# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 19:24:53 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (2S)-2-{[1-(2-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-chloropyridin-2-yl)-3-(2-hydroxyethoxy)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOC[C@H](Oc1ncnc2n(ncc12)c3ccccc3Cl)C(=O)Nc4ccc(Cl)cn4
#
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
 1J9  1J9  (2S)-2-{[1-(2-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-chloropyridin-2-yl)-3-(2-hydroxyethoxy)propanamide  ligand  51  33  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1J9
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
 1J9  C1   C   CR16  0  -0.255   7.8566  -0.7762  -0.4515
 1J9  C2   C   CR16  0  -0.246   8.4626   0.4559  -0.6523
 1J9  C3   C   CR16  0  -0.227   7.7168   1.6249  -0.6043
 1J9  C4   C   CR6   0  -0.068   6.3559   1.5540  -0.3539
 1J9  C5   C   CR6   0   0.383   5.7442   0.3231  -0.1368
 1J9  C6   C   CR16  0  -0.271   6.4967  -0.8404  -0.1898
 1J9  N1   N   NR5   0  -0.485   4.3586   0.2538   0.1157
 1J9  C7   C   CR56  0   0.570   3.3893  -0.1232  -0.7445
 1J9  C8   C   CR56  0  -0.225   2.1842   0.0050  -0.0545
 1J9  C9   C   CR15  0  -0.094   2.5493   0.4810   1.2288
 1J9  N2   N   N     0  -0.234   3.8442   0.6239   1.3077
 1J9  C10  C   CR6   0   0.556   1.0438  -0.3456  -0.7881
 1J9  N3   N   N     0  -0.485   1.1591  -0.7550  -2.0310
 1J9  C11  C   CR16  0   0.079   2.3840  -0.8255  -2.5724
 1J9  N4   N   N     0  -0.432   3.5318  -0.5341  -2.0043
 1J9  O1   O   O2    0  -0.448  -0.1317  -0.2476  -0.1990
 1J9  C12  C   CH1   0  -0.173  -1.3018  -0.5936  -0.9224
 1J9  C13  C   CH2   0  -0.155  -1.5516  -2.0918  -0.8880
 1J9  O2   O   O2    0  -0.478  -1.8355  -2.4601   0.4290
 1J9  C14  C   CH2   0  -0.162  -2.0599  -3.8433   0.5722
 1J9  C15  C   CH2   0  -0.185  -2.3286  -4.1708   2.0178
 1J9  O3   O   OH1   0  -0.668  -3.5448  -3.5839   2.4173
 1J9  C16  C   C     0   0.538  -2.4442   0.1626  -0.2396
 1J9  O4   O   O     0  -0.412  -2.3081   0.7499   0.8041
 1J9  N5   N   NH1   0  -0.734  -3.5986   0.0863  -0.9623
 1J9  C17  C   CR6   0   0.535  -4.8549   0.5848  -0.6332
 1J9  C18  C   CR16  0  -0.400  -5.7862   0.7471  -1.6632
 1J9  C19  C   CR16  0  -0.087  -7.0434   1.2153  -1.3476
 1J9  C20  C   CR6   0  -0.127  -7.3226   1.5114  -0.0206
 1J9  C21  C   CR16  0  -0.032  -6.3368   1.3195   0.9303
 1J9  N6   N   N     0  -0.416  -5.1308   0.8590   0.6282
 1J9  CL1  CL  CL    0  -0.117  -8.8742   2.1059   0.4464
 1J9  CL2  CL  CL    0  -0.092   5.4109   2.9953  -0.3269
 1J9  H1   H   HCR6  0   0.275   8.4407  -1.6849  -0.4937
 1J9  H2   H   HCR6  0   0.278   9.5243   0.5141  -0.8498
 1J9  H3   H   HCR6  0   0.290   8.1877   2.5839  -0.7699
 1J9  H4   H   HCR6  0   0.284   6.0122  -1.7923  -0.0171
 1J9  H5   H   HCR5  0   0.283   1.9174   0.7127   2.0719
 1J9  H6   H   HCR6  0   0.270   2.4212  -1.1663  -3.6003
 1J9  H7   H   HCH1  0   0.307  -1.2165  -0.2759  -1.9664
 1J9  H8   H   HCH2  0   0.225  -2.3834  -2.3273  -1.5670
 1J9  H9   H   HCH2  0   0.244  -0.6739  -2.6214  -1.2813
 1J9  H10  H   HCH2  0   0.209  -2.9039  -4.1677  -0.0530
 1J9  H11  H   HCH2  0   0.211  -1.1816  -4.4163   0.2455
 1J9  H12  H   HCH2  0   0.203  -2.3525  -5.2649   2.1045
 1J9  H13  H   HCH2  0   0.202  -1.4857  -3.8230   2.6291
 1J9  H14  H   HOH1  0   0.455  -3.6857  -3.7939   3.3446
 1J9  H15  H   HNH1  0   0.427  -3.5255  -0.2969  -1.8931
 1J9  H16  H   HCR6  0   0.295  -5.5285   0.5176  -2.6886
 1J9  H17  H   HCR6  0   0.300  -7.7873   1.3530  -2.1203
 1J9  H18  H   HCR6  0   0.286  -6.5292   1.5367   1.9748

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
 1J9  C1   C6   aromatic  1.386  0.020  1.386
 1J9  C1   C2   aromatic  1.388  0.020  1.388
 1J9  C6   C5   aromatic  1.387  0.020  1.387
 1J9  C2   C3   aromatic  1.387  0.020  1.387
 1J9  N4   C11  aromatic  1.313  0.020  1.313
 1J9  N4   C7   aromatic  1.333  0.020  1.333
 1J9  C11  N3   aromatic  1.341  0.020  1.341
 1J9  C5   N1   single    1.410  0.020  1.410
 1J9  C5   C4   aromatic  1.392  0.020  1.392
 1J9  N3   C10  aromatic  1.314  0.020  1.314
 1J9  C7   N1   aromatic  1.350  0.020  1.350
 1J9  C7   C8   aromatic  1.395  0.020  1.395
 1J9  C3   C4   aromatic  1.386  0.020  1.386
 1J9  O3   C15  single    1.408  0.020  1.408
 1J9  N1   N2   aromatic  1.350  0.020  1.350
 1J9  C4   CL2  single    1.724  0.020  1.724
 1J9  C10  C8   aromatic  1.401  0.020  1.401
 1J9  C10  O1   single    1.319  0.020  1.319
 1J9  C8   C9   aromatic  1.417  0.020  1.417
 1J9  C15  C14  single    1.506  0.020  1.506
 1J9  N2   C9   aromatic  1.305  0.020  1.305
 1J9  O2   C14  single    1.409  0.020  1.409
 1J9  O2   C13  single    1.397  0.020  1.397
 1J9  C12  O1   single    1.418  0.020  1.418
 1J9  C12  C13  single    1.519  0.020  1.519
 1J9  C12  C16  single    1.531  0.020  1.531
 1J9  N5   C16  single    1.364  0.020  1.364
 1J9  N5   C17  single    1.391  0.020  1.391
 1J9  C16  O4   double    1.205  0.020  1.205
 1J9  N6   C17  aromatic  1.320  0.020  1.320
 1J9  N6   C21  aromatic  1.326  0.020  1.326
 1J9  C17  C18  aromatic  1.398  0.020  1.398
 1J9  C21  C20  aromatic  1.383  0.020  1.383
 1J9  C18  C19  aromatic  1.378  0.020  1.378
 1J9  C20  C19  aromatic  1.388  0.020  1.388
 1J9  C20  CL1  single    1.726  0.020  1.726
 1J9  C1   H1   single    0.930  0.020  1.080
 1J9  C2   H2   single    0.930  0.020  1.080
 1J9  C3   H3   single    0.930  0.020  1.080
 1J9  C6   H4   single    0.930  0.020  1.080
 1J9  C9   H5   single    0.930  0.020  1.080
 1J9  C11  H6   single    0.930  0.020  1.080
 1J9  C12  H7   single    0.970  0.020  1.090
 1J9  C13  H8   single    0.970  0.020  1.090
 1J9  C13  H9   single    0.970  0.020  1.090
 1J9  C14  H10  single    0.970  0.020  1.090
 1J9  C14  H11  single    0.970  0.020  1.090
 1J9  C15  H12  single    0.970  0.020  1.090
 1J9  C15  H13  single    0.970  0.020  1.090
 1J9  O3   H14  single    0.850  0.020  0.980
 1J9  N5   H15  single    0.860  0.020  1.020
 1J9  C18  H16  single    0.930  0.020  1.080
 1J9  C19  H17  single    0.930  0.020  1.080
 1J9  C21  H18  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
 1J9  H1   C1   C6   119.90  3.000
 1J9  H1   C1   C2   120.31  3.000
 1J9  C6   C1   C2   119.79  3.000
 1J9  H2   C2   C3   119.25  3.000
 1J9  H2   C2   C1   120.20  3.000
 1J9  C3   C2   C1   120.55  3.000
 1J9  H3   C3   C4   120.06  3.000
 1J9  H3   C3   C2   120.52  3.000
 1J9  C4   C3   C2   119.41  3.000
 1J9  CL2  C4   C5   119.75  3.000
 1J9  CL2  C4   C3   119.90  3.000
 1J9  C5   C4   C3   120.35  3.000
 1J9  N1   C5   C6   119.93  3.000
 1J9  N1   C5   C4   120.22  3.000
 1J9  C6   C5   C4   119.84  3.000
 1J9  H4   C6   C5   119.28  3.000
 1J9  H4   C6   C1   120.67  3.000
 1J9  C5   C6   C1   120.05  3.000
 1J9  N2   N1   C7   111.45  3.000
 1J9  N2   N1   C5   121.26  3.000
 1J9  C7   N1   C5   127.25  3.000
 1J9  N4   C7   C8   126.04  3.000
 1J9  C8   C7   N1   106.24  3.000
 1J9  N4   C7   N1   127.72  3.000
 1J9  C10  C8   C9   140.21  3.000
 1J9  C9   C8   C7   104.86  3.000
 1J9  C10  C8   C7   114.93  3.000
 1J9  H5   C9   N2   120.69  3.000
 1J9  H5   C9   C8   129.00  3.000
 1J9  N2   C9   C8   110.32  3.000
 1J9  C9   N2   N1   107.13  3.000
 1J9  O1   C10  N3   121.61  3.000
 1J9  O1   C10  C8   118.25  3.000
 1J9  N3   C10  C8   120.14  3.000
 1J9  C11  N3   C10  118.59  3.000
 1J9  H6   C11  N4   116.76  3.000
 1J9  H6   C11  N3   115.52  3.000
 1J9  N4   C11  N3   127.73  3.000
 1J9  C11  N4   C7   112.58  3.000
 1J9  C12  O1   C10  119.30  3.000
 1J9  H7   C12  C16  109.89  3.000
 1J9  H7   C12  C13  108.70  3.000
 1J9  C16  C12  C13  110.75  3.000
 1J9  H7   C12  O1   110.57  3.000
 1J9  C16  C12  O1   105.52  3.000
 1J9  C13  C12  O1   111.39  3.000
 1J9  H9   C13  H8   106.28  3.000
 1J9  H9   C13  O2   111.91  3.000
 1J9  H8   C13  O2   111.85  3.000
 1J9  H9   C13  C12  109.64  3.000
 1J9  H8   C13  C12  108.77  3.000
 1J9  O2   C13  C12  108.35  3.000
 1J9  C14  O2   C13  112.78  3.000
 1J9  H11  C14  H10  106.91  3.000
 1J9  H11  C14  C15  108.34  3.000
 1J9  H10  C14  C15  110.16  3.000
 1J9  H11  C14  O2   110.77  3.000
 1J9  H10  C14  O2   110.75  3.000
 1J9  C15  C14  O2   109.84  3.000
 1J9  H13  C15  H12  106.77  3.000
 1J9  H13  C15  O3   111.91  3.000
 1J9  H12  C15  O3   111.97  3.000
 1J9  H13  C15  C14  109.18  3.000
 1J9  H12  C15  C14  107.24  3.000
 1J9  O3   C15  C14  109.61  3.000
 1J9  H14  O3   C15  108.01  3.000
 1J9  N5   C16  O4   125.56  3.000
 1J9  O4   C16  C12  122.87  3.000
 1J9  N5   C16  C12  111.57  3.000
 1J9  H15  N5   C17  114.81  3.000
 1J9  H15  N5   C16  116.65  3.000
 1J9  C17  N5   C16  128.24  3.000
 1J9  N6   C17  C18  122.73  3.000
 1J9  C18  C17  N5   117.96  3.000
 1J9  N6   C17  N5   119.29  3.000
 1J9  H16  C18  C19  120.42  3.000
 1J9  H16  C18  C17  121.00  3.000
 1J9  C19  C18  C17  118.58  3.000
 1J9  H17  C19  C20  121.17  3.000
 1J9  H17  C19  C18  120.48  3.000
 1J9  C20  C19  C18  118.35  3.000
 1J9  CL1  C20  C21  120.17  3.000
 1J9  CL1  C20  C19  120.86  3.000
 1J9  C21  C20  C19  118.97  3.000
 1J9  H18  C21  N6   116.79  3.000
 1J9  H18  C21  C20  120.54  3.000
 1J9  N6   C21  C20  122.68  3.000
 1J9  C21  N6   C17  118.69  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
 1J9  CONST_01  N1   C5   C6   C1   180.00   0.0  0
 1J9  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 1J9  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 1J9  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 1J9  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 1J9  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 1J9  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 1J9  CONST_08  N1   C5   C4   C3   180.00   0.0  0
 1J9  CONST_11  N4   C7   N1   C5     0.00   0.0  0
 1J9  CONST_12  C8   C7   N1   C5   180.00   0.0  0
 1J9  CONST_13  C9   N2   N1   C5   180.00   0.0  0
 1J9  CONST_16  C11  N4   C7   N1   180.00   0.0  0
 1J9  CONST_17  C10  C8   C7   N1   180.00   0.0  0
 1J9  CONST_18  C9   C8   C7   N1     0.00   0.0  0
 1J9  CONST_19  C8   C9   N2   N1     0.00   0.0  0
 1J9  CONST_20  N3   C11  N4   C7     0.00   0.0  0
 1J9  CONST_21  C9   N2   N1   C7     0.00   0.0  0
 1J9  CONST_22  N3   C10  C8   C7     0.00   0.0  0
 1J9  CONST_23  N2   C9   C8   C7     0.00   0.0  0
 1J9  CONST_24  C11  N4   C7   C8     0.00   0.0  0
 1J9  CONST_25  N2   N1   C7   C8     0.00   0.0  0
 1J9  CONST_26  C11  N3   C10  C8     0.00   0.0  0
 1J9  CONST_27  N4   C7   C8   C9   180.00   0.0  0
 1J9  CONST_28  N3   C10  C8   C9   180.00   0.0  0
 1J9  CONST_29  N4   C7   N1   N2   180.00   0.0  0
 1J9  CONST_30  C10  C8   C9   N2   180.00   0.0  0
 1J9  CONST_31  N4   C11  N3   C10    0.00   0.0  0
 1J9  CONST_32  N4   C7   C8   C10    0.00   0.0  0
 1J9  CONST_33  C20  C21  N6   C17    0.00   0.0  0
 1J9  CONST_34  C20  C19  C18  C17    0.00   0.0  0
 1J9  CONST_35  C21  N6   C17  C18    0.00   0.0  0
 1J9  CONST_36  C21  C20  C19  C18    0.00   0.0  0
 1J9  CONST_37  N6   C17  C18  C19    0.00   0.0  0
 1J9  CONST_38  N6   C21  C20  C19    0.00   0.0  0
 1J9  CONST_39  CL2  C4   C3   C2   180.00   0.0  0
 1J9  CONST_40  CL2  C4   C5   C6   180.00   0.0  0
 1J9  CONST_41  CL2  C4   C5   N1     0.00   0.0  0
 1J9  CONST_42  O1   C10  C8   C7   180.00   0.0  0
 1J9  CONST_43  O1   C10  C8   C9     0.00   0.0  0
 1J9  CONST_44  O1   C10  N3   C11  180.00   0.0  0
 1J9  CONST_45  C21  N6   C17  N5   180.00   0.0  0
 1J9  CONST_46  C19  C18  C17  N5   180.00   0.0  0
 1J9  CONST_47  CL1  C20  C19  C18  180.00   0.0  0
 1J9  CONST_48  CL1  C20  C21  N6   180.00   0.0  0
 1J9  CONST_49  H3   C3   C2   C1   180.00   0.0  0
 1J9  CONST_50  H4   C6   C1   C2   180.00   0.0  0
 1J9  CONST_51  H1   C1   C2   C3   180.00   0.0  0
 1J9  CONST_52  H2   C2   C3   C4   180.00   0.0  0
 1J9  CONST_53  H5   C9   N2   N1   180.00   0.0  0
 1J9  CONST_54  H6   C11  N4   C7   180.00   0.0  0
 1J9  CONST_55  H18  C21  N6   C17  180.00   0.0  0
 1J9  CONST_56  H17  C19  C18  C17  180.00   0.0  0
 1J9  CONST_57  H16  C18  C19  C20  180.00   0.0  0
 1J9  CONST_60  H15  N5   C17  C18    0.00   0.0  0
 1J9  CONST_61  C17  N5   C16  C12  180.00   0.0  0
 1J9  CONST_62  C17  N5   C16  O4     0.00   0.0  0
 1J9  Var_01    C15  C14  O2   C13  178.75  30.0  3
 1J9  Var_02    O3   C15  C14  O2    66.26  30.0  2
 1J9  Var_03    H8   C13  O2   C14   61.21  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
 1J9  chir_01  C12  O1  C13  C16  negativ

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
 1J9  plan-1  C1   0.020
 1J9  plan-1  C2   0.020
 1J9  plan-1  C3   0.020
 1J9  plan-1  C4   0.020
 1J9  plan-1  C5   0.020
 1J9  plan-1  C6   0.020
 1J9  plan-1  N1   0.020
 1J9  plan-1  CL2  0.020
 1J9  plan-1  H1   0.020
 1J9  plan-1  H2   0.020
 1J9  plan-1  H3   0.020
 1J9  plan-1  H4   0.020
 1J9  plan-2  N5   0.020
 1J9  plan-2  C17  0.020
 1J9  plan-2  C18  0.020
 1J9  plan-2  C19  0.020
 1J9  plan-2  C20  0.020
 1J9  plan-2  C21  0.020
 1J9  plan-2  N6   0.020
 1J9  plan-2  CL1  0.020
 1J9  plan-2  H16  0.020
 1J9  plan-2  H17  0.020
 1J9  plan-2  H18  0.020
 1J9  plan-3  C5   0.020
 1J9  plan-3  N1   0.020
 1J9  plan-3  C7   0.020
 1J9  plan-3  C8   0.020
 1J9  plan-3  C9   0.020
 1J9  plan-3  N2   0.020
 1J9  plan-3  C10  0.020
 1J9  plan-3  N3   0.020
 1J9  plan-3  C11  0.020
 1J9  plan-3  N4   0.020
 1J9  plan-3  O1   0.020
 1J9  plan-3  H5   0.020
 1J9  plan-3  H6   0.020
 1J9  plan-4  C12  0.020
 1J9  plan-4  C16  0.020
 1J9  plan-4  O4   0.020
 1J9  plan-4  N5   0.020
 1J9  plan-4  C17  0.020
 1J9  plan-4  H15  0.020

