# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 06:40:13 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: methyl (2S)-2-hydroxy-3-phenylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](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
 OPH  OPH  'methyl (2S)-2-hydroxy-3-phenylpropanoate'  ligand  25  13  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OPH
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
 OPH  CA   C  CH1   0  -0.055  -0.3201  -0.4658   0.9541
 OPH  CB   C  CH2   0  -0.582   0.2059   0.7272   0.1353
 OPH  CG   C  CR6   0   0.154   0.2034   0.4258  -1.3356
 OPH  CD1  C  CR16  0  -0.314  -0.8594   0.8168  -2.1451
 OPH  CD2  C  CR16  0  -0.301   1.2558  -0.2816  -1.9129
 OPH  CE1  C  CR16  0  -0.242  -0.8691   0.5165  -3.5010
 OPH  CE2  C  CR16  0  -0.240   1.2489  -0.5879  -3.2668
 OPH  CZ   C  CR16  0  -0.271   0.1850  -0.1892  -4.0660
 OPH  C    C  C     0   0.549  -0.3027  -0.1141   2.4350
 OPH  CS   C  CH3   0  -0.424   1.0983   0.3126   4.2788
 OPH  OP   O  OH1   0  -0.644  -1.5916  -0.8784   0.5580
 OPH  OS   O  O2    0  -0.449   0.9295  -0.0623   2.9096
 OPH  O    O  O     0  -0.443  -1.2920   0.1127   3.0835
 OPH  HA   H  HCH1  0   0.282   0.3494  -1.3164   0.7951
 OPH  HB1  H  HCH2  0   0.266  -0.4154   1.6051   0.3381
 OPH  HB2  H  HCH2  0   0.273   1.2168   0.9704   0.4674
 OPH  HD1  H  HCR6  0   0.245  -1.6854   1.3697  -1.7131
 OPH  HD2  H  HCR6  0   0.248   2.0932  -0.5941  -1.2991
 OPH  HE1  H  HCR6  0   0.254  -1.7013   0.8341  -4.1162
 OPH  HE2  H  HCR6  0   0.254   2.0775  -1.1339  -3.6993
 OPH  HZ   H  HCR6  0   0.254   0.1792  -0.4238  -5.1226
 OPH  HS1  H  HCH3  0   0.254   2.1687   0.3043   4.4599
 OPH  HS2  H  HCH3  0   0.242   0.7068   1.3116   4.4673
 OPH  HS3  H  HCH3  0   0.242   0.6125  -0.3982   4.9464
 OPH  HO   H  HOH1  0   0.447  -2.2146  -0.1542   0.6856

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
 OPH  CA   CB   single    1.540  0.020  1.540
 OPH  CA   C    single    1.522  0.020  1.522
 OPH  CA   OP   single    1.394  0.020  1.394
 OPH  CA   HA   single    0.970  0.020  1.090
 OPH  CB   CG   single    1.501  0.020  1.501
 OPH  CB   HB1  single    0.970  0.020  1.090
 OPH  CB   HB2  single    0.970  0.020  1.090
 OPH  CG   CD1  aromatic  1.392  0.020  1.392
 OPH  CG   CD2  aromatic  1.393  0.020  1.393
 OPH  CD1  CE1  aromatic  1.389  0.020  1.389
 OPH  CD1  HD1  single    0.930  0.020  1.080
 OPH  CD2  CE2  aromatic  1.388  0.020  1.388
 OPH  CD2  HD2  single    0.930  0.020  1.080
 OPH  CE1  CZ   aromatic  1.389  0.020  1.389
 OPH  CE1  HE1  single    0.930  0.020  1.080
 OPH  CE2  CZ   aromatic  1.389  0.020  1.389
 OPH  CE2  HE2  single    0.930  0.020  1.080
 OPH  CZ   HZ   single    0.930  0.020  1.080
 OPH  C    OS   single    1.321  0.020  1.321
 OPH  C    O    double    1.204  0.020  1.204
 OPH  CS   OS   single    1.430  0.020  1.430
 OPH  CS   HS1  single    0.970  0.020  1.090
 OPH  CS   HS2  single    0.970  0.020  1.090
 OPH  CS   HS3  single    0.970  0.020  1.090
 OPH  OP   HO   single    0.850  0.020  0.980

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
 OPH  HA   CA   OP   106.66  3.000
 OPH  HA   CA   C    108.30  3.000
 OPH  OP   CA   C    110.80  3.000
 OPH  HA   CA   CB   108.43  3.000
 OPH  OP   CA   CB   112.94  3.000
 OPH  C    CA   CB   109.54  3.000
 OPH  HB2  CB   HB1  106.89  3.000
 OPH  HB2  CB   CG   110.14  3.000
 OPH  HB1  CB   CG   109.97  3.000
 OPH  HB2  CB   CA   109.11  3.000
 OPH  HB1  CB   CA   109.21  3.000
 OPH  CG   CB   CA   111.40  3.000
 OPH  CD2  CG   CD1  118.58  3.000
 OPH  CD2  CG   CB   120.43  3.000
 OPH  CD1  CG   CB   120.97  3.000
 OPH  HD1  CD1  CE1  119.62  3.000
 OPH  HD1  CD1  CG   119.56  3.000
 OPH  CE1  CD1  CG   120.82  3.000
 OPH  HD2  CD2  CE2  119.49  3.000
 OPH  HD2  CD2  CG   119.69  3.000
 OPH  CE2  CD2  CG   120.82  3.000
 OPH  HE1  CE1  CZ   120.09  3.000
 OPH  HE1  CE1  CD1  119.79  3.000
 OPH  CZ   CE1  CD1  120.12  3.000
 OPH  HE2  CE2  CZ   120.08  3.000
 OPH  HE2  CE2  CD2  119.82  3.000
 OPH  CZ   CE2  CD2  120.11  3.000
 OPH  HZ   CZ   CE2  120.23  3.000
 OPH  HZ   CZ   CE1  120.22  3.000
 OPH  CE2  CZ   CE1  119.55  3.000
 OPH  O    C    OS   124.41  3.000
 OPH  O    C    CA   123.91  3.000
 OPH  OS   C    CA   111.66  3.000
 OPH  HS3  CS   HS2  109.39  3.000
 OPH  HS3  CS   HS1  109.42  3.000
 OPH  HS2  CS   HS1  109.41  3.000
 OPH  HS3  CS   OS   111.29  3.000
 OPH  HS2  CS   OS   111.33  3.000
 OPH  HS1  CS   OS   105.92  3.000
 OPH  HO   OP   CA   109.24  3.000
 OPH  CS   OS   C    117.67  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
 OPH  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 OPH  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 OPH  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 OPH  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 OPH  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 OPH  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 OPH  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 OPH  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 OPH  CONST_09  HE1  CE1  CD1  CG    180.00   0.0  0
 OPH  CONST_10  HE2  CE2  CD2  CG    180.00   0.0  0
 OPH  CONST_11  HD2  CD2  CG   CD1   180.00   0.0  0
 OPH  CONST_12  HZ   CZ   CE1  CD1   180.00   0.0  0
 OPH  CONST_13  HD1  CD1  CG   CD2   180.00   0.0  0
 OPH  Var_01    CD1  CG   CB   CA     95.62  30.0  2
 OPH  Var_02    O    C    OS   CS     -1.21  30.0  2
 OPH  Var_03    HS1  CS   OS   C    -179.37  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
 OPH  chir_01  CA  CB  C  OP  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
 OPH  plan-1  CB   0.020
 OPH  plan-1  CG   0.020
 OPH  plan-1  CD1  0.020
 OPH  plan-1  CD2  0.020
 OPH  plan-1  CE1  0.020
 OPH  plan-1  CE2  0.020
 OPH  plan-1  CZ   0.020
 OPH  plan-1  HD1  0.020
 OPH  plan-1  HD2  0.020
 OPH  plan-1  HE1  0.020
 OPH  plan-1  HE2  0.020
 OPH  plan-1  HZ   0.020
 OPH  plan-2  CA   0.020
 OPH  plan-2  C    0.020
 OPH  plan-2  OS   0.020
 OPH  plan-2  O    0.020

