# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:08:14 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (6S)-6-(4-cyano-2-methylsulfonyl-phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(C#N)[C@H](NC(=O)N1c2cccc(c2)C(F)(F)F)c3ccc(cc3[S](C)(=O)=O)C#N
#
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
 JJV  JJV  (6S)-6-(4-cyano-2-methylsulfonyl-phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile  ligand  47  32  .  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_JJV
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
 JJV  C28   C  CH3   0  -0.787   3.9718   2.4420  -2.1168
 JJV  S26   S  S     0   1.203   4.3081   2.0165  -0.4254
 JJV  O27   O  OS    0  -0.646   5.7516   2.0667  -0.2223
 JJV  O29   O  OS    0  -0.642   3.4589   2.8205   0.4489
 JJV  C4    C  CR6   0  -0.280   3.8075   0.2967  -0.3116
 JJV  C2    C  CR16  0  -0.216   4.8451  -0.6244  -0.2774
 JJV  C1    C  CR6   0   0.014   4.5534  -1.9787  -0.1855
 JJV  C31   C  CSP   0   0.068   5.6188  -2.9282  -0.1455
 JJV  N30   N  NS    0  -0.236   6.4765  -3.6959  -0.1197
 JJV  C3    C  CR16  0  -0.204   3.2303  -2.4098  -0.1294
 JJV  C5    C  CR16  0  -0.268   2.2140  -1.4780  -0.1673
 JJV  C6    C  CR6   0   0.244   2.4731  -0.1129  -0.2572
 JJV  C22   C  CH1   0  -0.192   1.2617   0.8194  -0.2734
 JJV  C9    C  C     0  -0.102   0.5432   0.7359   1.0475
 JJV  C11   C  C     0   0.375  -0.7018   0.2242   1.1720
 JJV  C25   C  CH3   0  -0.741  -1.4074   0.1005   2.4793
 JJV  C24   C  CSP   0   0.048   1.2567   1.1773   2.1847
 JJV  N32   N  NS    0  -0.261   1.8637   1.5307   3.1010
 JJV  N7    N  NH1   0  -0.658   0.3568   0.4588  -1.3368
 JJV  C8    C  C     0   0.699  -0.8835  -0.0522  -1.2407
 JJV  O23   O  O     0  -0.474  -1.5572  -0.3595  -2.2024
 JJV  N10   N  NT    0  -0.674  -1.3821  -0.2095   0.0543
 JJV  C12   C  CR6   0   0.285  -2.6836  -0.7871   0.1611
 JJV  C13   C  CR16  0  -0.277  -3.8004   0.0323   0.1203
 JJV  C14   C  CR16  0  -0.236  -2.8122  -2.1575   0.3096
 JJV  C16   C  CR16  0  -0.250  -4.0763  -2.7166   0.4269
 JJV  C17   C  CR16  0  -0.259  -5.2011  -1.9091   0.3946
 JJV  C15   C  CR6   0  -0.202  -5.0610  -0.5334   0.2430
 JJV  C18   C  CT    0   1.058  -6.2877   0.3220   0.1645
 JJV  F20   F  F     0  -0.312  -6.8582   0.2493  -1.0470
 JJV  F21   F  F     0  -0.308  -7.2169  -0.0576   1.0493
 JJV  F19   F  F     0  -0.302  -6.0276   1.6120   0.3946
 JJV  H281  H  HCH3  0   0.307   4.5586   1.8012  -2.7704
 JJV  H282  H  HCH3  0   0.289   2.9114   2.3325  -2.3327
 JJV  H283  H  HCH3  0   0.324   4.2653   3.4833  -2.2471
 JJV  H2    H  HCR6  0   0.312   5.8748  -0.2992  -0.3235
 JJV  H3    H  HCR6  0   0.300   3.0010  -3.4635  -0.0536
 JJV  H5    H  HCR6  0   0.284   1.1913  -1.8283  -0.1172
 JJV  H22   H  HCH1  0   0.307   1.5703   1.8505  -0.4325
 JJV  H7    H  HNH1  0   0.422   0.6824   0.6032  -2.2810
 JJV  H251  H  HCH3  0   0.282  -0.7757   0.4180   3.3034
 JJV  H252  H  HCH3  0   0.286  -2.3091   0.7138   2.4882
 JJV  H253  H  HCH3  0   0.284  -1.7111  -0.9304   2.6620
 JJV  H13   H  HCR6  0   0.287  -3.6684   1.0995   0.0000
 JJV  H14   H  HCR6  0   0.282  -1.9311  -2.7854   0.3380
 JJV  H16   H  HCR6  0   0.281  -4.1844  -3.7856   0.5447
 JJV  H17   H  HCR6  0   0.284  -6.1797  -2.3606   0.4914

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
 JJV  C28  S26   single    1.776  0.020  1.776
 JJV  S26  O27   double    1.459  0.020  1.459
 JJV  S26  O29   double    1.460  0.020  1.460
 JJV  S26  C4    single    1.795  0.020  1.795
 JJV  C4   C2    aromatic  1.388  0.020  1.388
 JJV  C4   C6    aromatic  1.397  0.020  1.397
 JJV  C2   C1    aromatic  1.388  0.020  1.388
 JJV  C1   C31   single    1.428  0.020  1.428
 JJV  C1   C3    aromatic  1.393  0.020  1.393
 JJV  C31  N30   triple    1.151  0.020  1.151
 JJV  C3   C5    aromatic  1.379  0.020  1.379
 JJV  C5   C6    aromatic  1.392  0.020  1.392
 JJV  C6   C22   single    1.529  0.020  1.529
 JJV  C22  C9    single    1.506  0.020  1.506
 JJV  C22  N7    single    1.442  0.020  1.442
 JJV  C9   C11   double    1.352  0.020  1.352
 JJV  C9   C24   single    1.413  0.020  1.413
 JJV  C11  C25   single    1.491  0.020  1.491
 JJV  C11  N10   single    1.378  0.020  1.378
 JJV  C24  N32   triple    1.155  0.020  1.155
 JJV  N7   C8    single    1.345  0.020  1.345
 JJV  C8   O23   double    1.214  0.020  1.214
 JJV  C8   N10   single    1.397  0.020  1.397
 JJV  N10  C12   single    1.428  0.020  1.428
 JJV  C12  C13   aromatic  1.386  0.020  1.386
 JJV  C12  C14   aromatic  1.384  0.020  1.384
 JJV  C13  C15   aromatic  1.387  0.020  1.387
 JJV  C14  C16   aromatic  1.387  0.020  1.387
 JJV  C16  C17   aromatic  1.385  0.020  1.385
 JJV  C17  C15   aromatic  1.391  0.020  1.391
 JJV  C15  C18   single    1.498  0.020  1.498
 JJV  C18  F20   single    1.341  0.020  1.341
 JJV  C18  F21   single    1.338  0.020  1.338
 JJV  C18  F19   single    1.336  0.020  1.336
 JJV  C28  H281  single    0.970  0.020  1.090
 JJV  C28  H282  single    0.970  0.020  1.090
 JJV  C28  H283  single    0.970  0.020  1.090
 JJV  C2   H2    single    0.930  0.020  1.080
 JJV  C3   H3    single    0.930  0.020  1.080
 JJV  C5   H5    single    0.930  0.020  1.080
 JJV  C22  H22   single    0.970  0.020  1.090
 JJV  N7   H7    single    0.860  0.020  1.020
 JJV  C25  H251  single    0.970  0.020  1.090
 JJV  C25  H252  single    0.970  0.020  1.090
 JJV  C25  H253  single    0.970  0.020  1.090
 JJV  C13  H13   single    0.930  0.020  1.080
 JJV  C14  H14   single    0.930  0.020  1.080
 JJV  C16  H16   single    0.930  0.020  1.080
 JJV  C17  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
 JJV  H283  C28  H282  109.57  3.000
 JJV  H283  C28  H281  110.24  3.000
 JJV  H282  C28  H281  110.33  3.000
 JJV  H283  C28  S26   106.97  3.000
 JJV  H282  C28  S26   110.46  3.000
 JJV  H281  C28  S26   109.22  3.000
 JJV  C4    S26  O29   109.12  3.000
 JJV  C4    S26  O27   107.46  3.000
 JJV  O29   S26  O27   118.25  3.000
 JJV  C4    S26  C28   103.72  3.000
 JJV  O29   S26  C28   109.16  3.000
 JJV  O27   S26  C28   108.16  3.000
 JJV  C6    C4   C2    121.24  3.000
 JJV  C6    C4   S26   123.36  3.000
 JJV  C2    C4   S26   115.41  3.000
 JJV  H2    C2   C1    119.77  3.000
 JJV  H2    C2   C4    120.76  3.000
 JJV  C1    C2   C4    119.47  3.000
 JJV  C3    C1   C31   120.13  3.000
 JJV  C3    C1   C2    120.28  3.000
 JJV  C31   C1   C2    119.59  3.000
 JJV  N30   C31  C1    180.00  3.000
 JJV  H3    C3   C5    120.28  3.000
 JJV  H3    C3   C1    120.40  3.000
 JJV  C5    C3   C1    119.32  3.000
 JJV  H5    C5   C6    119.75  3.000
 JJV  H5    C5   C3    118.44  3.000
 JJV  C6    C5   C3    121.81  3.000
 JJV  C22   C6   C5    116.82  3.000
 JJV  C22   C6   C4    125.29  3.000
 JJV  C5    C6   C4    117.89  3.000
 JJV  H22   C22  N7    107.89  3.000
 JJV  H22   C22  C9    108.44  3.000
 JJV  N7    C22  C9    109.48  3.000
 JJV  H22   C22  C6    110.78  3.000
 JJV  N7    C22  C6    110.64  3.000
 JJV  C9    C22  C6    109.57  3.000
 JJV  C24   C9   C11   120.61  3.000
 JJV  C24   C9   C22   116.59  3.000
 JJV  C11   C9   C22   122.76  3.000
 JJV  N10   C11  C25   116.84  3.000
 JJV  N10   C11  C9    119.93  3.000
 JJV  C25   C11  C9    123.24  3.000
 JJV  H253  C25  H252  107.46  3.000
 JJV  H253  C25  H251  108.15  3.000
 JJV  H252  C25  H251  108.08  3.000
 JJV  H253  C25  C11   110.93  3.000
 JJV  H252  C25  C11   110.60  3.000
 JJV  H251  C25  C11   111.46  3.000
 JJV  N32   C24  C9    180.00  3.000
 JJV  H7    N7   C8    114.76  3.000
 JJV  H7    N7   C22   116.86  3.000
 JJV  C8    N7   C22   128.39  3.000
 JJV  N10   C8   O23   120.53  3.000
 JJV  N10   C8   N7    116.00  3.000
 JJV  O23   C8   N7    123.47  3.000
 JJV  C12   N10  C8    116.12  3.000
 JJV  C12   N10  C11   121.10  3.000
 JJV  C8    N10  C11   122.70  3.000
 JJV  C14   C12  C13   120.90  3.000
 JJV  C14   C12  N10   119.54  3.000
 JJV  C13   C12  N10   119.55  3.000
 JJV  H13   C13  C15   121.53  3.000
 JJV  H13   C13  C12   119.21  3.000
 JJV  C15   C13  C12   119.26  3.000
 JJV  H14   C14  C16   120.38  3.000
 JJV  H14   C14  C12   120.10  3.000
 JJV  C16   C14  C12   119.52  3.000
 JJV  H16   C16  C17   119.86  3.000
 JJV  H16   C16  C14   119.93  3.000
 JJV  C17   C16  C14   120.21  3.000
 JJV  H17   C17  C15   120.90  3.000
 JJV  H17   C17  C16   119.28  3.000
 JJV  C15   C17  C16   119.82  3.000
 JJV  C18   C15  C17   119.22  3.000
 JJV  C18   C15  C13   120.46  3.000
 JJV  C17   C15  C13   120.29  3.000
 JJV  F19   C18  F21   107.17  3.000
 JJV  F19   C18  F20   106.91  3.000
 JJV  F21   C18  F20   106.65  3.000
 JJV  F19   C18  C15   112.52  3.000
 JJV  F21   C18  C15   111.84  3.000
 JJV  F20   C18  C15   111.40  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
 JJV  CONST_01  C3    C1   C2   C4     0.00   0.0  0
 JJV  CONST_02  C3    C5   C6   C4     0.00   0.0  0
 JJV  CONST_03  C5    C6   C4   C2     0.00   0.0  0
 JJV  CONST_04  C5    C3   C1   C2     0.00   0.0  0
 JJV  CONST_05  C6    C4   C2   C1     0.00   0.0  0
 JJV  CONST_06  C6    C5   C3   C1     0.00   0.0  0
 JJV  CONST_07  C17   C15  C13  C12    0.00   0.0  0
 JJV  CONST_08  C17   C16  C14  C12    0.00   0.0  0
 JJV  CONST_09  C16   C14  C12  C13    0.00   0.0  0
 JJV  CONST_10  C16   C17  C15  C13    0.00   0.0  0
 JJV  CONST_11  C15   C13  C12  C14    0.00   0.0  0
 JJV  CONST_12  C15   C17  C16  C14    0.00   0.0  0
 JJV  CONST_13  C22   C6   C4   C2   180.00   0.0  0
 JJV  CONST_14  C22   C6   C5   C3   180.00   0.0  0
 JJV  CONST_15  C15   C13  C12  N10  180.00   0.0  0
 JJV  CONST_16  C16   C14  C12  N10  180.00   0.0  0
 JJV  CONST_17  N10   C8   N7   C22    0.00   0.0  0
 JJV  CONST_18  N7    C8   N10  C11    0.00   0.0  0
 JJV  CONST_19  C12   N10  C8   N7   180.00   0.0  0
 JJV  CONST_20  C1    C2   C4   S26  180.00   0.0  0
 JJV  CONST_21  C5    C6   C4   S26  180.00   0.0  0
 JJV  CONST_22  C22   C6   C4   S26    0.00   0.0  0
 JJV  CONST_23  C31   C1   C2   C4   180.00   0.0  0
 JJV  CONST_24  C5    C3   C1   C31  180.00   0.0  0
 JJV  CONST_25  C18   C15  C13  C12  180.00   0.0  0
 JJV  CONST_26  C18   C15  C17  C16  180.00   0.0  0
 JJV  CONST_27  O23   C8   N7   C22  180.00   0.0  0
 JJV  CONST_28  O23   C8   N10  C11  180.00   0.0  0
 JJV  CONST_29  C12   N10  C8   O23    0.00   0.0  0
 JJV  CONST_30  H5    C5   C6   C4   180.00   0.0  0
 JJV  CONST_31  H3    C3   C1   C2   180.00   0.0  0
 JJV  CONST_32  H2    C2   C1   C3   180.00   0.0  0
 JJV  CONST_33  H13   C13  C12  N10    0.00   0.0  0
 JJV  CONST_34  H14   C14  C12  N10    0.00   0.0  0
 JJV  CONST_35  H16   C16  C14  C12  180.00   0.0  0
 JJV  CONST_36  H17   C17  C15  C13  180.00   0.0  0
 JJV  CONST_37  H7    N7   C8   N10  180.00   0.0  0
 JJV  Var_01    N10   C11  C9   C22   -2.04  30.0  1
 JJV  Var_02    C8    N10  C11  C9    -5.10  30.0  1
 JJV  Var_03    C13   C12  N10  C11   88.53  30.0  2
 JJV  Var_04    C2    C4   S26  C28  104.67  30.0  2
 JJV  Var_05    F20   C18  C15  C13  100.32  30.0  2
 JJV  Var_06    H251  C25  C11  C9    -3.18  30.0  3
 JJV  Var_07    H281  C28  S26  C4   -60.32  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
 JJV  chir_01  C22  C6  C9  N7  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
 JJV  plan-1  S26  0.020
 JJV  plan-1  C4   0.020
 JJV  plan-1  C2   0.020
 JJV  plan-1  C1   0.020
 JJV  plan-1  C31  0.020
 JJV  plan-1  N30  0.020
 JJV  plan-1  C3   0.020
 JJV  plan-1  C5   0.020
 JJV  plan-1  C6   0.020
 JJV  plan-1  C22  0.020
 JJV  plan-1  H2   0.020
 JJV  plan-1  H3   0.020
 JJV  plan-1  H5   0.020
 JJV  plan-2  N10  0.020
 JJV  plan-2  C12  0.020
 JJV  plan-2  C13  0.020
 JJV  plan-2  C14  0.020
 JJV  plan-2  C16  0.020
 JJV  plan-2  C17  0.020
 JJV  plan-2  C15  0.020
 JJV  plan-2  C18  0.020
 JJV  plan-2  H13  0.020
 JJV  plan-2  H14  0.020
 JJV  plan-2  H16  0.020
 JJV  plan-2  H17  0.020
 JJV  plan-3  C22  0.020
 JJV  plan-3  C11  0.020
 JJV  plan-3  N7   0.020
 JJV  plan-3  C8   0.020
 JJV  plan-3  O23  0.020
 JJV  plan-3  N10  0.020
 JJV  plan-3  C12  0.020
 JJV  plan-3  H7   0.020

