# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:09:14 2022
#   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  29  17  .  2022-08-10  2022-08-10
;
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  -0.667   7.0050  -16.8556  101.1142
 MH5  C4   C  CR15   0  -0.227   7.4893  -20.2166  100.0698
 MH5  C5   C  CR5    0  -0.147   7.3339  -19.3193  101.0817
 MH5  C6   C  CH2    0  -0.402   6.3809  -18.1605  101.1264
 MH5  C7   C  CR6    0   0.361   7.6628  -16.3503  102.2241
 MH5  C8   C  CR16   0  -0.350   8.6695  -15.3918  102.0489
 MH5  C10  C  CR16   0  -0.334   8.9605  -15.2110  104.4372
 MH5  C2   C  CR5    0  -0.163   9.1106  -21.0251  101.5290
 MH5  C3   C  CR15   0  -0.214   8.4983  -21.1883  100.3241
 MH5  S1   S  S2     0   0.189   8.4405  -19.6686  102.3636
 MH5  C9   C  CR16   0  -0.233   9.3028  -14.8324  103.1459
 MH5  C11  C  CR6    0  -0.092   7.9661  -16.1655  104.6326
 MH5  C12  C  CR16   0  -0.370   7.3293  -16.7248  103.5296
 MH5  O1   O  O      0  -0.587   6.6857  -17.4818  106.1237
 MH5  O2   O  OC    -1  -0.589   8.1621  -16.0494  106.9858
 MH5  H1   H  HNH1   0   0.371   7.4819  -16.6646  100.2457
 MH5  H2   H  HCR5   0   0.257   6.8971  -20.1855   99.1647
 MH5  H5   H  HCH2   0   0.278   5.7401  -18.2311  100.2463
 MH5  H6   H  HCH2   0   0.261   5.7139  -18.2352  101.9860
 MH5  H7   H  HCR6   0   0.247   8.9523  -15.0883  101.0468
 MH5  H8   H  HCR6   0   0.230   9.4632  -14.7731  105.2883
 MH5  H9   H  HCH3   0   0.251   9.9169  -22.2734  103.0841
 MH5  H10  H  HCH3   0   0.254  10.4863  -22.6438  101.4587
 MH5  H11  H  HCH3   0   0.251  11.1033  -21.2318  102.3111
 MH5  H13  H  HCR5   0   0.254   8.7621  -21.9778   99.6333
 MH5  H15  H  HCR6   0   0.240  10.0794  -14.0940  102.9860
 MH5  H16  H  HCR6   0   0.249   6.5578  -17.4612  103.7130
 MH5  C13  C  C      0   0.394   7.5684  -16.6060  106.0423
 MH5  C1   C  CH3    0  -0.713  10.2105  -21.8322  102.1306

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  1.361  0.020  1.361
 MH5  C5   C6   single    1.501  0.020  1.501
 MH5  C5   S1   aromatic  1.729  0.020  1.729
 MH5  C6   N1   single    1.447  0.020  1.447
 MH5  N1   C7   single    1.386  0.020  1.386
 MH5  C2   C1   single    1.491  0.020  1.491
 MH5  C2   S1   aromatic  1.728  0.020  1.728
 MH5  C8   C7   aromatic  1.401  0.020  1.401
 MH5  C8   C9   aromatic  1.385  0.020  1.385
 MH5  C7   C12  aromatic  1.399  0.020  1.399
 MH5  C9   C10  aromatic  1.389  0.020  1.389
 MH5  C12  C11  aromatic  1.391  0.020  1.391
 MH5  C10  C11  aromatic  1.392  0.020  1.392
 MH5  C11  C13  single    1.530  0.020  1.530
 MH5  C13  O1   deloc     1.246  0.020  1.246
 MH5  C13  O2   deloc     1.246  0.020  1.246
 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

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   113.34  3.000
 MH5  H1   N1   C6   112.45  3.000
 MH5  C7   N1   C6   121.81  3.000
 MH5  H2   C4   C3   123.84  3.000
 MH5  H2   C4   C5   122.71  3.000
 MH5  C3   C4   C5   113.45  3.000
 MH5  S1   C5   C6   122.70  3.000
 MH5  S1   C5   C4   110.17  3.000
 MH5  C6   C5   C4   127.12  3.000
 MH5  H6   C6   H5   105.79  3.000
 MH5  H6   C6   C5   111.03  3.000
 MH5  H5   C6   C5   107.40  3.000
 MH5  H6   C6   N1   109.41  3.000
 MH5  H5   C6   N1   107.76  3.000
 MH5  C5   C6   N1   114.98  3.000
 MH5  C12  C7   C8   118.12  3.000
 MH5  C12  C7   N1   122.47  3.000
 MH5  C8   C7   N1   119.37  3.000
 MH5  H7   C8   C9   119.97  3.000
 MH5  H7   C8   C7   119.63  3.000
 MH5  C9   C8   C7   120.39  3.000
 MH5  H8   C10  C11  119.95  3.000
 MH5  H8   C10  C9   120.47  3.000
 MH5  C11  C10  C9   119.58  3.000
 MH5  S1   C2   C3   110.31  3.000
 MH5  S1   C2   C1   121.07  3.000
 MH5  C3   C2   C1   128.61  3.000
 MH5  H13  C3   C2   122.89  3.000
 MH5  H13  C3   C4   123.84  3.000
 MH5  C2   C3   C4   113.27  3.000
 MH5  C2   S1   C5    92.79  3.000
 MH5  H15  C9   C10  119.99  3.000
 MH5  H15  C9   C8   119.09  3.000
 MH5  C10  C9   C8   120.92  3.000
 MH5  C12  C11  C13  119.73  3.000
 MH5  C13  C11  C10  120.84  3.000
 MH5  C12  C11  C10  119.43  3.000
 MH5  H16  C12  C11  117.75  3.000
 MH5  H16  C12  C7   120.69  3.000
 MH5  C11  C12  C7   121.56  3.000
 MH5  O2   C13  O1   127.01  3.000
 MH5  O2   C13  C11  116.45  3.000
 MH5  O1   C13  C11  116.54  3.000
 MH5  H11  C1   H10  107.75  3.000
 MH5  H11  C1   H9   107.35  3.000
 MH5  H10  C1   H9   107.82  3.000
 MH5  H11  C1   C2   111.87  3.000
 MH5  H10  C1   C2   109.96  3.000
 MH5  H9   C1   C2   111.90  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  Var_01    C4   C5   C6   N1   -113.16  30.0  2
 MH5  Var_02    C7   N1   C6   C5    -73.52  30.0  3
 MH5  Var_03    O1   C13  C11  C10  -178.78  30.0  2
 MH5  Var_04    H9   C1   C2   C3   -120.81  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  C13  0.020

