# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:50:51 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 3-chloro-6-fluoro-1-benzothiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sc2cc(F)ccc2c1Cl
#
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
 3R4  3R4  '3-chloro-6-fluoro-1-benzothiophene-2-carboxylic acid'  ligand  18  14  .  2021-08-04  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3R4
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
 3R4  C13   C   CR5   0   0.005   0.7579   0.7976  -0.0107
 3R4  O01   O   O     0  -0.416   3.7099   0.3318  -0.0064
 3R4  C02   C   C     0   0.533   2.9037  -0.5627  -0.0022
 3R4  O03   O   OH1   0  -0.600   3.2092  -1.8533   0.0052
 3R4  C04   C   CR5   0  -0.316   1.4492  -0.3735  -0.0039
 3R4  S05   S   S2    0   0.298   0.3927  -1.7555   0.0042
 3R4  C06   C   CR56  0  -0.219  -1.0014  -0.7393  -0.0014
 3R4  C07   C   CR16  0  -0.434  -2.3287  -1.1616   0.0010
 3R4  C08   C   CR6   0   0.543  -3.2874  -0.1781  -0.0053
 3R4  F09   F   F     0  -0.305  -4.5750  -0.5404  -0.0041
 3R4  C10   C   CR16  0  -0.411  -2.9890   1.1866  -0.0129
 3R4  C11   C   CR16  0  -0.267  -1.6737   1.5879  -0.0152
 3R4  C12   C   CR56  0   0.297  -0.6607   0.6223  -0.0093
 3R4  CL14  CL  CL    0  -0.074   1.4478   2.3567  -0.0206
 3R4  H1    H   HOH1  0   0.497   4.1708  -1.9764   0.0077
 3R4  H2    H   HCR6  0   0.300  -2.5989  -2.2093   0.0076
 3R4  H3    H   HCR6  0   0.294  -3.7901   1.9128  -0.0176
 3R4  H4    H   HCR6  0   0.275  -1.4293   2.6417  -0.0214

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
 3R4  S05  C04   aromatic  1.740  0.020  1.740
 3R4  S05  C06   aromatic  1.725  0.020  1.725
 3R4  O01  C02   double    1.204  0.020  1.204
 3R4  O03  C02   single    1.326  0.020  1.326
 3R4  C02  C04   single    1.467  0.020  1.467
 3R4  C04  C13   aromatic  1.360  0.020  1.360
 3R4  C07  C06   aromatic  1.393  0.020  1.393
 3R4  C07  C08   aromatic  1.374  0.020  1.374
 3R4  C06  C12   aromatic  1.404  0.020  1.404
 3R4  C13  C12   aromatic  1.429  0.020  1.429
 3R4  C13  CL14  single    1.705  0.020  1.705
 3R4  F09  C08   single    1.338  0.020  1.338
 3R4  C08  C10   aromatic  1.397  0.020  1.397
 3R4  C12  C11   aromatic  1.400  0.020  1.400
 3R4  C10  C11   aromatic  1.375  0.020  1.375
 3R4  O03  H1    single    0.850  0.020  0.980
 3R4  C07  H2    single    0.930  0.020  1.080
 3R4  C10  H3    single    0.930  0.020  1.080
 3R4  C11  H4    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
 3R4  CL14  C13  C12  120.91  3.000
 3R4  CL14  C13  C04  125.58  3.000
 3R4  C12   C13  C04  113.51  3.000
 3R4  C04   C02  O03  110.73  3.000
 3R4  C04   C02  O01  124.61  3.000
 3R4  O03   C02  O01  124.66  3.000
 3R4  H1    O03  C02  110.61  3.000
 3R4  S05   C04  C02  119.99  3.000
 3R4  C02   C04  C13  127.97  3.000
 3R4  S05   C04  C13  112.05  3.000
 3R4  C06   S05  C04   91.31  3.000
 3R4  C12   C06  C07  121.70  3.000
 3R4  C12   C06  S05  112.04  3.000
 3R4  C07   C06  S05  126.26  3.000
 3R4  H2    C07  C08  121.27  3.000
 3R4  H2    C07  C06  122.11  3.000
 3R4  C08   C07  C06  116.62  3.000
 3R4  C10   C08  F09  118.05  3.000
 3R4  C10   C08  C07  123.40  3.000
 3R4  F09   C08  C07  118.55  3.000
 3R4  H3    C10  C11  120.84  3.000
 3R4  H3    C10  C08  119.86  3.000
 3R4  C11   C10  C08  119.31  3.000
 3R4  H4    C11  C12  120.57  3.000
 3R4  H4    C11  C10  120.03  3.000
 3R4  C12   C11  C10  119.40  3.000
 3R4  C11   C12  C06  119.58  3.000
 3R4  C11   C12  C13  129.33  3.000
 3R4  C06   C12  C13  111.09  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
 3R4  CONST_01  C06   S05  C04  C13    0.00   0.0  0
 3R4  CONST_02  S05   C06  C12  C13    0.00   0.0  0
 3R4  CONST_03  C07   C06  C12  C13  180.00   0.0  0
 3R4  CONST_04  C10   C11  C12  C13  180.00   0.0  0
 3R4  CONST_05  C07   C06  S05  C04  180.00   0.0  0
 3R4  CONST_06  C12   C06  S05  C04    0.00   0.0  0
 3R4  CONST_07  C06   C12  C13  C04    0.00   0.0  0
 3R4  CONST_08  C11   C12  C13  C04  180.00   0.0  0
 3R4  CONST_09  C12   C13  C04  S05    0.00   0.0  0
 3R4  CONST_10  C08   C07  C06  S05  180.00   0.0  0
 3R4  CONST_11  C11   C12  C06  S05  180.00   0.0  0
 3R4  CONST_12  C10   C08  C07  C06    0.00   0.0  0
 3R4  CONST_13  C10   C11  C12  C06    0.00   0.0  0
 3R4  CONST_14  C11   C12  C06  C07    0.00   0.0  0
 3R4  CONST_15  C11   C10  C08  C07    0.00   0.0  0
 3R4  CONST_16  C12   C06  C07  C08    0.00   0.0  0
 3R4  CONST_17  C12   C11  C10  C08    0.00   0.0  0
 3R4  CONST_18  C06   S05  C04  C02  180.00   0.0  0
 3R4  CONST_19  C12   C13  C04  C02  180.00   0.0  0
 3R4  CONST_20  CL14  C13  C04  S05  180.00   0.0  0
 3R4  CONST_21  F09   C08  C07  C06  180.00   0.0  0
 3R4  CONST_22  CL14  C13  C12  C06  180.00   0.0  0
 3R4  CONST_23  C11   C10  C08  F09  180.00   0.0  0
 3R4  CONST_24  CL14  C13  C12  C11    0.00   0.0  0
 3R4  CONST_25  H4    C11  C12  C13    0.00   0.0  0
 3R4  CONST_26  H2    C07  C06  S05    0.00   0.0  0
 3R4  CONST_27  H3    C10  C08  C07  180.00   0.0  0
 3R4  CONST_28  H1    O03  C02  C04  180.00   0.0  0
 3R4  Var_01    O01   C02  C04  C13    0.02  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
 3R4  plan-1  C13   0.020
 3R4  plan-1  C02   0.020
 3R4  plan-1  C04   0.020
 3R4  plan-1  S05   0.020
 3R4  plan-1  C06   0.020
 3R4  plan-1  C07   0.020
 3R4  plan-1  C08   0.020
 3R4  plan-1  F09   0.020
 3R4  plan-1  C10   0.020
 3R4  plan-1  C11   0.020
 3R4  plan-1  C12   0.020
 3R4  plan-1  CL14  0.020
 3R4  plan-1  H2    0.020
 3R4  plan-1  H3    0.020
 3R4  plan-1  H4    0.020
 3R4  plan-2  O01   0.020
 3R4  plan-2  C02   0.020
 3R4  plan-2  O03   0.020
 3R4  plan-2  C04   0.020
 3R4  plan-2  H1    0.020

