# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:50:59 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-cyclopropyl-3-[1-(2,4-difluorophenyl)-7-methyl-6-oxo-pyrazolo[3,4-b]pyridin-5-yl]-4-methyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=Cc2cnn(c3ccc(F)cc3F)c12)c4cc(ccc4C)C(=O)NC5CC5
#
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
 LHJ  LHJ  N-cyclopropyl-3-[1-(2,4-difluorophenyl)-7-methyl-6-oxo-pyrazolo[3,4-b]pyridin-5-yl]-4-methyl-benzamide  ligand  52  32  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LHJ
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
 LHJ  N1    N  NR6   0  -0.584  -1.4680  -0.2907   0.8344
 LHJ  N3    N  NR5   0  -0.463  -3.2226  -0.4338  -0.8773
 LHJ  C4    C  CR6   0  -0.238   0.7115  -1.0194   0.0055
 LHJ  C5    C  CR16  0  -0.174   0.1794  -1.3179  -1.2058
 LHJ  C6    C  CR15  0  -0.084  -2.0972  -1.2335  -2.5028
 LHJ  C7    C  CH3   0  -0.569  -2.3206   0.1447   1.9336
 LHJ  C8    C  CR6   0   0.091   2.1506  -1.2290   0.2866
 LHJ  C10   C  CR6   0   0.579  -4.4837   1.5352  -0.2482
 LHJ  C13   C  CR16  0  -0.428  -6.5617  -0.0364   0.6754
 LHJ  C15   C  CR16  0  -0.306   3.0835  -0.3999  -0.3199
 LHJ  C17   C  CR16  0  -0.292   4.8761  -1.6054   0.7093
 LHJ  C22   C  CH1   0  -0.077   7.6277   1.2951  -0.8690
 LHJ  C24   C  CH2   0  -0.518   8.5603   2.0324   0.0346
 LHJ  C23   C  CH2   0  -0.482   7.5543   2.7870  -0.7794
 LHJ  N4    N  NH1   0  -0.660   6.6078   0.5039  -0.2641
 LHJ  O2    O  O     0  -0.485   5.0581   0.9432  -1.8374
 LHJ  C16   C  CR6   0  -0.034   4.4507  -0.5658  -0.1104
 LHJ  C18   C  CR16  0  -0.285   3.9485  -2.4470   1.3039
 LHJ  C19   C  CR6   0   0.080   2.5813  -2.2783   1.1119
 LHJ  C3    C  CR6   0   0.556  -0.0997  -0.4535   1.0781
 LHJ  O1    O  O     0  -0.469   0.3681  -0.1350   2.1617
 LHJ  C2    C  CR56  0   0.725  -1.9640  -0.5624  -0.3991
 LHJ  C1    C  CR56  0  -0.185  -1.1936  -1.0798  -1.4288
 LHJ  N2    N  N     0  -0.262  -3.2973  -0.8439  -2.1719
 LHJ  C9    C  CR6   0   0.076  -4.3720   0.1543  -0.3065
 LHJ  C14   C  CR16  0  -0.223  -5.4241  -0.6254   0.1500
 LHJ  C12   C  CR6   0   0.563  -6.6205   1.3444   0.7303
 LHJ  F2    F  F     0  -0.300  -7.7061   1.9257   1.2443
 LHJ  C11   C  CR16  0  -0.569  -5.5977   2.1562   0.2767
 LHJ  H5    H  HCR6  0   0.276   0.7954  -1.7376  -1.9917
 LHJ  H6    H  HCR5  0   0.280  -1.8950  -1.6146  -3.4924
 LHJ  H7    H  HCH3  0   0.289  -1.7841  -0.0002   2.8639
 LHJ  H7A   H  HCH3  0   0.268  -2.5787   1.1989   1.8466
 LHJ  H7B   H  HCH3  0   0.268  -3.2265  -0.4540   1.9626
 LHJ  H13   H  HCR6  0   0.299  -7.3828  -0.6380   1.0394
 LHJ  H15   H  HCR6  0   0.251   2.7372   0.4017  -0.9601
 LHJ  H17   H  HCR6  0   0.257   5.9286  -1.8010   0.8733
 LHJ  H20   H  HCH3  0   0.249   0.9549  -3.6841   1.0062
 LHJ  H20A  H  HCH3  0   0.252   2.1281  -4.0216   2.2761
 LHJ  H20B  H  HCH3  0   0.254   0.9676  -2.7110   2.4677
 LHJ  H22   H  HCH1  0   0.269   8.0483   0.8792  -1.7791
 LHJ  H24   H  HCH2  0   0.259   8.3900   1.9593   1.1018
 LHJ  H24A  H  HCH2  0   0.260   9.6032   2.0777  -0.2495
 LHJ  H23   H  HCH2  0   0.255   7.8982   3.3580  -1.6319
 LHJ  H23A  H  HCH2  0   0.255   6.7071   3.2146  -0.2595
 LHJ  HN4   H  HNH1  0   0.408   6.8264   0.0327   0.5980
 LHJ  H18   H  HCR6  0   0.257   4.2991  -3.2672   1.9183
 LHJ  H14   H  HCR6  0   0.300  -5.3450  -1.7028   0.0987
 LHJ  H11   H  HCR6  0   0.317  -5.6664   3.2348   0.3259
 LHJ  C20   C  CH3   0  -0.748   1.6084  -3.2233   1.7487
 LHJ  C21   C  C     0   0.534   5.3903   0.3573  -0.8163
 LHJ  F1    F  F     0  -0.289  -3.4729   2.2784  -0.6964

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
 LHJ  C2   N1    single    1.357  0.020  1.357
 LHJ  C3   N1    single    1.399  0.020  1.399
 LHJ  N1   C7    single    1.458  0.020  1.458
 LHJ  N2   N3    aromatic  1.360  0.020  1.360
 LHJ  N3   C2    aromatic  1.353  0.020  1.353
 LHJ  N3   C9    single    1.412  0.020  1.412
 LHJ  C5   C4    double    1.356  0.020  1.356
 LHJ  C8   C4    single    1.481  0.020  1.481
 LHJ  C4   C3    single    1.459  0.020  1.459
 LHJ  C5   C1    single    1.411  0.020  1.411
 LHJ  C5   H5    single    0.930  0.020  1.080
 LHJ  C6   C1    aromatic  1.412  0.020  1.412
 LHJ  C6   N2    aromatic  1.304  0.020  1.304
 LHJ  C6   H6    single    0.930  0.020  1.080
 LHJ  C7   H7    single    0.970  0.020  1.090
 LHJ  C7   H7A   single    0.970  0.020  1.090
 LHJ  C7   H7B   single    0.970  0.020  1.090
 LHJ  C15  C8    aromatic  1.388  0.020  1.388
 LHJ  C8   C19   aromatic  1.403  0.020  1.403
 LHJ  F1   C10   single    1.332  0.020  1.332
 LHJ  C10  C9    aromatic  1.387  0.020  1.387
 LHJ  C10  C11   aromatic  1.379  0.020  1.379
 LHJ  C14  C13   aromatic  1.385  0.020  1.385
 LHJ  C12  C13   aromatic  1.383  0.020  1.383
 LHJ  C13  H13   single    0.930  0.020  1.080
 LHJ  C16  C15   aromatic  1.393  0.020  1.393
 LHJ  C15  H15   single    0.930  0.020  1.080
 LHJ  C16  C17   aromatic  1.391  0.020  1.391
 LHJ  C17  C18   aromatic  1.386  0.020  1.386
 LHJ  C17  H17   single    0.930  0.020  1.080
 LHJ  C19  C20   single    1.498  0.020  1.498
 LHJ  C20  H20   single    0.970  0.020  1.090
 LHJ  C20  H20A  single    0.970  0.020  1.090
 LHJ  C20  H20B  single    0.970  0.020  1.090
 LHJ  O2   C21   double    1.223  0.020  1.223
 LHJ  N4   C21   single    1.345  0.020  1.345
 LHJ  C21  C16   single    1.494  0.020  1.494
 LHJ  C23  C22   single    1.496  0.020  1.496
 LHJ  C24  C22   single    1.493  0.020  1.493
 LHJ  C22  N4    single    1.426  0.020  1.426
 LHJ  C22  H22   single    0.970  0.020  1.090
 LHJ  C23  C24   single    1.498  0.020  1.498
 LHJ  C24  H24   single    0.970  0.020  1.090
 LHJ  C24  H24A  single    0.970  0.020  1.090
 LHJ  C23  H23   single    0.970  0.020  1.090
 LHJ  C23  H23A  single    0.970  0.020  1.090
 LHJ  N4   HN4   single    0.860  0.020  1.020
 LHJ  C18  C19   aromatic  1.391  0.020  1.391
 LHJ  C18  H18   single    0.930  0.020  1.080
 LHJ  C3   O1    double    1.222  0.020  1.222
 LHJ  C1   C2    aromatic  1.386  0.020  1.386
 LHJ  C9   C14   aromatic  1.387  0.020  1.387
 LHJ  C14  H14   single    0.930  0.020  1.080
 LHJ  C11  C12   aromatic  1.382  0.020  1.382
 LHJ  C12  F2    single    1.334  0.020  1.334
 LHJ  C11  H11   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
 LHJ  C2    N1   C3    119.50  3.000
 LHJ  C3    N1   C7    118.38  3.000
 LHJ  C2    N1   C7    122.11  3.000
 LHJ  C9    N3   N2    117.76  3.000
 LHJ  C9    N3   C2    130.86  3.000
 LHJ  N2    N3   C2    111.04  3.000
 LHJ  C3    C4   C8    117.10  3.000
 LHJ  C3    C4   C5    121.59  3.000
 LHJ  C8    C4   C5    121.30  3.000
 LHJ  H5    C5   C1    120.27  3.000
 LHJ  H5    C5   C4    120.67  3.000
 LHJ  C1    C5   C4    119.06  3.000
 LHJ  H6    C6   N2    120.68  3.000
 LHJ  H6    C6   C1    128.01  3.000
 LHJ  N2    C6   C1    111.31  3.000
 LHJ  H7B   C7   H7A   109.76  3.000
 LHJ  H7B   C7   H7    108.44  3.000
 LHJ  H7A   C7   H7    108.38  3.000
 LHJ  H7B   C7   N1    110.08  3.000
 LHJ  H7A   C7   N1    111.57  3.000
 LHJ  H7    C7   N1    108.54  3.000
 LHJ  C19   C8   C15   119.84  3.000
 LHJ  C19   C8   C4    121.05  3.000
 LHJ  C15   C8   C4    119.06  3.000
 LHJ  F1    C10  C11   119.32  3.000
 LHJ  C11   C10  C9    121.97  3.000
 LHJ  F1    C10  C9    118.70  3.000
 LHJ  H13   C13  C12   120.65  3.000
 LHJ  H13   C13  C14   121.01  3.000
 LHJ  C12   C13  C14   118.34  3.000
 LHJ  H15   C15  C16   119.40  3.000
 LHJ  H15   C15  C8    119.07  3.000
 LHJ  C16   C15  C8    121.53  3.000
 LHJ  H17   C17  C18   118.40  3.000
 LHJ  H17   C17  C16   121.44  3.000
 LHJ  C18   C17  C16   120.13  3.000
 LHJ  H22   C22  N4    114.85  3.000
 LHJ  H22   C22  C23   116.82  3.000
 LHJ  N4    C22  C23   119.53  3.000
 LHJ  H22   C22  C24   117.03  3.000
 LHJ  N4    C22  C24   117.65  3.000
 LHJ  C23   C22  C24    60.14  3.000
 LHJ  H24A  C24  H24   114.40  3.000
 LHJ  H24A  C24  C23   118.92  3.000
 LHJ  H24   C24  C23   117.63  3.000
 LHJ  H24A  C24  C22   117.63  3.000
 LHJ  H24   C24  C22   117.69  3.000
 LHJ  C23   C24  C22    60.03  3.000
 LHJ  H23A  C23  H23   114.76  3.000
 LHJ  H23A  C23  C24   117.63  3.000
 LHJ  H23   C23  C24   118.71  3.000
 LHJ  H23A  C23  C22   117.46  3.000
 LHJ  H23   C23  C22   117.60  3.000
 LHJ  C24   C23  C22    59.83  3.000
 LHJ  HN4   N4   C22   117.90  3.000
 LHJ  HN4   N4   C21   119.82  3.000
 LHJ  C22   N4   C21   122.27  3.000
 LHJ  C21   C16  C17   123.23  3.000
 LHJ  C21   C16  C15   118.19  3.000
 LHJ  C17   C16  C15   118.55  3.000
 LHJ  H18   C18  C19   119.23  3.000
 LHJ  H18   C18  C17   119.10  3.000
 LHJ  C19   C18  C17   121.66  3.000
 LHJ  C18   C19  C20   120.21  3.000
 LHJ  C18   C19  C8    118.28  3.000
 LHJ  C20   C19  C8    121.49  3.000
 LHJ  O1    C3   C4    122.68  3.000
 LHJ  O1    C3   N1    119.89  3.000
 LHJ  C4    C3   N1    117.44  3.000
 LHJ  C1    C2   N3    106.86  3.000
 LHJ  C1    C2   N1    123.15  3.000
 LHJ  N3    C2   N1    129.98  3.000
 LHJ  C2    C1   C6    104.48  3.000
 LHJ  C2    C1   C5    119.10  3.000
 LHJ  C6    C1   C5    136.43  3.000
 LHJ  C6    N2   N3    106.32  3.000
 LHJ  C14   C9   C10   119.01  3.000
 LHJ  C14   C9   N3    121.10  3.000
 LHJ  C10   C9   N3    119.84  3.000
 LHJ  H14   C14  C9    119.27  3.000
 LHJ  H14   C14  C13   120.12  3.000
 LHJ  C9    C14  C13   120.60  3.000
 LHJ  C11   C12  F2    118.20  3.000
 LHJ  F2    C12  C13   119.00  3.000
 LHJ  C11   C12  C13   122.80  3.000
 LHJ  H11   C11  C12   121.57  3.000
 LHJ  H11   C11  C10   121.16  3.000
 LHJ  C12   C11  C10   117.27  3.000
 LHJ  H20B  C20  H20A  107.78  3.000
 LHJ  H20B  C20  H20   107.16  3.000
 LHJ  H20A  C20  H20   107.81  3.000
 LHJ  H20B  C20  C19   111.43  3.000
 LHJ  H20A  C20  C19   111.00  3.000
 LHJ  H20   C20  C19   111.47  3.000
 LHJ  C16   C21  O2    121.29  3.000
 LHJ  C16   C21  N4    116.27  3.000
 LHJ  O2    C21  N4    122.44  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
 LHJ  CONST_01  C1   C6   N2   N3      0.00   0.0  0
 LHJ  CONST_02  C6   C1   C2   N3      0.00   0.0  0
 LHJ  CONST_03  C11  C10  C9   N3    180.00   0.0  0
 LHJ  CONST_04  C13  C14  C9   N3    180.00   0.0  0
 LHJ  CONST_05  C2   N3   N2   C6      0.00   0.0  0
 LHJ  CONST_06  C9   N3   N2   C6    180.00   0.0  0
 LHJ  CONST_07  C17  C16  C15  C8      0.00   0.0  0
 LHJ  CONST_08  C17  C18  C19  C8      0.00   0.0  0
 LHJ  CONST_11  C13  C14  C9   C10     0.00   0.0  0
 LHJ  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 LHJ  CONST_13  C18  C19  C8   C15     0.00   0.0  0
 LHJ  CONST_14  C18  C17  C16  C15     0.00   0.0  0
 LHJ  CONST_15  C19  C8   C15  C16     0.00   0.0  0
 LHJ  CONST_16  C19  C18  C17  C16     0.00   0.0  0
 LHJ  CONST_18  N2   C6   C1   C2      0.00   0.0  0
 LHJ  CONST_19  N2   N3   C2   C1      0.00   0.0  0
 LHJ  CONST_20  C9   N3   C2   C1    180.00   0.0  0
 LHJ  CONST_22  C12  C11  C10  C9      0.00   0.0  0
 LHJ  CONST_23  C12  C13  C14  C9      0.00   0.0  0
 LHJ  CONST_24  C11  C12  C13  C14     0.00   0.0  0
 LHJ  CONST_25  C11  C10  C9   C14     0.00   0.0  0
 LHJ  CONST_26  C9   N3   C2   N1      0.00   0.0  0
 LHJ  CONST_27  C16  C15  C8   C4    180.00   0.0  0
 LHJ  CONST_28  C18  C19  C8   C4    180.00   0.0  0
 LHJ  CONST_29  C2   N1   C3   C4      0.00   0.0  0
 LHJ  CONST_30  F1   C10  C9   N3      0.00   0.0  0
 LHJ  CONST_31  C20  C19  C8   C4      0.00   0.0  0
 LHJ  CONST_32  C21  C16  C15  C8    180.00   0.0  0
 LHJ  CONST_33  F2   C12  C11  C10   180.00   0.0  0
 LHJ  CONST_34  C20  C19  C8   C15   180.00   0.0  0
 LHJ  CONST_35  C20  C19  C18  C17   180.00   0.0  0
 LHJ  CONST_36  C18  C17  C16  C21   180.00   0.0  0
 LHJ  CONST_37  F2   C12  C13  C14   180.00   0.0  0
 LHJ  CONST_38  F1   C10  C9   C14   180.00   0.0  0
 LHJ  CONST_39  F1   C10  C11  C12   180.00   0.0  0
 LHJ  CONST_40  C7   N1   C3   C4    180.00   0.0  0
 LHJ  CONST_41  C2   N1   C3   O1    180.00   0.0  0
 LHJ  CONST_42  H6   C6   N2   N3    180.00   0.0  0
 LHJ  CONST_43  H14  C14  C9   N3      0.00   0.0  0
 LHJ  CONST_44  H15  C15  C8   C4      0.00   0.0  0
 LHJ  CONST_45  H18  C18  C19  C8    180.00   0.0  0
 LHJ  CONST_46  H11  C11  C12  C13   180.00   0.0  0
 LHJ  CONST_47  H17  C17  C16  C15   180.00   0.0  0
 LHJ  CONST_48  H13  C13  C14  C9    180.00   0.0  0
 LHJ  CONST_49  C16  C21  N4   C22   180.00   0.0  0
 LHJ  CONST_50  O1   C3   N1   C7      0.00   0.0  0
 LHJ  CONST_51  O2   C21  N4   C22     0.00   0.0  0
 LHJ  CONST_52  HN4  N4   C21  C16     0.00   0.0  0
 LHJ  Var_01    C15  C8   C4   C5     70.66  30.0  2
 LHJ  Var_02    N4   C22  C23  C24   106.85  30.0  1
 LHJ  Var_03    H24  C24  C23  C22  -107.67  30.0  1
 LHJ  Var_04    O2   C21  C16  C15   -22.75  30.0  3
 LHJ  Var_05    C23  C22  N4   C21    76.29  30.0  1
 LHJ  Var_06    H20  C20  C19  C8     54.61  30.0  2
 LHJ  Var_07    H7   C7   N1   C3    -16.38  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 LHJ  chir_01  C22  C23  C24  N4  both

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
 LHJ  plan-1  N3   0.020
 LHJ  plan-1  C10  0.020
 LHJ  plan-1  C13  0.020
 LHJ  plan-1  C9   0.020
 LHJ  plan-1  C14  0.020
 LHJ  plan-1  C12  0.020
 LHJ  plan-1  F2   0.020
 LHJ  plan-1  C11  0.020
 LHJ  plan-1  H13  0.020
 LHJ  plan-1  H14  0.020
 LHJ  plan-1  H11  0.020
 LHJ  plan-1  F1   0.020
 LHJ  plan-2  C4   0.020
 LHJ  plan-2  C8   0.020
 LHJ  plan-2  C15  0.020
 LHJ  plan-2  C17  0.020
 LHJ  plan-2  C16  0.020
 LHJ  plan-2  C18  0.020
 LHJ  plan-2  C19  0.020
 LHJ  plan-2  H15  0.020
 LHJ  plan-2  H17  0.020
 LHJ  plan-2  H18  0.020
 LHJ  plan-2  C20  0.020
 LHJ  plan-2  C21  0.020
 LHJ  plan-3  N1   0.020
 LHJ  plan-3  N3   0.020
 LHJ  plan-3  C4   0.020
 LHJ  plan-3  C5   0.020
 LHJ  plan-3  C6   0.020
 LHJ  plan-3  C7   0.020
 LHJ  plan-3  C8   0.020
 LHJ  plan-3  C3   0.020
 LHJ  plan-3  O1   0.020
 LHJ  plan-3  C2   0.020
 LHJ  plan-3  C1   0.020
 LHJ  plan-3  N2   0.020
 LHJ  plan-3  C9   0.020
 LHJ  plan-3  H5   0.020
 LHJ  plan-3  H6   0.020
 LHJ  plan-4  C22  0.020
 LHJ  plan-4  N4   0.020
 LHJ  plan-4  O2   0.020
 LHJ  plan-4  C16  0.020
 LHJ  plan-4  HN4  0.020
 LHJ  plan-4  C21  0.020

