# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:54:09 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: (3~{S},6~{S})-3-[(3-ethynyl-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(c3)C#C)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
 KEZ  KEZ  (3~{S},6~{S})-3-[(3-ethynyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione  ligand  44  26  .  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_KEZ
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
 KEZ  C02  C  CR6   0   0.324   -6.9722  18.1425  268.5469
 KEZ  C03  C  CR16  0  -0.337   -6.9812  17.0290  267.7124
 KEZ  C04  C  CR16  0  -0.273   -6.5804  17.1455  266.3939
 KEZ  C05  C  CR6   0   0.096   -6.1571  18.3651  265.8611
 KEZ  C06  C  CH2   0  -0.527   -5.7456  18.4766  264.4220
 KEZ  C07  C  CH1   0  -0.186   -6.8983  18.8813  263.4837
 KEZ  C08  C  C     0   0.539   -7.9941  17.8387  263.5122
 KEZ  C10  C  CH1   0  -0.181   -9.5544  19.4825  264.5635
 KEZ  C11  C  CH2   0  -0.514   -9.8644  19.3517  266.0651
 KEZ  C12  C  CR6   0   0.086  -10.9835  18.3838  266.3260
 KEZ  C13  C  CR16  0  -0.283  -12.3122  18.7576  266.1261
 KEZ  C14  C  CR16  0  -0.322  -13.3535  17.8702  266.3352
 KEZ  C15  C  CR6   0   0.342  -13.0840  16.5676  266.7541
 KEZ  C17  C  CR16  0  -0.371  -11.7648  16.1770  266.9583
 KEZ  C18  C  CR16  0  -0.299  -10.7333  17.0807  266.7416
 KEZ  C19  C  C     0   0.540   -8.5290  20.5711  264.3296
 KEZ  C23  C  CR16  0  -0.318   -6.1452  19.4694  266.6987
 KEZ  C24  C  CR6   0  -0.165   -6.5471  19.3775  268.0340
 KEZ  C25  C  CSP   0   0.271   -6.5330  20.5120  268.8932
 KEZ  C26  C  CSP1  0  -0.533   -6.5386  21.4386  269.6633
 KEZ  N09  N  NH1   0  -0.629   -9.1874  18.2124  263.9819
 KEZ  N20  N  NH1   0  -0.633   -7.3699  20.2153  263.7663
 KEZ  O01  O  OH1   0  -0.605   -7.3668  17.9864  269.8178
 KEZ  O16  O  OH1   0  -0.633  -14.1306  15.7396  266.9473
 KEZ  O21  O  O     0  -0.488   -8.7953  21.7238  264.6340
 KEZ  O22  O  O     0  -0.489   -7.7599  16.7090  263.1084
 KEZ  H1   H  HCR6  0   0.277   -7.2995  16.0716  268.1050
 KEZ  H2   H  HCR6  0   0.263   -6.5928  16.2636  265.7652
 KEZ  H3   H  HCH2  0   0.273   -5.3374  17.5292  264.0673
 KEZ  H4   H  HCH2  0   0.275   -4.9523  19.2189  264.3087
 KEZ  H5   H  HCH1  0   0.308   -6.5048  18.8750  262.4636
 KEZ  H6   H  HCH1  0   0.302  -10.4624  19.8286  264.0593
 KEZ  H7   H  HCH2  0   0.267   -8.9603  19.0320  266.5861
 KEZ  H8   H  HCH2  0   0.267  -10.1263  20.3410  266.4432
 KEZ  H9   H  HCR6  0   0.253  -12.5434  19.7672  265.8051
 KEZ  H10  H  HCR6  0   0.263  -14.3782  18.1836  266.1795
 KEZ  H11  H  HCR6  0   0.270  -11.5356  15.1698  267.2864
 KEZ  H12  H  HCR6  0   0.259   -9.7118  16.7606  266.9117
 KEZ  H13  H  HCR6  0   0.263   -5.8109  20.4302  266.3276
 KEZ  H14  H  H     0   0.287   -6.5358  22.2687  270.3327
 KEZ  H15  H  HNH1  0   0.406   -9.9053  17.5000  263.9860
 KEZ  H16  H  HNH1  0   0.407   -6.7097  20.9631  263.5977
 KEZ  H17  H  HOH1  0   0.474   -7.3252  18.8239  270.2989
 KEZ  H18  H  HOH1  0   0.474  -13.8249  14.8736  267.2395

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
 KEZ  O22  C08  double    1.222  0.020  1.222
 KEZ  N20  C07  single    1.443  0.020  1.443
 KEZ  N20  C19  single    1.337  0.020  1.337
 KEZ  C08  C07  single    1.513  0.020  1.513
 KEZ  C08  N09  single    1.336  0.020  1.336
 KEZ  C07  C06  single    1.540  0.020  1.540
 KEZ  O21  C19  double    1.222  0.020  1.222
 KEZ  C19  C10  single    1.514  0.020  1.514
 KEZ  N09  C10  single    1.444  0.020  1.444
 KEZ  C10  C11  single    1.539  0.020  1.539
 KEZ  C06  C05  single    1.501  0.020  1.501
 KEZ  C05  C04  aromatic  1.397  0.020  1.397
 KEZ  C05  C23  aromatic  1.386  0.020  1.386
 KEZ  C11  C12  single    1.502  0.020  1.502
 KEZ  C12  C13  aromatic  1.395  0.020  1.395
 KEZ  C12  C18  aromatic  1.390  0.020  1.390
 KEZ  C04  C03  aromatic  1.383  0.020  1.383
 KEZ  C13  C14  aromatic  1.384  0.020  1.384
 KEZ  C18  C17  aromatic  1.388  0.020  1.388
 KEZ  C14  C15  aromatic  1.395  0.020  1.395
 KEZ  C17  C15  aromatic  1.391  0.020  1.391
 KEZ  C15  O16  single    1.348  0.020  1.348
 KEZ  C23  C24  aromatic  1.398  0.020  1.398
 KEZ  C03  C02  aromatic  1.392  0.020  1.392
 KEZ  C24  C02  aromatic  1.403  0.020  1.403
 KEZ  C24  C25  single    1.423  0.020  1.423
 KEZ  C02  O01  single    1.340  0.020  1.340
 KEZ  C25  C26  triple    1.205  0.020  1.205
 KEZ  C03  H1   single    0.929  0.020  1.085
 KEZ  C04  H2   single    0.929  0.020  1.085
 KEZ  C06  H3   single    0.939  0.020  1.096
 KEZ  C06  H4   single    0.939  0.020  1.096
 KEZ  C07  H5   single    0.939  0.020  1.096
 KEZ  C10  H6   single    0.939  0.020  1.096
 KEZ  C11  H7   single    0.939  0.020  1.096
 KEZ  C11  H8   single    0.939  0.020  1.096
 KEZ  C13  H9   single    0.929  0.020  1.085
 KEZ  C14  H10  single    0.929  0.020  1.085
 KEZ  C17  H11  single    0.929  0.020  1.085
 KEZ  C18  H12  single    0.929  0.020  1.085
 KEZ  C23  H13  single    0.929  0.020  1.085
 KEZ  C26  H14  single    0.913  0.020  1.066
 KEZ  N09  H15  single    0.868  0.020  1.013
 KEZ  N20  H16  single    0.868  0.020  1.013
 KEZ  O01  H17  single    0.832  0.020  0.971
 KEZ  O16  H18  single    0.832  0.020  0.971

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
 KEZ  O01  C02  C24  122.58  3.000
 KEZ  O01  C02  C03  118.27  3.000
 KEZ  C24  C02  C03  119.14  3.000
 KEZ  H1   C03  C04  120.36  3.000
 KEZ  H1   C03  C02  119.47  3.000
 KEZ  C04  C03  C02  120.17  3.000
 KEZ  H2   C04  C05  119.54  3.000
 KEZ  H2   C04  C03  118.79  3.000
 KEZ  C05  C04  C03  121.67  3.000
 KEZ  C23  C05  C06  121.19  3.000
 KEZ  C23  C05  C04  117.90  3.000
 KEZ  C06  C05  C04  120.91  3.000
 KEZ  H4   C06  H3   106.54  3.000
 KEZ  H4   C06  C07  107.56  3.000
 KEZ  H3   C06  C07  108.07  3.000
 KEZ  H4   C06  C05  110.43  3.000
 KEZ  H3   C06  C05  110.48  3.000
 KEZ  C07  C06  C05  113.48  3.000
 KEZ  H5   C07  N20  107.80  3.000
 KEZ  H5   C07  C08  105.92  3.000
 KEZ  N20  C07  C08  113.38  3.000
 KEZ  H5   C07  C06  107.30  3.000
 KEZ  C08  C07  C06  110.46  3.000
 KEZ  N20  C07  C06  111.60  3.000
 KEZ  O22  C08  N09  123.09  3.000
 KEZ  N09  C08  C07  117.44  3.000
 KEZ  O22  C08  C07  119.47  3.000
 KEZ  H6   C10  N09  107.66  3.000
 KEZ  H6   C10  C19  105.27  3.000
 KEZ  N09  C10  C19  113.46  3.000
 KEZ  H6   C10  C11  108.01  3.000
 KEZ  N09  C10  C11  111.68  3.000
 KEZ  C19  C10  C11  110.38  3.000
 KEZ  H8   C11  H7   107.40  3.000
 KEZ  H8   C11  C12  110.20  3.000
 KEZ  H7   C11  C12  110.21  3.000
 KEZ  H8   C11  C10  108.03  3.000
 KEZ  H7   C11  C10  108.90  3.000
 KEZ  C12  C11  C10  111.97  3.000
 KEZ  C18  C12  C13  117.74  3.000
 KEZ  C18  C12  C11  121.44  3.000
 KEZ  C13  C12  C11  120.80  3.000
 KEZ  H9   C13  C14  118.77  3.000
 KEZ  H9   C13  C12  119.68  3.000
 KEZ  C14  C13  C12  121.55  3.000
 KEZ  H10  C14  C15  119.76  3.000
 KEZ  H10  C14  C13  120.31  3.000
 KEZ  C15  C14  C13  119.93  3.000
 KEZ  O16  C15  C17  122.86  3.000
 KEZ  O16  C15  C14  117.81  3.000
 KEZ  C17  C15  C14  119.32  3.000
 KEZ  H11  C17  C18  119.67  3.000
 KEZ  H11  C17  C15  120.40  3.000
 KEZ  C18  C17  C15  119.93  3.000
 KEZ  H12  C18  C17  118.91  3.000
 KEZ  H12  C18  C12  119.55  3.000
 KEZ  C17  C18  C12  121.53  3.000
 KEZ  O21  C19  N20  123.03  3.000
 KEZ  O21  C19  C10  119.50  3.000
 KEZ  N20  C19  C10  117.45  3.000
 KEZ  H13  C23  C24  118.33  3.000
 KEZ  H13  C23  C05  120.17  3.000
 KEZ  C24  C23  C05  121.50  3.000
 KEZ  C25  C24  C23  121.44  3.000
 KEZ  C25  C24  C02  118.94  3.000
 KEZ  C23  C24  C02  119.62  3.000
 KEZ  C26  C25  C24  180.00  3.000
 KEZ  H14  C26  C25  180.00  3.000
 KEZ  H15  N09  C10  115.93  3.000
 KEZ  H15  N09  C08  116.01  3.000
 KEZ  C10  N09  C08  127.93  3.000
 KEZ  H16  N20  C19  116.06  3.000
 KEZ  H16  N20  C07  115.95  3.000
 KEZ  C19  N20  C07  127.73  3.000
 KEZ  H17  O01  C02  111.00  3.000
 KEZ  H18  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
 KEZ  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 KEZ  CONST_02  C05  C23  C24  C02    0.00   0.0  0
 KEZ  CONST_03  C23  C05  C04  C03    0.00   0.0  0
 KEZ  CONST_04  C23  C24  C02  C03    0.00   0.0  0
 KEZ  CONST_05  C24  C23  C05  C04    0.00   0.0  0
 KEZ  CONST_06  C24  C02  C03  C04    0.00   0.0  0
 KEZ  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 KEZ  CONST_08  C15  C17  C18  C12    0.00   0.0  0
 KEZ  CONST_09  C17  C18  C12  C13    0.00   0.0  0
 KEZ  CONST_10  C17  C15  C14  C13    0.00   0.0  0
 KEZ  CONST_11  C18  C12  C13  C14    0.00   0.0  0
 KEZ  CONST_12  C18  C17  C15  C14    0.00   0.0  0
 KEZ  CONST_13  C10  C19  N20  C07    0.00   0.0  0
 KEZ  CONST_14  C10  N09  C08  C07    0.00   0.0  0
 KEZ  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 KEZ  CONST_16  C25  C24  C02  C03  180.00   0.0  0
 KEZ  CONST_17  O01  C02  C03  C04  180.00   0.0  0
 KEZ  CONST_18  C25  C24  C23  C05  180.00   0.0  0
 KEZ  CONST_19  C24  C23  C05  C06  180.00   0.0  0
 KEZ  CONST_20  C14  C13  C12  C11  180.00   0.0  0
 KEZ  CONST_21  C17  C18  C12  C11  180.00   0.0  0
 KEZ  CONST_22  O16  C15  C14  C13  180.00   0.0  0
 KEZ  CONST_23  O16  C15  C17  C18  180.00   0.0  0
 KEZ  CONST_24  O01  C02  C24  C23  180.00   0.0  0
 KEZ  CONST_25  O21  C19  N20  C07  180.00   0.0  0
 KEZ  CONST_26  O22  C08  N09  C10  180.00   0.0  0
 KEZ  CONST_27  H2   C04  C03  C02  180.00   0.0  0
 KEZ  CONST_28  H13  C23  C24  C02  180.00   0.0  0
 KEZ  CONST_29  H1   C03  C04  C05  180.00   0.0  0
 KEZ  CONST_30  H10  C14  C13  C12  180.00   0.0  0
 KEZ  CONST_31  H11  C17  C18  C12  180.00   0.0  0
 KEZ  CONST_32  H12  C18  C12  C13  180.00   0.0  0
 KEZ  CONST_33  H9   C13  C14  C15  180.00   0.0  0
 KEZ  CONST_34  H15  N09  C08  C07  180.00   0.0  0
 KEZ  CONST_35  H16  N20  C19  C10  180.00   0.0  0
 KEZ  Var_01    C07  C06  C05  C04   92.21  30.0  3
 KEZ  Var_02    C13  C12  C11  C10  -78.24  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
 KEZ  chir_01  C07  N20  C08  C06  positiv
 KEZ  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
 KEZ  plan-1  C02  0.020
 KEZ  plan-1  C03  0.020
 KEZ  plan-1  C04  0.020
 KEZ  plan-1  C05  0.020
 KEZ  plan-1  C06  0.020
 KEZ  plan-1  C23  0.020
 KEZ  plan-1  C24  0.020
 KEZ  plan-1  C25  0.020
 KEZ  plan-1  C26  0.020
 KEZ  plan-1  O01  0.020
 KEZ  plan-1  H1   0.020
 KEZ  plan-1  H2   0.020
 KEZ  plan-1  H13  0.020
 KEZ  plan-2  C11  0.020
 KEZ  plan-2  C12  0.020
 KEZ  plan-2  C13  0.020
 KEZ  plan-2  C14  0.020
 KEZ  plan-2  C15  0.020
 KEZ  plan-2  C17  0.020
 KEZ  plan-2  C18  0.020
 KEZ  plan-2  O16  0.020
 KEZ  plan-2  H9   0.020
 KEZ  plan-2  H10  0.020
 KEZ  plan-2  H11  0.020
 KEZ  plan-2  H12  0.020
 KEZ  plan-3  C07  0.020
 KEZ  plan-3  C08  0.020
 KEZ  plan-3  C10  0.020
 KEZ  plan-3  N09  0.020
 KEZ  plan-3  O22  0.020
 KEZ  plan-3  H15  0.020
 KEZ  plan-4  C07  0.020
 KEZ  plan-4  C10  0.020
 KEZ  plan-4  C19  0.020
 KEZ  plan-4  N20  0.020
 KEZ  plan-4  O21  0.020
 KEZ  plan-4  H16  0.020

