# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 16:02:38 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-(2,6-dioxo-5-propan-2-yl-3-propyl-pyrimidin-4-yl)carbonyl-5-methyl-benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN1C(=O)NC(=O)C(=C1C(=O)c2cc(C)cc(c2)C#N)C(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
 KRP  KRP  3-(2,6-dioxo-5-propan-2-yl-3-propyl-pyrimidin-4-yl)carbonyl-5-methyl-benzenecarbonitrile  ligand  46  25  .  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_KRP
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
 KRP  C1    C  CH2   0  -0.433  -2.5734  -2.8549   0.0027
 KRP  C2    C  CH3   0  -0.671  -2.3298  -4.3102  -0.3702
 KRP  C4    C  CH2   0  -0.324  -1.7010  -1.9295  -0.8318
 KRP  N5    N  NR6   0  -0.564  -1.8738  -0.5114  -0.4987
 KRP  C6    C  CR6   0   0.271  -1.0468   0.1409   0.3818
 KRP  C7    C  C     0   0.280   0.0342  -0.7013   1.0229
 KRP  O8    O  O     0  -0.331  -0.2303  -1.3347   2.0162
 KRP  C9    C  CR6   0   0.028   1.3782  -0.6971   0.4045
 KRP  C10   C  CR16  0  -0.293   1.6289   0.0307  -0.7504
 KRP  C11   C  CR6   0   0.053   2.9086   0.0006  -1.2960
 KRP  C12   C  CSP   0   0.058   3.1849   0.7429  -2.4847
 KRP  N13   N  NS    0  -0.240   3.4101   1.3410  -3.4426
 KRP  C14   C  CR16  0  -0.275   3.9230  -0.7420  -0.6985
 KRP  C15   C  CR6   0   0.125   3.6774  -1.4752   0.4599
 KRP  C16   C  CH3   0  -0.720   4.7762  -2.2571   1.1128
 KRP  C17   C  CR16  0  -0.293   2.3985  -1.4441   0.9968
 KRP  C18   C  CR6   0  -0.119  -1.1678   1.4419   0.7253
 KRP  C19   C  CH1   0  -0.334  -0.2117   2.1246   1.6760
 KRP  C20   C  CH3   0  -0.647   0.4884   3.3274   1.0409
 KRP  C21   C  CH3   0  -0.642  -0.8822   2.4875   3.0012
 KRP  C22   C  CR6   0   0.574  -2.2826   2.1827   0.1562
 KRP  O23   O  O     0  -0.444  -2.5541   3.3460   0.3877
 KRP  N24   N  NR16  0  -0.730  -3.0699   1.4539  -0.7140
 KRP  C25   C  CR6   0   0.723  -2.9382   0.1428  -1.0787
 KRP  O26   O  O     0  -0.476  -3.7012  -0.3939  -1.8544
 KRP  H1    H  HCH2  0   0.241  -3.6240  -2.6040  -0.1550
 KRP  H1A   H  HCH2  0   0.235  -2.3660  -2.6998   1.0631
 KRP  H2    H  HCH3  0   0.240  -2.9599  -4.9735   0.2211
 KRP  H2A   H  HCH3  0   0.227  -2.5543  -4.4926  -1.4219
 KRP  H2B   H  HCH3  0   0.226  -1.2917  -4.5989  -0.1970
 KRP  H4    H  HCH2  0   0.265  -0.6476  -2.1879  -0.7167
 KRP  H4A   H  HCH2  0   0.282  -1.9165  -2.0498  -1.8919
 KRP  H10   H  HCR6  0   0.294   0.8560   0.6140  -1.2324
 KRP  H14   H  HCR6  0   0.289   4.9112  -0.7466  -1.1408
 KRP  H16   H  HCH3  0   0.263   5.4569  -1.5908   1.6448
 KRP  H16A  H  HCH3  0   0.255   4.3794  -2.9704   1.8326
 KRP  H16B  H  HCH3  0   0.258   5.3649  -2.8046   0.3778
 KRP  H17   H  HCR6  0   0.280   2.1867  -2.0094   1.8957
 KRP  H19   H  HCH1  0   0.244   0.5825   1.4134   1.9174
 KRP  H20   H  HCH3  0   0.237  -0.1916   4.1626   0.8870
 KRP  H20A  H  HCH3  0   0.234   1.2935   3.6688   1.6929
 KRP  H20B  H  HCH3  0   0.226   0.9330   3.0668   0.0792
 KRP  H21   H  HCH3  0   0.231  -1.3161   1.6072   3.4766
 KRP  H21A  H  HCH3  0   0.233  -0.1455   2.9091   3.6865
 KRP  H21B  H  HCH3  0   0.233  -1.6703   3.2252   2.8618
 KRP  HN24  H  HNR6  0   0.428  -3.8529   1.9435  -1.1307

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
 KRP  C1   C2    single    1.522  0.020  1.522
 KRP  C1   C4    single    1.521  0.020  1.521
 KRP  C1   H1    single    0.970  0.020  1.090
 KRP  C1   H1A   single    0.970  0.020  1.090
 KRP  C2   H2    single    0.970  0.020  1.090
 KRP  C2   H2A   single    0.970  0.020  1.090
 KRP  C2   H2B   single    0.970  0.020  1.090
 KRP  N5   C4    single    1.467  0.020  1.467
 KRP  C4   H4    single    0.970  0.020  1.090
 KRP  C4   H4A   single    0.970  0.020  1.090
 KRP  C25  N5    single    1.377  0.020  1.377
 KRP  N5   C6    single    1.373  0.020  1.373
 KRP  C18  C6    double    1.351  0.020  1.351
 KRP  C6   C7    single    1.513  0.020  1.513
 KRP  C7   O8    double    1.207  0.020  1.207
 KRP  C7   C9    single    1.479  0.020  1.479
 KRP  C17  C9    aromatic  1.396  0.020  1.396
 KRP  C9   C10   aromatic  1.388  0.020  1.388
 KRP  C10  C11   aromatic  1.391  0.020  1.391
 KRP  C10  H10   single    0.930  0.020  1.080
 KRP  C14  C11   aromatic  1.392  0.020  1.392
 KRP  C11  C12   single    1.428  0.020  1.428
 KRP  C12  N13   triple    1.152  0.020  1.152
 KRP  C15  C14   aromatic  1.393  0.020  1.393
 KRP  C14  H14   single    0.930  0.020  1.080
 KRP  C17  C15   aromatic  1.387  0.020  1.387
 KRP  C16  C15   single    1.498  0.020  1.498
 KRP  C16  H16   single    0.970  0.020  1.090
 KRP  C16  H16A  single    0.970  0.020  1.090
 KRP  C16  H16B  single    0.970  0.020  1.090
 KRP  C17  H17   single    0.930  0.020  1.080
 KRP  C22  C18   single    1.454  0.020  1.454
 KRP  C18  C19   single    1.511  0.020  1.511
 KRP  C21  C19   single    1.529  0.020  1.529
 KRP  C20  C19   single    1.530  0.020  1.530
 KRP  C19  H19   single    0.970  0.020  1.090
 KRP  C20  H20   single    0.970  0.020  1.090
 KRP  C20  H20A  single    0.970  0.020  1.090
 KRP  C20  H20B  single    0.970  0.020  1.090
 KRP  C21  H21   single    0.970  0.020  1.090
 KRP  C21  H21A  single    0.970  0.020  1.090
 KRP  C21  H21B  single    0.970  0.020  1.090
 KRP  O23  C22   double    1.217  0.020  1.217
 KRP  N24  C22   single    1.381  0.020  1.381
 KRP  N24  C25   single    1.367  0.020  1.367
 KRP  N24  HN24  single    0.860  0.020  1.020
 KRP  O26  C25   double    1.213  0.020  1.213

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
 KRP  H1A   C1   H1    106.89  3.000
 KRP  H1A   C1   C4    109.73  3.000
 KRP  H1    C1   C4    109.45  3.000
 KRP  H1A   C1   C2    110.09  3.000
 KRP  H1    C1   C2    109.78  3.000
 KRP  C4    C1   C2    110.82  3.000
 KRP  H2B   C2   H2A   107.74  3.000
 KRP  H2B   C2   H2    107.63  3.000
 KRP  H2A   C2   H2    107.61  3.000
 KRP  H2B   C2   C1    111.49  3.000
 KRP  H2A   C2   C1    111.29  3.000
 KRP  H2    C2   C1    110.89  3.000
 KRP  H4A   C4   H4    105.53  3.000
 KRP  H4A   C4   N5    107.74  3.000
 KRP  H4    C4   N5    108.59  3.000
 KRP  H4A   C4   C1    110.71  3.000
 KRP  H4    C4   C1    110.60  3.000
 KRP  N5    C4   C1    113.33  3.000
 KRP  C25   N5   C6    120.66  3.000
 KRP  C6    N5   C4    122.28  3.000
 KRP  C25   N5   C4    117.04  3.000
 KRP  C18   C6   C7    119.49  3.000
 KRP  C7    C6   N5    115.96  3.000
 KRP  C18   C6   N5    124.52  3.000
 KRP  C9    C7   O8    122.98  3.000
 KRP  C9    C7   C6    118.06  3.000
 KRP  O8    C7   C6    118.95  3.000
 KRP  C17   C9   C10   120.09  3.000
 KRP  C10   C9   C7    120.89  3.000
 KRP  C17   C9   C7    119.01  3.000
 KRP  H10   C10  C11   119.61  3.000
 KRP  H10   C10  C9    121.63  3.000
 KRP  C11   C10  C9    118.76  3.000
 KRP  C14   C11  C12   119.57  3.000
 KRP  C12   C11  C10   119.53  3.000
 KRP  C14   C11  C10   120.89  3.000
 KRP  N13   C12  C11   180.00  3.000
 KRP  H14   C14  C15   119.90  3.000
 KRP  H14   C14  C11   119.48  3.000
 KRP  C15   C14  C11   120.62  3.000
 KRP  C17   C15  C16   121.27  3.000
 KRP  C16   C15  C14   120.52  3.000
 KRP  C17   C15  C14   118.21  3.000
 KRP  H16B  C16  H16A  108.29  3.000
 KRP  H16B  C16  H16   107.38  3.000
 KRP  H16A  C16  H16   107.78  3.000
 KRP  H16B  C16  C15   111.38  3.000
 KRP  H16A  C16  C15   111.28  3.000
 KRP  H16   C16  C15   110.57  3.000
 KRP  H17   C17  C15   119.33  3.000
 KRP  H17   C17  C9    119.24  3.000
 KRP  C15   C17  C9    121.43  3.000
 KRP  C22   C18  C19   120.06  3.000
 KRP  C19   C18  C6    122.57  3.000
 KRP  C22   C18  C6    117.36  3.000
 KRP  H19   C19  C21   106.36  3.000
 KRP  H19   C19  C20   105.71  3.000
 KRP  C21   C19  C20   111.96  3.000
 KRP  H19   C19  C18   107.73  3.000
 KRP  C20   C19  C18   112.55  3.000
 KRP  C21   C19  C18   112.03  3.000
 KRP  H20B  C20  H20A  107.51  3.000
 KRP  H20B  C20  H20   108.27  3.000
 KRP  H20A  C20  H20   107.80  3.000
 KRP  H20B  C20  C19   111.38  3.000
 KRP  H20A  C20  C19   109.61  3.000
 KRP  H20   C20  C19   112.10  3.000
 KRP  H21B  C21  H21A  107.90  3.000
 KRP  H21B  C21  H21   108.35  3.000
 KRP  H21A  C21  H21   107.87  3.000
 KRP  H21B  C21  C19   111.56  3.000
 KRP  H21A  C21  C19   109.88  3.000
 KRP  H21   C21  C19   111.15  3.000
 KRP  N24   C22  O23   119.81  3.000
 KRP  N24   C22  C18   114.49  3.000
 KRP  O23   C22  C18   125.70  3.000
 KRP  HN24  N24  C25   115.35  3.000
 KRP  HN24  N24  C22   116.40  3.000
 KRP  C25   N24  C22   128.25  3.000
 KRP  O26   C25  N24   122.29  3.000
 KRP  O26   C25  N5    123.03  3.000
 KRP  N24   C25  N5    114.68  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
 KRP  CONST_01  C14   C15  C17  C9      0.00   0.0  0
 KRP  CONST_02  C14   C11  C10  C9      0.00   0.0  0
 KRP  CONST_03  C15   C17  C9   C10     0.00   0.0  0
 KRP  CONST_04  C15   C14  C11  C10     0.00   0.0  0
 KRP  CONST_05  C17   C9   C10  C11     0.00   0.0  0
 KRP  CONST_06  C17   C15  C14  C11     0.00   0.0  0
 KRP  CONST_07  C22   N24  C25  N5      0.00   0.0  0
 KRP  CONST_08  N24   C25  N5   C6      0.00   0.0  0
 KRP  CONST_09  C25   N24  C22  C18     0.00   0.0  0
 KRP  CONST_10  C15   C17  C9   C7    180.00   0.0  0
 KRP  CONST_11  C11   C10  C9   C7    180.00   0.0  0
 KRP  CONST_12  C16   C15  C17  C9    180.00   0.0  0
 KRP  CONST_13  C12   C11  C10  C9    180.00   0.0  0
 KRP  CONST_14  C16   C15  C14  C11   180.00   0.0  0
 KRP  CONST_15  C15   C14  C11  C12   180.00   0.0  0
 KRP  CONST_16  N24   C25  N5   C4    180.00   0.0  0
 KRP  CONST_17  O26   C25  N5   C6    180.00   0.0  0
 KRP  CONST_18  O26   C25  N24  C22   180.00   0.0  0
 KRP  CONST_19  C25   N24  C22  O23   180.00   0.0  0
 KRP  CONST_20  H17   C17  C9   C10   180.00   0.0  0
 KRP  CONST_21  H14   C14  C11  C10   180.00   0.0  0
 KRP  CONST_22  H10   C10  C11  C14   180.00   0.0  0
 KRP  CONST_23  HN24  N24  C25  N5    180.00   0.0  0
 KRP  CONST_24  O26   C25  N5   C4      0.00   0.0  0
 KRP  Var_01    C9    C7   C6   N5     95.40  30.0  2
 KRP  Var_02    C17   C9   C7   C6    178.60  30.0  2
 KRP  Var_03    C25   N5   C4   C1    -82.75  30.0  1
 KRP  Var_04    C21   C19  C18  C6   -111.50  30.0  3
 KRP  Var_05    H16   C16  C15  C14    75.31  30.0  2
 KRP  Var_06    N5    C4   C1   C2   -178.91  30.0  3
 KRP  Var_07    H21   C21  C19  C18    56.48  30.0  3
 KRP  Var_08    H20   C20  C19  C18    70.76  30.0  3
 KRP  Var_09    H2    C2   C1   C4   -179.54  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
 KRP  plan-1  C7    0.020
 KRP  plan-1  C9    0.020
 KRP  plan-1  C10   0.020
 KRP  plan-1  C11   0.020
 KRP  plan-1  C12   0.020
 KRP  plan-1  N13   0.020
 KRP  plan-1  C14   0.020
 KRP  plan-1  C15   0.020
 KRP  plan-1  C16   0.020
 KRP  plan-1  C17   0.020
 KRP  plan-1  H10   0.020
 KRP  plan-1  H14   0.020
 KRP  plan-1  H17   0.020
 KRP  plan-2  C4    0.020
 KRP  plan-2  N5    0.020
 KRP  plan-2  C6    0.020
 KRP  plan-2  C7    0.020
 KRP  plan-2  C18   0.020
 KRP  plan-2  C19   0.020
 KRP  plan-2  C22   0.020
 KRP  plan-2  O23   0.020
 KRP  plan-2  N24   0.020
 KRP  plan-2  C25   0.020
 KRP  plan-2  O26   0.020
 KRP  plan-2  HN24  0.020
 KRP  plan-3  C6    0.020
 KRP  plan-3  C7    0.020
 KRP  plan-3  O8    0.020
 KRP  plan-3  C9    0.020

