# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 01:38:18 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-(3-butyl-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: CCCCN1C(=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
 KBT  KBT  3-(3-butyl-2,6-dioxo-5-propan-2-yl-pyrimidin-4-yl)carbonyl-5-methyl-benzenecarbonitrile  ligand  49  26  .  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_KBT
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
 KBT  C1    C  CH2   0  -0.421   3.0908   1.8706  -0.1559
 KBT  C2    C  CH2   0  -0.430   3.2076   3.3561  -0.4743
 KBT  C3    C  CH3   0  -0.662   4.3640   4.0177   0.2612
 KBT  C4    C  CH2   0  -0.331   1.9705   1.2209  -0.9545
 KBT  N5    N  NR6   0  -0.564   1.7421  -0.1819  -0.5931
 KBT  C6    C  CR6   0   0.271   0.8083  -0.5518   0.3430
 KBT  C7    C  C     0   0.277   0.0113   0.5746   0.9641
 KBT  O8    O  O     0  -0.331   0.4617   1.1578   1.9204
 KBT  C9    C  CR6   0   0.028  -1.3048   0.8940   0.3679
 KBT  C10   C  CR16  0  -0.292  -1.7548   0.2247  -0.7626
 KBT  C11   C  CR6   0   0.053  -2.9985   0.5587  -1.2887
 KBT  C12   C  CSP   0   0.058  -3.4754  -0.1205  -2.4510
 KBT  N13   N  NS    0  -0.239  -3.8641  -0.6768  -3.3814
 KBT  C14   C  CR16  0  -0.276  -3.7835   1.5438  -0.6956
 KBT  C15   C  CR6   0   0.125  -3.3376   2.2192   0.4373
 KBT  C16   C  CH3   0  -0.720  -4.1952   3.2602   1.0900
 KBT  C17   C  CR16  0  -0.292  -2.0935   1.8854   0.9541
 KBT  C18   C  CR6   0  -0.118   0.5843  -1.8234   0.7398
 KBT  C19   C  CH1   0  -0.335  -0.4745  -2.1848   1.7556
 KBT  C20   C  CH3   0  -0.647  -1.5433  -3.1142   1.1797
 KBT  C21   C  CH3   0  -0.642   0.1309  -2.7370   3.0469
 KBT  C22   C  CR6   0   0.574   1.4201  -2.8621   0.1586
 KBT  O23   O  O     0  -0.444   1.3633  -4.0491   0.4198
 KBT  N24   N  NR16  0  -0.730   2.3427  -2.4060  -0.7632
 KBT  C25   C  CR6   0   0.723   2.5648  -1.1210  -1.1737
 KBT  O26   O  O     0  -0.476   3.4191  -0.8380  -1.9876
 KBT  H1    H  HCH2  0   0.237   4.0346   1.3683  -0.3822
 KBT  H1A   H  HCH2  0   0.232   2.9108   1.7364   0.9138
 KBT  H2    H  HCH2  0   0.222   3.3348   3.4914  -1.5525
 KBT  H2A   H  HCH2  0   0.221   2.2712   3.8572  -0.2119
 KBT  H3    H  HCH3  0   0.220   4.2629   3.9023   1.3418
 KBT  H3A   H  HCH3  0   0.220   5.3194   3.5783  -0.0297
 KBT  H3B   H  HCH3  0   0.230   4.4114   5.0853   0.0458
 KBT  H4    H  HCH2  0   0.264   1.0372   1.7705  -0.8280
 KBT  H4A   H  HCH2  0   0.285   2.1882   1.2598  -2.0203
 KBT  H10   H  HCR6  0   0.295  -1.1592  -0.5404  -1.2424
 KBT  H14   H  HCR6  0   0.290  -4.7487   1.7851  -1.1229
 KBT  H16   H  HCH3  0   0.264  -4.9237   2.7925   1.7545
 KBT  H16A  H  HCH3  0   0.256  -3.6000   3.9502   1.6853
 KBT  H16B  H  HCH3  0   0.257  -4.7510   3.8374   0.3527
 KBT  H17   H  HCR6  0   0.280  -1.7284   2.4040   1.8317
 KBT  H19   H  HCH1  0   0.245  -0.9934  -1.2649   2.0386
 KBT  H20   H  HCH3  0   0.237  -1.1481  -4.1046   0.9628
 KBT  H20A  H  HCH3  0   0.234  -2.3581  -3.2265   1.8959
 KBT  H20B  H  HCH3  0   0.226  -1.9680  -2.7083   0.2601
 KBT  H21   H  HCH3  0   0.231   0.8716  -2.0501   3.4580
 KBT  H21A  H  HCH3  0   0.233  -0.6514  -2.8679   3.7958
 KBT  H21B  H  HCH3  0   0.233   0.6085  -3.7030   2.8924
 KBT  HN24  H  HNR6  0   0.428   2.9471  -3.1041  -1.1792

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
 KBT  C1   C4    single    1.522  0.020  1.522
 KBT  C1   C2    single    1.524  0.020  1.524
 KBT  C1   H1    single    0.970  0.020  1.090
 KBT  C1   H1A   single    0.970  0.020  1.090
 KBT  C3   C2    single    1.522  0.020  1.522
 KBT  C2   H2    single    0.970  0.020  1.090
 KBT  C2   H2A   single    0.970  0.020  1.090
 KBT  C3   H3    single    0.970  0.020  1.090
 KBT  C3   H3A   single    0.970  0.020  1.090
 KBT  C3   H3B   single    0.970  0.020  1.090
 KBT  N5   C4    single    1.466  0.020  1.466
 KBT  C4   H4    single    0.970  0.020  1.090
 KBT  C4   H4A   single    0.970  0.020  1.090
 KBT  C25  N5    single    1.377  0.020  1.377
 KBT  N5   C6    single    1.373  0.020  1.373
 KBT  C18  C6    double    1.351  0.020  1.351
 KBT  C6   C7    single    1.513  0.020  1.513
 KBT  C7   O8    double    1.207  0.020  1.207
 KBT  C7   C9    single    1.480  0.020  1.480
 KBT  C17  C9    aromatic  1.396  0.020  1.396
 KBT  C9   C10   aromatic  1.389  0.020  1.389
 KBT  C10  C11   aromatic  1.391  0.020  1.391
 KBT  C10  H10   single    0.930  0.020  1.080
 KBT  C14  C11   aromatic  1.392  0.020  1.392
 KBT  C11  C12   single    1.428  0.020  1.428
 KBT  C12  N13   triple    1.152  0.020  1.152
 KBT  C15  C14   aromatic  1.392  0.020  1.392
 KBT  C14  H14   single    0.930  0.020  1.080
 KBT  C17  C15   aromatic  1.388  0.020  1.388
 KBT  C16  C15   single    1.498  0.020  1.498
 KBT  C16  H16   single    0.970  0.020  1.090
 KBT  C16  H16A  single    0.970  0.020  1.090
 KBT  C16  H16B  single    0.970  0.020  1.090
 KBT  C17  H17   single    0.930  0.020  1.080
 KBT  C22  C18   single    1.454  0.020  1.454
 KBT  C18  C19   single    1.511  0.020  1.511
 KBT  C21  C19   single    1.529  0.020  1.529
 KBT  C19  C20   single    1.529  0.020  1.529
 KBT  C19  H19   single    0.970  0.020  1.090
 KBT  C20  H20   single    0.970  0.020  1.090
 KBT  C20  H20A  single    0.970  0.020  1.090
 KBT  C20  H20B  single    0.970  0.020  1.090
 KBT  C21  H21   single    0.970  0.020  1.090
 KBT  C21  H21A  single    0.970  0.020  1.090
 KBT  C21  H21B  single    0.970  0.020  1.090
 KBT  O23  C22   double    1.217  0.020  1.217
 KBT  N24  C22   single    1.382  0.020  1.382
 KBT  N24  C25   single    1.367  0.020  1.367
 KBT  N24  HN24  single    0.860  0.020  1.020
 KBT  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
 KBT  H1A   C1   H1    106.77  3.000
 KBT  H1A   C1   C4    109.88  3.000
 KBT  H1    C1   C4    109.33  3.000
 KBT  H1A   C1   C2    109.69  3.000
 KBT  H1    C1   C2    109.79  3.000
 KBT  C4    C1   C2    111.29  3.000
 KBT  H2A   C2   H2    106.22  3.000
 KBT  H2A   C2   C3    109.59  3.000
 KBT  H2    C2   C3    109.53  3.000
 KBT  H2A   C2   C1    109.32  3.000
 KBT  H2    C2   C1    109.59  3.000
 KBT  C3    C2   C1    112.40  3.000
 KBT  H3B   C3   H3A   107.67  3.000
 KBT  H3B   C3   H3    107.65  3.000
 KBT  H3A   C3   H3    107.60  3.000
 KBT  H3B   C3   C2    111.30  3.000
 KBT  H3A   C3   C2    111.19  3.000
 KBT  H3    C3   C2    111.24  3.000
 KBT  H4A   C4   H4    105.47  3.000
 KBT  H4A   C4   N5    107.86  3.000
 KBT  H4    C4   N5    108.68  3.000
 KBT  H4A   C4   C1    110.57  3.000
 KBT  H4    C4   C1    110.74  3.000
 KBT  N5    C4   C1    113.19  3.000
 KBT  C25   N5   C6    120.67  3.000
 KBT  C6    N5   C4    122.12  3.000
 KBT  C25   N5   C4    117.10  3.000
 KBT  C18   C6   C7    119.53  3.000
 KBT  C7    C6   N5    115.95  3.000
 KBT  C18   C6   N5    124.52  3.000
 KBT  C9    C7   O8    123.14  3.000
 KBT  C9    C7   C6    117.63  3.000
 KBT  O8    C7   C6    119.22  3.000
 KBT  C17   C9   C10   120.07  3.000
 KBT  C10   C9   C7    120.81  3.000
 KBT  C17   C9   C7    119.12  3.000
 KBT  H10   C10  C11   119.62  3.000
 KBT  H10   C10  C9    121.56  3.000
 KBT  C11   C10  C9    118.81  3.000
 KBT  C14   C11  C12   119.66  3.000
 KBT  C12   C11  C10   119.48  3.000
 KBT  C14   C11  C10   120.86  3.000
 KBT  N13   C12  C11   180.00  3.000
 KBT  H14   C14  C15   119.90  3.000
 KBT  H14   C14  C11   119.48  3.000
 KBT  C15   C14  C11   120.61  3.000
 KBT  C17   C15  C16   121.19  3.000
 KBT  C16   C15  C14   120.54  3.000
 KBT  C17   C15  C14   118.25  3.000
 KBT  H16B  C16  H16A  108.26  3.000
 KBT  H16B  C16  H16   107.39  3.000
 KBT  H16A  C16  H16   107.68  3.000
 KBT  H16B  C16  C15   111.43  3.000
 KBT  H16A  C16  C15   111.45  3.000
 KBT  H16   C16  C15   110.46  3.000
 KBT  H17   C17  C15   119.27  3.000
 KBT  H17   C17  C9    119.34  3.000
 KBT  C15   C17  C9    121.39  3.000
 KBT  C22   C18  C19   120.03  3.000
 KBT  C19   C18  C6    122.60  3.000
 KBT  C22   C18  C6    117.36  3.000
 KBT  H19   C19  C21   105.85  3.000
 KBT  H19   C19  C20   106.09  3.000
 KBT  C21   C19  C20   112.04  3.000
 KBT  H19   C19  C18   107.78  3.000
 KBT  C20   C19  C18   112.45  3.000
 KBT  C21   C19  C18   112.12  3.000
 KBT  H20B  C20  H20A  107.51  3.000
 KBT  H20B  C20  H20   108.17  3.000
 KBT  H20A  C20  H20   107.97  3.000
 KBT  H20B  C20  C19   111.31  3.000
 KBT  H20A  C20  C19   109.72  3.000
 KBT  H20   C20  C19   111.99  3.000
 KBT  H21B  C21  H21A  107.79  3.000
 KBT  H21B  C21  H21   108.32  3.000
 KBT  H21A  C21  H21   107.69  3.000
 KBT  H21B  C21  C19   111.97  3.000
 KBT  H21A  C21  C19   109.83  3.000
 KBT  H21   C21  C19   111.08  3.000
 KBT  N24   C22  O23   119.77  3.000
 KBT  N24   C22  C18   114.49  3.000
 KBT  O23   C22  C18   125.74  3.000
 KBT  HN24  N24  C25   115.31  3.000
 KBT  HN24  N24  C22   116.42  3.000
 KBT  C25   N24  C22   128.25  3.000
 KBT  O26   C25  N24   122.35  3.000
 KBT  O26   C25  N5    122.99  3.000
 KBT  N24   C25  N5    114.67  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
 KBT  CONST_01  C14   C15  C17  C9      0.00   0.0  0
 KBT  CONST_02  C14   C11  C10  C9      0.00   0.0  0
 KBT  CONST_03  C15   C17  C9   C10     0.00   0.0  0
 KBT  CONST_04  C15   C14  C11  C10     0.00   0.0  0
 KBT  CONST_05  C17   C9   C10  C11     0.00   0.0  0
 KBT  CONST_06  C17   C15  C14  C11     0.00   0.0  0
 KBT  CONST_07  C22   N24  C25  N5      0.00   0.0  0
 KBT  CONST_08  N24   C25  N5   C6      0.00   0.0  0
 KBT  CONST_09  C25   N24  C22  C18     0.00   0.0  0
 KBT  CONST_10  C15   C17  C9   C7    180.00   0.0  0
 KBT  CONST_11  C11   C10  C9   C7    180.00   0.0  0
 KBT  CONST_12  C16   C15  C17  C9    180.00   0.0  0
 KBT  CONST_13  C12   C11  C10  C9    180.00   0.0  0
 KBT  CONST_14  C16   C15  C14  C11   180.00   0.0  0
 KBT  CONST_15  C15   C14  C11  C12   180.00   0.0  0
 KBT  CONST_16  N24   C25  N5   C4    180.00   0.0  0
 KBT  CONST_17  O26   C25  N5   C6    180.00   0.0  0
 KBT  CONST_18  O26   C25  N24  C22   180.00   0.0  0
 KBT  CONST_19  C25   N24  C22  O23   180.00   0.0  0
 KBT  CONST_20  H17   C17  C9   C10   180.00   0.0  0
 KBT  CONST_21  H14   C14  C11  C10   180.00   0.0  0
 KBT  CONST_22  H10   C10  C11  C14   180.00   0.0  0
 KBT  CONST_23  HN24  N24  C25  N5    180.00   0.0  0
 KBT  CONST_24  O26   C25  N5   C4      0.00   0.0  0
 KBT  Var_01    C9    C7   C6   N5     94.98  30.0  2
 KBT  Var_02    C17   C9   C7   C6    177.05  30.0  2
 KBT  Var_03    C25   N5   C4   C1    -82.51  30.0  2
 KBT  Var_04    C21   C19  C18  C6   -114.16  30.0  3
 KBT  Var_05    H16   C16  C15  C14    82.61  30.0  2
 KBT  Var_06    N5    C4   C1   C2   -174.86  30.0  3
 KBT  Var_07    H21   C21  C19  C18    53.96  30.0  3
 KBT  Var_08    H20   C20  C19  C18    68.52  30.0  3
 KBT  Var_09    C4    C1   C2   C3   -177.27  30.0  1
 KBT  Var_10    H3    C3   C2   C1    -58.12  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
 KBT  plan-1  C7    0.020
 KBT  plan-1  C9    0.020
 KBT  plan-1  C10   0.020
 KBT  plan-1  C11   0.020
 KBT  plan-1  C12   0.020
 KBT  plan-1  N13   0.020
 KBT  plan-1  C14   0.020
 KBT  plan-1  C15   0.020
 KBT  plan-1  C16   0.020
 KBT  plan-1  C17   0.020
 KBT  plan-1  H10   0.020
 KBT  plan-1  H14   0.020
 KBT  plan-1  H17   0.020
 KBT  plan-2  C4    0.020
 KBT  plan-2  N5    0.020
 KBT  plan-2  C6    0.020
 KBT  plan-2  C7    0.020
 KBT  plan-2  C18   0.020
 KBT  plan-2  C19   0.020
 KBT  plan-2  C22   0.020
 KBT  plan-2  O23   0.020
 KBT  plan-2  N24   0.020
 KBT  plan-2  C25   0.020
 KBT  plan-2  O26   0.020
 KBT  plan-2  HN24  0.020
 KBT  plan-3  C6    0.020
 KBT  plan-3  C7    0.020
 KBT  plan-3  O8    0.020
 KBT  plan-3  C9    0.020

