# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:49:33 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc(c1)c2cc(Nc3ccc(OC(F)(F)F)cc3)ncn2
#
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
 STJ  STJ  3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)benzamide  ligand  40  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_STJ
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
 STJ  F1    F  F     0  -0.300  -6.9078  -1.1597  -0.9978
 STJ  C2    C  CT    0   1.071  -6.9597   0.1150  -0.6049
 STJ  F3    F  F     0  -0.300  -6.5965   0.8547  -1.6554
 STJ  F4    F  F     0  -0.278  -8.2159   0.4078  -0.3065
 STJ  O5    O  O2    0  -0.523  -6.2171   0.3544   0.4810
 STJ  C6    C  CR6   0   0.293  -4.8518   0.0933   0.4020
 STJ  C7    C  CR16  0  -0.287  -3.9851   1.0875  -0.0084
 STJ  C9    C  CR16  0  -0.309  -2.6174   0.8559  -0.0332
 STJ  C11   C  CR6   0   0.379  -2.1108  -0.3861   0.3568
 STJ  C12   C  CR16  0  -0.363  -3.0085  -1.3751   0.7765
 STJ  C14   C  CR16  0  -0.286  -4.3699  -1.1425   0.7998
 STJ  N16   N  NH1   0  -0.781  -0.7633  -0.7297   0.3808
 STJ  C18   C  CR6   0   0.593   0.3435  -0.0575  -0.0270
 STJ  N19   N  N     0  -0.473   0.2410   1.1616  -0.5456
 STJ  C20   C  CR16  0   0.073   1.3731   1.7453  -0.9120
 STJ  N22   N  N     0  -0.456   2.5893   1.2534  -0.8333
 STJ  C23   C  CR6   0   0.284   2.7032   0.0171  -0.3186
 STJ  C24   C  CR16  0  -0.459   1.5967  -0.6791   0.1141
 STJ  C26   C  CR6   0   0.085   4.0675  -0.5433  -0.2287
 STJ  C27   C  CR16  0  -0.311   5.1666   0.3105  -0.2481
 STJ  C29   C  CR6   0  -0.015   6.4601  -0.1853  -0.1338
 STJ  C30   C  CR16  0  -0.287   6.6605  -1.5605  -0.0398
 STJ  C32   C  CR16  0  -0.224   5.5728  -2.4208  -0.0477
 STJ  C34   C  CR16  0  -0.314   4.2852  -1.9182  -0.1345
 STJ  C36   C  C     0   0.492   7.5914   0.7966  -0.1615
 STJ  O37   O  O     0  -0.479   7.4545   1.8975  -0.6769
 STJ  N38   N  NH2   0  -0.813   8.7392   0.3937   0.4015
 STJ  H7    H  HCR6  0   0.281  -4.3606   2.0596  -0.2994
 STJ  H9    H  HCR6  0   0.296  -1.9554   1.6422  -0.3541
 STJ  H12   H  HCR6  0   0.281  -2.6363  -2.3419   1.0928
 STJ  H14   H  HCR6  0   0.282  -5.0428  -1.9185   1.1401
 STJ  HN16  H  HNH1  0   0.422  -0.5773  -1.6496   0.7505
 STJ  H20   H  HCR6  0   0.259   1.2778   2.7429  -1.3279
 STJ  H24   H  HCR6  0   0.285   1.6738  -1.6608   0.5615
 STJ  H27   H  HCR6  0   0.262   5.0089   1.3763  -0.3376
 STJ  H30   H  HCR6  0   0.266   7.6578  -1.9780   0.0126
 STJ  H32   H  HCR6  0   0.271   5.7303  -3.4895   0.0032
 STJ  H34   H  HCR6  0   0.265   3.4542  -2.6109  -0.1525
 STJ  HN38  H  HNH2  0   0.414   8.8155  -0.4547   0.9347
 STJ  HN3A  H  HNH2  0   0.407   9.5329   1.0134   0.4149

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
 STJ  F1   C2    single    1.335  0.020  1.335
 STJ  C2   F3    single    1.335  0.020  1.335
 STJ  C2   F4    single    1.324  0.020  1.324
 STJ  C2   O5    single    1.337  0.020  1.337
 STJ  O5   C6    single    1.392  0.020  1.392
 STJ  C6   C7    aromatic  1.381  0.020  1.381
 STJ  C6   C14   aromatic  1.385  0.020  1.385
 STJ  C7   C9    aromatic  1.387  0.020  1.387
 STJ  C9   C11   aromatic  1.397  0.020  1.397
 STJ  C11  C12   aromatic  1.400  0.020  1.400
 STJ  C11  N16   single    1.391  0.020  1.391
 STJ  C12  C14   aromatic  1.381  0.020  1.381
 STJ  N16  C18   single    1.358  0.020  1.358
 STJ  C18  N19   aromatic  1.329  0.020  1.329
 STJ  C18  C24   aromatic  1.406  0.020  1.406
 STJ  N19  C20   aromatic  1.325  0.020  1.325
 STJ  C20  N22   aromatic  1.314  0.020  1.314
 STJ  N22  C23   aromatic  1.344  0.020  1.344
 STJ  C23  C24   aromatic  1.377  0.020  1.377
 STJ  C23  C26   single    1.478  0.020  1.478
 STJ  C26  C27   aromatic  1.392  0.020  1.392
 STJ  C26  C34   aromatic  1.395  0.020  1.395
 STJ  C27  C29   aromatic  1.390  0.020  1.390
 STJ  C29  C30   aromatic  1.393  0.020  1.393
 STJ  C29  C36   single    1.498  0.020  1.498
 STJ  C30  C32   aromatic  1.387  0.020  1.387
 STJ  C32  C34   aromatic  1.385  0.020  1.385
 STJ  C36  O37   double    1.223  0.020  1.223
 STJ  C36  N38   single    1.340  0.020  1.340
 STJ  C7   H7    single    0.930  0.020  1.080
 STJ  C9   H9    single    0.930  0.020  1.080
 STJ  C12  H12   single    0.930  0.020  1.080
 STJ  C14  H14   single    0.930  0.020  1.080
 STJ  N16  HN16  single    0.860  0.020  1.020
 STJ  C20  H20   single    0.930  0.020  1.080
 STJ  C24  H24   single    0.930  0.020  1.080
 STJ  C27  H27   single    0.930  0.020  1.080
 STJ  C30  H30   single    0.930  0.020  1.080
 STJ  C32  H32   single    0.930  0.020  1.080
 STJ  C34  H34   single    0.930  0.020  1.080
 STJ  N38  HN38  single    0.860  0.020  1.020
 STJ  N38  HN3A  single    0.860  0.020  1.020

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
 STJ  O5    C2   F4    107.72  3.000
 STJ  O5    C2   F3    112.88  3.000
 STJ  F4    C2   F3    108.24  3.000
 STJ  O5    C2   F1    112.85  3.000
 STJ  F4    C2   F1    108.32  3.000
 STJ  F3    C2   F1    106.67  3.000
 STJ  C6    O5   C2    117.71  3.000
 STJ  C14   C6   C7    120.62  3.000
 STJ  C14   C6   O5    119.49  3.000
 STJ  C7    C6   O5    119.81  3.000
 STJ  H7    C7   C9    119.16  3.000
 STJ  H7    C7   C6    120.59  3.000
 STJ  C9    C7   C6    120.25  3.000
 STJ  H9    C9   C11   120.63  3.000
 STJ  H9    C9   C7    119.31  3.000
 STJ  C11   C9   C7    120.06  3.000
 STJ  N16   C11  C12   116.20  3.000
 STJ  N16   C11  C9    125.16  3.000
 STJ  C12   C11  C9    118.63  3.000
 STJ  H12   C12  C14   118.95  3.000
 STJ  H12   C12  C11   119.85  3.000
 STJ  C14   C12  C11   121.21  3.000
 STJ  H14   C14  C12   119.84  3.000
 STJ  H14   C14  C6    120.92  3.000
 STJ  C12   C14  C6    119.23  3.000
 STJ  HN16  N16  C18   114.29  3.000
 STJ  HN16  N16  C11   114.22  3.000
 STJ  C18   N16  C11   131.48  3.000
 STJ  C24   C18  N19   120.91  3.000
 STJ  C24   C18  N16   118.52  3.000
 STJ  N19   C18  N16   120.57  3.000
 STJ  C20   N19  C18   116.49  3.000
 STJ  H20   C20  N22   116.64  3.000
 STJ  H20   C20  N19   115.84  3.000
 STJ  N22   C20  N19   127.52  3.000
 STJ  C23   N22  C20   116.46  3.000
 STJ  C26   C23  C24   122.07  3.000
 STJ  C26   C23  N22   116.77  3.000
 STJ  C24   C23  N22   121.16  3.000
 STJ  H24   C24  C23   122.12  3.000
 STJ  H24   C24  C18   120.42  3.000
 STJ  C23   C24  C18   117.45  3.000
 STJ  C34   C26  C27   118.83  3.000
 STJ  C34   C26  C23   121.46  3.000
 STJ  C27   C26  C23   119.71  3.000
 STJ  H27   C27  C29   119.62  3.000
 STJ  H27   C27  C26   119.38  3.000
 STJ  C29   C27  C26   120.99  3.000
 STJ  C36   C29  C30   122.66  3.000
 STJ  C36   C29  C27   117.87  3.000
 STJ  C30   C29  C27   119.45  3.000
 STJ  H30   C30  C32   118.93  3.000
 STJ  H30   C30  C29   121.10  3.000
 STJ  C32   C30  C29   119.95  3.000
 STJ  H32   C32  C34   119.80  3.000
 STJ  H32   C32  C30   119.90  3.000
 STJ  C34   C32  C30   120.30  3.000
 STJ  H34   C34  C32   118.87  3.000
 STJ  H34   C34  C26   120.66  3.000
 STJ  C32   C34  C26   120.46  3.000
 STJ  N38   C36  O37   122.91  3.000
 STJ  N38   C36  C29   116.22  3.000
 STJ  O37   C36  C29   120.87  3.000
 STJ  HN3A  N38  HN38  116.91  3.000
 STJ  HN3A  N38  C36   119.70  3.000
 STJ  HN38  N38  C36   122.79  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
 STJ  CONST_01  C11   C9   C7   C6     0.00   0.0  0
 STJ  CONST_02  C11   C12  C14  C6     0.00   0.0  0
 STJ  CONST_03  C12   C14  C6   C7     0.00   0.0  0
 STJ  CONST_04  C12   C11  C9   C7     0.00   0.0  0
 STJ  CONST_05  C14   C6   C7   C9     0.00   0.0  0
 STJ  CONST_06  C14   C12  C11  C9     0.00   0.0  0
 STJ  CONST_07  N22   C20  N19  C18    0.00   0.0  0
 STJ  CONST_08  N22   C23  C24  C18    0.00   0.0  0
 STJ  CONST_09  C26   C23  C24  C18  180.00   0.0  0
 STJ  CONST_10  C23   C24  C18  N19    0.00   0.0  0
 STJ  CONST_11  C23   N22  C20  N19    0.00   0.0  0
 STJ  CONST_12  C24   C18  N19  C20    0.00   0.0  0
 STJ  CONST_13  C24   C23  N22  C20    0.00   0.0  0
 STJ  CONST_14  C26   C23  N22  C20  180.00   0.0  0
 STJ  CONST_17  C29   C27  C26  C23  180.00   0.0  0
 STJ  CONST_18  C32   C34  C26  C23  180.00   0.0  0
 STJ  CONST_21  C30   C29  C27  C26    0.00   0.0  0
 STJ  CONST_22  C30   C32  C34  C26    0.00   0.0  0
 STJ  CONST_23  C32   C34  C26  C27    0.00   0.0  0
 STJ  CONST_24  C32   C30  C29  C27    0.00   0.0  0
 STJ  CONST_25  C34   C26  C27  C29    0.00   0.0  0
 STJ  CONST_26  C34   C32  C30  C29    0.00   0.0  0
 STJ  CONST_27  C9    C7   C6   O5   180.00   0.0  0
 STJ  CONST_28  C12   C14  C6   O5   180.00   0.0  0
 STJ  CONST_29  N16   C11  C9   C7   180.00   0.0  0
 STJ  CONST_30  N16   C11  C12  C14  180.00   0.0  0
 STJ  CONST_31  C20   N19  C18  N16  180.00   0.0  0
 STJ  CONST_32  C23   C24  C18  N16  180.00   0.0  0
 STJ  CONST_33  C36   C29  C27  C26  180.00   0.0  0
 STJ  CONST_34  C36   C29  C30  C32  180.00   0.0  0
 STJ  CONST_35  H9    C9   C7   C6   180.00   0.0  0
 STJ  CONST_36  H12   C12  C14  C6   180.00   0.0  0
 STJ  CONST_37  H14   C14  C6   C7   180.00   0.0  0
 STJ  CONST_38  H7    C7   C9   C11  180.00   0.0  0
 STJ  CONST_39  H20   C20  N19  C18  180.00   0.0  0
 STJ  CONST_40  H24   C24  C18  N19  180.00   0.0  0
 STJ  CONST_41  H27   C27  C26  C23    0.00   0.0  0
 STJ  CONST_42  H34   C34  C26  C23    0.00   0.0  0
 STJ  CONST_43  H32   C32  C34  C26  180.00   0.0  0
 STJ  CONST_44  H30   C30  C29  C27  180.00   0.0  0
 STJ  CONST_45  HN38  N38  C36  C29    0.00   0.0  0
 STJ  CONST_46  HN3A  N38  C36  C29  180.00   0.0  0
 STJ  Var_01    C18   N16  C11  C9    -5.37  30.0  2
 STJ  Var_02    N19   C18  N16  C11    0.81  30.0  2
 STJ  Var_03    C7    C6   O5   C2    90.36  30.0  2
 STJ  Var_04    O37   C36  C29  C27  -22.78  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
 STJ  plan-1  O5    0.020
 STJ  plan-1  C6    0.020
 STJ  plan-1  C7    0.020
 STJ  plan-1  C9    0.020
 STJ  plan-1  C11   0.020
 STJ  plan-1  C12   0.020
 STJ  plan-1  C14   0.020
 STJ  plan-1  N16   0.020
 STJ  plan-1  H7    0.020
 STJ  plan-1  H9    0.020
 STJ  plan-1  H12   0.020
 STJ  plan-1  H14   0.020
 STJ  plan-2  N16   0.020
 STJ  plan-2  C18   0.020
 STJ  plan-2  N19   0.020
 STJ  plan-2  C20   0.020
 STJ  plan-2  N22   0.020
 STJ  plan-2  C23   0.020
 STJ  plan-2  C24   0.020
 STJ  plan-2  C26   0.020
 STJ  plan-2  H20   0.020
 STJ  plan-2  H24   0.020
 STJ  plan-3  C23   0.020
 STJ  plan-3  C26   0.020
 STJ  plan-3  C27   0.020
 STJ  plan-3  C29   0.020
 STJ  plan-3  C30   0.020
 STJ  plan-3  C32   0.020
 STJ  plan-3  C34   0.020
 STJ  plan-3  C36   0.020
 STJ  plan-3  H27   0.020
 STJ  plan-3  H30   0.020
 STJ  plan-3  H32   0.020
 STJ  plan-3  H34   0.020
 STJ  plan-4  C29   0.020
 STJ  plan-4  C36   0.020
 STJ  plan-4  O37   0.020
 STJ  plan-4  N38   0.020
 STJ  plan-4  HN38  0.020
 STJ  plan-4  HN3A  0.020

