# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 12:27:33 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2oc(C#Cc3cccc(c3)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
 XFS  XFS  "3-{[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_XFS
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
 XFS  C10  C  C      0  -0.096   1.3143   4.1807   -8.0517
 XFS  C13  C  C1     0  -0.288   0.7041   2.2805   -6.1203
 XFS  C15  C  C      0   0.399  -1.5654   1.8173   -7.1670
 XFS  C21  C  C      0   0.418  -0.9726   7.4192  -12.4320
 XFS  C24  C  CR56   0   0.072   2.2975   8.2855  -12.6242
 XFS  C02  C  CR6    0   0.096   3.1086  10.0301  -14.0582
 XFS  C03  C  CR16   0  -0.303   4.1506  10.2621  -13.1399
 XFS  C04  C  CR16   0  -0.335   4.2903   9.5325  -11.9720
 XFS  C05  C  CR56   0   0.328   3.3435   8.5485  -11.7419
 XFS  O06  O  O      0  -0.467   3.2796   7.7225  -10.6775
 XFS  C07  C  CR5    0   0.181   2.1834   6.9219  -10.8797
 XFS  C08  C  CSP    0   0.049   1.8914   5.9728   -9.8886
 XFS  C09  C  CSP    0   0.111   1.6258   5.1462   -9.0468
 XFS  C11  C  C1     0  -0.301   2.2315   3.9009   -7.0323
 XFS  C12  C  C1     0  -0.236   1.9174   2.9552   -6.0716
 XFS  C14  C  C      0  -0.085  -0.2248   2.5508   -7.1239
 XFS  O16  O  O      0  -0.582  -2.3790   2.2004   -8.0280
 XFS  O17  O  OC    -1  -0.583  -1.7184   0.9054   -6.3340
 XFS  C18  C  C1     0  -0.356   0.0903   3.5055   -8.0832
 XFS  C19  C  CR5    0   0.065   1.5416   7.2145  -12.0433
 XFS  O22  O  O      0  -0.607  -1.9009   7.1272  -13.2085
 XFS  O23  O  OC    -1  -0.590  -0.9773   8.2703  -11.5259
 XFS  C25  C  CR16   0  -0.418   2.1788   9.0370  -13.7960
 XFS  H1   H  H      0   0.248   0.4709   1.5398   -5.3669
 XFS  H2   H  HCH2   0   0.252   0.1585   5.6109  -12.1357
 XFS  H3   H  HCH2   0   0.239   0.4804   6.3788  -13.6699
 XFS  H4   H  HCH3   0   0.242   2.9626  11.9262  -15.0727
 XFS  H5   H  HCH3   0   0.243   3.9004  10.7240  -15.9375
 XFS  H6   H  HCH3   0   0.244   2.1445  10.6014  -15.8973
 XFS  H7   H  HCR6   0   0.250   4.8711  11.0429  -13.3533
 XFS  H8   H  HCR6   0   0.265   5.0961   9.7268  -11.2765
 XFS  H9   H  H      0   0.256   3.1784   4.4246   -6.9997
 XFS  H10  H  H      0   0.254   2.6250   2.7410   -5.2809
 XFS  H12  H  H      0   0.246  -0.6210   3.7278   -8.8675
 XFS  H14  H  HCR6   0   0.247   1.3712   8.8471  -14.4932
 XFS  C01  C  CH3    0  -0.721   3.0216  10.8621  -15.3060
 XFS  C20  C  CH2    0  -0.735   0.3270   6.5834  -12.6079

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
 XFS  C01  C02  single    1.502  0.020  1.502
 XFS  C02  C25  aromatic  1.385  0.020  1.385
 XFS  C02  C03  aromatic  1.408  0.020  1.408
 XFS  C25  C24  aromatic  1.397  0.020  1.397
 XFS  O22  C21  deloc     1.245  0.020  1.245
 XFS  C03  C04  aromatic  1.384  0.020  1.384
 XFS  C20  C21  single    1.555  0.020  1.555
 XFS  C20  C19  single    1.481  0.020  1.481
 XFS  C24  C19  aromatic  1.434  0.020  1.434
 XFS  C24  C05  aromatic  1.393  0.020  1.393
 XFS  C21  O23  deloc     1.243  0.020  1.243
 XFS  C19  C07  aromatic  1.361  0.020  1.361
 XFS  C04  C05  aromatic  1.385  0.020  1.385
 XFS  C05  O06  aromatic  1.349  0.020  1.349
 XFS  C07  O06  aromatic  1.372  0.020  1.372
 XFS  C07  C08  single    1.403  0.020  1.403
 XFS  C08  C09  triple    1.209  0.020  1.209
 XFS  C09  C10  single    1.421  0.020  1.421
 XFS  C10  C18  aromatic  1.398  0.020  1.398
 XFS  C10  C11  aromatic  1.399  0.020  1.399
 XFS  C18  C14  aromatic  1.390  0.020  1.390
 XFS  O16  C15  deloc     1.245  0.020  1.245
 XFS  C11  C12  aromatic  1.384  0.020  1.384
 XFS  C14  C15  single    1.529  0.020  1.529
 XFS  C14  C13  aromatic  1.394  0.020  1.394
 XFS  C15  O17  deloc     1.245  0.020  1.245
 XFS  C12  C13  aromatic  1.389  0.020  1.389
 XFS  C13  H1   single    0.930  0.020  1.080
 XFS  C20  H2   single    0.970  0.020  1.090
 XFS  C20  H3   single    0.970  0.020  1.090
 XFS  C01  H4   single    0.970  0.020  1.090
 XFS  C01  H5   single    0.970  0.020  1.090
 XFS  C01  H6   single    0.970  0.020  1.090
 XFS  C03  H7   single    0.930  0.020  1.080
 XFS  C04  H8   single    0.930  0.020  1.080
 XFS  C11  H9   single    0.930  0.020  1.080
 XFS  C12  H10  single    0.930  0.020  1.080
 XFS  C18  H12  single    0.930  0.020  1.080
 XFS  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
 XFS  C18  C10  C11  119.57  3.000
 XFS  C11  C10  C09  120.15  3.000
 XFS  C18  C10  C09  120.28  3.000
 XFS  H1   C13  C14  119.37  3.000
 XFS  H1   C13  C12  119.76  3.000
 XFS  C14  C13  C12  120.87  3.000
 XFS  O17  C15  O16  127.45  3.000
 XFS  O17  C15  C14  116.13  3.000
 XFS  O16  C15  C14  116.42  3.000
 XFS  O23  C21  O22  127.76  3.000
 XFS  O23  C21  C20  116.97  3.000
 XFS  O22  C21  C20  115.24  3.000
 XFS  C25  C24  C19  134.17  3.000
 XFS  C19  C24  C05  106.27  3.000
 XFS  C25  C24  C05  119.56  3.000
 XFS  C25  C02  C03  119.42  3.000
 XFS  C03  C02  C01  119.56  3.000
 XFS  C25  C02  C01  121.02  3.000
 XFS  H7   C03  C04  118.61  3.000
 XFS  H7   C03  C02  118.83  3.000
 XFS  C04  C03  C02  122.55  3.000
 XFS  H8   C04  C05  122.01  3.000
 XFS  H8   C04  C03  121.52  3.000
 XFS  C05  C04  C03  116.47  3.000
 XFS  O06  C05  C04  126.77  3.000
 XFS  O06  C05  C24  110.40  3.000
 XFS  C04  C05  C24  122.83  3.000
 XFS  C07  O06  C05  106.19  3.000
 XFS  C19  C07  C08  130.65  3.000
 XFS  C08  C07  O06  117.18  3.000
 XFS  C19  C07  O06  112.17  3.000
 XFS  C09  C08  C07  180.00  3.000
 XFS  C08  C09  C10  180.00  3.000
 XFS  H9   C11  C12  120.53  3.000
 XFS  H9   C11  C10  119.90  3.000
 XFS  C12  C11  C10  119.57  3.000
 XFS  H10  C12  C11  119.60  3.000
 XFS  H10  C12  C13  120.02  3.000
 XFS  C11  C12  C13  120.38  3.000
 XFS  C18  C14  C15  120.60  3.000
 XFS  C15  C14  C13  120.78  3.000
 XFS  C18  C14  C13  118.63  3.000
 XFS  H12  C18  C14  119.50  3.000
 XFS  H12  C18  C10  119.52  3.000
 XFS  C14  C18  C10  120.98  3.000
 XFS  C07  C19  C24  104.97  3.000
 XFS  C07  C19  C20  128.42  3.000
 XFS  C24  C19  C20  126.61  3.000
 XFS  H14  C25  C02  120.26  3.000
 XFS  H14  C25  C24  120.57  3.000
 XFS  C02  C25  C24  119.16  3.000
 XFS  H6   C01  H5   107.70  3.000
 XFS  H6   C01  H4   107.81  3.000
 XFS  H5   C01  H4   106.90  3.000
 XFS  H6   C01  C02  111.40  3.000
 XFS  H5   C01  C02  111.35  3.000
 XFS  H4   C01  C02  111.45  3.000
 XFS  H3   C20  H2   105.95  3.000
 XFS  H3   C20  C19  109.59  3.000
 XFS  H2   C20  C19  109.91  3.000
 XFS  H3   C20  C21  109.15  3.000
 XFS  H2   C20  C21  107.47  3.000
 XFS  C19  C20  C21  114.41  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
 XFS  CONST_01  C13  C14  C18  C10     0.00   0.0  0
 XFS  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 XFS  CONST_03  C03  C02  C25  C24     0.00   0.0  0
 XFS  CONST_04  O06  C07  C19  C24     0.00   0.0  0
 XFS  CONST_05  C03  C04  C05  C24     0.00   0.0  0
 XFS  CONST_06  C07  O06  C05  C24     0.00   0.0  0
 XFS  CONST_07  C19  C24  C25  C02   180.00   0.0  0
 XFS  CONST_08  C05  C24  C25  C02     0.00   0.0  0
 XFS  CONST_09  C05  C04  C03  C02     0.00   0.0  0
 XFS  CONST_10  O06  C05  C04  C03   180.00   0.0  0
 XFS  CONST_11  C25  C02  C03  C04     0.00   0.0  0
 XFS  CONST_12  C25  C24  C05  C04     0.00   0.0  0
 XFS  CONST_13  C19  C24  C05  C04   180.00   0.0  0
 XFS  CONST_14  C07  O06  C05  C04   180.00   0.0  0
 XFS  CONST_15  C07  C19  C24  C05     0.00   0.0  0
 XFS  CONST_16  C19  C07  O06  C05     0.00   0.0  0
 XFS  CONST_17  C25  C24  C05  O06   180.00   0.0  0
 XFS  CONST_18  C19  C24  C05  O06     0.00   0.0  0
 XFS  CONST_19  C25  C24  C19  C07   180.00   0.0  0
 XFS  CONST_20  C14  C18  C10  C11     0.00   0.0  0
 XFS  CONST_21  C14  C13  C12  C11     0.00   0.0  0
 XFS  CONST_22  C18  C10  C11  C12     0.00   0.0  0
 XFS  CONST_23  C18  C14  C13  C12     0.00   0.0  0
 XFS  CONST_24  C15  C14  C18  C10   180.00   0.0  0
 XFS  CONST_25  C12  C13  C14  C15   180.00   0.0  0
 XFS  CONST_26  C25  C24  C19  C20     0.00   0.0  0
 XFS  CONST_27  C05  C24  C19  C20   180.00   0.0  0
 XFS  CONST_28  O06  C07  C19  C20   180.00   0.0  0
 XFS  CONST_29  C01  C02  C25  C24   180.00   0.0  0
 XFS  CONST_30  C08  C07  C19  C24   180.00   0.0  0
 XFS  CONST_31  C04  C03  C02  C01   180.00   0.0  0
 XFS  CONST_32  C08  C07  O06  C05   180.00   0.0  0
 XFS  CONST_33  C14  C18  C10  C09   180.00   0.0  0
 XFS  CONST_34  C12  C11  C10  C09   180.00   0.0  0
 XFS  CONST_35  H10  C12  C11  C10   180.00   0.0  0
 XFS  CONST_36  H12  C18  C14  C13   180.00   0.0  0
 XFS  CONST_37  H9   C11  C12  C13   180.00   0.0  0
 XFS  CONST_38  H8   C04  C05  C24   180.00   0.0  0
 XFS  CONST_39  H8   C04  C03  C02   180.00   0.0  0
 XFS  CONST_40  H14  C25  C02  C03   180.00   0.0  0
 XFS  CONST_41  H14  C25  C24  C05   180.00   0.0  0
 XFS  CONST_42  H7   C03  C04  C05   180.00   0.0  0
 XFS  CONST_43  H8   C04  C05  O06     0.00   0.0  0
 XFS  CONST_44  H12  C18  C10  C11   180.00   0.0  0
 XFS  CONST_45  H1   C13  C12  C11   180.00   0.0  0
 XFS  CONST_46  H10  C12  C13  C14   180.00   0.0  0
 XFS  CONST_47  H9   C11  C10  C18   180.00   0.0  0
 XFS  CONST_48  H1   C13  C14  C18   180.00   0.0  0
 XFS  CONST_49  H14  C25  C24  C19     0.00   0.0  0
 XFS  CONST_50  H7   C03  C02  C25   180.00   0.0  0
 XFS  Var_01    C07  C08  C09  C10  -140.67  30.0  2
 XFS  Var_02    O16  C15  C14  C13   174.10  30.0  2
 XFS  Var_03    O17  C15  C14  C13    -5.80  30.0  2
 XFS  Var_04    C24  C19  C20  C21   -77.23  30.0  2
 XFS  Var_05    C07  C19  C20  C21   102.64  30.0  2
 XFS  Var_06    C18  C14  C15  O16    -5.66  30.0  3
 XFS  Var_07    C18  C14  C15  O17   174.45  30.0  3
 XFS  Var_08    H2   C20  C19  C24   161.77  30.0  2
 XFS  Var_09    H3   C20  C19  C24    45.72  30.0  2
 XFS  Var_10    H4   C01  C02  C03   -57.03  30.0  2
 XFS  Var_11    H5   C01  C02  C03    62.24  30.0  2
 XFS  Var_12    H6   C01  C02  C03  -177.50  30.0  2
 XFS  Var_13    H2   C20  C19  C07   -18.35  30.0  2
 XFS  Var_14    H3   C20  C19  C07  -134.40  30.0  2
 XFS  Var_15    H4   C01  C02  C25   122.96  30.0  2
 XFS  Var_16    H5   C01  C02  C25  -117.76  30.0  2
 XFS  Var_17    H6   C01  C02  C25     2.49  30.0  2
 XFS  Var_18    O22  C21  C20  C19   159.85  30.0  3
 XFS  Var_19    O23  C21  C20  C19   -21.69  30.0  3
 XFS  Var_20    H2   C20  C21  O22   -77.82  30.0  2
 XFS  Var_21    H3   C20  C21  O22    36.66  30.0  2
 XFS  Var_22    H2   C20  C21  O23   100.65  30.0  2
 XFS  Var_23    H3   C20  C21  O23  -144.88  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
 XFS  plan-1  C10  0.020
 XFS  plan-1  C13  0.020
 XFS  plan-1  C15  0.020
 XFS  plan-1  C08  0.020
 XFS  plan-1  C09  0.020
 XFS  plan-1  C11  0.020
 XFS  plan-1  C12  0.020
 XFS  plan-1  C14  0.020
 XFS  plan-1  C18  0.020
 XFS  plan-1  H1   0.020
 XFS  plan-1  H9   0.020
 XFS  plan-1  H10  0.020
 XFS  plan-1  H12  0.020
 XFS  plan-2  C24  0.020
 XFS  plan-2  C02  0.020
 XFS  plan-2  C03  0.020
 XFS  plan-2  C04  0.020
 XFS  plan-2  C05  0.020
 XFS  plan-2  O06  0.020
 XFS  plan-2  C07  0.020
 XFS  plan-2  C08  0.020
 XFS  plan-2  C09  0.020
 XFS  plan-2  C19  0.020
 XFS  plan-2  C25  0.020
 XFS  plan-2  H7   0.020
 XFS  plan-2  H8   0.020
 XFS  plan-2  H14  0.020
 XFS  plan-2  C01  0.020
 XFS  plan-2  C20  0.020
 XFS  plan-3  C15  0.020
 XFS  plan-3  C14  0.020
 XFS  plan-3  O16  0.020
 XFS  plan-3  O17  0.020
 XFS  plan-4  C21  0.020
 XFS  plan-4  O22  0.020
 XFS  plan-4  O23  0.020
 XFS  plan-4  C20  0.020

