# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 08:33:02 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  15  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 PERFECT
;

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   0.211  -1.0108   0.1820  -1.1982
 SPA  C2   C  CR5   0  -0.123   0.3038  -0.4608  -0.2909
 SPA  C3   C  CR15  0  -0.230   1.4442  -0.4701  -1.0362
 SPA  C4   C  CR15  0  -0.184   1.2589   0.0470  -2.3483
 SPA  C5   C  CR15  0  -0.470  -0.0239   0.4387  -2.5762
 SPA  C6   C  CH2   0  -0.670   0.1310  -0.9272   1.1120
 SPA  C7   C  C     0   0.557  -0.0793   0.1966   2.1005
 SPA  O1   O  O     0  -0.430  -0.1728   1.3619   1.8164
 SPA  O2   O  OH1   0  -0.591  -0.1531  -0.2689   3.3409
 SPA  H3   H  HCR5  0   0.265   2.3884  -0.8364  -0.6570
 SPA  H4   H  HCR5  0   0.266   2.0447   0.1218  -3.0859
 SPA  H5   H  HCR5  0   0.294  -0.4415   0.8616  -3.4768
 SPA  H61  H  HCH2  0   0.312   1.0154  -1.4929   1.4149
 SPA  H62  H  HCH2  0   0.311  -0.7097  -1.6219   1.2043
 SPA  HO2  H  HOH1  0   0.483  -0.2965   0.4596   3.9635

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  1.722  0.020  1.722
 SPA  S1  C5   aromatic  1.714  0.020  1.714
 SPA  C2  C3   aromatic  1.362  0.020  1.362
 SPA  C2  C6   single    1.488  0.020  1.488
 SPA  C3  C4   aromatic  1.422  0.020  1.422
 SPA  C3  H3   single    0.930  0.020  1.080
 SPA  C4  C5   aromatic  1.360  0.020  1.360
 SPA  C4  H4   single    0.930  0.020  1.080
 SPA  C5  H5   single    0.930  0.020  1.080
 SPA  C6  C7   single    1.511  0.020  1.511
 SPA  C6  H61  single    0.970  0.020  1.090
 SPA  C6  H62  single    0.970  0.020  1.090
 SPA  C7  O1   double    1.203  0.020  1.203
 SPA  C7  O2   single    1.327  0.020  1.327
 SPA  O2  HO2  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
 SPA  C5   S1  C2    92.29  3.000
 SPA  C6   C2  C3   127.64  3.000
 SPA  C6   C2  S1   121.67  3.000
 SPA  C3   C2  S1   110.69  3.000
 SPA  H3   C3  C4   124.08  3.000
 SPA  H3   C3  C2   122.77  3.000
 SPA  C4   C3  C2   113.15  3.000
 SPA  H4   C4  C5   123.48  3.000
 SPA  H4   C4  C3   124.06  3.000
 SPA  C5   C4  C3   112.46  3.000
 SPA  H5   C5  C4   128.14  3.000
 SPA  H5   C5  S1   120.45  3.000
 SPA  C4   C5  S1   111.41  3.000
 SPA  H62  C6  H61  105.65  3.000
 SPA  H62  C6  C7   108.06  3.000
 SPA  H61  C6  C7   108.43  3.000
 SPA  H62  C6  C2   111.57  3.000
 SPA  H61  C6  C2   109.24  3.000
 SPA  C7   C6  C2   113.55  3.000
 SPA  O2   C7  O1   123.80  3.000
 SPA  O2   C7  C6   110.99  3.000
 SPA  O1   C7  C6   125.21  3.000
 SPA  HO2  O2  C7   110.19  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  CONST_11  HO2  O2  C7  C6  180.00   0.0  0
 SPA  Var_01    C7   C6  C2  S1  -71.40  30.0  2
 SPA  Var_02    O1   C7  C6  C2    3.65  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
 SPA  plan-2  HO2  0.020

