# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:24:50 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC(O)=O)cc1c2sccc2
#
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
 5V5  5V5  '2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid'  ligand  28  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5V5
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
 5V5  C1   C  CH2    0  -0.690   3.2105   0.4530   0.9647
 5V5  C2   C  CR6    0   0.200   1.9231  -0.2616   0.7027
 5V5  C3   C  CR16   0  -0.288   1.8865  -1.6313   0.4782
 5V5  O2   O  OC    -1  -0.621   5.0237   1.5383  -0.0996
 5V5  C11  C  C1     0  -0.471  -3.9708   1.5967  -0.0087
 5V5  C12  C  CR16   0  -0.378   0.7189   0.4276   0.6458
 5V5  O    O  O      0  -0.593   3.5606   0.4758  -1.4046
 5V5  C    C  C      0   0.412   3.9981   0.8596  -0.3072
 5V5  C4   C  CR16   0  -0.352   0.6945  -2.2851   0.2057
 5V5  C5   C  CR6    0   0.337  -0.5001  -1.5768   0.1566
 5V5  C6   C  CH3    0  -0.408  -1.7681  -3.5220  -0.3470
 5V5  C7   C  CR6    0   0.068  -0.5048  -0.1922   0.3908
 5V5  C8   C  C      0  -0.175  -1.7333   0.6033   0.3954
 5V5  C9   C  C1     0  -0.218  -1.9104   1.8218   1.0004
 5V5  C10  C  C1     0  -0.147  -3.1853   2.3894   0.7713
 5V5  S    S  S2     0   0.248  -3.1737   0.1509  -0.4484
 5V5  H1   H  HCH2   0   0.234   3.0302   1.3500   1.5645
 5V5  H2   H  HCH2   0   0.237   3.8687  -0.1753   1.5734
 5V5  H3   H  HCR6   0   0.225   2.8005  -2.2118   0.5124
 5V5  H5   H  H      0   0.263  -4.9861   1.7765  -0.3256
 5V5  H6   H  HCR6   0   0.215   0.7354   1.5013   0.7906
 5V5  H7   H  HCR6   0   0.241   0.7132  -3.3530   0.0358
 5V5  H8   H  HCH3   0   0.209  -1.4304  -4.1081   0.5129
 5V5  H9   H  HCH3   0   0.249  -2.8158  -3.7470  -0.5309
 5V5  H10  H  HCH3   0   0.211  -1.1868  -3.8185  -1.2253
 5V5  H11  H  H      0   0.223  -1.1560   2.2938   1.6123
 5V5  H12  H  H      0   0.232  -3.5041   3.3384   1.1764
 5V5  O1   O  O2     0  -0.462  -1.6952  -2.1403  -0.1038

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
 5V5  C11  C10  aromatic  1.362  0.020  1.362
 5V5  C11  S    aromatic  1.708  0.020  1.708
 5V5  C10  C9   aromatic  1.414  0.020  1.414
 5V5  C9   C8   aromatic  1.372  0.020  1.372
 5V5  S    C8   aromatic  1.730  0.020  1.730
 5V5  C8   C7   single    1.464  0.020  1.464
 5V5  C7   C12  aromatic  1.395  0.020  1.395
 5V5  C7   C5   aromatic  1.404  0.020  1.404
 5V5  O1   C5   single    1.347  0.020  1.347
 5V5  O1   C6   single    1.405  0.020  1.405
 5V5  C12  C2   aromatic  1.389  0.020  1.389
 5V5  C5   C4   aromatic  1.390  0.020  1.390
 5V5  C2   C1   single    1.496  0.020  1.496
 5V5  C2   C3   aromatic  1.388  0.020  1.388
 5V5  C4   C3   aromatic  1.387  0.020  1.387
 5V5  O    C    deloc     1.242  0.020  1.242
 5V5  C1   C    single    1.550  0.020  1.550
 5V5  C    O2   deloc     1.247  0.020  1.247
 5V5  C1   H1   single    0.970  0.020  1.090
 5V5  C1   H2   single    0.970  0.020  1.090
 5V5  C3   H3   single    0.930  0.020  1.080
 5V5  C11  H5   single    0.930  0.020  1.080
 5V5  C12  H6   single    0.930  0.020  1.080
 5V5  C4   H7   single    0.930  0.020  1.080
 5V5  C6   H8   single    0.970  0.020  1.090
 5V5  C6   H9   single    0.970  0.020  1.090
 5V5  C6   H10  single    0.970  0.020  1.090
 5V5  C9   H11  single    0.930  0.020  1.080
 5V5  C10  H12  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
 5V5  H2   C1   H1   105.36  3.000
 5V5  H2   C1   C    107.53  3.000
 5V5  H1   C1   C    108.57  3.000
 5V5  H2   C1   C2   109.92  3.000
 5V5  H1   C1   C2   110.25  3.000
 5V5  C    C1   C2   114.77  3.000
 5V5  C12  C2   C3   117.39  3.000
 5V5  C3   C2   C1   121.50  3.000
 5V5  C12  C2   C1   121.09  3.000
 5V5  H3   C3   C4   118.61  3.000
 5V5  H3   C3   C2   120.09  3.000
 5V5  C4   C3   C2   121.30  3.000
 5V5  H5   C11  S    120.31  3.000
 5V5  H5   C11  C10  127.89  3.000
 5V5  S    C11  C10  111.78  3.000
 5V5  H6   C12  C7   118.55  3.000
 5V5  H6   C12  C2   118.24  3.000
 5V5  C7   C12  C2   123.20  3.000
 5V5  O    C    O2   127.21  3.000
 5V5  O2   C    C1   115.09  3.000
 5V5  O    C    C1   117.70  3.000
 5V5  H7   C4   C5   120.84  3.000
 5V5  H7   C4   C3   118.79  3.000
 5V5  C5   C4   C3   120.37  3.000
 5V5  C7   C5   C4   119.97  3.000
 5V5  C4   C5   O1   123.81  3.000
 5V5  C7   C5   O1   116.22  3.000
 5V5  H10  C6   H9   108.67  3.000
 5V5  H10  C6   H8   108.77  3.000
 5V5  H9   C6   H8   108.63  3.000
 5V5  H10  C6   O1   112.20  3.000
 5V5  H9   C6   O1   106.43  3.000
 5V5  H8   C6   O1   112.02  3.000
 5V5  C8   C7   C5   122.63  3.000
 5V5  C5   C7   C12  117.75  3.000
 5V5  C8   C7   C12  119.62  3.000
 5V5  S    C8   C9   109.87  3.000
 5V5  S    C8   C7   123.73  3.000
 5V5  C9   C8   C7   126.34  3.000
 5V5  H11  C9   C10  123.10  3.000
 5V5  H11  C9   C8   123.22  3.000
 5V5  C10  C9   C8   113.67  3.000
 5V5  H12  C10  C9   123.92  3.000
 5V5  H12  C10  C11  123.80  3.000
 5V5  C9   C10  C11  112.28  3.000
 5V5  C8   S    C11   92.39  3.000
 5V5  C6   O1   C5   119.41  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
 5V5  CONST_01  C8   C7   C12  C2    180.00   0.0  0
 5V5  CONST_02  C5   C7   C12  C2      0.00   0.0  0
 5V5  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 5V5  CONST_04  C7   C12  C2   C3      0.00   0.0  0
 5V5  CONST_05  C7   C5   C4   C3      0.00   0.0  0
 5V5  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 5V5  CONST_07  C9   C8   S    C11     0.00   0.0  0
 5V5  CONST_08  C7   C8   S    C11   180.00   0.0  0
 5V5  CONST_11  C4   C5   C7   C12     0.00   0.0  0
 5V5  CONST_12  C4   C3   C2   C12     0.00   0.0  0
 5V5  CONST_13  C8   C7   C5   C4    180.00   0.0  0
 5V5  CONST_16  C10  C9   C8   C7    180.00   0.0  0
 5V5  CONST_17  C10  C11  S    C8      0.00   0.0  0
 5V5  CONST_18  S    C11  C10  C9      0.00   0.0  0
 5V5  CONST_19  S    C8   C9   C10     0.00   0.0  0
 5V5  CONST_20  C7   C12  C2   C1    180.00   0.0  0
 5V5  CONST_21  C4   C3   C2   C1    180.00   0.0  0
 5V5  CONST_22  O1   C5   C4   C3    180.00   0.0  0
 5V5  CONST_23  C8   C7   C5   O1      0.00   0.0  0
 5V5  CONST_24  C12  C7   C5   O1    180.00   0.0  0
 5V5  CONST_25  H7   C4   C3   C2    180.00   0.0  0
 5V5  CONST_26  H6   C12  C2   C3    180.00   0.0  0
 5V5  CONST_27  H11  C9   C10  C11   180.00   0.0  0
 5V5  CONST_28  H3   C3   C2   C12   180.00   0.0  0
 5V5  CONST_29  H12  C10  C9   C8    180.00   0.0  0
 5V5  CONST_30  H5   C11  S    C8    180.00   0.0  0
 5V5  Var_01    C    C1   C2   C3     84.11  30.0  2
 5V5  Var_02    C7   C5   O1   C6   -179.94  30.0  2
 5V5  Var_03    O    C    C1   C2     -5.45  30.0  3
 5V5  Var_04    H8   C6   O1   C5     61.46  30.0  3

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
 5V5  plan-1  C11  0.020
 5V5  plan-1  C7   0.020
 5V5  plan-1  C8   0.020
 5V5  plan-1  C9   0.020
 5V5  plan-1  C10  0.020
 5V5  plan-1  S    0.020
 5V5  plan-1  H5   0.020
 5V5  plan-1  H11  0.020
 5V5  plan-1  H12  0.020
 5V5  plan-2  C1   0.020
 5V5  plan-2  C2   0.020
 5V5  plan-2  C3   0.020
 5V5  plan-2  C12  0.020
 5V5  plan-2  C4   0.020
 5V5  plan-2  C5   0.020
 5V5  plan-2  C7   0.020
 5V5  plan-2  C8   0.020
 5V5  plan-2  H3   0.020
 5V5  plan-2  H6   0.020
 5V5  plan-2  H7   0.020
 5V5  plan-2  O1   0.020
 5V5  plan-3  C1   0.020
 5V5  plan-3  O2   0.020
 5V5  plan-3  O    0.020
 5V5  plan-3  C    0.020

