# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 09:25:27 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{R})-2-[[2-[4-(3-chloranyl-2-fluoranyl-phenyl)phenyl]-3-cyano-1,7-naphthyridin-4-yl]amino]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](Nc1c2ccncc2nc(c3ccc(cc3)c4cccc(Cl)c4F)c1C#N)C(N)=O
#
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
 P4Z  P4Z  (2~{R})-2-[[2-[4-(3-chloranyl-2-fluoranyl-phenyl)phenyl]-3-cyano-1,7-naphthyridin-4-yl]amino]butanamide  ligand  52  33  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P4Z
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
 P4Z  C4   C   CR16  0  -0.280   9.5083  -0.2360   -7.6908
 P4Z  C5   C   CR6   0   0.094   9.9118  -1.0734   -8.7309
 P4Z  C6   C   CR16  0  -0.281   9.6594  -0.6770  -10.0431
 P4Z  C7   C   CR6   0  -0.145  10.5582  -2.3768   -8.4741
 P4Z  C8   C   CR6   0   0.610  11.6461  -2.5025   -7.6208
 P4Z  C10  C   CR16  0  -0.217  11.7845  -4.8647   -8.0186
 P4Z  C15  C   CR6   0   0.212   7.9012   2.6262   -9.5246
 P4Z  C17  C   CR66  0   0.087   7.7632   4.8538   -9.0875
 P4Z  C20  C   CR16  0  -0.077   6.7452   7.3694   -9.3230
 P4Z  C21  C   CR16  0  -0.375   6.1736   6.3651  -10.0607
 P4Z  C22  C   CR66  0   0.092   6.6807   5.0578   -9.9562
 P4Z  C24  C   CR6   0  -0.116   6.7735   2.6870  -10.4021
 P4Z  C28  C   CH1   0  -0.218   4.6106   3.2572  -12.5497
 P4Z  C1   C   CR16  0  -0.262   9.0030   0.5127  -10.3113
 P4Z  C2   C   CR6   0   0.016   8.5870   1.3385   -9.2711
 P4Z  C3   C   CR16  0  -0.268   8.8601   0.9571   -7.9590
 P4Z  C9   C   CR6   0  -0.223  12.2575  -3.7242   -7.3909
 P4Z  C11  C   CR16  0  -0.262  10.7014  -4.7619   -8.8784
 P4Z  C12  C   CR16  0  -0.271  10.0997  -3.5345   -9.1035
 P4Z  CL1  CL  CL    0  -0.091  13.6127  -3.7967   -6.3286
 P4Z  F14  F   F     0  -0.285  12.1432  -1.4223   -7.0159
 P4Z  N16  N   N     0  -0.466   8.3713   3.6596   -8.8909
 P4Z  C18  C   CR16  0  -0.096   8.2653   5.9703   -8.3811
 P4Z  N19  N   N     0  -0.383   7.7822   7.1791   -8.4890
 P4Z  C23  C   CR6   0   0.535   6.1559   3.9178  -10.6783
 P4Z  C25  C   CSP   0   0.001   6.2408   1.4573  -10.8683
 P4Z  N26  N   NS    0  -0.248   5.8105   0.4393  -11.2019
 P4Z  N27  N   NH1   0  -0.705   5.1302   4.1156  -11.5052
 P4Z  C29  C   CH2   0  -0.435   5.6217   3.1115  -13.7021
 P4Z  C30  C   CH3   0  -0.677   5.2178   2.0930  -14.7572
 P4Z  C31  C   C     0   0.535   3.3278   3.9298  -13.0408
 P4Z  O32  O   O     0  -0.473   3.2147   5.1468  -13.0160
 P4Z  N33  N   NH2   0  -0.792   2.3921   3.1006  -13.5026
 P4Z  H1   H   HCR6  0   0.260   9.6706  -0.5254   -6.6611
 P4Z  H2   H   HCR6  0   0.264   9.9899  -1.2970  -10.8667
 P4Z  H3   H   HCR6  0   0.290  12.2610  -5.8178   -7.8351
 P4Z  H4   H   HCR6  0   0.275   6.3643   8.3806   -9.3960
 P4Z  H5   H   HCR6  0   0.276   5.3429   6.6238  -10.7034
 P4Z  H6   H   HCH1  0   0.297   4.3584   2.2747  -12.1521
 P4Z  H7   H   HCR6  0   0.268   8.8408   0.8029  -11.3415
 P4Z  H8   H   HCR6  0   0.260   8.5444   1.5898   -7.1399
 P4Z  H9   H   HCR6  0   0.273  10.3237  -5.6476   -9.3702
 P4Z  H10  H   HCR6  0   0.274   9.2476  -3.4672   -9.7672
 P4Z  H11  H   HCR6  0   0.275   9.1029   5.8135   -7.7085
 P4Z  H12  H   HNH1  0   0.421   4.7947   5.0646  -11.6018
 P4Z  H13  H   HCH2  0   0.252   6.5827   2.8184  -13.2731
 P4Z  H14  H   HCH2  0   0.248   5.7769   4.0948  -14.1527
 P4Z  H15  H   HCH3  0   0.244   6.0270   1.9562  -15.4738
 P4Z  H16  H   HCH3  0   0.229   5.0073   1.1203  -14.3087
 P4Z  H17  H   HCH3  0   0.232   4.3363   2.4043  -15.3161
 P4Z  H18  H   HNH2  0   0.409   1.5400   3.4641  -13.9000
 P4Z  H19  H   HNH2  0   0.418   2.5031   2.1008  -13.4809

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
 P4Z  C30  C29  single    1.521  0.020  1.521
 P4Z  N33  C31  single    1.333  0.020  1.333
 P4Z  C29  C28  single    1.540  0.020  1.540
 P4Z  C31  O32  double    1.222  0.020  1.222
 P4Z  C31  C28  single    1.529  0.020  1.529
 P4Z  C28  N27  single    1.448  0.020  1.448
 P4Z  N27  C23  single    1.332  0.020  1.332
 P4Z  N26  C25  triple    1.155  0.020  1.155
 P4Z  C23  C24  aromatic  1.405  0.020  1.405
 P4Z  C23  C22  aromatic  1.448  0.020  1.448
 P4Z  C25  C24  single    1.419  0.020  1.419
 P4Z  C1   C6   aromatic  1.385  0.020  1.385
 P4Z  C1   C2   aromatic  1.392  0.020  1.392
 P4Z  C21  C22  aromatic  1.406  0.020  1.406
 P4Z  C21  C20  aromatic  1.371  0.020  1.371
 P4Z  C24  C15  aromatic  1.430  0.020  1.430
 P4Z  C6   C5   aromatic  1.394  0.020  1.394
 P4Z  C22  C17  aromatic  1.403  0.020  1.403
 P4Z  C20  N19  aromatic  1.344  0.020  1.344
 P4Z  C15  C2   single    1.481  0.020  1.481
 P4Z  C15  N16  aromatic  1.300  0.020  1.300
 P4Z  C17  N16  aromatic  1.354  0.020  1.354
 P4Z  C17  C18  aromatic  1.413  0.020  1.413
 P4Z  C2   C3   aromatic  1.393  0.020  1.393
 P4Z  C12  C11  aromatic  1.385  0.020  1.385
 P4Z  C12  C7   aromatic  1.395  0.020  1.395
 P4Z  N19  C18  aromatic  1.306  0.020  1.306
 P4Z  C11  C10  aromatic  1.387  0.020  1.387
 P4Z  C5   C7   single    1.477  0.020  1.477
 P4Z  C5   C4   aromatic  1.395  0.020  1.395
 P4Z  C7   C8   aromatic  1.388  0.020  1.388
 P4Z  C10  C9   aromatic  1.385  0.020  1.385
 P4Z  C3   C4   aromatic  1.384  0.020  1.384
 P4Z  C8   C9   aromatic  1.385  0.020  1.385
 P4Z  C8   F14  single    1.334  0.020  1.334
 P4Z  C9   CL1  single    1.724  0.020  1.724
 P4Z  C4   H1   single    0.930  0.020  1.080
 P4Z  C6   H2   single    0.930  0.020  1.080
 P4Z  C10  H3   single    0.930  0.020  1.080
 P4Z  C20  H4   single    0.930  0.020  1.080
 P4Z  C21  H5   single    0.930  0.020  1.080
 P4Z  C28  H6   single    0.970  0.020  1.090
 P4Z  C1   H7   single    0.930  0.020  1.080
 P4Z  C3   H8   single    0.930  0.020  1.080
 P4Z  C11  H9   single    0.930  0.020  1.080
 P4Z  C12  H10  single    0.930  0.020  1.080
 P4Z  C18  H11  single    0.930  0.020  1.080
 P4Z  N27  H12  single    0.860  0.020  1.020
 P4Z  C29  H13  single    0.970  0.020  1.090
 P4Z  C29  H14  single    0.970  0.020  1.090
 P4Z  C30  H15  single    0.970  0.020  1.090
 P4Z  C30  H16  single    0.970  0.020  1.090
 P4Z  C30  H17  single    0.970  0.020  1.090
 P4Z  N33  H18  single    0.860  0.020  1.020
 P4Z  N33  H19  single    0.860  0.020  1.020

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
 P4Z  H1   C4   C3   119.03  3.000
 P4Z  H1   C4   C5   120.38  3.000
 P4Z  C3   C4   C5   120.56  3.000
 P4Z  C7   C5   C6   119.59  3.000
 P4Z  C7   C5   C4   121.77  3.000
 P4Z  C6   C5   C4   118.61  3.000
 P4Z  H2   C6   C1   119.30  3.000
 P4Z  H2   C6   C5   119.87  3.000
 P4Z  C1   C6   C5   120.83  3.000
 P4Z  C12  C7   C8   117.36  3.000
 P4Z  C8   C7   C5   121.98  3.000
 P4Z  C12  C7   C5   120.65  3.000
 P4Z  F14  C8   C9   118.32  3.000
 P4Z  F14  C8   C7   119.82  3.000
 P4Z  C9   C8   C7   121.85  3.000
 P4Z  H3   C10  C11  120.98  3.000
 P4Z  H3   C10  C9   119.89  3.000
 P4Z  C11  C10  C9   119.12  3.000
 P4Z  N16  C15  C2   116.12  3.000
 P4Z  N16  C15  C24  123.39  3.000
 P4Z  C2   C15  C24  120.48  3.000
 P4Z  C18  C17  N16  117.67  3.000
 P4Z  C18  C17  C22  117.96  3.000
 P4Z  N16  C17  C22  124.37  3.000
 P4Z  H4   C20  N19  116.44  3.000
 P4Z  H4   C20  C21  120.07  3.000
 P4Z  N19  C20  C21  123.49  3.000
 P4Z  H5   C21  C22  122.93  3.000
 P4Z  H5   C21  C20  117.69  3.000
 P4Z  C22  C21  C20  119.39  3.000
 P4Z  C23  C22  C21  124.35  3.000
 P4Z  C21  C22  C17  117.35  3.000
 P4Z  C23  C22  C17  118.30  3.000
 P4Z  C25  C24  C23  121.99  3.000
 P4Z  C25  C24  C15  117.44  3.000
 P4Z  C23  C24  C15  120.31  3.000
 P4Z  H6   C28  C31  108.64  3.000
 P4Z  H6   C28  C29  109.86  3.000
 P4Z  C31  C28  C29  110.60  3.000
 P4Z  H6   C28  N27  110.75  3.000
 P4Z  C31  C28  N27  105.77  3.000
 P4Z  C29  C28  N27  111.11  3.000
 P4Z  H7   C1   C2   120.49  3.000
 P4Z  H7   C1   C6   119.05  3.000
 P4Z  C2   C1   C6   120.44  3.000
 P4Z  C3   C2   C1   118.87  3.000
 P4Z  C3   C2   C15  119.34  3.000
 P4Z  C1   C2   C15  121.76  3.000
 P4Z  H8   C3   C2   119.70  3.000
 P4Z  H8   C3   C4   119.61  3.000
 P4Z  C2   C3   C4   120.68  3.000
 P4Z  CL1  C9   C10  120.88  3.000
 P4Z  CL1  C9   C8   119.10  3.000
 P4Z  C10  C9   C8   120.02  3.000
 P4Z  H9   C11  C12  120.01  3.000
 P4Z  H9   C11  C10  119.62  3.000
 P4Z  C12  C11  C10  120.37  3.000
 P4Z  H10  C12  C11  119.78  3.000
 P4Z  H10  C12  C7   118.94  3.000
 P4Z  C11  C12  C7   121.27  3.000
 P4Z  C17  N16  C15  117.88  3.000
 P4Z  H11  C18  N19  118.04  3.000
 P4Z  H11  C18  C17  118.02  3.000
 P4Z  N19  C18  C17  123.94  3.000
 P4Z  C18  N19  C20  117.87  3.000
 P4Z  N27  C23  C24  126.20  3.000
 P4Z  C24  C23  C22  115.63  3.000
 P4Z  N27  C23  C22  118.15  3.000
 P4Z  N26  C25  C24  180.00  3.000
 P4Z  H12  N27  C23  117.00  3.000
 P4Z  H12  N27  C28  111.62  3.000
 P4Z  C23  N27  C28  129.48  3.000
 P4Z  H14  C29  H13  106.16  3.000
 P4Z  H14  C29  C30  110.74  3.000
 P4Z  H13  C29  C30  109.04  3.000
 P4Z  H14  C29  C28  108.47  3.000
 P4Z  H13  C29  C28  108.00  3.000
 P4Z  C30  C29  C28  114.08  3.000
 P4Z  H17  C30  H16  108.03  3.000
 P4Z  H17  C30  H15  107.43  3.000
 P4Z  H16  C30  H15  107.55  3.000
 P4Z  H17  C30  C29  112.30  3.000
 P4Z  H16  C30  C29  111.27  3.000
 P4Z  H15  C30  C29  110.06  3.000
 P4Z  N33  C31  O32  124.16  3.000
 P4Z  O32  C31  C28  120.59  3.000
 P4Z  N33  C31  C28  115.24  3.000
 P4Z  H19  N33  H18  117.39  3.000
 P4Z  H19  N33  C31  122.23  3.000
 P4Z  H18  N33  C31  120.38  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
 P4Z  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 P4Z  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 P4Z  CONST_05  C15  C2   C3   C4    180.00   0.0  0
 P4Z  CONST_06  C2   C1   C6   C5      0.00   0.0  0
 P4Z  CONST_07  C11  C12  C7   C5    180.00   0.0  0
 P4Z  CONST_08  C9   C8   C7   C5    180.00   0.0  0
 P4Z  CONST_09  C2   C3   C4   C5      0.00   0.0  0
 P4Z  CONST_10  C15  C2   C1   C6    180.00   0.0  0
 P4Z  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 P4Z  CONST_14  C3   C4   C5   C6      0.00   0.0  0
 P4Z  CONST_15  C10  C11  C12  C7      0.00   0.0  0
 P4Z  CONST_16  C1   C6   C5   C7    180.00   0.0  0
 P4Z  CONST_17  C3   C4   C5   C7    180.00   0.0  0
 P4Z  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 P4Z  CONST_19  C11  C12  C7   C8      0.00   0.0  0
 P4Z  CONST_20  C11  C10  C9   C8      0.00   0.0  0
 P4Z  CONST_21  C22  C23  C24  C15     0.00   0.0  0
 P4Z  CONST_22  C22  C17  N16  C15     0.00   0.0  0
 P4Z  CONST_23  C18  C17  N16  C15   180.00   0.0  0
 P4Z  CONST_24  C24  C23  C22  C17     0.00   0.0  0
 P4Z  CONST_25  C20  C21  C22  C17     0.00   0.0  0
 P4Z  CONST_26  C24  C15  N16  C17     0.00   0.0  0
 P4Z  CONST_27  C2   C15  N16  C17   180.00   0.0  0
 P4Z  CONST_28  C20  N19  C18  C17     0.00   0.0  0
 P4Z  CONST_29  C23  C22  C21  C20   180.00   0.0  0
 P4Z  CONST_30  C24  C23  C22  C21   180.00   0.0  0
 P4Z  CONST_31  N16  C17  C22  C21   180.00   0.0  0
 P4Z  CONST_32  C18  C17  C22  C21     0.00   0.0  0
 P4Z  CONST_33  C18  N19  C20  C21     0.00   0.0  0
 P4Z  CONST_34  N19  C20  C21  C22     0.00   0.0  0
 P4Z  CONST_35  N19  C18  C17  C22     0.00   0.0  0
 P4Z  CONST_39  C23  C24  C15  C2    180.00   0.0  0
 P4Z  CONST_41  C12  C11  C10  C9      0.00   0.0  0
 P4Z  CONST_42  C12  C7   C8   C9      0.00   0.0  0
 P4Z  CONST_43  C23  C24  C15  N16     0.00   0.0  0
 P4Z  CONST_44  C23  C22  C17  N16     0.00   0.0  0
 P4Z  CONST_45  N19  C18  C17  N16   180.00   0.0  0
 P4Z  CONST_46  C23  C22  C17  C18   180.00   0.0  0
 P4Z  CONST_47  F14  C8   C7   C5      0.00   0.0  0
 P4Z  CONST_48  CL1  C9   C8   C7    180.00   0.0  0
 P4Z  CONST_49  F14  C8   C9   C10   180.00   0.0  0
 P4Z  CONST_50  N27  C23  C24  C15   180.00   0.0  0
 P4Z  CONST_51  N27  C23  C22  C17   180.00   0.0  0
 P4Z  CONST_52  N27  C23  C22  C21     0.00   0.0  0
 P4Z  CONST_53  C25  C24  C23  C22   180.00   0.0  0
 P4Z  CONST_54  C25  C24  C15  C2      0.00   0.0  0
 P4Z  CONST_55  CL1  C9   C10  C11   180.00   0.0  0
 P4Z  CONST_56  F14  C8   C7   C12   180.00   0.0  0
 P4Z  CONST_57  C25  C24  C15  N16   180.00   0.0  0
 P4Z  CONST_58  H2   C6   C5   C4    180.00   0.0  0
 P4Z  CONST_59  H7   C1   C6   C5    180.00   0.0  0
 P4Z  CONST_60  H10  C12  C7   C5      0.00   0.0  0
 P4Z  CONST_61  H8   C3   C4   C5    180.00   0.0  0
 P4Z  CONST_62  H1   C4   C5   C6    180.00   0.0  0
 P4Z  CONST_63  H9   C11  C12  C7    180.00   0.0  0
 P4Z  CONST_64  H3   C10  C9   C8    180.00   0.0  0
 P4Z  CONST_65  H5   C21  C22  C17   180.00   0.0  0
 P4Z  CONST_66  H11  C18  N19  C20   180.00   0.0  0
 P4Z  CONST_67  H4   C20  C21  C22   180.00   0.0  0
 P4Z  CONST_70  H12  N27  C23  C22     0.00   0.0  0
 P4Z  CONST_71  H18  N33  C31  C28   180.00   0.0  0
 P4Z  CONST_72  H19  N33  C31  C28     0.00   0.0  0
 P4Z  Var_01    H15  C30  C29  C28  -173.31  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
 P4Z  chir_01  C28  C29  C31  N27  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
 P4Z  plan-1  C4   0.020
 P4Z  plan-1  C5   0.020
 P4Z  plan-1  C6   0.020
 P4Z  plan-1  C7   0.020
 P4Z  plan-1  C15  0.020
 P4Z  plan-1  C1   0.020
 P4Z  plan-1  C2   0.020
 P4Z  plan-1  C3   0.020
 P4Z  plan-1  H1   0.020
 P4Z  plan-1  H2   0.020
 P4Z  plan-1  H7   0.020
 P4Z  plan-1  H8   0.020
 P4Z  plan-2  C5   0.020
 P4Z  plan-2  C7   0.020
 P4Z  plan-2  C8   0.020
 P4Z  plan-2  C10  0.020
 P4Z  plan-2  C9   0.020
 P4Z  plan-2  C11  0.020
 P4Z  plan-2  C12  0.020
 P4Z  plan-2  CL1  0.020
 P4Z  plan-2  F14  0.020
 P4Z  plan-2  H3   0.020
 P4Z  plan-2  H9   0.020
 P4Z  plan-2  H10  0.020
 P4Z  plan-3  C15  0.020
 P4Z  plan-3  C17  0.020
 P4Z  plan-3  C20  0.020
 P4Z  plan-3  C21  0.020
 P4Z  plan-3  C22  0.020
 P4Z  plan-3  C24  0.020
 P4Z  plan-3  C2   0.020
 P4Z  plan-3  N16  0.020
 P4Z  plan-3  C18  0.020
 P4Z  plan-3  N19  0.020
 P4Z  plan-3  C23  0.020
 P4Z  plan-3  C25  0.020
 P4Z  plan-3  N26  0.020
 P4Z  plan-3  N27  0.020
 P4Z  plan-3  H4   0.020
 P4Z  plan-3  H5   0.020
 P4Z  plan-3  H11  0.020
 P4Z  plan-4  C28  0.020
 P4Z  plan-4  C31  0.020
 P4Z  plan-4  O32  0.020
 P4Z  plan-4  N33  0.020
 P4Z  plan-4  H18  0.020
 P4Z  plan-4  H19  0.020
 P4Z  plan-5  C28  0.020
 P4Z  plan-5  C23  0.020
 P4Z  plan-5  N27  0.020
 P4Z  plan-5  H12  0.020

