# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 14:07:38 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2S)-2-{[1-(3-chloropyridin-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-methylpyridin-2-yl)-3-(propan-2-yloxy)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)OC[C@H](Oc1ncnc2n(ncc12)c3ncccc3Cl)C(=O)Nc4ccc(C)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
 1JD  1JD  (2S)-2-{[1-(3-chloropyridin-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-methylpyridin-2-yl)-3-(propan-2-yloxy)propanamide  ligand  55  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_1JD
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
 1JD  C1   C   CH3   0  -0.725   9.1025  -2.3570   0.4952
 1JD  C2   C   CR6   0   0.003   7.7723  -1.7916   0.1032
 1JD  C3   C   CR16  0  -0.170   7.5693  -1.1563  -1.1231
 1JD  C4   C   CR16  0  -0.391   6.3279  -0.6527  -1.4455
 1JD  C5   C   CR6   0   0.516   5.2943  -0.7918  -0.5138
 1JD  N1   N   N     0  -0.418   5.4647  -1.3819   0.6517
 1JD  C6   C   CR16  0  -0.108   6.6694  -1.8679   0.9390
 1JD  N2   N   NH1   0  -0.733   4.0481  -0.2559  -0.8413
 1JD  C7   C   C     0   0.535   2.8480  -0.4579  -0.2327
 1JD  O1   O   O     0  -0.419   2.6407  -1.2207   0.6785
 1JD  C8   C   CH1   0  -0.169   1.7411   0.4040  -0.8509
 1JD  C9   C   CH2   0  -0.164   1.9944   1.8785  -0.5833
 1JD  O2   O   O2    0  -0.486   2.2240   2.0289   0.7863
 1JD  C10  C   CH1   0   0.049   2.6828   3.3136   1.1803
 1JD  C11  C   CH3   0  -0.684   1.5823   4.3619   1.0916
 1JD  C12  C   CH3   0  -0.673   3.2119   3.1757   2.5948
 1JD  O3   O   O2    0  -0.447   0.5427  -0.0282  -0.2253
 1JD  C13  C   CR6   0   0.559  -0.6158   0.1796  -0.8156
 1JD  C14  C   CR56  0  -0.238  -1.7776  -0.2249  -0.1461
 1JD  C15  C   CR15  0  -0.084  -2.1690  -0.8287   1.0747
 1JD  N3   N   N     0  -0.229  -3.4674  -0.9281   1.1352
 1JD  N4   N   NR5   0  -0.469  -3.9596  -0.4085  -0.0102
 1JD  C16  C   CR56  0   0.588  -2.9694   0.0278  -0.8233
 1JD  N5   N   N     0  -0.431  -3.0807   0.6073  -2.0174
 1JD  C17  C   CR16  0   0.078  -1.9160   0.9298  -2.5332
 1JD  N6   N   N     0  -0.484  -0.7005   0.7472  -1.9976
 1JD  C18  C   CR6   0   0.514  -5.3440  -0.4027  -0.2632
 1JD  C19  C   CR6   0  -0.143  -6.2210   0.2572   0.5931
 1JD  C20  C   CR16  0  -0.094  -7.5766   0.2084   0.3109
 1JD  C21  C   CR16  0  -0.328  -7.9937  -0.4672  -0.8227
 1JD  C22  C   CR16  0  -0.054  -7.0373  -1.0649  -1.6292
 1JD  N7   N   N     0  -0.394  -5.7433  -1.0400  -1.3439
 1JD  CL1  CL  CL    0  -0.077  -5.6516   1.1489   1.9466
 1JD  H1   H   HCH3  0   0.250   9.4050  -3.1628  -0.1753
 1JD  H2   H   HCH3  0   0.249   9.8831  -1.5963   0.4567
 1JD  H3   H   HCH3  0   0.246   9.0789  -2.7596   1.5071
 1JD  H4   H   HCR6  0   0.268   8.3854  -1.0581  -1.8289
 1JD  H5   H   HCR6  0   0.279   6.1582  -0.1627  -2.3960
 1JD  H6   H   HCR6  0   0.254   6.7615  -2.3478   1.9088
 1JD  H7   H   HNH1  0   0.423   4.0459   0.3241  -1.6672
 1JD  H8   H   HCH1  0   0.307   1.6944   0.2381  -1.9317
 1JD  H9   H   HCH2  0   0.224   2.8589   2.2070  -1.1774
 1JD  H10  H   HCH2  0   0.244   1.1386   2.4647  -0.9394
 1JD  H11  H   HCH1  0   0.204   3.5100   3.6150   0.5201
 1JD  H12  H   HCH3  0   0.225   0.7278   4.0783   1.7092
 1JD  H13  H   HCH3  0   0.234   1.9523   5.3233   1.4486
 1JD  H14  H   HCH3  0   0.236   1.2309   4.5121   0.0701
 1JD  H15  H   HCH3  0   0.235   4.0062   2.4307   2.6497
 1JD  H16  H   HCH3  0   0.228   3.6193   4.1265   2.9375
 1JD  H17  H   HCH3  0   0.225   2.4165   2.8839   3.2837
 1JD  H18  H   HCR5  0   0.285  -1.5522  -1.1861   1.8842
 1JD  H19  H   HCR6  0   0.271  -1.9300   1.4047  -3.5069
 1JD  H20  H   HCR6  0   0.306  -8.2872   0.7039   0.9580
 1JD  H21  H   HCR6  0   0.292  -9.0419  -0.5222  -1.0794
 1JD  H22  H   HCR6  0   0.284  -7.3241  -1.5901  -2.5314

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
 1JD  C1   C2   single    1.498  0.020  1.498
 1JD  C3   C2   aromatic  1.396  0.020  1.396
 1JD  C3   C4   aromatic  1.378  0.020  1.378
 1JD  C2   C6   aromatic  1.386  0.020  1.386
 1JD  C4   C5   aromatic  1.398  0.020  1.398
 1JD  C6   N1   aromatic  1.331  0.020  1.331
 1JD  O1   C7   double    1.206  0.020  1.206
 1JD  C5   N1   aromatic  1.317  0.020  1.317
 1JD  C5   N2   single    1.396  0.020  1.396
 1JD  C11  C10  single    1.522  0.020  1.522
 1JD  C7   N2   single    1.361  0.020  1.361
 1JD  C7   C8   single    1.533  0.020  1.533
 1JD  C9   C8   single    1.520  0.020  1.520
 1JD  C9   O2   single    1.397  0.020  1.397
 1JD  C10  O2   single    1.420  0.020  1.420
 1JD  C10  C12  single    1.516  0.020  1.516
 1JD  CL1  C19  single    1.718  0.020  1.718
 1JD  C8   O3   single    1.419  0.020  1.419
 1JD  C15  N3   aromatic  1.304  0.020  1.304
 1JD  C15  C14  aromatic  1.417  0.020  1.417
 1JD  O3   C13  single    1.317  0.020  1.317
 1JD  N3   N4   aromatic  1.351  0.020  1.351
 1JD  C14  C13  aromatic  1.401  0.020  1.401
 1JD  C14  C16  aromatic  1.394  0.020  1.394
 1JD  C13  N6   aromatic  1.314  0.020  1.314
 1JD  N4   C16  aromatic  1.353  0.020  1.353
 1JD  N4   C18  single    1.407  0.020  1.407
 1JD  C19  C20  aromatic  1.386  0.020  1.386
 1JD  C19  C18  aromatic  1.392  0.020  1.392
 1JD  C16  N5   aromatic  1.332  0.020  1.332
 1JD  N6   C17  aromatic  1.341  0.020  1.341
 1JD  C20  C21  aromatic  1.384  0.020  1.384
 1JD  C18  N7   aromatic  1.317  0.020  1.317
 1JD  C17  N5   aromatic  1.314  0.020  1.314
 1JD  N7   C22  aromatic  1.325  0.020  1.325
 1JD  C21  C22  aromatic  1.387  0.020  1.387
 1JD  C1   H1   single    0.970  0.020  1.090
 1JD  C1   H2   single    0.970  0.020  1.090
 1JD  C1   H3   single    0.970  0.020  1.090
 1JD  C3   H4   single    0.930  0.020  1.080
 1JD  C4   H5   single    0.930  0.020  1.080
 1JD  C6   H6   single    0.930  0.020  1.080
 1JD  N2   H7   single    0.860  0.020  1.020
 1JD  C8   H8   single    0.970  0.020  1.090
 1JD  C9   H9   single    0.970  0.020  1.090
 1JD  C9   H10  single    0.970  0.020  1.090
 1JD  C10  H11  single    0.970  0.020  1.090
 1JD  C11  H12  single    0.970  0.020  1.090
 1JD  C11  H13  single    0.970  0.020  1.090
 1JD  C11  H14  single    0.970  0.020  1.090
 1JD  C12  H15  single    0.970  0.020  1.090
 1JD  C12  H16  single    0.970  0.020  1.090
 1JD  C12  H17  single    0.970  0.020  1.090
 1JD  C15  H18  single    0.930  0.020  1.080
 1JD  C17  H19  single    0.930  0.020  1.080
 1JD  C20  H20  single    0.930  0.020  1.080
 1JD  C21  H21  single    0.930  0.020  1.080
 1JD  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
 1JD  H3   C1   H2   107.82  3.000
 1JD  H3   C1   H1   107.69  3.000
 1JD  H2   C1   H1   107.16  3.000
 1JD  H3   C1   C2   111.31  3.000
 1JD  H2   C1   C2   111.29  3.000
 1JD  H1   C1   C2   111.36  3.000
 1JD  C6   C2   C3   116.05  3.000
 1JD  C6   C2   C1   121.88  3.000
 1JD  C3   C2   C1   122.07  3.000
 1JD  H4   C3   C4   119.54  3.000
 1JD  H4   C3   C2   120.27  3.000
 1JD  C4   C3   C2   120.19  3.000
 1JD  H5   C4   C5   120.93  3.000
 1JD  H5   C4   C3   120.80  3.000
 1JD  C5   C4   C3   118.27  3.000
 1JD  N2   C5   N1   119.68  3.000
 1JD  N2   C5   C4   117.74  3.000
 1JD  N1   C5   C4   122.58  3.000
 1JD  C6   N1   C5   118.15  3.000
 1JD  H6   C6   N1   115.53  3.000
 1JD  H6   C6   C2   119.70  3.000
 1JD  N1   C6   C2   124.76  3.000
 1JD  H7   N2   C7   116.71  3.000
 1JD  H7   N2   C5   114.50  3.000
 1JD  C7   N2   C5   128.72  3.000
 1JD  C8   C7   O1   122.42  3.000
 1JD  C8   C7   N2   111.90  3.000
 1JD  O1   C7   N2   125.69  3.000
 1JD  H8   C8   O3   110.67  3.000
 1JD  H8   C8   C9   109.15  3.000
 1JD  O3   C8   C9   111.01  3.000
 1JD  H8   C8   C7   110.11  3.000
 1JD  O3   C8   C7   105.11  3.000
 1JD  C9   C8   C7   110.74  3.000
 1JD  H10  C9   H9   106.17  3.000
 1JD  H10  C9   O2   112.90  3.000
 1JD  H9   C9   O2   111.62  3.000
 1JD  H10  C9   C8   109.35  3.000
 1JD  H9   C9   C8   109.01  3.000
 1JD  O2   C9   C8   107.73  3.000
 1JD  C10  O2   C9   115.01  3.000
 1JD  H11  C10  C12  108.80  3.000
 1JD  H11  C10  C11  108.65  3.000
 1JD  C12  C10  C11  111.66  3.000
 1JD  H11  C10  O2   108.91  3.000
 1JD  C12  C10  O2   106.82  3.000
 1JD  C11  C10  O2   111.92  3.000
 1JD  H14  C11  H13  107.13  3.000
 1JD  H14  C11  H12  108.27  3.000
 1JD  H13  C11  H12  108.03  3.000
 1JD  H14  C11  C10  112.47  3.000
 1JD  H13  C11  C10  110.05  3.000
 1JD  H12  C11  C10  110.72  3.000
 1JD  H17  C12  H16  107.88  3.000
 1JD  H17  C12  H15  108.44  3.000
 1JD  H16  C12  H15  107.93  3.000
 1JD  H17  C12  C10  111.02  3.000
 1JD  H16  C12  C10  110.15  3.000
 1JD  H15  C12  C10  111.30  3.000
 1JD  C13  O3   C8   119.82  3.000
 1JD  N6   C13  C14  120.09  3.000
 1JD  N6   C13  O3   121.88  3.000
 1JD  C14  C13  O3   118.03  3.000
 1JD  C16  C14  C15  105.05  3.000
 1JD  C16  C14  C13  115.13  3.000
 1JD  C15  C14  C13  139.81  3.000
 1JD  H18  C15  N3   120.63  3.000
 1JD  H18  C15  C14  129.04  3.000
 1JD  N3   C15  C14  110.34  3.000
 1JD  N4   N3   C15  107.11  3.000
 1JD  C18  N4   C16  127.62  3.000
 1JD  C18  N4   N3   120.83  3.000
 1JD  C16  N4   N3   111.52  3.000
 1JD  N5   C16  N4   128.15  3.000
 1JD  N5   C16  C14  125.86  3.000
 1JD  N4   C16  C14  105.98  3.000
 1JD  C17  N5   C16  112.62  3.000
 1JD  H19  C17  N6   115.50  3.000
 1JD  H19  C17  N5   116.68  3.000
 1JD  N6   C17  N5   127.83  3.000
 1JD  C17  N6   C13  118.47  3.000
 1JD  N7   C18  C19  122.91  3.000
 1JD  N7   C18  N4   116.35  3.000
 1JD  C19  C18  N4   120.74  3.000
 1JD  CL1  C19  C20  120.20  3.000
 1JD  C20  C19  C18  118.32  3.000
 1JD  CL1  C19  C18  121.46  3.000
 1JD  H20  C20  C21  121.05  3.000
 1JD  H20  C20  C19  120.33  3.000
 1JD  C21  C20  C19  118.61  3.000
 1JD  H21  C21  C22  120.60  3.000
 1JD  H21  C21  C20  120.78  3.000
 1JD  C22  C21  C20  118.61  3.000
 1JD  H22  C22  N7   116.56  3.000
 1JD  H22  C22  C21  120.74  3.000
 1JD  N7   C22  C21  122.70  3.000
 1JD  C22  N7   C18  118.81  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
 1JD  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 1JD  CONST_02  C5   N1   C6   C2      0.00   0.0  0
 1JD  CONST_03  N1   C6   C2   C3      0.00   0.0  0
 1JD  CONST_04  N1   C5   C4   C3      0.00   0.0  0
 1JD  CONST_05  C6   C2   C3   C4      0.00   0.0  0
 1JD  CONST_06  C6   N1   C5   C4      0.00   0.0  0
 1JD  CONST_07  N3   C15  C14  C13   180.00   0.0  0
 1JD  CONST_08  N4   C16  C14  C13   180.00   0.0  0
 1JD  CONST_09  N5   C16  C14  C13     0.00   0.0  0
 1JD  CONST_10  N5   C17  N6   C13     0.00   0.0  0
 1JD  CONST_11  N4   N3   C15  C14     0.00   0.0  0
 1JD  CONST_12  C17  N6   C13  C14     0.00   0.0  0
 1JD  CONST_13  N3   N4   C16  C14     0.00   0.0  0
 1JD  CONST_14  C18  N4   C16  C14   180.00   0.0  0
 1JD  CONST_15  C17  N5   C16  C14     0.00   0.0  0
 1JD  CONST_16  C16  N4   N3   C15     0.00   0.0  0
 1JD  CONST_17  C18  N4   N3   C15   180.00   0.0  0
 1JD  CONST_18  N6   C13  C14  C15   180.00   0.0  0
 1JD  CONST_19  N4   C16  C14  C15     0.00   0.0  0
 1JD  CONST_20  N5   C16  C14  C15   180.00   0.0  0
 1JD  CONST_21  C16  C14  C15  N3      0.00   0.0  0
 1JD  CONST_22  N5   C16  N4   N3    180.00   0.0  0
 1JD  CONST_25  C17  N5   C16  N4    180.00   0.0  0
 1JD  CONST_26  C20  C19  C18  N4    180.00   0.0  0
 1JD  CONST_27  C22  N7   C18  N4    180.00   0.0  0
 1JD  CONST_28  N6   C13  C14  C16     0.00   0.0  0
 1JD  CONST_31  N6   C17  N5   C16     0.00   0.0  0
 1JD  CONST_32  C18  N4   C16  N5      0.00   0.0  0
 1JD  CONST_33  C21  C20  C19  C18     0.00   0.0  0
 1JD  CONST_34  C21  C22  N7   C18     0.00   0.0  0
 1JD  CONST_35  C22  C21  C20  C19     0.00   0.0  0
 1JD  CONST_36  C22  N7   C18  C19     0.00   0.0  0
 1JD  CONST_37  N7   C18  C19  C20     0.00   0.0  0
 1JD  CONST_38  N7   C22  C21  C20     0.00   0.0  0
 1JD  CONST_39  C4   C3   C2   C1    180.00   0.0  0
 1JD  CONST_40  N1   C6   C2   C1    180.00   0.0  0
 1JD  CONST_41  N2   C5   C4   C3    180.00   0.0  0
 1JD  CONST_42  N2   C5   N1   C6    180.00   0.0  0
 1JD  CONST_43  C15  C14  C13  O3      0.00   0.0  0
 1JD  CONST_44  C16  C14  C13  O3    180.00   0.0  0
 1JD  CONST_45  C17  N6   C13  O3    180.00   0.0  0
 1JD  CONST_46  CL1  C19  C18  N4      0.00   0.0  0
 1JD  CONST_47  CL1  C19  C20  C21   180.00   0.0  0
 1JD  CONST_48  CL1  C19  C18  N7    180.00   0.0  0
 1JD  CONST_49  H5   C4   C3   C2    180.00   0.0  0
 1JD  CONST_50  H6   C6   C2   C3    180.00   0.0  0
 1JD  CONST_51  H4   C3   C4   C5    180.00   0.0  0
 1JD  CONST_52  H18  C15  C14  C13     0.00   0.0  0
 1JD  CONST_53  H19  C17  N6   C13   180.00   0.0  0
 1JD  CONST_54  H20  C20  C19  C18   180.00   0.0  0
 1JD  CONST_55  H22  C22  N7   C18   180.00   0.0  0
 1JD  CONST_56  H21  C21  C20  C19   180.00   0.0  0
 1JD  CONST_57  C7   N2   C5   C4    180.00   0.0  0
 1JD  CONST_58  C7   N2   C5   N1      0.00   0.0  0
 1JD  CONST_59  H7   N2   C5   C4      0.00   0.0  0
 1JD  CONST_60  O1   C7   N2   C5      0.00   0.0  0
 1JD  CONST_61  C8   C7   N2   C5    180.00   0.0  0
 1JD  Var_01    C14  C13  O3   C8   -178.05  30.0  2
 1JD  Var_02    H1   C1   C2   C3    -63.12  30.0  2
 1JD  Var_03    C11  C10  O2   C9     72.02  30.0  2
 1JD  Var_04    H12  C11  C10  O2     57.75  30.0  3
 1JD  Var_05    H15  C12  C10  O2     57.90  30.0  3
 1JD  Var_06    H9   C9   O2   C10    51.00  30.0  1

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
 1JD  chir_01  C8  C7  C9  O3  positiv

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
 1JD  plan-1  C1   0.020
 1JD  plan-1  C2   0.020
 1JD  plan-1  C3   0.020
 1JD  plan-1  C4   0.020
 1JD  plan-1  C5   0.020
 1JD  plan-1  N1   0.020
 1JD  plan-1  C6   0.020
 1JD  plan-1  N2   0.020
 1JD  plan-1  H4   0.020
 1JD  plan-1  H5   0.020
 1JD  plan-1  H6   0.020
 1JD  plan-2  N4   0.020
 1JD  plan-2  C18  0.020
 1JD  plan-2  C19  0.020
 1JD  plan-2  C20  0.020
 1JD  plan-2  C21  0.020
 1JD  plan-2  C22  0.020
 1JD  plan-2  N7   0.020
 1JD  plan-2  CL1  0.020
 1JD  plan-2  H20  0.020
 1JD  plan-2  H21  0.020
 1JD  plan-2  H22  0.020
 1JD  plan-3  O3   0.020
 1JD  plan-3  C13  0.020
 1JD  plan-3  C14  0.020
 1JD  plan-3  C15  0.020
 1JD  plan-3  N3   0.020
 1JD  plan-3  N4   0.020
 1JD  plan-3  C16  0.020
 1JD  plan-3  N5   0.020
 1JD  plan-3  C17  0.020
 1JD  plan-3  N6   0.020
 1JD  plan-3  C18  0.020
 1JD  plan-3  H18  0.020
 1JD  plan-3  H19  0.020
 1JD  plan-4  C5   0.020
 1JD  plan-4  N2   0.020
 1JD  plan-4  C7   0.020
 1JD  plan-4  O1   0.020
 1JD  plan-4  C8   0.020
 1JD  plan-4  H7   0.020

