# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:40:24 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: (3~{S},6~{S})-3-[(3,5-dimethyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C[C@@H]2NC(=O)[C@H](Cc3ccc(O)cc3)NC2=O)cc(C)c1O
#
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
 KEB  KEB  (3~{S},6~{S})-3-[(3,5-dimethyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione  ligand  48  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 GRAND
;

data_comp_KEB
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
 KEB  C01  C  CH3   0  -0.722   -7.2693  15.5415   4.8539
 KEB  C02  C  CR6   0   0.007   -6.8452  16.8485   4.2522
 KEB  C03  C  CR16  0  -0.342   -6.5654  16.9588   2.8962
 KEB  C04  C  CR6   0   0.116   -6.1575  18.1582   2.3191
 KEB  C05  C  CH2   0  -0.526   -5.8753  18.2479   0.8471
 KEB  C06  C  CH1   0  -0.184   -7.0874  18.6896   0.0052
 KEB  C08  C  C     0   0.540   -8.5893  20.4367   0.9663
 KEB  C10  C  CH1   0  -0.179   -9.6168  19.3790   1.3073
 KEB  C11  C  CH2   0  -0.520   -9.7583  19.2523   2.8359
 KEB  C12  C  CR6   0   0.089  -10.8363  18.2813   3.2236
 KEB  C13  C  CR16  0  -0.285  -12.1707  18.6745   3.2765
 KEB  C14  C  CR16  0  -0.369  -13.1773  17.7792   3.6044
 KEB  C15  C  CR6   0   0.341  -12.8628  16.4519   3.8880
 KEB  C17  C  CR16  0  -0.326  -11.5340  16.0396   3.8359
 KEB  C18  C  CR16  0  -0.301  -10.5420  16.9491   3.5049
 KEB  C20  C  C     0   0.541   -8.2131  17.6864   0.1235
 KEB  C22  C  CR16  0  -0.362   -6.0328  19.2688   3.1454
 KEB  C23  C  CR6   0   0.008   -6.3054  19.2092   4.5079
 KEB  C24  C  CH3   0  -0.775   -6.1605  20.4221   5.3817
 KEB  C25  C  CR6   0   0.273   -6.7162  17.9885   5.0505
 KEB  N07  N  NH1   0  -0.632   -7.4927  20.0400   0.3131
 KEB  N19  N  NH1   0  -0.630   -9.3531  18.1045   0.6805
 KEB  O09  O  O     0  -0.490   -8.7961  21.6003   1.2767
 KEB  O16  O  OH1   0  -0.633  -13.7964  15.5366   4.2188
 KEB  O21  O  O     0  -0.492   -8.0543  16.5498  -0.2977
 KEB  O26  O  OH1   0  -0.622   -6.9976  17.8436   6.3649
 KEB  H1   H  HCH3  0   0.249   -6.5698  15.1991   5.6188
 KEB  H2   H  HCH3  0   0.240   -8.2487  15.6103   5.3318
 KEB  H3   H  HCH3  0   0.244   -7.3283  14.7686   4.0889
 KEB  H4   H  HCR6  0   0.242   -6.6599  16.0752   2.2743
 KEB  H5   H  HCH2  0   0.266   -5.5351  17.2854   0.4620
 KEB  H6   H  HCH2  0   0.268   -5.0696  18.9612   0.6570
 KEB  H7   H  HCH1  0   0.304   -6.7792  18.6670  -1.0438
 KEB  H8   H  HCH1  0   0.300  -10.5665  19.7506   0.9106
 KEB  H9   H  HCH2  0   0.279   -8.8001  18.9434   3.2569
 KEB  H10  H  HCH2  0   0.263   -9.9841  20.2427   3.2344
 KEB  H11  H  HCR6  0   0.254  -12.4350  19.7035   3.0604
 KEB  H12  H  HCR6  0   0.270  -14.2072  18.1170   3.6422
 KEB  H13  H  HCR6  0   0.261  -11.2809  15.0101   4.0577
 KEB  H14  H  HCR6  0   0.264   -9.5119  16.6147   3.4676
 KEB  H15  H  HCR6  0   0.240   -5.7032  20.2132   2.7267
 KEB  H16  H  HCH3  0   0.253   -7.1063  20.7070   5.8499
 KEB  H17  H  HCH3  0   0.250   -5.4324  20.2691   6.1826
 KEB  H18  H  HCH3  0   0.266   -5.8189  21.2780   4.8028
 KEB  H19  H  HNH1  0   0.405   -6.8258  20.7653   0.0845
 KEB  H20  H  HNH1  0   0.406  -10.0948  17.4196   0.7392
 KEB  H21  H  HOH1  0   0.474  -14.6738  15.9349   4.2137
 KEB  H22  H  HOH1  0   0.481   -6.8502  18.6664   6.8432

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
 KEB  O21  C20  double    1.222  0.020  1.222
 KEB  C06  N07  single    1.443  0.020  1.443
 KEB  C06  C20  single    1.513  0.020  1.513
 KEB  C06  C05  single    1.541  0.020  1.541
 KEB  N07  C08  single    1.337  0.020  1.337
 KEB  C20  N19  single    1.336  0.020  1.336
 KEB  C08  O09  double    1.222  0.020  1.222
 KEB  C08  C10  single    1.514  0.020  1.514
 KEB  N19  C10  single    1.445  0.020  1.445
 KEB  C05  C04  single    1.502  0.020  1.502
 KEB  C10  C11  single    1.540  0.020  1.540
 KEB  C04  C03  aromatic  1.392  0.020  1.392
 KEB  C04  C22  aromatic  1.390  0.020  1.390
 KEB  C11  C12  single    1.502  0.020  1.502
 KEB  C03  C02  aromatic  1.389  0.020  1.389
 KEB  C12  C18  aromatic  1.393  0.020  1.393
 KEB  C12  C13  aromatic  1.392  0.020  1.392
 KEB  C22  C23  aromatic  1.391  0.020  1.391
 KEB  C18  C17  aromatic  1.386  0.020  1.386
 KEB  C13  C14  aromatic  1.387  0.020  1.387
 KEB  C17  C15  aromatic  1.392  0.020  1.392
 KEB  C14  C15  aromatic  1.393  0.020  1.393
 KEB  C15  O16  single    1.349  0.020  1.349
 KEB  C02  C01  single    1.500  0.020  1.500
 KEB  C02  C25  aromatic  1.398  0.020  1.398
 KEB  C23  C25  aromatic  1.398  0.020  1.398
 KEB  C23  C24  single    1.502  0.020  1.502
 KEB  C25  O26  single    1.352  0.020  1.352
 KEB  C01  H1   single    0.970  0.020  1.090
 KEB  C01  H2   single    0.970  0.020  1.090
 KEB  C01  H3   single    0.970  0.020  1.090
 KEB  C03  H4   single    0.930  0.020  1.080
 KEB  C05  H5   single    0.970  0.020  1.090
 KEB  C05  H6   single    0.970  0.020  1.090
 KEB  C06  H7   single    0.970  0.020  1.090
 KEB  C10  H8   single    0.970  0.020  1.090
 KEB  C11  H9   single    0.970  0.020  1.090
 KEB  C11  H10  single    0.970  0.020  1.090
 KEB  C13  H11  single    0.930  0.020  1.080
 KEB  C14  H12  single    0.930  0.020  1.080
 KEB  C17  H13  single    0.930  0.020  1.080
 KEB  C18  H14  single    0.930  0.020  1.080
 KEB  C22  H15  single    0.930  0.020  1.080
 KEB  C24  H16  single    0.970  0.020  1.090
 KEB  C24  H17  single    0.970  0.020  1.090
 KEB  C24  H18  single    0.970  0.020  1.090
 KEB  N07  H19  single    0.860  0.020  1.020
 KEB  N19  H20  single    0.860  0.020  1.020
 KEB  O16  H21  single    0.850  0.020  0.980
 KEB  O26  H22  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
 KEB  H3   C01  H2   107.67  3.000
 KEB  H3   C01  H1   107.71  3.000
 KEB  H2   C01  H1   106.73  3.000
 KEB  H3   C01  C02  110.61  3.000
 KEB  H2   C01  C02  111.97  3.000
 KEB  H1   C01  C02  111.91  3.000
 KEB  C25  C02  C03  118.31  3.000
 KEB  C25  C02  C01  120.51  3.000
 KEB  C03  C02  C01  121.18  3.000
 KEB  H4   C03  C04  119.32  3.000
 KEB  H4   C03  C02  118.53  3.000
 KEB  C04  C03  C02  122.15  3.000
 KEB  C22  C04  C05  121.21  3.000
 KEB  C22  C04  C03  117.92  3.000
 KEB  C05  C04  C03  120.86  3.000
 KEB  H6   C05  H5   106.53  3.000
 KEB  H6   C05  C06  107.33  3.000
 KEB  H5   C05  C06  107.78  3.000
 KEB  H6   C05  C04  110.37  3.000
 KEB  H5   C05  C04  110.60  3.000
 KEB  C06  C05  C04  113.89  3.000
 KEB  H7   C06  N07  107.65  3.000
 KEB  H7   C06  C20  105.73  3.000
 KEB  N07  C06  C20  113.26  3.000
 KEB  H7   C06  C05  107.25  3.000
 KEB  C20  C06  C05  110.65  3.000
 KEB  N07  C06  C05  111.88  3.000
 KEB  O09  C08  N07  123.07  3.000
 KEB  O09  C08  C10  119.56  3.000
 KEB  N07  C08  C10  117.37  3.000
 KEB  H8   C10  N19  107.51  3.000
 KEB  H8   C10  C11  107.94  3.000
 KEB  N19  C10  C11  112.01  3.000
 KEB  H8   C10  C08  105.67  3.000
 KEB  C11  C10  C08  110.08  3.000
 KEB  N19  C10  C08  113.26  3.000
 KEB  H10  C11  H9   107.32  3.000
 KEB  H10  C11  C12  110.12  3.000
 KEB  H9   C11  C12  110.35  3.000
 KEB  H10  C11  C10  107.87  3.000
 KEB  H9   C11  C10  108.99  3.000
 KEB  C12  C11  C10  112.04  3.000
 KEB  C18  C12  C13  117.71  3.000
 KEB  C13  C12  C11  121.01  3.000
 KEB  C18  C12  C11  121.25  3.000
 KEB  H11  C13  C14  118.88  3.000
 KEB  H11  C13  C12  119.62  3.000
 KEB  C14  C13  C12  121.50  3.000
 KEB  H12  C14  C15  120.27  3.000
 KEB  H12  C14  C13  119.77  3.000
 KEB  C15  C14  C13  119.96  3.000
 KEB  O16  C15  C17  117.96  3.000
 KEB  O16  C15  C14  122.70  3.000
 KEB  C17  C15  C14  119.34  3.000
 KEB  H13  C17  C18  120.36  3.000
 KEB  H13  C17  C15  119.79  3.000
 KEB  C18  C17  C15  119.85  3.000
 KEB  H14  C18  C17  119.08  3.000
 KEB  H14  C18  C12  119.28  3.000
 KEB  C17  C18  C12  121.64  3.000
 KEB  O21  C20  N19  123.06  3.000
 KEB  N19  C20  C06  117.40  3.000
 KEB  O21  C20  C06  119.54  3.000
 KEB  H15  C22  C23  118.37  3.000
 KEB  H15  C22  C04  119.58  3.000
 KEB  C23  C22  C04  122.04  3.000
 KEB  C25  C23  C24  120.52  3.000
 KEB  C24  C23  C22  121.09  3.000
 KEB  C25  C23  C22  118.38  3.000
 KEB  H18  C24  H17  106.90  3.000
 KEB  H18  C24  H16  107.12  3.000
 KEB  H17  C24  H16  107.40  3.000
 KEB  H18  C24  C23  110.85  3.000
 KEB  H17  C24  C23  112.18  3.000
 KEB  H16  C24  C23  112.10  3.000
 KEB  O26  C25  C23  122.15  3.000
 KEB  O26  C25  C02  116.66  3.000
 KEB  C23  C25  C02  121.19  3.000
 KEB  H19  N07  C08  116.01  3.000
 KEB  H19  N07  C06  115.96  3.000
 KEB  C08  N07  C06  127.76  3.000
 KEB  H20  N19  C20  115.98  3.000
 KEB  H20  N19  C10  116.01  3.000
 KEB  C20  N19  C10  127.79  3.000
 KEB  H21  O16  C15  110.39  3.000
 KEB  H22  O26  C25  111.07  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
 KEB  CONST_01  C22  C04  C03  C02    0.00   0.0  0
 KEB  CONST_02  C22  C23  C25  C02    0.00   0.0  0
 KEB  CONST_03  C23  C22  C04  C03    0.00   0.0  0
 KEB  CONST_04  C23  C25  C02  C03    0.00   0.0  0
 KEB  CONST_05  C25  C02  C03  C04    0.00   0.0  0
 KEB  CONST_06  C25  C23  C22  C04    0.00   0.0  0
 KEB  CONST_07  C15  C17  C18  C12    0.00   0.0  0
 KEB  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 KEB  CONST_09  C17  C18  C12  C13    0.00   0.0  0
 KEB  CONST_10  C17  C15  C14  C13    0.00   0.0  0
 KEB  CONST_11  C18  C12  C13  C14    0.00   0.0  0
 KEB  CONST_12  C18  C17  C15  C14    0.00   0.0  0
 KEB  CONST_13  C10  C08  N07  C06    0.00   0.0  0
 KEB  CONST_14  C10  N19  C20  C06    0.00   0.0  0
 KEB  CONST_15  C04  C03  C02  C01  180.00   0.0  0
 KEB  CONST_16  C23  C25  C02  C01  180.00   0.0  0
 KEB  CONST_17  C05  C04  C03  C02  180.00   0.0  0
 KEB  CONST_18  C24  C23  C25  C02  180.00   0.0  0
 KEB  CONST_19  O26  C25  C02  C03  180.00   0.0  0
 KEB  CONST_20  C24  C23  C22  C04  180.00   0.0  0
 KEB  CONST_21  C23  C22  C04  C05  180.00   0.0  0
 KEB  CONST_22  C17  C18  C12  C11  180.00   0.0  0
 KEB  CONST_23  C14  C13  C12  C11  180.00   0.0  0
 KEB  CONST_24  O16  C15  C14  C13  180.00   0.0  0
 KEB  CONST_25  O16  C15  C17  C18  180.00   0.0  0
 KEB  CONST_26  O26  C25  C23  C22  180.00   0.0  0
 KEB  CONST_27  O09  C08  N07  C06  180.00   0.0  0
 KEB  CONST_28  O21  C20  N19  C10  180.00   0.0  0
 KEB  CONST_29  H15  C22  C04  C03  180.00   0.0  0
 KEB  CONST_30  H13  C17  C18  C12  180.00   0.0  0
 KEB  CONST_31  H12  C14  C13  C12  180.00   0.0  0
 KEB  CONST_32  H14  C18  C12  C13  180.00   0.0  0
 KEB  CONST_33  H11  C13  C14  C15  180.00   0.0  0
 KEB  CONST_34  H4   C03  C04  C22  180.00   0.0  0
 KEB  CONST_35  H20  N19  C20  C06  180.00   0.0  0
 KEB  CONST_36  H19  N07  C08  C10  180.00   0.0  0
 KEB  Var_01    C06  C05  C04  C03   92.58  30.0  2
 KEB  Var_02    C18  C12  C11  C10   94.70  30.0  2
 KEB  Var_03    H1   C01  C02  C03  119.15  30.0  2
 KEB  Var_04    H16  C24  C23  C22  118.93  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
 KEB  chir_01  C06  N07  C20  C05  positiv
 KEB  chir_02  C10  N19  C11  C08  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
 KEB  plan-1  C01  0.020
 KEB  plan-1  C02  0.020
 KEB  plan-1  C03  0.020
 KEB  plan-1  C04  0.020
 KEB  plan-1  C05  0.020
 KEB  plan-1  C22  0.020
 KEB  plan-1  C23  0.020
 KEB  plan-1  C24  0.020
 KEB  plan-1  C25  0.020
 KEB  plan-1  O26  0.020
 KEB  plan-1  H4   0.020
 KEB  plan-1  H15  0.020
 KEB  plan-2  C11  0.020
 KEB  plan-2  C12  0.020
 KEB  plan-2  C13  0.020
 KEB  plan-2  C14  0.020
 KEB  plan-2  C15  0.020
 KEB  plan-2  C17  0.020
 KEB  plan-2  C18  0.020
 KEB  plan-2  O16  0.020
 KEB  plan-2  H11  0.020
 KEB  plan-2  H12  0.020
 KEB  plan-2  H13  0.020
 KEB  plan-2  H14  0.020
 KEB  plan-3  C06  0.020
 KEB  plan-3  C10  0.020
 KEB  plan-3  C20  0.020
 KEB  plan-3  N19  0.020
 KEB  plan-3  O21  0.020
 KEB  plan-3  H20  0.020
 KEB  plan-4  C06  0.020
 KEB  plan-4  C08  0.020
 KEB  plan-4  C10  0.020
 KEB  plan-4  N07  0.020
 KEB  plan-4  O09  0.020
 KEB  plan-4  H19  0.020

