# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 20:03:48 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-[3-[(2-azanyl-6-fluoro-pyridin-4-yl)methyl]-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: CC(C)C1=C(N(Cc2cc(N)nc(F)c2)C(=O)NC1=O)C(=O)c3cc(C)cc(c3)C#N
#
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
 KR1  KR1  3-[3-[(2-azanyl-6-fluoro-pyridin-4-yl)methyl]-2,6-dioxo-5-propan-2-yl-pyrimidin-4-yl]carbonyl-5-methyl-benzenecarbonitrile  ligand  51  31  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KR1
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
 KR1  F1    F  F     0  -0.303   2.5238  -2.0414  -2.3012
 KR1  N1    N  NS    0  -0.241  -0.7786  -2.0230  -4.0234
 KR1  O1    O  O     0  -0.335  -1.0968   0.5376   2.5696
 KR1  C2    C  CR16  0  -0.276  -1.9348  -2.9759  -0.8768
 KR1  N2    N  NR16  0  -0.730   1.0104   3.7563  -0.3394
 KR1  O2    O  O     0  -0.439  -0.9083   4.6492  -1.0937
 KR1  C3    C  CR6   0   0.048  -1.3459  -1.8864  -1.5108
 KR1  N3    N  NR6   0  -0.574   1.1154   1.7790   0.8506
 KR1  C4    C  CR16  0  -0.289  -1.0294  -0.7318  -0.8026
 KR1  C5    C  CR6   0   0.022  -1.3043  -0.6860   0.5563
 KR1  N5    N  N     0  -0.481   1.7700  -2.9828  -0.4325
 KR1  C6    C  CR16  0  -0.291  -1.9083  -1.7761   1.1842
 KR1  C7    C  CR6   0   0.122  -2.2287  -2.9290   0.4832
 KR1  C8    C  C     0   0.303  -0.9105   0.4811   1.3776
 KR1  C9    C  CR6   0   0.288  -0.2500   1.6617   0.6939
 KR1  C10   C  CH3   0  -0.722  -2.8735  -4.0990   1.1619
 KR1  C11   C  CR6   0  -0.124  -1.0202   2.5623   0.0467
 KR1  C12   C  CR6   0   0.580  -0.3590   3.7340  -0.5116
 KR1  C13   C  CR6   0   0.731   1.7985   2.8453   0.3034
 KR1  C14   C  CH1   0  -0.337  -2.5224   2.4287  -0.0626
 KR1  C15   C  CH3   0  -0.641  -3.2379   3.4808   0.7874
 KR1  C16   C  CH3   0  -0.647  -3.0212   2.4241  -1.5079
 KR1  C17   C  CH2   0  -0.422   1.8887   0.7767   1.5880
 KR1  C18   C  CR6   0   0.192   1.8974  -0.5544   0.8882
 KR1  C19   C  CR16  0  -0.438   1.4833  -1.6835   1.5562
 KR1  C20   C  CR6   0   0.508   1.4165  -2.9021   0.8522
 KR1  C21   C  CR6   0   0.583   2.1820  -1.8915  -1.0166
 KR1  C22   C  CR16  0  -0.531   2.2773  -0.6395  -0.4533
 KR1  H2    H  HCR6  0   0.285  -2.1595  -3.8679  -1.4479
 KR1  HN2   H  HNR6  0   0.430   1.5017   4.5472  -0.7391
 KR1  H4    H  HCR6  0   0.295  -0.5565   0.0983  -1.3093
 KR1  HN4   H  HNH2  0   0.396   0.7993  -4.8421   0.8922
 KR1  HN4A  H  HNH2  0   0.404   0.5807  -3.9947   2.3651
 KR1  H6    H  HCR6  0   0.278  -2.1112  -1.7292   2.2468
 KR1  H10   H  HCH3  0   0.262  -3.9476  -4.1121   0.9704
 KR1  H10A  H  HCH3  0   0.254  -2.4660  -5.0414   0.7978
 KR1  H10B  H  HCH3  0   0.254  -2.7308  -4.0614   2.2405
 KR1  H14   H  HCH1  0   0.248  -2.8061   1.4597   0.3552
 KR1  H15   H  HCH3  0   0.233  -3.0196   4.4928   0.4501
 KR1  H15A  H  HCH3  0   0.234  -4.3170   3.3341   0.7278
 KR1  H15B  H  HCH3  0   0.232  -2.9480   3.4007   1.8357
 KR1  H16   H  HCH3  0   0.238  -2.8907   3.3904  -1.9894
 KR1  H16A  H  HCH3  0   0.227  -2.5037   1.6737  -2.1070
 KR1  H16B  H  HCH3  0   0.234  -4.0840   2.1802  -1.5254
 KR1  H17   H  HCH2  0   0.323   2.9035   1.1561   1.6783
 KR1  H17A  H  HCH2  0   0.306   1.4973   0.6841   2.5995
 KR1  H19   H  HCR6  0   0.280   1.1691  -1.6345   2.5910
 KR1  H22   H  HCR6  0   0.276   2.6234   0.2133  -1.0207
 KR1  N4    N  NH2   0  -0.830   0.9994  -4.0319   1.4526
 KR1  O3    O  O     0  -0.475   3.0025   2.9762   0.3782
 KR1  C1    C  CSP   0   0.055  -1.0333  -1.9623  -2.9019

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
 KR1  C3   C1    single    1.428  0.020  1.428
 KR1  C1   N1    triple    1.152  0.020  1.152
 KR1  C21  F1    single    1.338  0.020  1.338
 KR1  O1   C8    double    1.208  0.020  1.208
 KR1  C7   C2    aromatic  1.392  0.020  1.392
 KR1  C3   C2    aromatic  1.391  0.020  1.391
 KR1  C2   H2    single    0.930  0.020  1.080
 KR1  N2   C12   single    1.380  0.020  1.380
 KR1  N2   C13   single    1.365  0.020  1.365
 KR1  N2   HN2   single    0.860  0.020  1.020
 KR1  O2   C12   double    1.216  0.020  1.216
 KR1  C4   C3    aromatic  1.391  0.020  1.391
 KR1  C13  N3    single    1.379  0.020  1.379
 KR1  N3   C9    single    1.379  0.020  1.379
 KR1  N3   C17   single    1.465  0.020  1.465
 KR1  O3   C13   double    1.213  0.020  1.213
 KR1  C5   C4    aromatic  1.387  0.020  1.387
 KR1  C4   H4    single    0.930  0.020  1.080
 KR1  N4   C20   single    1.346  0.020  1.346
 KR1  N4   HN4   single    0.890  0.020  1.040
 KR1  N4   HN4A  single    0.890  0.020  1.040
 KR1  C8   C5    single    1.480  0.020  1.480
 KR1  C5   C6    aromatic  1.396  0.020  1.396
 KR1  C20  N5    aromatic  1.335  0.020  1.335
 KR1  N5   C21   aromatic  1.305  0.020  1.305
 KR1  C6   C7    aromatic  1.387  0.020  1.387
 KR1  C6   H6    single    0.930  0.020  1.080
 KR1  C7   C10   single    1.498  0.020  1.498
 KR1  C9   C8    single    1.516  0.020  1.516
 KR1  C11  C9    double    1.350  0.020  1.350
 KR1  C10  H10   single    0.970  0.020  1.090
 KR1  C10  H10A  single    0.970  0.020  1.090
 KR1  C10  H10B  single    0.970  0.020  1.090
 KR1  C12  C11   single    1.457  0.020  1.457
 KR1  C11  C14   single    1.512  0.020  1.512
 KR1  C15  C14   single    1.530  0.020  1.530
 KR1  C14  C16   single    1.529  0.020  1.529
 KR1  C14  H14   single    0.970  0.020  1.090
 KR1  C15  H15   single    0.970  0.020  1.090
 KR1  C15  H15A  single    0.970  0.020  1.090
 KR1  C15  H15B  single    0.970  0.020  1.090
 KR1  C16  H16   single    0.970  0.020  1.090
 KR1  C16  H16A  single    0.970  0.020  1.090
 KR1  C16  H16B  single    0.970  0.020  1.090
 KR1  C18  C17   single    1.504  0.020  1.504
 KR1  C17  H17   single    0.970  0.020  1.090
 KR1  C17  H17A  single    0.970  0.020  1.090
 KR1  C19  C18   aromatic  1.376  0.020  1.376
 KR1  C18  C22   aromatic  1.397  0.020  1.397
 KR1  C20  C19   aromatic  1.409  0.020  1.409
 KR1  C19  H19   single    0.930  0.020  1.080
 KR1  C21  C22   aromatic  1.376  0.020  1.376
 KR1  C22  H22   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
 KR1  H2    C2   C7    119.95  3.000
 KR1  H2    C2   C3    119.51  3.000
 KR1  C7    C2   C3    120.54  3.000
 KR1  HN2   N2   C13   115.25  3.000
 KR1  HN2   N2   C12   116.39  3.000
 KR1  C13   N2   C12   128.36  3.000
 KR1  C4    C3   C2    120.95  3.000
 KR1  C4    C3   C1    119.36  3.000
 KR1  C2    C3   C1    119.67  3.000
 KR1  C17   N3   C13   117.84  3.000
 KR1  C17   N3   C9    121.43  3.000
 KR1  C13   N3   C9    120.72  3.000
 KR1  H4    C4   C5    121.35  3.000
 KR1  H4    C4   C3    119.88  3.000
 KR1  C5    C4   C3    118.76  3.000
 KR1  C8    C5   C6    118.77  3.000
 KR1  C6    C5   C4    120.05  3.000
 KR1  C8    C5   C4    121.12  3.000
 KR1  C21   N5   C20   117.64  3.000
 KR1  H6    C6   C7    119.26  3.000
 KR1  H6    C6   C5    119.26  3.000
 KR1  C7    C6   C5    121.47  3.000
 KR1  C10   C7   C6    121.30  3.000
 KR1  C10   C7   C2    120.47  3.000
 KR1  C6    C7   C2    118.23  3.000
 KR1  C9    C8   C5    118.67  3.000
 KR1  C9    C8   O1    118.42  3.000
 KR1  C5    C8   O1    122.92  3.000
 KR1  C11   C9   C8    119.15  3.000
 KR1  C11   C9   N3    124.22  3.000
 KR1  C8    C9   N3    116.51  3.000
 KR1  H10B  C10  H10A  108.18  3.000
 KR1  H10B  C10  H10   107.66  3.000
 KR1  H10A  C10  H10   107.41  3.000
 KR1  H10B  C10  C7    111.43  3.000
 KR1  H10A  C10  C7    111.29  3.000
 KR1  H10   C10  C7    110.70  3.000
 KR1  C14   C11  C12   119.63  3.000
 KR1  C14   C11  C9    122.85  3.000
 KR1  C12   C11  C9    117.47  3.000
 KR1  C11   C12  O2    125.72  3.000
 KR1  C11   C12  N2    114.55  3.000
 KR1  O2    C12  N2    119.73  3.000
 KR1  O3    C13  N3    123.39  3.000
 KR1  O3    C13  N2    121.99  3.000
 KR1  N3    C13  N2    114.62  3.000
 KR1  H14   C14  C16   105.91  3.000
 KR1  H14   C14  C15   106.02  3.000
 KR1  C16   C14  C15   112.00  3.000
 KR1  H14   C14  C11   107.98  3.000
 KR1  C16   C14  C11   113.12  3.000
 KR1  C15   C14  C11   111.32  3.000
 KR1  H15B  C15  H15A  107.80  3.000
 KR1  H15B  C15  H15   108.22  3.000
 KR1  H15A  C15  H15   107.85  3.000
 KR1  H15B  C15  C14   111.05  3.000
 KR1  H15A  C15  C14   109.86  3.000
 KR1  H15   C15  C14   111.91  3.000
 KR1  H16B  C16  H16A  107.44  3.000
 KR1  H16B  C16  H16   107.98  3.000
 KR1  H16A  C16  H16   108.12  3.000
 KR1  H16B  C16  C14   109.49  3.000
 KR1  H16A  C16  C14   111.50  3.000
 KR1  H16   C16  C14   112.13  3.000
 KR1  H17A  C17  H17   106.75  3.000
 KR1  H17A  C17  C18   111.05  3.000
 KR1  H17   C17  C18   110.01  3.000
 KR1  H17A  C17  N3    109.64  3.000
 KR1  H17   C17  N3    107.20  3.000
 KR1  C18   C17  N3    111.98  3.000
 KR1  C22   C18  C19   119.89  3.000
 KR1  C22   C18  C17   120.16  3.000
 KR1  C19   C18  C17   119.92  3.000
 KR1  H19   C19  C20   120.20  3.000
 KR1  H19   C19  C18   120.95  3.000
 KR1  C20   C19  C18   118.78  3.000
 KR1  C19   C20  N5    121.37  3.000
 KR1  C19   C20  N4    121.20  3.000
 KR1  N5    C20  N4    117.43  3.000
 KR1  C22   C21  N5    126.85  3.000
 KR1  C22   C21  F1    118.51  3.000
 KR1  N5    C21  F1    114.64  3.000
 KR1  H22   C22  C21   121.66  3.000
 KR1  H22   C22  C18   122.89  3.000
 KR1  C21   C22  C18   115.44  3.000
 KR1  HN4A  N4   HN4   116.95  3.000
 KR1  HN4A  N4   C20   120.22  3.000
 KR1  HN4   N4   C20   119.32  3.000
 KR1  C3    C1   N1    180.00  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
 KR1  CONST_01  C5    C6   C7   C2      0.00   0.0  0
 KR1  CONST_02  C5    C4   C3   C2      0.00   0.0  0
 KR1  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 KR1  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 KR1  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 KR1  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 KR1  CONST_07  C18   C19  C20  N5      0.00   0.0  0
 KR1  CONST_08  C18   C22  C21  N5      0.00   0.0  0
 KR1  CONST_09  C21   C22  C18  C19     0.00   0.0  0
 KR1  CONST_10  C21   N5   C20  C19     0.00   0.0  0
 KR1  CONST_11  C22   C21  N5   C20     0.00   0.0  0
 KR1  CONST_12  C22   C18  C19  C20     0.00   0.0  0
 KR1  CONST_13  C9    N3   C13  N2      0.00   0.0  0
 KR1  CONST_14  C12   N2   C13  N3      0.00   0.0  0
 KR1  CONST_15  C13   N2   C12  C11     0.00   0.0  0
 KR1  CONST_16  C7    C2   C3   C1    180.00   0.0  0
 KR1  CONST_17  C5    C4   C3   C1    180.00   0.0  0
 KR1  CONST_18  C20   N5   C21  F1    180.00   0.0  0
 KR1  CONST_19  C18   C22  C21  F1    180.00   0.0  0
 KR1  CONST_20  C10   C7   C2   C3    180.00   0.0  0
 KR1  CONST_21  C8    C5   C4   C3    180.00   0.0  0
 KR1  CONST_22  C21   N5   C20  N4    180.00   0.0  0
 KR1  CONST_23  C18   C19  C20  N4    180.00   0.0  0
 KR1  CONST_24  C10   C7   C6   C5    180.00   0.0  0
 KR1  CONST_25  C8    C5   C6   C7    180.00   0.0  0
 KR1  CONST_26  C20   C19  C18  C17   180.00   0.0  0
 KR1  CONST_27  C21   C22  C18  C17   180.00   0.0  0
 KR1  CONST_28  C17   N3   C13  N2    180.00   0.0  0
 KR1  CONST_29  C13   N2   C12  O2    180.00   0.0  0
 KR1  CONST_30  C12   N2   C13  O3    180.00   0.0  0
 KR1  CONST_31  C9    N3   C13  O3    180.00   0.0  0
 KR1  CONST_32  H6    C6   C7   C2    180.00   0.0  0
 KR1  CONST_33  H4    C4   C3   C2    180.00   0.0  0
 KR1  CONST_34  H2    C2   C3   C4    180.00   0.0  0
 KR1  CONST_35  H19   C19  C20  N5    180.00   0.0  0
 KR1  CONST_36  H22   C22  C21  N5    180.00   0.0  0
 KR1  CONST_37  HN2   N2   C13  N3    180.00   0.0  0
 KR1  CONST_38  C17   N3   C13  O3      0.00   0.0  0
 KR1  CONST_39  HN4   N4   C20  N5      0.00   0.0  0
 KR1  CONST_40  HN4A  N4   C20  N5    180.00   0.0  0
 KR1  Var_01    C5    C8   C9   N3   -103.20  30.0  2
 KR1  Var_02    C19   C18  C17  N3   -124.94  30.0  2
 KR1  Var_03    C9    C8   C5   C4      2.63  30.0  2
 KR1  Var_04    C18   C17  N3   C9     66.33  30.0  3
 KR1  Var_05    C15   C14  C11  C9    109.55  30.0  3
 KR1  Var_06    H10   C10  C7   C2    -79.76  30.0  2
 KR1  Var_07    H15   C15  C14  C11    62.83  30.0  3
 KR1  Var_08    H16   C16  C14  C11   -68.39  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
 KR1  plan-1  N2    0.020
 KR1  plan-1  O2    0.020
 KR1  plan-1  N3    0.020
 KR1  plan-1  C8    0.020
 KR1  plan-1  C9    0.020
 KR1  plan-1  C11   0.020
 KR1  plan-1  C12   0.020
 KR1  plan-1  C13   0.020
 KR1  plan-1  C14   0.020
 KR1  plan-1  C17   0.020
 KR1  plan-1  HN2   0.020
 KR1  plan-1  O3    0.020
 KR1  plan-2  N1    0.020
 KR1  plan-2  C2    0.020
 KR1  plan-2  C3    0.020
 KR1  plan-2  C4    0.020
 KR1  plan-2  C5    0.020
 KR1  plan-2  C6    0.020
 KR1  plan-2  C7    0.020
 KR1  plan-2  C8    0.020
 KR1  plan-2  C10   0.020
 KR1  plan-2  H2    0.020
 KR1  plan-2  H4    0.020
 KR1  plan-2  H6    0.020
 KR1  plan-2  C1    0.020
 KR1  plan-3  F1    0.020
 KR1  plan-3  N5    0.020
 KR1  plan-3  C17   0.020
 KR1  plan-3  C18   0.020
 KR1  plan-3  C19   0.020
 KR1  plan-3  C20   0.020
 KR1  plan-3  C21   0.020
 KR1  plan-3  C22   0.020
 KR1  plan-3  H19   0.020
 KR1  plan-3  H22   0.020
 KR1  plan-3  N4    0.020
 KR1  plan-4  C20   0.020
 KR1  plan-4  HN4   0.020
 KR1  plan-4  HN4A  0.020
 KR1  plan-4  N4    0.020
 KR1  plan-5  O1    0.020
 KR1  plan-5  C5    0.020
 KR1  plan-5  C8    0.020
 KR1  plan-5  C9    0.020

