# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 13:05:52 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2oc(C#Cc3ccc(cc3)C(O)=O)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
 XHY  XHY  "4-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid"  ligand  37  25  .  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_XHY
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
 XHY  C10  C  C      0  -0.125   0.7678   4.0287   -8.5817
 XHY  C13  C  C      0  -0.097  -0.0475   2.0912   -6.7183
 XHY  C15  C  C1     0  -0.280   1.5720   3.7218   -7.4791
 XHY  C21  C  C      0   0.402  -1.2036   7.6025  -13.1223
 XHY  C24  C  CR56   0   0.078   1.9905   8.1398  -13.0756
 XHY  C02  C  CR6    0   0.097   2.8735   9.8438  -14.5126
 XHY  C03  C  CR16   0  -0.302   3.9402  10.0130  -13.6088
 XHY  C04  C  CR16   0  -0.335   4.0566   9.2718  -12.4450
 XHY  C05  C  CR56   0   0.328   3.0598   8.3407  -12.2053
 XHY  O06  O  O      0  -0.467   2.9628   7.5158  -11.1423
 XHY  C07  C  CR5    0   0.183   1.8238   6.7761  -11.3346
 XHY  C08  C  CSP    0   0.059   1.4917   5.8289  -10.3549
 XHY  C09  C  CSP    0   0.103   1.1705   5.0035   -9.5315
 XHY  C11  C  C1     0  -0.294  -0.4479   3.3552   -8.7426
 XHY  C12  C  C1     0  -0.279  -0.8400   2.3995   -7.8227
 XHY  C14  C  C1     0  -0.283   1.1602   2.7691   -6.5635
 XHY  C16  C  C      0   0.395  -0.4959   1.0422   -5.7031
 XHY  O17  O  OC    -1  -0.584   0.2312   0.8914   -4.7033
 XHY  O18  O  O      0  -0.583  -1.5491   0.4337   -5.9689
 XHY  C19  C  CR5    0   0.030   1.1870   7.1064  -12.4911
 XHY  O22  O  OC    -1  -0.592  -1.3975   8.2480  -12.0766
 XHY  O23  O  O      0  -0.600  -1.8205   7.6936  -14.1990
 XHY  C25  C  CR16   0  -0.415   1.8949   8.9014  -14.2422
 XHY  H1   H  H      0   0.252   2.5152   4.2353   -7.3437
 XHY  H2   H  HCH2   0   0.243  -0.4041   5.7133  -12.4319
 XHY  H3   H  HCH2   0   0.230   0.1354   6.1338  -14.0497
 XHY  H4   H  HCH3   0   0.242   2.8892  11.7475  -15.5212
 XHY  H5   H  HCH3   0   0.243   3.6413  10.4508  -16.4314
 XHY  H6   H  HCH3   0   0.244   1.8872  10.5272  -16.3021
 XHY  H7   H  HCR6   0   0.251   4.6980  10.7550  -13.8306
 XHY  H8   H  HCR6   0   0.265   4.8804   9.4214  -11.7599
 XHY  H9   H  H      0   0.253  -1.0792   3.5865   -9.5911
 XHY  H10  H  H      0   0.247  -1.7803   1.8833   -7.9610
 XHY  H11  H  H      0   0.247   1.7886   2.5473   -5.7111
 XHY  H14  H  HCR6   0   0.245   1.0616   8.7625  -14.9216
 XHY  C01  C  CH3    0  -0.721   2.8163  10.6845  -15.7558
 XHY  C20  C  CH2    0  -0.681  -0.0631   6.5445  -13.0573

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
 XHY  C01  C02  single    1.502  0.020  1.502
 XHY  C02  C25  aromatic  1.385  0.020  1.385
 XHY  C02  C03  aromatic  1.408  0.020  1.408
 XHY  C25  C24  aromatic  1.396  0.020  1.396
 XHY  O23  C21  deloc     1.244  0.020  1.244
 XHY  C03  C04  aromatic  1.385  0.020  1.385
 XHY  C20  C21  single    1.557  0.020  1.557
 XHY  C20  C19  single    1.483  0.020  1.483
 XHY  C24  C19  aromatic  1.434  0.020  1.434
 XHY  C24  C05  aromatic  1.393  0.020  1.393
 XHY  C21  O22  deloc     1.244  0.020  1.244
 XHY  C19  C07  aromatic  1.361  0.020  1.361
 XHY  C04  C05  aromatic  1.385  0.020  1.385
 XHY  C05  O06  aromatic  1.349  0.020  1.349
 XHY  C07  O06  aromatic  1.372  0.020  1.372
 XHY  C07  C08  single    1.403  0.020  1.403
 XHY  C08  C09  triple    1.209  0.020  1.209
 XHY  C09  C10  single    1.419  0.020  1.419
 XHY  C11  C10  aromatic  1.399  0.020  1.399
 XHY  C11  C12  aromatic  1.383  0.020  1.383
 XHY  C10  C15  aromatic  1.399  0.020  1.399
 XHY  C12  C13  aromatic  1.394  0.020  1.394
 XHY  C15  C14  aromatic  1.384  0.020  1.384
 XHY  C13  C14  aromatic  1.394  0.020  1.394
 XHY  C13  C16  single    1.527  0.020  1.527
 XHY  O18  C16  deloc     1.245  0.020  1.245
 XHY  C16  O17  deloc     1.245  0.020  1.245
 XHY  C15  H1   single    0.930  0.020  1.080
 XHY  C20  H2   single    0.970  0.020  1.090
 XHY  C20  H3   single    0.970  0.020  1.090
 XHY  C01  H4   single    0.970  0.020  1.090
 XHY  C01  H5   single    0.970  0.020  1.090
 XHY  C01  H6   single    0.970  0.020  1.090
 XHY  C03  H7   single    0.930  0.020  1.080
 XHY  C04  H8   single    0.930  0.020  1.080
 XHY  C11  H9   single    0.930  0.020  1.080
 XHY  C12  H10  single    0.930  0.020  1.080
 XHY  C14  H11  single    0.930  0.020  1.080
 XHY  C25  H14  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
 XHY  C11  C10  C09  120.01  3.000
 XHY  C11  C10  C15  118.99  3.000
 XHY  C09  C10  C15  121.00  3.000
 XHY  C16  C13  C14  120.98  3.000
 XHY  C16  C13  C12  120.78  3.000
 XHY  C14  C13  C12  118.24  3.000
 XHY  H1   C15  C14  120.20  3.000
 XHY  H1   C15  C10  119.70  3.000
 XHY  C14  C15  C10  120.10  3.000
 XHY  O23  C21  O22  127.74  3.000
 XHY  O22  C21  C20  115.57  3.000
 XHY  O23  C21  C20  116.68  3.000
 XHY  C25  C24  C19  134.06  3.000
 XHY  C19  C24  C05  106.23  3.000
 XHY  C25  C24  C05  119.72  3.000
 XHY  C25  C02  C03  119.44  3.000
 XHY  C03  C02  C01  119.53  3.000
 XHY  C25  C02  C01  121.03  3.000
 XHY  H7   C03  C04  118.68  3.000
 XHY  H7   C03  C02  118.72  3.000
 XHY  C04  C03  C02  122.60  3.000
 XHY  H8   C04  C05  122.10  3.000
 XHY  H8   C04  C03  121.48  3.000
 XHY  C05  C04  C03  116.41  3.000
 XHY  O06  C05  C04  126.81  3.000
 XHY  O06  C05  C24  110.42  3.000
 XHY  C04  C05  C24  122.77  3.000
 XHY  C07  O06  C05  106.20  3.000
 XHY  C19  C07  C08  130.29  3.000
 XHY  C08  C07  O06  117.57  3.000
 XHY  C19  C07  O06  112.14  3.000
 XHY  C09  C08  C07  180.00  3.000
 XHY  C08  C09  C10  180.00  3.000
 XHY  H9   C11  C12  120.24  3.000
 XHY  H9   C11  C10  119.60  3.000
 XHY  C12  C11  C10  120.16  3.000
 XHY  H10  C12  C11  119.42  3.000
 XHY  H10  C12  C13  119.34  3.000
 XHY  C11  C12  C13  121.24  3.000
 XHY  H11  C14  C15  119.30  3.000
 XHY  H11  C14  C13  119.41  3.000
 XHY  C15  C14  C13  121.28  3.000
 XHY  O18  C16  O17  127.31  3.000
 XHY  O17  C16  C13  116.45  3.000
 XHY  O18  C16  C13  116.24  3.000
 XHY  C07  C19  C24  105.02  3.000
 XHY  C07  C19  C20  128.82  3.000
 XHY  C24  C19  C20  126.16  3.000
 XHY  H14  C25  C02  120.53  3.000
 XHY  H14  C25  C24  120.41  3.000
 XHY  C02  C25  C24  119.06  3.000
 XHY  H6   C01  H5   107.66  3.000
 XHY  H6   C01  H4   107.79  3.000
 XHY  H5   C01  H4   106.93  3.000
 XHY  H6   C01  C02  111.52  3.000
 XHY  H5   C01  C02  111.32  3.000
 XHY  H4   C01  C02  111.39  3.000
 XHY  H3   C20  H2   106.87  3.000
 XHY  H3   C20  C19  109.64  3.000
 XHY  H2   C20  C19  109.41  3.000
 XHY  H3   C20  C21  110.53  3.000
 XHY  H2   C20  C21  108.16  3.000
 XHY  C19  C20  C21  112.08  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
 XHY  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 XHY  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 XHY  CONST_03  C12  C11  C10  C15     0.00   0.0  0
 XHY  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 XHY  CONST_05  C03  C02  C25  C24     0.00   0.0  0
 XHY  CONST_06  O06  C07  C19  C24     0.00   0.0  0
 XHY  CONST_07  C03  C04  C05  C24     0.00   0.0  0
 XHY  CONST_08  C07  O06  C05  C24     0.00   0.0  0
 XHY  CONST_09  C19  C24  C25  C02   180.00   0.0  0
 XHY  CONST_10  C05  C24  C25  C02     0.00   0.0  0
 XHY  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 XHY  CONST_12  O06  C05  C04  C03   180.00   0.0  0
 XHY  CONST_13  C25  C02  C03  C04     0.00   0.0  0
 XHY  CONST_14  C25  C24  C05  C04     0.00   0.0  0
 XHY  CONST_15  C19  C24  C05  C04   180.00   0.0  0
 XHY  CONST_16  C07  O06  C05  C04   180.00   0.0  0
 XHY  CONST_17  C07  C19  C24  C05     0.00   0.0  0
 XHY  CONST_18  C19  C07  O06  C05     0.00   0.0  0
 XHY  CONST_19  C25  C24  C05  O06   180.00   0.0  0
 XHY  CONST_20  C19  C24  C05  O06     0.00   0.0  0
 XHY  CONST_21  C25  C24  C19  C07   180.00   0.0  0
 XHY  CONST_22  C14  C15  C10  C11     0.00   0.0  0
 XHY  CONST_23  C14  C13  C12  C11     0.00   0.0  0
 XHY  CONST_24  C16  C13  C14  C15   180.00   0.0  0
 XHY  CONST_25  C25  C24  C19  C20     0.00   0.0  0
 XHY  CONST_26  C05  C24  C19  C20   180.00   0.0  0
 XHY  CONST_27  O06  C07  C19  C20   180.00   0.0  0
 XHY  CONST_28  C01  C02  C25  C24   180.00   0.0  0
 XHY  CONST_29  C08  C07  C19  C24   180.00   0.0  0
 XHY  CONST_30  C04  C03  C02  C01   180.00   0.0  0
 XHY  CONST_31  C08  C07  O06  C05   180.00   0.0  0
 XHY  CONST_32  C12  C11  C10  C09   180.00   0.0  0
 XHY  CONST_33  C14  C15  C10  C09   180.00   0.0  0
 XHY  CONST_34  C16  C13  C12  C11   180.00   0.0  0
 XHY  CONST_35  H10  C12  C11  C10   180.00   0.0  0
 XHY  CONST_36  H11  C14  C15  C10   180.00   0.0  0
 XHY  CONST_37  H9   C11  C12  C13   180.00   0.0  0
 XHY  CONST_38  H1   C15  C14  C13   180.00   0.0  0
 XHY  CONST_39  H9   C11  C10  C15   180.00   0.0  0
 XHY  CONST_40  H8   C04  C05  C24   180.00   0.0  0
 XHY  CONST_41  H8   C04  C03  C02   180.00   0.0  0
 XHY  CONST_42  H14  C25  C02  C03   180.00   0.0  0
 XHY  CONST_43  H14  C25  C24  C05   180.00   0.0  0
 XHY  CONST_44  H7   C03  C04  C05   180.00   0.0  0
 XHY  CONST_45  H8   C04  C05  O06     0.00   0.0  0
 XHY  CONST_46  H1   C15  C10  C11   180.00   0.0  0
 XHY  CONST_47  H11  C14  C13  C12   180.00   0.0  0
 XHY  CONST_48  H10  C12  C13  C14   180.00   0.0  0
 XHY  CONST_49  H14  C25  C24  C19     0.00   0.0  0
 XHY  CONST_50  H7   C03  C02  C25   180.00   0.0  0
 XHY  Var_01    C07  C08  C09  C10     0.29  30.0  3
 XHY  Var_02    C24  C19  C20  C21   -64.84  30.0  2
 XHY  Var_03    C07  C19  C20  C21   115.21  30.0  2
 XHY  Var_04    O18  C16  C13  C12     4.44  30.0  2
 XHY  Var_05    O17  C16  C13  C12  -175.54  30.0  2
 XHY  Var_06    O18  C16  C13  C14  -175.82  30.0  2
 XHY  Var_07    O17  C16  C13  C14     4.20  30.0  2
 XHY  Var_08    H2   C20  C19  C24   175.19  30.0  2
 XHY  Var_09    H3   C20  C19  C24    58.29  30.0  2
 XHY  Var_10    H4   C01  C02  C03   -53.19  30.0  2
 XHY  Var_11    H5   C01  C02  C03    66.07  30.0  2
 XHY  Var_12    H6   C01  C02  C03  -173.67  30.0  2
 XHY  Var_13    H2   C20  C19  C07    -4.76  30.0  2
 XHY  Var_14    H3   C20  C19  C07  -121.66  30.0  2
 XHY  Var_15    H4   C01  C02  C25   126.98  30.0  2
 XHY  Var_16    H5   C01  C02  C25  -113.76  30.0  2
 XHY  Var_17    H6   C01  C02  C25     6.50  30.0  2
 XHY  Var_18    O23  C21  C20  C19   131.79  30.0  3
 XHY  Var_19    O22  C21  C20  C19   -49.00  30.0  3
 XHY  Var_20    H2   C20  C21  O22    71.70  30.0  2
 XHY  Var_21    H3   C20  C21  O22  -171.63  30.0  2
 XHY  Var_22    H2   C20  C21  O23  -107.52  30.0  2
 XHY  Var_23    H3   C20  C21  O23     9.15  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
 XHY  plan-1  C10  0.020
 XHY  plan-1  C13  0.020
 XHY  plan-1  C15  0.020
 XHY  plan-1  C08  0.020
 XHY  plan-1  C09  0.020
 XHY  plan-1  C11  0.020
 XHY  plan-1  C12  0.020
 XHY  plan-1  C14  0.020
 XHY  plan-1  C16  0.020
 XHY  plan-1  H1   0.020
 XHY  plan-1  H9   0.020
 XHY  plan-1  H10  0.020
 XHY  plan-1  H11  0.020
 XHY  plan-2  C24  0.020
 XHY  plan-2  C02  0.020
 XHY  plan-2  C03  0.020
 XHY  plan-2  C04  0.020
 XHY  plan-2  C05  0.020
 XHY  plan-2  O06  0.020
 XHY  plan-2  C07  0.020
 XHY  plan-2  C08  0.020
 XHY  plan-2  C09  0.020
 XHY  plan-2  C19  0.020
 XHY  plan-2  C25  0.020
 XHY  plan-2  H7   0.020
 XHY  plan-2  H8   0.020
 XHY  plan-2  H14  0.020
 XHY  plan-2  C01  0.020
 XHY  plan-2  C20  0.020
 XHY  plan-3  C21  0.020
 XHY  plan-3  O22  0.020
 XHY  plan-3  O23  0.020
 XHY  plan-3  C20  0.020
 XHY  plan-4  C13  0.020
 XHY  plan-4  C16  0.020
 XHY  plan-4  O17  0.020
 XHY  plan-4  O18  0.020

