# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 09:04:49 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-[2-[(3R,4S)-3-fluoranyl-4-methoxy-piperidin-1-yl]pyrimidin-4-yl]-2-methyl-1-propan-2-yl-imidazo[4,5-c]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1CCN(C[C@H]1F)c2nccc(Nc3cc4n(C(C)C)c(C)nc4cn3)n2
#
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
 4ZJ  4ZJ  N-[2-[(3R,4S)-3-fluoranyl-4-methoxy-piperidin-1-yl]pyrimidin-4-yl]-2-methyl-1-propan-2-yl-imidazo[4,5-c]pyridin-6-amine  ligand  55  29  .  2022-07-23  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_4ZJ
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
 4ZJ  C4   C  CR56  0   0.041   2.8713   0.9061   1.8160
 4ZJ  C5   C  CR16  0  -0.135   1.8018   0.3917   2.5359
 4ZJ  C11  C  CH1   0  -0.143   5.2020   0.6171  -0.9539
 4ZJ  C7   C  CR6   0   0.461   1.6481  -1.4001   1.1142
 4ZJ  C8   C  CR16  0  -0.436   2.7036  -0.9859   0.3104
 4ZJ  C9   C  CR56  0   0.454   3.3279   0.1921   0.6987
 4ZJ  C12  C  CH3   0  -0.654   5.9769  -0.6775  -0.7479
 4ZJ  C13  C  CH3   0  -0.654   4.3761   0.6241  -2.2333
 4ZJ  N3   N  N     0  -0.478   3.6219   2.0404   1.9945
 4ZJ  C1   C  CH3   0  -0.777   5.5327   3.0644   0.8182
 4ZJ  C2   C  CR5   0   0.433   4.4972   2.0220   1.0295
 4ZJ  N6   N  N     0  -0.416   1.2219  -0.7454   2.1953
 4ZJ  N10  N  NR5   0  -0.544   4.3717   0.9264   0.2094
 4ZJ  N14  N  NH1   0  -0.754   1.0157  -2.6120   0.8047
 4ZJ  C15  C  CR6   0   0.533  -0.3266  -2.8074   0.6769
 4ZJ  C16  C  CR16  0  -0.467  -0.8104  -4.0779   0.3114
 4ZJ  C17  C  CR16  0  -0.019  -2.1742  -4.1731   0.1823
 4ZJ  N18  N  N     0  -0.503  -3.0159  -3.1637   0.3891
 4ZJ  C19  C  CR6   0   0.633  -2.4522  -2.0053   0.7402
 4ZJ  N20  N  N     0  -0.492  -1.1435  -1.7918   0.8802
 4ZJ  N21  N  NT    0  -0.491  -3.2771  -0.9579   1.0138
 4ZJ  C22  C  CH2   0  -0.329  -4.6941  -0.9958   0.7138
 4ZJ  C23  C  CH2   0  -0.472  -5.0051  -0.2008  -0.5511
 4ZJ  C24  C  CH1   0   0.031  -4.4750   1.2215  -0.4308
 4ZJ  C25  C  CH1   0   0.159  -2.9981   1.2176  -0.0526
 4ZJ  C26  C  CH2   0  -0.382  -2.7608   0.3799   1.1916
 4ZJ  F27  F  F     0  -0.377  -2.2692   0.6723  -1.1103
 4ZJ  O28  O  O2    0  -0.493  -4.7277   1.8937  -1.6382
 4ZJ  C29  C  CH3   0  -0.410  -4.6467   3.2967  -1.5596
 4ZJ  H1   H  HCR6  0   0.260   1.4211   0.9033   3.4138
 4ZJ  H2   H  HCH1  0   0.280   5.9288   1.4265  -1.0227
 4ZJ  H3   H  HCR6  0   0.279   2.9943  -1.5559  -0.5610
 4ZJ  H4   H  HCH3  0   0.233   5.3275  -1.5523  -0.7168
 4ZJ  H5   H  HCH3  0   0.247   6.6761  -0.8162  -1.5722
 4ZJ  H6   H  HCH3  0   0.246   6.5525  -0.6454   0.1771
 4ZJ  H7   H  HCH3  0   0.233   3.6472  -0.1860  -2.2599
 4ZJ  H8   H  HCH3  0   0.245   3.8427   1.5677  -2.3470
 4ZJ  H9   H  HCH3  0   0.247   5.0344   0.5040  -3.0933
 4ZJ  H10  H  HCH3  0   0.267   6.5399   2.6488   0.8710
 4ZJ  H11  H  HCH3  0   0.268   5.4266   3.5481  -0.1539
 4ZJ  H12  H  HCH3  0   0.278   5.4355   3.8231   1.5899
 4ZJ  H13  H  HNH1  0   0.410   1.6032  -3.3334   0.4174
 4ZJ  H14  H  HCR6  0   0.269  -0.1577  -4.9212   0.1373
 4ZJ  H15  H  HCR6  0   0.261  -2.6239  -5.1177  -0.1056
 4ZJ  H16  H  HCH2  0   0.274  -5.0163  -2.0268   0.6078
 4ZJ  H17  H  HCH2  0   0.241  -5.2367  -0.5689   1.5638
 4ZJ  H18  H  HCH2  0   0.238  -4.5603  -0.6993  -1.4162
 4ZJ  H19  H  HCH2  0   0.250  -6.0853  -0.1772  -0.7089
 4ZJ  H20  H  HCH1  0   0.210  -5.0026   1.7210   0.3990
 4ZJ  H21  H  HCH1  0   0.235  -2.6251   2.2320   0.1174
 4ZJ  H22  H  HCH2  0   0.254  -3.2743   0.8573   2.0324
 4ZJ  H23  H  HCH2  0   0.296  -1.7016   0.3397   1.4314
 4ZJ  H24  H  HCH3  0   0.238  -4.9819   3.6998  -2.5144
 4ZJ  H25  H  HCH3  0   0.208  -5.2921   3.6975  -0.7696
 4ZJ  H26  H  HCH3  0   0.210  -3.6293   3.6601  -1.3806

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
 4ZJ  F27  C25  single    1.396  0.020  1.396
 4ZJ  C25  C26  single    1.519  0.020  1.519
 4ZJ  C25  C24  single    1.525  0.020  1.525
 4ZJ  O28  C29  single    1.407  0.020  1.407
 4ZJ  O28  C24  single    1.405  0.020  1.405
 4ZJ  C26  N21  single    1.445  0.020  1.445
 4ZJ  C24  C23  single    1.523  0.020  1.523
 4ZJ  N18  C17  aromatic  1.330  0.020  1.330
 4ZJ  N18  C19  aromatic  1.335  0.020  1.335
 4ZJ  C17  C16  aromatic  1.373  0.020  1.373
 4ZJ  N21  C19  single    1.361  0.020  1.361
 4ZJ  N21  C22  single    1.449  0.020  1.449
 4ZJ  C23  C22  single    1.526  0.020  1.526
 4ZJ  C19  N20  aromatic  1.333  0.020  1.333
 4ZJ  C16  C15  aromatic  1.408  0.020  1.408
 4ZJ  N20  C15  aromatic  1.319  0.020  1.319
 4ZJ  C15  N14  single    1.362  0.020  1.362
 4ZJ  N14  C7   single    1.402  0.020  1.402
 4ZJ  C7   C8   aromatic  1.390  0.020  1.390
 4ZJ  C7   N6   aromatic  1.334  0.020  1.334
 4ZJ  C8   C9   aromatic  1.389  0.020  1.389
 4ZJ  C13  C11  single    1.523  0.020  1.523
 4ZJ  C11  C12  single    1.523  0.020  1.523
 4ZJ  C11  N10  single    1.462  0.020  1.462
 4ZJ  N6   C5   aromatic  1.321  0.020  1.321
 4ZJ  C9   N10  aromatic  1.367  0.020  1.367
 4ZJ  C9   C4   aromatic  1.402  0.020  1.402
 4ZJ  N10  C2   aromatic  1.374  0.020  1.374
 4ZJ  C5   C4   aromatic  1.388  0.020  1.388
 4ZJ  C4   N3   aromatic  1.372  0.020  1.372
 4ZJ  C2   N3   aromatic  1.303  0.020  1.303
 4ZJ  C2   C1   single    1.484  0.020  1.484
 4ZJ  C5   H1   single    0.930  0.020  1.080
 4ZJ  C11  H2   single    0.970  0.020  1.090
 4ZJ  C8   H3   single    0.930  0.020  1.080
 4ZJ  C12  H4   single    0.970  0.020  1.090
 4ZJ  C12  H5   single    0.970  0.020  1.090
 4ZJ  C12  H6   single    0.970  0.020  1.090
 4ZJ  C13  H7   single    0.970  0.020  1.090
 4ZJ  C13  H8   single    0.970  0.020  1.090
 4ZJ  C13  H9   single    0.970  0.020  1.090
 4ZJ  C1   H10  single    0.970  0.020  1.090
 4ZJ  C1   H11  single    0.970  0.020  1.090
 4ZJ  C1   H12  single    0.970  0.020  1.090
 4ZJ  N14  H13  single    0.860  0.020  1.020
 4ZJ  C16  H14  single    0.930  0.020  1.080
 4ZJ  C17  H15  single    0.930  0.020  1.080
 4ZJ  C22  H16  single    0.970  0.020  1.090
 4ZJ  C22  H17  single    0.970  0.020  1.090
 4ZJ  C23  H18  single    0.970  0.020  1.090
 4ZJ  C23  H19  single    0.970  0.020  1.090
 4ZJ  C24  H20  single    0.970  0.020  1.090
 4ZJ  C25  H21  single    0.970  0.020  1.090
 4ZJ  C26  H22  single    0.970  0.020  1.090
 4ZJ  C26  H23  single    0.970  0.020  1.090
 4ZJ  C29  H24  single    0.970  0.020  1.090
 4ZJ  C29  H25  single    0.970  0.020  1.090
 4ZJ  C29  H26  single    0.970  0.020  1.090

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
 4ZJ  N3   C4   C9   110.28  3.000
 4ZJ  N3   C4   C5   131.34  3.000
 4ZJ  C9   C4   C5   118.38  3.000
 4ZJ  H1   C5   N6   117.41  3.000
 4ZJ  H1   C5   C4   121.01  3.000
 4ZJ  N6   C5   C4   121.57  3.000
 4ZJ  H2   C11  N10  105.77  3.000
 4ZJ  H2   C11  C13  107.77  3.000
 4ZJ  N10  C11  C13  111.07  3.000
 4ZJ  H2   C11  C12  107.49  3.000
 4ZJ  N10  C11  C12  111.17  3.000
 4ZJ  C13  C11  C12  113.18  3.000
 4ZJ  N14  C7   N6   117.33  3.000
 4ZJ  N6   C7   C8   124.42  3.000
 4ZJ  N14  C7   C8   118.20  3.000
 4ZJ  H3   C8   C9   123.49  3.000
 4ZJ  H3   C8   C7   120.88  3.000
 4ZJ  C9   C8   C7   115.63  3.000
 4ZJ  N10  C9   C8   134.35  3.000
 4ZJ  N10  C9   C4   105.09  3.000
 4ZJ  C8   C9   C4   120.55  3.000
 4ZJ  H6   C12  H5   107.87  3.000
 4ZJ  H6   C12  H4   108.31  3.000
 4ZJ  H5   C12  H4   107.55  3.000
 4ZJ  H6   C12  C11  111.01  3.000
 4ZJ  H5   C12  C11  109.41  3.000
 4ZJ  H4   C12  C11  112.52  3.000
 4ZJ  H9   C13  H8   107.99  3.000
 4ZJ  H9   C13  H7   107.62  3.000
 4ZJ  H8   C13  H7   108.28  3.000
 4ZJ  H9   C13  C11  109.57  3.000
 4ZJ  H8   C13  C11  110.92  3.000
 4ZJ  H7   C13  C11  112.31  3.000
 4ZJ  C2   N3   C4   105.04  3.000
 4ZJ  H12  C1   H11  108.34  3.000
 4ZJ  H12  C1   H10  108.32  3.000
 4ZJ  H11  C1   H10  107.57  3.000
 4ZJ  H12  C1   C2   109.08  3.000
 4ZJ  H11  C1   C2   111.73  3.000
 4ZJ  H10  C1   C2   111.69  3.000
 4ZJ  N10  C2   C1   122.59  3.000
 4ZJ  C1   C2   N3   124.34  3.000
 4ZJ  N10  C2   N3   113.07  3.000
 4ZJ  C7   N6   C5   119.41  3.000
 4ZJ  C2   N10  C9   106.52  3.000
 4ZJ  C2   N10  C11  126.26  3.000
 4ZJ  C9   N10  C11  127.22  3.000
 4ZJ  H13  N14  C15  115.82  3.000
 4ZJ  H13  N14  C7   116.16  3.000
 4ZJ  C15  N14  C7   126.11  3.000
 4ZJ  N20  C15  C16  121.46  3.000
 4ZJ  N20  C15  N14  119.03  3.000
 4ZJ  C16  C15  N14  119.50  3.000
 4ZJ  H14  C16  C17  122.05  3.000
 4ZJ  H14  C16  C15  122.59  3.000
 4ZJ  C17  C16  C15  115.36  3.000
 4ZJ  H15  C17  N18  116.07  3.000
 4ZJ  H15  C17  C16  119.79  3.000
 4ZJ  N18  C17  C16  124.13  3.000
 4ZJ  C19  N18  C17  115.59  3.000
 4ZJ  N21  C19  N20  116.78  3.000
 4ZJ  N20  C19  N18  125.51  3.000
 4ZJ  N21  C19  N18  117.68  3.000
 4ZJ  C19  N20  C15  117.93  3.000
 4ZJ  C26  N21  C22  113.52  3.000
 4ZJ  C22  N21  C19  122.07  3.000
 4ZJ  C26  N21  C19  121.37  3.000
 4ZJ  H17  C22  H16  107.40  3.000
 4ZJ  H17  C22  C23  109.84  3.000
 4ZJ  H16  C22  C23  110.69  3.000
 4ZJ  H17  C22  N21  108.28  3.000
 4ZJ  H16  C22  N21  109.59  3.000
 4ZJ  C23  C22  N21  110.94  3.000
 4ZJ  H19  C23  H18  107.33  3.000
 4ZJ  H19  C23  C24  109.61  3.000
 4ZJ  H18  C23  C24  110.30  3.000
 4ZJ  H19  C23  C22  109.44  3.000
 4ZJ  H18  C23  C22  109.61  3.000
 4ZJ  C24  C23  C22  110.50  3.000
 4ZJ  H20  C24  O28  110.11  3.000
 4ZJ  H20  C24  C25  106.14  3.000
 4ZJ  O28  C24  C25  112.87  3.000
 4ZJ  H20  C24  C23  108.42  3.000
 4ZJ  O28  C24  C23  108.45  3.000
 4ZJ  C25  C24  C23  110.76  3.000
 4ZJ  H21  C25  F27  107.57  3.000
 4ZJ  H21  C25  C26  109.32  3.000
 4ZJ  F27  C25  C26  108.89  3.000
 4ZJ  H21  C25  C24  111.50  3.000
 4ZJ  C26  C25  C24  110.86  3.000
 4ZJ  F27  C25  C24  108.60  3.000
 4ZJ  H23  C26  H22  107.69  3.000
 4ZJ  H23  C26  C25  110.70  3.000
 4ZJ  H22  C26  C25  108.38  3.000
 4ZJ  H23  C26  N21  109.95  3.000
 4ZJ  H22  C26  N21  109.30  3.000
 4ZJ  C25  C26  N21  110.74  3.000
 4ZJ  C29  O28  C24  114.75  3.000
 4ZJ  H26  C29  H25  107.93  3.000
 4ZJ  H26  C29  H24  107.84  3.000
 4ZJ  H25  C29  H24  108.38  3.000
 4ZJ  H26  C29  O28  113.16  3.000
 4ZJ  H25  C29  O28  111.77  3.000
 4ZJ  H24  C29  O28  107.59  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
 4ZJ  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 4ZJ  CONST_02  C2   N10  C9   C4      0.00   0.0  0
 4ZJ  CONST_03  C7   N6   C5   C4      0.00   0.0  0
 4ZJ  CONST_04  N10  C2   N3   C4      0.00   0.0  0
 4ZJ  CONST_05  C8   C7   N6   C5      0.00   0.0  0
 4ZJ  CONST_06  C8   C9   C4   C5      0.00   0.0  0
 4ZJ  CONST_07  N10  C9   C4   C5    180.00   0.0  0
 4ZJ  CONST_08  C2   N3   C4   C5    180.00   0.0  0
 4ZJ  CONST_09  N10  C9   C8   C7    180.00   0.0  0
 4ZJ  CONST_10  C2   N10  C9   C8    180.00   0.0  0
 4ZJ  CONST_11  N3   C4   C9   C8    180.00   0.0  0
 4ZJ  CONST_12  N6   C7   C8   C9      0.00   0.0  0
 4ZJ  CONST_13  N3   C2   N10  C9      0.00   0.0  0
 4ZJ  CONST_14  N6   C5   C4   C9      0.00   0.0  0
 4ZJ  CONST_15  C2   N3   C4   C9      0.00   0.0  0
 4ZJ  CONST_16  N10  C9   C4   N3      0.00   0.0  0
 4ZJ  CONST_17  N6   C5   C4   N3    180.00   0.0  0
 4ZJ  CONST_18  N18  C17  C16  C15     0.00   0.0  0
 4ZJ  CONST_19  N18  C19  N20  C15     0.00   0.0  0
 4ZJ  CONST_20  C19  N18  C17  C16     0.00   0.0  0
 4ZJ  CONST_21  C19  N20  C15  C16     0.00   0.0  0
 4ZJ  CONST_22  N20  C19  N18  C17     0.00   0.0  0
 4ZJ  CONST_23  N20  C15  C16  C17     0.00   0.0  0
 4ZJ  CONST_24  N21  C19  N20  C15   180.00   0.0  0
 4ZJ  CONST_25  N21  C19  N18  C17   180.00   0.0  0
 4ZJ  CONST_26  C11  N10  C9   C4    180.00   0.0  0
 4ZJ  CONST_27  C1   C2   N3   C4    180.00   0.0  0
 4ZJ  CONST_28  N14  C7   N6   C5    180.00   0.0  0
 4ZJ  CONST_29  C8   C9   N10  C11     0.00   0.0  0
 4ZJ  CONST_30  N3   C2   N10  C11   180.00   0.0  0
 4ZJ  CONST_31  N14  C7   C8   C9    180.00   0.0  0
 4ZJ  CONST_32  C1   C2   N10  C9    180.00   0.0  0
 4ZJ  CONST_33  C17  C16  C15  N14   180.00   0.0  0
 4ZJ  CONST_34  C19  N20  C15  N14   180.00   0.0  0
 4ZJ  CONST_35  H3   C8   C9   C4    180.00   0.0  0
 4ZJ  CONST_36  H1   C5   N6   C7    180.00   0.0  0
 4ZJ  CONST_37  H15  C17  C16  C15   180.00   0.0  0
 4ZJ  CONST_38  H14  C16  C17  N18   180.00   0.0  0
 4ZJ  Var_01    C26  N21  C19  N18  -169.99  30.0  2
 4ZJ  Var_02    C25  C26  N21  C19   102.30  30.0  1
 4ZJ  Var_03    C23  C22  N21  C19  -102.25  30.0  1
 4ZJ  Var_04    C24  C23  C22  N21   -54.63  30.0  1
 4ZJ  Var_05    C16  C15  N14  C7    177.62  30.0  1
 4ZJ  Var_06    C15  N14  C7   C8   -130.05  30.0  1
 4ZJ  Var_07    C13  C11  N10  C9     63.79  30.0  2
 4ZJ  Var_08    H10  C1   C2   N3    119.80  30.0  2
 4ZJ  Var_09    H7   C13  C11  N10   -66.84  30.0  3
 4ZJ  Var_10    H4   C12  C11  N10    67.51  30.0  3
 4ZJ  Var_11    H24  C29  O28  C24  -173.02  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
 4ZJ  chir_01  C24  C25  O28  C23  negativ
 4ZJ  chir_02  C25  F27  C24  C26  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
 4ZJ  plan-1  N14  0.020
 4ZJ  plan-1  C15  0.020
 4ZJ  plan-1  C16  0.020
 4ZJ  plan-1  C17  0.020
 4ZJ  plan-1  N18  0.020
 4ZJ  plan-1  C19  0.020
 4ZJ  plan-1  N20  0.020
 4ZJ  plan-1  N21  0.020
 4ZJ  plan-1  H14  0.020
 4ZJ  plan-1  H15  0.020
 4ZJ  plan-2  C4   0.020
 4ZJ  plan-2  C5   0.020
 4ZJ  plan-2  C11  0.020
 4ZJ  plan-2  C7   0.020
 4ZJ  plan-2  C8   0.020
 4ZJ  plan-2  C9   0.020
 4ZJ  plan-2  N3   0.020
 4ZJ  plan-2  C1   0.020
 4ZJ  plan-2  C2   0.020
 4ZJ  plan-2  N6   0.020
 4ZJ  plan-2  N10  0.020
 4ZJ  plan-2  N14  0.020
 4ZJ  plan-2  H1   0.020
 4ZJ  plan-2  H3   0.020

