# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:51:19 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-[(3-fluoro-3'-methoxybiphenyl-4-yl)carbamoyl]thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2ccc(NC(=O)c3ccsc3C(O)=O)c(F)c2
#
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
 ILC  ILC  '3-[(3-fluoro-3'-methoxybiphenyl-4-yl)carbamoyl]thiophene-2-carboxylic acid'  ligand  39  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ILC
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
 ILC  C1    C  CR16   0  -0.395   6.8246  -0.4381  -0.6520
 ILC  C2    C  CR6    0   0.409   6.1583  -0.4057   0.5703
 ILC  C8    C  CR16   0  -0.417   4.7717  -0.2520   0.5983
 ILC  C9    C  CR6    0   0.114   4.0413  -0.1279  -0.5779
 ILC  C10   C  CR6    0   0.096   2.5753   0.0378  -0.5327
 ILC  C11   C  CR16   0  -0.338   4.7162  -0.1588  -1.8024
 ILC  C12   C  CR16   0  -0.226   6.0903  -0.3137  -1.8260
 ILC  C13   C  CR16   0  -0.319   1.7523  -0.5150  -1.5110
 ILC  C14   C  CR16   0  -0.288   0.3748  -0.3631  -1.4803
 ILC  C16   C  CR6    0   0.191  -0.2405   0.3499  -0.4513
 ILC  C20   C  CR16   0  -0.475   1.9674   0.7609   0.4942
 ILC  C21   C  C      0   0.480  -2.6121  -0.1744  -0.8493
 ILC  C22   C  CR5    0   0.032  -3.9874   0.2661  -0.4849
 ILC  C24   C  CR15   0  -0.189  -4.9590   0.4404  -1.5132
 ILC  C27   C  CR5    0  -0.380  -4.4958   0.4984   0.7680
 ILC  O3    O  O2     0  -0.473   6.7628  -0.5238   1.7676
 ILC  C4    C  CH3    0  -0.437   8.1659  -0.6936   1.8016
 ILC  N17   N  NH1    0  -0.707  -1.6080   0.5854  -0.3448
 ILC  C18   C  CR6    0   0.505   0.6005   0.8982   0.5174
 ILC  F19   F  F      0  -0.312   0.0410   1.6153   1.5072
 ILC  O23   O  O      0  -0.457  -2.4446  -1.1042  -1.6184
 ILC  C25   C  CR15   0  -0.470  -6.1710   0.8198  -1.0259
 ILC  S26   S  S2     0   0.239  -6.1512   0.9461   0.6795
 ILC  C28   C  C      0   0.396  -3.9028   0.3587   2.1513
 ILC  O29   O  O      0  -0.568  -2.7578  -0.1143   2.2266
 ILC  O30   O  OC    -1  -0.588  -4.6507   0.7312   3.0735
 ILC  H1    H  HCR6   0   0.280   7.8978  -0.5551  -0.7109
 ILC  H8    H  HCR6   0   0.260   4.2700  -0.2512   1.5589
 ILC  H11   H  HCR6   0   0.252   4.1720  -0.0374  -2.7298
 ILC  H12   H  HCR6   0   0.261   6.6116  -0.3307  -2.7744
 ILC  H13   H  HCR6   0   0.260   2.1843  -1.0939  -2.3165
 ILC  H14   H  HCR6   0   0.286  -0.2162  -0.8059  -2.2648
 ILC  H20   H  HCR6   0   0.278   2.5522   1.2344   1.2727
 ILC  H24   H  HCR5   0   0.271  -4.7521   0.3053  -2.5655
 ILC  H41   H  HCH3   0   0.260   8.4407  -0.7791   2.8499
 ILC  H42   H  HCH3   0   0.229   8.4807  -1.6015   1.2805
 ILC  H43   H  HCH3   0   0.229   8.6930   0.1614   1.3697
 ILC  HN17  H  HNH1   0   0.418  -1.8828   1.2331   0.3775
 ILC  H25   H  HCR5   0   0.294  -7.0671   1.0303  -1.5897

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
 ILC  C1   C2    aromatic  1.393  0.020  1.393
 ILC  C1   C12   aromatic  1.390  0.020  1.390
 ILC  C1   H1    single    0.930  0.020  1.080
 ILC  C2   C8    aromatic  1.395  0.020  1.395
 ILC  C2   O3    single    1.346  0.020  1.346
 ILC  C8   C9    aromatic  1.390  0.020  1.390
 ILC  C8   H8    single    0.930  0.020  1.080
 ILC  C9   C10   single    1.476  0.020  1.476
 ILC  C9   C11   aromatic  1.399  0.020  1.399
 ILC  C10  C13   aromatic  1.393  0.020  1.393
 ILC  C10  C20   aromatic  1.395  0.020  1.395
 ILC  C11  C12   aromatic  1.383  0.020  1.383
 ILC  C11  H11   single    0.930  0.020  1.080
 ILC  C12  H12   single    0.930  0.020  1.080
 ILC  C13  C14   aromatic  1.386  0.020  1.386
 ILC  C13  H13   single    0.930  0.020  1.080
 ILC  C14  C16   aromatic  1.395  0.020  1.395
 ILC  C14  H14   single    0.930  0.020  1.080
 ILC  C16  N17   single    1.392  0.020  1.392
 ILC  C16  C18   aromatic  1.395  0.020  1.395
 ILC  C20  C18   aromatic  1.374  0.020  1.374
 ILC  C20  H20   single    0.930  0.020  1.080
 ILC  C21  C22   single    1.489  0.020  1.489
 ILC  C21  N17   single    1.356  0.020  1.356
 ILC  C21  O23   double    1.218  0.020  1.218
 ILC  C22  C24   aromatic  1.426  0.020  1.426
 ILC  C22  C27   aromatic  1.372  0.020  1.372
 ILC  C24  C25   aromatic  1.360  0.020  1.360
 ILC  C24  H24   single    0.930  0.020  1.080
 ILC  C27  S26   aromatic  1.717  0.020  1.717
 ILC  C27  C28   single    1.512  0.020  1.512
 ILC  O3   C4    single    1.414  0.020  1.414
 ILC  C4   H41   single    0.970  0.020  1.090
 ILC  C4   H42   single    0.970  0.020  1.090
 ILC  C4   H43   single    0.970  0.020  1.090
 ILC  N17  HN17  single    0.860  0.020  1.020
 ILC  C18  F19   single    1.344  0.020  1.344
 ILC  C25  S26   aromatic  1.710  0.020  1.710
 ILC  C25  H25   single    0.930  0.020  1.080
 ILC  C28  O29   deloc     1.241  0.020  1.241
 ILC  C28  O30   deloc     1.244  0.020  1.244

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
 ILC  H1    C1   C12  119.21  3.000
 ILC  H1    C1   C2   121.69  3.000
 ILC  C12   C1   C2   119.10  3.000
 ILC  O3    C2   C8   115.97  3.000
 ILC  O3    C2   C1   124.31  3.000
 ILC  C8    C2   C1   119.72  3.000
 ILC  H8    C8   C9   120.44  3.000
 ILC  H8    C8   C2   118.55  3.000
 ILC  C9    C8   C2   121.00  3.000
 ILC  C11   C9   C10  120.57  3.000
 ILC  C11   C9   C8   119.03  3.000
 ILC  C10   C9   C8   120.40  3.000
 ILC  C20   C10  C13  117.72  3.000
 ILC  C20   C10  C9   120.89  3.000
 ILC  C13   C10  C9   121.39  3.000
 ILC  H11   C11  C12  119.84  3.000
 ILC  H11   C11  C9   120.34  3.000
 ILC  C12   C11  C9   119.80  3.000
 ILC  H12   C12  C11  119.69  3.000
 ILC  H12   C12  C1   118.95  3.000
 ILC  C11   C12  C1   121.36  3.000
 ILC  H13   C13  C14  118.15  3.000
 ILC  H13   C13  C10  119.96  3.000
 ILC  C14   C13  C10  121.88  3.000
 ILC  H14   C14  C16  120.35  3.000
 ILC  H14   C14  C13  118.94  3.000
 ILC  C16   C14  C13  120.71  3.000
 ILC  C18   C16  N17  118.21  3.000
 ILC  C18   C16  C14  116.57  3.000
 ILC  N17   C16  C14  125.19  3.000
 ILC  H20   C20  C18  118.78  3.000
 ILC  H20   C20  C10  121.37  3.000
 ILC  C18   C20  C10  119.84  3.000
 ILC  O23   C21  N17  124.09  3.000
 ILC  O23   C21  C22  120.47  3.000
 ILC  N17   C21  C22  115.27  3.000
 ILC  C27   C22  C24  112.67  3.000
 ILC  C27   C22  C21  128.01  3.000
 ILC  C24   C22  C21  119.28  3.000
 ILC  H24   C24  C25  123.65  3.000
 ILC  H24   C24  C22  123.82  3.000
 ILC  C25   C24  C22  112.52  3.000
 ILC  C28   C27  S26  116.71  3.000
 ILC  C28   C27  C22  132.43  3.000
 ILC  S26   C27  C22  110.76  3.000
 ILC  C4    O3   C2   118.52  3.000
 ILC  H43   C4   H42  108.80  3.000
 ILC  H43   C4   H41  108.70  3.000
 ILC  H42   C4   H41  108.75  3.000
 ILC  H43   C4   O3   112.03  3.000
 ILC  H42   C4   O3   111.97  3.000
 ILC  H41   C4   O3   106.48  3.000
 ILC  HN17  N17  C21  115.12  3.000
 ILC  HN17  N17  C16  115.55  3.000
 ILC  C21   N17  C16  127.17  3.000
 ILC  F19   C18  C20  118.67  3.000
 ILC  F19   C18  C16  118.04  3.000
 ILC  C20   C18  C16  123.28  3.000
 ILC  H25   C25  S26  121.07  3.000
 ILC  H25   C25  C24  127.37  3.000
 ILC  S26   C25  C24  111.57  3.000
 ILC  C25   S26  C27   92.48  3.000
 ILC  O30   C28  O29  128.58  3.000
 ILC  O30   C28  C27  114.51  3.000
 ILC  O29   C28  C27  116.91  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
 ILC  CONST_01  C9    C8   C2   C1      0.00   0.0  0
 ILC  CONST_02  C9    C11  C12  C1      0.00   0.0  0
 ILC  CONST_03  C11   C12  C1   C2      0.00   0.0  0
 ILC  CONST_04  C10   C9   C8   C2    180.00   0.0  0
 ILC  CONST_05  C11   C9   C8   C2      0.00   0.0  0
 ILC  CONST_06  C12   C1   C2   C8      0.00   0.0  0
 ILC  CONST_09  C12   C11  C9   C8      0.00   0.0  0
 ILC  CONST_10  C14   C13  C10  C9    180.00   0.0  0
 ILC  CONST_11  C18   C20  C10  C9    180.00   0.0  0
 ILC  CONST_12  C12   C11  C9   C10   180.00   0.0  0
 ILC  CONST_13  C16   C14  C13  C10     0.00   0.0  0
 ILC  CONST_14  C16   C18  C20  C10     0.00   0.0  0
 ILC  CONST_17  C18   C20  C10  C13     0.00   0.0  0
 ILC  CONST_18  C18   C16  C14  C13     0.00   0.0  0
 ILC  CONST_19  C20   C10  C13  C14     0.00   0.0  0
 ILC  CONST_20  C20   C18  C16  C14     0.00   0.0  0
 ILC  CONST_21  S26   C25  C24  C22     0.00   0.0  0
 ILC  CONST_22  C25   S26  C27  C22     0.00   0.0  0
 ILC  CONST_23  S26   C27  C22  C24     0.00   0.0  0
 ILC  CONST_24  C27   S26  C25  C24     0.00   0.0  0
 ILC  CONST_25  C25   C24  C22  C27     0.00   0.0  0
 ILC  CONST_26  O3    C2   C8   C9    180.00   0.0  0
 ILC  CONST_27  F19   C18  C20  C10   180.00   0.0  0
 ILC  CONST_28  O3    C2   C1   C12   180.00   0.0  0
 ILC  CONST_29  N17   C16  C14  C13   180.00   0.0  0
 ILC  CONST_30  F19   C18  C16  C14   180.00   0.0  0
 ILC  CONST_31  N17   C16  C18  C20   180.00   0.0  0
 ILC  CONST_32  C25   C24  C22  C21   180.00   0.0  0
 ILC  CONST_33  S26   C27  C22  C21   180.00   0.0  0
 ILC  CONST_34  C28   C27  C22  C24   180.00   0.0  0
 ILC  CONST_35  C28   C27  S26  C25   180.00   0.0  0
 ILC  CONST_36  H8    C8   C2   C1    180.00   0.0  0
 ILC  CONST_37  H11   C11  C12  C1    180.00   0.0  0
 ILC  CONST_38  H12   C12  C1   C2    180.00   0.0  0
 ILC  CONST_39  H1    C1   C2   C8    180.00   0.0  0
 ILC  CONST_40  H13   C13  C10  C9      0.00   0.0  0
 ILC  CONST_41  H20   C20  C10  C9      0.00   0.0  0
 ILC  CONST_42  H14   C14  C13  C10   180.00   0.0  0
 ILC  CONST_43  H25   C25  C24  C22   180.00   0.0  0
 ILC  CONST_44  H24   C24  C22  C27   180.00   0.0  0
 ILC  CONST_45  C22   C21  N17  C16   180.00   0.0  0
 ILC  CONST_48  HN17  N17  C16  C14   180.00   0.0  0
 ILC  CONST_49  O23   C21  N17  C16     0.00   0.0  0
 ILC  Var_01    O29   C28  C27  C22    -4.09  30.0  2
 ILC  Var_02    N17   C21  C22  C24   128.93  30.0  2
 ILC  Var_03    H41   C4   O3   C2   -179.31  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
 ILC  plan-1  C21   0.020
 ILC  plan-1  C22   0.020
 ILC  plan-1  C24   0.020
 ILC  plan-1  C27   0.020
 ILC  plan-1  C25   0.020
 ILC  plan-1  S26   0.020
 ILC  plan-1  C28   0.020
 ILC  plan-1  H24   0.020
 ILC  plan-1  H25   0.020
 ILC  plan-2  C1    0.020
 ILC  plan-2  C2    0.020
 ILC  plan-2  C8    0.020
 ILC  plan-2  C9    0.020
 ILC  plan-2  C10   0.020
 ILC  plan-2  C11   0.020
 ILC  plan-2  C12   0.020
 ILC  plan-2  O3    0.020
 ILC  plan-2  H1    0.020
 ILC  plan-2  H8    0.020
 ILC  plan-2  H11   0.020
 ILC  plan-2  H12   0.020
 ILC  plan-3  C9    0.020
 ILC  plan-3  C10   0.020
 ILC  plan-3  C13   0.020
 ILC  plan-3  C14   0.020
 ILC  plan-3  C16   0.020
 ILC  plan-3  C20   0.020
 ILC  plan-3  N17   0.020
 ILC  plan-3  C18   0.020
 ILC  plan-3  F19   0.020
 ILC  plan-3  H13   0.020
 ILC  plan-3  H14   0.020
 ILC  plan-3  H20   0.020
 ILC  plan-4  C16   0.020
 ILC  plan-4  C21   0.020
 ILC  plan-4  C22   0.020
 ILC  plan-4  N17   0.020
 ILC  plan-4  O23   0.020
 ILC  plan-4  HN17  0.020
 ILC  plan-5  C27   0.020
 ILC  plan-5  C28   0.020
 ILC  plan-5  O29   0.020
 ILC  plan-5  O30   0.020

