# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:11:06 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2S)-2-[6-(methylsulfanyl)naphthalen-2-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccc2cc(ccc2c1)[C@H](C)C(O)=O
#
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
 T1N  T1N  '(2S)-2-[6-(methylsulfanyl)naphthalen-2-yl]propanoic acid'  ligand  30  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T1N
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
 T1N  CAA   C  CH3    0  -0.796   5.7219   0.7887  -0.3157
 T1N  CAB   C  CH3    0  -0.646  -3.9623   0.3277   1.8134
 T1N  OAD   O  O      0  -0.596  -3.7408  -0.4776  -1.7108
 T1N  CAE   C  CR16   0  -0.261   2.7316   1.2594  -0.1241
 T1N  CAF   C  CR16   0  -0.284  -1.6297  -1.1928   0.4029
 T1N  CAG   C  CR16   0  -0.301   1.4200   1.6504  -0.0819
 T1N  CAH   C  CR16   0  -0.312  -0.3275  -1.5982   0.3612
 T1N  CAI   C  CR16   0  -0.334   2.0756  -1.0423   0.1484
 T1N  CAJ   C  CR16   0  -0.421  -0.9848   1.0953   0.1345
 T1N  SAK   S  S2     0   0.035   4.7359  -0.6940  -0.0382
 T1N  CAL   C  C      0   0.431  -4.3186  -0.0476  -0.6954
 T1N  CAM   C  CR6    0  -0.119   3.0734  -0.1068  -0.0076
 T1N  CAN   C  CR6    0   0.219  -1.9880   0.1769   0.2918
 T1N  CAO   C  CR66   0   0.108   0.7206  -0.6571   0.1968
 T1N  CAP   C  CR66   0   0.133   0.3778   0.7128   0.0797
 T1N  CAQ   C  CH1    0  -0.497  -3.4283   0.5888   0.4051
 T1N  HAA   H  HCH3   0   0.274   5.6066   1.5103   0.4904
 T1N  HAAA  H  HCH3   0   0.295   6.7572   0.4538  -0.3349
 T1N  HAAB  H  HCH3   0   0.275   5.4918   1.2569  -1.2708
 T1N  HAB   H  HCH3   0   0.214  -3.9514  -0.7365   2.0581
 T1N  HABA  H  HCH3   0   0.216  -3.3617   0.8451   2.5631
 T1N  HABB  H  HCH3   0   0.227  -4.9893   0.6757   1.9067
 T1N  HAE   H  HCR6   0   0.264   3.4990   2.0109  -0.2425
 T1N  HAF   H  HCR6   0   0.242  -2.4088  -1.9351   0.5254
 T1N  HAG   H  HCR6   0   0.254   1.1763   2.7024  -0.1720
 T1N  HAH   H  HCR6   0   0.246  -0.0817  -2.6500   0.4494
 T1N  HAI   H  HCR6   0   0.256   2.3192  -2.0956   0.2388
 T1N  HAJ   H  HCR6   0   0.239  -1.2259   2.1501   0.0502
 T1N  HAQ   H  HCH1   0   0.247  -3.4746   1.6732   0.2369
 T1N  OAC   O  OC    -1  -0.609  -5.5475  -0.0409  -0.4868

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
 T1N  SAK  CAA   single    1.802  0.020  1.802
 T1N  CAA  HAA   single    0.970  0.020  1.090
 T1N  CAA  HAAA  single    0.970  0.020  1.090
 T1N  CAA  HAAB  single    0.970  0.020  1.090
 T1N  CAB  CAQ   single    1.529  0.020  1.529
 T1N  CAB  HAB   single    0.970  0.020  1.090
 T1N  CAB  HABA  single    0.970  0.020  1.090
 T1N  CAB  HABB  single    0.970  0.020  1.090
 T1N  CAL  OAC   deloc     1.247  0.020  1.247
 T1N  OAD  CAL   deloc     1.245  0.020  1.245
 T1N  CAG  CAE   aromatic  1.369  0.020  1.369
 T1N  CAE  CAM   aromatic  1.413  0.020  1.413
 T1N  CAE  HAE   single    0.930  0.020  1.080
 T1N  CAN  CAF   aromatic  1.420  0.020  1.420
 T1N  CAF  CAH   aromatic  1.365  0.020  1.365
 T1N  CAF  HAF   single    0.930  0.020  1.080
 T1N  CAP  CAG   aromatic  1.411  0.020  1.411
 T1N  CAG  HAG   single    0.930  0.020  1.080
 T1N  CAH  CAO   aromatic  1.418  0.020  1.418
 T1N  CAH  HAH   single    0.930  0.020  1.080
 T1N  CAO  CAI   aromatic  1.410  0.020  1.410
 T1N  CAI  CAM   aromatic  1.377  0.020  1.377
 T1N  CAI  HAI   single    0.930  0.020  1.080
 T1N  CAN  CAJ   aromatic  1.369  0.020  1.369
 T1N  CAJ  CAP   aromatic  1.416  0.020  1.416
 T1N  CAJ  HAJ   single    0.930  0.020  1.080
 T1N  CAM  SAK   single    1.763  0.020  1.763
 T1N  CAQ  CAL   single    1.552  0.020  1.552
 T1N  CAQ  CAN   single    1.502  0.020  1.502
 T1N  CAP  CAO   aromatic  1.417  0.020  1.417
 T1N  CAQ  HAQ   single    0.970  0.020  1.090

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
 T1N  HAAB  CAA  HAAA  108.54  3.000
 T1N  HAAB  CAA  HAA   110.03  3.000
 T1N  HAAA  CAA  HAA   108.54  3.000
 T1N  HAAB  CAA  SAK   111.93  3.000
 T1N  HAAA  CAA  SAK   105.66  3.000
 T1N  HAA   CAA  SAK   111.94  3.000
 T1N  HABB  CAB  HABA  107.99  3.000
 T1N  HABB  CAB  HAB   107.56  3.000
 T1N  HABA  CAB  HAB   107.62  3.000
 T1N  HABB  CAB  CAQ   110.73  3.000
 T1N  HABA  CAB  CAQ   111.09  3.000
 T1N  HAB   CAB  CAQ   111.68  3.000
 T1N  HAE   CAE  CAM   120.64  3.000
 T1N  HAE   CAE  CAG   119.01  3.000
 T1N  CAM   CAE  CAG   120.34  3.000
 T1N  HAF   CAF  CAN   119.23  3.000
 T1N  HAF   CAF  CAH   119.10  3.000
 T1N  CAN   CAF  CAH   121.67  3.000
 T1N  HAG   CAG  CAP   119.24  3.000
 T1N  HAG   CAG  CAE   119.35  3.000
 T1N  CAP   CAG  CAE   121.41  3.000
 T1N  HAH   CAH  CAO   119.07  3.000
 T1N  HAH   CAH  CAF   120.16  3.000
 T1N  CAO   CAH  CAF   120.77  3.000
 T1N  HAI   CAI  CAO   118.58  3.000
 T1N  HAI   CAI  CAM   120.43  3.000
 T1N  CAO   CAI  CAM   121.00  3.000
 T1N  HAJ   CAJ  CAP   118.24  3.000
 T1N  HAJ   CAJ  CAN   119.87  3.000
 T1N  CAP   CAJ  CAN   121.88  3.000
 T1N  CAM   SAK  CAA   104.15  3.000
 T1N  CAQ   CAL  OAD   116.98  3.000
 T1N  CAQ   CAL  OAC   116.40  3.000
 T1N  OAD   CAL  OAC   126.58  3.000
 T1N  SAK   CAM  CAI   117.33  3.000
 T1N  SAK   CAM  CAE   123.27  3.000
 T1N  CAI   CAM  CAE   119.41  3.000
 T1N  CAQ   CAN  CAJ   121.82  3.000
 T1N  CAQ   CAN  CAF   120.03  3.000
 T1N  CAJ   CAN  CAF   118.10  3.000
 T1N  CAP   CAO  CAI   119.60  3.000
 T1N  CAP   CAO  CAH   118.19  3.000
 T1N  CAI   CAO  CAH   122.21  3.000
 T1N  CAO   CAP  CAJ   119.38  3.000
 T1N  CAO   CAP  CAG   118.24  3.000
 T1N  CAJ   CAP  CAG   122.38  3.000
 T1N  HAQ   CAQ  CAN   107.43  3.000
 T1N  HAQ   CAQ  CAL   105.79  3.000
 T1N  CAN   CAQ  CAL   112.58  3.000
 T1N  HAQ   CAQ  CAB   107.16  3.000
 T1N  CAN   CAQ  CAB   110.95  3.000
 T1N  CAL   CAQ  CAB   112.51  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
 T1N  CONST_01  CAJ  CAP  CAG  CAE  180.00   0.0  0
 T1N  CONST_02  CAO  CAP  CAG  CAE    0.00   0.0  0
 T1N  CONST_03  CAO  CAI  CAM  CAE    0.00   0.0  0
 T1N  CONST_04  CAP  CAJ  CAN  CAF    0.00   0.0  0
 T1N  CONST_05  CAI  CAO  CAH  CAF  180.00   0.0  0
 T1N  CONST_06  CAP  CAO  CAH  CAF    0.00   0.0  0
 T1N  CONST_07  CAI  CAM  CAE  CAG    0.00   0.0  0
 T1N  CONST_08  CAN  CAJ  CAP  CAG  180.00   0.0  0
 T1N  CONST_09  CAH  CAO  CAP  CAG  180.00   0.0  0
 T1N  CONST_10  CAI  CAO  CAP  CAG    0.00   0.0  0
 T1N  CONST_11  CAJ  CAN  CAF  CAH    0.00   0.0  0
 T1N  CONST_12  CAM  CAI  CAO  CAH  180.00   0.0  0
 T1N  CONST_13  CAJ  CAP  CAO  CAH    0.00   0.0  0
 T1N  CONST_14  CAJ  CAP  CAO  CAI  180.00   0.0  0
 T1N  CONST_15  CAP  CAG  CAE  CAM    0.00   0.0  0
 T1N  CONST_16  CAP  CAO  CAI  CAM    0.00   0.0  0
 T1N  CONST_17  CAO  CAH  CAF  CAN    0.00   0.0  0
 T1N  CONST_18  CAO  CAP  CAJ  CAN    0.00   0.0  0
 T1N  CONST_19  SAK  CAM  CAE  CAG  180.00   0.0  0
 T1N  CONST_20  CAQ  CAN  CAF  CAH  180.00   0.0  0
 T1N  CONST_21  CAO  CAI  CAM  SAK  180.00   0.0  0
 T1N  CONST_22  CAQ  CAN  CAJ  CAP  180.00   0.0  0
 T1N  CONST_23  HAI  CAI  CAM  CAE  180.00   0.0  0
 T1N  CONST_24  HAJ  CAJ  CAN  CAF  180.00   0.0  0
 T1N  CONST_25  HAH  CAH  CAO  CAI    0.00   0.0  0
 T1N  CONST_26  HAE  CAE  CAM  CAI  180.00   0.0  0
 T1N  CONST_27  HAF  CAF  CAN  CAJ  180.00   0.0  0
 T1N  CONST_28  HAG  CAG  CAP  CAJ    0.00   0.0  0
 T1N  Var_01    CAE  CAM  SAK  CAA   -2.57  30.0  1
 T1N  Var_02    HAA  CAA  SAK  CAM   61.80  30.0  3

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
 T1N  chir_01  CAQ  CAB  CAL  CAN  positiv

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
 T1N  plan-1  CAE  0.020
 T1N  plan-1  CAF  0.020
 T1N  plan-1  CAG  0.020
 T1N  plan-1  CAH  0.020
 T1N  plan-1  CAI  0.020
 T1N  plan-1  CAJ  0.020
 T1N  plan-1  SAK  0.020
 T1N  plan-1  CAM  0.020
 T1N  plan-1  CAN  0.020
 T1N  plan-1  CAO  0.020
 T1N  plan-1  CAP  0.020
 T1N  plan-1  CAQ  0.020
 T1N  plan-1  HAE  0.020
 T1N  plan-1  HAF  0.020
 T1N  plan-1  HAG  0.020
 T1N  plan-1  HAH  0.020
 T1N  plan-1  HAI  0.020
 T1N  plan-1  HAJ  0.020
 T1N  plan-2  OAD  0.020
 T1N  plan-2  CAL  0.020
 T1N  plan-2  CAQ  0.020
 T1N  plan-2  OAC  0.020

