# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 05:28:20 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 3,4-dichloro-5-(5-hydroxypyridin-3-yl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(Cl)c(Cl)c(c1)c2cncc(O)c2)C(O)=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
 4ZK  4ZK  3,4-dichloro-5-(5-hydroxypyridin-3-yl)-L-phenylalanine  ligand  32  21  .  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_4ZK
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
 4ZK  N1   N   NH2    0  -0.791  -3.7004  -0.3010   1.5020
 4ZK  C4   C   CR6    0   0.161  -1.5749  -0.1922  -0.6667
 4ZK  C5   C   CR16   0  -0.362  -0.4065   0.5539  -0.5478
 4ZK  C6   C   CR16   0  -0.309  -1.4772  -1.5777  -0.6262
 4ZK  C7   C   CR6    0   0.041  -0.2429  -2.1914  -0.4764
 4ZK  C8   C   CR6    0  -0.105   0.9166  -1.4344  -0.3595
 4ZK  C10  C   CR6    0  -0.024   2.0364   0.8215  -0.2922
 4ZK  C13  C   CR16   0  -0.193   4.1520   2.5279  -0.2197
 4ZK  C1   C   C      0   0.406  -4.7940   1.6246   0.4091
 4ZK  O2   O   O      0  -0.603  -5.8607   0.9931   0.5322
 4ZK  C2   C   CH1    0  -0.201  -3.4819   0.8392   0.6362
 4ZK  C3   C   CH2    0  -0.533  -2.9054   0.4883  -0.7597
 4ZK  CL1  CL  CL     0  -0.098  -0.1669  -3.9135  -0.4499
 4ZK  CL2  CL  CL     0  -0.096   2.4431  -2.2212  -0.2216
 4ZK  C9   C   CR6    0   0.167   0.8402  -0.0406  -0.3932
 4ZK  C11  C   CR16   0  -0.255   2.8446   0.8290   0.8361
 4ZK  C12  C   CR16   0  -0.101   2.3481   1.6921  -1.3343
 4ZK  N2   N   N      0  -0.380   3.3804   2.5205  -1.2948
 4ZK  C14  C   CR6    0   0.292   3.9266   1.6984   0.8784
 4ZK  O3   O   OH1    0  -0.621   4.7036   1.7075   1.9732
 4ZK  H1   H   HNH2   0   0.330  -4.4634  -0.8535   1.1321
 4ZK  H2   H   HNH2   0   0.338  -2.8826  -0.8979   1.5222
 4ZK  H4   H   HCR6   0   0.261  -0.4651   1.6357  -0.5662
 4ZK  H5   H   HCR6   0   0.285  -2.3646  -2.1891  -0.7268
 4ZK  H6   H   HCR6   0   0.275   4.9902   3.2196  -0.2167
 4ZK  H8   H   HCH1   0   0.219  -2.7646   1.5077   1.1249
 4ZK  H9   H   HCH2   0   0.249  -2.8071   1.4074  -1.3407
 4ZK  H10  H   HCH2   0   0.245  -3.6181  -0.1547  -1.2847
 4ZK  H11  H   HCR6   0   0.280   2.6342   0.1818   1.6789
 4ZK  H12  H   HCR6   0   0.262   1.7388   1.7069  -2.2314
 4ZK  H13  H   HOH1   0   0.479   5.4077   2.3605   1.8856
 4ZK  O1   O   OC    -1  -0.617  -4.6653   2.8188   0.0762

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
 4ZK  O2   C1   deloc     1.246  0.020  1.246
 4ZK  O1   C1   deloc     1.246  0.020  1.246
 4ZK  C1   C2   single    1.546  0.020  1.546
 4ZK  C2   C3   single    1.551  0.020  1.551
 4ZK  C2   N1   single    1.448  0.020  1.448
 4ZK  C3   C4   single    1.497  0.020  1.497
 4ZK  C4   C6   aromatic  1.389  0.020  1.389
 4ZK  C4   C5   aromatic  1.391  0.020  1.391
 4ZK  C6   C7   aromatic  1.387  0.020  1.387
 4ZK  C5   C9   aromatic  1.390  0.020  1.390
 4ZK  C7   CL1  single    1.724  0.020  1.724
 4ZK  C7   C8   aromatic  1.390  0.020  1.390
 4ZK  C9   C8   aromatic  1.396  0.020  1.396
 4ZK  C9   C10  single    1.478  0.020  1.478
 4ZK  C8   CL2  single    1.723  0.020  1.723
 4ZK  C10  C12  aromatic  1.393  0.020  1.393
 4ZK  C10  C11  aromatic  1.388  0.020  1.388
 4ZK  C12  N2   aromatic  1.324  0.020  1.324
 4ZK  C11  C14  aromatic  1.389  0.020  1.389
 4ZK  N2   C13  aromatic  1.323  0.020  1.323
 4ZK  C14  C13  aromatic  1.395  0.020  1.395
 4ZK  C14  O3   single    1.343  0.020  1.343
 4ZK  N1   H1   single    0.890  0.020  1.040
 4ZK  N1   H2   single    0.890  0.020  1.040
 4ZK  C5   H4   single    0.930  0.020  1.080
 4ZK  C6   H5   single    0.930  0.020  1.080
 4ZK  C13  H6   single    0.930  0.020  1.080
 4ZK  C2   H8   single    0.970  0.020  1.090
 4ZK  C3   H9   single    0.970  0.020  1.090
 4ZK  C3   H10  single    0.970  0.020  1.090
 4ZK  C11  H11  single    0.930  0.020  1.080
 4ZK  C12  H12  single    0.930  0.020  1.080
 4ZK  O3   H13  single    0.850  0.020  0.980

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
 4ZK  H2   N1   H1   107.12  3.000
 4ZK  H2   N1   C2   110.74  3.000
 4ZK  H1   N1   C2   108.97  3.000
 4ZK  C3   C4   C6   121.16  3.000
 4ZK  C6   C4   C5   118.24  3.000
 4ZK  C3   C4   C5   120.52  3.000
 4ZK  H4   C5   C9   118.52  3.000
 4ZK  H4   C5   C4   119.24  3.000
 4ZK  C9   C5   C4   122.23  3.000
 4ZK  H5   C6   C7   119.33  3.000
 4ZK  H5   C6   C4   120.20  3.000
 4ZK  C7   C6   C4   120.47  3.000
 4ZK  CL1  C7   C8   120.40  3.000
 4ZK  C8   C7   C6   120.71  3.000
 4ZK  CL1  C7   C6   118.89  3.000
 4ZK  C9   C8   CL2  120.42  3.000
 4ZK  CL2  C8   C7   119.82  3.000
 4ZK  C9   C8   C7   119.74  3.000
 4ZK  C12  C10  C11  118.32  3.000
 4ZK  C11  C10  C9   122.00  3.000
 4ZK  C12  C10  C9   119.63  3.000
 4ZK  H6   C13  C14  120.07  3.000
 4ZK  H6   C13  N2   117.10  3.000
 4ZK  C14  C13  N2   122.83  3.000
 4ZK  C2   C1   O2   117.04  3.000
 4ZK  C2   C1   O1   116.00  3.000
 4ZK  O2   C1   O1   126.91  3.000
 4ZK  H8   C2   C3   107.23  3.000
 4ZK  H8   C2   C1   108.14  3.000
 4ZK  C3   C2   C1   107.36  3.000
 4ZK  H8   C2   N1   108.21  3.000
 4ZK  C3   C2   N1   114.59  3.000
 4ZK  C1   C2   N1   111.08  3.000
 4ZK  H10  C3   H9   107.34  3.000
 4ZK  H10  C3   C2   108.84  3.000
 4ZK  H9   C3   C2   108.79  3.000
 4ZK  H10  C3   C4   109.97  3.000
 4ZK  H9   C3   C4   109.61  3.000
 4ZK  C2   C3   C4   112.17  3.000
 4ZK  C10  C9   C8   122.43  3.000
 4ZK  C10  C9   C5   118.95  3.000
 4ZK  C8   C9   C5   118.61  3.000
 4ZK  H11  C11  C14  120.11  3.000
 4ZK  H11  C11  C10  121.08  3.000
 4ZK  C14  C11  C10  118.81  3.000
 4ZK  H12  C12  N2   117.01  3.000
 4ZK  H12  C12  C10  120.10  3.000
 4ZK  N2   C12  C10  122.89  3.000
 4ZK  C12  N2   C13  118.83  3.000
 4ZK  O3   C14  C11  118.69  3.000
 4ZK  O3   C14  C13  123.00  3.000
 4ZK  C11  C14  C13  118.32  3.000
 4ZK  H13  O3   C14  110.68  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
 4ZK  CONST_01  C8   C7   C6   C4     0.00   0.0  0
 4ZK  CONST_02  C8   C9   C5   C4     0.00   0.0  0
 4ZK  CONST_03  C10  C9   C5   C4   180.00   0.0  0
 4ZK  CONST_04  C7   C6   C4   C5     0.00   0.0  0
 4ZK  CONST_05  C7   C8   C9   C5     0.00   0.0  0
 4ZK  CONST_08  C9   C5   C4   C6     0.00   0.0  0
 4ZK  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 4ZK  CONST_10  C10  C9   C8   C7   180.00   0.0  0
 4ZK  CONST_13  C13  N2   C12  C10    0.00   0.0  0
 4ZK  CONST_14  C13  C14  C11  C10    0.00   0.0  0
 4ZK  CONST_15  N2   C12  C10  C9   180.00   0.0  0
 4ZK  CONST_16  C14  C11  C10  C9   180.00   0.0  0
 4ZK  CONST_17  N2   C12  C10  C11    0.00   0.0  0
 4ZK  CONST_18  N2   C13  C14  C11    0.00   0.0  0
 4ZK  CONST_19  C14  C11  C10  C12    0.00   0.0  0
 4ZK  CONST_20  C14  C13  N2   C12    0.00   0.0  0
 4ZK  CONST_21  CL1  C7   C6   C4   180.00   0.0  0
 4ZK  CONST_22  CL2  C8   C9   C5   180.00   0.0  0
 4ZK  CONST_23  CL2  C8   C7   C6   180.00   0.0  0
 4ZK  CONST_24  C3   C4   C6   C7   180.00   0.0  0
 4ZK  CONST_25  CL2  C8   C9   C10    0.00   0.0  0
 4ZK  CONST_26  O3   C14  C11  C10  180.00   0.0  0
 4ZK  CONST_27  C9   C5   C4   C3   180.00   0.0  0
 4ZK  CONST_28  C9   C8   C7   CL1  180.00   0.0  0
 4ZK  CONST_29  O3   C14  C13  N2   180.00   0.0  0
 4ZK  CONST_30  H5   C6   C4   C5   180.00   0.0  0
 4ZK  CONST_31  H4   C5   C4   C6   180.00   0.0  0
 4ZK  CONST_32  H12  C12  N2   C13  180.00   0.0  0
 4ZK  CONST_33  H11  C11  C14  C13  180.00   0.0  0
 4ZK  CONST_34  H6   C13  C14  C11  180.00   0.0  0
 4ZK  Var_01    C2   C3   C4   C5   -84.41  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
 4ZK  chir_01  C2  C1  C3  N1  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
 4ZK  plan-1  C4   0.020
 4ZK  plan-1  C5   0.020
 4ZK  plan-1  C6   0.020
 4ZK  plan-1  C7   0.020
 4ZK  plan-1  C8   0.020
 4ZK  plan-1  C10  0.020
 4ZK  plan-1  C3   0.020
 4ZK  plan-1  CL1  0.020
 4ZK  plan-1  CL2  0.020
 4ZK  plan-1  C9   0.020
 4ZK  plan-1  H4   0.020
 4ZK  plan-1  H5   0.020
 4ZK  plan-2  C10  0.020
 4ZK  plan-2  C13  0.020
 4ZK  plan-2  C9   0.020
 4ZK  plan-2  C11  0.020
 4ZK  plan-2  C12  0.020
 4ZK  plan-2  N2   0.020
 4ZK  plan-2  C14  0.020
 4ZK  plan-2  O3   0.020
 4ZK  plan-2  H6   0.020
 4ZK  plan-2  H11  0.020
 4ZK  plan-2  H12  0.020
 4ZK  plan-3  C1   0.020
 4ZK  plan-3  O2   0.020
 4ZK  plan-3  C2   0.020
 4ZK  plan-3  O1   0.020

