# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:37:52 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-{2-[(E)-iminomethyl]-6-propylpyrimidin-4-yl}-N,N-dimethyl-5-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1cc(nc(C=N)n1)c2cc(cc(c2)C(F)(F)F)C(=O)N(C)C
#
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
 O47  O47  3-{2-[(E)-iminomethyl]-6-propylpyrimidin-4-yl}-N,N-dimethyl-5-(trifluoromethyl)benzamide  ligand  45  26  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O47
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
 O47  C1    C  CR6   0  -0.151  -1.8636   1.7449  -0.3465
 O47  C2    C  CR16  0  -0.322  -2.7841   0.7708  -0.0000
 O47  C3    C  CR6   0  -0.024  -2.3542  -0.5347   0.2187
 O47  C4    C  CR16  0  -0.282  -1.0071  -0.8430   0.1213
 O47  C5    C  CR6   0   0.096  -0.0718   0.1415  -0.1966
 O47  C6    C  CR16  0  -0.352  -0.5117   1.4362  -0.4399
 O47  C7    C  CT    0   1.062  -2.2904   3.1530  -0.6290
 O47  F8    F  F     0  -0.312  -1.9839   3.5170  -1.8817
 O47  F9    F  F     0  -0.299  -3.6038   3.3324  -0.4766
 O47  F10   F  F     0  -0.312  -1.6755   4.0243   0.1822
 O47  N11   N  N     0  -0.425   1.6459  -1.5064  -0.4062
 O47  C12   C  CR6   0   0.296   1.3603  -0.2154  -0.2841
 O47  C13   C  CR16  0  -0.387   2.3748   0.7356  -0.2352
 O47  C14   C  CR6   0   0.308   3.6848   0.2923  -0.3479
 O47  N15   N  N     0  -0.434   3.9522  -1.0056  -0.4843
 O47  C16   C  CR6   0   0.333   2.9227  -1.8397  -0.4970
 O47  C17   C  CH2   0  -0.494   4.8438   1.2352  -0.2830
 O47  C18   C  CH2   0  -0.426   5.6495   1.0638   1.0074
 O47  C19   C  CH3   0  -0.667   6.8046   2.0502   1.0879
 O47  C20   C  C     0   0.521  -3.3602  -1.5417   0.6889
 O47  N21   N  NT    0  -0.441  -3.3571  -2.7550   0.1107
 O47  O22   O  O     0  -0.487  -4.1200  -1.2308   1.5980
 O47  C23   C  CH3   0  -0.525  -4.2057  -3.8033   0.6406
 O47  C24   C  CH3   0  -0.534  -2.7219  -3.0736  -1.1533
 O47  C25   C  C1    0  -0.114   3.2763  -3.2737  -0.6310
 O47  N26   N  N     0  -0.509   2.3954  -4.1771  -0.6437
 O47  H2    H  HCR6  0   0.281  -3.8359   1.0045   0.0914
 O47  H4    H  HCR6  0   0.283  -0.6584  -1.8505   0.3080
 O47  H6    H  HCR6  0   0.280   0.1978   2.2059  -0.7157
 O47  H13   H  HCR6  0   0.280   2.1735   1.7888  -0.1012
 O47  H17   H  HCH2  0   0.255   5.4954   1.0577  -1.1431
 O47  H17A  H  HCH2  0   0.247   4.4844   2.2633  -0.3599
 O47  H18   H  HCH2  0   0.229   4.9876   1.1970   1.8671
 O47  H18A  H  HCH2  0   0.230   6.0266   0.0401   1.0622
 O47  H19   H  HCH3  0   0.233   7.3755   1.9157   2.0067
 O47  H19A  H  HCH3  0   0.222   7.4903   1.9247   0.2486
 O47  H19B  H  HCH3  0   0.222   6.4444   3.0802   1.0698
 O47  H23   H  HCH3  0   0.243  -5.1409  -3.8768   0.0808
 O47  H23A  H  HCH3  0   0.248  -3.6849  -4.7572   0.5599
 O47  H23B  H  HCH3  0   0.257  -4.4370  -3.6238   1.6857
 O47  H24   H  HCH3  0   0.247  -1.8882  -3.7643  -1.0175
 O47  H24A  H  HCH3  0   0.260  -3.4531  -3.5497  -1.8080
 O47  H24B  H  HCH3  0   0.265  -2.3615  -2.1845  -1.6606
 O47  H25   H  H     0   0.241   4.3494  -3.4543  -0.7117
 O47  HN26  H  H     0   0.358   2.8354  -5.0884  -0.7388

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
 O47  C7   C1    single    1.498  0.020  1.498
 O47  C6   C1    aromatic  1.390  0.020  1.390
 O47  C1   C2    aromatic  1.384  0.020  1.384
 O47  C2   C3    aromatic  1.392  0.020  1.392
 O47  C2   H2    single    0.930  0.020  1.080
 O47  C4   C3    aromatic  1.385  0.020  1.385
 O47  C3   C20   single    1.499  0.020  1.499
 O47  C5   C4    aromatic  1.395  0.020  1.395
 O47  C4   H4    single    0.930  0.020  1.080
 O47  C6   C5    aromatic  1.389  0.020  1.389
 O47  C12  C5    single    1.479  0.020  1.479
 O47  C6   H6    single    0.930  0.020  1.080
 O47  F8   C7    single    1.340  0.020  1.340
 O47  F10  C7    single    1.340  0.020  1.340
 O47  C7   F9    single    1.334  0.020  1.334
 O47  C16  N11   aromatic  1.323  0.020  1.323
 O47  N11  C12   aromatic  1.328  0.020  1.328
 O47  C12  C13   aromatic  1.391  0.020  1.391
 O47  C14  C13   aromatic  1.388  0.020  1.388
 O47  C13  H13   single    0.930  0.020  1.080
 O47  N15  C14   aromatic  1.332  0.020  1.332
 O47  C14  C17   single    1.496  0.020  1.496
 O47  C16  N15   aromatic  1.325  0.020  1.325
 O47  C25  C16   single    1.483  0.020  1.483
 O47  C17  C18   single    1.531  0.020  1.531
 O47  C17  H17   single    0.970  0.020  1.090
 O47  C17  H17A  single    0.970  0.020  1.090
 O47  C18  C19   single    1.521  0.020  1.521
 O47  C18  H18   single    0.970  0.020  1.090
 O47  C18  H18A  single    0.970  0.020  1.090
 O47  C19  H19   single    0.970  0.020  1.090
 O47  C19  H19A  single    0.970  0.020  1.090
 O47  C19  H19B  single    0.970  0.020  1.090
 O47  N21  C20   single    1.344  0.020  1.344
 O47  C20  O22   double    1.225  0.020  1.225
 O47  C24  N21   single    1.450  0.020  1.450
 O47  N21  C23   single    1.449  0.020  1.449
 O47  C23  H23   single    0.970  0.020  1.090
 O47  C23  H23A  single    0.970  0.020  1.090
 O47  C23  H23B  single    0.970  0.020  1.090
 O47  C24  H24   single    0.970  0.020  1.090
 O47  C24  H24A  single    0.970  0.020  1.090
 O47  C24  H24B  single    0.970  0.020  1.090
 O47  N26  C25   double    1.262  0.020  1.262
 O47  C25  H25   single    0.930  0.020  1.080
 O47  N26  HN26  single    0.890  0.020  1.040

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
 O47  C7    C1   C6    118.24  3.000
 O47  C6    C1   C2    120.48  3.000
 O47  C7    C1   C2    121.27  3.000
 O47  H2    C2   C3    119.34  3.000
 O47  H2    C2   C1    121.05  3.000
 O47  C3    C2   C1    119.61  3.000
 O47  C20   C3   C4    121.68  3.000
 O47  C20   C3   C2    118.17  3.000
 O47  C4    C3   C2    119.87  3.000
 O47  H4    C4   C5    118.71  3.000
 O47  H4    C4   C3    120.55  3.000
 O47  C5    C4   C3    120.74  3.000
 O47  C12   C5   C6    121.42  3.000
 O47  C12   C5   C4    119.52  3.000
 O47  C6    C5   C4    119.05  3.000
 O47  H6    C6   C5    119.99  3.000
 O47  H6    C6   C1    119.78  3.000
 O47  C5    C6   C1    120.22  3.000
 O47  F10   C7   F9    107.16  3.000
 O47  F9    C7   F8    107.18  3.000
 O47  F10   C7   F8    106.52  3.000
 O47  F9    C7   C1    112.66  3.000
 O47  F10   C7   C1    111.49  3.000
 O47  F8    C7   C1    111.49  3.000
 O47  C16   N11  C12   117.31  3.000
 O47  C13   C12  N11   120.73  3.000
 O47  C13   C12  C5    122.63  3.000
 O47  N11   C12  C5    116.64  3.000
 O47  H13   C13  C14   119.83  3.000
 O47  H13   C13  C12   122.33  3.000
 O47  C14   C13  C12   117.84  3.000
 O47  C17   C14  N15   117.59  3.000
 O47  C17   C14  C13   121.78  3.000
 O47  N15   C14  C13   120.61  3.000
 O47  C16   N15  C14   117.27  3.000
 O47  C25   C16  N15   115.10  3.000
 O47  C25   C16  N11   118.69  3.000
 O47  N15   C16  N11   126.21  3.000
 O47  H17A  C17  H17   107.07  3.000
 O47  H17A  C17  C18   109.76  3.000
 O47  H17   C17  C18   109.34  3.000
 O47  H17A  C17  C14   109.61  3.000
 O47  H17   C17  C14   108.99  3.000
 O47  C18   C17  C14   111.95  3.000
 O47  H18A  C18  H18   106.48  3.000
 O47  H18A  C18  C19   110.06  3.000
 O47  H18   C18  C19   109.82  3.000
 O47  H18A  C18  C17   109.20  3.000
 O47  H18   C18  C17   109.30  3.000
 O47  C19   C18  C17   111.82  3.000
 O47  H19B  C19  H19A  107.66  3.000
 O47  H19B  C19  H19   107.66  3.000
 O47  H19A  C19  H19   107.76  3.000
 O47  H19B  C19  C18   111.14  3.000
 O47  H19A  C19  C18   111.22  3.000
 O47  H19   C19  C18   111.24  3.000
 O47  O22   C20  N21   123.36  3.000
 O47  O22   C20  C3    118.59  3.000
 O47  N21   C20  C3    118.03  3.000
 O47  C24   N21  C23   114.61  3.000
 O47  C23   N21  C20   119.63  3.000
 O47  C24   N21  C20   125.05  3.000
 O47  H23B  C23  H23A  108.54  3.000
 O47  H23B  C23  H23   108.79  3.000
 O47  H23A  C23  H23   108.19  3.000
 O47  H23B  C23  N21   110.94  3.000
 O47  H23A  C23  N21   109.04  3.000
 O47  H23   C23  N21   111.26  3.000
 O47  H24B  C24  H24A  107.44  3.000
 O47  H24B  C24  H24   108.85  3.000
 O47  H24A  C24  H24   108.09  3.000
 O47  H24B  C24  N21   111.90  3.000
 O47  H24A  C24  N21   108.99  3.000
 O47  H24   C24  N21   111.42  3.000
 O47  H25   C25  N26   124.56  3.000
 O47  H25   C25  C16   113.65  3.000
 O47  N26   C25  C16   121.78  3.000
 O47  HN26  N26  C25   109.92  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
 O47  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 O47  CONST_02  C12  C5   C6   C1    180.00   0.0  0
 O47  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 O47  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 O47  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 O47  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 O47  CONST_07  C6   C5   C4   C3      0.00   0.0  0
 O47  CONST_08  C12  C5   C4   C3    180.00   0.0  0
 O47  CONST_11  C16  N11  C12  C5    180.00   0.0  0
 O47  CONST_12  C14  C13  C12  C5    180.00   0.0  0
 O47  CONST_15  C14  N15  C16  N11     0.00   0.0  0
 O47  CONST_16  C14  C13  C12  N11     0.00   0.0  0
 O47  CONST_17  N15  C16  N11  C12     0.00   0.0  0
 O47  CONST_18  N15  C14  C13  C12     0.00   0.0  0
 O47  CONST_19  C16  N11  C12  C13     0.00   0.0  0
 O47  CONST_20  C16  N15  C14  C13     0.00   0.0  0
 O47  CONST_21  C20  C3   C2   C1    180.00   0.0  0
 O47  CONST_22  C7   C1   C2   C3    180.00   0.0  0
 O47  CONST_23  C20  C3   C4   C5    180.00   0.0  0
 O47  CONST_24  C7   C1   C6   C5    180.00   0.0  0
 O47  CONST_25  C25  C16  N11  C12   180.00   0.0  0
 O47  CONST_26  C17  C14  C13  C12   180.00   0.0  0
 O47  CONST_27  C25  C16  N15  C14   180.00   0.0  0
 O47  CONST_28  C17  C14  N15  C16   180.00   0.0  0
 O47  CONST_29  H6   C6   C1   C2    180.00   0.0  0
 O47  CONST_30  H4   C4   C3   C2    180.00   0.0  0
 O47  CONST_31  H2   C2   C3   C4    180.00   0.0  0
 O47  CONST_32  H13  C13  C12  C5      0.00   0.0  0
 O47  CONST_34  C23  N21  C20  C3    180.00   0.0  0
 O47  CONST_36  C23  N21  C20  O22     0.00   0.0  0
 O47  Var_01    F8   C7   C1   C2   -119.12  30.0  3
 O47  Var_02    N21  C20  C3   C2    135.82  30.0  2
 O47  Var_03    N26  C25  C16  N11    -0.88  30.0  3
 O47  Var_04    C18  C17  C14  C13   109.82  30.0  2
 O47  Var_05    C19  C18  C17  C14  -178.42  30.0  3
 O47  Var_06    H19  C19  C18  C17  -179.63  30.0  3
 O47  Var_07    H24  C24  N21  C20   113.99  30.0  3
 O47  Var_08    H23  C23  N21  C20    97.09  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
 O47  plan-1  C1    0.020
 O47  plan-1  C2    0.020
 O47  plan-1  C3    0.020
 O47  plan-1  C4    0.020
 O47  plan-1  C5    0.020
 O47  plan-1  C6    0.020
 O47  plan-1  C7    0.020
 O47  plan-1  C12   0.020
 O47  plan-1  C20   0.020
 O47  plan-1  H2    0.020
 O47  plan-1  H4    0.020
 O47  plan-1  H6    0.020
 O47  plan-2  C5    0.020
 O47  plan-2  N11   0.020
 O47  plan-2  C12   0.020
 O47  plan-2  C13   0.020
 O47  plan-2  C14   0.020
 O47  plan-2  N15   0.020
 O47  plan-2  C16   0.020
 O47  plan-2  C17   0.020
 O47  plan-2  C25   0.020
 O47  plan-2  H13   0.020
 O47  plan-3  C3    0.020
 O47  plan-3  C20   0.020
 O47  plan-3  N21   0.020
 O47  plan-3  O22   0.020
 O47  plan-3  C23   0.020
 O47  plan-3  C24   0.020
 O47  plan-4  C16   0.020
 O47  plan-4  C25   0.020
 O47  plan-4  N26   0.020
 O47  plan-4  H25   0.020
 O47  plan-4  HN26  0.020

