# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 21:29:27 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2S)-2-(4-chlorophenoxy)-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)Oc2ccc(Cl)cc2
#
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
 YRG  YRG  '(2S)-2-(4-chlorophenoxy)-3-phenylpropanoic acid'  ligand  32  19  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YRG
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
 YRG  CAK   C   CR16  0  -0.352   1.5819   0.6861  -1.2797
 YRG  CAI   C   CR16  0  -0.197   2.8937   1.0608  -1.0583
 YRG  CAP   C   CR6   0  -0.064   3.5614   0.5864   0.0625
 YRG  CLAC  CL  CL    0  -0.137   5.2080   1.0554   0.3434
 YRG  CAJ   C   CR16  0  -0.199   2.9243  -0.2560   0.9544
 YRG  CAL   C   CR16  0  -0.374   1.6061  -0.6351   0.7312
 YRG  CAR   C   CR6   0   0.408   0.9285  -0.1662  -0.3898
 YRG  OAN   O   O2    0  -0.467  -0.3517  -0.4621  -0.6981
 YRG  CAS   C   CH1   0  -0.084  -1.1082  -1.2790   0.1512
 YRG  CAO   C   C     0   0.511  -0.6854  -2.7330  -0.0115
 YRG  OAB   O   OH1   0  -0.587  -1.1961  -3.4858   0.9489
 YRG  OAA   O   O     0  -0.415   0.0015  -3.1385  -0.9099
 YRG  CAM   C   CH2   0  -0.551  -2.5798  -1.1088  -0.2444
 YRG  CAQ   C   CR6   0   0.138  -3.0358   0.3119  -0.0632
 YRG  CAG   C   CR16  0  -0.296  -2.9786   1.2240  -1.1136
 YRG  CAE   C   CR16  0  -0.243  -3.3785   2.5409  -0.9302
 YRG  CAD   C   CR16  0  -0.269  -3.8370   2.9647   0.3103
 YRG  CAF   C   CR16  0  -0.240  -3.8976   2.0626   1.3645
 YRG  CAH   C   CR16  0  -0.306  -3.4999   0.7459   1.1763
 YRG  HAK   H   HCR6  0   0.276   1.0551   1.0557  -2.1500
 YRG  HAI   H   HCR6  0   0.283   3.3897   1.7211  -1.7565
 YRG  HAJ   H   HCR6  0   0.284   3.4422  -0.6275   1.8281
 YRG  HAL   H   HCR6  0   0.285   1.1424  -1.2935   1.4531
 YRG  HAS   H   HCH1  0   0.285  -0.9939  -0.9817   1.2016
 YRG  HOAB  H   HOH1  0   0.490  -0.9607  -4.4167   0.8133
 YRG  HAM   H   HCH2  0   0.276  -2.7112  -1.4283  -1.2809
 YRG  HAMA  H   HCH2  0   0.283  -3.1796  -1.7767   0.3751
 YRG  HAG   H   HCR6  0   0.246  -2.6235   0.9016  -2.0845
 YRG  HAE   H   HCR6  0   0.255  -3.3317   3.2375  -1.7573
 YRG  HAD   H   HCR6  0   0.255  -4.1492   3.9911   0.4540
 YRG  HAF   H   HCR6  0   0.255  -4.2585   2.3832   2.3333
 YRG  HAH   H   HCR6  0   0.250  -3.5568   0.0462   2.0026

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
 YRG  CAR   CAK   aromatic  1.395  0.020  1.395
 YRG  CAI   CAK   aromatic  1.382  0.020  1.382
 YRG  CAK   HAK   single    0.930  0.020  1.080
 YRG  CAP   CAI   aromatic  1.388  0.020  1.388
 YRG  CAI   HAI   single    0.930  0.020  1.080
 YRG  CAJ   CAP   aromatic  1.382  0.020  1.382
 YRG  CLAC  CAP   single    1.735  0.020  1.735
 YRG  CAJ   CAL   aromatic  1.390  0.020  1.390
 YRG  CAJ   HAJ   single    0.930  0.020  1.080
 YRG  CAL   CAR   aromatic  1.391  0.020  1.391
 YRG  CAL   HAL   single    0.930  0.020  1.080
 YRG  OAN   CAR   single    1.350  0.020  1.350
 YRG  OAN   CAS   single    1.400  0.020  1.400
 YRG  CAM   CAS   single    1.533  0.020  1.533
 YRG  CAS   CAO   single    1.523  0.020  1.523
 YRG  CAS   HAS   single    0.970  0.020  1.090
 YRG  CAO   OAA   double    1.201  0.020  1.201
 YRG  CAO   OAB   single    1.323  0.020  1.323
 YRG  OAB   HOAB  single    0.850  0.020  0.980
 YRG  CAQ   CAM   single    1.503  0.020  1.503
 YRG  CAM   HAM   single    0.970  0.020  1.090
 YRG  CAM   HAMA  single    0.970  0.020  1.090
 YRG  CAH   CAQ   aromatic  1.393  0.020  1.393
 YRG  CAG   CAQ   aromatic  1.392  0.020  1.392
 YRG  CAE   CAG   aromatic  1.388  0.020  1.388
 YRG  CAG   HAG   single    0.930  0.020  1.080
 YRG  CAD   CAE   aromatic  1.389  0.020  1.389
 YRG  CAE   HAE   single    0.930  0.020  1.080
 YRG  CAD   CAF   aromatic  1.389  0.020  1.389
 YRG  CAD   HAD   single    0.930  0.020  1.080
 YRG  CAF   CAH   aromatic  1.388  0.020  1.388
 YRG  CAF   HAF   single    0.930  0.020  1.080
 YRG  CAH   HAH   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
 YRG  HAK   CAK  CAR   119.58  3.000
 YRG  HAK   CAK  CAI   119.88  3.000
 YRG  CAR   CAK  CAI   120.54  3.000
 YRG  HAI   CAI  CAP   120.61  3.000
 YRG  HAI   CAI  CAK   119.83  3.000
 YRG  CAP   CAI  CAK   119.55  3.000
 YRG  CAJ   CAP  CLAC  119.85  3.000
 YRG  CLAC  CAP  CAI   119.66  3.000
 YRG  CAJ   CAP  CAI   120.49  3.000
 YRG  HAJ   CAJ  CAL   119.36  3.000
 YRG  HAJ   CAJ  CAP   120.65  3.000
 YRG  CAL   CAJ  CAP   119.99  3.000
 YRG  HAL   CAL  CAR   122.29  3.000
 YRG  HAL   CAL  CAJ   117.75  3.000
 YRG  CAR   CAL  CAJ   119.96  3.000
 YRG  OAN   CAR  CAL   124.90  3.000
 YRG  OAN   CAR  CAK   115.64  3.000
 YRG  CAL   CAR  CAK   119.46  3.000
 YRG  CAS   OAN  CAR   120.12  3.000
 YRG  HAS   CAS  CAM   108.47  3.000
 YRG  HAS   CAS  CAO   109.39  3.000
 YRG  CAM   CAS  CAO   110.17  3.000
 YRG  HAS   CAS  OAN   111.48  3.000
 YRG  CAO   CAS  OAN   110.01  3.000
 YRG  CAM   CAS  OAN   107.29  3.000
 YRG  OAA   CAO  OAB   124.86  3.000
 YRG  OAB   CAO  CAS   111.01  3.000
 YRG  OAA   CAO  CAS   124.11  3.000
 YRG  HOAB  OAB  CAO   110.55  3.000
 YRG  HAMA  CAM  HAM   107.08  3.000
 YRG  HAMA  CAM  CAQ   110.09  3.000
 YRG  HAM   CAM  CAQ   110.76  3.000
 YRG  HAMA  CAM  CAS   108.25  3.000
 YRG  HAM   CAM  CAS   109.13  3.000
 YRG  CAQ   CAM  CAS   111.40  3.000
 YRG  CAH   CAQ  CAG   118.74  3.000
 YRG  CAG   CAQ  CAM   121.05  3.000
 YRG  CAH   CAQ  CAM   120.19  3.000
 YRG  HAG   CAG  CAE   119.69  3.000
 YRG  HAG   CAG  CAQ   119.66  3.000
 YRG  CAE   CAG  CAQ   120.66  3.000
 YRG  HAE   CAE  CAD   120.03  3.000
 YRG  HAE   CAE  CAG   119.81  3.000
 YRG  CAD   CAE  CAG   120.16  3.000
 YRG  HAD   CAD  CAF   120.17  3.000
 YRG  HAD   CAD  CAE   120.21  3.000
 YRG  CAF   CAD  CAE   119.62  3.000
 YRG  HAF   CAF  CAH   119.86  3.000
 YRG  HAF   CAF  CAD   120.10  3.000
 YRG  CAH   CAF  CAD   120.04  3.000
 YRG  HAH   CAH  CAF   119.59  3.000
 YRG  HAH   CAH  CAQ   119.64  3.000
 YRG  CAF   CAH  CAQ   120.77  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
 YRG  CONST_01  CAJ   CAL  CAR  CAK     0.00   0.0  0
 YRG  CONST_02  CAJ   CAP  CAI  CAK     0.00   0.0  0
 YRG  CONST_03  CAL   CAR  CAK  CAI     0.00   0.0  0
 YRG  CONST_04  CAL   CAJ  CAP  CAI     0.00   0.0  0
 YRG  CONST_05  CAR   CAK  CAI  CAP     0.00   0.0  0
 YRG  CONST_06  CAR   CAL  CAJ  CAP     0.00   0.0  0
 YRG  CONST_07  CAD   CAF  CAH  CAQ     0.00   0.0  0
 YRG  CONST_08  CAD   CAE  CAG  CAQ     0.00   0.0  0
 YRG  CONST_09  CAF   CAH  CAQ  CAG     0.00   0.0  0
 YRG  CONST_10  CAF   CAD  CAE  CAG     0.00   0.0  0
 YRG  CONST_11  CAH   CAQ  CAG  CAE     0.00   0.0  0
 YRG  CONST_12  CAH   CAF  CAD  CAE     0.00   0.0  0
 YRG  CONST_13  CLAC  CAP  CAI  CAK   180.00   0.0  0
 YRG  CONST_14  OAN   CAR  CAK  CAI   180.00   0.0  0
 YRG  CONST_15  CAL   CAJ  CAP  CLAC  180.00   0.0  0
 YRG  CONST_16  OAN   CAR  CAL  CAJ   180.00   0.0  0
 YRG  CONST_17  CAF   CAH  CAQ  CAM   180.00   0.0  0
 YRG  CONST_18  CAE   CAG  CAQ  CAM   180.00   0.0  0
 YRG  CONST_19  HAL   CAL  CAR  CAK   180.00   0.0  0
 YRG  CONST_20  HAJ   CAJ  CAP  CAI   180.00   0.0  0
 YRG  CONST_21  HAK   CAK  CAI  CAP   180.00   0.0  0
 YRG  CONST_22  HAI   CAI  CAP  CAJ   180.00   0.0  0
 YRG  CONST_23  HAF   CAF  CAH  CAQ   180.00   0.0  0
 YRG  CONST_24  HAE   CAE  CAG  CAQ   180.00   0.0  0
 YRG  CONST_25  HAH   CAH  CAQ  CAG   180.00   0.0  0
 YRG  CONST_26  HAD   CAD  CAE  CAG   180.00   0.0  0
 YRG  CONST_27  HAG   CAG  CAE  CAD   180.00   0.0  0
 YRG  CONST_28  HOAB  OAB  CAO  CAS   180.00   0.0  0
 YRG  Var_01    CAH   CAQ  CAM  CAS   -85.81  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
 YRG  chir_01  CAS  OAN  CAM  CAO  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
 YRG  plan-1  CAK   0.020
 YRG  plan-1  CAI   0.020
 YRG  plan-1  CAP   0.020
 YRG  plan-1  CLAC  0.020
 YRG  plan-1  CAJ   0.020
 YRG  plan-1  CAL   0.020
 YRG  plan-1  CAR   0.020
 YRG  plan-1  OAN   0.020
 YRG  plan-1  HAK   0.020
 YRG  plan-1  HAI   0.020
 YRG  plan-1  HAJ   0.020
 YRG  plan-1  HAL   0.020
 YRG  plan-2  CAM   0.020
 YRG  plan-2  CAQ   0.020
 YRG  plan-2  CAG   0.020
 YRG  plan-2  CAE   0.020
 YRG  plan-2  CAD   0.020
 YRG  plan-2  CAF   0.020
 YRG  plan-2  CAH   0.020
 YRG  plan-2  HAG   0.020
 YRG  plan-2  HAE   0.020
 YRG  plan-2  HAD   0.020
 YRG  plan-2  HAF   0.020
 YRG  plan-2  HAH   0.020
 YRG  plan-3  CAS   0.020
 YRG  plan-3  CAO   0.020
 YRG  plan-3  OAB   0.020
 YRG  plan-3  OAA   0.020
 YRG  plan-3  HOAB  0.020

