# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:43:26 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: (2S)-2-[4-(thiophene-2-carbonyl)phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C(O)=O)c1ccc(cc1)C(=O)c2sccc2
#
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
 M5A  M5A  '(2S)-2-[4-(thiophene-2-carbonyl)phenyl]propanoic acid'  ligand  29  18  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M5A
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
 M5A  O2   O  O      0  -0.398  -2.2053  -2.5237   0.0816
 M5A  C9   C  C      0   0.364  -1.9618  -1.3331   0.0021
 M5A  C10  C  CR5    0  -0.315  -3.0564  -0.3570   0.0964
 M5A  C11  C  CR15   0  -0.185  -4.3912  -0.6386  -0.0532
 M5A  C12  C  CR15   0  -0.178  -5.2188   0.4820   0.1718
 M5A  C13  C  CR15   0  -0.446  -4.5022   1.5959   0.5100
 M5A  S    S  S2     0   0.257  -2.8265   1.2961   0.5366
 M5A  C4   C  CR6    0  -0.065  -0.5703  -0.8490  -0.1610
 M5A  C6   C  CR16   0  -0.265   0.4664  -1.5409   0.4733
 M5A  C2   C  CR16   0  -0.287   1.7773  -1.1373   0.3195
 M5A  C7   C  CR16   0  -0.265  -0.2492   0.2284  -0.9825
 M5A  C3   C  CR16   0  -0.326   1.0757   0.6064  -1.1540
 M5A  C1   C  CR6    0   0.220   2.1101  -0.0562  -0.5026
 M5A  C    C  CH1    0  -0.500   3.5406   0.3430  -0.7181
 M5A  C5   C  CH3    0  -0.648   4.3332  -0.7827  -1.3859
 M5A  C8   C  C      0   0.438   4.2311   0.8478   0.5789
 M5A  O    O  OC    -1  -0.609   5.4624   1.0214   0.5027
 M5A  O1   O  O      0  -0.595   3.5078   1.0676   1.5672
 M5A  H1   H  HCR5   0   0.278  -4.7589  -1.6178  -0.3242
 M5A  H2   H  HCR5   0   0.276  -6.2959   0.4669   0.0945
 M5A  H3   H  HCR5   0   0.308  -4.8806   2.5794   0.7436
 M5A  H4   H  HCR6   0   0.257   0.2378  -2.3866   1.1095
 M5A  H5   H  HCR6   0   0.248   2.5575  -1.6769   0.8415
 M5A  H6   H  HCR6   0   0.266  -1.0188   0.7541  -1.5329
 M5A  H7   H  HCR6   0   0.251   1.3044   1.4340  -1.8149
 M5A  H8   H  HCH1   0   0.249   3.5434   1.1938  -1.4113
 M5A  H9   H  HCH3   0   0.217   4.4062  -1.6616  -0.7429
 M5A  H10  H  HCH3   0   0.220   3.8607  -1.0933  -2.3188
 M5A  H11  H  HCH3   0   0.231   5.3445  -0.4521  -1.6136

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
 M5A  O1   C8   deloc     1.244  0.020  1.244
 M5A  C8   O    deloc     1.246  0.020  1.246
 M5A  C8   C    single    1.554  0.020  1.554
 M5A  O2   C9   double    1.218  0.020  1.218
 M5A  C3   C7   aromatic  1.388  0.020  1.388
 M5A  C3   C1   aromatic  1.390  0.020  1.390
 M5A  C7   C4   aromatic  1.392  0.020  1.392
 M5A  C    C1   single    1.501  0.020  1.501
 M5A  C    C5   single    1.530  0.020  1.530
 M5A  C1   C2   aromatic  1.398  0.020  1.398
 M5A  C9   C4   single    1.482  0.020  1.482
 M5A  C9   C10  single    1.470  0.020  1.470
 M5A  C4   C6   aromatic  1.398  0.020  1.398
 M5A  C2   C6   aromatic  1.380  0.020  1.380
 M5A  S    C10  aromatic  1.726  0.020  1.726
 M5A  S    C13  aromatic  1.703  0.020  1.703
 M5A  C10  C11  aromatic  1.372  0.020  1.372
 M5A  C11  C12  aromatic  1.411  0.020  1.411
 M5A  C13  C12  aromatic  1.367  0.020  1.367
 M5A  C11  H1   single    0.930  0.020  1.080
 M5A  C12  H2   single    0.930  0.020  1.080
 M5A  C13  H3   single    0.930  0.020  1.080
 M5A  C6   H4   single    0.930  0.020  1.080
 M5A  C2   H5   single    0.930  0.020  1.080
 M5A  C7   H6   single    0.930  0.020  1.080
 M5A  C3   H7   single    0.930  0.020  1.080
 M5A  C    H8   single    0.970  0.020  1.090
 M5A  C5   H9   single    0.970  0.020  1.090
 M5A  C5   H10  single    0.970  0.020  1.090
 M5A  C5   H11  single    0.970  0.020  1.090

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
 M5A  C4   C9   C10  119.30  3.000
 M5A  C10  C9   O2   119.75  3.000
 M5A  C4   C9   O2   120.94  3.000
 M5A  S    C10  C11  110.73  3.000
 M5A  C11  C10  C9   125.53  3.000
 M5A  S    C10  C9   123.59  3.000
 M5A  H1   C11  C12  124.06  3.000
 M5A  H1   C11  C10  122.98  3.000
 M5A  C12  C11  C10  112.96  3.000
 M5A  H2   C12  C13  123.50  3.000
 M5A  H2   C12  C11  124.22  3.000
 M5A  C13  C12  C11  112.28  3.000
 M5A  H3   C13  S    120.15  3.000
 M5A  H3   C13  C12  127.75  3.000
 M5A  S    C13  C12  112.10  3.000
 M5A  C13  S    C10   91.92  3.000
 M5A  C7   C4   C6   118.66  3.000
 M5A  C6   C4   C9   118.97  3.000
 M5A  C7   C4   C9   122.28  3.000
 M5A  H4   C6   C2   119.63  3.000
 M5A  H4   C6   C4   119.77  3.000
 M5A  C2   C6   C4   120.58  3.000
 M5A  H5   C2   C1   119.82  3.000
 M5A  H5   C2   C6   119.00  3.000
 M5A  C1   C2   C6   121.17  3.000
 M5A  H6   C7   C3   118.91  3.000
 M5A  H6   C7   C4   120.79  3.000
 M5A  C3   C7   C4   120.24  3.000
 M5A  H7   C3   C1   119.52  3.000
 M5A  H7   C3   C7   118.99  3.000
 M5A  C1   C3   C7   121.49  3.000
 M5A  C    C1   C3   121.01  3.000
 M5A  C    C1   C2   121.13  3.000
 M5A  C3   C1   C2   117.83  3.000
 M5A  H8   C    C8   105.92  3.000
 M5A  H8   C    C5   107.06  3.000
 M5A  C8   C    C5   111.91  3.000
 M5A  H8   C    C1   107.42  3.000
 M5A  C5   C    C1   111.14  3.000
 M5A  C8   C    C1   112.97  3.000
 M5A  H11  C5   H10  108.07  3.000
 M5A  H11  C5   H9   107.81  3.000
 M5A  H10  C5   H9   107.67  3.000
 M5A  H11  C5   C    110.44  3.000
 M5A  H10  C5   C    111.00  3.000
 M5A  H9   C5   C    111.71  3.000
 M5A  O1   C8   O    126.76  3.000
 M5A  O    C8   C    115.69  3.000
 M5A  O1   C8   C    117.52  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
 M5A  CONST_01  C12  C13  S    C10    0.00   0.0  0
 M5A  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 M5A  CONST_03  C13  S    C10  C11    0.00   0.0  0
 M5A  CONST_04  S    C13  C12  C11    0.00   0.0  0
 M5A  CONST_05  S    C10  C11  C12    0.00   0.0  0
 M5A  CONST_06  C1   C3   C7   C4     0.00   0.0  0
 M5A  CONST_07  C1   C2   C6   C4     0.00   0.0  0
 M5A  CONST_08  C3   C7   C4   C6     0.00   0.0  0
 M5A  CONST_09  C3   C1   C2   C6     0.00   0.0  0
 M5A  CONST_10  C7   C3   C1   C2     0.00   0.0  0
 M5A  CONST_11  C7   C4   C6   C2     0.00   0.0  0
 M5A  CONST_12  C3   C7   C4   C9   180.00   0.0  0
 M5A  CONST_13  C2   C6   C4   C9   180.00   0.0  0
 M5A  CONST_14  C13  S    C10  C9   180.00   0.0  0
 M5A  CONST_15  C12  C11  C10  C9   180.00   0.0  0
 M5A  CONST_16  C    C1   C2   C6   180.00   0.0  0
 M5A  CONST_17  C    C1   C3   C7   180.00   0.0  0
 M5A  CONST_18  H3   C13  S    C10  180.00   0.0  0
 M5A  CONST_19  H2   C12  C11  C10  180.00   0.0  0
 M5A  CONST_20  H1   C11  C12  C13  180.00   0.0  0
 M5A  CONST_21  H7   C3   C7   C4   180.00   0.0  0
 M5A  CONST_22  H5   C2   C6   C4   180.00   0.0  0
 M5A  CONST_23  H6   C7   C4   C6   180.00   0.0  0
 M5A  CONST_24  H4   C6   C4   C7   180.00   0.0  0
 M5A  Var_01    C7   C4   C9   C10  -39.89  30.0  2
 M5A  Var_02    C4   C9   C10  C11  164.44  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
 M5A  chir_01  C  C8  C1  C5  positiv

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
 M5A  plan-1  C9   0.020
 M5A  plan-1  C10  0.020
 M5A  plan-1  C11  0.020
 M5A  plan-1  C12  0.020
 M5A  plan-1  C13  0.020
 M5A  plan-1  S    0.020
 M5A  plan-1  H1   0.020
 M5A  plan-1  H2   0.020
 M5A  plan-1  H3   0.020
 M5A  plan-2  C9   0.020
 M5A  plan-2  C4   0.020
 M5A  plan-2  C6   0.020
 M5A  plan-2  C2   0.020
 M5A  plan-2  C7   0.020
 M5A  plan-2  C3   0.020
 M5A  plan-2  C1   0.020
 M5A  plan-2  C    0.020
 M5A  plan-2  H4   0.020
 M5A  plan-2  H5   0.020
 M5A  plan-2  H6   0.020
 M5A  plan-2  H7   0.020
 M5A  plan-3  O2   0.020
 M5A  plan-3  C9   0.020
 M5A  plan-3  C10  0.020
 M5A  plan-3  C4   0.020
 M5A  plan-4  C    0.020
 M5A  plan-4  C8   0.020
 M5A  plan-4  O    0.020
 M5A  plan-4  O1   0.020

