# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 00:37:33 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2R)-phenyl(sulfanyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](S)c1ccccc1
#
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
 RTD  RTD  '(2R)-phenyl(sulfanyl)ethanoic acid'  ligand  19  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RTD
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
 RTD  O1   O  O     0  -0.420  -1.4381   1.6830   0.8207
 RTD  C    C  C     0   0.592  -1.7283   0.9499  -0.0881
 RTD  O2   O  OH1   0  -0.582  -2.8216   1.0773  -0.8234
 RTD  CA   C  CH1   0  -0.656  -0.9079  -0.2516  -0.5126
 RTD  S1   S  S2    0  -0.161  -1.6636  -1.7398   0.2446
 RTD  CB   C  CR6   0   0.217   0.5600  -0.0964  -0.2357
 RTD  CG1  C  CR16  0  -0.300   1.4385   0.0149  -1.3086
 RTD  CD1  C  CR16  0  -0.240   2.8031   0.1686  -1.0959
 RTD  CE   C  CR16  0  -0.264   3.3028   0.2135   0.1967
 RTD  CD2  C  CR16  0  -0.243   2.4311   0.1031   1.2741
 RTD  CG2  C  CR16  0  -0.292   1.0704  -0.0512   1.0599
 RTD  H1   H  HOH1  0   0.486  -3.3552   1.8179  -0.4972
 RTD  HA   H  HCH1  0   0.346  -1.0571  -0.4176  -1.5814
 RTD  H2   H  HSH1  0   0.231  -1.4836  -1.3985   1.5260
 RTD  HG1  H  HCR6  0   0.260   1.0560  -0.0202  -2.3219
 RTD  HD1  H  HCR6  0   0.259   3.4725   0.2506  -1.9421
 RTD  HE   H  HCR6  0   0.259   4.3654   0.3291   0.3662
 RTD  HD2  H  HCR6  0   0.259   2.8132   0.1359   2.2862
 RTD  HG2  H  HCR6  0   0.249   0.4127  -0.1411   1.9144

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
 RTD  CD2  CG2  aromatic  1.386  0.020  1.386
 RTD  CD2  CE   aromatic  1.390  0.020  1.390
 RTD  CG2  CB   aromatic  1.393  0.020  1.393
 RTD  O1   C    double    1.203  0.020  1.203
 RTD  CE   CD1  aromatic  1.387  0.020  1.387
 RTD  O2   C    single    1.324  0.020  1.324
 RTD  C    CA   single    1.515  0.020  1.515
 RTD  CB   CA   single    1.502  0.020  1.502
 RTD  CB   CG1  aromatic  1.391  0.020  1.391
 RTD  S1   CA   single    1.833  0.020  1.833
 RTD  CD1  CG1  aromatic  1.390  0.020  1.390
 RTD  O2   H1   single    0.850  0.020  0.980
 RTD  CA   HA   single    0.970  0.020  1.090
 RTD  S1   H2   single    1.200  0.020  1.300
 RTD  CG1  HG1  single    0.930  0.020  1.080
 RTD  CD1  HD1  single    0.930  0.020  1.080
 RTD  CE   HE   single    0.930  0.020  1.080
 RTD  CD2  HD2  single    0.930  0.020  1.080
 RTD  CG2  HG2  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
 RTD  CA   C    O2   111.58  3.000
 RTD  CA   C    O1   124.34  3.000
 RTD  O2   C    O1   124.06  3.000
 RTD  H1   O2   C    109.96  3.000
 RTD  HA   CA   CB   109.25  3.000
 RTD  HA   CA   S1   102.98  3.000
 RTD  CB   CA   S1   114.25  3.000
 RTD  HA   CA   C    108.71  3.000
 RTD  S1   CA   C    107.75  3.000
 RTD  CB   CA   C    113.30  3.000
 RTD  H2   S1   CA    97.65  3.000
 RTD  CG2  CB   CG1  118.90  3.000
 RTD  CG1  CB   CA   118.90  3.000
 RTD  CG2  CB   CA   122.20  3.000
 RTD  HG1  CG1  CD1  119.55  3.000
 RTD  HG1  CG1  CB   119.72  3.000
 RTD  CD1  CG1  CB   120.73  3.000
 RTD  HD1  CD1  CE   120.24  3.000
 RTD  HD1  CD1  CG1  119.75  3.000
 RTD  CE   CD1  CG1  120.01  3.000
 RTD  HE   CE   CD2  120.18  3.000
 RTD  HE   CE   CD1  120.22  3.000
 RTD  CD2  CE   CD1  119.60  3.000
 RTD  HD2  CD2  CG2  119.63  3.000
 RTD  HD2  CD2  CE   120.06  3.000
 RTD  CG2  CD2  CE   120.30  3.000
 RTD  HG2  CG2  CD2  118.94  3.000
 RTD  HG2  CG2  CB   120.60  3.000
 RTD  CD2  CG2  CB   120.46  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
 RTD  CONST_01  CE   CD2  CG2  CB     0.00  0.0  0
 RTD  CONST_02  CE   CD1  CG1  CB     0.00  0.0  0
 RTD  CONST_03  CD2  CG2  CB   CG1    0.00  0.0  0
 RTD  CONST_04  CD2  CE   CD1  CG1    0.00  0.0  0
 RTD  CONST_05  CG2  CD2  CE   CD1    0.00  0.0  0
 RTD  CONST_06  CG2  CB   CG1  CD1    0.00  0.0  0
 RTD  CONST_07  CD2  CG2  CB   CA   180.00  0.0  0
 RTD  CONST_08  CD1  CG1  CB   CA   180.00  0.0  0
 RTD  CONST_09  HD2  CD2  CG2  CB   180.00  0.0  0
 RTD  CONST_10  HD1  CD1  CG1  CB   180.00  0.0  0
 RTD  CONST_11  HG2  CG2  CB   CG1  180.00  0.0  0
 RTD  CONST_12  HE   CE   CD1  CG1  180.00  0.0  0
 RTD  CONST_13  HG1  CG1  CD1  CE   180.00  0.0  0
 RTD  CONST_14  H1   O2   C    O1     0.00  0.0  0

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
 RTD  chir_01  CA  C  CB  S1  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
 RTD  plan-1  CA   0.020
 RTD  plan-1  CB   0.020
 RTD  plan-1  CG1  0.020
 RTD  plan-1  CD1  0.020
 RTD  plan-1  CE   0.020
 RTD  plan-1  CD2  0.020
 RTD  plan-1  CG2  0.020
 RTD  plan-1  HG1  0.020
 RTD  plan-1  HD1  0.020
 RTD  plan-1  HE   0.020
 RTD  plan-1  HD2  0.020
 RTD  plan-1  HG2  0.020
 RTD  plan-2  O1   0.020
 RTD  plan-2  C    0.020
 RTD  plan-2  O2   0.020
 RTD  plan-2  CA   0.020
 RTD  plan-2  H1   0.020

