# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 16:29:12 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: 3-[(5-methylthiophen-2-yl)methylamino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(CNc2cccc(c2)C(O)=O)cc1
#
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
 MH5  MH5  '3-[(5-methylthiophen-2-yl)methylamino]benzoic acid'  ligand  30  17  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MH5
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
 MH5  N1   N  NH1   0  -0.671   7.0325  -16.8942  101.1421
 MH5  C4   C  CR15  0  -0.227   7.4893  -20.2263  100.0622
 MH5  C5   C  CR5   0  -0.147   7.3273  -19.3567  101.0970
 MH5  C6   C  CH2   0  -0.409   6.3876  -18.1885  101.1610
 MH5  C7   C  CR6   0   0.382   7.6926  -16.3779  102.2335
 MH5  C8   C  CR16  0  -0.332   8.6631  -15.3815  102.0462
 MH5  C10  C  CR16  0  -0.307   9.0259  -15.2049  104.4245
 MH5  C2   C  CR5   0  -0.162   9.0831  -21.0889  101.5210
 MH5  C3   C  CR15  0  -0.215   8.4871  -21.2126  100.3030
 MH5  S1   S  S2    0   0.191   8.4133  -19.7503  102.3835
 MH5  C9   C  CR16  0  -0.232   9.3114  -14.8095  103.1241
 MH5  C11  C  CR6   0  -0.072   8.0650  -16.1916  104.6233
 MH5  C12  C  CR16  0  -0.341   7.4066  -16.7725  103.5430
 MH5  O1   O  O     0  -0.439   6.8725  -17.5235  106.1979
 MH5  O2   O  OH1   0  -0.595   8.3722  -16.0573  106.9465
 MH5  H1   H  HNH1  0   0.382   7.4632  -16.6750  100.2573
 MH5  H2   H  HCR5  0   0.261   6.9096  -20.1659   99.1505
 MH5  H5   H  HCH2  0   0.287   5.7325  -18.2435  100.2913
 MH5  H6   H  HCH2  0   0.266   5.7312  -18.2547  102.0297
 MH5  H7   H  HCR6  0   0.267   8.9052  -15.0564  101.0410
 MH5  H8   H  HCR6  0   0.260   9.5493  -14.7493  105.2522
 MH5  H9   H  HCH3  0   0.252   9.8784  -22.3476  103.0733
 MH5  H10  H  HCH3  0   0.255  10.4218  -22.7381  101.4438
 MH5  H11  H  HCH3  0   0.253  11.0781  -21.3352  102.2818
 MH5  H13  H  HCR5  0   0.257   8.7554  -21.9827   99.5924
 MH5  H15  H  HCR6  0   0.262  10.0568  -14.0448  102.9488
 MH5  H16  H  HCR6  0   0.270   6.6603  -17.5303  103.7390
 MH5  H17  H  HOH1  0   0.486   8.0950  -16.3996  107.8094
 MH5  C13  C  C     0   0.532   7.6984  -16.6688  105.9818
 MH5  C1   C  CH3   0  -0.714  10.1709  -21.9176  102.1145

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
 MH5  C4   C3   aromatic  1.424  0.020  1.424
 MH5  C4   C5   aromatic  1.361  0.020  1.361
 MH5  C3   C2   aromatic  1.362  0.020  1.362
 MH5  C5   C6   single    1.501  0.020  1.501
 MH5  C5   S1   aromatic  1.729  0.020  1.729
 MH5  C6   N1   single    1.446  0.020  1.446
 MH5  N1   C7   single    1.376  0.020  1.376
 MH5  C2   C1   single    1.491  0.020  1.491
 MH5  C2   S1   aromatic  1.728  0.020  1.728
 MH5  C8   C7   aromatic  1.403  0.020  1.403
 MH5  C8   C9   aromatic  1.382  0.020  1.382
 MH5  C7   C12  aromatic  1.397  0.020  1.397
 MH5  C9   C10  aromatic  1.389  0.020  1.389
 MH5  C12  C11  aromatic  1.392  0.020  1.392
 MH5  C10  C11  aromatic  1.392  0.020  1.392
 MH5  C11  C13  single    1.486  0.020  1.486
 MH5  C13  O1   double    1.208  0.020  1.208
 MH5  C13  O2   single    1.326  0.020  1.326
 MH5  N1   H1   single    0.890  0.020  1.040
 MH5  C4   H2   single    0.930  0.020  1.080
 MH5  C6   H5   single    0.970  0.020  1.090
 MH5  C6   H6   single    0.970  0.020  1.090
 MH5  C8   H7   single    0.930  0.020  1.080
 MH5  C10  H8   single    0.930  0.020  1.080
 MH5  C1   H9   single    0.970  0.020  1.090
 MH5  C1   H10  single    0.970  0.020  1.090
 MH5  C1   H11  single    0.970  0.020  1.090
 MH5  C3   H13  single    0.930  0.020  1.080
 MH5  C9   H15  single    0.930  0.020  1.080
 MH5  C12  H16  single    0.930  0.020  1.080
 MH5  O2   H17  single    0.850  0.020  0.980

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
 MH5  H1   N1   C7   114.18  3.000
 MH5  H1   N1   C6   113.36  3.000
 MH5  C7   N1   C6   122.64  3.000
 MH5  H2   C4   C3   123.82  3.000
 MH5  H2   C4   C5   122.76  3.000
 MH5  C3   C4   C5   113.42  3.000
 MH5  S1   C5   C6   122.60  3.000
 MH5  S1   C5   C4   110.21  3.000
 MH5  C6   C5   C4   127.17  3.000
 MH5  H6   C6   H5   105.70  3.000
 MH5  H6   C6   C5   111.32  3.000
 MH5  H5   C6   C5   107.64  3.000
 MH5  H6   C6   N1   109.45  3.000
 MH5  H5   C6   N1   107.62  3.000
 MH5  C5   C6   N1   114.64  3.000
 MH5  C12  C7   C8   117.85  3.000
 MH5  C12  C7   N1   122.63  3.000
 MH5  C8   C7   N1   119.49  3.000
 MH5  H7   C8   C9   119.64  3.000
 MH5  H7   C8   C7   119.42  3.000
 MH5  C9   C8   C7   120.95  3.000
 MH5  H8   C10  C11  121.61  3.000
 MH5  H8   C10  C9   119.86  3.000
 MH5  C11  C10  C9   118.53  3.000
 MH5  S1   C2   C3   110.32  3.000
 MH5  S1   C2   C1   120.99  3.000
 MH5  C3   C2   C1   128.68  3.000
 MH5  H13  C3   C2   122.94  3.000
 MH5  H13  C3   C4   123.78  3.000
 MH5  C2   C3   C4   113.28  3.000
 MH5  C2   S1   C5    92.78  3.000
 MH5  H15  C9   C10  119.64  3.000
 MH5  H15  C9   C8   119.29  3.000
 MH5  C10  C9   C8   121.07  3.000
 MH5  C12  C11  C13  117.32  3.000
 MH5  C13  C11  C10  121.92  3.000
 MH5  C12  C11  C10  120.77  3.000
 MH5  H16  C12  C11  118.56  3.000
 MH5  H16  C12  C7   120.60  3.000
 MH5  C11  C12  C7   120.84  3.000
 MH5  H17  O2   C13  109.86  3.000
 MH5  O2   C13  O1   122.92  3.000
 MH5  O2   C13  C11  113.06  3.000
 MH5  O1   C13  C11  124.02  3.000
 MH5  H11  C1   H10  107.77  3.000
 MH5  H11  C1   H9   107.38  3.000
 MH5  H10  C1   H9   107.83  3.000
 MH5  H11  C1   C2   111.78  3.000
 MH5  H10  C1   C2   109.98  3.000
 MH5  H9   C1   C2   111.92  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
 MH5  CONST_01  S1   C2   C3   C4      0.00   0.0  0
 MH5  CONST_02  C2   S1   C5   C4      0.00   0.0  0
 MH5  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 MH5  CONST_04  C3   C2   S1   C5      0.00   0.0  0
 MH5  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 MH5  CONST_06  C10  C11  C12  C7      0.00   0.0  0
 MH5  CONST_07  C11  C12  C7   C8      0.00   0.0  0
 MH5  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 MH5  CONST_09  S1   C5   C4   C3      0.00   0.0  0
 MH5  CONST_10  C12  C7   C8   C9      0.00   0.0  0
 MH5  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 MH5  CONST_12  C9   C8   C7   N1    180.00   0.0  0
 MH5  CONST_13  C11  C12  C7   N1    180.00   0.0  0
 MH5  CONST_14  C1   C2   C3   C4    180.00   0.0  0
 MH5  CONST_15  C1   C2   S1   C5    180.00   0.0  0
 MH5  CONST_16  C3   C4   C5   C6    180.00   0.0  0
 MH5  CONST_17  C2   S1   C5   C6    180.00   0.0  0
 MH5  CONST_18  C13  C11  C12  C7    180.00   0.0  0
 MH5  CONST_19  C9   C10  C11  C13   180.00   0.0  0
 MH5  CONST_20  H13  C3   C4   C5    180.00   0.0  0
 MH5  CONST_21  H15  C9   C8   C7    180.00   0.0  0
 MH5  CONST_22  H16  C12  C7   C8    180.00   0.0  0
 MH5  CONST_23  H8   C10  C9   C8    180.00   0.0  0
 MH5  CONST_24  H7   C8   C9   C10   180.00   0.0  0
 MH5  CONST_25  H2   C4   C3   C2    180.00   0.0  0
 MH5  CONST_28  H1   N1   C7   C8      0.00   0.0  0
 MH5  CONST_29  H17  O2   C13  C11   180.00   0.0  0
 MH5  Var_01    C4   C5   C6   N1   -110.76  30.0  2
 MH5  Var_02    C7   N1   C6   C5    -74.90  30.0  3
 MH5  Var_03    O1   C13  C11  C10  -179.88  30.0  2
 MH5  Var_04    H9   C1   C2   C3   -123.50  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
 MH5  plan-1  C4   0.020
 MH5  plan-1  C5   0.020
 MH5  plan-1  C6   0.020
 MH5  plan-1  C2   0.020
 MH5  plan-1  C3   0.020
 MH5  plan-1  S1   0.020
 MH5  plan-1  H2   0.020
 MH5  plan-1  H13  0.020
 MH5  plan-1  C1   0.020
 MH5  plan-2  N1   0.020
 MH5  plan-2  C7   0.020
 MH5  plan-2  C8   0.020
 MH5  plan-2  C10  0.020
 MH5  plan-2  C9   0.020
 MH5  plan-2  C11  0.020
 MH5  plan-2  C12  0.020
 MH5  plan-2  H7   0.020
 MH5  plan-2  H8   0.020
 MH5  plan-2  H15  0.020
 MH5  plan-2  H16  0.020
 MH5  plan-2  C13  0.020
 MH5  plan-3  N1   0.020
 MH5  plan-3  C6   0.020
 MH5  plan-3  C7   0.020
 MH5  plan-3  H1   0.020
 MH5  plan-4  C11  0.020
 MH5  plan-4  O1   0.020
 MH5  plan-4  O2   0.020
 MH5  plan-4  H17  0.020
 MH5  plan-4  C13  0.020

