# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 04:54:29 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-benzothiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(OCCCc2c(sc3ccccc23)C(O)=O)cc(C)c1Cl
#
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
 19G  19G  '3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-benzothiophene-2-carboxylic acid'  ligand  43  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_19G
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
 19G  OAC  O   O      0  -0.569   2.3480  -3.0625  -0.2517
 19G  CAQ  C   C      0   0.401   3.4751  -2.6993   0.1266
 19G  OAD  O   OC    -1  -0.596   4.3897  -3.4079   0.5918
 19G  CAW  C   CR5    0  -0.448   3.8118  -1.2331   0.0322
 19G  S    S   S2     0   0.187   5.3881  -0.7987   0.6306
 19G  CAX  C   CR56   0  -0.212   5.1155   0.8692   0.2653
 19G  CAH  C   CR16   0  -0.288   5.9895   1.9333   0.4799
 19G  CAF  C   CR16   0  -0.272   5.5816   3.2037   0.1212
 19G  CAG  C   CR16   0  -0.256   4.3187   3.4159  -0.4468
 19G  CAI  C   CR16   0  -0.343   3.4549   2.3608  -0.6605
 19G  CAY  C   CR56   0   0.175   3.8434   1.0626  -0.3043
 19G  CAV  C   CR5    0   0.233   3.1051  -0.1694  -0.4364
 19G  CAN  C   CH2    0  -0.521   1.7119  -0.2133  -0.9841
 19G  CAL  C   CH2    0  -0.454   0.6626  -0.0963   0.1217
 19G  CAM  C   CH2    0  -0.180  -0.7372  -0.1183  -0.4546
 19G  OAO  O   O2     0  -0.478  -1.6574   0.0071   0.6191
 19G  CAT  C   CR6    0   0.434  -2.9749   0.0571   0.3522
 19G  CAJ  C   CR16   0  -0.473  -3.5219  -0.0511  -0.9214
 19G  CAR  C   CR6    0   0.219  -4.9013   0.0166  -1.1128
 19G  CAA  C   CH3    0  -0.722  -5.4710  -0.1030  -2.4939
 19G  CAU  C   CR6    0  -0.218  -5.7117   0.1963   0.0017
 19G  CL   CL  CL     0  -0.139  -7.4356   0.2973  -0.2204
 19G  CAS  C   CR6    0   0.209  -5.1938   0.3046   1.2937
 19G  CAB  C   CH3    0  -0.722  -6.0791   0.5004   2.4867
 19G  CAK  C   CR16   0  -0.441  -3.8183   0.2308   1.4487
 19G  H2   H   HCR6   0   0.263   6.9650   1.7697   0.9201
 19G  H3   H   HCR6   0   0.257   6.2450   4.0435   0.2817
 19G  H4   H   HCR6   0   0.255   4.0178   4.4191  -0.7188
 19G  H5   H   HCR6   0   0.247   2.4825   2.5412  -1.1024
 19G  H6   H   HCH2   0   0.235   1.5776   0.5996  -1.7026
 19G  H7   H   HCH2   0   0.254   1.5598  -1.1457  -1.5244
 19G  H8   H   HCH2   0   0.244   0.7893  -0.9279   0.8175
 19G  H9   H   HCH2   0   0.235   0.8118   0.8294   0.6845
 19G  H10  H   HCH2   0   0.222  -0.8712   0.7036  -1.1680
 19G  H11  H   HCH2   0   0.222  -0.9077  -1.0558  -0.9972
 19G  H12  H   HCR6   0   0.278  -2.8938  -0.1851  -1.7918
 19G  H13  H   HCH3   0   0.251  -6.1536  -0.9505  -2.5723
 19G  H14  H   HCH3   0   0.251  -6.0352   0.7884  -2.7718
 19G  H15  H   HCH3   0   0.251  -4.6797  -0.2410  -3.2282
 19G  H16  H   HCH3   0   0.251  -6.7944  -0.3163   2.5936
 19G  H17  H   HCH3   0   0.252  -5.4899   0.5522   3.4004
 19G  H18  H   HCH3   0   0.251  -6.6569   1.4224   2.4070
 19G  H19  H   HCR6   0   0.259  -3.3884   0.3142   2.4398

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
 19G  OAC  CAQ  deloc     1.243  0.020  1.243
 19G  OAD  CAQ  deloc     1.247  0.020  1.247
 19G  CAQ  CAW  single    1.507  0.020  1.507
 19G  CAW  S    aromatic  1.741  0.020  1.741
 19G  CAW  CAV  aromatic  1.360  0.020  1.360
 19G  S    CAX  aromatic  1.729  0.020  1.729
 19G  CAN  CAL  single    1.529  0.020  1.529
 19G  CAN  CAV  single    1.498  0.020  1.498
 19G  CAL  CAM  single    1.514  0.020  1.514
 19G  CAV  CAY  aromatic  1.442  0.020  1.442
 19G  CAX  CAY  aromatic  1.407  0.020  1.407
 19G  CAX  CAH  aromatic  1.394  0.020  1.394
 19G  CAY  CAI  aromatic  1.401  0.020  1.401
 19G  CAM  OAO  single    1.420  0.020  1.420
 19G  OAO  CAT  single    1.345  0.020  1.345
 19G  CAH  CAF  aromatic  1.382  0.020  1.382
 19G  CAI  CAG  aromatic  1.380  0.020  1.380
 19G  CAT  CAK  aromatic  1.394  0.020  1.394
 19G  CAT  CAJ  aromatic  1.390  0.020  1.390
 19G  CAF  CAG  aromatic  1.401  0.020  1.401
 19G  CAK  CAS  aromatic  1.386  0.020  1.386
 19G  CAJ  CAR  aromatic  1.394  0.020  1.394
 19G  CAS  CAB  single    1.498  0.020  1.498
 19G  CAS  CAU  aromatic  1.396  0.020  1.396
 19G  CAR  CAU  aromatic  1.390  0.020  1.390
 19G  CAR  CAA  single    1.499  0.020  1.499
 19G  CAU  CL   single    1.741  0.020  1.741
 19G  CAH  H2   single    0.930  0.020  1.080
 19G  CAF  H3   single    0.930  0.020  1.080
 19G  CAG  H4   single    0.930  0.020  1.080
 19G  CAI  H5   single    0.930  0.020  1.080
 19G  CAN  H6   single    0.970  0.020  1.090
 19G  CAN  H7   single    0.970  0.020  1.090
 19G  CAL  H8   single    0.970  0.020  1.090
 19G  CAL  H9   single    0.970  0.020  1.090
 19G  CAM  H10  single    0.970  0.020  1.090
 19G  CAM  H11  single    0.970  0.020  1.090
 19G  CAJ  H12  single    0.930  0.020  1.080
 19G  CAA  H13  single    0.970  0.020  1.090
 19G  CAA  H14  single    0.970  0.020  1.090
 19G  CAA  H15  single    0.970  0.020  1.090
 19G  CAB  H16  single    0.970  0.020  1.090
 19G  CAB  H17  single    0.970  0.020  1.090
 19G  CAB  H18  single    0.970  0.020  1.090
 19G  CAK  H19  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
 19G  CAW  CAQ  OAD  114.35  3.000
 19G  CAW  CAQ  OAC  117.88  3.000
 19G  OAD  CAQ  OAC  127.77  3.000
 19G  CAV  CAW  S    113.18  3.000
 19G  CAV  CAW  CAQ  131.77  3.000
 19G  S    CAW  CAQ  115.05  3.000
 19G  CAX  S    CAW   91.45  3.000
 19G  CAY  CAX  CAH  121.62  3.000
 19G  CAH  CAX  S    127.24  3.000
 19G  CAY  CAX  S    111.14  3.000
 19G  H2   CAH  CAF  120.70  3.000
 19G  H2   CAH  CAX  120.81  3.000
 19G  CAF  CAH  CAX  118.49  3.000
 19G  H3   CAF  CAG  119.68  3.000
 19G  H3   CAF  CAH  119.61  3.000
 19G  CAG  CAF  CAH  120.71  3.000
 19G  H4   CAG  CAI  119.71  3.000
 19G  H4   CAG  CAF  119.55  3.000
 19G  CAI  CAG  CAF  120.74  3.000
 19G  H5   CAI  CAY  120.46  3.000
 19G  H5   CAI  CAG  119.85  3.000
 19G  CAY  CAI  CAG  119.70  3.000
 19G  CAV  CAY  CAI  128.77  3.000
 19G  CAI  CAY  CAX  118.74  3.000
 19G  CAV  CAY  CAX  112.48  3.000
 19G  CAN  CAV  CAY  122.32  3.000
 19G  CAY  CAV  CAW  111.75  3.000
 19G  CAN  CAV  CAW  125.89  3.000
 19G  H7   CAN  H6   107.07  3.000
 19G  H7   CAN  CAL  109.20  3.000
 19G  H6   CAN  CAL  109.52  3.000
 19G  H7   CAN  CAV  109.68  3.000
 19G  H6   CAN  CAV  109.44  3.000
 19G  CAL  CAN  CAV  111.82  3.000
 19G  H9   CAL  H8   107.52  3.000
 19G  H9   CAL  CAM  109.53  3.000
 19G  H8   CAL  CAM  109.80  3.000
 19G  H9   CAL  CAN  110.09  3.000
 19G  H8   CAL  CAN  108.84  3.000
 19G  CAM  CAL  CAN  110.98  3.000
 19G  H11  CAM  H10  107.45  3.000
 19G  H11  CAM  OAO  110.43  3.000
 19G  H10  CAM  OAO  110.28  3.000
 19G  H11  CAM  CAL  110.16  3.000
 19G  H10  CAM  CAL  110.47  3.000
 19G  OAO  CAM  CAL  108.07  3.000
 19G  CAT  OAO  CAM  119.21  3.000
 19G  CAK  CAT  CAJ  119.48  3.000
 19G  CAJ  CAT  OAO  124.35  3.000
 19G  CAK  CAT  OAO  116.17  3.000
 19G  H12  CAJ  CAR  118.04  3.000
 19G  H12  CAJ  CAT  121.22  3.000
 19G  CAR  CAJ  CAT  120.74  3.000
 19G  CAU  CAR  CAA  121.85  3.000
 19G  CAA  CAR  CAJ  119.91  3.000
 19G  CAU  CAR  CAJ  118.24  3.000
 19G  H15  CAA  H14  107.92  3.000
 19G  H15  CAA  H13  107.94  3.000
 19G  H14  CAA  H13  107.03  3.000
 19G  H15  CAA  CAR  110.83  3.000
 19G  H14  CAA  CAR  111.47  3.000
 19G  H13  CAA  CAR  111.47  3.000
 19G  CAS  CAU  CL   118.74  3.000
 19G  CL   CAU  CAR  118.86  3.000
 19G  CAS  CAU  CAR  122.40  3.000
 19G  CAK  CAS  CAB  120.28  3.000
 19G  CAB  CAS  CAU  121.86  3.000
 19G  CAK  CAS  CAU  117.87  3.000
 19G  H18  CAB  H17  107.93  3.000
 19G  H18  CAB  H16  107.01  3.000
 19G  H17  CAB  H16  107.95  3.000
 19G  H18  CAB  CAS  111.42  3.000
 19G  H17  CAB  CAS  110.78  3.000
 19G  H16  CAB  CAS  111.57  3.000
 19G  H19  CAK  CAS  119.47  3.000
 19G  H19  CAK  CAT  119.27  3.000
 19G  CAS  CAK  CAT  121.26  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
 19G  CONST_01  CAY  CAX  S    CAW     0.00   0.0  0
 19G  CONST_02  CAH  CAX  S    CAW   180.00   0.0  0
 19G  CONST_03  CAX  CAY  CAV  CAW     0.00   0.0  0
 19G  CONST_04  CAI  CAY  CAV  CAW   180.00   0.0  0
 19G  CONST_05  CAY  CAV  CAW  S       0.00   0.0  0
 19G  CONST_06  CAV  CAY  CAX  S       0.00   0.0  0
 19G  CONST_07  CAI  CAY  CAX  S     180.00   0.0  0
 19G  CONST_08  CAF  CAH  CAX  S     180.00   0.0  0
 19G  CONST_09  CAV  CAW  S    CAX     0.00   0.0  0
 19G  CONST_10  CAG  CAI  CAY  CAX     0.00   0.0  0
 19G  CONST_11  CAG  CAF  CAH  CAX     0.00   0.0  0
 19G  CONST_12  CAV  CAY  CAX  CAH   180.00   0.0  0
 19G  CONST_13  CAI  CAY  CAX  CAH     0.00   0.0  0
 19G  CONST_14  CAI  CAG  CAF  CAH     0.00   0.0  0
 19G  CONST_15  CAY  CAX  CAH  CAF     0.00   0.0  0
 19G  CONST_16  CAY  CAI  CAG  CAF     0.00   0.0  0
 19G  CONST_17  CAV  CAY  CAI  CAG   180.00   0.0  0
 19G  CONST_18  CAU  CAS  CAK  CAT     0.00   0.0  0
 19G  CONST_19  CAU  CAR  CAJ  CAT     0.00   0.0  0
 19G  CONST_20  CAS  CAK  CAT  CAJ     0.00   0.0  0
 19G  CONST_21  CAS  CAU  CAR  CAJ     0.00   0.0  0
 19G  CONST_22  CAK  CAT  CAJ  CAR     0.00   0.0  0
 19G  CONST_23  CAK  CAS  CAU  CAR     0.00   0.0  0
 19G  CONST_24  CAX  S    CAW  CAQ   180.00   0.0  0
 19G  CONST_25  CAY  CAV  CAW  CAQ   180.00   0.0  0
 19G  CONST_26  CAN  CAV  CAW  S     180.00   0.0  0
 19G  CONST_27  CAN  CAV  CAY  CAX   180.00   0.0  0
 19G  CONST_28  CAN  CAV  CAY  CAI     0.00   0.0  0
 19G  CONST_29  CAS  CAK  CAT  OAO   180.00   0.0  0
 19G  CONST_30  CAR  CAJ  CAT  OAO   180.00   0.0  0
 19G  CONST_31  CAB  CAS  CAK  CAT   180.00   0.0  0
 19G  CONST_32  CAA  CAR  CAJ  CAT   180.00   0.0  0
 19G  CONST_33  CL   CAU  CAR  CAJ   180.00   0.0  0
 19G  CONST_34  CAB  CAS  CAU  CAR   180.00   0.0  0
 19G  CONST_35  CAS  CAU  CAR  CAA   180.00   0.0  0
 19G  CONST_36  CAK  CAS  CAU  CL    180.00   0.0  0
 19G  CONST_37  H2   CAH  CAX  S       0.00   0.0  0
 19G  CONST_38  H5   CAI  CAY  CAX   180.00   0.0  0
 19G  CONST_39  H3   CAF  CAH  CAX   180.00   0.0  0
 19G  CONST_40  H4   CAG  CAF  CAH   180.00   0.0  0
 19G  CONST_41  H19  CAK  CAT  CAJ   180.00   0.0  0
 19G  CONST_42  H12  CAJ  CAR  CAU   180.00   0.0  0
 19G  Var_01    S    CAW  CAQ  OAC   178.05  30.0  2
 19G  Var_02    CAL  CAN  CAV  CAW    86.14  30.0  2
 19G  Var_03    CAK  CAT  OAO  CAM  -177.69  30.0  2
 19G  Var_04    H13  CAA  CAR  CAJ   120.43  30.0  2
 19G  Var_05    H16  CAB  CAS  CAU    59.19  30.0  2
 19G  Var_06    CAM  CAL  CAN  CAV   179.01  30.0  3
 19G  Var_07    H10  CAM  OAO  CAT    57.00  30.0  1
 19G  Var_08    OAO  CAM  CAL  CAN  -179.42  30.0  3

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
 19G  plan-1  OAO  0.020
 19G  plan-1  CAT  0.020
 19G  plan-1  CAJ  0.020
 19G  plan-1  CAR  0.020
 19G  plan-1  CAA  0.020
 19G  plan-1  CAU  0.020
 19G  plan-1  CL   0.020
 19G  plan-1  CAS  0.020
 19G  plan-1  CAB  0.020
 19G  plan-1  CAK  0.020
 19G  plan-1  H12  0.020
 19G  plan-1  H19  0.020
 19G  plan-2  CAQ  0.020
 19G  plan-2  CAW  0.020
 19G  plan-2  S    0.020
 19G  plan-2  CAX  0.020
 19G  plan-2  CAH  0.020
 19G  plan-2  CAF  0.020
 19G  plan-2  CAG  0.020
 19G  plan-2  CAI  0.020
 19G  plan-2  CAY  0.020
 19G  plan-2  CAV  0.020
 19G  plan-2  CAN  0.020
 19G  plan-2  H2   0.020
 19G  plan-2  H3   0.020
 19G  plan-2  H4   0.020
 19G  plan-2  H5   0.020
 19G  plan-3  OAC  0.020
 19G  plan-3  CAQ  0.020
 19G  plan-3  OAD  0.020
 19G  plan-3  CAW  0.020

