# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 07:04:01 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: 2-amino-N-cyclopropyl-5-(4-{[(2R)-2-(3,5-difluorophenyl)-2-hydroxyacetyl]amino}-2-methylphenyl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(NC(=O)[C@H](O)c2cc(F)cc(F)c2)ccc1c3cnc(N)c(c3)C(=O)NC4CC4
#
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
 Z6P  Z6P  2-amino-N-cyclopropyl-5-(4-{[(2R)-2-(3,5-difluorophenyl)-2-hydroxyacetyl]amino}-2-methylphenyl)pyridine-3-carboxamide  ligand  55  33  .  2022-08-11  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_Z6P
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
 Z6P  C1   C  CR6   0   0.043   1.9614  12.9548  -21.0916
 Z6P  C2   C  CR6   0   0.080   1.1723  13.2155  -19.9590
 Z6P  C3   C  CR16  0  -0.392  -0.1885  12.9487  -20.0173
 Z6P  C4   C  CR6   0   0.388  -0.8001  12.4210  -21.1551
 Z6P  C5   C  CR16  0  -0.317  -0.0127  12.1351  -22.2676
 Z6P  C6   C  CH3   0  -0.756   1.7502  13.7476  -18.6775
 Z6P  C7   C  CR6   0  -0.047   3.4103  13.2292  -21.1278
 Z6P  C8   C  C     0   0.502  -3.0030  11.6317  -21.9816
 Z6P  C9   C  CH1   0  -0.111  -4.4804  11.6218  -21.5715
 Z6P  C10  C  CR6   0   0.087  -4.8332  10.2156  -21.1331
 Z6P  C12  C  CR6   0   0.563  -5.6183   8.0253  -21.6467
 Z6P  O2   O  O     0  -0.487   6.8746  16.4938  -21.0350
 Z6P  N3   N  NH1   0  -0.648   5.2406  16.6767  -19.4966
 Z6P  C21  C  CH1   0  -0.079   5.6604  17.9594  -19.0371
 Z6P  C22  C  CH2   0  -0.510   4.5980  18.9090  -18.5896
 Z6P  C23  C  CH2   0  -0.482   5.3439  19.1656  -19.8625
 Z6P  C18  C  CR6   0  -0.183   5.3161  14.7027  -20.8618
 Z6P  C19  C  CR16  0  -0.225   3.9548  14.4621  -20.7805
 Z6P  C17  C  CR6   0   0.447   6.1385  13.6585  -21.3581
 Z6P  N2   N  NH2   0  -0.831   7.4768  13.7851  -21.4854
 Z6P  N1   N  N     0  -0.449   5.6222  12.4689  -21.6767
 Z6P  C16  C  CR16  0  -0.090   4.3211  12.2710  -21.5601
 Z6P  C    C  CR16  0  -0.289   1.3446  12.4098  -22.2156
 Z6P  N    N  NH1   0  -0.734  -2.1848  12.2321  -21.0937
 Z6P  O    O  O     0  -0.452  -2.6610  11.0997  -23.0201
 Z6P  O1   O  OH1   0  -0.653  -4.6864  12.5769  -20.5722
 Z6P  C11  C  CR16  0  -0.467  -5.3196   9.3071  -22.0653
 Z6P  C15  C  CR16  0  -0.461  -4.6520   9.8364  -19.8075
 Z6P  C14  C  CR6   0   0.565  -4.9688   8.5426  -19.4447
 Z6P  F    F  F     0  -0.307  -4.8020   8.1722  -18.1690
 Z6P  C13  C  CR16  0  -0.562  -5.4552   7.6087  -20.3396
 Z6P  F1   F  F     0  -0.306  -6.0942   7.1477  -22.5384
 Z6P  H1   H  HCR6  0   0.263  -0.7947  13.1489  -19.1398
 Z6P  H2   H  HCR6  0   0.276  -0.4359  11.7229  -23.1686
 Z6P  H3   H  HCH3  0   0.251   1.8850  14.8304  -18.7094
 Z6P  H4   H  HCH3  0   0.256   1.0896  13.5329  -17.8386
 Z6P  H5   H  HCH3  0   0.248   2.7242  13.3099  -18.4596
 Z6P  H6   H  HCH1  0   0.285  -5.0469  11.8586  -22.4811
 Z6P  H7   H  HNH1  0   0.408   4.5593  16.1821  -18.9428
 Z6P  H8   H  HCH1  0   0.267   6.5966  17.9703  -18.4870
 Z6P  H9   H  HCH2  0   0.259   4.8099  19.5273  -17.7277
 Z6P  H10  H  HCH2  0   0.258   3.5685  18.5816  -18.6655
 Z6P  H11  H  HCH2  0   0.255   6.0735  19.9642  -19.8859
 Z6P  H12  H  HCH2  0   0.255   4.8175  19.0072  -20.7947
 Z6P  H13  H  HCR6  0   0.272   3.2916  15.2626  -20.4763
 Z6P  H14  H  HNH2  0   0.386   7.9569  13.0572  -21.9874
 Z6P  H15  H  HNH2  0   0.401   7.8711  14.7094  -21.5301
 Z6P  H16  H  HCR6  0   0.259   3.9688  11.2794  -21.8299
 Z6P  H17  H  HCR6  0   0.251   1.9414  12.2085  -23.0972
 Z6P  H18  H  HNH1  0   0.424  -2.6395  12.6147  -20.2756
 Z6P  H19  H  HOH1  0   0.473  -5.6112  12.5665  -20.3012
 Z6P  H20  H  HCR6  0   0.283  -5.4761   9.5956  -23.0969
 Z6P  H21  H  HCR6  0   0.285  -4.2775  10.5296  -19.0659
 Z6P  H22  H  HCR6  0   0.304  -5.7021   6.6015  -20.0303
 Z6P  C20  C  C     0   0.544   5.8845  16.0251  -20.4843

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
 Z6P  F1   C12  single    1.339  0.020  1.339
 Z6P  O    C8   double    1.216  0.020  1.216
 Z6P  C11  C12  aromatic  1.381  0.020  1.381
 Z6P  C11  C10  aromatic  1.390  0.020  1.390
 Z6P  C12  C13  aromatic  1.382  0.020  1.382
 Z6P  C5   C    aromatic  1.386  0.020  1.386
 Z6P  C5   C4   aromatic  1.393  0.020  1.393
 Z6P  C    C1   aromatic  1.393  0.020  1.393
 Z6P  C8   C9   single    1.533  0.020  1.533
 Z6P  C8   N    single    1.348  0.020  1.348
 Z6P  N1   C16  aromatic  1.321  0.020  1.321
 Z6P  N1   C17  aromatic  1.335  0.020  1.335
 Z6P  C9   C10  single    1.515  0.020  1.515
 Z6P  C9   O1   single    1.398  0.020  1.398
 Z6P  N2   C17  single    1.350  0.020  1.350
 Z6P  C16  C7   aromatic  1.391  0.020  1.391
 Z6P  C17  C18  aromatic  1.419  0.020  1.419
 Z6P  C10  C15  aromatic  1.391  0.020  1.391
 Z6P  C7   C1   single    1.475  0.020  1.475
 Z6P  C7   C19  aromatic  1.392  0.020  1.392
 Z6P  C13  C14  aromatic  1.382  0.020  1.382
 Z6P  C4   N    single    1.399  0.020  1.399
 Z6P  C4   C3   aromatic  1.395  0.020  1.395
 Z6P  C1   C2   aromatic  1.405  0.020  1.405
 Z6P  C18  C19  aromatic  1.385  0.020  1.385
 Z6P  C18  C20  single    1.488  0.020  1.488
 Z6P  O2   C20  double    1.226  0.020  1.226
 Z6P  C23  C21  single    1.495  0.020  1.495
 Z6P  C23  C22  single    1.497  0.020  1.497
 Z6P  C20  N3   single    1.347  0.020  1.347
 Z6P  C15  C14  aromatic  1.381  0.020  1.381
 Z6P  N3   C21  single    1.426  0.020  1.426
 Z6P  C14  F    single    1.339  0.020  1.339
 Z6P  C3   C2   aromatic  1.388  0.020  1.388
 Z6P  C2   C6   single    1.503  0.020  1.503
 Z6P  C21  C22  single    1.494  0.020  1.494
 Z6P  C3   H1   single    0.930  0.020  1.080
 Z6P  C5   H2   single    0.930  0.020  1.080
 Z6P  C6   H3   single    0.970  0.020  1.090
 Z6P  C6   H4   single    0.970  0.020  1.090
 Z6P  C6   H5   single    0.970  0.020  1.090
 Z6P  C9   H6   single    0.970  0.020  1.090
 Z6P  N3   H7   single    0.860  0.020  1.020
 Z6P  C21  H8   single    0.970  0.020  1.090
 Z6P  C22  H9   single    0.970  0.020  1.090
 Z6P  C22  H10  single    0.970  0.020  1.090
 Z6P  C23  H11  single    0.970  0.020  1.090
 Z6P  C23  H12  single    0.970  0.020  1.090
 Z6P  C19  H13  single    0.930  0.020  1.080
 Z6P  N2   H14  single    0.890  0.020  1.040
 Z6P  N2   H15  single    0.890  0.020  1.040
 Z6P  C16  H16  single    0.930  0.020  1.080
 Z6P  C    H17  single    0.930  0.020  1.080
 Z6P  N    H18  single    0.860  0.020  1.020
 Z6P  O1   H19  single    0.850  0.020  0.980
 Z6P  C11  H20  single    0.930  0.020  1.080
 Z6P  C15  H21  single    0.930  0.020  1.080
 Z6P  C13  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
 Z6P  C    C1   C7   119.20  3.000
 Z6P  C7   C1   C2   122.48  3.000
 Z6P  C    C1   C2   118.32  3.000
 Z6P  C6   C2   C3   118.74  3.000
 Z6P  C6   C2   C1   122.49  3.000
 Z6P  C3   C2   C1   118.77  3.000
 Z6P  H1   C3   C4   118.96  3.000
 Z6P  H1   C3   C2   118.58  3.000
 Z6P  C4   C3   C2   122.46  3.000
 Z6P  N    C4   C5   124.54  3.000
 Z6P  N    C4   C3   116.69  3.000
 Z6P  C5   C4   C3   118.77  3.000
 Z6P  H2   C5   C    119.47  3.000
 Z6P  H2   C5   C4   121.63  3.000
 Z6P  C    C5   C4   118.89  3.000
 Z6P  H5   C6   H4   107.99  3.000
 Z6P  H5   C6   H3   107.09  3.000
 Z6P  H4   C6   H3   107.03  3.000
 Z6P  H5   C6   C2   111.83  3.000
 Z6P  H4   C6   C2   110.71  3.000
 Z6P  H3   C6   C2   111.94  3.000
 Z6P  C16  C7   C19  115.57  3.000
 Z6P  C19  C7   C1   122.89  3.000
 Z6P  C16  C7   C1   121.51  3.000
 Z6P  O    C8   N    125.91  3.000
 Z6P  N    C8   C9   114.30  3.000
 Z6P  O    C8   C9   119.78  3.000
 Z6P  H6   C9   O1   111.66  3.000
 Z6P  H6   C9   C10  108.66  3.000
 Z6P  O1   C9   C10  113.16  3.000
 Z6P  H6   C9   C8   105.92  3.000
 Z6P  O1   C9   C8   109.20  3.000
 Z6P  C10  C9   C8   107.93  3.000
 Z6P  C15  C10  C11  120.45  3.000
 Z6P  C15  C10  C9   119.91  3.000
 Z6P  C11  C10  C9   119.63  3.000
 Z6P  F1   C12  C13  118.33  3.000
 Z6P  C13  C12  C11  122.76  3.000
 Z6P  F1   C12  C11  118.91  3.000
 Z6P  H7   N3   C21  117.62  3.000
 Z6P  H7   N3   C20  119.25  3.000
 Z6P  C21  N3   C20  122.05  3.000
 Z6P  H8   C21  C23  117.00  3.000
 Z6P  H8   C21  C22  117.07  3.000
 Z6P  C23  C21  C22   60.13  3.000
 Z6P  H8   C21  N3   115.22  3.000
 Z6P  C22  C21  N3   117.33  3.000
 Z6P  C23  C21  N3   119.04  3.000
 Z6P  H10  C22  H9   114.51  3.000
 Z6P  H10  C22  C23  117.76  3.000
 Z6P  H9   C22  C23  118.80  3.000
 Z6P  H10  C22  C21  117.58  3.000
 Z6P  H9   C22  C21  117.57  3.000
 Z6P  C23  C22  C21   59.99  3.000
 Z6P  H12  C23  H11  114.66  3.000
 Z6P  H12  C23  C22  117.70  3.000
 Z6P  H11  C23  C22  118.73  3.000
 Z6P  H12  C23  C21  117.41  3.000
 Z6P  H11  C23  C21  117.68  3.000
 Z6P  C22  C23  C21   59.87  3.000
 Z6P  C17  C18  C19  117.55  3.000
 Z6P  C19  C18  C20  121.00  3.000
 Z6P  C17  C18  C20  121.42  3.000
 Z6P  H13  C19  C18  119.34  3.000
 Z6P  H13  C19  C7   119.02  3.000
 Z6P  C18  C19  C7   121.59  3.000
 Z6P  N1   C17  N2   116.38  3.000
 Z6P  N2   C17  C18  122.58  3.000
 Z6P  N1   C17  C18  120.99  3.000
 Z6P  H15  N2   H14  117.10  3.000
 Z6P  H15  N2   C17  118.61  3.000
 Z6P  H14  N2   C17  116.88  3.000
 Z6P  C16  N1   C17  119.55  3.000
 Z6P  H16  C16  N1   115.73  3.000
 Z6P  H16  C16  C7   119.58  3.000
 Z6P  N1   C16  C7   124.69  3.000
 Z6P  H17  C    C5   118.18  3.000
 Z6P  H17  C    C1   119.03  3.000
 Z6P  C5   C    C1   122.78  3.000
 Z6P  H18  N    C8   115.36  3.000
 Z6P  H18  N    C4   115.44  3.000
 Z6P  C8   N    C4   129.19  3.000
 Z6P  H19  O1   C9   109.59  3.000
 Z6P  H20  C11  C12  120.32  3.000
 Z6P  H20  C11  C10  121.04  3.000
 Z6P  C12  C11  C10  118.63  3.000
 Z6P  H21  C15  C14  119.98  3.000
 Z6P  H21  C15  C10  121.59  3.000
 Z6P  C14  C15  C10  118.43  3.000
 Z6P  C13  C14  F    118.29  3.000
 Z6P  F    C14  C15  118.76  3.000
 Z6P  C13  C14  C15  122.95  3.000
 Z6P  H22  C13  C14  121.62  3.000
 Z6P  H22  C13  C12  121.61  3.000
 Z6P  C14  C13  C12  116.77  3.000
 Z6P  C18  C20  N3   115.68  3.000
 Z6P  N3   C20  O2   122.03  3.000
 Z6P  C18  C20  O2   122.29  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
 Z6P  CONST_01  C4   C5   C    C1     0.00   0.0  0
 Z6P  CONST_02  N1   C16  C7   C1   180.00   0.0  0
 Z6P  CONST_03  C18  C19  C7   C1   180.00   0.0  0
 Z6P  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 Z6P  CONST_05  C5   C    C1   C2     0.00   0.0  0
 Z6P  CONST_08  C5   C4   C3   C2     0.00   0.0  0
 Z6P  CONST_09  C    C5   C4   C3     0.00   0.0  0
 Z6P  CONST_10  C    C1   C2   C3     0.00   0.0  0
 Z6P  CONST_11  C7   C1   C2   C3   180.00   0.0  0
 Z6P  CONST_12  C7   C1   C    C5   180.00   0.0  0
 Z6P  CONST_13  C17  N1   C16  C7     0.00   0.0  0
 Z6P  CONST_14  C17  C18  C19  C7     0.00   0.0  0
 Z6P  CONST_15  C13  C12  C11  C10    0.00   0.0  0
 Z6P  CONST_16  C13  C14  C15  C10    0.00   0.0  0
 Z6P  CONST_17  C15  C10  C11  C12    0.00   0.0  0
 Z6P  CONST_18  C15  C14  C13  C12    0.00   0.0  0
 Z6P  CONST_19  C16  N1   C17  C18    0.00   0.0  0
 Z6P  CONST_20  C16  C7   C19  C18    0.00   0.0  0
 Z6P  CONST_21  N1   C16  C7   C19    0.00   0.0  0
 Z6P  CONST_23  N1   C17  C18  C19    0.00   0.0  0
 Z6P  CONST_25  C14  C13  C12  C11    0.00   0.0  0
 Z6P  CONST_26  C14  C15  C10  C11    0.00   0.0  0
 Z6P  CONST_27  N    C4   C3   C2   180.00   0.0  0
 Z6P  CONST_28  C6   C2   C3   C4   180.00   0.0  0
 Z6P  CONST_29  C    C1   C2   C6   180.00   0.0  0
 Z6P  CONST_30  C7   C1   C2   C6     0.00   0.0  0
 Z6P  CONST_31  C20  C18  C19  C7   180.00   0.0  0
 Z6P  CONST_32  C12  C11  C10  C9   180.00   0.0  0
 Z6P  CONST_33  C14  C15  C10  C9   180.00   0.0  0
 Z6P  CONST_34  F1   C12  C11  C10  180.00   0.0  0
 Z6P  CONST_35  F    C14  C15  C10  180.00   0.0  0
 Z6P  CONST_36  F    C14  C13  C12  180.00   0.0  0
 Z6P  CONST_37  N1   C17  C18  C20  180.00   0.0  0
 Z6P  CONST_38  N2   C17  C18  C19  180.00   0.0  0
 Z6P  CONST_39  C16  N1   C17  N2   180.00   0.0  0
 Z6P  CONST_40  N    C4   C5   C    180.00   0.0  0
 Z6P  CONST_41  F1   C12  C13  C14  180.00   0.0  0
 Z6P  CONST_42  H2   C5   C    C1   180.00   0.0  0
 Z6P  CONST_43  H16  C16  C7   C1     0.00   0.0  0
 Z6P  CONST_44  H13  C19  C7   C1     0.00   0.0  0
 Z6P  CONST_45  H1   C3   C2   C1   180.00   0.0  0
 Z6P  CONST_46  H17  C    C1   C2   180.00   0.0  0
 Z6P  CONST_47  H22  C13  C12  C11  180.00   0.0  0
 Z6P  CONST_48  H21  C15  C10  C11  180.00   0.0  0
 Z6P  CONST_49  H20  C11  C10  C15  180.00   0.0  0
 Z6P  CONST_50  C18  C20  N3   C21  180.00   0.0  0
 Z6P  CONST_51  C8   N    C4   C3   180.00   0.0  0
 Z6P  CONST_52  C8   N    C4   C5     0.00   0.0  0
 Z6P  CONST_53  H18  N    C4   C3     0.00   0.0  0
 Z6P  CONST_54  H14  N2   C17  C18  180.00   0.0  0
 Z6P  CONST_56  O    C8   N    C4     0.00   0.0  0
 Z6P  CONST_57  C9   C8   N    C4   180.00   0.0  0
 Z6P  CONST_58  C21  N3   C20  O2     0.00   0.0  0
 Z6P  CONST_59  H7   N3   C20  C18    0.00   0.0  0
 Z6P  Var_01    C22  C23  C21  N3   106.66  30.0  1
 Z6P  Var_02    H9   C22  C23  C21  107.00  30.0  1
 Z6P  Var_03    C17  C18  C20  O2    30.37  30.0  2
 Z6P  Var_04    C23  C21  N3   C20   76.66  30.0  3
 Z6P  Var_05    H3   C6   C2   C1    81.95  30.0  2

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
 Z6P  chir_01  C9   C8   C10  O1   negativ
 Z6P  chir_02  C21  C23  N3   C22  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
 Z6P  plan-1  C1   0.020
 Z6P  plan-1  C2   0.020
 Z6P  plan-1  C3   0.020
 Z6P  plan-1  C4   0.020
 Z6P  plan-1  C5   0.020
 Z6P  plan-1  C6   0.020
 Z6P  plan-1  C7   0.020
 Z6P  plan-1  C    0.020
 Z6P  plan-1  N    0.020
 Z6P  plan-1  H1   0.020
 Z6P  plan-1  H2   0.020
 Z6P  plan-1  H17  0.020
 Z6P  plan-2  C1   0.020
 Z6P  plan-2  C7   0.020
 Z6P  plan-2  C18  0.020
 Z6P  plan-2  C19  0.020
 Z6P  plan-2  C17  0.020
 Z6P  plan-2  N2   0.020
 Z6P  plan-2  N1   0.020
 Z6P  plan-2  C16  0.020
 Z6P  plan-2  H13  0.020
 Z6P  plan-2  H16  0.020
 Z6P  plan-2  C20  0.020
 Z6P  plan-3  C9   0.020
 Z6P  plan-3  C10  0.020
 Z6P  plan-3  C12  0.020
 Z6P  plan-3  C11  0.020
 Z6P  plan-3  C15  0.020
 Z6P  plan-3  C14  0.020
 Z6P  plan-3  F    0.020
 Z6P  plan-3  C13  0.020
 Z6P  plan-3  F1   0.020
 Z6P  plan-3  H20  0.020
 Z6P  plan-3  H21  0.020
 Z6P  plan-3  H22  0.020
 Z6P  plan-4  O2   0.020
 Z6P  plan-4  N3   0.020
 Z6P  plan-4  C21  0.020
 Z6P  plan-4  C18  0.020
 Z6P  plan-4  H7   0.020
 Z6P  plan-4  C20  0.020
 Z6P  plan-5  C17  0.020
 Z6P  plan-5  N2   0.020
 Z6P  plan-5  H14  0.020
 Z6P  plan-5  H15  0.020
 Z6P  plan-6  C4   0.020
 Z6P  plan-6  C8   0.020
 Z6P  plan-6  C9   0.020
 Z6P  plan-6  N    0.020
 Z6P  plan-6  O    0.020
 Z6P  plan-6  H18  0.020

