# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:41:10 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 1-benzothiophen-2-ylacetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1sc2ccccc2c1
#
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
 2FX  2FX  '1-benzothiophen-2-ylacetic acid'  ligand  21  13  .  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_2FX
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
 2FX  O1    O  OH1   0  -0.590  -4.4854  -0.0832   0.0052
 2FX  C2    C  C     0   0.558  -3.2062  -0.0798   0.3547
 2FX  O3    O  O     0  -0.428  -2.8208   0.0210   1.4898
 2FX  C4    C  CR5   0  -0.123  -0.8627  -0.1957  -0.5334
 2FX  C5    C  CR15  0  -0.253   0.0288  -1.2020  -0.6753
 2FX  C6    C  CR56  0   0.216   1.3634  -0.8321  -0.3037
 2FX  C7    C  CR16  0  -0.321   2.5328  -1.6007  -0.3191
 2FX  C8    C  CR16  0  -0.256   3.7237  -1.0324   0.0861
 2FX  C9    C  CR16  0  -0.272   3.7731   0.3005   0.5139
 2FX  C10   C  CR16  0  -0.277   2.6323   1.0807   0.5386
 2FX  C11   C  CR56  0  -0.225   1.4338   0.5050   0.1257
 2FX  S12   S  S2    0   0.215  -0.1231   1.2636   0.0592
 2FX  C13   C  CH2   0  -0.674  -2.3148  -0.2255  -0.8562
 2FX  HO1   H  HOH1  0   0.484  -5.0470   0.0053   0.7901
 2FX  H5    H  HCR5  0   0.270  -0.2442  -2.1841  -1.0374
 2FX  H7    H  HCR6  0   0.257   2.4989  -2.6313  -0.6490
 2FX  H8    H  HCR6  0   0.258   4.6310  -1.6218   0.0726
 2FX  H9    H  HCR6  0   0.261   4.7163   0.7273   0.8283
 2FX  H10   H  HCR6  0   0.268   2.6728   2.1103   0.8694
 2FX  H13   H  HCH2  0   0.318  -2.5565  -1.1734  -1.3429
 2FX  H13A  H  HCH2  0   0.313  -2.5754   0.5557  -1.5769

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
 2FX  C2   O1    single    1.326  0.020  1.326
 2FX  O1   HO1   single    0.850  0.020  0.980
 2FX  C13  C2    single    1.511  0.020  1.511
 2FX  O3   C2    double    1.203  0.020  1.203
 2FX  S12  C4    aromatic  1.740  0.020  1.740
 2FX  C5   C4    aromatic  1.352  0.020  1.352
 2FX  C4   C13   single    1.488  0.020  1.488
 2FX  C6   C5    aromatic  1.434  0.020  1.434
 2FX  C5   H5    single    0.930  0.020  1.080
 2FX  C7   C6    aromatic  1.399  0.020  1.399
 2FX  C11  C6    aromatic  1.406  0.020  1.406
 2FX  C8   C7    aromatic  1.380  0.020  1.380
 2FX  C7   H7    single    0.930  0.020  1.080
 2FX  C9   C8    aromatic  1.401  0.020  1.401
 2FX  C8   H8    single    0.930  0.020  1.080
 2FX  C9   C10   aromatic  1.382  0.020  1.382
 2FX  C9   H9    single    0.930  0.020  1.080
 2FX  C10  C11   aromatic  1.392  0.020  1.392
 2FX  C10  H10   single    0.930  0.020  1.080
 2FX  C11  S12   aromatic  1.733  0.020  1.733
 2FX  C13  H13   single    0.970  0.020  1.090
 2FX  C13  H13A  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
 2FX  HO1   O1   C2   110.19  3.000
 2FX  C13   C2   O3   125.12  3.000
 2FX  O3    C2   O1   123.92  3.000
 2FX  C13   C2   O1   110.96  3.000
 2FX  C13   C4   S12  120.37  3.000
 2FX  C13   C4   C5   127.29  3.000
 2FX  S12   C4   C5   112.32  3.000
 2FX  H5    C5   C6   123.76  3.000
 2FX  H5    C5   C4   123.00  3.000
 2FX  C6    C5   C4   113.24  3.000
 2FX  C11   C6   C7   118.94  3.000
 2FX  C11   C6   C5   111.78  3.000
 2FX  C7    C6   C5   129.29  3.000
 2FX  H7    C7   C8   120.56  3.000
 2FX  H7    C7   C6   120.00  3.000
 2FX  C8    C7   C6   119.44  3.000
 2FX  H8    C8   C9   119.51  3.000
 2FX  H8    C8   C7   119.70  3.000
 2FX  C9    C8   C7   120.79  3.000
 2FX  H9    C9   C10  119.45  3.000
 2FX  H9    C9   C8   119.66  3.000
 2FX  C10   C9   C8   120.89  3.000
 2FX  H10   C10  C11  121.08  3.000
 2FX  H10   C10  C9   120.76  3.000
 2FX  C11   C10  C9   118.15  3.000
 2FX  S12   C11  C10  127.13  3.000
 2FX  S12   C11  C6   111.08  3.000
 2FX  C10   C11  C6   121.79  3.000
 2FX  C11   S12  C4    91.59  3.000
 2FX  H13A  C13  H13  105.86  3.000
 2FX  H13A  C13  C4   111.16  3.000
 2FX  H13   C13  C4   109.26  3.000
 2FX  H13A  C13  C2   108.57  3.000
 2FX  H13   C13  C2   108.07  3.000
 2FX  C4    C13  C2   113.58  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
 2FX  CONST_01  C6   C11  S12  C4     0.00   0.0  0
 2FX  CONST_02  C10  C11  S12  C4   180.00   0.0  0
 2FX  CONST_03  C7   C6   C5   C4   180.00   0.0  0
 2FX  CONST_04  C11  C6   C5   C4     0.00   0.0  0
 2FX  CONST_05  C11  S12  C4   C5     0.00   0.0  0
 2FX  CONST_06  C8   C7   C6   C5   180.00   0.0  0
 2FX  CONST_07  C10  C11  C6   C5   180.00   0.0  0
 2FX  CONST_08  S12  C11  C6   C5     0.00   0.0  0
 2FX  CONST_09  S12  C4   C5   C6     0.00   0.0  0
 2FX  CONST_10  C9   C8   C7   C6     0.00   0.0  0
 2FX  CONST_11  C9   C10  C11  C6     0.00   0.0  0
 2FX  CONST_12  C10  C11  C6   C7     0.00   0.0  0
 2FX  CONST_13  S12  C11  C6   C7   180.00   0.0  0
 2FX  CONST_14  C10  C9   C8   C7     0.00   0.0  0
 2FX  CONST_15  C11  C6   C7   C8     0.00   0.0  0
 2FX  CONST_16  C11  C10  C9   C8     0.00   0.0  0
 2FX  CONST_17  S12  C11  C10  C9   180.00   0.0  0
 2FX  CONST_18  C13  C4   C5   C6   180.00   0.0  0
 2FX  CONST_19  C13  C4   S12  C11  180.00   0.0  0
 2FX  CONST_20  H7   C7   C6   C5     0.00   0.0  0
 2FX  CONST_21  H8   C8   C7   C6   180.00   0.0  0
 2FX  CONST_22  H10  C10  C11  C6   180.00   0.0  0
 2FX  CONST_23  H5   C5   C6   C7     0.00   0.0  0
 2FX  CONST_24  H9   C9   C8   C7   180.00   0.0  0
 2FX  CONST_25  HO1  O1   C2   O3     0.00   0.0  0
 2FX  Var_01    S12  C4   C13  C2   -67.29  30.0  2
 2FX  Var_02    C4   C13  C2   O1   178.60  30.0  1

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
 2FX  plan-1  C4   0.020
 2FX  plan-1  C5   0.020
 2FX  plan-1  C6   0.020
 2FX  plan-1  C7   0.020
 2FX  plan-1  C8   0.020
 2FX  plan-1  C9   0.020
 2FX  plan-1  C10  0.020
 2FX  plan-1  C11  0.020
 2FX  plan-1  S12  0.020
 2FX  plan-1  C13  0.020
 2FX  plan-1  H5   0.020
 2FX  plan-1  H7   0.020
 2FX  plan-1  H8   0.020
 2FX  plan-1  H9   0.020
 2FX  plan-1  H10  0.020
 2FX  plan-2  O1   0.020
 2FX  plan-2  C2   0.020
 2FX  plan-2  O3   0.020
 2FX  plan-2  C13  0.020
 2FX  plan-2  HO1  0.020

