# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:04:29 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-(2-ethynyl-5-methyl-1-benzofuran-3-yl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2oc(C#C)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
 S0Y  S0Y  '2-(2-ethynyl-5-methyl-1-benzofuran-3-yl)ethanoic acid'  ligand  25  16  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S0Y
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
 S0Y  C10  C  C      0   0.056   1.3651   7.1189  -12.1961
 S0Y  C15  C  CR6    0   0.074   2.1573   8.2050  -12.6991
 S0Y  C01  C  CH3    0  -0.722   2.9928  10.9131  -15.2105
 S0Y  C02  C  CR6    0   0.096   3.0361  10.0048  -14.0158
 S0Y  C03  C  CR16   0  -0.299   4.0781  10.1428  -13.0771
 S0Y  C04  C  CR16   0  -0.335   4.1786   9.3449  -11.9508
 S0Y  C05  C  CR6    0   0.340   3.1991   8.3781  -11.7914
 S0Y  O06  O  OC2    0  -0.462   3.0972   7.4899  -10.7818
 S0Y  C07  C  C      0   0.223   1.9827   6.7371  -11.0482
 S0Y  C08  C  CSP    0   0.223   1.6636   5.7185  -10.1302
 S0Y  C09  C  CSP1   0  -0.562   1.3742   4.8483   -9.3494
 S0Y  C11  C  CH2    0  -0.683   0.1439   6.5634  -12.8268
 S0Y  C12  C  C      0   0.403  -1.0321   7.5823  -12.8249
 S0Y  O13  O  O      0  -0.601  -1.6734   7.6916  -13.8862
 S0Y  O14  O  OC    -1  -0.591  -1.2311   8.1777  -11.7518
 S0Y  C16  C  CR16   0  -0.414   2.0718   9.0297  -13.8232
 S0Y  H1   H  HCH3   0   0.242   2.9714  11.9620  -14.9100
 S0Y  H2   H  HCH3   0   0.243   3.8702  10.7811  -15.8461
 S0Y  H3   H  HCH3   0   0.244   2.1104  10.7272  -15.8218
 S0Y  H4   H  HCR6   0   0.252   4.8244  10.9116  -13.2383
 S0Y  H5   H  HCR6   0   0.266   4.9849   9.4720  -11.2402
 S0Y  H6   H  H      0   0.284   1.1154   4.0802   -8.6561
 S0Y  H7   H  HCH2   0   0.245  -0.1754   5.6743  -12.2753
 S0Y  H8   H  HCH2   0   0.232   0.3695   6.2341  -13.8430
 S0Y  H10  H  HCR6   0   0.246   1.2582   8.9086  -14.5292

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
 S0Y  C01  C02  single    1.501  0.020  1.501
 S0Y  C02  C16  aromatic  1.385  0.020  1.385
 S0Y  C02  C03  aromatic  1.409  0.020  1.409
 S0Y  C16  C15  aromatic  1.397  0.020  1.397
 S0Y  O13  C12  deloc     1.245  0.020  1.245
 S0Y  C03  C04  aromatic  1.384  0.020  1.384
 S0Y  C11  C12  single    1.556  0.020  1.556
 S0Y  C11  C10  single    1.482  0.020  1.482
 S0Y  C15  C10  aromatic  1.435  0.020  1.435
 S0Y  C15  C05  aromatic  1.393  0.020  1.393
 S0Y  C12  O14  deloc     1.243  0.020  1.243
 S0Y  C10  C07  aromatic  1.358  0.020  1.358
 S0Y  C04  C05  aromatic  1.386  0.020  1.386
 S0Y  C05  O06  aromatic  1.348  0.020  1.348
 S0Y  C07  O06  aromatic  1.371  0.020  1.371
 S0Y  C07  C08  single    1.408  0.020  1.408
 S0Y  C08  C09  triple    1.204  0.020  1.204
 S0Y  C01  H1   single    0.939  0.020  1.096
 S0Y  C01  H2   single    0.939  0.020  1.096
 S0Y  C01  H3   single    0.939  0.020  1.096
 S0Y  C03  H4   single    0.929  0.020  1.085
 S0Y  C04  H5   single    0.929  0.020  1.085
 S0Y  C09  H6   single    0.913  0.020  1.066
 S0Y  C11  H7   single    0.939  0.020  1.096
 S0Y  C11  H8   single    0.939  0.020  1.096
 S0Y  C16  H10  single    0.929  0.020  1.085

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
 S0Y  C11  C10  C07  128.96  3.000
 S0Y  C07  C10  C15  104.95  3.000
 S0Y  C11  C10  C15  126.10  3.000
 S0Y  C16  C15  C05  119.80  3.000
 S0Y  C05  C15  C10  106.17  3.000
 S0Y  C16  C15  C10  134.03  3.000
 S0Y  H3   C01  H2   107.68  3.000
 S0Y  H3   C01  H1   107.62  3.000
 S0Y  H2   C01  H1   107.00  3.000
 S0Y  H3   C01  C02  111.51  3.000
 S0Y  H2   C01  C02  111.53  3.000
 S0Y  H1   C01  C02  111.28  3.000
 S0Y  C16  C02  C03  119.42  3.000
 S0Y  C03  C02  C01  119.48  3.000
 S0Y  C16  C02  C01  121.10  3.000
 S0Y  H4   C03  C04  118.70  3.000
 S0Y  H4   C03  C02  118.66  3.000
 S0Y  C04  C03  C02  122.64  3.000
 S0Y  H5   C04  C05  122.21  3.000
 S0Y  H5   C04  C03  121.38  3.000
 S0Y  C05  C04  C03  116.40  3.000
 S0Y  O06  C05  C04  126.81  3.000
 S0Y  O06  C05  C15  110.46  3.000
 S0Y  C04  C05  C15  122.72  3.000
 S0Y  C07  O06  C05  106.12  3.000
 S0Y  C08  C07  O06  117.05  3.000
 S0Y  C08  C07  C10  130.65  3.000
 S0Y  O06  C07  C10  112.30  3.000
 S0Y  C09  C08  C07  180.00  3.000
 S0Y  H6   C09  C08  180.00  3.000
 S0Y  H8   C11  H7   106.53  3.000
 S0Y  H8   C11  C12  110.78  3.000
 S0Y  H7   C11  C12  108.12  3.000
 S0Y  H8   C11  C10  109.80  3.000
 S0Y  H7   C11  C10  109.30  3.000
 S0Y  C12  C11  C10  112.13  3.000
 S0Y  O14  C12  O13  127.69  3.000
 S0Y  O14  C12  C11  115.82  3.000
 S0Y  O13  C12  C11  116.48  3.000
 S0Y  H10  C16  C02  120.71  3.000
 S0Y  H10  C16  C15  120.27  3.000
 S0Y  C02  C16  C15  119.02  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
 S0Y  CONST_01  C02  C16  C15  C10  180.00   0.0  0
 S0Y  CONST_02  C04  C05  C15  C10  180.00   0.0  0
 S0Y  CONST_03  O06  C05  C15  C10    0.00   0.0  0
 S0Y  CONST_04  C05  O06  C07  C10    0.00   0.0  0
 S0Y  CONST_05  C03  C02  C16  C15    0.00   0.0  0
 S0Y  CONST_06  O06  C07  C10  C15    0.00   0.0  0
 S0Y  CONST_07  C03  C04  C05  C15    0.00   0.0  0
 S0Y  CONST_08  C07  O06  C05  C15    0.00   0.0  0
 S0Y  CONST_09  C05  C15  C16  C02    0.00   0.0  0
 S0Y  CONST_10  C05  C04  C03  C02    0.00   0.0  0
 S0Y  CONST_11  O06  C05  C04  C03  180.00   0.0  0
 S0Y  CONST_12  C16  C02  C03  C04    0.00   0.0  0
 S0Y  CONST_13  C16  C15  C05  C04    0.00   0.0  0
 S0Y  CONST_14  C07  O06  C05  C04  180.00   0.0  0
 S0Y  CONST_15  C07  C10  C15  C05    0.00   0.0  0
 S0Y  CONST_16  C16  C15  C05  O06  180.00   0.0  0
 S0Y  CONST_17  C16  C15  C10  C07  180.00   0.0  0
 S0Y  CONST_18  C01  C02  C16  C15  180.00   0.0  0
 S0Y  CONST_19  C08  C07  C10  C15  180.00   0.0  0
 S0Y  CONST_20  C04  C03  C02  C01  180.00   0.0  0
 S0Y  CONST_21  C11  C10  C15  C05  180.00   0.0  0
 S0Y  CONST_22  C08  C07  O06  C05  180.00   0.0  0
 S0Y  CONST_23  C11  C10  C07  O06  180.00   0.0  0
 S0Y  CONST_24  C16  C15  C10  C11    0.00   0.0  0
 S0Y  CONST_25  H10  C16  C15  C10    0.00   0.0  0
 S0Y  CONST_26  H5   C04  C05  C15  180.00   0.0  0
 S0Y  CONST_27  H4   C03  C04  C05  180.00   0.0  0
 S0Y  Var_01    C12  C11  C10  C15  -66.39  30.0  3
 S0Y  Var_02    H1   C01  C02  C03  -57.01  30.0  2
 S0Y  Var_03    O13  C12  C11  C10  134.99  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
 S0Y  plan-1  C10  0.020
 S0Y  plan-1  C15  0.020
 S0Y  plan-1  C01  0.020
 S0Y  plan-1  C02  0.020
 S0Y  plan-1  C03  0.020
 S0Y  plan-1  C04  0.020
 S0Y  plan-1  C05  0.020
 S0Y  plan-1  O06  0.020
 S0Y  plan-1  C07  0.020
 S0Y  plan-1  C08  0.020
 S0Y  plan-1  C09  0.020
 S0Y  plan-1  C11  0.020
 S0Y  plan-1  C16  0.020
 S0Y  plan-1  H4   0.020
 S0Y  plan-1  H5   0.020
 S0Y  plan-1  H10  0.020
 S0Y  plan-2  C11  0.020
 S0Y  plan-2  C12  0.020
 S0Y  plan-2  O13  0.020
 S0Y  plan-2  O14  0.020

