# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 21:15:02 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-[5-methyl-2-(2-thiophen-2-ylethynyl)-1-benzofuran-3-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2oc(C#Cc3sccc3)c(CC(O)=O)c2c1
#
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
 SJY  SJY  "2-[5-methyl-2-(2-thiophen-2-ylethynyl)-1-benzofuran-3-yl]ethanoic acid"  ligand  32  21  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SJY
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
 SJY  C10  C  CR5    0  -0.435   1.2803   3.9615   -8.7636
 SJY  C13  C  CR15   0  -0.460   0.3558   1.9487   -7.6714
 SJY  C15  C  CR5    0   0.070   1.4655   7.3260  -12.4487
 SJY  C17  C  C      0   0.425  -1.0361   7.8210  -12.5869
 SJY  C20  C  CR56   0   0.080   2.2660   8.3767  -13.0064
 SJY  C21  C  CR16   0  -0.419   2.1150   9.2496  -14.0867
 SJY  C02  C  CR6    0   0.095   3.1105  10.1755  -14.3506
 SJY  C03  C  CR16   0  -0.302   4.2493  10.2239  -13.5226
 SJY  C04  C  CR16   0  -0.335   4.4215   9.3750  -12.4435
 SJY  C05  C  CR56   0   0.328   3.4080   8.4597  -12.2123
 SJY  O06  O  O      0  -0.465   3.3642   7.5418  -11.2254
 SJY  C07  C  CR5    0   0.179   2.1834   6.8652  -11.3879
 SJY  C08  C  CSP    0   0.080   1.8937   5.8473  -10.4671
 SJY  C09  C  CSP    0   0.152   1.6161   4.9719   -9.6796
 SJY  C11  C  CR15   0  -0.223   1.6437   3.8563   -7.4440
 SJY  C12  C  CR15   0  -0.177   1.1127   2.7016   -6.8232
 SJY  S14  S  S2     0   0.236   0.2842   2.6287   -9.2377
 SJY  O18  O  O      0  -0.608  -2.1439   7.4553  -13.0205
 SJY  O19  O  OC    -1  -0.587  -0.7741   8.8426  -11.9301
 SJY  H1   H  HCR5   0   0.304  -0.1661   1.0290   -7.4554
 SJY  H2   H  HCR6   0   0.247   1.2336   9.2000  -14.7149
 SJY  H3   H  HCH3   0   0.243   2.9701  12.1701  -15.1501
 SJY  H4   H  HCH3   0   0.242   3.8411  11.0479  -16.1793
 SJY  H5   H  HCH3   0   0.244   2.0847  10.9621  -16.0754
 SJY  H6   H  HCR6   0   0.251   5.0194  10.9552  -13.7380
 SJY  H7   H  HCR6   0   0.265   5.3023   9.4277  -11.8172
 SJY  H8   H  HCR5   0   0.272   2.2648   4.5867   -6.9461
 SJY  H9   H  HCR5   0   0.274   1.2818   2.4431   -5.7882
 SJY  H10  H  HCH2   0   0.247   0.1678   6.7063  -14.0015
 SJY  H11  H  HCH2   0   0.248  -0.0829   5.8779  -12.4861
 SJY  C01  C  CH3    0  -0.721   2.9926  11.1363  -15.4992
 SJY  C16  C  CH2    0  -0.747   0.1416   6.8574  -12.9179

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
 SJY  C10  C09  single    1.405  0.020  1.405
 SJY  C10  C11  aromatic  1.373  0.020  1.373
 SJY  C10  S14  aromatic  1.730  0.020  1.730
 SJY  C13  C12  aromatic  1.364  0.020  1.364
 SJY  C13  S14  aromatic  1.709  0.020  1.709
 SJY  C15  C20  aromatic  1.434  0.020  1.434
 SJY  C15  C07  aromatic  1.361  0.020  1.361
 SJY  C15  C16  single    1.481  0.020  1.481
 SJY  C17  O18  deloc     1.245  0.020  1.245
 SJY  C17  O19  deloc     1.243  0.020  1.243
 SJY  C20  C21  aromatic  1.397  0.020  1.397
 SJY  C20  C05  aromatic  1.393  0.020  1.393
 SJY  C21  C02  aromatic  1.385  0.020  1.385
 SJY  C01  C02  single    1.502  0.020  1.502
 SJY  C02  C03  aromatic  1.409  0.020  1.409
 SJY  C03  C04  aromatic  1.384  0.020  1.384
 SJY  C04  C05  aromatic  1.385  0.020  1.385
 SJY  C05  O06  aromatic  1.348  0.020  1.348
 SJY  O06  C07  aromatic  1.371  0.020  1.371
 SJY  C07  C08  single    1.403  0.020  1.403
 SJY  C08  C09  triple    1.210  0.020  1.210
 SJY  C11  C12  aromatic  1.414  0.020  1.414
 SJY  C16  C17  single    1.557  0.020  1.557
 SJY  C13  H1   single    0.930  0.020  1.080
 SJY  C21  H2   single    0.930  0.020  1.080
 SJY  C01  H3   single    0.970  0.020  1.090
 SJY  C01  H4   single    0.970  0.020  1.090
 SJY  C01  H5   single    0.970  0.020  1.090
 SJY  C03  H6   single    0.930  0.020  1.080
 SJY  C04  H7   single    0.930  0.020  1.080
 SJY  C11  H8   single    0.930  0.020  1.080
 SJY  C12  H9   single    0.930  0.020  1.080
 SJY  C16  H10  single    0.970  0.020  1.090
 SJY  C16  H11  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
 SJY  S14  C10  C11  110.90  3.000
 SJY  S14  C10  C09  120.87  3.000
 SJY  C11  C10  C09  128.23  3.000
 SJY  H1   C13  S14  120.15  3.000
 SJY  H1   C13  C12  127.91  3.000
 SJY  S14  C13  C12  111.94  3.000
 SJY  C16  C15  C07  127.69  3.000
 SJY  C16  C15  C20  127.44  3.000
 SJY  C07  C15  C20  104.87  3.000
 SJY  O19  C17  O18  127.84  3.000
 SJY  O19  C17  C16  117.50  3.000
 SJY  O18  C17  C16  114.66  3.000
 SJY  C05  C20  C21  119.48  3.000
 SJY  C05  C20  C15  106.23  3.000
 SJY  C21  C20  C15  134.29  3.000
 SJY  H2   C21  C02  120.32  3.000
 SJY  H2   C21  C20  120.51  3.000
 SJY  C02  C21  C20  119.17  3.000
 SJY  C03  C02  C01  119.40  3.000
 SJY  C03  C02  C21  119.47  3.000
 SJY  C01  C02  C21  121.13  3.000
 SJY  H6   C03  C04  118.72  3.000
 SJY  H6   C03  C02  118.74  3.000
 SJY  C04  C03  C02  122.54  3.000
 SJY  H7   C04  C05  122.09  3.000
 SJY  H7   C04  C03  121.52  3.000
 SJY  C05  C04  C03  116.39  3.000
 SJY  O06  C05  C04  126.57  3.000
 SJY  O06  C05  C20  110.48  3.000
 SJY  C04  C05  C20  122.95  3.000
 SJY  C07  O06  C05  106.10  3.000
 SJY  C08  C07  O06  117.28  3.000
 SJY  C08  C07  C15  130.41  3.000
 SJY  O06  C07  C15  112.31  3.000
 SJY  C09  C08  C07  180.00  3.000
 SJY  C08  C09  C10  180.00  3.000
 SJY  H8   C11  C12  124.44  3.000
 SJY  H8   C11  C10  122.91  3.000
 SJY  C12  C11  C10  112.65  3.000
 SJY  H9   C12  C11  123.86  3.000
 SJY  H9   C12  C13  123.42  3.000
 SJY  C11  C12  C13  112.72  3.000
 SJY  C13  S14  C10   91.79  3.000
 SJY  H5   C01  H4   107.79  3.000
 SJY  H5   C01  H3   107.67  3.000
 SJY  H4   C01  H3   106.99  3.000
 SJY  H5   C01  C02  111.57  3.000
 SJY  H4   C01  C02  111.33  3.000
 SJY  H3   C01  C02  111.28  3.000
 SJY  H11  C16  H10  105.80  3.000
 SJY  H11  C16  C17  108.36  3.000
 SJY  H10  C16  C17  108.30  3.000
 SJY  H11  C16  C15  109.99  3.000
 SJY  H10  C16  C15  109.63  3.000
 SJY  C17  C16  C15  114.39  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
 SJY  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 SJY  CONST_02  C12  C13  S14  C10     0.00   0.0  0
 SJY  CONST_03  C11  C10  S14  C13     0.00   0.0  0
 SJY  CONST_04  C02  C21  C20  C15   180.00   0.0  0
 SJY  CONST_05  C04  C05  C20  C15   180.00   0.0  0
 SJY  CONST_06  O06  C05  C20  C15     0.00   0.0  0
 SJY  CONST_07  C05  O06  C07  C15     0.00   0.0  0
 SJY  CONST_08  O06  C07  C15  C20     0.00   0.0  0
 SJY  CONST_09  C03  C02  C21  C20     0.00   0.0  0
 SJY  CONST_10  C03  C04  C05  C20     0.00   0.0  0
 SJY  CONST_11  C07  O06  C05  C20     0.00   0.0  0
 SJY  CONST_12  C07  C15  C20  C21   180.00   0.0  0
 SJY  CONST_13  C04  C05  C20  C21     0.00   0.0  0
 SJY  CONST_14  O06  C05  C20  C21   180.00   0.0  0
 SJY  CONST_15  C04  C03  C02  C21     0.00   0.0  0
 SJY  CONST_16  C05  C20  C21  C02     0.00   0.0  0
 SJY  CONST_17  C05  C04  C03  C02     0.00   0.0  0
 SJY  CONST_18  O06  C05  C04  C03   180.00   0.0  0
 SJY  CONST_19  C07  O06  C05  C04   180.00   0.0  0
 SJY  CONST_20  C07  C15  C20  C05     0.00   0.0  0
 SJY  CONST_21  S14  C13  C12  C11     0.00   0.0  0
 SJY  CONST_22  S14  C10  C11  C12     0.00   0.0  0
 SJY  CONST_23  C09  C10  S14  C13   180.00   0.0  0
 SJY  CONST_24  C08  C07  C15  C20   180.00   0.0  0
 SJY  CONST_25  C01  C02  C21  C20   180.00   0.0  0
 SJY  CONST_26  C16  C15  C20  C21     0.00   0.0  0
 SJY  CONST_27  C04  C03  C02  C01   180.00   0.0  0
 SJY  CONST_28  C16  C15  C20  C05   180.00   0.0  0
 SJY  CONST_29  C08  C07  O06  C05   180.00   0.0  0
 SJY  CONST_30  C16  C15  C07  O06   180.00   0.0  0
 SJY  CONST_31  C12  C11  C10  C09   180.00   0.0  0
 SJY  CONST_32  H9   C12  C11  C10   180.00   0.0  0
 SJY  CONST_33  H1   C13  S14  C10   180.00   0.0  0
 SJY  CONST_34  H8   C11  C12  C13   180.00   0.0  0
 SJY  CONST_35  H2   C21  C20  C15     0.00   0.0  0
 SJY  CONST_36  H7   C04  C05  C20   180.00   0.0  0
 SJY  CONST_37  H6   C03  C02  C21   180.00   0.0  0
 SJY  CONST_38  H7   C04  C03  C02   180.00   0.0  0
 SJY  CONST_39  H2   C21  C02  C03   180.00   0.0  0
 SJY  CONST_40  H2   C21  C20  C05   180.00   0.0  0
 SJY  CONST_41  H6   C03  C04  C05   180.00   0.0  0
 SJY  CONST_42  H7   C04  C05  O06     0.00   0.0  0
 SJY  CONST_43  H1   C13  C12  C11   180.00   0.0  0
 SJY  CONST_44  H8   C11  C10  S14   180.00   0.0  0
 SJY  CONST_45  H9   C12  C13  S14   180.00   0.0  0
 SJY  Var_01    C07  C08  C09  C10   -27.06  30.0  1
 SJY  Var_02    C20  C15  C16  C17   -73.98  30.0  3
 SJY  Var_03    C07  C15  C16  C17   105.30  30.0  3
 SJY  Var_04    H10  C16  C15  C20    47.88  30.0  2
 SJY  Var_05    H11  C16  C15  C20   163.81  30.0  2
 SJY  Var_06    H3   C01  C02  C21   117.63  30.0  2
 SJY  Var_07    H4   C01  C02  C21  -123.11  30.0  2
 SJY  Var_08    H5   C01  C02  C21    -2.64  30.0  2
 SJY  Var_09    H3   C01  C02  C03   -61.93  30.0  2
 SJY  Var_10    H4   C01  C02  C03    57.33  30.0  2
 SJY  Var_11    H5   C01  C02  C03   177.80  30.0  2
 SJY  Var_12    H10  C16  C15  C07  -132.84  30.0  2
 SJY  Var_13    H11  C16  C15  C07   -16.90  30.0  2
 SJY  Var_14    O18  C17  C16  C15   177.56  30.0  3
 SJY  Var_15    O19  C17  C16  C15    -2.73  30.0  3
 SJY  Var_16    H10  C16  C17  O18    54.97  30.0  2
 SJY  Var_17    H11  C16  C17  O18   -59.35  30.0  2
 SJY  Var_18    H10  C16  C17  O19  -125.32  30.0  2
 SJY  Var_19    H11  C16  C17  O19   120.36  30.0  2

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
 SJY  plan-1  C10  0.020
 SJY  plan-1  C13  0.020
 SJY  plan-1  C08  0.020
 SJY  plan-1  C09  0.020
 SJY  plan-1  C11  0.020
 SJY  plan-1  C12  0.020
 SJY  plan-1  S14  0.020
 SJY  plan-1  H1   0.020
 SJY  plan-1  H8   0.020
 SJY  plan-1  H9   0.020
 SJY  plan-2  C15  0.020
 SJY  plan-2  C20  0.020
 SJY  plan-2  C21  0.020
 SJY  plan-2  C02  0.020
 SJY  plan-2  C03  0.020
 SJY  plan-2  C04  0.020
 SJY  plan-2  C05  0.020
 SJY  plan-2  O06  0.020
 SJY  plan-2  C07  0.020
 SJY  plan-2  C08  0.020
 SJY  plan-2  C09  0.020
 SJY  plan-2  H2   0.020
 SJY  plan-2  H6   0.020
 SJY  plan-2  H7   0.020
 SJY  plan-2  C01  0.020
 SJY  plan-2  C16  0.020
 SJY  plan-3  C17  0.020
 SJY  plan-3  O18  0.020
 SJY  plan-3  O19  0.020
 SJY  plan-3  C16  0.020

