# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:07:46 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: {2,6-dimethyl-5-[(4,5,7-trifluoro-1,3-benzothiazol-2-yl)methyl]pyridin-3-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(C)c(Cc2sc3c(F)cc(F)c(F)c3n2)cc1CC(O)=O
#
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
 2X9  2X9  '{2,6-dimethyl-5-[(4,5,7-trifluoro-1,3-benzothiazol-2-yl)methyl]pyridin-3-yl}acetic acid'  ligand  38  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2X9
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
 2X9  C1   C  CH3   0  -0.748   4.6221   0.9442  -2.0763
 2X9  C2   C  CR6   0   0.206   3.5428   0.9352  -1.0357
 2X9  C3   C  CR6   0   0.029   1.5544   1.0603   0.8462
 2X9  F4   F  F     0  -0.301  -5.0192  -2.9920  -0.4286
 2X9  C5   C  CR6   0   0.072   3.1217  -0.2541  -0.4327
 2X9  C6   C  CR16  0  -0.198   2.1140  -0.1646   0.5108
 2X9  C7   C  CR6   0   0.199   2.0435   2.1935   0.1968
 2X9  N8   N  N     0  -0.447   3.0091   2.1083  -0.7155
 2X9  C9   C  CH2   0  -0.712   3.7263  -1.5803  -0.7743
 2X9  C11  C  CH3   0  -0.753   1.5163   3.5683   0.4864
 2X9  C12  C  CH2   0  -0.636   0.4377   1.1098   1.8617
 2X9  F13  F  F     0  -0.289  -2.7894  -2.9819   1.0948
 2X9  C20  C  C     0   0.559   5.0443  -1.8209  -0.0779
 2X9  O23  O  OH1   0  -0.591   5.5602  -2.9966  -0.4142
 2X9  O24  O  O     0  -0.432   5.5692  -1.0584   0.6917
 2X9  C28  C  CR5   0   0.084  -0.8418   0.6506   1.2417
 2X9  N29  N  N     0  -0.383  -1.2912  -0.5516   1.3256
 2X9  S30  S  S2    0   0.273  -1.7817   1.7474   0.2549
 2X9  C32  C  CR56  0  -0.467  -2.8712   0.4539  -0.0739
 2X9  C33  C  CR6   0   0.408  -4.3148  -1.8661  -0.3072
 2X9  C34  C  CR6   0   0.570  -4.0184   0.4328  -0.8457
 2X9  C35  C  CR56  0   0.241  -2.4389  -0.6999   0.5941
 2X9  C36  C  CR6   0   0.369  -3.1782  -1.8726   0.4705
 2X9  C37  C  CR16  0  -0.585  -4.7503  -0.7241  -0.9719
 2X9  F38  F  F     0  -0.292  -4.4030   1.5473  -1.4681
 2X9  H1   H  HCH3  0   0.252   5.5837   0.6421  -1.6570
 2X9  H2   H  HCH3  0   0.250   4.4002   0.2570  -2.8946
 2X9  H3   H  HCH3  0   0.258   4.7361   1.9424  -2.4930
 2X9  H4   H  HCR6  0   0.261   1.7529  -1.0658   0.9956
 2X9  H5   H  HCH2  0   0.316   3.0466  -2.3896  -0.4928
 2X9  H6   H  HCH2  0   0.303   3.8797  -1.6928  -1.8514
 2X9  H7   H  HCH3  0   0.257   1.6123   3.8247   1.5428
 2X9  H8   H  HCH3  0   0.263   2.0634   4.3074  -0.0940
 2X9  H9   H  HCH3  0   0.242   0.4592   3.6650   0.2308
 2X9  H10  H  HCH2  0   0.312   0.6602   0.4372   2.6905
 2X9  H11  H  HCH2  0   0.303   0.3205   2.1086   2.2829
 2X9  H12  H  HOH1  0   0.483   6.3985  -3.1374   0.0512
 2X9  H13  H  HCR6  0   0.324  -5.6484  -0.7543  -1.5749

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
 2X9  F4   C33  single    1.334  0.020  1.334
 2X9  C37  C33  aromatic  1.391  0.020  1.391
 2X9  C37  C34  aromatic  1.375  0.020  1.375
 2X9  F38  C34  single    1.333  0.020  1.333
 2X9  C33  C36  aromatic  1.377  0.020  1.377
 2X9  C34  C32  aromatic  1.383  0.020  1.383
 2X9  O24  C20  double    1.204  0.020  1.204
 2X9  O23  C20  single    1.327  0.020  1.327
 2X9  C36  F13  single    1.331  0.020  1.331
 2X9  C36  C35  aromatic  1.392  0.020  1.392
 2X9  C20  C9   single    1.510  0.020  1.510
 2X9  C32  C35  aromatic  1.402  0.020  1.402
 2X9  C32  S30  aromatic  1.723  0.020  1.723
 2X9  C35  N29  aromatic  1.369  0.020  1.369
 2X9  S30  C28  aromatic  1.749  0.020  1.749
 2X9  C9   C5   single    1.497  0.020  1.497
 2X9  N29  C28  aromatic  1.286  0.020  1.286
 2X9  C28  C12  single    1.494  0.020  1.494
 2X9  C5   C6   aromatic  1.383  0.020  1.383
 2X9  C5   C2   aromatic  1.398  0.020  1.398
 2X9  C6   C3   aromatic  1.388  0.020  1.388
 2X9  C1   C2   single    1.499  0.020  1.499
 2X9  C2   N8   aromatic  1.328  0.020  1.328
 2X9  C3   C12  single    1.510  0.020  1.510
 2X9  C3   C7   aromatic  1.395  0.020  1.395
 2X9  N8   C7   aromatic  1.331  0.020  1.331
 2X9  C7   C11  single    1.501  0.020  1.501
 2X9  C1   H1   single    0.970  0.020  1.090
 2X9  C1   H2   single    0.970  0.020  1.090
 2X9  C1   H3   single    0.970  0.020  1.090
 2X9  C6   H4   single    0.930  0.020  1.080
 2X9  C9   H5   single    0.970  0.020  1.090
 2X9  C9   H6   single    0.970  0.020  1.090
 2X9  C11  H7   single    0.970  0.020  1.090
 2X9  C11  H8   single    0.970  0.020  1.090
 2X9  C11  H9   single    0.970  0.020  1.090
 2X9  C12  H10  single    0.970  0.020  1.090
 2X9  C12  H11  single    0.970  0.020  1.090
 2X9  O23  H12  single    0.850  0.020  0.980
 2X9  C37  H13  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
 2X9  H3   C1   H2   108.17  3.000
 2X9  H3   C1   H1   107.98  3.000
 2X9  H2   C1   H1   107.03  3.000
 2X9  H3   C1   C2   110.30  3.000
 2X9  H2   C1   C2   111.73  3.000
 2X9  H1   C1   C2   111.46  3.000
 2X9  N8   C2   C5   121.76  3.000
 2X9  N8   C2   C1   116.83  3.000
 2X9  C5   C2   C1   121.41  3.000
 2X9  C12  C3   C7   123.08  3.000
 2X9  C7   C3   C6   117.60  3.000
 2X9  C12  C3   C6   119.31  3.000
 2X9  C9   C5   C6   120.48  3.000
 2X9  C6   C5   C2   117.29  3.000
 2X9  C9   C5   C2   122.24  3.000
 2X9  H4   C6   C5   119.56  3.000
 2X9  H4   C6   C3   119.40  3.000
 2X9  C5   C6   C3   121.04  3.000
 2X9  C11  C7   N8   116.47  3.000
 2X9  C11  C7   C3   122.09  3.000
 2X9  N8   C7   C3   121.43  3.000
 2X9  C7   N8   C2   120.89  3.000
 2X9  H6   C9   H5   105.33  3.000
 2X9  H6   C9   C20  108.38  3.000
 2X9  H5   C9   C20  107.81  3.000
 2X9  H6   C9   C5   111.87  3.000
 2X9  H5   C9   C5   110.23  3.000
 2X9  C20  C9   C5   112.86  3.000
 2X9  H9   C11  H8   107.57  3.000
 2X9  H9   C11  H7   106.92  3.000
 2X9  H8   C11  H7   108.22  3.000
 2X9  H9   C11  C7   112.09  3.000
 2X9  H8   C11  C7   110.06  3.000
 2X9  H7   C11  C7   111.79  3.000
 2X9  H11  C12  H10  107.06  3.000
 2X9  H11  C12  C28  110.48  3.000
 2X9  H10  C12  C28  107.49  3.000
 2X9  H11  C12  C3   111.67  3.000
 2X9  H10  C12  C3   109.87  3.000
 2X9  C28  C12  C3   110.13  3.000
 2X9  O24  C20  O23  123.61  3.000
 2X9  O23  C20  C9   111.32  3.000
 2X9  O24  C20  C9   125.07  3.000
 2X9  H12  O23  C20  110.07  3.000
 2X9  S30  C28  N29  115.79  3.000
 2X9  N29  C28  C12  124.02  3.000
 2X9  S30  C28  C12  120.10  3.000
 2X9  C35  N29  C28  111.06  3.000
 2X9  C32  S30  C28   88.67  3.000
 2X9  C35  C32  C34  120.62  3.000
 2X9  C35  C32  S30  109.39  3.000
 2X9  C34  C32  S30  129.99  3.000
 2X9  C37  C33  C36  122.14  3.000
 2X9  C36  C33  F4   118.90  3.000
 2X9  C37  C33  F4   118.96  3.000
 2X9  F38  C34  C37  120.46  3.000
 2X9  F38  C34  C32  119.16  3.000
 2X9  C37  C34  C32  120.38  3.000
 2X9  C36  C35  C32  119.17  3.000
 2X9  C32  C35  N29  115.09  3.000
 2X9  C36  C35  N29  125.74  3.000
 2X9  C35  C36  C33  118.99  3.000
 2X9  C35  C36  F13  120.36  3.000
 2X9  C33  C36  F13  120.66  3.000
 2X9  H13  C37  C34  121.10  3.000
 2X9  H13  C37  C33  120.20  3.000
 2X9  C34  C37  C33  118.70  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
 2X9  CONST_01  C3   C6   C5   C2     0.00   0.0  0
 2X9  CONST_02  C3   C7   N8   C2     0.00   0.0  0
 2X9  CONST_03  C7   C3   C6   C5     0.00   0.0  0
 2X9  CONST_04  C7   N8   C2   C5     0.00   0.0  0
 2X9  CONST_05  N8   C2   C5   C6     0.00   0.0  0
 2X9  CONST_06  N8   C7   C3   C6     0.00   0.0  0
 2X9  CONST_07  C34  C32  S30  C28  180.00   0.0  0
 2X9  CONST_08  C35  C32  S30  C28    0.00   0.0  0
 2X9  CONST_09  C36  C35  N29  C28  180.00   0.0  0
 2X9  CONST_10  C32  C35  N29  C28    0.00   0.0  0
 2X9  CONST_11  C33  C36  C35  N29  180.00   0.0  0
 2X9  CONST_12  C34  C32  C35  N29  180.00   0.0  0
 2X9  CONST_13  S30  C32  C35  N29    0.00   0.0  0
 2X9  CONST_14  C32  S30  C28  N29    0.00   0.0  0
 2X9  CONST_15  C37  C34  C32  S30  180.00   0.0  0
 2X9  CONST_16  C36  C35  C32  S30  180.00   0.0  0
 2X9  CONST_17  C35  N29  C28  S30    0.00   0.0  0
 2X9  CONST_18  C33  C37  C34  C32    0.00   0.0  0
 2X9  CONST_19  C33  C36  C35  C32    0.00   0.0  0
 2X9  CONST_20  C36  C33  C37  C34    0.00   0.0  0
 2X9  CONST_21  C36  C35  C32  C34    0.00   0.0  0
 2X9  CONST_22  C37  C33  C36  C35    0.00   0.0  0
 2X9  CONST_23  C37  C34  C32  C35    0.00   0.0  0
 2X9  CONST_24  C6   C5   C2   C1   180.00   0.0  0
 2X9  CONST_25  C7   N8   C2   C1   180.00   0.0  0
 2X9  CONST_26  C11  C7   N8   C2   180.00   0.0  0
 2X9  CONST_27  C9   C5   C6   C3   180.00   0.0  0
 2X9  CONST_28  C34  C37  C33  F4   180.00   0.0  0
 2X9  CONST_29  C35  C36  C33  F4   180.00   0.0  0
 2X9  CONST_30  C12  C3   C6   C5   180.00   0.0  0
 2X9  CONST_31  C11  C7   C3   C6   180.00   0.0  0
 2X9  CONST_32  C9   C5   C2   N8   180.00   0.0  0
 2X9  CONST_33  C12  C3   C7   N8   180.00   0.0  0
 2X9  CONST_34  C32  S30  C28  C12  180.00   0.0  0
 2X9  CONST_35  C35  N29  C28  C12  180.00   0.0  0
 2X9  CONST_36  C37  C33  C36  F13  180.00   0.0  0
 2X9  CONST_37  C32  C35  C36  F13  180.00   0.0  0
 2X9  CONST_38  N29  C35  C36  F13    0.00   0.0  0
 2X9  CONST_39  F38  C34  C32  S30    0.00   0.0  0
 2X9  CONST_40  F38  C34  C37  C33  180.00   0.0  0
 2X9  CONST_41  F38  C34  C32  C35  180.00   0.0  0
 2X9  CONST_42  H4   C6   C5   C2   180.00   0.0  0
 2X9  CONST_43  H13  C37  C34  C32  180.00   0.0  0
 2X9  CONST_44  H12  O23  C20  C9   180.00   0.0  0
 2X9  Var_01    S30  C28  C12  C3   -80.51  30.0  2
 2X9  Var_02    C28  C12  C3   C6   -76.23  30.0  2
 2X9  Var_03    C20  C9   C5   C2    79.98  30.0  2
 2X9  Var_04    H7   C11  C7   C3    57.20  30.0  2
 2X9  Var_05    H1   C1   C2   C5   -65.74  30.0  2
 2X9  Var_06    O24  C20  C9   C5     1.14  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
 2X9  plan-1  C1   0.020
 2X9  plan-1  C2   0.020
 2X9  plan-1  C3   0.020
 2X9  plan-1  C5   0.020
 2X9  plan-1  C6   0.020
 2X9  plan-1  C7   0.020
 2X9  plan-1  N8   0.020
 2X9  plan-1  C9   0.020
 2X9  plan-1  C11  0.020
 2X9  plan-1  C12  0.020
 2X9  plan-1  H4   0.020
 2X9  plan-2  F4   0.020
 2X9  plan-2  C12  0.020
 2X9  plan-2  F13  0.020
 2X9  plan-2  C28  0.020
 2X9  plan-2  N29  0.020
 2X9  plan-2  S30  0.020
 2X9  plan-2  C32  0.020
 2X9  plan-2  C33  0.020
 2X9  plan-2  C34  0.020
 2X9  plan-2  C35  0.020
 2X9  plan-2  C36  0.020
 2X9  plan-2  C37  0.020
 2X9  plan-2  F38  0.020
 2X9  plan-2  H13  0.020
 2X9  plan-3  C9   0.020
 2X9  plan-3  C20  0.020
 2X9  plan-3  O23  0.020
 2X9  plan-3  O24  0.020
 2X9  plan-3  H12  0.020

