# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 06:11:52 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5-(2-chlorophenyl)-N-[5-(cyclopropylcarbamoyl)-2-methylphenyl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1NC(=O)c2sc(cc2)c3ccccc3Cl)C(=O)NC4CC4
#
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
 1M8  1M8  5-(2-chlorophenyl)-N-[5-(cyclopropylcarbamoyl)-2-methylphenyl]thiophene-2-carboxamide  ligand  47  28  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1M8
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
 1M8  C1   C   CR16  0  -0.301   3.0128   0.2672  -0.3346
 1M8  C2   C   CR6   0  -0.051   4.3467   0.5861  -0.5625
 1M8  C3   C   CR16  0  -0.295   4.7248   1.9250  -0.6041
 1M8  C4   C   CR16  0  -0.291   3.7813   2.9177  -0.3978
 1M8  C5   C   CR6   0   0.062   2.4510   2.6155  -0.1290
 1M8  C6   C   CR6   0   0.334   2.0773   1.2661  -0.1043
 1M8  C7   C   CH3   0  -0.750   1.4511   3.7032   0.1209
 1M8  N8   N   NH1   0  -0.776   0.7258   0.9459   0.1182
 1M8  C9   C   C     0   0.542   5.2989  -0.5418  -0.8071
 1M8  N10  N   NH1   0  -0.662   6.5981  -0.2870  -0.5736
 1M8  O11  O   O     0  -0.484   4.9028  -1.6332  -1.1911
 1M8  C12  C   CH1   0  -0.077   7.6165  -1.2532  -0.8230
 1M8  C13  C   CH2   0  -0.517   8.7846  -1.2884   0.1065
 1M8  C14  C   CH2   0  -0.483   7.7836  -2.4031   0.1191
 1M8  C15  C   C     0   0.545   0.2833  -0.0166   0.9704
 1M8  C16  C   CR5   0  -0.340  -1.1785  -0.2091   1.0183
 1M8  C17  C   CR15  0  -0.163  -1.8343  -0.9337   1.9757
 1M8  C18  C   CR15  0  -0.189  -3.2314  -0.9660   1.7838
 1M8  C19  C   CR5   0  -0.207  -3.6349  -0.2681   0.6778
 1M8  S20  S   S2    0   0.263  -2.2865   0.4210  -0.1389
 1M8  O21  O   O     0  -0.450   1.0224  -0.6896   1.6657
 1M8  C22  C   CR6   0   0.187  -4.9846  -0.0327   0.1583
 1M8  C23  C   CR16  0  -0.314  -5.3894   1.2716  -0.1386
 1M8  C24  C   CR16  0  -0.227  -6.6526   1.5413  -0.6363
 1M8  C25  C   CR16  0  -0.267  -7.5464   0.5013  -0.8468
 1M8  C26  C   CR16  0  -0.190  -7.1707  -0.8026  -0.5641
 1M8  C27  C   CR6   0  -0.118  -5.9019  -1.0623  -0.0686
 1M8  CL1  CL  CL    0  -0.118  -5.4707  -2.7131   0.2247
 1M8  H1   H   HCR6  0   0.268   2.7057  -0.7687  -0.3470
 1M8  H2   H   HCR6  0   0.258   5.7429   2.2181  -0.8255
 1M8  H3   H   HCR6  0   0.261   4.0861   3.9557  -0.4430
 1M8  H4   H   HCH3  0   0.255   0.6905   3.7489  -0.6625
 1M8  H5   H   HCH3  0   0.257   0.9296   3.5592   1.0686
 1M8  H6   H   HCH3  0   0.265   1.9374   4.6761   0.1524
 1M8  H7   H   HNH1  0   0.409   0.0503   1.5742  -0.2900
 1M8  H8   H   HNH1  0   0.409   6.8799   0.6182  -0.2355
 1M8  H9   H   HCH1  0   0.269   7.8162  -1.4456  -1.8725
 1M8  H10  H   HCH2  0   0.260   9.7605  -1.4702  -0.3234
 1M8  H11  H   HCH2  0   0.259   8.7858  -0.6020   0.9444
 1M8  H12  H   HCH2  0   0.256   7.1065  -2.4609   0.9613
 1M8  H13  H   HCH2  0   0.256   8.0662  -3.3597  -0.3002
 1M8  H14  H   HCR5  0   0.279  -1.3285  -1.4161   2.7993
 1M8  H15  H   HCR5  0   0.274  -3.9151  -1.4724   2.4487
 1M8  H16  H   HCR6  0   0.270  -4.7014   2.0878   0.0422
 1M8  H17  H   HCR6  0   0.271  -6.9393   2.5615  -0.8510
 1M8  H18  H   HCR6  0   0.274  -8.5369   0.6992  -1.2337
 1M8  H19  H   HCR6  0   0.285  -7.8601  -1.6183  -0.7341

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
 1M8  C4   C3   aromatic  1.385  0.020  1.385
 1M8  C4   C5   aromatic  1.390  0.020  1.390
 1M8  C3   C2   aromatic  1.392  0.020  1.392
 1M8  C14  C13  single    1.498  0.020  1.498
 1M8  C14  C12  single    1.496  0.020  1.496
 1M8  C7   C5   single    1.498  0.020  1.498
 1M8  C5   C6   aromatic  1.400  0.020  1.400
 1M8  N10  C12  single    1.426  0.020  1.426
 1M8  N10  C9   single    1.344  0.020  1.344
 1M8  C13  C12  single    1.493  0.020  1.493
 1M8  C2   C9   single    1.496  0.020  1.496
 1M8  C2   C1   aromatic  1.390  0.020  1.390
 1M8  C9   O11  double    1.223  0.020  1.223
 1M8  C6   C1   aromatic  1.388  0.020  1.388
 1M8  C6   N8   single    1.407  0.020  1.407
 1M8  N8   C15  single    1.360  0.020  1.360
 1M8  C15  O21  double    1.218  0.020  1.218
 1M8  C15  C16  single    1.475  0.020  1.475
 1M8  C17  C16  aromatic  1.368  0.020  1.368
 1M8  C17  C18  aromatic  1.411  0.020  1.411
 1M8  C16  S20  aromatic  1.722  0.020  1.722
 1M8  C18  C19  aromatic  1.369  0.020  1.369
 1M8  S20  C19  aromatic  1.720  0.020  1.720
 1M8  C19  C22  single    1.465  0.020  1.465
 1M8  C22  C23  aromatic  1.398  0.020  1.398
 1M8  C22  C27  aromatic  1.397  0.020  1.397
 1M8  C23  C24  aromatic  1.384  0.020  1.384
 1M8  CL1  C27  single    1.731  0.020  1.731
 1M8  C27  C26  aromatic  1.387  0.020  1.387
 1M8  C24  C25  aromatic  1.387  0.020  1.387
 1M8  C26  C25  aromatic  1.386  0.020  1.386
 1M8  C1   H1   single    0.930  0.020  1.080
 1M8  C3   H2   single    0.930  0.020  1.080
 1M8  C4   H3   single    0.930  0.020  1.080
 1M8  C7   H4   single    0.970  0.020  1.090
 1M8  C7   H5   single    0.970  0.020  1.090
 1M8  C7   H6   single    0.970  0.020  1.090
 1M8  N8   H7   single    0.860  0.020  1.020
 1M8  N10  H8   single    0.860  0.020  1.020
 1M8  C12  H9   single    0.970  0.020  1.090
 1M8  C13  H10  single    0.970  0.020  1.090
 1M8  C13  H11  single    0.970  0.020  1.090
 1M8  C14  H12  single    0.970  0.020  1.090
 1M8  C14  H13  single    0.970  0.020  1.090
 1M8  C17  H14  single    0.930  0.020  1.080
 1M8  C18  H15  single    0.930  0.020  1.080
 1M8  C23  H16  single    0.930  0.020  1.080
 1M8  C24  H17  single    0.930  0.020  1.080
 1M8  C25  H18  single    0.930  0.020  1.080
 1M8  C26  H19  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
 1M8  H1   C1   C6   120.02  3.000
 1M8  H1   C1   C2   119.39  3.000
 1M8  C6   C1   C2   120.59  3.000
 1M8  C9   C2   C3   123.19  3.000
 1M8  C9   C2   C1   117.68  3.000
 1M8  C3   C2   C1   119.09  3.000
 1M8  H2   C3   C4   118.51  3.000
 1M8  H2   C3   C2   121.47  3.000
 1M8  C4   C3   C2   119.99  3.000
 1M8  H3   C4   C5   119.07  3.000
 1M8  H3   C4   C3   119.28  3.000
 1M8  C5   C4   C3   121.66  3.000
 1M8  C7   C5   C6   121.23  3.000
 1M8  C6   C5   C4   117.91  3.000
 1M8  C7   C5   C4   120.86  3.000
 1M8  N8   C6   C5   118.59  3.000
 1M8  N8   C6   C1   120.67  3.000
 1M8  C5   C6   C1   120.71  3.000
 1M8  H6   C7   H5   107.85  3.000
 1M8  H6   C7   H4   107.12  3.000
 1M8  H5   C7   H4   107.18  3.000
 1M8  H6   C7   C5   110.83  3.000
 1M8  H5   C7   C5   111.59  3.000
 1M8  H4   C7   C5   112.04  3.000
 1M8  H7   N8   C15  118.47  3.000
 1M8  H7   N8   C6   115.95  3.000
 1M8  C15  N8   C6   124.96  3.000
 1M8  O11  C9   N10  122.46  3.000
 1M8  O11  C9   C2   121.19  3.000
 1M8  N10  C9   C2   116.35  3.000
 1M8  H8   N10  C12  117.92  3.000
 1M8  H8   N10  C9   119.95  3.000
 1M8  C12  N10  C9   122.10  3.000
 1M8  H9   C12  C14  116.88  3.000
 1M8  H9   C12  C13  116.98  3.000
 1M8  C14  C12  C13   60.16  3.000
 1M8  H9   C12  N10  114.88  3.000
 1M8  C13  C12  N10  117.76  3.000
 1M8  C14  C12  N10  119.37  3.000
 1M8  H11  C13  H10  114.39  3.000
 1M8  H11  C13  C14  117.75  3.000
 1M8  H10  C13  C14  118.75  3.000
 1M8  H11  C13  C12  117.87  3.000
 1M8  H10  C13  C12  117.54  3.000
 1M8  C14  C13  C12   60.01  3.000
 1M8  H13  C14  H12  114.70  3.000
 1M8  H13  C14  C13  118.69  3.000
 1M8  H12  C14  C13  117.67  3.000
 1M8  H13  C14  C12  117.69  3.000
 1M8  H12  C14  C12  117.47  3.000
 1M8  C13  C14  C12   59.83  3.000
 1M8  O21  C15  C16  120.71  3.000
 1M8  C16  C15  N8   115.80  3.000
 1M8  O21  C15  N8   123.49  3.000
 1M8  S20  C16  C17  110.84  3.000
 1M8  S20  C16  C15  124.62  3.000
 1M8  C17  C16  C15  124.53  3.000
 1M8  H14  C17  C18  123.87  3.000
 1M8  H14  C17  C16  123.07  3.000
 1M8  C18  C17  C16  113.06  3.000
 1M8  H15  C18  C19  123.37  3.000
 1M8  H15  C18  C17  123.65  3.000
 1M8  C19  C18  C17  112.97  3.000
 1M8  C22  C19  S20  119.30  3.000
 1M8  C22  C19  C18  129.79  3.000
 1M8  S20  C19  C18  110.91  3.000
 1M8  C19  S20  C16   92.22  3.000
 1M8  C27  C22  C23  117.58  3.000
 1M8  C27  C22  C19  122.95  3.000
 1M8  C23  C22  C19  119.47  3.000
 1M8  H16  C23  C24  119.54  3.000
 1M8  H16  C23  C22  118.95  3.000
 1M8  C24  C23  C22  121.50  3.000
 1M8  H17  C24  C25  120.42  3.000
 1M8  H17  C24  C23  119.81  3.000
 1M8  C25  C24  C23  119.77  3.000
 1M8  H18  C25  C26  119.56  3.000
 1M8  H18  C25  C24  120.47  3.000
 1M8  C26  C25  C24  119.97  3.000
 1M8  H19  C26  C27  119.88  3.000
 1M8  H19  C26  C25  120.31  3.000
 1M8  C27  C26  C25  119.81  3.000
 1M8  CL1  C27  C26  117.84  3.000
 1M8  C26  C27  C22  121.37  3.000
 1M8  CL1  C27  C22  120.77  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
 1M8  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 1M8  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 1M8  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 1M8  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 1M8  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 1M8  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 1M8  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 1M8  CONST_08  C18  C19  S20  C16     0.00   0.0  0
 1M8  CONST_09  C22  C19  S20  C16   180.00   0.0  0
 1M8  CONST_10  C19  S20  C16  C17     0.00   0.0  0
 1M8  CONST_11  S20  C19  C18  C17     0.00   0.0  0
 1M8  CONST_12  C22  C19  C18  C17   180.00   0.0  0
 1M8  CONST_13  S20  C16  C17  C18     0.00   0.0  0
 1M8  CONST_16  C24  C23  C22  C19   180.00   0.0  0
 1M8  CONST_17  C26  C27  C22  C19   180.00   0.0  0
 1M8  CONST_20  C25  C24  C23  C22     0.00   0.0  0
 1M8  CONST_21  C25  C26  C27  C22     0.00   0.0  0
 1M8  CONST_22  C26  C27  C22  C23     0.00   0.0  0
 1M8  CONST_23  C26  C25  C24  C23     0.00   0.0  0
 1M8  CONST_24  C27  C22  C23  C24     0.00   0.0  0
 1M8  CONST_25  C27  C26  C25  C24     0.00   0.0  0
 1M8  CONST_26  C7   C5   C6   C1    180.00   0.0  0
 1M8  CONST_27  N8   C6   C1   C2    180.00   0.0  0
 1M8  CONST_28  C7   C5   C4   C3    180.00   0.0  0
 1M8  CONST_29  C9   C2   C3   C4    180.00   0.0  0
 1M8  CONST_30  N8   C6   C5   C4    180.00   0.0  0
 1M8  CONST_31  C9   C2   C1   C6    180.00   0.0  0
 1M8  CONST_32  C18  C17  C16  C15   180.00   0.0  0
 1M8  CONST_33  C19  S20  C16  C15   180.00   0.0  0
 1M8  CONST_34  CL1  C27  C22  C19     0.00   0.0  0
 1M8  CONST_35  CL1  C27  C22  C23   180.00   0.0  0
 1M8  CONST_36  CL1  C27  C26  C25   180.00   0.0  0
 1M8  CONST_37  H2   C3   C2   C1    180.00   0.0  0
 1M8  CONST_38  H3   C4   C3   C2    180.00   0.0  0
 1M8  CONST_39  H1   C1   C2   C3    180.00   0.0  0
 1M8  CONST_40  H15  C18  C17  C16   180.00   0.0  0
 1M8  CONST_41  H14  C17  C18  C19   180.00   0.0  0
 1M8  CONST_42  H16  C23  C22  C19     0.00   0.0  0
 1M8  CONST_43  H17  C24  C23  C22   180.00   0.0  0
 1M8  CONST_44  H19  C26  C27  C22   180.00   0.0  0
 1M8  CONST_45  H18  C25  C24  C23   180.00   0.0  0
 1M8  CONST_46  C12  N10  C9   C2    180.00   0.0  0
 1M8  CONST_47  C16  C15  N8   C6    180.00   0.0  0
 1M8  CONST_51  O21  C15  N8   C6      0.00   0.0  0
 1M8  CONST_52  C12  N10  C9   O11     0.00   0.0  0
 1M8  CONST_53  H8   N10  C9   C2      0.00   0.0  0
 1M8  Var_01    C13  C14  C12  N10  -107.06  30.0  1
 1M8  Var_02    H10  C13  C14  C12  -106.99  30.0  1
 1M8  Var_03    N10  C9   C2   C1   -158.05  30.0  2
 1M8  Var_04    C17  C16  C15  N8   -167.07  30.0  2
 1M8  Var_05    C14  C12  N10  C9    -75.17  30.0  3
 1M8  Var_06    H4   C7   C5   C4    114.16  30.0  2

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
 1M8  chir_01  C12  C14  N10  C13  both

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
 1M8  plan-1  C15  0.020
 1M8  plan-1  C16  0.020
 1M8  plan-1  C17  0.020
 1M8  plan-1  C18  0.020
 1M8  plan-1  C19  0.020
 1M8  plan-1  S20  0.020
 1M8  plan-1  C22  0.020
 1M8  plan-1  H14  0.020
 1M8  plan-1  H15  0.020
 1M8  plan-2  C1   0.020
 1M8  plan-2  C2   0.020
 1M8  plan-2  C3   0.020
 1M8  plan-2  C4   0.020
 1M8  plan-2  C5   0.020
 1M8  plan-2  C6   0.020
 1M8  plan-2  C7   0.020
 1M8  plan-2  N8   0.020
 1M8  plan-2  C9   0.020
 1M8  plan-2  H1   0.020
 1M8  plan-2  H2   0.020
 1M8  plan-2  H3   0.020
 1M8  plan-3  C19  0.020
 1M8  plan-3  C22  0.020
 1M8  plan-3  C23  0.020
 1M8  plan-3  C24  0.020
 1M8  plan-3  C25  0.020
 1M8  plan-3  C26  0.020
 1M8  plan-3  C27  0.020
 1M8  plan-3  CL1  0.020
 1M8  plan-3  H16  0.020
 1M8  plan-3  H17  0.020
 1M8  plan-3  H18  0.020
 1M8  plan-3  H19  0.020
 1M8  plan-4  C6   0.020
 1M8  plan-4  N8   0.020
 1M8  plan-4  C15  0.020
 1M8  plan-4  C16  0.020
 1M8  plan-4  O21  0.020
 1M8  plan-4  H7   0.020
 1M8  plan-5  C2   0.020
 1M8  plan-5  C9   0.020
 1M8  plan-5  N10  0.020
 1M8  plan-5  O11  0.020
 1M8  plan-5  C12  0.020
 1M8  plan-5  H8   0.020

