# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:29:13 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-(3-ethyl-2,6-dioxo-5-propan-2-yl-pyrimidin-4-yl)carbonyl-5-methyl-benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=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
 KRV  KRV  3-(3-ethyl-2,6-dioxo-5-propan-2-yl-pyrimidin-4-yl)carbonyl-5-methyl-benzenecarbonitrile  ligand  43  24  .  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_KRV
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
 KRV  C1    C  CH2   0  -0.338   1.4574   2.3119  -1.0074
 KRV  C2    C  CH3   0  -0.660   2.2206   3.3798  -0.2466
 KRV  N8    N  NR6   0  -0.558   1.8216   0.9485  -0.5995
 KRV  C9    C  CR6   0   0.723   2.9557   0.4093  -1.1646
 KRV  N10   N  NR16  0  -0.729   3.2761  -0.8434  -0.7203
 KRV  C11   C  CR6   0   0.575   2.6143  -1.6123   0.2171
 KRV  C12   C  CR6   0  -0.118   1.4241  -0.9901   0.7766
 KRV  C13   C  CR6   0   0.268   1.1129   0.2529   0.3486
 KRV  C14   C  C     0   0.284  -0.0759   0.9753   0.9448
 KRV  O15   O  O     0  -0.332   0.0932   1.7037   1.8926
 KRV  C16   C  CR6   0   0.026  -1.4023   0.7393   0.3323
 KRV  C17   C  CR16  0  -0.292  -1.5464  -0.1356  -0.7356
 KRV  C18   C  CR6   0   0.054  -2.8132  -0.3301  -1.2778
 KRV  C19   C  CSP   0   0.058  -2.9772  -1.2306  -2.3740
 KRV  N20   N  NS    0  -0.239  -3.1072  -1.9523  -3.2619
 KRV  C21   C  CR16  0  -0.274  -3.9194   0.3415  -0.7667
 KRV  C22   C  CR6   0   0.126  -3.7808   1.2257   0.3008
 KRV  C23   C  CR16  0  -0.295  -2.5161   1.4126   0.8395
 KRV  C24   C  CH3   0  -0.721  -4.9780   1.9400   0.8500
 KRV  C25   C  CH1   0  -0.337   0.5907  -1.7344   1.7943
 KRV  C26   C  CH3   0  -0.644  -0.0002  -3.0261   1.2275
 KRV  C27   C  CH3   0  -0.643   1.3534  -1.9789   3.0973
 KRV  O28   O  O     0  -0.444   3.0421  -2.7139   0.5066
 KRV  O29   O  O     0  -0.476   3.6217   0.9925  -1.9945
 KRV  H1    H  HCH2  0   0.268   0.3836   2.4360  -0.8774
 KRV  H1A   H  HCH2  0   0.285   1.6344   2.3954  -2.0768
 KRV  H2    H  HCH3  0   0.247   1.8978   4.3637  -0.5851
 KRV  H2A   H  HCH3  0   0.237   2.0401   3.3151   0.8252
 KRV  H2B   H  HCH3  0   0.243   3.2925   3.3003  -0.4199
 KRV  HN10  H  HNR6  0   0.428   4.1089  -1.2493  -1.1306
 KRV  H17   H  HCR6  0   0.293  -0.7000  -0.6617  -1.1558
 KRV  H21   H  HCR6  0   0.290  -4.8944   0.1758  -1.2075
 KRV  H23   H  HCR6  0   0.281  -2.3900   2.0983   1.6680
 KRV  H24   H  HCH3  0   0.263  -5.6319   1.2459   1.3796
 KRV  H24A  H  HCH3  0   0.256  -4.6889   2.7242   1.5469
 KRV  H24B  H  HCH3  0   0.258  -5.5652   2.3946   0.0525
 KRV  H25   H  HCH1  0   0.245  -0.2618  -1.1019   2.0581
 KRV  H26   H  HCH3  0   0.236   0.7689  -3.7688   1.0245
 KRV  H26A  H  HCH3  0   0.234  -0.6993  -3.4578   1.9448
 KRV  H26B  H  HCH3  0   0.225  -0.5487  -2.8400   0.3027
 KRV  H27   H  HCH3  0   0.231   1.7386  -1.0458   3.5097
 KRV  H27A  H  HCH3  0   0.233   0.6861  -2.4218   3.8382
 KRV  H27B  H  HCH3  0   0.234   2.1896  -2.6605   2.9527

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
 KRV  N8   C1    single    1.469  0.020  1.469
 KRV  C2   C1    single    1.517  0.020  1.517
 KRV  C1   H1    single    0.970  0.020  1.090
 KRV  C1   H1A   single    0.970  0.020  1.090
 KRV  C2   H2    single    0.970  0.020  1.090
 KRV  C2   H2A   single    0.970  0.020  1.090
 KRV  C2   H2B   single    0.970  0.020  1.090
 KRV  C9   N8    single    1.377  0.020  1.377
 KRV  N8   C13   single    1.373  0.020  1.373
 KRV  N10  C9    single    1.367  0.020  1.367
 KRV  O29  C9    double    1.213  0.020  1.213
 KRV  N10  C11   single    1.381  0.020  1.381
 KRV  N10  HN10  single    0.860  0.020  1.020
 KRV  O28  C11   double    1.217  0.020  1.217
 KRV  C11  C12   single    1.455  0.020  1.455
 KRV  C12  C25   single    1.511  0.020  1.511
 KRV  C12  C13   double    1.351  0.020  1.351
 KRV  C13  C14   single    1.513  0.020  1.513
 KRV  C14  O15   double    1.207  0.020  1.207
 KRV  C14  C16   single    1.480  0.020  1.480
 KRV  C16  C23   aromatic  1.397  0.020  1.397
 KRV  C16  C17   aromatic  1.388  0.020  1.388
 KRV  C17  C18   aromatic  1.392  0.020  1.392
 KRV  C17  H17   single    0.930  0.020  1.080
 KRV  C18  C21   aromatic  1.391  0.020  1.391
 KRV  C18  C19   single    1.428  0.020  1.428
 KRV  C19  N20   triple    1.152  0.020  1.152
 KRV  C22  C21   aromatic  1.393  0.020  1.393
 KRV  C21  H21   single    0.930  0.020  1.080
 KRV  C23  C22   aromatic  1.387  0.020  1.387
 KRV  C22  C24   single    1.498  0.020  1.498
 KRV  C23  H23   single    0.930  0.020  1.080
 KRV  C24  H24   single    0.970  0.020  1.090
 KRV  C24  H24A  single    0.970  0.020  1.090
 KRV  C24  H24B  single    0.970  0.020  1.090
 KRV  C27  C25   single    1.529  0.020  1.529
 KRV  C25  C26   single    1.529  0.020  1.529
 KRV  C25  H25   single    0.970  0.020  1.090
 KRV  C26  H26   single    0.970  0.020  1.090
 KRV  C26  H26A  single    0.970  0.020  1.090
 KRV  C26  H26B  single    0.970  0.020  1.090
 KRV  C27  H27   single    0.970  0.020  1.090
 KRV  C27  H27A  single    0.970  0.020  1.090
 KRV  C27  H27B  single    0.970  0.020  1.090

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
 KRV  H1A   C1   H1    105.62  3.000
 KRV  H1A   C1   N8    107.70  3.000
 KRV  H1    C1   N8    108.49  3.000
 KRV  H1A   C1   C2    110.94  3.000
 KRV  H1    C1   C2    110.86  3.000
 KRV  N8    C1   C2    112.91  3.000
 KRV  H2B   C2   H2A   108.39  3.000
 KRV  H2B   C2   H2    107.95  3.000
 KRV  H2A   C2   H2    108.08  3.000
 KRV  H2B   C2   C1    111.35  3.000
 KRV  H2A   C2   C1    111.62  3.000
 KRV  H2    C2   C1    109.32  3.000
 KRV  C13   N8   C9    120.67  3.000
 KRV  C13   N8   C1    122.28  3.000
 KRV  C9    N8   C1    116.98  3.000
 KRV  O29   C9   N10   122.28  3.000
 KRV  O29   C9   N8    122.99  3.000
 KRV  N10   C9   N8    114.73  3.000
 KRV  HN10  N10  C11   116.46  3.000
 KRV  HN10  N10  C9    115.34  3.000
 KRV  C11   N10  C9    128.19  3.000
 KRV  O28   C11  C12   125.69  3.000
 KRV  C12   C11  N10   114.51  3.000
 KRV  O28   C11  N10   119.80  3.000
 KRV  C25   C12  C13   122.65  3.000
 KRV  C13   C12  C11   117.39  3.000
 KRV  C25   C12  C11   119.96  3.000
 KRV  C14   C13  C12   119.69  3.000
 KRV  C14   C13  N8    115.83  3.000
 KRV  C12   C13  N8    124.47  3.000
 KRV  C16   C14  O15   123.14  3.000
 KRV  C16   C14  C13   117.70  3.000
 KRV  O15   C14  C13   119.16  3.000
 KRV  C23   C16  C17   120.03  3.000
 KRV  C17   C16  C14   120.80  3.000
 KRV  C23   C16  C14   119.18  3.000
 KRV  H17   C17  C18   119.54  3.000
 KRV  H17   C17  C16   121.62  3.000
 KRV  C18   C17  C16   118.84  3.000
 KRV  C21   C18  C19   119.67  3.000
 KRV  C19   C18  C17   119.45  3.000
 KRV  C21   C18  C17   120.87  3.000
 KRV  N20   C19  C18   180.00  3.000
 KRV  H21   C21  C22   119.91  3.000
 KRV  H21   C21  C18   119.51  3.000
 KRV  C22   C21  C18   120.58  3.000
 KRV  C24   C22  C23   121.46  3.000
 KRV  C24   C22  C21   120.26  3.000
 KRV  C23   C22  C21   118.28  3.000
 KRV  H23   C23  C22   119.25  3.000
 KRV  H23   C23  C16   119.35  3.000
 KRV  C22   C23  C16   121.40  3.000
 KRV  H24B  C24  H24A  108.14  3.000
 KRV  H24B  C24  H24   107.33  3.000
 KRV  H24A  C24  H24   107.87  3.000
 KRV  H24B  C24  C22   111.17  3.000
 KRV  H24A  C24  C22   111.46  3.000
 KRV  H24   C24  C22   110.70  3.000
 KRV  H25   C25  C27   106.00  3.000
 KRV  H25   C25  C26   106.06  3.000
 KRV  C27   C25  C26   111.92  3.000
 KRV  H25   C25  C12   107.90  3.000
 KRV  C26   C25  C12   112.30  3.000
 KRV  C27   C25  C12   112.17  3.000
 KRV  H26B  C26  H26A  107.62  3.000
 KRV  H26B  C26  H26   108.27  3.000
 KRV  H26A  C26  H26   107.79  3.000
 KRV  H26B  C26  C25   111.36  3.000
 KRV  H26A  C26  C25   109.76  3.000
 KRV  H26   C26  C25   111.87  3.000
 KRV  H27B  C27  H27A  107.81  3.000
 KRV  H27B  C27  H27   108.34  3.000
 KRV  H27A  C27  H27   107.85  3.000
 KRV  H27B  C27  C25   111.72  3.000
 KRV  H27A  C27  C25   109.78  3.000
 KRV  H27   C27  C25   111.19  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
 KRV  CONST_01  C21   C22  C23  C16     0.00   0.0  0
 KRV  CONST_02  C21   C18  C17  C16     0.00   0.0  0
 KRV  CONST_03  C22   C23  C16  C17     0.00   0.0  0
 KRV  CONST_04  C22   C21  C18  C17     0.00   0.0  0
 KRV  CONST_05  C23   C16  C17  C18     0.00   0.0  0
 KRV  CONST_06  C23   C22  C21  C18     0.00   0.0  0
 KRV  CONST_07  C11   N10  C9   N8      0.00   0.0  0
 KRV  CONST_08  C12   C11  N10  C9      0.00   0.0  0
 KRV  CONST_09  C13   N8   C9   N10     0.00   0.0  0
 KRV  CONST_10  C22   C23  C16  C14   180.00   0.0  0
 KRV  CONST_11  C18   C17  C16  C14   180.00   0.0  0
 KRV  CONST_12  C24   C22  C23  C16   180.00   0.0  0
 KRV  CONST_13  C19   C18  C17  C16   180.00   0.0  0
 KRV  CONST_14  C24   C22  C21  C18   180.00   0.0  0
 KRV  CONST_15  C22   C21  C18  C19   180.00   0.0  0
 KRV  CONST_16  N10   C9   N8   C1    180.00   0.0  0
 KRV  CONST_17  O28   C11  N10  C9    180.00   0.0  0
 KRV  CONST_18  O29   C9   N10  C11   180.00   0.0  0
 KRV  CONST_19  O29   C9   N8   C13   180.00   0.0  0
 KRV  CONST_20  H23   C23  C16  C17   180.00   0.0  0
 KRV  CONST_21  H21   C21  C18  C17   180.00   0.0  0
 KRV  CONST_22  H17   C17  C18  C21   180.00   0.0  0
 KRV  CONST_23  HN10  N10  C9   N8    180.00   0.0  0
 KRV  CONST_24  O29   C9   N8   C1      0.00   0.0  0
 KRV  Var_01    C16   C14  C13  N8     93.96  30.0  2
 KRV  Var_02    C23   C16  C14  C13  -178.62  30.0  2
 KRV  Var_03    C9    N8   C1   C2    -82.33  30.0  2
 KRV  Var_04    C27   C25  C12  C11    65.15  30.0  3
 KRV  Var_05    H24   C24  C22  C21    70.50  30.0  2
 KRV  Var_06    H2    C2   C1   N8   -179.31  30.0  3
 KRV  Var_07    H27   C27  C25  C12    54.78  30.0  3
 KRV  Var_08    H26   C26  C25  C12    68.08  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
 KRV  plan-1  C1    0.020
 KRV  plan-1  N8    0.020
 KRV  plan-1  C9    0.020
 KRV  plan-1  N10   0.020
 KRV  plan-1  C11   0.020
 KRV  plan-1  C12   0.020
 KRV  plan-1  C13   0.020
 KRV  plan-1  C14   0.020
 KRV  plan-1  C25   0.020
 KRV  plan-1  O28   0.020
 KRV  plan-1  O29   0.020
 KRV  plan-1  HN10  0.020
 KRV  plan-2  C14   0.020
 KRV  plan-2  C16   0.020
 KRV  plan-2  C17   0.020
 KRV  plan-2  C18   0.020
 KRV  plan-2  C19   0.020
 KRV  plan-2  N20   0.020
 KRV  plan-2  C21   0.020
 KRV  plan-2  C22   0.020
 KRV  plan-2  C23   0.020
 KRV  plan-2  C24   0.020
 KRV  plan-2  H17   0.020
 KRV  plan-2  H21   0.020
 KRV  plan-2  H23   0.020
 KRV  plan-3  C13   0.020
 KRV  plan-3  C14   0.020
 KRV  plan-3  O15   0.020
 KRV  plan-3  C16   0.020

