# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 11:47:24 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: N-methyl-4-[4-({[3-(trifluoromethyl)phenyl]carbamoyl}amino)phenoxy]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3cccc(c3)C(F)(F)F)cc2)ccn1
#
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
 ZFS  ZFS  "N-methyl-4-[4-({[3-(trifluoromethyl)phenyl]carbamoyl}amino)phenoxy]pyridine-2-carboxamide"
  ligand  48  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZFS
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
 ZFS  N1   N  NH1   0  -0.635  10.0973   -9.0478   3.0229
 ZFS  C2   C  C     0   0.539  10.1201   -9.1694   1.6951
 ZFS  O2   O  O2    0  -0.498   9.6499   -6.8060  -2.4707
 ZFS  C3   C  CR6   0   0.124   9.8531   -7.8953   0.9398
 ZFS  O3   O  O     0  -0.481   7.1424   -1.3191  -4.6146
 ZFS  C4   C  CR16  0  -0.389   9.8669   -7.9251  -0.4409
 ZFS  C5   C  CR6   0   0.478   9.6241   -6.7388  -1.1277
 ZFS  C7   C  CR16  0  -0.295   8.1716   -5.2733  -3.5610
 ZFS  C8   C  CR16  0  -0.289   7.9796   -4.1541  -4.3554
 ZFS  C9   C  CR6   0   0.365   9.0747   -3.4090  -4.7918
 ZFS  C10  C  C     0   0.699   7.9813   -1.3266  -5.4940
 ZFS  C11  C  CR6   0   0.391   7.2578    0.7707  -6.5405
 ZFS  C12  C  CR16  0  -0.313   6.8088    1.1887  -7.7895
 ZFS  C13  C  CR16  0  -0.235   6.0412    2.3366  -7.9107
 ZFS  C14  C  CR16  0  -0.286   5.7018    3.0763  -6.7913
 ZFS  C15  C  CR6   0  -0.188   6.1557    2.6587  -5.5438
 ZFS  C16  C  CR16  0  -0.334   6.9333    1.5197  -5.4094
 ZFS  C17  C  CT    0   1.051   5.8136    3.4944  -4.3494
 ZFS  C18  C  CR16  0  -0.322  10.3581   -3.8122  -4.4287
 ZFS  C20  C  CR16  0  -0.401   9.3769   -5.5820  -0.3994
 ZFS  C21  C  CR16  0  -0.062   9.3857   -5.6756   0.9851
 ZFS  C1   C  CH3   0  -0.514  10.3293  -10.1630   3.9075
 ZFS  O1   O  O     0  -0.479  10.3392  -10.2196   1.1065
 ZFS  C6   C  CR6   0   0.286   9.4546   -5.6601  -3.2114
 ZFS  N3   N  NH1   0  -0.784   8.0757   -0.3590  -6.4628
 ZFS  F1   F  F     0  -0.314   6.3440    4.7229  -4.4403
 ZFS  F2   F  F     0  -0.314   4.4893    3.6627  -4.2269
 ZFS  F3   F  F     0  -0.301   6.2481    2.9690  -3.2009
 ZFS  C19  C  CR16  0  -0.293  10.5524   -4.9371  -3.6439
 ZFS  N4   N  N     0  -0.449   9.6172   -6.7949   1.6508
 ZFS  H1   H  HNH1  0   0.406   9.9025   -8.1356   3.4054
 ZFS  H2   H  HCR6  0   0.283  10.0649   -8.8439  -0.9758
 ZFS  H3   H  HCR6  0   0.278   7.3188   -5.8535  -3.2314
 ZFS  H4   H  HCR6  0   0.274   6.9757   -3.8830  -4.6460
 ZFS  H5   H  HCR6  0   0.277   7.0603    0.6110  -8.6707
 ZFS  H6   H  HCR6  0   0.270   5.6985    2.6489  -8.8879
 ZFS  H7   H  HCR6  0   0.273   5.0946    3.9659  -6.8978
 ZFS  H8   H  HCR6  0   0.279   7.3066    1.2194  -4.4423
 ZFS  H9   H  HCR6  0   0.276  11.2156   -3.2412  -4.7631
 ZFS  H10  H  HCR6  0   0.297   9.1806   -4.6286  -0.8697
 ZFS  H11  H  HCR6  0   0.274   9.1938   -4.7884   1.5775
 ZFS  H12  H  HCH3  0   0.252  10.2771   -9.8074   4.9324
 ZFS  H13  H  HCH3  0   0.239   9.5794  -10.9440   3.7757
 ZFS  H14  H  HCH3  0   0.240  11.3133  -10.6045   3.7468
 ZFS  H15  H  HNH1  0   0.412   9.7314   -2.0913  -6.2186
 ZFS  H16  H  HNH1  0   0.413   8.6029   -0.5780  -7.2950
 ZFS  H17  H  HCR6  0   0.278  11.5540   -5.2449  -3.3717
 ZFS  N2   N  NH1   0  -0.780   8.9367   -2.2985  -5.6321

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
 ZFS  C13  C12  aromatic  1.386  0.020  1.386
 ZFS  C13  C14  aromatic  1.384  0.020  1.384
 ZFS  C12  C11  aromatic  1.392  0.020  1.392
 ZFS  C14  C15  aromatic  1.392  0.020  1.392
 ZFS  C11  N3   single    1.397  0.020  1.397
 ZFS  C11  C16  aromatic  1.395  0.020  1.395
 ZFS  N3   C10  single    1.373  0.020  1.373
 ZFS  N2   C10  single    1.370  0.020  1.370
 ZFS  N2   C9   single    1.399  0.020  1.399
 ZFS  C15  C16  aromatic  1.386  0.020  1.386
 ZFS  C15  C17  single    1.497  0.020  1.497
 ZFS  C10  O3   double    1.215  0.020  1.215
 ZFS  C18  C9   aromatic  1.393  0.020  1.393
 ZFS  C18  C19  aromatic  1.385  0.020  1.385
 ZFS  C9   C8   aromatic  1.395  0.020  1.395
 ZFS  F1   C17  single    1.341  0.020  1.341
 ZFS  C17  F2   single    1.341  0.020  1.341
 ZFS  C17  F3   single    1.336  0.020  1.336
 ZFS  C19  C6   aromatic  1.384  0.020  1.384
 ZFS  C8   C7   aromatic  1.386  0.020  1.386
 ZFS  C6   C7   aromatic  1.385  0.020  1.385
 ZFS  C6   O2   single    1.378  0.020  1.378
 ZFS  O2   C5   single    1.345  0.020  1.345
 ZFS  C5   C20  aromatic  1.389  0.020  1.389
 ZFS  C5   C4   aromatic  1.392  0.020  1.392
 ZFS  C20  C21  aromatic  1.388  0.020  1.388
 ZFS  C4   C3   aromatic  1.381  0.020  1.381
 ZFS  C21  N4   aromatic  1.323  0.020  1.323
 ZFS  C3   N4   aromatic  1.331  0.020  1.331
 ZFS  C3   C2   single    1.505  0.020  1.505
 ZFS  O1   C2   double    1.224  0.020  1.224
 ZFS  C2   N1   single    1.334  0.020  1.334
 ZFS  N1   C1   single    1.442  0.020  1.442
 ZFS  N1   H1   single    0.860  0.020  1.020
 ZFS  C4   H2   single    0.930  0.020  1.080
 ZFS  C7   H3   single    0.930  0.020  1.080
 ZFS  C8   H4   single    0.930  0.020  1.080
 ZFS  C12  H5   single    0.930  0.020  1.080
 ZFS  C13  H6   single    0.930  0.020  1.080
 ZFS  C14  H7   single    0.930  0.020  1.080
 ZFS  C16  H8   single    0.930  0.020  1.080
 ZFS  C18  H9   single    0.930  0.020  1.080
 ZFS  C20  H10  single    0.930  0.020  1.080
 ZFS  C21  H11  single    0.930  0.020  1.080
 ZFS  C1   H12  single    0.970  0.020  1.090
 ZFS  C1   H13  single    0.970  0.020  1.090
 ZFS  C1   H14  single    0.970  0.020  1.090
 ZFS  N2   H15  single    0.860  0.020  1.020
 ZFS  N3   H16  single    0.860  0.020  1.020
 ZFS  C19  H17  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
 ZFS  H1   N1   C1   119.87  3.000
 ZFS  H1   N1   C2   117.62  3.000
 ZFS  C1   N1   C2   122.51  3.000
 ZFS  O1   C2   C3   121.13  3.000
 ZFS  O1   C2   N1   124.07  3.000
 ZFS  C3   C2   N1   114.80  3.000
 ZFS  C6   O2   C5   119.49  3.000
 ZFS  N4   C3   C4   123.61  3.000
 ZFS  N4   C3   C2   117.59  3.000
 ZFS  C4   C3   C2   118.79  3.000
 ZFS  H2   C4   C5   120.79  3.000
 ZFS  H2   C4   C3   120.98  3.000
 ZFS  C5   C4   C3   118.23  3.000
 ZFS  C20  C5   C4   118.81  3.000
 ZFS  C4   C5   O2   116.53  3.000
 ZFS  C20  C5   O2   124.65  3.000
 ZFS  H3   C7   C6   120.21  3.000
 ZFS  H3   C7   C8   119.88  3.000
 ZFS  C6   C7   C8   119.91  3.000
 ZFS  H4   C8   C9   120.78  3.000
 ZFS  H4   C8   C7   119.07  3.000
 ZFS  C9   C8   C7   120.14  3.000
 ZFS  N2   C9   C18  118.49  3.000
 ZFS  C18  C9   C8   119.15  3.000
 ZFS  N2   C9   C8   122.31  3.000
 ZFS  N3   C10  N2   112.40  3.000
 ZFS  N2   C10  O3   123.97  3.000
 ZFS  N3   C10  O3   123.63  3.000
 ZFS  N3   C11  C16  121.70  3.000
 ZFS  C16  C11  C12  119.43  3.000
 ZFS  N3   C11  C12  118.80  3.000
 ZFS  H5   C12  C13  119.93  3.000
 ZFS  H5   C12  C11  119.67  3.000
 ZFS  C13  C12  C11  120.39  3.000
 ZFS  H6   C13  C14  119.91  3.000
 ZFS  H6   C13  C12  119.57  3.000
 ZFS  C14  C13  C12  120.51  3.000
 ZFS  H7   C14  C15  121.18  3.000
 ZFS  H7   C14  C13  119.83  3.000
 ZFS  C15  C14  C13  118.99  3.000
 ZFS  C17  C15  C16  120.64  3.000
 ZFS  C17  C15  C14  118.23  3.000
 ZFS  C16  C15  C14  121.10  3.000
 ZFS  H8   C16  C15  120.64  3.000
 ZFS  H8   C16  C11  119.78  3.000
 ZFS  C15  C16  C11  119.56  3.000
 ZFS  F3   C17  F2   106.99  3.000
 ZFS  F3   C17  F1   106.85  3.000
 ZFS  F2   C17  F1   106.37  3.000
 ZFS  F3   C17  C15  113.08  3.000
 ZFS  F2   C17  C15  111.64  3.000
 ZFS  F1   C17  C15  111.52  3.000
 ZFS  H9   C18  C19  119.47  3.000
 ZFS  H9   C18  C9   119.75  3.000
 ZFS  C19  C18  C9   120.79  3.000
 ZFS  H10  C20  C21  119.64  3.000
 ZFS  H10  C20  C5   122.59  3.000
 ZFS  C21  C20  C5   117.76  3.000
 ZFS  H11  C21  N4   116.65  3.000
 ZFS  H11  C21  C20  119.28  3.000
 ZFS  N4   C21  C20  124.07  3.000
 ZFS  H14  C1   H13  108.22  3.000
 ZFS  H14  C1   H12  108.36  3.000
 ZFS  H13  C1   H12  108.39  3.000
 ZFS  H14  C1   N1   111.58  3.000
 ZFS  H13  C1   N1   111.65  3.000
 ZFS  H12  C1   N1   108.54  3.000
 ZFS  C19  C6   C7   120.67  3.000
 ZFS  C7   C6   O2   119.94  3.000
 ZFS  C19  C6   O2   119.33  3.000
 ZFS  H16  N3   C11  115.82  3.000
 ZFS  H16  N3   C10  117.70  3.000
 ZFS  C11  N3   C10  124.69  3.000
 ZFS  H17  C19  C6   120.45  3.000
 ZFS  H17  C19  C18  120.20  3.000
 ZFS  C6   C19  C18  119.34  3.000
 ZFS  C21  N4   C3   117.50  3.000
 ZFS  H15  N2   C10  117.53  3.000
 ZFS  H15  N2   C9   115.74  3.000
 ZFS  C10  N2   C9   124.84  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
 ZFS  CONST_01  C20  C5   C4   C3      0.00   0.0  0
 ZFS  CONST_02  C20  C21  N4   C3      0.00   0.0  0
 ZFS  CONST_03  C21  C20  C5   C4      0.00   0.0  0
 ZFS  CONST_04  C21  N4   C3   C4      0.00   0.0  0
 ZFS  CONST_05  N4   C21  C20  C5      0.00   0.0  0
 ZFS  CONST_06  N4   C3   C4   C5      0.00   0.0  0
 ZFS  CONST_07  C18  C9   C8   C7      0.00   0.0  0
 ZFS  CONST_08  C18  C19  C6   C7      0.00   0.0  0
 ZFS  CONST_09  C19  C18  C9   C8      0.00   0.0  0
 ZFS  CONST_10  C19  C6   C7   C8      0.00   0.0  0
 ZFS  CONST_11  C6   C19  C18  C9      0.00   0.0  0
 ZFS  CONST_12  C6   C7   C8   C9      0.00   0.0  0
 ZFS  CONST_13  C14  C13  C12  C11     0.00   0.0  0
 ZFS  CONST_14  C14  C15  C16  C11     0.00   0.0  0
 ZFS  CONST_15  C15  C14  C13  C12     0.00   0.0  0
 ZFS  CONST_16  C15  C16  C11  C12     0.00   0.0  0
 ZFS  CONST_17  C16  C11  C12  C13     0.00   0.0  0
 ZFS  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 ZFS  CONST_19  C5   C4   C3   C2    180.00   0.0  0
 ZFS  CONST_20  C21  N4   C3   C2    180.00   0.0  0
 ZFS  CONST_21  C18  C19  C6   O2    180.00   0.0  0
 ZFS  CONST_22  C8   C7   C6   O2    180.00   0.0  0
 ZFS  CONST_23  C21  C20  C5   O2    180.00   0.0  0
 ZFS  CONST_24  C3   C4   C5   O2    180.00   0.0  0
 ZFS  CONST_25  N2   C9   C8   C7    180.00   0.0  0
 ZFS  CONST_26  C17  C15  C16  C11   180.00   0.0  0
 ZFS  CONST_27  N3   C11  C12  C13   180.00   0.0  0
 ZFS  CONST_28  C17  C15  C14  C13   180.00   0.0  0
 ZFS  CONST_29  N3   C11  C16  C15   180.00   0.0  0
 ZFS  CONST_30  C19  C18  C9   N2    180.00   0.0  0
 ZFS  CONST_31  H11  C21  N4   C3    180.00   0.0  0
 ZFS  CONST_32  H10  C20  C5   C4    180.00   0.0  0
 ZFS  CONST_33  H11  C21  C20  C5    180.00   0.0  0
 ZFS  CONST_34  H17  C19  C6   C7    180.00   0.0  0
 ZFS  CONST_35  H9   C18  C9   C8    180.00   0.0  0
 ZFS  CONST_36  H17  C19  C18  C9    180.00   0.0  0
 ZFS  CONST_37  H3   C7   C8   C9    180.00   0.0  0
 ZFS  CONST_38  H6   C13  C12  C11   180.00   0.0  0
 ZFS  CONST_39  H7   C14  C13  C12   180.00   0.0  0
 ZFS  CONST_40  H8   C16  C11  C12   180.00   0.0  0
 ZFS  CONST_41  H5   C12  C13  C14   180.00   0.0  0
 ZFS  CONST_42  H8   C16  C15  C14   180.00   0.0  0
 ZFS  CONST_43  H6   C13  C14  C15   180.00   0.0  0
 ZFS  CONST_44  H5   C12  C11  C16   180.00   0.0  0
 ZFS  CONST_45  H7   C14  C15  C16   180.00   0.0  0
 ZFS  CONST_46  H4   C8   C9   C18   180.00   0.0  0
 ZFS  CONST_47  H2   C4   C5   C20   180.00   0.0  0
 ZFS  CONST_48  H9   C18  C19  C6    180.00   0.0  0
 ZFS  CONST_49  H4   C8   C7   C6    180.00   0.0  0
 ZFS  CONST_50  H3   C7   C6   C19   180.00   0.0  0
 ZFS  CONST_51  H10  C20  C21  N4    180.00   0.0  0
 ZFS  CONST_52  H2   C4   C3   N4    180.00   0.0  0
 ZFS  CONST_61  C1   N1   C2   C3    180.00   0.0  0
 ZFS  CONST_62  C11  N3   C10  O3      0.00   0.0  0
 ZFS  CONST_63  C9   N2   C10  O3      0.00   0.0  0
 ZFS  CONST_64  N3   C10  N2   C9    180.00   0.0  0
 ZFS  CONST_65  N2   C10  N3   C11   180.00   0.0  0
 ZFS  CONST_66  H1   N1   C2   C3      0.00   0.0  0
 ZFS  CONST_67  O1   C2   N1   C1      0.00   0.0  0
 ZFS  CONST_70  H1   N1   C2   O1    180.00   0.0  0
 ZFS  Var_01    C6   O2   C5   C4   -178.20  30.0  2
 ZFS  Var_02    C19  C6   O2   C5     94.54  30.0  2
 ZFS  Var_03    C7   C6   O2   C5    -88.07  30.0  2
 ZFS  Var_04    C6   O2   C5   C20     1.71  30.0  2
 ZFS  Var_05    C4   C3   C2   N1    179.53  30.0  2
 ZFS  Var_06    N4   C3   C2   N1     -0.37  30.0  2
 ZFS  Var_07    O1   C2   C3   C4     -0.40  30.0  2
 ZFS  Var_08    F1   C17  C15  C14   -62.37  30.0  2
 ZFS  Var_09    F2   C17  C15  C14    56.47  30.0  2
 ZFS  Var_10    F3   C17  C15  C14   177.18  30.0  2
 ZFS  Var_11    F1   C17  C15  C16   115.98  30.0  2
 ZFS  Var_12    F2   C17  C15  C16  -125.18  30.0  2
 ZFS  Var_13    F3   C17  C15  C16    -4.47  30.0  2
 ZFS  Var_14    N4   C3   C2   O1    179.70  30.0  2
 ZFS  Var_15    H12  C1   N1   C2    178.94  30.0  3
 ZFS  Var_16    H13  C1   N1   C2    -61.66  30.0  3
 ZFS  Var_17    H14  C1   N1   C2     59.60  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
 ZFS  plan-1  C2   0.020
 ZFS  plan-1  O2   0.020
 ZFS  plan-1  C3   0.020
 ZFS  plan-1  C4   0.020
 ZFS  plan-1  C5   0.020
 ZFS  plan-1  C20  0.020
 ZFS  plan-1  C21  0.020
 ZFS  plan-1  N4   0.020
 ZFS  plan-1  H2   0.020
 ZFS  plan-1  H10  0.020
 ZFS  plan-1  H11  0.020
 ZFS  plan-2  C11  0.020
 ZFS  plan-2  C12  0.020
 ZFS  plan-2  C13  0.020
 ZFS  plan-2  C14  0.020
 ZFS  plan-2  C15  0.020
 ZFS  plan-2  C16  0.020
 ZFS  plan-2  C17  0.020
 ZFS  plan-2  N3   0.020
 ZFS  plan-2  H5   0.020
 ZFS  plan-2  H6   0.020
 ZFS  plan-2  H7   0.020
 ZFS  plan-2  H8   0.020
 ZFS  plan-3  O2   0.020
 ZFS  plan-3  C7   0.020
 ZFS  plan-3  C8   0.020
 ZFS  plan-3  C9   0.020
 ZFS  plan-3  C18  0.020
 ZFS  plan-3  C6   0.020
 ZFS  plan-3  C19  0.020
 ZFS  plan-3  H3   0.020
 ZFS  plan-3  H4   0.020
 ZFS  plan-3  H9   0.020
 ZFS  plan-3  H17  0.020
 ZFS  plan-3  N2   0.020
 ZFS  plan-4  N1   0.020
 ZFS  plan-4  C2   0.020
 ZFS  plan-4  C3   0.020
 ZFS  plan-4  C1   0.020
 ZFS  plan-4  O1   0.020
 ZFS  plan-4  H1   0.020
 ZFS  plan-5  O3   0.020
 ZFS  plan-5  C9   0.020
 ZFS  plan-5  C10  0.020
 ZFS  plan-5  C11  0.020
 ZFS  plan-5  N3   0.020
 ZFS  plan-5  H15  0.020
 ZFS  plan-5  H16  0.020
 ZFS  plan-5  N2   0.020

