# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:22:15 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-[(6R)-5-ethanoyl-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidin-6-yl]pyridine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)C1=C(C)N(C(=O)N[C@@H]1c2ccc(nc2)C#N)c3cccc(c3)C(F)(F)F
#
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
 JJS  JJS  5-[(6R)-5-ethanoyl-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidin-6-yl]pyridine-2-carbonitrile  ligand  44  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JJS
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
 JJS  F25   F  F     0  -0.300  -4.9287   2.4844  -0.7428
 JJS  C24   C  CT    0   1.057  -3.6396   2.1418  -0.7028
 JJS  F27   F  F     0  -0.312  -3.1894   2.1487  -1.9652
 JJS  F26   F  F     0  -0.313  -2.9912   3.1255  -0.0629
 JJS  C20   C  CR6   0  -0.191  -3.4138   0.8159  -0.0457
 JJS  C21   C  CR16  0  -0.280  -4.4538   0.1067   0.5348
 JJS  C22   C  CR16  0  -0.247  -4.1961  -1.1168   1.1408
 JJS  C23   C  CR16  0  -0.232  -2.9124  -1.6320   1.1656
 JJS  C19   C  CR16  0  -0.276  -2.1180   0.3093  -0.0149
 JJS  C18   C  CR6   0   0.280  -1.8755  -0.9132   0.5835
 JJS  N4    N  NR6   0  -0.660  -0.5442  -1.4231   0.5778
 JJS  C3    C  CR6   0   0.687   0.1105  -1.4648   1.8124
 JJS  O29   O  O     0  -0.480  -0.4784  -1.2181   2.8462
 JJS  C5    C  CR6   0   0.355   0.0225  -1.9180  -0.5943
 JJS  C28   C  CH3   0  -0.729  -0.9437  -2.2523  -1.6873
 JJS  C6    C  CR6   0  -0.148   1.3679  -2.0837  -0.6608
 JJS  C15   C  C     0   0.357   2.0696  -2.5473  -1.8691
 JJS  O16   O  O     0  -0.414   1.5259  -2.6435  -2.9553
 JJS  C17   C  CH3   0  -0.805   3.5343  -2.8861  -1.7305
 JJS  C1    C  CR16  0  -0.240   2.1953  -1.7164   0.5429
 JJS  N2    N  NR16  0  -0.635   1.3970  -1.8463   1.7423
 JJS  C7    C  CR6   0   0.081   2.8126  -0.3296   0.4521
 JJS  C8    C  CR16  0  -0.081   2.1951   0.7167  -0.2330
 JJS  N9    N  N     0  -0.400   2.6790   1.9448  -0.2846
 JJS  C10   C  CR6   0   0.194   3.8238   2.1811   0.3475
 JJS  C13   C  CSP   0   0.065   4.3212   3.5276   0.2655
 JJS  N14   N  NS    0  -0.233   4.7244   4.6037   0.2062
 JJS  C11   C  CR16  0  -0.257   4.5369   1.2220   1.0511
 JJS  C12   C  CR16  0  -0.187   4.0088  -0.0573   1.0998
 JJS  H21   H  HCR6  0   0.279  -5.4660   0.4856   0.5208
 JJS  H19   H  HCR6  0   0.285  -1.2946   0.8557  -0.4593
 JJS  H22   H  HCR6  0   0.279  -5.0079  -1.6723   1.5896
 JJS  H23   H  HCR6  0   0.280  -2.7177  -2.5941   1.6195
 JJS  H2    H  HNR6  0   0.417   1.8898  -1.8836   2.6226
 JJS  H281  H  HCH3  0   0.264  -1.9346  -2.4547  -1.2896
 JJS  H282  H  HCH3  0   0.275  -1.0337  -1.4307  -2.3995
 JJS  H283  H  HCH3  0   0.281  -0.6135  -3.1236  -2.2415
 JJS  H1    H  HCR6  0   0.307   3.0117  -2.4303   0.6555
 JJS  H171  H  HCH3  0   0.272   3.6937  -3.6652  -0.9830
 JJS  H172  H  HCH3  0   0.274   3.9254  -3.2308  -2.6845
 JJS  H173  H  HCH3  0   0.261   4.1176  -2.0172  -1.4182
 JJS  H8    H  HCR6  0   0.275   1.2726   0.5499  -0.7775
 JJS  H12   H  HCR6  0   0.294   4.5331  -0.8372   1.6384
 JJS  H11   H  HCR6  0   0.303   5.4697   1.4681   1.5384

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
 JJS  F25  C24   single    1.334  0.020  1.334
 JJS  C24  F27   single    1.340  0.020  1.340
 JJS  C24  F26   single    1.341  0.020  1.341
 JJS  C24  C20   single    1.497  0.020  1.497
 JJS  C20  C21   aromatic  1.386  0.020  1.386
 JJS  C20  C19   aromatic  1.392  0.020  1.392
 JJS  C21  C22   aromatic  1.390  0.020  1.390
 JJS  C22  C23   aromatic  1.383  0.020  1.383
 JJS  C23  C18   aromatic  1.389  0.020  1.389
 JJS  C19  C18   aromatic  1.383  0.020  1.383
 JJS  C18  N4    single    1.426  0.020  1.426
 JJS  N4   C3    single    1.398  0.020  1.398
 JJS  N4   C5    single    1.393  0.020  1.393
 JJS  C3   O29   double    1.215  0.020  1.215
 JJS  C3   N2    single    1.344  0.020  1.344
 JJS  C5   C28   single    1.497  0.020  1.497
 JJS  C5   C6    double    1.357  0.020  1.357
 JJS  C6   C15   single    1.472  0.020  1.472
 JJS  C6   C1    single    1.506  0.020  1.506
 JJS  C15  O16   double    1.219  0.020  1.219
 JJS  C15  C17   single    1.510  0.020  1.510
 JJS  C1   N2    single    1.447  0.020  1.447
 JJS  C1   C7    single    1.521  0.020  1.521
 JJS  C7   C8    aromatic  1.395  0.020  1.395
 JJS  C7   C12   aromatic  1.387  0.020  1.387
 JJS  C8   N9    aromatic  1.321  0.020  1.321
 JJS  N9   C10   aromatic  1.329  0.020  1.329
 JJS  C10  C13   single    1.438  0.020  1.438
 JJS  C10  C11   aromatic  1.387  0.020  1.387
 JJS  C13  N14   triple    1.151  0.020  1.151
 JJS  C11  C12   aromatic  1.385  0.020  1.385
 JJS  C21  H21   single    0.930  0.020  1.080
 JJS  C19  H19   single    0.930  0.020  1.080
 JJS  C22  H22   single    0.930  0.020  1.080
 JJS  C23  H23   single    0.930  0.020  1.080
 JJS  N2   H2    single    0.890  0.020  1.040
 JJS  C28  H281  single    0.970  0.020  1.090
 JJS  C28  H282  single    0.970  0.020  1.090
 JJS  C28  H283  single    0.970  0.020  1.090
 JJS  C1   H1    single    0.970  0.020  1.090
 JJS  C17  H171  single    0.970  0.020  1.090
 JJS  C17  H172  single    0.970  0.020  1.090
 JJS  C17  H173  single    0.970  0.020  1.090
 JJS  C8   H8    single    0.930  0.020  1.080
 JJS  C12  H12   single    0.930  0.020  1.080
 JJS  C11  H11   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
 JJS  C20   C24  F26   111.56  3.000
 JJS  C20   C24  F27   111.55  3.000
 JJS  F26   C24  F27   106.45  3.000
 JJS  C20   C24  F25   112.73  3.000
 JJS  F26   C24  F25   107.04  3.000
 JJS  F27   C24  F25   107.16  3.000
 JJS  C19   C20  C21   120.20  3.000
 JJS  C19   C20  C24   118.21  3.000
 JJS  C21   C20  C24   121.59  3.000
 JJS  H21   C21  C22   119.21  3.000
 JJS  H21   C21  C20   121.19  3.000
 JJS  C22   C21  C20   119.60  3.000
 JJS  H22   C22  C23   119.87  3.000
 JJS  H22   C22  C21   119.62  3.000
 JJS  C23   C22  C21   120.52  3.000
 JJS  H23   C23  C18   120.11  3.000
 JJS  H23   C23  C22   120.38  3.000
 JJS  C18   C23  C22   119.49  3.000
 JJS  H19   C19  C18   119.35  3.000
 JJS  H19   C19  C20   121.00  3.000
 JJS  C18   C19  C20   119.66  3.000
 JJS  N4    C18  C19   118.58  3.000
 JJS  N4    C18  C23   120.90  3.000
 JJS  C19   C18  C23   120.52  3.000
 JJS  C5    N4   C3    122.82  3.000
 JJS  C5    N4   C18   120.69  3.000
 JJS  C3    N4   C18   116.39  3.000
 JJS  N2    C3   O29   124.47  3.000
 JJS  N2    C3   N4    114.26  3.000
 JJS  O29   C3   N4    121.22  3.000
 JJS  C6    C5   C28   125.23  3.000
 JJS  C6    C5   N4    119.21  3.000
 JJS  C28   C5   N4    115.55  3.000
 JJS  H283  C28  H282  107.26  3.000
 JJS  H283  C28  H281  108.37  3.000
 JJS  H282  C28  H281  107.70  3.000
 JJS  H283  C28  C5    110.87  3.000
 JJS  H282  C28  C5    111.20  3.000
 JJS  H281  C28  C5    111.28  3.000
 JJS  C1    C6   C15   118.09  3.000
 JJS  C1    C6   C5    118.40  3.000
 JJS  C15   C6   C5    123.45  3.000
 JJS  C17   C15  O16   119.80  3.000
 JJS  C17   C15  C6    117.24  3.000
 JJS  O16   C15  C6    122.94  3.000
 JJS  H173  C17  H172  108.13  3.000
 JJS  H173  C17  H171  107.10  3.000
 JJS  H172  C17  H171  108.79  3.000
 JJS  H173  C17  C15   111.46  3.000
 JJS  H172  C17  C15   109.86  3.000
 JJS  H171  C17  C15   111.39  3.000
 JJS  H1    C1   C7    107.42  3.000
 JJS  H1    C1   N2    105.59  3.000
 JJS  C7    C1   N2    110.82  3.000
 JJS  H1    C1   C6    109.53  3.000
 JJS  C7    C1   C6    113.44  3.000
 JJS  N2    C1   C6    109.73  3.000
 JJS  H2    N2   C1    117.19  3.000
 JJS  H2    N2   C3    115.62  3.000
 JJS  C1    N2   C3    123.10  3.000
 JJS  C12   C7   C8    117.64  3.000
 JJS  C12   C7   C1    120.07  3.000
 JJS  C8    C7   C1    122.26  3.000
 JJS  H8    C8   N9    115.80  3.000
 JJS  H8    C8   C7    120.53  3.000
 JJS  N9    C8   C7    123.67  3.000
 JJS  C10   N9   C8    117.54  3.000
 JJS  C11   C10  C13   119.91  3.000
 JJS  C11   C10  N9    124.15  3.000
 JJS  C13   C10  N9    115.94  3.000
 JJS  N14   C13  C10   180.00  3.000
 JJS  H11   C11  C12   121.57  3.000
 JJS  H11   C11  C10   121.00  3.000
 JJS  C12   C11  C10   117.43  3.000
 JJS  H12   C12  C11   119.87  3.000
 JJS  H12   C12  C7    120.55  3.000
 JJS  C11   C12  C7    119.58  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
 JJS  CONST_01  C23   C22  C21  C20    0.00   0.0  0
 JJS  CONST_02  C23   C18  C19  C20    0.00   0.0  0
 JJS  CONST_03  C18   C19  C20  C21    0.00   0.0  0
 JJS  CONST_04  C18   C23  C22  C21    0.00   0.0  0
 JJS  CONST_05  C19   C20  C21  C22    0.00   0.0  0
 JJS  CONST_06  C19   C18  C23  C22    0.00   0.0  0
 JJS  CONST_07  C10   N9   C8   C7     0.00   0.0  0
 JJS  CONST_08  C10   C11  C12  C7     0.00   0.0  0
 JJS  CONST_09  C11   C12  C7   C8     0.00   0.0  0
 JJS  CONST_10  C11   C10  N9   C8     0.00   0.0  0
 JJS  CONST_11  C12   C7   C8   N9     0.00   0.0  0
 JJS  CONST_12  C12   C11  C10  N9     0.00   0.0  0
 JJS  CONST_13  N4    C18  C19  C20  180.00   0.0  0
 JJS  CONST_14  N4    C18  C23  C22  180.00   0.0  0
 JJS  CONST_15  N9    C8   C7   C1   180.00   0.0  0
 JJS  CONST_16  C11   C12  C7   C1   180.00   0.0  0
 JJS  CONST_17  N2    C3   N4   C18  180.00   0.0  0
 JJS  CONST_19  N2    C3   N4   C5     0.00   0.0  0
 JJS  CONST_20  C22   C21  C20  C24  180.00   0.0  0
 JJS  CONST_21  C18   C19  C20  C24  180.00   0.0  0
 JJS  CONST_22  C13   C10  N9   C8   180.00   0.0  0
 JJS  CONST_23  C12   C11  C10  C13  180.00   0.0  0
 JJS  CONST_24  O29   C3   N4   C18    0.00   0.0  0
 JJS  CONST_25  C5    N4   C3   O29  180.00   0.0  0
 JJS  CONST_27  H22   C22  C21  C20  180.00   0.0  0
 JJS  CONST_28  H19   C19  C20  C21  180.00   0.0  0
 JJS  CONST_29  H23   C23  C22  C21  180.00   0.0  0
 JJS  CONST_30  H21   C21  C22  C23  180.00   0.0  0
 JJS  CONST_31  H8    C8   C7   C1     0.00   0.0  0
 JJS  CONST_32  H12   C12  C7   C1     0.00   0.0  0
 JJS  CONST_33  H11   C11  C12  C7   180.00   0.0  0
 JJS  CONST_34  H2    N2   C3   N4   180.00   0.0  0
 JJS  Var_01    C3    N4   C18  C23  -69.90  30.0  2
 JJS  Var_02    C6    C5   N4   C18  163.73  30.0  1
 JJS  Var_03    C1    C6   C5   N4    -0.28  30.0  1
 JJS  Var_04    C21   C20  C24  F25   -4.58  30.0  2
 JJS  Var_05    O16   C15  C6   C5    10.38  30.0  2
 JJS  Var_06    H281  C28  C5   N4   -23.77  30.0  3
 JJS  Var_07    H171  C17  C15  C6    58.33  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JJS  chir_01  C1  C6  N2  C7  positiv

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
 JJS  plan-1  C24  0.020
 JJS  plan-1  C20  0.020
 JJS  plan-1  C21  0.020
 JJS  plan-1  C22  0.020
 JJS  plan-1  C23  0.020
 JJS  plan-1  C19  0.020
 JJS  plan-1  C18  0.020
 JJS  plan-1  N4   0.020
 JJS  plan-1  H21  0.020
 JJS  plan-1  H19  0.020
 JJS  plan-1  H22  0.020
 JJS  plan-1  H23  0.020
 JJS  plan-2  C1   0.020
 JJS  plan-2  C7   0.020
 JJS  plan-2  C8   0.020
 JJS  plan-2  N9   0.020
 JJS  plan-2  C10  0.020
 JJS  plan-2  C13  0.020
 JJS  plan-2  N14  0.020
 JJS  plan-2  C11  0.020
 JJS  plan-2  C12  0.020
 JJS  plan-2  H8   0.020
 JJS  plan-2  H12  0.020
 JJS  plan-2  H11  0.020
 JJS  plan-3  C18  0.020
 JJS  plan-3  N4   0.020
 JJS  plan-3  C3   0.020
 JJS  plan-3  O29  0.020
 JJS  plan-3  C5   0.020
 JJS  plan-3  C1   0.020
 JJS  plan-3  N2   0.020
 JJS  plan-3  H2   0.020
 JJS  plan-4  C6   0.020
 JJS  plan-4  C15  0.020
 JJS  plan-4  O16  0.020
 JJS  plan-4  C17  0.020

