# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:41:07 2021
#   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  30  18  .  2022-03-22  2022-11-17
;
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  -0.400  62.5325  28.3554  52.3200
 M5A  C9   C  C     0   0.390  62.0834  28.8205  53.3530
 M5A  C10  C  CR5   0  -0.300  62.8957  28.8242  54.5679
 M5A  C11  C  CR15  0  -0.232  62.5420  28.9797  55.8849
 M5A  C12  C  CR15  0  -0.174  63.6384  28.8339  56.7641
 M5A  C13  C  CR15  0  -0.446  64.8024  28.5687  56.0996
 M5A  S    S  S2    0   0.265  64.5786  28.4783  54.4132
 M5A  C4   C  CR6   0  -0.044  60.7061  29.3723  53.4046
 M5A  C6   C  CR16  0  -0.270  60.3918  30.5136  54.1357
 M5A  C2   C  CR16  0  -0.304  59.1026  31.0264  54.1082
 M5A  C7   C  CR16  0  -0.259  59.7090  28.7617  52.6414
 M5A  C3   C  CR16  0  -0.283  58.4219  29.2649  52.6377
 M5A  C1   C  CR6   0   0.185  58.1009  30.4075  53.3709
 M5A  C    C  CH1   0  -0.501  56.6976  30.9511  53.3993
 M5A  C5   C  CH3   0  -0.648  55.6863  29.9027  53.8876
 M5A  C8   C  C     0   0.577  56.2901  31.5058  52.0483
 M5A  O    O  OH1   0  -0.591  55.1095  32.1088  52.1106
 M5A  O1   O  O     0  -0.430  56.9363  31.4230  51.0354
 M5A  H1   H  HCR5  0   0.287  61.5313  29.1674  56.2171
 M5A  H2   H  HCR5  0   0.280  63.5687  28.9175  57.8385
 M5A  H3   H  HCR5  0   0.308  65.7831  28.4226  56.5266
 M5A  H4   H  HCR6  0   0.276  61.1516  31.0294  54.7075
 M5A  H5   H  HCR6  0   0.263  58.8777  31.9237  54.6716
 M5A  H6   H  HCR6  0   0.265  59.9376  27.8762  52.0628
 M5A  H7   H  HCR6  0   0.257  57.6632  28.7564  52.0566
 M5A  H8   H  HCH1  0   0.305  56.6672  31.7905  54.1019
 M5A  H9   H  HCH3  0   0.251  56.0054  29.5106  54.8522
 M5A  H10  H  HCH3  0   0.254  54.6962  30.3364  54.0141
 M5A  H11  H  HCH3  0   0.237  55.6064  29.0662  53.1937
 M5A  H12  H  HOH1  0   0.482  54.8606  32.4434  51.2359

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   double    1.204  0.020  1.204
 M5A  C8   O    single    1.327  0.020  1.327
 M5A  C8   C    single    1.516  0.020  1.516
 M5A  O2   C9   double    1.219  0.020  1.219
 M5A  C3   C7   aromatic  1.382  0.020  1.382
 M5A  C3   C1   aromatic  1.395  0.020  1.395
 M5A  C7   C4   aromatic  1.396  0.020  1.396
 M5A  C    C1   single    1.505  0.020  1.505
 M5A  C    C5   single    1.536  0.020  1.536
 M5A  C1   C2   aromatic  1.389  0.020  1.389
 M5A  C9   C4   single    1.485  0.020  1.485
 M5A  C9   C10  single    1.461  0.020  1.461
 M5A  C4   C6   aromatic  1.391  0.020  1.391
 M5A  C2   C6   aromatic  1.388  0.020  1.388
 M5A  S    C10  aromatic  1.725  0.020  1.725
 M5A  S    C13  aromatic  1.704  0.020  1.704
 M5A  C10  C11  aromatic  1.372  0.020  1.372
 M5A  C11  C12  aromatic  1.413  0.020  1.413
 M5A  C13  C12  aromatic  1.366  0.020  1.366
 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
 M5A  O    H12  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
 M5A  C4   C9   C10  119.06  3.000
 M5A  C10  C9   O2   120.05  3.000
 M5A  C4   C9   O2   120.88  3.000
 M5A  S    C10  C11  111.11  3.000
 M5A  C11  C10  C9   130.90  3.000
 M5A  S    C10  C9   117.85  3.000
 M5A  H1   C11  C12  123.54  3.000
 M5A  H1   C11  C10  123.77  3.000
 M5A  C12  C11  C10  112.67  3.000
 M5A  H2   C12  C13  123.63  3.000
 M5A  H2   C12  C11  124.13  3.000
 M5A  C13  C12  C11  112.24  3.000
 M5A  H3   C13  S    120.24  3.000
 M5A  H3   C13  C12  127.44  3.000
 M5A  S    C13  C12  112.32  3.000
 M5A  C13  S    C10   91.65  3.000
 M5A  C7   C4   C6   118.99  3.000
 M5A  C6   C4   C9   122.19  3.000
 M5A  C7   C4   C9   118.75  3.000
 M5A  H4   C6   C2   119.13  3.000
 M5A  H4   C6   C4   120.68  3.000
 M5A  C2   C6   C4   120.16  3.000
 M5A  H5   C2   C1   119.70  3.000
 M5A  H5   C2   C6   119.26  3.000
 M5A  C1   C2   C6   121.05  3.000
 M5A  H6   C7   C3   119.55  3.000
 M5A  H6   C7   C4   119.95  3.000
 M5A  C3   C7   C4   120.49  3.000
 M5A  H7   C3   C1   120.37  3.000
 M5A  H7   C3   C7   118.90  3.000
 M5A  C1   C3   C7   120.73  3.000
 M5A  C    C1   C3   121.35  3.000
 M5A  C    C1   C2   120.09  3.000
 M5A  C3   C1   C2   118.55  3.000
 M5A  H8   C    C8   106.48  3.000
 M5A  H8   C    C5   107.51  3.000
 M5A  C8   C    C5   110.85  3.000
 M5A  H8   C    C1   108.35  3.000
 M5A  C5   C    C1   111.92  3.000
 M5A  C8   C    C1   111.46  3.000
 M5A  H11  C5   H10  108.25  3.000
 M5A  H11  C5   H9   108.00  3.000
 M5A  H10  C5   H9   107.89  3.000
 M5A  H11  C5   C    111.70  3.000
 M5A  H10  C5   C    111.34  3.000
 M5A  H9   C5   C    109.53  3.000
 M5A  O1   C8   O    123.23  3.000
 M5A  O    C8   C    111.32  3.000
 M5A  O1   C8   C    125.45  3.000
 M5A  H12  O    C8   110.06  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  CONST_25  H12  O    C8   C     180.00   0.0  0
 M5A  Var_01    C7   C4   C9   C10  -143.85  30.0  2
 M5A  Var_02    C4   C9   C10  C11    16.75  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
 M5A  plan-4  H12  0.020

