# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:02:15 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-[(4R)-4-(4-cyanophenyl)-5-ethanoyl-6-methyl-2-oxidanylidene-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidin-3-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)C1=C(C)N(C(=O)N(CC(O)=O)[C@@H]1c2ccc(cc2)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
 JJD  JJD  '2-[(4R)-4-(4-cyanophenyl)-5-ethanoyl-6-methyl-2-oxidanylidene-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidin-3-yl]ethanoic acid'  ligand  50  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JJD
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
 JJD  C1    C  CR16   0  -0.246   1.6313  -0.8125   1.2528
 JJD  N2    N  NR6    0  -0.460   0.8361   0.3393   1.6372
 JJD  C3    C  CR6    0   0.747  -0.3001   0.6862   1.0150
 JJD  N4    N  NR6    0  -0.680  -0.8658  -0.2956   0.1859
 JJD  C5    C  CR6    0   0.348  -0.4371  -1.6146   0.1702
 JJD  C6    C  CR6    0  -0.148   0.7716  -1.9203   0.7020
 JJD  C7    C  CR6    0   0.216   2.7539  -0.4300   0.3001
 JJD  C8    C  CR16   0  -0.308   4.0429  -0.2514   0.7860
 JJD  C9    C  CR16   0  -0.228   5.0728   0.1328  -0.0559
 JJD  C10   C  CR6    0  -0.009   4.8066   0.3378  -1.4070
 JJD  C11   C  CR16   0  -0.230   3.5175   0.1482  -1.9101
 JJD  C12   C  CR16   0  -0.253   2.5052  -0.2346  -1.0549
 JJD  C13   C  CSP    0   0.054   5.8599   0.7321  -2.2849
 JJD  N14   N  NS     0  -0.255   6.7099   1.0480  -2.9963
 JJD  C15   C  C      0   0.350   1.3306  -3.2823   0.7108
 JJD  O16   O  O      0  -0.420   0.9166  -4.1764  -0.0079
 JJD  C17   C  CH3    0  -0.805   2.4889  -3.5531   1.6412
 JJD  C18   C  C      0   0.283  -1.9841   0.1148  -0.5951
 JJD  C19   C  C1     0  -0.262  -3.2118   0.3557   0.0008
 JJD  C20   C  C      0  -0.204  -4.2884   0.7449  -0.7852
 JJD  C21   C  C1     0  -0.276  -4.1404   0.8924  -2.1593
 JJD  C22   C  C1     0  -0.244  -2.9089   0.6453  -2.7455
 JJD  C23   C  C1     0  -0.249  -1.8286   0.2631  -1.9652
 JJD  C24   C  CT     0   1.056  -5.5958   1.0396  -0.1181
 JJD  F25   F  F      0  -0.313  -5.5699   2.2242   0.5107
 JJD  F26   F  F      0  -0.303  -6.6137   1.0806  -0.9818
 JJD  F27   F  F      0  -0.310  -5.9025   0.1227   0.8089
 JJD  C28   C  CH3    0  -0.736  -1.4082  -2.5943  -0.4103
 JJD  O29   O  O      0  -0.496  -0.8777   1.7441   1.1783
 JJD  C30   C  CH2    0  -0.470   1.4982   1.3414   2.4451
 JJD  C31   C  C      0   0.429   2.2143   2.4602   1.6516
 JJD  O32   O  OC    -1  -0.627   2.9085   3.2170   2.3604
 JJD  O33   O  O      0  -0.572   2.0217   2.5198   0.4305
 JJD  H1    H  HCR6   0   0.290   2.0991  -1.1554   2.1795
 JJD  H8    H  HCR6   0   0.271   4.2530  -0.4148   1.8362
 JJD  H9    H  HCR6   0   0.279   6.0738   0.2703   0.3302
 JJD  H11   H  HCR6   0   0.277   3.3182   0.3010  -2.9621
 JJD  H12   H  HCR6   0   0.260   1.5104  -0.3835  -1.4537
 JJD  H17   H  HCH3   0   0.267   2.2783  -3.2275   2.6605
 JJD  H17A  H  HCH3   0   0.271   2.7138  -4.6170   1.6488
 JJD  H17B  H  HCH3   0   0.263   3.3853  -3.0221   1.3124
 JJD  H19   H  H      0   0.280  -3.3176   0.2213   1.0693
 JJD  H21   H  H      0   0.278  -4.9725   1.1932  -2.7806
 JJD  H22   H  H      0   0.277  -2.7898   0.7560  -3.8143
 JJD  H23   H  H      0   0.280  -0.8649   0.0767  -2.4221
 JJD  H28   H  HCH3   0   0.261  -2.4321  -2.3042  -0.1842
 JJD  H28A  H  HCH3   0   0.272  -1.3133  -2.6418  -1.4966
 JJD  H28B  H  HCH3   0   0.282  -1.2407  -3.5934  -0.0291
 JJD  H30   H  HCH2   0   0.265   0.7719   1.8026   3.1173
 JJD  H30A  H  HCH2   0   0.250   2.2162   0.8240   3.0849

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
 JJD  C7   C1    single    1.521  0.020  1.521
 JJD  C1   C6    single    1.507  0.020  1.507
 JJD  C1   N2    single    1.451  0.020  1.451
 JJD  C1   H1    single    0.970  0.020  1.090
 JJD  C30  N2    single    1.447  0.020  1.447
 JJD  N2   C3    single    1.341  0.020  1.341
 JJD  C3   N4    single    1.404  0.020  1.404
 JJD  C3   O29   double    1.216  0.020  1.216
 JJD  C5   N4    single    1.387  0.020  1.387
 JJD  N4   C18   single    1.425  0.020  1.425
 JJD  C6   C5    double    1.355  0.020  1.355
 JJD  C5   C28   single    1.497  0.020  1.497
 JJD  C15  C6    single    1.472  0.020  1.472
 JJD  C8   C7    aromatic  1.389  0.020  1.389
 JJD  C7   C12   aromatic  1.391  0.020  1.391
 JJD  C9   C8    aromatic  1.385  0.020  1.385
 JJD  C8   H8    single    0.930  0.020  1.080
 JJD  C9   C10   aromatic  1.392  0.020  1.392
 JJD  C9   H9    single    0.930  0.020  1.080
 JJD  C13  C10   single    1.427  0.020  1.427
 JJD  C10  C11   aromatic  1.397  0.020  1.397
 JJD  C11  C12   aromatic  1.379  0.020  1.379
 JJD  C11  H11   single    0.930  0.020  1.080
 JJD  C12  H12   single    0.930  0.020  1.080
 JJD  N14  C13   triple    1.153  0.020  1.153
 JJD  C17  C15   single    1.510  0.020  1.510
 JJD  C15  O16   double    1.220  0.020  1.220
 JJD  C17  H17   single    0.970  0.020  1.090
 JJD  C17  H17A  single    0.970  0.020  1.090
 JJD  C17  H17B  single    0.970  0.020  1.090
 JJD  C19  C18   aromatic  1.386  0.020  1.386
 JJD  C18  C23   aromatic  1.387  0.020  1.387
 JJD  C19  C20   aromatic  1.389  0.020  1.389
 JJD  C19  H19   single    0.930  0.020  1.080
 JJD  C24  C20   single    1.497  0.020  1.497
 JJD  C20  C21   aromatic  1.390  0.020  1.390
 JJD  C21  C22   aromatic  1.386  0.020  1.386
 JJD  C21  H21   single    0.930  0.020  1.080
 JJD  C23  C22   aromatic  1.386  0.020  1.386
 JJD  C22  H22   single    0.930  0.020  1.080
 JJD  C23  H23   single    0.930  0.020  1.080
 JJD  F26  C24   single    1.336  0.020  1.336
 JJD  F27  C24   single    1.339  0.020  1.339
 JJD  C24  F25   single    1.341  0.020  1.341
 JJD  C28  H28   single    0.970  0.020  1.090
 JJD  C28  H28A  single    0.970  0.020  1.090
 JJD  C28  H28B  single    0.970  0.020  1.090
 JJD  C31  C30   single    1.547  0.020  1.547
 JJD  C30  H30   single    0.970  0.020  1.090
 JJD  C30  H30A  single    0.970  0.020  1.090
 JJD  O33  C31   deloc     1.238  0.020  1.238
 JJD  C31  O32   deloc     1.248  0.020  1.248

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
 JJD  H1    C1   C7    107.09  3.000
 JJD  H1    C1   C6    108.87  3.000
 JJD  C7    C1   C6    112.15  3.000
 JJD  H1    C1   N2    105.00  3.000
 JJD  C6    C1   N2    111.57  3.000
 JJD  C7    C1   N2    111.76  3.000
 JJD  C30   N2   C3    117.87  3.000
 JJD  C3    N2   C1    123.13  3.000
 JJD  C30   N2   C1    116.52  3.000
 JJD  O29   C3   N4    119.75  3.000
 JJD  O29   C3   N2    124.41  3.000
 JJD  N4    C3   N2    115.75  3.000
 JJD  C18   N4   C5    120.69  3.000
 JJD  C18   N4   C3    116.01  3.000
 JJD  C5    N4   C3    123.17  3.000
 JJD  C28   C5   C6    125.68  3.000
 JJD  C28   C5   N4    115.24  3.000
 JJD  C6    C5   N4    119.05  3.000
 JJD  C15   C6   C5    123.33  3.000
 JJD  C15   C6   C1    117.48  3.000
 JJD  C5    C6   C1    119.11  3.000
 JJD  C12   C7   C8    119.24  3.000
 JJD  C12   C7   C1    120.88  3.000
 JJD  C8    C7   C1    119.87  3.000
 JJD  H8    C8   C9    119.15  3.000
 JJD  H8    C8   C7    119.97  3.000
 JJD  C9    C8   C7    120.88  3.000
 JJD  H9    C9   C10   120.31  3.000
 JJD  H9    C9   C8    120.44  3.000
 JJD  C10   C9   C8    119.25  3.000
 JJD  C13   C10  C11   119.82  3.000
 JJD  C11   C10  C9    120.40  3.000
 JJD  C13   C10  C9    119.77  3.000
 JJD  H11   C11  C12   120.47  3.000
 JJD  H11   C11  C10   120.08  3.000
 JJD  C12   C11  C10   119.45  3.000
 JJD  H12   C12  C11   118.97  3.000
 JJD  H12   C12  C7    120.26  3.000
 JJD  C11   C12  C7    120.77  3.000
 JJD  N14   C13  C10   180.00  3.000
 JJD  C17   C15  O16   119.47  3.000
 JJD  O16   C15  C6    123.08  3.000
 JJD  C17   C15  C6    117.44  3.000
 JJD  H17B  C17  H17A  107.93  3.000
 JJD  H17B  C17  H17   107.14  3.000
 JJD  H17A  C17  H17   109.00  3.000
 JJD  H17B  C17  C15   110.90  3.000
 JJD  H17A  C17  C15   109.78  3.000
 JJD  H17   C17  C15   111.97  3.000
 JJD  C23   C18  C19   120.37  3.000
 JJD  C23   C18  N4    118.98  3.000
 JJD  C19   C18  N4    120.65  3.000
 JJD  H19   C19  C20   121.19  3.000
 JJD  H19   C19  C18   119.31  3.000
 JJD  C20   C19  C18   119.48  3.000
 JJD  C24   C20  C21   120.84  3.000
 JJD  C21   C20  C19   120.45  3.000
 JJD  C24   C20  C19   118.69  3.000
 JJD  H21   C21  C22   119.37  3.000
 JJD  H21   C21  C20   121.05  3.000
 JJD  C22   C21  C20   119.58  3.000
 JJD  H22   C22  C23   119.92  3.000
 JJD  H22   C22  C21   119.84  3.000
 JJD  C23   C22  C21   120.23  3.000
 JJD  H23   C23  C22   120.23  3.000
 JJD  H23   C23  C18   119.89  3.000
 JJD  C22   C23  C18   119.88  3.000
 JJD  F27   C24  F26   107.10  3.000
 JJD  F27   C24  F25   106.52  3.000
 JJD  F26   C24  F25   106.90  3.000
 JJD  F25   C24  C20   111.46  3.000
 JJD  F27   C24  C20   111.94  3.000
 JJD  F26   C24  C20   112.55  3.000
 JJD  H28B  C28  H28A  107.27  3.000
 JJD  H28B  C28  H28   108.58  3.000
 JJD  H28A  C28  H28   107.47  3.000
 JJD  H28B  C28  C5    111.54  3.000
 JJD  H28A  C28  C5    110.98  3.000
 JJD  H28   C28  C5    110.82  3.000
 JJD  H30A  C30  H30   106.07  3.000
 JJD  H30A  C30  C31   109.80  3.000
 JJD  H30   C30  C31   108.55  3.000
 JJD  H30A  C30  N2    107.44  3.000
 JJD  H30   C30  N2    109.37  3.000
 JJD  C31   C30  N2    115.22  3.000
 JJD  O33   C31  O32   128.15  3.000
 JJD  O32   C31  C30   113.87  3.000
 JJD  O33   C31  C30   117.96  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
 JJD  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 JJD  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 JJD  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 JJD  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 JJD  CONST_05  C12  C7   C8   C9      0.00   0.0  0
 JJD  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 JJD  CONST_07  C21  C20  C19  C18     0.00   0.0  0
 JJD  CONST_08  C21  C22  C23  C18     0.00   0.0  0
 JJD  CONST_09  C22  C23  C18  C19     0.00   0.0  0
 JJD  CONST_10  C22  C21  C20  C19     0.00   0.0  0
 JJD  CONST_11  C23  C18  C19  C20     0.00   0.0  0
 JJD  CONST_12  C23  C22  C21  C20     0.00   0.0  0
 JJD  CONST_13  C9   C8   C7   C1    180.00   0.0  0
 JJD  CONST_14  C11  C12  C7   C1    180.00   0.0  0
 JJD  CONST_15  C20  C19  C18  N4    180.00   0.0  0
 JJD  CONST_16  C22  C23  C18  N4    180.00   0.0  0
 JJD  CONST_18  C5   N4   C3   N2      0.00   0.0  0
 JJD  CONST_19  C18  N4   C3   N2    180.00   0.0  0
 JJD  CONST_20  C13  C10  C9   C8    180.00   0.0  0
 JJD  CONST_21  C13  C10  C11  C12   180.00   0.0  0
 JJD  CONST_22  C24  C20  C19  C18   180.00   0.0  0
 JJD  CONST_23  C24  C20  C21  C22   180.00   0.0  0
 JJD  CONST_24  O29  C3   N2   C1    180.00   0.0  0
 JJD  CONST_25  C30  N2   C3   N4    180.00   0.0  0
 JJD  CONST_26  O29  C3   N4   C5    180.00   0.0  0
 JJD  CONST_27  O29  C3   N4   C18     0.00   0.0  0
 JJD  CONST_28  H8   C8   C7   C1      0.00   0.0  0
 JJD  CONST_29  H12  C12  C7   C1      0.00   0.0  0
 JJD  CONST_30  H19  C19  C18  N4      0.00   0.0  0
 JJD  CONST_31  H23  C23  C18  N4      0.00   0.0  0
 JJD  CONST_32  H9   C9   C8   C7    180.00   0.0  0
 JJD  CONST_33  H11  C11  C12  C7    180.00   0.0  0
 JJD  CONST_34  H22  C22  C23  C18   180.00   0.0  0
 JJD  CONST_35  H21  C21  C20  C19   180.00   0.0  0
 JJD  CONST_36  C30  N2   C3   O29     0.00   0.0  0
 JJD  Var_01    N4   C5   C6   C1     -1.98  30.0  1
 JJD  Var_02    C6   C5   N4   C3    -17.20  30.0  1
 JJD  Var_03    C19  C18  N4   C3    -71.75  30.0  2
 JJD  Var_04    C17  C15  C6   C1     19.19  30.0  2
 JJD  Var_05    C31  C30  N2   C1     89.58  30.0  2
 JJD  Var_06    F26  C24  C20  C19  -164.69  30.0  3
 JJD  Var_07    H28  C28  C5   N4    -34.31  30.0  3
 JJD  Var_08    O33  C31  C30  N2      9.47  30.0  2
 JJD  Var_09    H17  C17  C15  C6     51.14  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
 JJD  chir_01  C1  C7  C6  N2  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
 JJD  plan-1  C1   0.020
 JJD  plan-1  C7   0.020
 JJD  plan-1  C8   0.020
 JJD  plan-1  C9   0.020
 JJD  plan-1  C10  0.020
 JJD  plan-1  C11  0.020
 JJD  plan-1  C12  0.020
 JJD  plan-1  C13  0.020
 JJD  plan-1  N14  0.020
 JJD  plan-1  H8   0.020
 JJD  plan-1  H9   0.020
 JJD  plan-1  H11  0.020
 JJD  plan-1  H12  0.020
 JJD  plan-2  N4   0.020
 JJD  plan-2  C18  0.020
 JJD  plan-2  C19  0.020
 JJD  plan-2  C20  0.020
 JJD  plan-2  C21  0.020
 JJD  plan-2  C22  0.020
 JJD  plan-2  C23  0.020
 JJD  plan-2  C24  0.020
 JJD  plan-2  H19  0.020
 JJD  plan-2  H21  0.020
 JJD  plan-2  H22  0.020
 JJD  plan-2  H23  0.020
 JJD  plan-3  C1   0.020
 JJD  plan-3  N2   0.020
 JJD  plan-3  C3   0.020
 JJD  plan-3  N4   0.020
 JJD  plan-3  C5   0.020
 JJD  plan-3  C18  0.020
 JJD  plan-3  O29  0.020
 JJD  plan-3  C30  0.020
 JJD  plan-4  C30  0.020
 JJD  plan-4  C31  0.020
 JJD  plan-4  O32  0.020
 JJD  plan-4  O33  0.020
 JJD  plan-5  C6   0.020
 JJD  plan-5  C15  0.020
 JJD  plan-5  O16  0.020
 JJD  plan-5  C17  0.020

