# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:51:13 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: thiophen-2-ylacetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1sccc1
#
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
 SPA  SPA  'thiophen-2-ylacetic acid '  ligand  14  9  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SPA
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
 SPA  S1   S  S2     0   0.047  -0.6703   0.7869  -0.8408
 SPA  C2   C  CR5    0  -0.074   0.4871  -0.3370  -0.2231
 SPA  C3   C  CR15   0  -0.216   1.3828  -0.7260  -1.1753
 SPA  C4   C  CR15   0  -0.149   1.1364  -0.1003  -2.4407
 SPA  C5   C  CR15   0  -0.459   0.0605   0.7120  -2.4147
 SPA  C6   C  CH2    0  -0.643   0.3873  -0.8127   1.1797
 SPA  C7   C  C      0   0.465  -0.4558   0.1474   2.0732
 SPA  O1   O  O      0  -0.591  -1.2677   0.8145   1.3854
 SPA  O2   O  OC    -1  -0.708  -0.2781   0.0532   3.2648
 SPA  H3   H  HCR5   0   0.231   2.1856  -1.4257  -0.9908
 SPA  H4   H  HCR5   0   0.271   1.7475  -0.2527  -3.3183
 SPA  H5   H  HCR5   0   0.302  -0.3209   1.3219  -3.2202
 SPA  H61  H  HCH2   0   0.254   1.3809  -0.9915   1.5990
 SPA  H62  H  HCH2   0   0.271  -0.1142  -1.7867   1.1910

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
 SPA  S1  C2   aromatic  1.727  0.020  1.727
 SPA  S1  C5   aromatic  1.737  0.020  1.737
 SPA  C2  C3   aromatic  1.364  0.020  1.364
 SPA  C2  C6   single    1.485  0.020  1.485
 SPA  C3  C4   aromatic  1.433  0.020  1.433
 SPA  C3  H3   single    0.930  0.020  1.080
 SPA  C4  C5   aromatic  1.348  0.020  1.348
 SPA  C4  H4   single    0.930  0.020  1.080
 SPA  C5  H5   single    0.930  0.020  1.080
 SPA  C6  C7   single    1.559  0.020  1.559
 SPA  C6  H61  single    0.970  0.020  1.090
 SPA  C6  H62  single    0.970  0.020  1.090
 SPA  C7  O1   deloc     1.256  0.020  1.256
 SPA  C7  O2   deloc     1.208  0.020  1.208

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
 SPA  C5   S1  C2    90.81  3.000
 SPA  C6   C2  C3   127.77  3.000
 SPA  C6   C2  S1   120.08  3.000
 SPA  C3   C2  S1   112.08  3.000
 SPA  H3   C3  C4   124.13  3.000
 SPA  H3   C3  C2   123.59  3.000
 SPA  C4   C3  C2   112.28  3.000
 SPA  H4   C4  C5   123.51  3.000
 SPA  H4   C4  C3   123.96  3.000
 SPA  C5   C4  C3   112.53  3.000
 SPA  H5   C5  C4   127.42  3.000
 SPA  H5   C5  S1   120.20  3.000
 SPA  C4   C5  S1   112.28  3.000
 SPA  H62  C6  H61  105.47  3.000
 SPA  H62  C6  C7   107.10  3.000
 SPA  H61  C6  C7   111.86  3.000
 SPA  H62  C6  C2   108.99  3.000
 SPA  H61  C6  C2   110.72  3.000
 SPA  C7   C6  C2   112.36  3.000
 SPA  O2   C7  O1   132.57  3.000
 SPA  O2   C7  C6   115.95  3.000
 SPA  O1   C7  C6   111.27  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
 SPA  CONST_01  C4  C3  C2  S1    0.00   0.0  0
 SPA  CONST_02  C3  C4  C5  S1    0.00   0.0  0
 SPA  CONST_03  C4  C5  S1  C2    0.00   0.0  0
 SPA  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 SPA  CONST_05  C5  S1  C2  C3    0.00   0.0  0
 SPA  CONST_06  C6  C2  C3  C4  180.00   0.0  0
 SPA  CONST_07  C6  C2  S1  C5  180.00   0.0  0
 SPA  CONST_08  H3  C3  C2  S1  180.00   0.0  0
 SPA  CONST_09  H4  C4  C5  S1  180.00   0.0  0
 SPA  CONST_10  H5  C5  S1  C2  180.00   0.0  0
 SPA  Var_01    C7  C6  C2  S1  -20.66  30.0  2
 SPA  Var_02    O1  C7  C6  C2   24.80  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
 SPA  plan-1  S1  0.020
 SPA  plan-1  C2  0.020
 SPA  plan-1  C3  0.020
 SPA  plan-1  C4  0.020
 SPA  plan-1  C5  0.020
 SPA  plan-1  C6  0.020
 SPA  plan-1  H3  0.020
 SPA  plan-1  H4  0.020
 SPA  plan-1  H5  0.020
 SPA  plan-2  C6  0.020
 SPA  plan-2  C7  0.020
 SPA  plan-2  O1  0.020
 SPA  plan-2  O2  0.020

