# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:14:44 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 2-hydroxy-5-(methylsulfanyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccc(O)c(c1)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
 3R6  3R6  '2-hydroxy-5-(methylsulfanyl)benzoic acid'  ligand  19  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3R6
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
 3R6  C01  C  CH3    0  -0.755   3.8415  -0.1627   0.5277
 3R6  S02  S  S2     0  -0.037   2.9864  -0.3920  -1.0556
 3R6  C03  C  CR6    0  -0.148   1.4002   0.3067  -0.6953
 3R6  C04  C  CR16   0  -0.226   1.1784   1.6777  -0.8442
 3R6  C05  C  CR16   0  -0.348  -0.0624   2.2265  -0.5874
 3R6  C06  C  CR6    0   0.360  -1.1247   1.4100  -0.1808
 3R6  O07  O  OH1    0  -0.651  -2.3141   1.9455   0.0572
 3R6  C08  C  CR6    0  -0.273  -0.9141   0.0237  -0.0329
 3R6  C09  C  CR16   0  -0.268   0.3457  -0.5017  -0.2936
 3R6  C10  C  C      0   0.495  -2.0496  -0.8678   0.4012
 3R6  O11  O  OC    -1  -0.548  -1.8565  -2.0788   0.5243
 3R6  O12  O  O      0  -0.632  -3.1560  -0.2756   0.6126
 3R6  H1   H  HCH3   0   0.264   3.3452  -0.7150   1.3232
 3R6  H2   H  HCH3   0   0.269   4.8529  -0.5485   0.4076
 3R6  H3   H  HCH3   0   0.263   3.8968   0.8915   0.7918
 3R6  H4   H  HCR6   0   0.261   1.9893   2.3208  -1.1640
 3R6  H5   H  HCR6   0   0.256  -0.2244   3.2911  -0.7042
 3R6  H6   H  HOH1   0   0.461  -2.8872   1.1319   0.3313
 3R6  H7   H  HCR6   0   0.256   0.4989  -1.5676  -0.1790

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
 3R6  O12  C10  deloc     1.273  0.020  1.273
 3R6  O11  C10  deloc     1.233  0.020  1.233
 3R6  C10  C08  single    1.507  0.020  1.507
 3R6  C09  C08  aromatic  1.390  0.020  1.390
 3R6  C09  C03  aromatic  1.388  0.020  1.388
 3R6  C08  C06  aromatic  1.410  0.020  1.410
 3R6  S02  C03  single    1.770  0.020  1.770
 3R6  S02  C01  single    1.814  0.020  1.814
 3R6  C03  C04  aromatic  1.397  0.020  1.397
 3R6  C06  O07  single    1.326  0.020  1.326
 3R6  C06  C05  aromatic  1.400  0.020  1.400
 3R6  C04  C05  aromatic  1.381  0.020  1.381
 3R6  C01  H1   single    0.970  0.020  1.090
 3R6  C01  H2   single    0.970  0.020  1.090
 3R6  C01  H3   single    0.970  0.020  1.090
 3R6  C04  H4   single    0.930  0.020  1.080
 3R6  C05  H5   single    0.930  0.020  1.080
 3R6  O07  H6   single    0.850  0.020  0.980
 3R6  C09  H7   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
 3R6  H3   C01  H2   108.83  3.000
 3R6  H3   C01  H1   109.72  3.000
 3R6  H2   C01  H1   108.93  3.000
 3R6  H3   C01  S02  110.99  3.000
 3R6  H2   C01  S02  107.26  3.000
 3R6  H1   C01  S02  111.03  3.000
 3R6  C03  S02  C01  101.23  3.000
 3R6  C09  C03  C04  118.81  3.000
 3R6  C04  C03  S02  120.53  3.000
 3R6  C09  C03  S02  120.64  3.000
 3R6  H4   C04  C05  119.44  3.000
 3R6  H4   C04  C03  119.69  3.000
 3R6  C05  C04  C03  120.86  3.000
 3R6  H5   C05  C06  119.40  3.000
 3R6  H5   C05  C04  120.33  3.000
 3R6  C06  C05  C04  120.26  3.000
 3R6  C08  C06  O07  120.81  3.000
 3R6  O07  C06  C05  119.82  3.000
 3R6  C08  C06  C05  119.37  3.000
 3R6  H6   O07  C06  103.14  3.000
 3R6  C10  C08  C09  120.88  3.000
 3R6  C09  C08  C06  119.17  3.000
 3R6  C10  C08  C06  119.94  3.000
 3R6  H7   C09  C08  118.72  3.000
 3R6  H7   C09  C03  119.77  3.000
 3R6  C08  C09  C03  121.52  3.000
 3R6  O12  C10  O11  125.23  3.000
 3R6  O11  C10  C08  119.46  3.000
 3R6  O12  C10  C08  115.31  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
 3R6  CONST_01  C06  C08  C09  C03    0.00   0.0  0
 3R6  CONST_02  C06  C05  C04  C03    0.00   0.0  0
 3R6  CONST_03  C08  C09  C03  C04    0.00   0.0  0
 3R6  CONST_04  C08  C06  C05  C04    0.00   0.0  0
 3R6  CONST_05  C09  C08  C06  C05    0.00   0.0  0
 3R6  CONST_06  C09  C03  C04  C05    0.00   0.0  0
 3R6  CONST_07  C08  C09  C03  S02  180.00   0.0  0
 3R6  CONST_08  C05  C04  C03  S02  180.00   0.0  0
 3R6  CONST_09  C10  C08  C09  C03  180.00   0.0  0
 3R6  CONST_10  O07  C06  C05  C04  180.00   0.0  0
 3R6  CONST_11  C10  C08  C06  C05  180.00   0.0  0
 3R6  CONST_12  C09  C08  C06  O07  180.00   0.0  0
 3R6  CONST_13  H5   C05  C04  C03  180.00   0.0  0
 3R6  CONST_14  H7   C09  C03  C04  180.00   0.0  0
 3R6  CONST_15  H4   C04  C05  C06  180.00   0.0  0
 3R6  Var_01    C09  C03  S02  C01  -95.43  30.0  2
 3R6  Var_02    O12  C10  C08  C06   -0.16  30.0  2
 3R6  Var_03    H1   C01  S02  C03   62.20  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
 3R6  plan-1  S02  0.020
 3R6  plan-1  C03  0.020
 3R6  plan-1  C04  0.020
 3R6  plan-1  C05  0.020
 3R6  plan-1  C06  0.020
 3R6  plan-1  O07  0.020
 3R6  plan-1  C08  0.020
 3R6  plan-1  C09  0.020
 3R6  plan-1  C10  0.020
 3R6  plan-1  H4   0.020
 3R6  plan-1  H5   0.020
 3R6  plan-1  H7   0.020
 3R6  plan-2  C08  0.020
 3R6  plan-2  C10  0.020
 3R6  plan-2  O11  0.020
 3R6  plan-2  O12  0.020

