# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 21:40:14 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: {2-amino-4-[3,5-bis(trifluoromethyl)phenyl]thiophen-3-yl}(4-chlorophenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1scc(c2cc(cc(c2)C(F)(F)F)C(F)(F)F)c1C(=O)c3ccc(Cl)cc3
#
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
 XTD  XTD  "{2-amino-4-[3,5-bis(trifluoromethyl)phenyl]thiophen-3-yl}(4-chlorophenyl)methanone"
  ligand  39  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XTD
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
 XTD  C1   C   CR6   0  -0.050  102.5143  121.9788  112.2584
 XTD  C2   C   CR16  0  -0.269  103.5643  121.8120  111.3621
 XTD  C3   C   CR16  0  -0.190  103.9027  122.8209  110.4757
 XTD  C4   C   CR6   0  -0.038  103.1836  124.0059  110.5014
 XTD  C5   C   CR16  0  -0.202  102.1072  124.1783  111.3578
 XTD  C6   C   CR16  0  -0.281  101.7662  123.1514  112.2225
 XTD  C7   C   CR5   0  -0.092  103.1904  120.3672  114.1034
 XTD  C9   C   CR15  0  -0.554  105.2681  120.0188  115.1210
 XTD  C8   C   CR5   0   0.127  102.9508  119.1788  114.8110
 XTD  C10  C   CR5   0   0.184  104.5443  120.8392  114.3281
 XTD  C11  C   CR6   0   0.052  105.1327  122.0963  113.8280
 XTD  C12  C   CR16  0  -0.322  104.5364  123.3277  114.1003
 XTD  N    N   NH2   0  -0.817  101.8312  118.4624  114.8624
 XTD  C    C   C     0   0.351  102.1607  120.9218  113.2493
 XTD  O    O   O     0  -0.442  100.9917  120.5475  113.3087
 XTD  C13  C   CR6   0  -0.149  105.0807  124.4928  113.5934
 XTD  C14  C   CT    0   1.064  104.4550  125.8253  113.8817
 XTD  C15  C   CR16  0  -0.329  106.2335  124.4549  112.8114
 XTD  C16  C   CR6   0  -0.154  106.8417  123.2373  112.5697
 XTD  C17  C   CT    0   1.060  108.0615  123.1279  111.7072
 XTD  C18  C   CR16  0  -0.301  106.2981  122.0631  113.0798
 XTD  F    F   F     0  -0.313  105.2584  126.5931  114.6326
 XTD  F1   F   F     0  -0.309  104.2103  126.5129  112.7593
 XTD  F2   F   F     0  -0.299  103.2974  125.7177  114.5364
 XTD  F3   F   F     0  -0.312  107.8116  122.4077  110.6038
 XTD  F4   F   F     0  -0.312  109.0648  122.5111  112.3455
 XTD  F5   F   F     0  -0.299  108.5187  124.3150  111.3043
 XTD  S    S   S2    0   0.217  104.3592  118.6491  115.6627
 XTD  CL   CL  CL    0  -0.122  103.6446  125.2980  109.4463
 XTD  H1   H   HCR6  0   0.280  104.1351  120.8921  111.3563
 XTD  H2   H   HCR6  0   0.282  104.7297  122.6924  109.7908
 XTD  H3   H   HCR6  0   0.281  101.5444  125.1016  111.3560
 XTD  H4   H   HCR6  0   0.269  100.9358  123.2866  112.9034
 XTD  H5   H   HCR5  0   0.297  106.2795  120.1605  115.4688
 XTD  H6   H   HCR6  0   0.284  103.6413  123.3522  114.7072
 XTD  H7   H   HNH2  0   0.415  101.7843  117.5778  115.3386
 XTD  H8   H   HNH2  0   0.423  101.0085  118.8156  114.4001
 XTD  H9   H   HCR6  0   0.288  106.6446  125.3679  112.4013
 XTD  H10  H   HCR6  0   0.281  106.7537  121.1044  112.8639

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
 XTD  CL   C4   single    1.731  0.020  1.731
 XTD  C4   C3   aromatic  1.386  0.020  1.386
 XTD  C4   C5   aromatic  1.386  0.020  1.386
 XTD  C3   C2   aromatic  1.385  0.020  1.385
 XTD  F5   C17  single    1.334  0.020  1.334
 XTD  F3   C17  single    1.341  0.020  1.341
 XTD  C5   C6   aromatic  1.385  0.020  1.385
 XTD  C2   C1   aromatic  1.391  0.020  1.391
 XTD  C17  F4   single    1.340  0.020  1.340
 XTD  C17  C16  single    1.498  0.020  1.498
 XTD  C6   C1   aromatic  1.391  0.020  1.391
 XTD  C1   C    single    1.491  0.020  1.491
 XTD  C16  C18  aromatic  1.391  0.020  1.391
 XTD  C16  C15  aromatic  1.382  0.020  1.382
 XTD  C18  C11  aromatic  1.385  0.020  1.385
 XTD  C15  C13  aromatic  1.394  0.020  1.394
 XTD  C    O    double    1.229  0.020  1.229
 XTD  C    C7   single    1.448  0.020  1.448
 XTD  C11  C10  single    1.475  0.020  1.475
 XTD  C11  C12  aromatic  1.395  0.020  1.395
 XTD  C7   C10  aromatic  1.451  0.020  1.451
 XTD  C7   C8   aromatic  1.404  0.020  1.404
 XTD  F1   C14  single    1.339  0.020  1.339
 XTD  C13  C12  aromatic  1.382  0.020  1.382
 XTD  C13  C14  single    1.500  0.020  1.500
 XTD  C10  C9   aromatic  1.351  0.020  1.351
 XTD  N    C8   single    1.330  0.020  1.330
 XTD  C8   S    aromatic  1.729  0.020  1.729
 XTD  C14  F2   single    1.334  0.020  1.334
 XTD  C14  F    single    1.341  0.020  1.341
 XTD  C9   S    aromatic  1.731  0.020  1.731
 XTD  C2   H1   single    0.930  0.020  1.080
 XTD  C3   H2   single    0.930  0.020  1.080
 XTD  C5   H3   single    0.930  0.020  1.080
 XTD  C6   H4   single    0.930  0.020  1.080
 XTD  C9   H5   single    0.930  0.020  1.080
 XTD  C12  H6   single    0.930  0.020  1.080
 XTD  N    H7   single    0.860  0.020  1.020
 XTD  N    H8   single    0.860  0.020  1.020
 XTD  C15  H9   single    0.930  0.020  1.080
 XTD  C18  H10  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
 XTD  C    C1   C6   119.14  3.000
 XTD  C    C1   C2   121.49  3.000
 XTD  C6   C1   C2   119.37  3.000
 XTD  H1   C2   C3   119.12  3.000
 XTD  H1   C2   C1   120.23  3.000
 XTD  C3   C2   C1   120.64  3.000
 XTD  H2   C3   C4   120.66  3.000
 XTD  H2   C3   C2   120.38  3.000
 XTD  C4   C3   C2   118.95  3.000
 XTD  CL   C4   C5   119.38  3.000
 XTD  C5   C4   C3   121.36  3.000
 XTD  CL   C4   C3   119.26  3.000
 XTD  H3   C5   C6   120.40  3.000
 XTD  H3   C5   C4   120.61  3.000
 XTD  C6   C5   C4   118.99  3.000
 XTD  H4   C6   C5   119.27  3.000
 XTD  H4   C6   C1   120.10  3.000
 XTD  C5   C6   C1   120.57  3.000
 XTD  C    C7   C10  129.06  3.000
 XTD  C10  C7   C8   110.89  3.000
 XTD  C    C7   C8   120.01  3.000
 XTD  H5   C9   S    119.69  3.000
 XTD  H5   C9   C10  127.70  3.000
 XTD  S    C9   C10  112.51  3.000
 XTD  S    C8   N    120.10  3.000
 XTD  S    C8   C7   111.63  3.000
 XTD  N    C8   C7   128.25  3.000
 XTD  C11  C10  C9   120.17  3.000
 XTD  C9   C10  C7   113.15  3.000
 XTD  C11  C10  C7   126.64  3.000
 XTD  C18  C11  C12  119.09  3.000
 XTD  C12  C11  C10  121.03  3.000
 XTD  C18  C11  C10  119.88  3.000
 XTD  H6   C12  C13  120.83  3.000
 XTD  H6   C12  C11  118.89  3.000
 XTD  C13  C12  C11  120.27  3.000
 XTD  H8   N    H7   119.18  3.000
 XTD  H8   N    C8   118.73  3.000
 XTD  H7   N    C8   122.09  3.000
 XTD  O    C    C7   122.09  3.000
 XTD  C7   C    C1   119.65  3.000
 XTD  O    C    C1   118.26  3.000
 XTD  C15  C13  C14  118.49  3.000
 XTD  C14  C13  C12  120.93  3.000
 XTD  C15  C13  C12  120.57  3.000
 XTD  F2   C14  F1   107.11  3.000
 XTD  F2   C14  F    106.93  3.000
 XTD  F1   C14  F    106.55  3.000
 XTD  F    C14  C13  111.49  3.000
 XTD  F2   C14  C13  112.62  3.000
 XTD  F1   C14  C13  111.80  3.000
 XTD  H9   C15  C16  120.65  3.000
 XTD  H9   C15  C13  120.27  3.000
 XTD  C16  C15  C13  119.08  3.000
 XTD  C18  C16  C17  117.89  3.000
 XTD  C18  C16  C15  120.50  3.000
 XTD  C17  C16  C15  121.55  3.000
 XTD  F5   C17  F4   107.27  3.000
 XTD  F4   C17  F3   106.52  3.000
 XTD  F5   C17  F3   107.05  3.000
 XTD  F4   C17  C16  111.66  3.000
 XTD  F3   C17  C16  111.17  3.000
 XTD  F5   C17  C16  112.83  3.000
 XTD  H10  C18  C16  120.64  3.000
 XTD  H10  C18  C11  118.87  3.000
 XTD  C16  C18  C11  120.44  3.000
 XTD  C8   S    C9    91.78  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
 XTD  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 XTD  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 XTD  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 XTD  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 XTD  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 XTD  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 XTD  CONST_09  S    C9   C10  C7      0.00   0.0  0
 XTD  CONST_10  C9   S    C8   C7      0.00   0.0  0
 XTD  CONST_13  C8   C7   C10  C9      0.00   0.0  0
 XTD  CONST_14  C11  C10  C7   C8    180.00   0.0  0
 XTD  CONST_15  C10  C9   S    C8      0.00   0.0  0
 XTD  CONST_16  C16  C18  C11  C10   180.00   0.0  0
 XTD  CONST_17  C13  C12  C11  C10   180.00   0.0  0
 XTD  CONST_18  S    C8   C7   C10     0.00   0.0  0
 XTD  CONST_19  C15  C16  C18  C11     0.00   0.0  0
 XTD  CONST_20  S    C9   C10  C11   180.00   0.0  0
 XTD  CONST_21  C15  C13  C12  C11     0.00   0.0  0
 XTD  CONST_22  C16  C18  C11  C12     0.00   0.0  0
 XTD  CONST_23  C16  C15  C13  C12     0.00   0.0  0
 XTD  CONST_24  C18  C16  C15  C13     0.00   0.0  0
 XTD  CONST_25  C18  C11  C12  C13     0.00   0.0  0
 XTD  CONST_26  CL   C4   C3   C2    180.00   0.0  0
 XTD  CONST_27  C    C1   C2   C3    180.00   0.0  0
 XTD  CONST_28  C    C1   C6   C5    180.00   0.0  0
 XTD  CONST_29  CL   C4   C5   C6    180.00   0.0  0
 XTD  CONST_30  C    C7   C10  C9    180.00   0.0  0
 XTD  CONST_31  N    C8   S    C9    180.00   0.0  0
 XTD  CONST_32  N    C8   C7   C10   180.00   0.0  0
 XTD  CONST_33  C17  C16  C18  C11   180.00   0.0  0
 XTD  CONST_34  C    C7   C10  C11     0.00   0.0  0
 XTD  CONST_35  C14  C13  C12  C11   180.00   0.0  0
 XTD  CONST_36  S    C8   C7   C     180.00   0.0  0
 XTD  CONST_37  C17  C16  C15  C13   180.00   0.0  0
 XTD  CONST_38  C16  C15  C13  C14   180.00   0.0  0
 XTD  CONST_39  H2   C3   C2   C1    180.00   0.0  0
 XTD  CONST_40  H3   C5   C6   C1    180.00   0.0  0
 XTD  CONST_41  H4   C6   C1   C2    180.00   0.0  0
 XTD  CONST_42  H3   C5   C4   C3    180.00   0.0  0
 XTD  CONST_43  H1   C2   C3   C4    180.00   0.0  0
 XTD  CONST_44  H4   C6   C5   C4    180.00   0.0  0
 XTD  CONST_45  H2   C3   C4   C5    180.00   0.0  0
 XTD  CONST_46  H1   C2   C1   C6    180.00   0.0  0
 XTD  CONST_47  H5   C9   C10  C7    180.00   0.0  0
 XTD  CONST_48  H5   C9   S    C8    180.00   0.0  0
 XTD  CONST_49  H10  C18  C11  C10     0.00   0.0  0
 XTD  CONST_50  H6   C12  C11  C10     0.00   0.0  0
 XTD  CONST_51  H5   C9   C10  C11     0.00   0.0  0
 XTD  CONST_52  H10  C18  C11  C12   180.00   0.0  0
 XTD  CONST_53  H9   C15  C13  C12   180.00   0.0  0
 XTD  CONST_54  H10  C18  C16  C15   180.00   0.0  0
 XTD  CONST_55  H6   C12  C13  C15   180.00   0.0  0
 XTD  CONST_56  H9   C15  C16  C18   180.00   0.0  0
 XTD  CONST_57  H6   C12  C11  C18   180.00   0.0  0
 XTD  CONST_58  H7   N    C8   C7    180.00   0.0  0
 XTD  CONST_59  H8   N    C8   C7      0.00   0.0  0
 XTD  CONST_60  H7   N    C8   S       0.00   0.0  0
 XTD  CONST_61  H8   N    C8   S     180.00   0.0  0
 XTD  Var_01    C10  C7   C    C1     11.87  30.0  2
 XTD  Var_02    C8   C7   C    C1   -165.33  30.0  2
 XTD  Var_03    C7   C    C1   C2     51.52  30.0  2
 XTD  Var_04    C7   C    C1   C6   -129.16  30.0  2
 XTD  Var_05    O    C    C1   C2   -128.31  30.0  2
 XTD  Var_06    O    C    C1   C6     51.01  30.0  2
 XTD  Var_07    O    C    C7   C8     14.50  30.0  2
 XTD  Var_08    O    C    C7   C10  -168.31  30.0  2
 XTD  Var_09    F1   C14  C13  C12  -126.84  30.0  2
 XTD  Var_10    F2   C14  C13  C12    -6.18  30.0  2
 XTD  Var_11    F    C14  C13  C12   114.01  30.0  2
 XTD  Var_12    F5   C17  C16  C15     4.47  30.0  3
 XTD  Var_13    F3   C17  C16  C15  -115.80  30.0  3
 XTD  Var_14    F4   C17  C16  C15   125.39  30.0  3
 XTD  Var_15    F1   C14  C13  C15    53.76  30.0  2
 XTD  Var_16    F2   C14  C13  C15   174.42  30.0  2
 XTD  Var_17    F    C14  C13  C15   -65.39  30.0  2
 XTD  Var_18    F5   C17  C16  C18  -178.24  30.0  3
 XTD  Var_19    F3   C17  C16  C18    61.49  30.0  3
 XTD  Var_20    F4   C17  C16  C18   -57.32  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
 XTD  plan-1  C7   0.020
 XTD  plan-1  C9   0.020
 XTD  plan-1  C8   0.020
 XTD  plan-1  C10  0.020
 XTD  plan-1  C11  0.020
 XTD  plan-1  N    0.020
 XTD  plan-1  C    0.020
 XTD  plan-1  S    0.020
 XTD  plan-1  H5   0.020
 XTD  plan-2  C1   0.020
 XTD  plan-2  C2   0.020
 XTD  plan-2  C3   0.020
 XTD  plan-2  C4   0.020
 XTD  plan-2  C5   0.020
 XTD  plan-2  C6   0.020
 XTD  plan-2  C    0.020
 XTD  plan-2  CL   0.020
 XTD  plan-2  H1   0.020
 XTD  plan-2  H2   0.020
 XTD  plan-2  H3   0.020
 XTD  plan-2  H4   0.020
 XTD  plan-3  C10  0.020
 XTD  plan-3  C11  0.020
 XTD  plan-3  C12  0.020
 XTD  plan-3  C13  0.020
 XTD  plan-3  C14  0.020
 XTD  plan-3  C15  0.020
 XTD  plan-3  C16  0.020
 XTD  plan-3  C17  0.020
 XTD  plan-3  C18  0.020
 XTD  plan-3  H6   0.020
 XTD  plan-3  H9   0.020
 XTD  plan-3  H10  0.020
 XTD  plan-4  C8   0.020
 XTD  plan-4  N    0.020
 XTD  plan-4  H7   0.020
 XTD  plan-4  H8   0.020
 XTD  plan-5  C1   0.020
 XTD  plan-5  C7   0.020
 XTD  plan-5  C    0.020
 XTD  plan-5  O    0.020

