# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:24:54 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (6~{S})-6-[2,4-bis(fluoranyl)phenyl]-~{N},~{N},4-trimethyl-2-oxidanylidene-5,6-dihydro-1~{H}-pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)[C@H]1[C@H](NC(=O)N=C1C)c2ccc(F)cc2F
#
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
 JSN  JSN  (6~{S})-6-[2,4-bis(fluoranyl)phenyl]-~{N},~{N},4-trimethyl-2-oxidanylidene-5,6-dihydro-1~{H}-pyrimidine-5-carboxamide  ligand  36  21  .  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_JSN
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
 JSN  N1   N  N     0  -0.441   1.8486   2.2279   0.8285
 JSN  N3   N  NH1   0  -0.622   1.0159   1.8306  -1.3418
 JSN  C4   C  C     0   0.590   1.1369  -1.4036   0.5671
 JSN  C5   C  CH3   0  -0.529   1.2829  -3.8049   0.5579
 JSN  C6   C  CH3   0  -0.543   2.5969  -2.5365  -1.0881
 JSN  C7   C  CH1   0  -0.122   0.6014   0.4920  -1.0116
 JSN  C8   C  CR6   0  -0.053  -0.8503   0.4265  -0.5781
 JSN  C10  C  CR16  0  -0.411  -2.8127   1.3860   0.4828
 JSN  C13  C  CR6   0   0.565  -1.6212  -0.6900  -0.8632
 JSN  C1   C  CH3   0  -0.741   2.1579   0.5666   2.4985
 JSN  C2   C  C     0   0.341   1.8299   0.9829   1.1060
 JSN  C3   C  CH1   0  -0.514   1.5991  -0.0561   0.0304
 JSN  N2   N  NT    0  -0.449   1.6817  -2.5104   0.0378
 JSN  O1   O  O     0  -0.485   0.2786  -1.4417   1.4387
 JSN  C9   C  CR16  0  -0.287  -1.4826   1.4639   0.0969
 JSN  C11  C  CR6   0   0.536  -3.5215   0.2438   0.1696
 JSN  F1   F  F     0  -0.308  -4.8076   0.1519   0.5290
 JSN  C12  C  CR16  0  -0.554  -2.9488  -0.8141  -0.5088
 JSN  F2   F  F     0  -0.308  -1.0524  -1.7147  -1.5168
 JSN  C14  C  C     0   0.558   1.6297   2.6708  -0.4863
 JSN  O2   O  O     0  -0.478   1.9866   3.7908  -0.8054
 JSN  H1   H  HNH1  0   0.411   0.7849   2.1847  -2.2580
 JSN  H2   H  HCH3  0   0.244   0.4195  -4.2002   0.0187
 JSN  H3   H  HCH3  0   0.251   2.1100  -4.5020   0.4418
 JSN  H4   H  HCH3  0   0.255   1.0347  -3.7402   1.6130
 JSN  H5   H  HCH3  0   0.255   3.6388  -2.5490  -0.7631
 JSN  H6   H  HCH3  0   0.268   2.4131  -3.4364  -1.6717
 JSN  H7   H  HCH3  0   0.256   2.4508  -1.6968  -1.7617
 JSN  H8   H  HCH1  0   0.309   0.7167  -0.1055  -1.9170
 JSN  H9   H  HCR6  0   0.287  -3.2859   2.2034   1.0092
 JSN  H10  H  HCH3  0   0.264   2.5845   1.4020   3.0474
 JSN  H11  H  HCH3  0   0.277   1.2626   0.2221   3.0144
 JSN  H12  H  HCH3  0   0.260   2.8640  -0.2655   2.4995
 JSN  H13  H  HCH1  0   0.342   2.5691  -0.1383  -0.4706
 JSN  H14  H  HCR6  0   0.272  -0.9394   2.3679   0.3349
 JSN  H15  H  HCR6  0   0.304  -3.5127  -1.7040  -0.7563

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
 JSN  C1   C2   single    1.490  0.020  1.490
 JSN  N1   C2   double    1.276  0.020  1.276
 JSN  N1   C14  single    1.405  0.020  1.405
 JSN  C2   C3   single    1.513  0.020  1.513
 JSN  O1   C4   double    1.224  0.020  1.224
 JSN  O2   C14  double    1.218  0.020  1.218
 JSN  C14  N3   single    1.347  0.020  1.347
 JSN  C3   C4   single    1.522  0.020  1.522
 JSN  C3   C7   single    1.543  0.020  1.543
 JSN  C4   N2   single    1.342  0.020  1.342
 JSN  N3   C7   single    1.440  0.020  1.440
 JSN  N2   C5   single    1.451  0.020  1.451
 JSN  N2   C6   single    1.451  0.020  1.451
 JSN  C7   C8   single    1.516  0.020  1.516
 JSN  C9   C8   aromatic  1.390  0.020  1.390
 JSN  C9   C10  aromatic  1.387  0.020  1.387
 JSN  C8   C13  aromatic  1.386  0.020  1.386
 JSN  C10  C11  aromatic  1.380  0.020  1.380
 JSN  C13  F2   single    1.342  0.020  1.342
 JSN  C13  C12  aromatic  1.380  0.020  1.380
 JSN  C11  C12  aromatic  1.381  0.020  1.381
 JSN  C11  F1   single    1.339  0.020  1.339
 JSN  N3   H1   single    0.860  0.020  1.020
 JSN  C5   H2   single    0.970  0.020  1.090
 JSN  C5   H3   single    0.970  0.020  1.090
 JSN  C5   H4   single    0.970  0.020  1.090
 JSN  C6   H5   single    0.970  0.020  1.090
 JSN  C6   H6   single    0.970  0.020  1.090
 JSN  C6   H7   single    0.970  0.020  1.090
 JSN  C7   H8   single    0.970  0.020  1.090
 JSN  C10  H9   single    0.930  0.020  1.080
 JSN  C1   H10  single    0.970  0.020  1.090
 JSN  C1   H11  single    0.970  0.020  1.090
 JSN  C1   H12  single    0.970  0.020  1.090
 JSN  C3   H13  single    0.970  0.020  1.090
 JSN  C9   H14  single    0.930  0.020  1.080
 JSN  C12  H15  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
 JSN  C14  N1   C2   120.61  3.000
 JSN  H1   N3   C14  117.51  3.000
 JSN  H1   N3   C7   117.95  3.000
 JSN  C14  N3   C7   124.44  3.000
 JSN  O1   C4   N2   122.66  3.000
 JSN  N2   C4   C3   117.88  3.000
 JSN  O1   C4   C3   119.44  3.000
 JSN  H4   C5   H3   108.40  3.000
 JSN  H4   C5   H2   108.70  3.000
 JSN  H3   C5   H2   108.45  3.000
 JSN  H4   C5   N2   110.98  3.000
 JSN  H3   C5   N2   108.94  3.000
 JSN  H2   C5   N2   111.30  3.000
 JSN  H7   C6   H6   106.50  3.000
 JSN  H7   C6   H5   108.78  3.000
 JSN  H6   C6   H5   108.15  3.000
 JSN  H7   C6   N2   112.48  3.000
 JSN  H6   C6   N2   108.93  3.000
 JSN  H5   C6   N2   111.79  3.000
 JSN  H8   C7   C3   107.31  3.000
 JSN  H8   C7   C8   108.35  3.000
 JSN  C3   C7   C8   114.24  3.000
 JSN  H8   C7   N3   106.76  3.000
 JSN  C8   C7   N3   112.42  3.000
 JSN  C3   C7   N3   107.40  3.000
 JSN  C9   C8   C13  116.62  3.000
 JSN  C13  C8   C7   120.55  3.000
 JSN  C9   C8   C7   122.83  3.000
 JSN  H9   C10  C11  120.75  3.000
 JSN  H9   C10  C9   120.84  3.000
 JSN  C11  C10  C9   118.41  3.000
 JSN  F2   C13  C12  117.66  3.000
 JSN  C12  C13  C8   123.69  3.000
 JSN  F2   C13  C8   118.65  3.000
 JSN  H12  C1   H11  106.87  3.000
 JSN  H12  C1   H10  109.37  3.000
 JSN  H11  C1   H10  109.06  3.000
 JSN  H12  C1   C2   110.88  3.000
 JSN  H11  C1   C2   110.49  3.000
 JSN  H10  C1   C2   110.10  3.000
 JSN  C3   C2   C1   120.40  3.000
 JSN  C3   C2   N1   121.18  3.000
 JSN  C1   C2   N1   118.22  3.000
 JSN  H13  C3   C2   103.99  3.000
 JSN  H13  C3   C7   106.89  3.000
 JSN  C2   C3   C7   109.55  3.000
 JSN  H13  C3   C4   111.33  3.000
 JSN  C7   C3   C4   110.86  3.000
 JSN  C2   C3   C4   113.80  3.000
 JSN  C6   N2   C5   115.81  3.000
 JSN  C6   N2   C4   125.22  3.000
 JSN  C5   N2   C4   118.87  3.000
 JSN  H14  C9   C10  117.87  3.000
 JSN  H14  C9   C8   120.16  3.000
 JSN  C10  C9   C8   121.97  3.000
 JSN  C12  C11  F1   118.54  3.000
 JSN  F1   C11  C10  119.29  3.000
 JSN  C12  C11  C10  122.16  3.000
 JSN  H15  C12  C11  121.74  3.000
 JSN  H15  C12  C13  121.11  3.000
 JSN  C11  C12  C13  117.15  3.000
 JSN  O2   C14  N3   122.74  3.000
 JSN  N3   C14  N1   117.95  3.000
 JSN  O2   C14  N1   119.31  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
 JSN  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 JSN  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 JSN  CONST_03  C13  C8   C9   C10    0.00   0.0  0
 JSN  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 JSN  CONST_05  C12  C13  C8   C9     0.00   0.0  0
 JSN  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 JSN  CONST_07  C10  C9   C8   C7   180.00   0.0  0
 JSN  CONST_08  C12  C13  C8   C7   180.00   0.0  0
 JSN  CONST_09  C7   N3   C14  N1     0.00   0.0  0
 JSN  CONST_11  F2   C13  C8   C7     0.00   0.0  0
 JSN  CONST_12  F1   C11  C12  C13  180.00   0.0  0
 JSN  CONST_13  F2   C13  C8   C9   180.00   0.0  0
 JSN  CONST_14  F1   C11  C10  C9   180.00   0.0  0
 JSN  CONST_15  F2   C13  C12  C11  180.00   0.0  0
 JSN  CONST_16  O2   C14  N3   C7   180.00   0.0  0
 JSN  CONST_18  H14  C9   C8   C7     0.00   0.0  0
 JSN  CONST_19  H9   C10  C9   C8   180.00   0.0  0
 JSN  CONST_20  H15  C12  C13  C8   180.00   0.0  0
 JSN  CONST_21  H1   N3   C14  N1   180.00   0.0  0
 JSN  CONST_22  C3   C4   N2   C5   180.00   0.0  0
 JSN  CONST_23  C3   C4   N2   C6     0.00   0.0  0
 JSN  CONST_24  O1   C4   N2   C5     0.00   0.0  0
 JSN  CONST_25  O1   C4   N2   C6   180.00   0.0  0
 JSN  Var_01    H10  C1   C2   N1   -12.29  30.0  3
 JSN  Var_02    H2   C5   N2   C4    89.79  30.0  3
 JSN  Var_03    H5   C6   N2   C4    94.94  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
 JSN  chir_01  C7  C3  N3  C8  positiv
 JSN  chir_02  C3  C7  C4  C2  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
 JSN  plan-1  C7   0.020
 JSN  plan-1  C8   0.020
 JSN  plan-1  C10  0.020
 JSN  plan-1  C13  0.020
 JSN  plan-1  C9   0.020
 JSN  plan-1  C11  0.020
 JSN  plan-1  F1   0.020
 JSN  plan-1  C12  0.020
 JSN  plan-1  F2   0.020
 JSN  plan-1  H9   0.020
 JSN  plan-1  H14  0.020
 JSN  plan-1  H15  0.020
 JSN  plan-2  C4   0.020
 JSN  plan-2  C5   0.020
 JSN  plan-2  C6   0.020
 JSN  plan-2  C3   0.020
 JSN  plan-2  N2   0.020
 JSN  plan-2  O1   0.020
 JSN  plan-3  N1   0.020
 JSN  plan-3  N3   0.020
 JSN  plan-3  C7   0.020
 JSN  plan-3  C2   0.020
 JSN  plan-3  C14  0.020
 JSN  plan-3  O2   0.020
 JSN  plan-3  H1   0.020

