# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Nov 20 13:17:24 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: (2S)-3-methyl-2-{5-methyl-2-[(thiophen-2-yl)ethynyl]-1-benzofuran-3-yl}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](C(O)=O)c1c(oc2ccc(C)cc12)C#Cc3sccc3
#
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
 TXM  TXM  "(2S)-3-methyl-2-{5-methyl-2-[(thiophen-2-yl)ethynyl]-1-benzofuran-3-yl}butanoic acid"  ligand  42  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TXM
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
 TXM  C13   C  CR16  0  -0.302   3.3952   9.0063  -13.4150
 TXM  C15   C  CH3   0  -0.720   2.0173  10.0406  -15.2474
 TXM  C17   C  CR56  0   0.091   1.3550   7.2645  -12.7556
 TXM  C20   C  CR5   0  -0.447   0.3983   2.8900   -8.4669
 TXM  C21   C  CR15  0  -0.220   0.7297   2.8182   -7.1364
 TXM  C22   C  CR15  0  -0.177   0.1841   1.6790   -6.5014
 TXM  C02   C  CH1   0  -0.211  -0.8510   4.6766  -13.5104
 TXM  C03   C  CH3   0  -0.664  -0.2990   5.0771  -14.8741
 TXM  C04   C  CH1   0  -0.492  -0.8360   5.7998  -12.4529
 TXM  C05   C  C     0   0.554  -1.7290   6.9927  -12.7423
 TXM  O06   O  O     0  -0.419  -2.4261   7.1422  -13.7122
 TXM  O07   O  OH1   0  -0.586  -1.6639   7.8825  -11.7571
 TXM  C08   C  CR5   0   0.045   0.5514   6.2570  -12.1244
 TXM  C09   C  CR5   0   0.205   1.3331   5.7401  -11.1366
 TXM  O10   O  O     0  -0.457   2.5600   6.3318  -11.0922
 TXM  C11   C  CR56  0   0.330   2.5685   7.2633  -12.0689
 TXM  C12   C  CR16  0  -0.332   3.6112   8.1213  -12.3749
 TXM  C14   C  CR6   0   0.102   2.1852   9.0455  -14.1352
 TXM  C16   C  CR16  0  -0.434   1.1655   8.1701  -13.8046
 TXM  C18   C  CSP   0   0.083   1.0503   4.7379  -10.1962
 TXM  C19   C  CSP   0   0.167   0.7540   3.8803   -9.3966
 TXM  C23   C  CR15  0  -0.457  -0.5512   0.9054   -7.3508
 TXM  S24   S  S2    0   0.243  -0.5854   1.5458   -8.9334
 TXM  H131  H  HCR6  0   0.255   4.1855   9.6966  -13.6846
 TXM  H151  H  HCH3  0   0.245   2.0718  11.0639  -14.8725
 TXM  H152  H  HCH3  0   0.244   2.8016   9.9326  -15.9977
 TXM  H153  H  HCH3  0   0.245   1.0574   9.9219  -15.7479
 TXM  H211  H  HCR5  0   0.274   1.3377   3.5619   -6.6420
 TXM  H221  H  HCR5  0   0.276   0.3272   1.4451   -5.4567
 TXM  H012  H  HCH3  0   0.226  -2.6164   3.7403  -12.6479
 TXM  H013  H  HCH3  0   0.229  -2.9509   4.6558  -14.1193
 TXM  H011  H  HCH3  0   0.231  -2.1416   3.0982  -14.2152
 TXM  H021  H  HCH1  0   0.238  -0.1731   3.9203  -13.1005
 TXM  H032  H  HCH3  0   0.233   0.7139   5.4740  -14.8039
 TXM  H033  H  HCH3  0   0.232  -0.2585   4.2014  -15.5233
 TXM  H031  H  HCH3  0   0.227  -0.9230   5.8216  -15.3661
 TXM  H041  H  HCH1  0   0.300  -1.2447   5.3588  -11.5334
 TXM  H1    H  HOH1  0   0.479  -2.2443   8.6339  -11.9535
 TXM  H121  H  HCR6  0   0.270   4.5455   8.1051  -11.8295
 TXM  H161  H  HCR6  0   0.251   0.2385   8.1899  -14.3642
 TXM  H231  H  HCR5  0   0.306  -1.0770  -0.0097   -7.1248
 TXM  C01   C  CH3   0  -0.664  -2.2214   4.0141  -13.6281

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
 TXM  C15  C14   single    1.502  0.020  1.502
 TXM  C03  C02   single    1.525  0.020  1.525
 TXM  C14  C16   aromatic  1.384  0.020  1.384
 TXM  C14  C13   aromatic  1.409  0.020  1.409
 TXM  C16  C17   aromatic  1.399  0.020  1.399
 TXM  C02  C01   single    1.527  0.020  1.527
 TXM  C02  C04   single    1.543  0.020  1.543
 TXM  O06  C05   double    1.204  0.020  1.204
 TXM  C13  C12   aromatic  1.383  0.020  1.383
 TXM  C17  C08   aromatic  1.435  0.020  1.435
 TXM  C17  C11   aromatic  1.394  0.020  1.394
 TXM  C05  C04   single    1.518  0.020  1.518
 TXM  C05  O07   single    1.329  0.020  1.329
 TXM  C04  C08   single    1.497  0.020  1.497
 TXM  C12  C11   aromatic  1.385  0.020  1.385
 TXM  C08  C09   aromatic  1.362  0.020  1.362
 TXM  C11  O10   aromatic  1.350  0.020  1.350
 TXM  C09  O10   aromatic  1.363  0.020  1.363
 TXM  C09  C18   single    1.403  0.020  1.403
 TXM  C18  C19   triple    1.209  0.020  1.209
 TXM  C19  C20   single    1.404  0.020  1.404
 TXM  C20  S24   aromatic  1.730  0.020  1.730
 TXM  C20  C21   aromatic  1.373  0.020  1.373
 TXM  S24  C23   aromatic  1.708  0.020  1.708
 TXM  C21  C22   aromatic  1.414  0.020  1.414
 TXM  C23  C22   aromatic  1.364  0.020  1.364
 TXM  C13  H131  single    0.930  0.020  1.080
 TXM  C15  H151  single    0.970  0.020  1.090
 TXM  C15  H152  single    0.970  0.020  1.090
 TXM  C15  H153  single    0.970  0.020  1.090
 TXM  C21  H211  single    0.930  0.020  1.080
 TXM  C22  H221  single    0.930  0.020  1.080
 TXM  C01  H012  single    0.970  0.020  1.090
 TXM  C01  H013  single    0.970  0.020  1.090
 TXM  C01  H011  single    0.970  0.020  1.090
 TXM  C02  H021  single    0.970  0.020  1.090
 TXM  C03  H032  single    0.970  0.020  1.090
 TXM  C03  H033  single    0.970  0.020  1.090
 TXM  C03  H031  single    0.970  0.020  1.090
 TXM  C04  H041  single    0.970  0.020  1.090
 TXM  O07  H1    single    0.850  0.020  0.980
 TXM  C12  H121  single    0.930  0.020  1.080
 TXM  C16  H161  single    0.930  0.020  1.080
 TXM  C23  H231  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
 TXM  H131  C13  C14   118.79  3.000
 TXM  H131  C13  C12   118.75  3.000
 TXM  C14   C13  C12   122.45  3.000
 TXM  H153  C15  H152  107.86  3.000
 TXM  H153  C15  H151  107.70  3.000
 TXM  H152  C15  H151  107.06  3.000
 TXM  H153  C15  C14   111.51  3.000
 TXM  H152  C15  C14   111.32  3.000
 TXM  H151  C15  C14   111.18  3.000
 TXM  C16   C17  C11   119.20  3.000
 TXM  C11   C17  C08   105.67  3.000
 TXM  C16   C17  C08   135.12  3.000
 TXM  S24   C20  C19   120.90  3.000
 TXM  S24   C20  C21   110.98  3.000
 TXM  C19   C20  C21   128.13  3.000
 TXM  H211  C21  C22   124.49  3.000
 TXM  H211  C21  C20   122.91  3.000
 TXM  C22   C21  C20   112.60  3.000
 TXM  H221  C22  C23   123.43  3.000
 TXM  H221  C22  C21   123.91  3.000
 TXM  C23   C22  C21   112.66  3.000
 TXM  H021  C02  C04   103.89  3.000
 TXM  H021  C02  C03   106.98  3.000
 TXM  C04   C02  C03   114.73  3.000
 TXM  H021  C02  C01   106.55  3.000
 TXM  C04   C02  C01   112.18  3.000
 TXM  C03   C02  C01   111.71  3.000
 TXM  H031  C03  H033  107.53  3.000
 TXM  H031  C03  H032  108.22  3.000
 TXM  H033  C03  H032  107.22  3.000
 TXM  H031  C03  C02   112.10  3.000
 TXM  H033  C03  C02   109.56  3.000
 TXM  H032  C03  C02   111.99  3.000
 TXM  H041  C04  C08   106.48  3.000
 TXM  H041  C04  C05   104.84  3.000
 TXM  C08   C04  C05   110.30  3.000
 TXM  H041  C04  C02   106.13  3.000
 TXM  C08   C04  C02   112.44  3.000
 TXM  C05   C04  C02   115.83  3.000
 TXM  O07   C05  O06   122.85  3.000
 TXM  O07   C05  C04   110.86  3.000
 TXM  O06   C05  C04   126.29  3.000
 TXM  H1    O07  C05   109.84  3.000
 TXM  C09   C08  C04   125.12  3.000
 TXM  C09   C08  C17   105.32  3.000
 TXM  C04   C08  C17   129.55  3.000
 TXM  C18   C09  O10   118.02  3.000
 TXM  C18   C09  C08   129.92  3.000
 TXM  O10   C09  C08   112.06  3.000
 TXM  C11   O10  C09   106.36  3.000
 TXM  C12   C11  O10   126.33  3.000
 TXM  O10   C11  C17   110.58  3.000
 TXM  C12   C11  C17   123.10  3.000
 TXM  H121  C12  C11   121.98  3.000
 TXM  H121  C12  C13   121.58  3.000
 TXM  C11   C12  C13   116.44  3.000
 TXM  C16   C14  C15   120.91  3.000
 TXM  C16   C14  C13   119.55  3.000
 TXM  C15   C14  C13   119.54  3.000
 TXM  H161  C16  C14   119.71  3.000
 TXM  H161  C16  C17   121.02  3.000
 TXM  C14   C16  C17   119.27  3.000
 TXM  C19   C18  C09   180.00  3.000
 TXM  C18   C19  C20   180.00  3.000
 TXM  H231  C23  S24   120.15  3.000
 TXM  H231  C23  C22   127.81  3.000
 TXM  S24   C23  C22   112.04  3.000
 TXM  C23   S24  C20    91.72  3.000
 TXM  H011  C01  H013  107.52  3.000
 TXM  H011  C01  H012  107.40  3.000
 TXM  H013  C01  H012  108.09  3.000
 TXM  H011  C01  C02   109.89  3.000
 TXM  H013  C01  C02   112.37  3.000
 TXM  H012  C01  C02   111.37  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
 TXM  CONST_01  C17   C16  C14  C13     0.00   0.0  0
 TXM  CONST_02  C17   C11  C12  C13     0.00   0.0  0
 TXM  CONST_03  O10   C11  C12  C13   180.00   0.0  0
 TXM  CONST_04  O10   C09  C08  C17     0.00   0.0  0
 TXM  CONST_05  C09   O10  C11  C17     0.00   0.0  0
 TXM  CONST_06  C22   C23  S24  C20     0.00   0.0  0
 TXM  CONST_07  C23   C22  C21  C20     0.00   0.0  0
 TXM  CONST_08  C23   S24  C20  C21     0.00   0.0  0
 TXM  CONST_09  S24   C23  C22  C21     0.00   0.0  0
 TXM  CONST_10  S24   C20  C21  C22     0.00   0.0  0
 TXM  CONST_11  C14   C16  C17  C08   180.00   0.0  0
 TXM  CONST_12  C12   C11  C17  C08   180.00   0.0  0
 TXM  CONST_13  O10   C11  C17  C08     0.00   0.0  0
 TXM  CONST_14  C11   O10  C09  C08     0.00   0.0  0
 TXM  CONST_15  C16   C17  C08  C09   180.00   0.0  0
 TXM  CONST_16  C11   C17  C08  C09     0.00   0.0  0
 TXM  CONST_17  C12   C11  O10  C09   180.00   0.0  0
 TXM  CONST_18  C16   C17  C11  O10   180.00   0.0  0
 TXM  CONST_19  C14   C16  C17  C11     0.00   0.0  0
 TXM  CONST_20  C14   C13  C12  C11     0.00   0.0  0
 TXM  CONST_21  C16   C14  C13  C12     0.00   0.0  0
 TXM  CONST_22  C16   C17  C11  C12     0.00   0.0  0
 TXM  CONST_23  C17   C16  C14  C15   180.00   0.0  0
 TXM  CONST_24  C12   C13  C14  C15   180.00   0.0  0
 TXM  CONST_25  C18   C09  C08  C17   180.00   0.0  0
 TXM  CONST_26  C19   C20  C21  C22   180.00   0.0  0
 TXM  CONST_27  C16   C17  C08  C04     0.00   0.0  0
 TXM  CONST_28  C11   C17  C08  C04   180.00   0.0  0
 TXM  CONST_29  O10   C09  C08  C04   180.00   0.0  0
 TXM  CONST_30  C18   C09  O10  C11   180.00   0.0  0
 TXM  CONST_31  C23   S24  C20  C19   180.00   0.0  0
 TXM  CONST_32  H161  C16  C14  C13   180.00   0.0  0
 TXM  CONST_33  H121  C12  C11  C17   180.00   0.0  0
 TXM  CONST_34  H231  C23  S24  C20   180.00   0.0  0
 TXM  CONST_35  H221  C22  C21  C20   180.00   0.0  0
 TXM  CONST_36  H231  C23  C22  C21   180.00   0.0  0
 TXM  CONST_37  H161  C16  C17  C08     0.00   0.0  0
 TXM  CONST_38  H121  C12  C11  O10     0.00   0.0  0
 TXM  CONST_39  H161  C16  C17  C11   180.00   0.0  0
 TXM  CONST_40  H131  C13  C12  C11   180.00   0.0  0
 TXM  CONST_41  H121  C12  C13  C14   180.00   0.0  0
 TXM  CONST_42  H131  C13  C14  C16   180.00   0.0  0
 TXM  CONST_43  H211  C21  C22  C23   180.00   0.0  0
 TXM  CONST_44  H211  C21  C20  S24   180.00   0.0  0
 TXM  CONST_45  H221  C22  C23  S24   180.00   0.0  0
 TXM  CONST_46  H1    O07  C05  C04   180.00   0.0  0
 TXM  CONST_47  H1    O07  C05  O06     0.00   0.0  0
 TXM  Var_01    C09   C18  C19  C20   -25.52  30.0  1
 TXM  Var_02    H151  C15  C14  C13   -62.82  30.0  2
 TXM  Var_03    H152  C15  C14  C13    56.45  30.0  2
 TXM  Var_04    H153  C15  C14  C13   176.96  30.0  2
 TXM  Var_05    H151  C15  C14  C16   116.92  30.0  2
 TXM  Var_06    H152  C15  C14  C16  -123.81  30.0  2
 TXM  Var_07    H153  C15  C14  C16    -3.29  30.0  2
 TXM  Var_08    H032  C03  C02  C01  -175.21  30.0  3
 TXM  Var_09    H033  C03  C02  C01   -56.37  30.0  3
 TXM  Var_10    H031  C03  C02  C01    62.93  30.0  3
 TXM  Var_11    H012  C01  C02  C03  -179.34  30.0  3
 TXM  Var_12    H013  C01  C02  C03   -57.90  30.0  3
 TXM  Var_13    H011  C01  C02  C03    61.78  30.0  3
 TXM  Var_14    H032  C03  C02  C04    55.68  30.0  3
 TXM  Var_15    H033  C03  C02  C04   174.52  30.0  3
 TXM  Var_16    H031  C03  C02  C04   -66.18  30.0  3
 TXM  Var_17    H012  C01  C02  C04   -48.90  30.0  3
 TXM  Var_18    H013  C01  C02  C04    72.54  30.0  3
 TXM  Var_19    H011  C01  C02  C04  -167.79  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 TXM  chir_01  C04  C02  C05  C08  positiv

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
 TXM  plan-1  C20   0.020
 TXM  plan-1  C21   0.020
 TXM  plan-1  C22   0.020
 TXM  plan-1  C18   0.020
 TXM  plan-1  C19   0.020
 TXM  plan-1  C23   0.020
 TXM  plan-1  S24   0.020
 TXM  plan-1  H211  0.020
 TXM  plan-1  H221  0.020
 TXM  plan-1  H231  0.020
 TXM  plan-2  C13   0.020
 TXM  plan-2  C15   0.020
 TXM  plan-2  C17   0.020
 TXM  plan-2  C04   0.020
 TXM  plan-2  C08   0.020
 TXM  plan-2  C09   0.020
 TXM  plan-2  O10   0.020
 TXM  plan-2  C11   0.020
 TXM  plan-2  C12   0.020
 TXM  plan-2  C14   0.020
 TXM  plan-2  C16   0.020
 TXM  plan-2  C18   0.020
 TXM  plan-2  C19   0.020
 TXM  plan-2  H131  0.020
 TXM  plan-2  H121  0.020
 TXM  plan-2  H161  0.020
 TXM  plan-3  C04   0.020
 TXM  plan-3  C05   0.020
 TXM  plan-3  O06   0.020
 TXM  plan-3  O07   0.020
 TXM  plan-3  H1    0.020

