# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:05:02 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  31  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.364   1.6016   0.6968  -1.2877
 YRG  CAI   C   CR16   0  -0.199   2.9334   1.0159  -1.0978
 YRG  CAP   C   CR6    0  -0.070   3.6078   0.5100   0.0045
 YRG  CLAC  CL  CL     0  -0.147   5.2816   0.9074   0.2481
 YRG  CAJ   C   CR16   0  -0.203   2.9549  -0.3085   0.9085
 YRG  CAL   C   CR16   0  -0.379   1.6182  -0.6316   0.7165
 YRG  CAR   C   CR6    0   0.420   0.9270  -0.1326  -0.3877
 YRG  OAN   O   O2     0  -0.469  -0.3660  -0.3584  -0.6490
 YRG  CAS   C   CH1    0  -0.091  -1.1003  -1.2373   0.1826
 YRG  CAO   C   C      0   0.385  -0.6556  -2.7131   0.0325
 YRG  OAB   O   OC    -1  -0.609  -1.0930  -3.4750   0.9158
 YRG  OAA   O   O      0  -0.581   0.0514  -2.9994  -0.9454
 YRG  CAM   C   CH2    0  -0.547  -2.5676  -1.0879  -0.2173
 YRG  CAQ   C   CR6    0   0.148  -3.0695   0.3199  -0.0629
 YRG  CAG   C   CR16   0  -0.304  -3.0930   1.1981  -1.1436
 YRG  CAE   C   CR16   0  -0.244  -3.5314   2.5067  -0.9891
 YRG  CAD   C   CR16   0  -0.274  -3.9493   2.9604   0.2552
 YRG  CAF   C   CR16   0  -0.241  -3.9299   2.0941   1.3410
 YRG  CAH   C   CR16   0  -0.311  -3.4942   0.7858   1.1799
 YRG  HAK   H   HCR6   0   0.267   1.0718   1.0925  -2.1449
 YRG  HAI   H   HCR6   0   0.276   3.4400   1.6569  -1.8068
 YRG  HAJ   H   HCR6   0   0.278   3.4784  -0.7052   1.7681
 YRG  HAL   H   HCR6   0   0.281   1.1419  -1.2748   1.4431
 YRG  HAS   H   HCH1   0   0.230  -0.9982  -0.9303   1.2323
 YRG  HAM   H   HCH2   0   0.251  -2.6959  -1.4249  -1.2497
 YRG  HAMA  H   HCH2   0   0.260  -3.1460  -1.7650   0.4127
 YRG  HAG   H   HCR6   0   0.241  -2.7693   0.8534  -2.1182
 YRG  HAE   H   HCR6   0   0.251  -3.5462   3.1738  -1.8418
 YRG  HAD   H   HCR6   0   0.252  -4.2915   3.9802   0.3774
 YRG  HAF   H   HCR6   0   0.252  -4.2578   2.4370   2.3141
 YRG  HAH   H   HCR6   0   0.245  -3.4888   0.1152   2.0321

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  1.398  0.020  1.398
 YRG  CAI   CAK   aromatic  1.383  0.020  1.383
 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  1.383  0.020  1.383
 YRG  CLAC  CAP   single    1.738  0.020  1.738
 YRG  CAJ   CAL   aromatic  1.389  0.020  1.389
 YRG  CAJ   HAJ   single    0.930  0.020  1.080
 YRG  CAL   CAR   aromatic  1.395  0.020  1.395
 YRG  CAL   HAL   single    0.930  0.020  1.080
 YRG  OAN   CAR   single    1.338  0.020  1.338
 YRG  OAN   CAS   single    1.415  0.020  1.415
 YRG  CAM   CAS   single    1.528  0.020  1.528
 YRG  CAS   CAO   single    1.549  0.020  1.549
 YRG  CAS   HAS   single    0.970  0.020  1.090
 YRG  CAO   OAA   deloc     1.240  0.020  1.240
 YRG  CAO   OAB   deloc     1.246  0.020  1.246
 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  1.394  0.020  1.394
 YRG  CAG   CAQ   aromatic  1.393  0.020  1.393
 YRG  CAE   CAG   aromatic  1.389  0.020  1.389
 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   119.38  3.000
 YRG  HAK   CAK  CAI   119.72  3.000
 YRG  CAR   CAK  CAI   120.90  3.000
 YRG  HAI   CAI  CAP   120.60  3.000
 YRG  HAI   CAI  CAK   119.85  3.000
 YRG  CAP   CAI  CAK   119.54  3.000
 YRG  CAJ   CAP  CLAC  119.89  3.000
 YRG  CLAC  CAP  CAI   119.74  3.000
 YRG  CAJ   CAP  CAI   120.37  3.000
 YRG  HAJ   CAJ  CAL   119.37  3.000
 YRG  HAJ   CAJ  CAP   120.53  3.000
 YRG  CAL   CAJ  CAP   120.11  3.000
 YRG  HAL   CAL  CAR   121.78  3.000
 YRG  HAL   CAL  CAJ   118.01  3.000
 YRG  CAR   CAL  CAJ   120.22  3.000
 YRG  OAN   CAR  CAL   124.95  3.000
 YRG  OAN   CAR  CAK   116.15  3.000
 YRG  CAL   CAR  CAK   118.87  3.000
 YRG  CAS   OAN  CAR   119.42  3.000
 YRG  HAS   CAS  CAM   108.18  3.000
 YRG  HAS   CAS  CAO   109.41  3.000
 YRG  CAM   CAS  CAO   110.09  3.000
 YRG  HAS   CAS  OAN   109.86  3.000
 YRG  CAO   CAS  OAN   112.70  3.000
 YRG  CAM   CAS  OAN   106.48  3.000
 YRG  OAA   CAO  OAB   128.17  3.000
 YRG  OAB   CAO  CAS   114.41  3.000
 YRG  OAA   CAO  CAS   117.40  3.000
 YRG  HAMA  CAM  HAM   106.97  3.000
 YRG  HAMA  CAM  CAQ   110.19  3.000
 YRG  HAM   CAM  CAQ   110.27  3.000
 YRG  HAMA  CAM  CAS   107.30  3.000
 YRG  HAM   CAM  CAS   109.24  3.000
 YRG  CAQ   CAM  CAS   112.67  3.000
 YRG  CAH   CAQ  CAG   118.43  3.000
 YRG  CAG   CAQ  CAM   121.11  3.000
 YRG  CAH   CAQ  CAM   120.44  3.000
 YRG  HAG   CAG  CAE   119.62  3.000
 YRG  HAG   CAG  CAQ   119.50  3.000
 YRG  CAE   CAG  CAQ   120.88  3.000
 YRG  HAE   CAE  CAD   120.01  3.000
 YRG  HAE   CAE  CAG   119.82  3.000
 YRG  CAD   CAE  CAG   120.16  3.000
 YRG  HAD   CAD  CAF   120.24  3.000
 YRG  HAD   CAD  CAE   120.26  3.000
 YRG  CAF   CAD  CAE   119.50  3.000
 YRG  HAF   CAF  CAH   119.86  3.000
 YRG  HAF   CAF  CAD   120.06  3.000
 YRG  CAH   CAF  CAD   120.09  3.000
 YRG  HAH   CAH  CAF   119.55  3.000
 YRG  HAH   CAH  CAQ   119.51  3.000
 YRG  CAF   CAH  CAQ   120.94  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  Var_01    CAH   CAQ  CAM  CAS   -82.54  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

