# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 20:43:52 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-[1H-indazol-4-yl(2-{[3-(4-methyl-1,3-oxazol-5-yl)phenyl]amino}pyrimidin-4-yl)amino]propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncoc1c2cccc(Nc3nccc(n3)N(CCCO)c4cccc5[nH]ncc45)c2
#
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
 4DK  4DK  3-[1H-indazol-4-yl(2-{[3-(4-methyl-1,3-oxazol-5-yl)phenyl]amino}pyrimidin-4-yl)amino]propan-1-ol  ligand  56  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4DK
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
 4DK  C01  C  CH3   0  -0.765   8.0177  -0.8489   0.1918
 4DK  C05  C  CR5   0   0.104   7.0991   0.2289  -0.2600
 4DK  N06  N  N     0  -0.425   7.5640   1.4983  -0.5446
 4DK  C07  C  CR15  0   0.160   6.5206   2.1723  -0.8724
 4DK  O09  O  O     0  -0.403   5.3897   1.4703  -0.8355
 4DK  C10  C  CR5   0   0.305   5.7511   0.2153  -0.4481
 4DK  C11  C  CR6   0   0.036   4.7064  -0.7861  -0.3054
 4DK  C12  C  CR16  0  -0.355   5.0167  -2.1408  -0.4168
 4DK  C14  C  CR16  0  -0.226   4.0102  -3.0815  -0.2542
 4DK  C16  C  CR16  0  -0.363   2.7092  -2.6919  -0.0017
 4DK  C18  C  CR6   0   0.390   2.3812  -1.3328   0.0955
 4DK  N19  N  NH1   0  -0.777   1.0498  -1.0380   0.3501
 4DK  C21  C  CR6   0   0.601   0.3747   0.1474   0.4238
 4DK  N22  N  N     0  -0.493   1.0229   1.2932   0.2612
 4DK  C23  C  CR16  0  -0.005   0.2621   2.3856   0.3382
 4DK  C25  C  CR16  0  -0.441  -1.0909   2.3709   0.5640
 4DK  C27  C  CR6   0   0.539  -1.6746   1.0959   0.7288
 4DK  N28  N  N     0  -0.517  -0.9261   0.0024   0.6627
 4DK  N29  N  NT    0  -0.589  -2.9992   0.9234   0.9745
 4DK  C30  C  CH2   0  -0.345  -3.9057   2.0555   1.1040
 4DK  C33  C  CH2   0  -0.467  -4.4142   2.5653  -0.2392
 4DK  C36  C  CH2   0  -0.140  -5.3669   3.7312  -0.0582
 4DK  O39  O  OH1   0  -0.672  -5.7969   4.1659  -1.3290
 4DK  C41  C  CR6   0   0.259  -3.5790  -0.3674   0.9039
 4DK  C42  C  CR16  0  -0.320  -4.2213  -0.9096   1.9941
 4DK  C44  C  CR16  0  -0.274  -4.8623  -2.1627   1.9163
 4DK  C46  C  CR16  0  -0.296  -4.8707  -2.9063   0.7596
 4DK  C48  C  CR56  0   0.410  -4.2139  -2.3512  -0.3449
 4DK  N49  N  NR15  0  -0.548  -4.0471  -2.7968  -1.6121
 4DK  N51  N  N     0  -0.226  -3.3639  -1.9356  -2.3674
 4DK  C52  C  CR15  0  -0.130  -3.0680  -0.9127  -1.6056
 4DK  C54  C  CR56  0  -0.068  -3.5778  -1.0996  -0.2943
 4DK  C55  C  CR16  0  -0.375   3.3914  -0.3835  -0.0539
 4DK  H02  H  HCH3  0   0.255   8.3976  -1.4345  -0.6478
 4DK  H04  H  HCH3  0   0.261   8.8765  -0.4182   0.7045
 4DK  H03  H  HCH3  0   0.251   7.5254  -1.5379   0.8770
 4DK  H08  H  HCR5  0   0.295   6.4585   3.2095  -1.1647
 4DK  H13  H  HCR6  0   0.260   6.0198  -2.4645  -0.6561
 4DK  H15  H  HCR6  0   0.262   4.2410  -4.1351  -0.3406
 4DK  H17  H  HCR6  0   0.270   1.9354  -3.4420   0.1125
 4DK  H20  H  HNH1  0   0.406   0.4467  -1.8380   0.4668
 4DK  H24  H  HCR6  0   0.268   0.7727   3.3321   0.1999
 4DK  H26  H  HCR6  0   0.275  -1.6505   3.2923   0.5920
 4DK  H32  H  HCH2  0   0.275  -4.7445   1.7347   1.7223
 4DK  H31  H  HCH2  0   0.256  -3.4108   2.8510   1.6638
 4DK  H34  H  HCH2  0   0.237  -3.5706   2.8770  -0.8619
 4DK  H35  H  HCH2  0   0.238  -4.9206   1.7520  -0.7665
 4DK  H38  H  HCH2  0   0.194  -6.2133   3.4148   0.5662
 4DK  H37  H  HCH2  0   0.195  -4.8554   4.5339   0.4895
 4DK  H40  H  HOH1  0   0.454  -6.3829   4.9181  -1.2068
 4DK  H43  H  HCR6  0   0.264  -4.2374  -0.3652   2.9299
 4DK  H45  H  HCR6  0   0.264  -5.3569  -2.5475   2.7983
 4DK  H47  H  HCR6  0   0.272  -5.3645  -3.8672   0.7064
 4DK  H50  H  HNR5  0   0.417  -4.3814  -3.6579  -2.0124
 4DK  H53  H  HCR5  0   0.262  -2.5088  -0.0791  -2.0010
 4DK  H56  H  HCR6  0   0.286   3.1484   0.6624   0.0369

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
 4DK  C44  C46  aromatic  1.375  0.020  1.375
 4DK  C44  C42  aromatic  1.410  0.020  1.410
 4DK  C07  N06  aromatic  1.285  0.020  1.285
 4DK  C07  O09  aromatic  1.332  0.020  1.332
 4DK  C46  C48  aromatic  1.400  0.020  1.400
 4DK  N06  C05  aromatic  1.381  0.020  1.381
 4DK  C42  C41  aromatic  1.377  0.020  1.377
 4DK  C33  C30  single    1.524  0.020  1.524
 4DK  C33  C36  single    1.516  0.020  1.516
 4DK  O09  C10  aromatic  1.362  0.020  1.362
 4DK  C30  N29  single    1.456  0.020  1.456
 4DK  C48  N49  aromatic  1.354  0.020  1.354
 4DK  C48  C54  aromatic  1.405  0.020  1.405
 4DK  C41  C54  aromatic  1.404  0.020  1.404
 4DK  C41  N29  single    1.417  0.020  1.417
 4DK  C05  C10  aromatic  1.361  0.020  1.361
 4DK  C05  C01  single    1.487  0.020  1.487
 4DK  N49  N51  aromatic  1.334  0.020  1.334
 4DK  C54  C52  aromatic  1.419  0.020  1.419
 4DK  C10  C11  single    1.454  0.020  1.454
 4DK  N29  C27  single    1.358  0.020  1.358
 4DK  O39  C36  single    1.410  0.020  1.410
 4DK  N51  C52  aromatic  1.309  0.020  1.309
 4DK  C11  C55  aromatic  1.398  0.020  1.398
 4DK  C11  C12  aromatic  1.394  0.020  1.394
 4DK  C27  N28  aromatic  1.327  0.020  1.327
 4DK  C27  C25  aromatic  1.412  0.020  1.412
 4DK  C55  C18  aromatic  1.394  0.020  1.394
 4DK  N28  C21  aromatic  1.331  0.020  1.331
 4DK  C12  C14  aromatic  1.387  0.020  1.387
 4DK  C25  C23  aromatic  1.372  0.020  1.372
 4DK  C18  N19  single    1.387  0.020  1.387
 4DK  C18  C16  aromatic  1.402  0.020  1.402
 4DK  C14  C16  aromatic  1.381  0.020  1.381
 4DK  C21  N19  single    1.366  0.020  1.366
 4DK  C21  N22  aromatic  1.326  0.020  1.326
 4DK  C23  N22  aromatic  1.333  0.020  1.333
 4DK  C01  H02  single    0.970  0.020  1.090
 4DK  C01  H04  single    0.970  0.020  1.090
 4DK  C01  H03  single    0.970  0.020  1.090
 4DK  C07  H08  single    0.930  0.020  1.080
 4DK  C12  H13  single    0.930  0.020  1.080
 4DK  C14  H15  single    0.930  0.020  1.080
 4DK  C16  H17  single    0.930  0.020  1.080
 4DK  N19  H20  single    0.860  0.020  1.020
 4DK  C23  H24  single    0.930  0.020  1.080
 4DK  C25  H26  single    0.930  0.020  1.080
 4DK  C30  H32  single    0.970  0.020  1.090
 4DK  C30  H31  single    0.970  0.020  1.090
 4DK  C33  H34  single    0.970  0.020  1.090
 4DK  C33  H35  single    0.970  0.020  1.090
 4DK  C36  H38  single    0.970  0.020  1.090
 4DK  C36  H37  single    0.970  0.020  1.090
 4DK  O39  H40  single    0.850  0.020  0.980
 4DK  C42  H43  single    0.930  0.020  1.080
 4DK  C44  H45  single    0.930  0.020  1.080
 4DK  C46  H47  single    0.930  0.020  1.080
 4DK  N49  H50  single    0.860  0.020  1.020
 4DK  C52  H53  single    0.930  0.020  1.080
 4DK  C55  H56  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
 4DK  H03  C01  H04  108.09  3.000
 4DK  H03  C01  H02  107.56  3.000
 4DK  H04  C01  H02  107.45  3.000
 4DK  H03  C01  C05  111.74  3.000
 4DK  H04  C01  C05  110.10  3.000
 4DK  H02  C01  C05  111.72  3.000
 4DK  C10  C05  N06  108.30  3.000
 4DK  C10  C05  C01  130.30  3.000
 4DK  N06  C05  C01  121.39  3.000
 4DK  C07  N06  C05  105.15  3.000
 4DK  H08  C07  O09  117.72  3.000
 4DK  H08  C07  N06  128.32  3.000
 4DK  O09  C07  N06  113.96  3.000
 4DK  C10  O09  C07  105.56  3.000
 4DK  C11  C10  O09  118.15  3.000
 4DK  C11  C10  C05  134.82  3.000
 4DK  O09  C10  C05  107.03  3.000
 4DK  C55  C11  C12  120.23  3.000
 4DK  C12  C11  C10  120.09  3.000
 4DK  C55  C11  C10  119.68  3.000
 4DK  H13  C12  C14  119.76  3.000
 4DK  H13  C12  C11  121.01  3.000
 4DK  C14  C12  C11  119.21  3.000
 4DK  H15  C14  C16  119.34  3.000
 4DK  H15  C14  C12  119.74  3.000
 4DK  C16  C14  C12  120.90  3.000
 4DK  H17  C16  C18  119.79  3.000
 4DK  H17  C16  C14  119.77  3.000
 4DK  C18  C16  C14  120.43  3.000
 4DK  C55  C18  N19  124.78  3.000
 4DK  N19  C18  C16  116.32  3.000
 4DK  C55  C18  C16  118.90  3.000
 4DK  H20  N19  C21  112.74  3.000
 4DK  H20  N19  C18  115.25  3.000
 4DK  C21  N19  C18  131.96  3.000
 4DK  N28  C21  N22  126.43  3.000
 4DK  N22  C21  N19  120.10  3.000
 4DK  N28  C21  N19  113.47  3.000
 4DK  C23  N22  C21  114.95  3.000
 4DK  H24  C23  C25  119.66  3.000
 4DK  H24  C23  N22  116.05  3.000
 4DK  C25  C23  N22  124.30  3.000
 4DK  H26  C25  C27  123.65  3.000
 4DK  H26  C25  C23  120.46  3.000
 4DK  C27  C25  C23  115.89  3.000
 4DK  N29  C27  N28  117.03  3.000
 4DK  N28  C27  C25  120.35  3.000
 4DK  N29  C27  C25  122.61  3.000
 4DK  C27  N28  C21  118.08  3.000
 4DK  C41  N29  C30  117.26  3.000
 4DK  C41  N29  C27  120.39  3.000
 4DK  C30  N29  C27  121.63  3.000
 4DK  H31  C30  H32  105.81  3.000
 4DK  H31  C30  C33  111.07  3.000
 4DK  H32  C30  C33  109.97  3.000
 4DK  H31  C30  N29  109.28  3.000
 4DK  H32  C30  N29  107.50  3.000
 4DK  C33  C30  N29  112.92  3.000
 4DK  H35  C33  H34  107.13  3.000
 4DK  H35  C33  C36  109.78  3.000
 4DK  H34  C33  C36  109.48  3.000
 4DK  H35  C33  C30  109.31  3.000
 4DK  H34  C33  C30  109.86  3.000
 4DK  C36  C33  C30  111.20  3.000
 4DK  H37  C36  H38  106.61  3.000
 4DK  H37  C36  O39  111.48  3.000
 4DK  H38  C36  O39  111.47  3.000
 4DK  H37  C36  C33  109.20  3.000
 4DK  H38  C36  C33  109.30  3.000
 4DK  O39  C36  C33  108.72  3.000
 4DK  H40  O39  C36  108.21  3.000
 4DK  C54  C41  C42  118.08  3.000
 4DK  C54  C41  N29  121.14  3.000
 4DK  C42  C41  N29  120.69  3.000
 4DK  H43  C42  C44  119.20  3.000
 4DK  H43  C42  C41  119.56  3.000
 4DK  C44  C42  C41  121.24  3.000
 4DK  H45  C44  C46  119.38  3.000
 4DK  H45  C44  C42  118.62  3.000
 4DK  C46  C44  C42  122.00  3.000
 4DK  H47  C46  C48  121.85  3.000
 4DK  H47  C46  C44  121.64  3.000
 4DK  C48  C46  C44  116.51  3.000
 4DK  C54  C48  N49  105.73  3.000
 4DK  C54  C48  C46  122.51  3.000
 4DK  N49  C48  C46  131.75  3.000
 4DK  H50  N49  N51  119.82  3.000
 4DK  H50  N49  C48  127.80  3.000
 4DK  N51  N49  C48  112.38  3.000
 4DK  C52  N51  N49  106.90  3.000
 4DK  H53  C52  C54  128.80  3.000
 4DK  H53  C52  N51  120.50  3.000
 4DK  C54  C52  N51  110.70  3.000
 4DK  C52  C54  C48  104.28  3.000
 4DK  C52  C54  C41  136.06  3.000
 4DK  C48  C54  C41  119.66  3.000
 4DK  H56  C55  C18  119.24  3.000
 4DK  H56  C55  C11  120.45  3.000
 4DK  C18  C55  C11  120.31  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
 4DK  CONST_01  O09  C07  N06  C05     0.00   0.0  0
 4DK  CONST_02  C07  O09  C10  C05     0.00   0.0  0
 4DK  CONST_05  C10  O09  C07  N06     0.00   0.0  0
 4DK  CONST_06  O09  C10  C05  N06     0.00   0.0  0
 4DK  CONST_07  C11  C10  C05  N06   180.00   0.0  0
 4DK  CONST_08  C10  C05  N06  C07     0.00   0.0  0
 4DK  CONST_09  C11  C10  O09  C07   180.00   0.0  0
 4DK  CONST_12  C18  C55  C11  C10   180.00   0.0  0
 4DK  CONST_13  C14  C12  C11  C10   180.00   0.0  0
 4DK  CONST_14  C16  C18  C55  C11     0.00   0.0  0
 4DK  CONST_15  C16  C14  C12  C11     0.00   0.0  0
 4DK  CONST_16  C18  C55  C11  C12     0.00   0.0  0
 4DK  CONST_17  C18  C16  C14  C12     0.00   0.0  0
 4DK  CONST_18  C55  C11  C12  C14     0.00   0.0  0
 4DK  CONST_19  C55  C18  C16  C14     0.00   0.0  0
 4DK  CONST_20  C25  C27  N28  C21     0.00   0.0  0
 4DK  CONST_21  C25  C23  N22  C21     0.00   0.0  0
 4DK  CONST_22  C27  N28  C21  N22     0.00   0.0  0
 4DK  CONST_23  C27  C25  C23  N22     0.00   0.0  0
 4DK  CONST_24  N28  C27  C25  C23     0.00   0.0  0
 4DK  CONST_25  N28  C21  N22  C23     0.00   0.0  0
 4DK  CONST_26  C46  C44  C42  C41     0.00   0.0  0
 4DK  CONST_27  C46  C48  C54  C41     0.00   0.0  0
 4DK  CONST_28  N49  C48  C54  C41   180.00   0.0  0
 4DK  CONST_29  N51  C52  C54  C41   180.00   0.0  0
 4DK  CONST_30  C48  C46  C44  C42     0.00   0.0  0
 4DK  CONST_31  C48  C54  C41  C42     0.00   0.0  0
 4DK  CONST_32  C52  C54  C41  C42   180.00   0.0  0
 4DK  CONST_33  N49  C48  C46  C44   180.00   0.0  0
 4DK  CONST_34  C54  C48  C46  C44     0.00   0.0  0
 4DK  CONST_35  C54  C41  C42  C44     0.00   0.0  0
 4DK  CONST_36  N51  N49  C48  C46   180.00   0.0  0
 4DK  CONST_37  C52  C54  C48  C46   180.00   0.0  0
 4DK  CONST_38  C52  N51  N49  C48     0.00   0.0  0
 4DK  CONST_39  N51  C52  C54  C48     0.00   0.0  0
 4DK  CONST_40  C52  C54  C48  N49     0.00   0.0  0
 4DK  CONST_41  C54  C52  N51  N49     0.00   0.0  0
 4DK  CONST_42  C54  C48  N49  N51     0.00   0.0  0
 4DK  CONST_43  C07  N06  C05  C01   180.00   0.0  0
 4DK  CONST_44  O09  C10  C05  C01   180.00   0.0  0
 4DK  CONST_45  C11  C10  C05  C01     0.00   0.0  0
 4DK  CONST_46  N19  C18  C55  C11   180.00   0.0  0
 4DK  CONST_47  N19  C18  C16  C14   180.00   0.0  0
 4DK  CONST_48  C27  N28  C21  N19   180.00   0.0  0
 4DK  CONST_49  C23  N22  C21  N19   180.00   0.0  0
 4DK  CONST_50  N29  C27  N28  C21   180.00   0.0  0
 4DK  CONST_51  N29  C27  C25  C23   180.00   0.0  0
 4DK  CONST_52  C44  C42  C41  N29   180.00   0.0  0
 4DK  CONST_53  C48  C54  C41  N29   180.00   0.0  0
 4DK  CONST_54  C52  C54  C41  N29     0.00   0.0  0
 4DK  CONST_55  H08  C07  N06  C05   180.00   0.0  0
 4DK  CONST_56  H56  C55  C11  C10     0.00   0.0  0
 4DK  CONST_57  H13  C12  C11  C10     0.00   0.0  0
 4DK  CONST_58  H15  C14  C12  C11   180.00   0.0  0
 4DK  CONST_59  H17  C16  C14  C12   180.00   0.0  0
 4DK  CONST_60  H24  C23  N22  C21   180.00   0.0  0
 4DK  CONST_61  H26  C25  C23  N22   180.00   0.0  0
 4DK  CONST_62  H45  C44  C42  C41   180.00   0.0  0
 4DK  CONST_63  H53  C52  C54  C41     0.00   0.0  0
 4DK  CONST_64  H47  C46  C44  C42   180.00   0.0  0
 4DK  CONST_65  H43  C42  C44  C46   180.00   0.0  0
 4DK  CONST_66  H50  N49  C48  C46     0.00   0.0  0
 4DK  Var_01    C21  N19  C18  C16  -175.39  30.0  2
 4DK  Var_02    N28  C21  N19  C18   178.48  30.0  1
 4DK  Var_03    C41  N29  C27  C25   169.08  30.0  3
 4DK  Var_04    C42  C41  N29  C27   121.73  30.0  2
 4DK  Var_05    H02  C01  C05  N06   -91.77  30.0  2
 4DK  Var_06    C33  C30  N29  C27    84.09  30.0  2
 4DK  Var_07    C36  C33  C30  N29   179.29  30.0  1
 4DK  Var_08    O39  C36  C33  C30   179.62  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
 4DK  plan-1  C01  0.020
 4DK  plan-1  C05  0.020
 4DK  plan-1  N06  0.020
 4DK  plan-1  C07  0.020
 4DK  plan-1  O09  0.020
 4DK  plan-1  C10  0.020
 4DK  plan-1  C11  0.020
 4DK  plan-1  H08  0.020
 4DK  plan-2  C10  0.020
 4DK  plan-2  C11  0.020
 4DK  plan-2  C12  0.020
 4DK  plan-2  C14  0.020
 4DK  plan-2  C16  0.020
 4DK  plan-2  C18  0.020
 4DK  plan-2  N19  0.020
 4DK  plan-2  C55  0.020
 4DK  plan-2  H13  0.020
 4DK  plan-2  H15  0.020
 4DK  plan-2  H17  0.020
 4DK  plan-2  H56  0.020
 4DK  plan-3  N19  0.020
 4DK  plan-3  C21  0.020
 4DK  plan-3  N22  0.020
 4DK  plan-3  C23  0.020
 4DK  plan-3  C25  0.020
 4DK  plan-3  C27  0.020
 4DK  plan-3  N28  0.020
 4DK  plan-3  N29  0.020
 4DK  plan-3  H24  0.020
 4DK  plan-3  H26  0.020
 4DK  plan-4  N29  0.020
 4DK  plan-4  C41  0.020
 4DK  plan-4  C42  0.020
 4DK  plan-4  C44  0.020
 4DK  plan-4  C46  0.020
 4DK  plan-4  C48  0.020
 4DK  plan-4  N49  0.020
 4DK  plan-4  N51  0.020
 4DK  plan-4  C52  0.020
 4DK  plan-4  C54  0.020
 4DK  plan-4  H43  0.020
 4DK  plan-4  H45  0.020
 4DK  plan-4  H47  0.020
 4DK  plan-4  H50  0.020
 4DK  plan-4  H53  0.020

