# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 06:16:03 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-({2-chloro-6-[(2,4-dichlorophenyl)sulfanyl]benzyl}carbamoyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1C(=O)NCc2c(Cl)cccc2Sc3ccc(Cl)cc3Cl
#
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
 03L  03L  '2-({2-chloro-6-[(2,4-dichlorophenyl)sulfanyl]benzyl}carbamoyl)benzoic acid'  ligand  42  29  .  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_03L
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
 03L  OAA   O   O      0  -0.577   3.5823   2.1805   1.4815
 03L  OAB   O   O      0  -0.493   3.4683  -0.8583   1.5309
 03L  OAC   O   OC    -1  -0.588   5.3762   3.4374   1.0672
 03L  CAF   C   CR16   0  -0.249   6.5701   0.8542  -1.9907
 03L  CAG   C   CR16   0  -0.254   5.8813  -0.3369  -2.1772
 03L  CAH   C   CR16   0  -0.271  -1.7582  -2.3023  -2.3337
 03L  CAI   C   CR16   0  -0.202  -0.6279  -2.9625  -1.8756
 03L  CAJ   C   CR16   0  -0.181  -2.0461  -1.0282  -1.8815
 03L  CAK   C   CR16   0  -0.286   6.1709   1.7319  -0.9943
 03L  CAL   C   CR16   0  -0.260   4.8004  -0.6380  -1.3622
 03L  CAM   C   CR16   0  -0.193  -5.5844   1.7735  -0.3661
 03L  CAN   C   CR16   0  -0.156  -5.0435   0.3058   1.4759
 03L  CAO   C   CR16   0  -0.254  -4.2449   1.8061  -0.7174
 03L  CAP   C   CR6    0  -0.013  -3.7065   0.3679   1.1193
 03L  CAQ   C   CH2    0  -0.364   0.8214  -0.4460   0.5884
 03L  NAR   N   NH1    0  -0.599   2.0531  -0.0087  -0.0221
 03L  CAT   C   C      0   0.399   4.6461   2.4450   0.8910
 03L  CAU   C   C      0   0.515   3.2695  -0.2123   0.5142
 03L  CAV   C   CR6    0  -0.051  -5.9694   1.0156   0.7268
 03L  CAW   C   CR6    0  -0.099   0.1888  -2.3354  -0.9519
 03L  CAX   C   CR6    0  -0.090  -3.2885   1.1072   0.0118
 03L  CAY   C   CR6    0  -0.220  -1.2203  -0.4170  -0.9420
 03L  CAZ   C   CR6    0  -0.117   5.0859   1.4454  -0.1692
 03L  CBA   C   CR6    0  -0.070   4.4018   0.2448  -0.3615
 03L  CBB   C   CR6    0   0.206  -0.0878  -1.0653  -0.4400
 03L  HAF   H   HCR6   0   0.253   7.4145   1.0985  -2.6225
 03L  HAG   H   HCR6   0   0.256   6.1837  -1.0293  -2.9522
 03L  HAH   H   HCR6   0   0.276  -2.4025  -2.7797  -3.0593
 03L  HAI   H   HCR6   0   0.286  -0.3843  -3.9520  -2.2369
 03L  HAJ   H   HCR6   0   0.274  -2.9132  -0.5045  -2.2618
 03L  HAK   H   HCR6   0   0.248   6.7028   2.6631  -0.8519
 03L  HAL   H   HCR6   0   0.246   4.2632  -1.5683  -1.5075
 03L  HAM   H   HCR6   0   0.293  -6.3124   2.3248  -0.9442
 03L  HAN   H   HCR6   0   0.307  -5.3550  -0.2760   2.3322
 03L  HAO   H   HCR6   0   0.292  -3.9359   2.3799  -1.5808
 03L  HAQ   H   HCH2   0   0.275   1.0618  -1.1806   1.3554
 03L  HAQA  H   HCH2   0   0.268   0.3180   0.3804   1.0923
 03L  HNAR  H   HNH1   0   0.396   1.9856   0.6163  -0.8091
 03L  SAS   S   S2     0   0.092  -1.5907   1.2534  -0.4440
 03L  CLAF  CL  CL     0  -0.084  -2.5648  -0.4942   2.0775
 03L  CLAE  CL  CL     0  -0.110   1.5958  -3.1910  -0.4062
 03L  CLAD  CL  CL     0  -0.104  -7.6352   0.9478   1.1755

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
 03L  OAA  CAT   deloc     1.245  0.020  1.245
 03L  OAB  CAU   double    1.221  0.020  1.221
 03L  OAC  CAT   deloc     1.245  0.020  1.245
 03L  CAV  CLAD  single    1.726  0.020  1.726
 03L  CAW  CLAE  single    1.735  0.020  1.735
 03L  CAG  CAF   aromatic  1.388  0.020  1.388
 03L  CAK  CAF   aromatic  1.387  0.020  1.387
 03L  CAF  HAF   single    0.930  0.020  1.080
 03L  CAP  CLAF  single    1.722  0.020  1.722
 03L  CAL  CAG   aromatic  1.387  0.020  1.387
 03L  CAG  HAG   single    0.930  0.020  1.080
 03L  CAH  CAI   aromatic  1.387  0.020  1.387
 03L  CAH  CAJ   aromatic  1.382  0.020  1.382
 03L  CAH  HAH   single    0.930  0.020  1.080
 03L  CAI  CAW   aromatic  1.383  0.020  1.383
 03L  CAI  HAI   single    0.930  0.020  1.080
 03L  CAJ  CAY   aromatic  1.392  0.020  1.392
 03L  CAJ  HAJ   single    0.930  0.020  1.080
 03L  CAZ  CAK   aromatic  1.393  0.020  1.393
 03L  CAK  HAK   single    0.930  0.020  1.080
 03L  CBA  CAL   aromatic  1.393  0.020  1.393
 03L  CAL  HAL   single    0.930  0.020  1.080
 03L  CAO  CAM   aromatic  1.385  0.020  1.385
 03L  CAM  CAV   aromatic  1.385  0.020  1.385
 03L  CAM  HAM   single    0.930  0.020  1.080
 03L  CAP  CAN   aromatic  1.385  0.020  1.385
 03L  CAV  CAN   aromatic  1.386  0.020  1.386
 03L  CAN  HAN   single    0.930  0.020  1.080
 03L  CAO  CAX   aromatic  1.391  0.020  1.391
 03L  CAO  HAO   single    0.930  0.020  1.080
 03L  CAX  CAP   aromatic  1.396  0.020  1.396
 03L  CBB  CAQ   single    1.506  0.020  1.506
 03L  CAQ  NAR   single    1.443  0.020  1.443
 03L  CAQ  HAQ   single    0.970  0.020  1.090
 03L  CAQ  HAQA  single    0.970  0.020  1.090
 03L  NAR  CAU   single    1.345  0.020  1.345
 03L  NAR  HNAR  single    0.860  0.020  1.020
 03L  CAY  SAS   single    1.782  0.020  1.782
 03L  SAS  CAX   single    1.764  0.020  1.764
 03L  CAT  CAZ   single    1.522  0.020  1.522
 03L  CAU  CBA   single    1.503  0.020  1.503
 03L  CAW  CBB   aromatic  1.397  0.020  1.397
 03L  CAY  CBB   aromatic  1.398  0.020  1.398
 03L  CBA  CAZ   aromatic  1.395  0.020  1.395

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
 03L  HAF   CAF  CAK   120.07  3.000
 03L  HAF   CAF  CAG   120.14  3.000
 03L  CAK   CAF  CAG   119.79  3.000
 03L  HAG   CAG  CAL   119.97  3.000
 03L  HAG   CAG  CAF   120.43  3.000
 03L  CAL   CAG  CAF   119.60  3.000
 03L  HAH   CAH  CAJ   120.15  3.000
 03L  HAH   CAH  CAI   119.80  3.000
 03L  CAJ   CAH  CAI   120.04  3.000
 03L  HAI   CAI  CAW   120.33  3.000
 03L  HAI   CAI  CAH   120.60  3.000
 03L  CAW   CAI  CAH   119.07  3.000
 03L  HAJ   CAJ  CAY   120.00  3.000
 03L  HAJ   CAJ  CAH   119.88  3.000
 03L  CAY   CAJ  CAH   120.12  3.000
 03L  HAK   CAK  CAZ   118.83  3.000
 03L  HAK   CAK  CAF   119.86  3.000
 03L  CAZ   CAK  CAF   121.31  3.000
 03L  HAL   CAL  CBA   119.90  3.000
 03L  HAL   CAL  CAG   119.59  3.000
 03L  CBA   CAL  CAG   120.51  3.000
 03L  HAM   CAM  CAV   120.94  3.000
 03L  HAM   CAM  CAO   120.25  3.000
 03L  CAV   CAM  CAO   118.81  3.000
 03L  HAN   CAN  CAV   120.74  3.000
 03L  HAN   CAN  CAP   120.41  3.000
 03L  CAV   CAN  CAP   118.85  3.000
 03L  HAO   CAO  CAX   119.24  3.000
 03L  HAO   CAO  CAM   119.42  3.000
 03L  CAX   CAO  CAM   121.34  3.000
 03L  CAX   CAP  CAN   121.14  3.000
 03L  CAX   CAP  CLAF  120.54  3.000
 03L  CAN   CAP  CLAF  118.31  3.000
 03L  HAQA  CAQ  HAQ   106.71  3.000
 03L  HAQA  CAQ  CBB   110.38  3.000
 03L  HAQ   CAQ  CBB   109.68  3.000
 03L  HAQA  CAQ  NAR   111.09  3.000
 03L  HAQ   CAQ  NAR   108.31  3.000
 03L  CBB   CAQ  NAR   110.56  3.000
 03L  HNAR  NAR  CAU   117.79  3.000
 03L  HNAR  NAR  CAQ   117.49  3.000
 03L  CAU   NAR  CAQ   123.89  3.000
 03L  CAZ   CAT  OAC   116.92  3.000
 03L  CAZ   CAT  OAA   115.96  3.000
 03L  OAC   CAT  OAA   127.12  3.000
 03L  CBA   CAU  NAR   113.77  3.000
 03L  CBA   CAU  OAB   121.57  3.000
 03L  NAR   CAU  OAB   124.02  3.000
 03L  CAN   CAV  CAM   121.40  3.000
 03L  CAN   CAV  CLAD  118.94  3.000
 03L  CAM   CAV  CLAD  119.66  3.000
 03L  CBB   CAW  CAI   122.68  3.000
 03L  CBB   CAW  CLAE  119.58  3.000
 03L  CAI   CAW  CLAE  117.73  3.000
 03L  SAS   CAX  CAP   122.49  3.000
 03L  SAS   CAX  CAO   118.99  3.000
 03L  CAP   CAX  CAO   118.44  3.000
 03L  CBB   CAY  SAS   120.18  3.000
 03L  CBB   CAY  CAJ   121.28  3.000
 03L  SAS   CAY  CAJ   118.48  3.000
 03L  CBA   CAZ  CAT   121.30  3.000
 03L  CBA   CAZ  CAK   118.51  3.000
 03L  CAT   CAZ  CAK   120.17  3.000
 03L  CAZ   CBA  CAU   123.44  3.000
 03L  CAZ   CBA  CAL   120.28  3.000
 03L  CAU   CBA  CAL   116.20  3.000
 03L  CAY   CBB  CAW   116.77  3.000
 03L  CAY   CBB  CAQ   122.93  3.000
 03L  CAW   CBB  CAQ   120.30  3.000
 03L  CAY   SAS  CAX   101.22  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
 03L  CONST_01  CBA  CAL  CAG  CAF      0.00   0.0  0
 03L  CONST_02  CBA  CAZ  CAK  CAF      0.00   0.0  0
 03L  CONST_03  CAZ  CAK  CAF  CAG      0.00   0.0  0
 03L  CONST_04  CAZ  CBA  CAL  CAG      0.00   0.0  0
 03L  CONST_05  CBB  CAW  CAI  CAH      0.00   0.0  0
 03L  CONST_06  CBB  CAY  CAJ  CAH      0.00   0.0  0
 03L  CONST_07  CAY  CAJ  CAH  CAI      0.00   0.0  0
 03L  CONST_08  CAY  CBB  CAW  CAI      0.00   0.0  0
 03L  CONST_09  CAW  CAI  CAH  CAJ      0.00   0.0  0
 03L  CONST_10  CAW  CBB  CAY  CAJ      0.00   0.0  0
 03L  CONST_11  CAL  CAG  CAF  CAK      0.00   0.0  0
 03L  CONST_12  CAL  CBA  CAZ  CAK      0.00   0.0  0
 03L  CONST_13  CAP  CAX  CAO  CAM      0.00   0.0  0
 03L  CONST_14  CAP  CAN  CAV  CAM      0.00   0.0  0
 03L  CONST_15  CAO  CAX  CAP  CAN      0.00   0.0  0
 03L  CONST_16  CAO  CAM  CAV  CAN      0.00   0.0  0
 03L  CONST_17  CAX  CAO  CAM  CAV      0.00   0.0  0
 03L  CONST_18  CAX  CAP  CAN  CAV      0.00   0.0  0
 03L  CONST_19  CAO  CAM  CAV  CLAD   180.00   0.0  0
 03L  CONST_20  CAP  CAN  CAV  CLAD   180.00   0.0  0
 03L  CONST_21  CAH  CAI  CAW  CLAE   180.00   0.0  0
 03L  CONST_22  CAY  CBB  CAW  CLAE   180.00   0.0  0
 03L  CONST_23  CAT  CAZ  CAK  CAF    180.00   0.0  0
 03L  CONST_24  CAV  CAN  CAP  CLAF   180.00   0.0  0
 03L  CONST_25  CAO  CAX  CAP  CLAF   180.00   0.0  0
 03L  CONST_26  CAU  CBA  CAL  CAG    180.00   0.0  0
 03L  CONST_27  SAS  CAY  CAJ  CAH    180.00   0.0  0
 03L  CONST_28  CAQ  CBB  CAW  CAI    180.00   0.0  0
 03L  CONST_29  CAQ  CBB  CAY  CAJ    180.00   0.0  0
 03L  CONST_30  CAU  CBA  CAZ  CAK    180.00   0.0  0
 03L  CONST_31  CAT  CAZ  CBA  CAL    180.00   0.0  0
 03L  CONST_32  SAS  CAX  CAO  CAM    180.00   0.0  0
 03L  CONST_33  SAS  CAX  CAP  CAN    180.00   0.0  0
 03L  CONST_34  CAW  CBB  CAY  SAS    180.00   0.0  0
 03L  CONST_35  HAL  CAL  CAG  CAF    180.00   0.0  0
 03L  CONST_36  HAK  CAK  CAF  CAG    180.00   0.0  0
 03L  CONST_37  HAJ  CAJ  CAH  CAI    180.00   0.0  0
 03L  CONST_38  HAI  CAI  CAH  CAJ    180.00   0.0  0
 03L  CONST_39  HAG  CAG  CAF  CAK    180.00   0.0  0
 03L  CONST_40  HAF  CAF  CAG  CAL    180.00   0.0  0
 03L  CONST_41  HAN  CAN  CAV  CAM    180.00   0.0  0
 03L  CONST_42  HAM  CAM  CAV  CAN    180.00   0.0  0
 03L  CONST_43  HAO  CAO  CAX  CAP    180.00   0.0  0
 03L  CONST_44  HAH  CAH  CAI  CAW    180.00   0.0  0
 03L  CONST_45  CBA  CAU  NAR  CAQ    180.00   0.0  0
 03L  CONST_47  CAQ  NAR  CAU  OAB      0.00   0.0  0
 03L  Var_01    CBB  CAY  SAS  CAX   -130.49  30.0  1
 03L  Var_02    CAK  CAZ  CAT  OAA    172.23  30.0  2
 03L  Var_03    CAL  CBA  CAU  OAB     88.89  30.0  2
 03L  Var_04    CAW  CBB  CAQ  NAR     73.79  30.0  1
 03L  Var_05    CBB  CAQ  NAR  CAU   -136.13  30.0  2

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
 03L  plan-1  CAF   0.020
 03L  plan-1  CAG   0.020
 03L  plan-1  CAK   0.020
 03L  plan-1  CAL   0.020
 03L  plan-1  CAT   0.020
 03L  plan-1  CAU   0.020
 03L  plan-1  CAZ   0.020
 03L  plan-1  CBA   0.020
 03L  plan-1  HAF   0.020
 03L  plan-1  HAG   0.020
 03L  plan-1  HAK   0.020
 03L  plan-1  HAL   0.020
 03L  plan-2  CAH   0.020
 03L  plan-2  CAI   0.020
 03L  plan-2  CAJ   0.020
 03L  plan-2  CAQ   0.020
 03L  plan-2  CAW   0.020
 03L  plan-2  CAY   0.020
 03L  plan-2  CBB   0.020
 03L  plan-2  HAH   0.020
 03L  plan-2  HAI   0.020
 03L  plan-2  HAJ   0.020
 03L  plan-2  SAS   0.020
 03L  plan-2  CLAE  0.020
 03L  plan-3  CAM   0.020
 03L  plan-3  CAN   0.020
 03L  plan-3  CAO   0.020
 03L  plan-3  CAP   0.020
 03L  plan-3  CAV   0.020
 03L  plan-3  CAX   0.020
 03L  plan-3  HAM   0.020
 03L  plan-3  HAN   0.020
 03L  plan-3  HAO   0.020
 03L  plan-3  SAS   0.020
 03L  plan-3  CLAF  0.020
 03L  plan-3  CLAD  0.020
 03L  plan-4  OAB   0.020
 03L  plan-4  CAQ   0.020
 03L  plan-4  NAR   0.020
 03L  plan-4  CAU   0.020
 03L  plan-4  CBA   0.020
 03L  plan-4  HNAR  0.020
 03L  plan-5  OAA   0.020
 03L  plan-5  OAC   0.020
 03L  plan-5  CAT   0.020
 03L  plan-5  CAZ   0.020

