# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 02:58:37 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  31  17  .  2021-08-24  2021-08-24  
;
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  -0.798   5.7158   0.8105  -0.3413
 T1N  CAB   C  CH3   0  -0.646  -4.0321   0.1997   1.7839
 T1N  OAD   O  O     0  -0.431  -3.8353  -0.7798  -1.5408
 T1N  CAE   C  CR16  0  -0.258   2.7211   1.2533  -0.1859
 T1N  CAF   C  CR16  0  -0.283  -1.6083  -1.2181   0.5040
 T1N  CAG   C  CR16  0  -0.296   1.4077   1.6348  -0.1425
 T1N  CAH   C  CR16  0  -0.308  -0.3017  -1.6105   0.4595
 T1N  CAI   C  CR16  0  -0.333   2.0908  -1.0421   0.1923
 T1N  CAJ   C  CR16  0  -0.392  -0.9865   1.0663   0.1217
 T1N  SAK   S  S2    0   0.042   4.7419  -0.6784  -0.0541
 T1N  CAL   C  C     0   0.575  -4.2342   0.0010  -0.7146
 T1N  CAM   C  CR6   0  -0.115   3.0768  -0.1047  -0.0166
 T1N  CAN   C  CR6   0   0.186  -1.9729   0.1415   0.3333
 T1N  CAO   C  CR66  0   0.117   0.7330  -0.6671   0.2405
 T1N  CAP   C  CR66  0   0.130   0.3777   0.6939   0.0704
 T1N  CAQ   C  CH1   0  -0.505  -3.4136   0.5670   0.4268
 T1N  HAA   H  HCH3  0   0.276   5.5871   1.5388   0.4566
 T1N  HAAA  H  HCH3  0   0.296   6.7541   0.4846  -0.3491
 T1N  HAAB  H  HCH3  0   0.276   5.4891   1.2659  -1.3033
 T1N  HAB   H  HCH3  0   0.235  -4.0676  -0.8797   1.9321
 T1N  HABA  H  HCH3  0   0.249  -3.4318   0.6299   2.5843
 T1N  HABB  H  HCH3  0   0.251  -5.0443   0.5881   1.8815
 T1N  HOAC  H  HOH1  0   0.481  -5.9809   0.0900  -1.4357
 T1N  HAE   H  HCR6  0   0.267   3.4803   2.0050  -0.3471
 T1N  HAF   H  HCR6  0   0.250  -2.3751  -1.9631   0.6750
 T1N  HAG   H  HCR6  0   0.259   1.1521   2.6795  -0.2733
 T1N  HAH   H  HCR6  0   0.253  -0.0440  -2.6543   0.5920
 T1N  HAI   H  HCR6  0   0.259   2.3460  -2.0878   0.3266
 T1N  HAJ   H  HCR6  0   0.252  -1.2414   2.1124  -0.0101
 T1N  HAQ   H  HCH1  0   0.302  -3.4587   1.6572   0.3305
 T1N  OAC   O  OH1   0  -0.592  -5.4741   0.4763  -0.7060

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    1.536  0.020  1.536
 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   single    1.328  0.020  1.328
 T1N  OAC  HOAC  single    0.850  0.020  0.980
 T1N  OAD  CAL   double    1.205  0.020  1.205
 T1N  CAG  CAE   aromatic  1.368  0.020  1.368
 T1N  CAE  CAM   aromatic  1.414  0.020  1.414
 T1N  CAE  HAE   single    0.930  0.020  1.080
 T1N  CAN  CAF   aromatic  1.418  0.020  1.418
 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  1.417  0.020  1.417
 T1N  CAH  HAH   single    0.930  0.020  1.080
 T1N  CAO  CAI   aromatic  1.409  0.020  1.409
 T1N  CAI  CAM   aromatic  1.376  0.020  1.376
 T1N  CAI  HAI   single    0.930  0.020  1.080
 T1N  CAN  CAJ   aromatic  1.369  0.020  1.369
 T1N  CAJ  CAP   aromatic  1.415  0.020  1.415
 T1N  CAJ  HAJ   single    0.930  0.020  1.080
 T1N  CAM  SAK   single    1.762  0.020  1.762
 T1N  CAQ  CAL   single    1.515  0.020  1.515
 T1N  CAQ  CAN   single    1.505  0.020  1.505
 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  108.53  3.000
 T1N  HAAB  CAA  HAA   110.09  3.000
 T1N  HAAA  CAA  HAA   108.57  3.000
 T1N  HAAB  CAA  SAK   111.97  3.000
 T1N  HAAA  CAA  SAK   105.62  3.000
 T1N  HAA   CAA  SAK   111.86  3.000
 T1N  HABB  CAB  HABA  107.80  3.000
 T1N  HABB  CAB  HAB   108.11  3.000
 T1N  HABA  CAB  HAB   108.01  3.000
 T1N  HABB  CAB  CAQ   111.61  3.000
 T1N  HABA  CAB  CAQ   109.44  3.000
 T1N  HAB   CAB  CAQ   111.71  3.000
 T1N  HAE   CAE  CAM   120.62  3.000
 T1N  HAE   CAE  CAG   119.02  3.000
 T1N  CAM   CAE  CAG   120.36  3.000
 T1N  HAF   CAF  CAN   119.78  3.000
 T1N  HAF   CAF  CAH   119.03  3.000
 T1N  CAN   CAF  CAH   121.19  3.000
 T1N  HAG   CAG  CAP   119.27  3.000
 T1N  HAG   CAG  CAE   119.44  3.000
 T1N  CAP   CAG  CAE   121.29  3.000
 T1N  HAH   CAH  CAO   119.12  3.000
 T1N  HAH   CAH  CAF   120.05  3.000
 T1N  CAO   CAH  CAF   120.83  3.000
 T1N  HAI   CAI  CAO   118.62  3.000
 T1N  HAI   CAI  CAM   120.45  3.000
 T1N  CAO   CAI  CAM   120.94  3.000
 T1N  HAJ   CAJ  CAP   118.42  3.000
 T1N  HAJ   CAJ  CAN   120.06  3.000
 T1N  CAP   CAJ  CAN   121.51  3.000
 T1N  CAM   SAK  CAA   104.19  3.000
 T1N  CAQ   CAL  OAD   125.40  3.000
 T1N  CAQ   CAL  OAC   111.53  3.000
 T1N  OAD   CAL  OAC   123.07  3.000
 T1N  SAK   CAM  CAI   117.29  3.000
 T1N  SAK   CAM  CAE   123.23  3.000
 T1N  CAI   CAM  CAE   119.47  3.000
 T1N  CAQ   CAN  CAJ   120.57  3.000
 T1N  CAQ   CAN  CAF   120.64  3.000
 T1N  CAJ   CAN  CAF   118.76  3.000
 T1N  CAP   CAO  CAI   119.54  3.000
 T1N  CAP   CAO  CAH   118.36  3.000
 T1N  CAI   CAO  CAH   122.10  3.000
 T1N  CAO   CAP  CAJ   119.35  3.000
 T1N  CAO   CAP  CAG   118.40  3.000
 T1N  CAJ   CAP  CAG   122.25  3.000
 T1N  HAQ   CAQ  CAN   108.38  3.000
 T1N  HAQ   CAQ  CAL   106.46  3.000
 T1N  CAN   CAQ  CAL   111.47  3.000
 T1N  HAQ   CAQ  CAB   107.40  3.000
 T1N  CAN   CAQ  CAB   111.88  3.000
 T1N  CAL   CAQ  CAB   110.98  3.000
 T1N  HOAC  OAC  CAL   109.93  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  CONST_29  HOAC  OAC  CAL  OAD    0.00   0.0  0
 T1N  Var_01    CAE   CAM  SAK  CAA   -0.11  30.0  1
 T1N  Var_02    HAA   CAA  SAK  CAM   60.97  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  HOAC  0.020
 T1N  plan-2  OAC   0.020

