-2  O    0.020
 DPH  plan-2  OXT  0.020

