# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 00:23:02 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: naphthalene-1-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Sc1cccc2ccccc12
#
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
 2XH  2XH  'naphthalene-1-thiol      '  ligand  19  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2XH
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
 2XH  C14  C  CR16  0  -0.247   1.9315  -1.8351   0.0009
 2XH  C5   C  CR16  0  -0.257   2.8830  -0.7967   0.0164
 2XH  C6   C  CR16  0  -0.310   2.4687   0.5065   0.0331
 2XH  C11  C  CR66  0   0.110   1.0924   0.8324   0.0258
 2XH  C7   C  CR16  0  -0.316   0.6643   2.1802   0.0672
 2XH  C8   C  CR16  0  -0.254  -0.6669   2.4845   0.0608
 2XH  C9   C  CR16  0  -0.245  -1.6287   1.4570  -0.0094
 2XH  C10  C  CR6   0  -0.225  -1.2498   0.1390  -0.0456
 2XH  C12  C  CR66  0   0.198   0.1307  -0.2145  -0.0091
 2XH  C13  C  CR16  0  -0.330   0.5917  -1.5511  -0.0103
 2XH  SAH  S  S2    0  -0.192  -2.5369  -1.0813  -0.0304
 2XH  H1   H  HCR6  0   0.262   2.2618  -2.8657   0.0026
 2XH  H2   H  HCR6  0   0.261   3.9392  -1.0320   0.0218
 2XH  H3   H  HCR6  0   0.260   3.1929   1.3116   0.0540
 2XH  H4   H  HCR6  0   0.261   1.4086   2.9658   0.1047
 2XH  H5   H  HCR6  0   0.264  -0.9948   3.5151   0.0943
 2XH  H6   H  HCR6  0   0.271  -2.6792   1.7155  -0.0431
 2XH  H7   H  HCR6  0   0.252  -0.1224  -2.3631  -0.0076
 2XH  H8   H  HSH1  0   0.238  -2.1329  -1.8207  -1.0720

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
 2XH  C8   C9   aromatic  1.409  0.020  1.409
 2XH  C8   C7   aromatic  1.366  0.020  1.366
 2XH  C9   C10  aromatic  1.372  0.020  1.372
 2XH  C7   C11  aromatic  1.415  0.020  1.415
 2XH  C10  SAH  single    1.774  0.020  1.774
 2XH  C10  C12  aromatic  1.426  0.020  1.426
 2XH  C11  C12  aromatic  1.422  0.020  1.422
 2XH  C11  C6   aromatic  1.414  0.020  1.414
 2XH  C12  C13  aromatic  1.414  0.020  1.414
 2XH  C6   C5   aromatic  1.368  0.020  1.368
 2XH  C13  C14  aromatic  1.370  0.020  1.370
 2XH  C5   C14  aromatic  1.408  0.020  1.408
 2XH  C14  H1   single    0.930  0.020  1.080
 2XH  C5   H2   single    0.930  0.020  1.080
 2XH  C6   H3   single    0.930  0.020  1.080
 2XH  C7   H4   single    0.930  0.020  1.080
 2XH  C8   H5   single    0.930  0.020  1.080
 2XH  C9   H6   single    0.930  0.020  1.080
 2XH  C13  H7   single    0.930  0.020  1.080
 2XH  SAH  H8   single    1.200  0.020  1.300

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
 2XH  H1   C14  C13  119.74  3.000
 2XH  H1   C14  C5   119.72  3.000
 2XH  C13  C14  C5   120.54  3.000
 2XH  H2   C5   C6   120.19  3.000
 2XH  H2   C5   C14  119.94  3.000
 2XH  C6   C5   C14  119.87  3.000
 2XH  H3   C6   C11  118.66  3.000
 2XH  H3   C6   C5   120.40  3.000
 2XH  C11  C6   C5   120.95  3.000
 2XH  C12  C11  C7   119.83  3.000
 2XH  C12  C11  C6   119.25  3.000
 2XH  C7   C11  C6   120.91  3.000
 2XH  H4   C7   C8   120.57  3.000
 2XH  H4   C7   C11  118.96  3.000
 2XH  C8   C7   C11  120.47  3.000
 2XH  H5   C8   C9   119.29  3.000
 2XH  H5   C8   C7   120.50  3.000
 2XH  C9   C8   C7   120.20  3.000
 2XH  H6   C9   C10  119.78  3.000
 2XH  H6   C9   C8   119.33  3.000
 2XH  C10  C9   C8   120.89  3.000
 2XH  SAH  C10  C12  122.13  3.000
 2XH  C12  C10  C9   120.34  3.000
 2XH  SAH  C10  C9   117.41  3.000
 2XH  C13  C12  C10  123.38  3.000
 2XH  C13  C12  C11  118.39  3.000
 2XH  C10  C12  C11  118.23  3.000
 2XH  H7   C13  C12  119.64  3.000
 2XH  H7   C13  C14  119.36  3.000
 2XH  C12  C13  C14  120.99  3.000
 2XH  H8   SAH  C10   98.87  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
 2XH  CONST_01  C10  C12  C13  C14  180.00  0.0  0
 2XH  CONST_02  C11  C12  C13  C14    0.00  0.0  0
 2XH  CONST_03  C11  C6   C5   C14    0.00  0.0  0
 2XH  CONST_04  C7   C11  C6   C5   180.00  0.0  0
 2XH  CONST_05  C12  C11  C6   C5     0.00  0.0  0
 2XH  CONST_06  C12  C13  C14  C5     0.00  0.0  0
 2XH  CONST_07  C8   C7   C11  C6   180.00  0.0  0
 2XH  CONST_08  C10  C12  C11  C6   180.00  0.0  0
 2XH  CONST_09  C13  C12  C11  C6     0.00  0.0  0
 2XH  CONST_10  C13  C14  C5   C6     0.00  0.0  0
 2XH  CONST_11  C9   C8   C7   C11    0.00  0.0  0
 2XH  CONST_12  C9   C10  C12  C11    0.00  0.0  0
 2XH  CONST_13  C10  C9   C8   C7     0.00  0.0  0
 2XH  CONST_14  C10  C12  C11  C7     0.00  0.0  0
 2XH  CONST_15  C13  C12  C11  C7   180.00  0.0  0
 2XH  CONST_16  C12  C10  C9   C8     0.00  0.0  0
 2XH  CONST_17  C12  C11  C7   C8     0.00  0.0  0
 2XH  CONST_18  C13  C12  C10  C9   180.00  0.0  0
 2XH  CONST_19  SAH  C10  C12  C11  180.00  0.0  0
 2XH  CONST_20  SAH  C10  C9   C8   180.00  0.0  0
 2XH  CONST_21  SAH  C10  C12  C13    0.00  0.0  0
 2XH  CONST_22  H3   C6   C5   C14  180.00  0.0  0
 2XH  CONST_23  H7   C13  C14  C5   180.00  0.0  0
 2XH  CONST_24  H4   C7   C11  C6     0.00  0.0  0
 2XH  CONST_25  H1   C14  C5   C6   180.00  0.0  0
 2XH  CONST_26  H5   C8   C7   C11  180.00  0.0  0
 2XH  CONST_27  H2   C5   C6   C11  180.00  0.0  0
 2XH  CONST_28  H6   C9   C8   C7   180.00  0.0  0

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
 2XH  plan-1  C14  0.020
 2XH  plan-1  C5   0.020
 2XH  plan-1  C6   0.020
 2XH  plan-1  C11  0.020
 2XH  plan-1  C7   0.020
 2XH  plan-1  C8   0.020
 2XH  plan-1  C9   0.020
 2XH  plan-1  C10  0.020
 2XH  plan-1  C12  0.020
 2XH  plan-1  C13  0.020
 2XH  plan-1  SAH  0.020
 2XH  plan-1  H1   0.020
 2XH  plan-1  H2   0.020
 2XH  plan-1  H3   0.020
 2XH  plan-1  H4   0.020
 2XH  plan-1  H5   0.020
 2XH  plan-1  H6   0.020
 2XH  plan-1  H7   0.020

