# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:29:58 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: (3~{S},6~{S})-3-[(3-chloranyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C[C@@H]2NC(=O)[C@H](Cc3ccc(O)c(Cl)c3)NC2=O)cc1
#
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
 KEW  KEW  (3~{S},6~{S})-3-[(3-chloranyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione  ligand  42  25  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KEW
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
 KEW  C02  C   CR6   0   0.405   -6.9404  18.2741  269.2014
 KEW  C03  C   CR16  0  -0.337   -6.9381  17.1538  268.3734
 KEW  C04  C   CR16  0  -0.273   -6.5499  17.2540  267.0493
 KEW  C05  C   CR6   0   0.082   -6.1472  18.4703  266.4997
 KEW  C06  C   CH2   0  -0.525   -5.7487  18.5762  265.0567
 KEW  C07  C   CH1   0  -0.186   -6.9115  18.9666  264.1251
 KEW  C08  C   C     0   0.540   -7.9960  17.9122  264.1597
 KEW  C10  C   CH1   0  -0.182   -9.5689  19.5401  265.2154
 KEW  C11  C   CH2   0  -0.512   -9.8628  19.4013  266.7200
 KEW  C12  C   CR6   0   0.086  -10.9608  18.4119  266.9888
 KEW  C13  C   CR16  0  -0.299  -10.6793  17.1014  267.3670
 KEW  C14  C   CR16  0  -0.325  -11.6881  16.1767  267.5878
 KEW  C15  C   CR6   0   0.342  -13.0194  16.5514  267.4286
 KEW  C17  C   CR16  0  -0.369  -13.3202  17.8578  267.0489
 KEW  C18  C   CR16  0  -0.283  -12.2979  18.7686  266.8325
 KEW  C19  C   C     0   0.540   -8.5575  20.6400  264.9746
 KEW  C23  C   CR16  0  -0.265   -6.1443  19.5891  267.3241
 KEW  C24  C   CR6   0  -0.155   -6.5363  19.4891  268.6490
 KEW  N09  N   NH1   0  -0.630   -9.1939  18.2767  264.6246
 KEW  N20  N   NH1   0  -0.633   -7.3968  20.2960  264.4063
 KEW  O01  O   OH1   0  -0.610   -7.3215  18.1235  270.4769
 KEW  O16  O   OH1   0  -0.633  -13.9691  15.6217  267.6561
 KEW  O21  O   O     0  -0.487   -8.8346  21.7899  265.2794
 KEW  O22  O   O     0  -0.489   -7.7493  16.7834  263.7609
 KEW  CL1  CL  CL    0  -0.115   -6.5275  20.9019  269.6571
 KEW  H1   H   HCR6  0   0.280   -7.2423  16.1988  268.7833
 KEW  H2   H   HCR6  0   0.262   -6.5564  16.3633  266.4335
 KEW  H3   H   HCH2  0   0.274   -5.3379  17.6290  264.7049
 KEW  H4   H   HCH2  0   0.276   -4.9605  19.3219  264.9315
 KEW  H5   H   HCH1  0   0.309   -6.5230  18.9618  263.1030
 KEW  H6   H   HCH1  0   0.303  -10.4860  19.8770  264.7221
 KEW  H7   H   HCH2  0   0.265   -8.9489  19.0972  267.2327
 KEW  H8   H   HCH2  0   0.267  -10.1393  20.3849  267.1023
 KEW  H9   H   HCR6  0   0.256   -9.6485  16.7953  267.5019
 KEW  H10  H   HCR6  0   0.262  -11.4448  15.1648  267.8871
 KEW  H11  H   HCR6  0   0.271  -14.3521  18.1670  266.9249
 KEW  H12  H   HCR6  0   0.255  -12.5533  19.7807  266.5398
 KEW  H13  H   HCR6  0   0.276   -5.8254  20.5502  266.9418
 KEW  H14  H   HNH1  0   0.407   -9.9055  17.5580  264.6284
 KEW  H15  H   HNH1  0   0.407   -6.7475  21.0516  264.2303
 KEW  H16  H   HOH1  0   0.470   -7.2890  18.9622  270.9549
 KEW  H17  H   HOH1  0   0.474  -14.8463  15.9985  267.5260

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
 KEW  O22  C08  double    1.222  0.020  1.222
 KEW  C07  N20  single    1.443  0.020  1.443
 KEW  C07  C08  single    1.513  0.020  1.513
 KEW  C07  C06  single    1.540  0.020  1.540
 KEW  N20  C19  single    1.337  0.020  1.337
 KEW  C08  N09  single    1.336  0.020  1.336
 KEW  C19  O21  double    1.222  0.020  1.222
 KEW  C19  C10  single    1.513  0.020  1.513
 KEW  N09  C10  single    1.444  0.020  1.444
 KEW  C10  C11  single    1.539  0.020  1.539
 KEW  C06  C05  single    1.501  0.020  1.501
 KEW  C11  C12  single    1.502  0.020  1.502
 KEW  C05  C04  aromatic  1.394  0.020  1.394
 KEW  C05  C23  aromatic  1.390  0.020  1.390
 KEW  C12  C13  aromatic  1.393  0.020  1.393
 KEW  C12  C18  aromatic  1.393  0.020  1.393
 KEW  C04  C03  aromatic  1.383  0.020  1.383
 KEW  C13  C14  aromatic  1.386  0.020  1.386
 KEW  C18  C17  aromatic  1.386  0.020  1.386
 KEW  C14  C15  aromatic  1.392  0.020  1.392
 KEW  C17  C15  aromatic  1.393  0.020  1.393
 KEW  C15  O16  single    1.348  0.020  1.348
 KEW  C23  C24  aromatic  1.385  0.020  1.385
 KEW  C03  C02  aromatic  1.393  0.020  1.393
 KEW  C24  C02  aromatic  1.395  0.020  1.395
 KEW  C24  CL1  single    1.736  0.020  1.736
 KEW  C02  O01  single    1.340  0.020  1.340
 KEW  C03  H1   single    0.930  0.020  1.080
 KEW  C04  H2   single    0.930  0.020  1.080
 KEW  C06  H3   single    0.970  0.020  1.090
 KEW  C06  H4   single    0.970  0.020  1.090
 KEW  C07  H5   single    0.970  0.020  1.090
 KEW  C10  H6   single    0.970  0.020  1.090
 KEW  C11  H7   single    0.970  0.020  1.090
 KEW  C11  H8   single    0.970  0.020  1.090
 KEW  C13  H9   single    0.930  0.020  1.080
 KEW  C14  H10  single    0.930  0.020  1.080
 KEW  C17  H11  single    0.930  0.020  1.080
 KEW  C18  H12  single    0.930  0.020  1.080
 KEW  C23  H13  single    0.930  0.020  1.080
 KEW  N09  H14  single    0.860  0.020  1.020
 KEW  N20  H15  single    0.860  0.020  1.020
 KEW  O01  H16  single    0.850  0.020  0.980
 KEW  O16  H17  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
 KEW  O01  C02  C24  123.88  3.000
 KEW  O01  C02  C03  118.42  3.000
 KEW  C24  C02  C03  117.69  3.000
 KEW  H1   C03  C04  120.33  3.000
 KEW  H1   C03  C02  118.93  3.000
 KEW  C04  C03  C02  120.74  3.000
 KEW  H2   C04  C05  119.68  3.000
 KEW  H2   C04  C03  118.89  3.000
 KEW  C05  C04  C03  121.43  3.000
 KEW  C23  C05  C06  120.86  3.000
 KEW  C23  C05  C04  117.98  3.000
 KEW  C06  C05  C04  121.15  3.000
 KEW  H4   C06  H3   106.51  3.000
 KEW  H4   C06  C07  107.60  3.000
 KEW  H3   C06  C07  108.02  3.000
 KEW  H4   C06  C05  110.49  3.000
 KEW  H3   C06  C05  110.42  3.000
 KEW  C07  C06  C05  113.51  3.000
 KEW  H5   C07  N20  107.80  3.000
 KEW  H5   C07  C08  105.84  3.000
 KEW  N20  C07  C08  113.36  3.000
 KEW  H5   C07  C06  107.22  3.000
 KEW  C08  C07  C06  110.53  3.000
 KEW  N20  C07  C06  111.69  3.000
 KEW  O22  C08  N09  123.13  3.000
 KEW  N09  C08  C07  117.43  3.000
 KEW  O22  C08  C07  119.44  3.000
 KEW  H6   C10  N09  107.61  3.000
 KEW  H6   C10  C19  105.35  3.000
 KEW  N09  C10  C19  113.40  3.000
 KEW  H6   C10  C11  107.96  3.000
 KEW  N09  C10  C11  111.74  3.000
 KEW  C19  C10  C11  110.40  3.000
 KEW  H8   C11  H7   107.39  3.000
 KEW  H8   C11  C12  110.23  3.000
 KEW  H7   C11  C12  110.15  3.000
 KEW  H8   C11  C10  108.04  3.000
 KEW  H7   C11  C10  108.94  3.000
 KEW  C12  C11  C10  111.95  3.000
 KEW  C18  C12  C13  117.75  3.000
 KEW  C18  C12  C11  120.86  3.000
 KEW  C13  C12  C11  121.37  3.000
 KEW  H9   C13  C14  118.94  3.000
 KEW  H9   C13  C12  119.46  3.000
 KEW  C14  C13  C12  121.59  3.000
 KEW  H10  C14  C15  119.87  3.000
 KEW  H10  C14  C13  120.25  3.000
 KEW  C15  C14  C13  119.88  3.000
 KEW  O16  C15  C17  122.71  3.000
 KEW  O16  C15  C14  117.95  3.000
 KEW  C17  C15  C14  119.34  3.000
 KEW  H11  C17  C18  119.78  3.000
 KEW  H11  C17  C15  120.26  3.000
 KEW  C18  C17  C15  119.96  3.000
 KEW  H12  C18  C17  118.81  3.000
 KEW  H12  C18  C12  119.71  3.000
 KEW  C17  C18  C12  121.48  3.000
 KEW  O21  C19  N20  123.03  3.000
 KEW  O21  C19  C10  119.53  3.000
 KEW  N20  C19  C10  117.43  3.000
 KEW  H13  C23  C24  119.03  3.000
 KEW  H13  C23  C05  120.39  3.000
 KEW  C24  C23  C05  120.58  3.000
 KEW  CL1  C24  C23  119.69  3.000
 KEW  CL1  C24  C02  118.73  3.000
 KEW  C23  C24  C02  121.58  3.000
 KEW  H14  N09  C10  115.94  3.000
 KEW  H14  N09  C08  116.01  3.000
 KEW  C10  N09  C08  127.88  3.000
 KEW  H15  N20  C19  116.03  3.000
 KEW  H15  N20  C07  116.00  3.000
 KEW  C19  N20  C07  127.71  3.000
 KEW  H16  O01  C02  111.35  3.000
 KEW  H17  O16  C15  110.42  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
 KEW  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 KEW  CONST_02  C05  C23  C24  C02    0.00   0.0  0
 KEW  CONST_03  C23  C05  C04  C03    0.00   0.0  0
 KEW  CONST_04  C23  C24  C02  C03    0.00   0.0  0
 KEW  CONST_05  C24  C23  C05  C04    0.00   0.0  0
 KEW  CONST_06  C24  C02  C03  C04    0.00   0.0  0
 KEW  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 KEW  CONST_08  C15  C17  C18  C12    0.00   0.0  0
 KEW  CONST_09  C17  C18  C12  C13    0.00   0.0  0
 KEW  CONST_10  C17  C15  C14  C13    0.00   0.0  0
 KEW  CONST_11  C18  C12  C13  C14    0.00   0.0  0
 KEW  CONST_12  C18  C17  C15  C14    0.00   0.0  0
 KEW  CONST_13  C10  C19  N20  C07    0.00   0.0  0
 KEW  CONST_14  C10  N09  C08  C07    0.00   0.0  0
 KEW  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 KEW  CONST_16  CL1  C24  C02  C03  180.00   0.0  0
 KEW  CONST_17  O01  C02  C03  C04  180.00   0.0  0
 KEW  CONST_18  CL1  C24  C23  C05  180.00   0.0  0
 KEW  CONST_19  C24  C23  C05  C06  180.00   0.0  0
 KEW  CONST_20  C14  C13  C12  C11  180.00   0.0  0
 KEW  CONST_21  C17  C18  C12  C11  180.00   0.0  0
 KEW  CONST_22  O16  C15  C14  C13  180.00   0.0  0
 KEW  CONST_23  O16  C15  C17  C18  180.00   0.0  0
 KEW  CONST_24  O01  C02  C24  C23  180.00   0.0  0
 KEW  CONST_25  O21  C19  N20  C07  180.00   0.0  0
 KEW  CONST_26  O22  C08  N09  C10  180.00   0.0  0
 KEW  CONST_27  H2   C04  C03  C02  180.00   0.0  0
 KEW  CONST_28  H13  C23  C24  C02  180.00   0.0  0
 KEW  CONST_29  H1   C03  C04  C05  180.00   0.0  0
 KEW  CONST_30  H10  C14  C13  C12  180.00   0.0  0
 KEW  CONST_31  H11  C17  C18  C12  180.00   0.0  0
 KEW  CONST_32  H12  C18  C12  C13  180.00   0.0  0
 KEW  CONST_33  H9   C13  C14  C15  180.00   0.0  0
 KEW  CONST_34  H14  N09  C08  C07  180.00   0.0  0
 KEW  CONST_35  H15  N20  C19  C10  180.00   0.0  0
 KEW  Var_01    C07  C06  C05  C04   92.57  30.0  3
 KEW  Var_02    C13  C12  C11  C10   98.51  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
 KEW  chir_01  C07  N20  C08  C06  positiv
 KEW  chir_02  C10  N09  C11  C19  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
 KEW  plan-1  C02  0.020
 KEW  plan-1  C03  0.020
 KEW  plan-1  C04  0.020
 KEW  plan-1  C05  0.020
 KEW  plan-1  C06  0.020
 KEW  plan-1  C23  0.020
 KEW  plan-1  C24  0.020
 KEW  plan-1  O01  0.020
 KEW  plan-1  CL1  0.020
 KEW  plan-1  H1   0.020
 KEW  plan-1  H2   0.020
 KEW  plan-1  H13  0.020
 KEW  plan-2  C11  0.020
 KEW  plan-2  C12  0.020
 KEW  plan-2  C13  0.020
 KEW  plan-2  C14  0.020
 KEW  plan-2  C15  0.020
 KEW  plan-2  C17  0.020
 KEW  plan-2  C18  0.020
 KEW  plan-2  O16  0.020
 KEW  plan-2  H9   0.020
 KEW  plan-2  H10  0.020
 KEW  plan-2  H11  0.020
 KEW  plan-2  H12  0.020
 KEW  plan-3  C07  0.020
 KEW  plan-3  C10  0.020
 KEW  plan-3  C19  0.020
 KEW  plan-3  N20  0.020
 KEW  plan-3  O21  0.020
 KEW  plan-3  H15  0.020
 KEW  plan-4  C07  0.020
 KEW  plan-4  C08  0.020
 KEW  plan-4  C10  0.020
 KEW  plan-4  N09  0.020
 KEW  plan-4  O22  0.020
 KEW  plan-4  H14  0.020

