# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:12:32 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: (3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(2-methyl-4-oxidanyl-phenyl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(O)ccc1C[C@@H]2NC(=O)[C@H](Cc3ccc(O)cc3)NC2=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
 KE5  KE5  (3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(2-methyl-4-oxidanyl-phenyl)methyl]piperazine-2,5-dione  ligand  45  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 GRAND
;

data_comp_KE5
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
 KE5  CAB  C  CR16  0  -0.188   -6.0555  18.7578   5.1894
 KE5  CAX  C  CH3   0  -0.750  -10.8976  14.9190   3.6488
 KE5  CA   C  CR6   0   0.543   -6.7945  16.7197   3.9518
 KE5  CB   C  CR6   0   0.541   -7.4437  18.8791   5.7783
 KE5  NB   N  NR16  0  -0.633   -5.8589  17.5413   4.4383
 KE5  OB   O  O     0  -0.490   -7.6831  19.7721   6.5779
 KE5  CD1  C  CR16  0  -0.294  -11.0855  18.7118   3.6612
 KE5  CD2  C  CR6   0   0.078  -11.3941  16.3331   3.7534
 KE5  CD3  C  CR16  0  -0.278   -7.7429  21.0206   3.2555
 KE5  CE1  C  CR16  0  -0.345  -12.4028  18.9317   4.0250
 KE5  CE2  C  CR16  0  -0.424  -12.7218  16.5526   4.1102
 KE5  CE3  C  CR16  0  -0.383   -8.5882  21.2041   2.1707
 KE5  CAA  C  CR16  0  -0.183   -8.2250  16.9623   4.3803
 KE5  CBA  C  CH2   0  -0.542   -9.1055  17.2714   3.1553
 KE5  CBB  C  CH2   0  -0.523   -5.7137  20.0058   4.3541
 KE5  CD4  C  CR16  0  -0.286   -6.3611  19.5798   1.9517
 KE5  CE4  C  CR16  0  -0.326   -7.1974  19.7466   0.8599
 KE5  CGA  C  CR6   0   0.057  -10.5552  17.4312   3.5189
 KE5  CGB  C  CR6   0   0.086   -6.6159  20.2076   3.1706
 KE5  CZA  C  CR6   0   0.361  -13.2319  17.8392   4.2544
 KE5  CZB  C  CR6   0   0.342   -8.3207  20.5640   0.9637
 KE5  NA   N  NR16  0  -0.628   -8.3542  17.9787   5.3979
 KE5  OA   O  O     0  -0.488   -6.5376  15.7811   3.2130
 KE5  OHA  O  OH1   0  -0.635  -14.5124  18.0774   4.6051
 KE5  OHB  O  OH1   0  -0.631   -9.1019  20.7054  -0.1260
 KE5  H1   H  HCR6  0   0.306   -5.3697  18.7378   6.0410
 KE5  H2   H  HCH3  0   0.249  -10.3981  14.6055   4.5684
 KE5  H3   H  HCH3  0   0.257  -11.7200  14.2248   3.4821
 KE5  H4   H  HCH3  0   0.247  -10.1819  14.7878   2.8374
 KE5  H5   H  HNR6  0   0.404   -4.9073  17.3410   4.1614
 KE5  H7   H  HCR6  0   0.255   -7.9682  21.5315   4.1843
 KE5  H8   H  HCR6  0   0.259  -12.7856  19.9393   4.1282
 KE5  H9   H  HCR6  0   0.261  -13.3707  15.6983   4.2766
 KE5  H10  H  HCR6  0   0.275   -9.4495  21.8565   2.2649
 KE5  H11  H  HCR6  0   0.301   -8.5554  16.0143   4.8157
 KE5  H12  H  HCH2  0   0.266   -8.9675  16.4730   2.4250
 KE5  H13  H  HCH2  0   0.279   -8.7403  18.1900   2.6930
 KE5  H14  H  HCH2  0   0.270   -4.6756  19.9089   4.0279
 KE5  H15  H  HCH2  0   0.269   -5.7490  20.8718   5.0159
 KE5  H16  H  HCR6  0   0.249   -5.4864  18.9492   1.8448
 KE5  H17  H  HCR6  0   0.263   -6.9785  19.2495  -0.0772
 KE5  H18  H  HNR6  0   0.403   -9.2732  18.0777   5.8087
 KE5  H19  H  HOH1  0   0.473  -14.9799  17.2479   4.7527
 KE5  H20  H  HOH1  0   0.473   -9.8416  21.2925   0.0650
 KE5  H6   H  HCR6  0   0.259  -10.4432  19.5648   3.4759

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
 KE5  OHB  CZB  single    1.348  0.020  1.348
 KE5  CE4  CZB  aromatic  1.393  0.020  1.393
 KE5  CE4  CD4  aromatic  1.385  0.020  1.385
 KE5  CZB  CE3  aromatic  1.392  0.020  1.392
 KE5  CD4  CGB  aromatic  1.395  0.020  1.395
 KE5  CE3  CD3  aromatic  1.387  0.020  1.387
 KE5  OA   CA   double    1.222  0.020  1.222
 KE5  CGB  CD3  aromatic  1.392  0.020  1.392
 KE5  CGB  CBB  single    1.502  0.020  1.502
 KE5  CBA  CGA  single    1.503  0.020  1.503
 KE5  CBA  CAA  single    1.540  0.020  1.540
 KE5  CD1  CGA  aromatic  1.393  0.020  1.393
 KE5  CD1  CE1  aromatic  1.384  0.020  1.384
 KE5  CGA  CD2  aromatic  1.402  0.020  1.402
 KE5  CE1  CZA  aromatic  1.391  0.020  1.391
 KE5  CD2  CAX  single    1.502  0.020  1.502
 KE5  CD2  CE2  aromatic  1.392  0.020  1.392
 KE5  CA   NB   single    1.337  0.020  1.337
 KE5  CA   CAA  single    1.513  0.020  1.513
 KE5  CZA  CE2  aromatic  1.392  0.020  1.392
 KE5  CZA  OHA  single    1.349  0.020  1.349
 KE5  NB   CAB  single    1.443  0.020  1.443
 KE5  CBB  CAB  single    1.540  0.020  1.540
 KE5  CAA  NA   single    1.444  0.020  1.444
 KE5  CAB  CB   single    1.513  0.020  1.513
 KE5  NA   CB   single    1.336  0.020  1.336
 KE5  CB   OB   double    1.222  0.020  1.222
 KE5  CAB  H1   single    0.970  0.020  1.090
 KE5  CAX  H2   single    0.970  0.020  1.090
 KE5  CAX  H3   single    0.970  0.020  1.090
 KE5  CAX  H4   single    0.970  0.020  1.090
 KE5  NB   H5   single    0.860  0.020  1.020
 KE5  CD1  H6   single    0.930  0.020  1.080
 KE5  CD3  H7   single    0.930  0.020  1.080
 KE5  CE1  H8   single    0.930  0.020  1.080
 KE5  CE2  H9   single    0.930  0.020  1.080
 KE5  CE3  H10  single    0.930  0.020  1.080
 KE5  CAA  H11  single    0.970  0.020  1.090
 KE5  CBA  H12  single    0.970  0.020  1.090
 KE5  CBA  H13  single    0.970  0.020  1.090
 KE5  CBB  H14  single    0.970  0.020  1.090
 KE5  CBB  H15  single    0.970  0.020  1.090
 KE5  CD4  H16  single    0.930  0.020  1.080
 KE5  CE4  H17  single    0.930  0.020  1.080
 KE5  NA   H18  single    0.860  0.020  1.020
 KE5  OHA  H19  single    0.850  0.020  0.980
 KE5  OHB  H20  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
 KE5  H1   CAB  CBB  107.33  3.000
 KE5  H1   CAB  NB   107.72  3.000
 KE5  CBB  CAB  NB   111.75  3.000
 KE5  H1   CAB  CB   105.89  3.000
 KE5  CBB  CAB  CB   110.47  3.000
 KE5  NB   CAB  CB   113.28  3.000
 KE5  H4   CAX  H3   107.77  3.000
 KE5  H4   CAX  H2   106.98  3.000
 KE5  H3   CAX  H2   106.93  3.000
 KE5  H4   CAX  CD2  112.47  3.000
 KE5  H3   CAX  CD2  111.16  3.000
 KE5  H2   CAX  CD2  111.26  3.000
 KE5  OA   CA   CAA  119.56  3.000
 KE5  CAA  CA   NB   117.39  3.000
 KE5  OA   CA   NB   123.03  3.000
 KE5  NA   CB   OB   123.04  3.000
 KE5  OB   CB   CAB  119.54  3.000
 KE5  NA   CB   CAB  117.42  3.000
 KE5  H5   NB   CA   115.93  3.000
 KE5  H5   NB   CAB  115.96  3.000
 KE5  CA   NB   CAB  127.74  3.000
 KE5  H6   CD1  CGA  118.71  3.000
 KE5  H6   CD1  CE1  118.94  3.000
 KE5  CGA  CD1  CE1  122.35  3.000
 KE5  CGA  CD2  CE2  119.35  3.000
 KE5  CE2  CD2  CAX  118.78  3.000
 KE5  CGA  CD2  CAX  121.87  3.000
 KE5  H7   CD3  CGB  119.73  3.000
 KE5  H7   CD3  CE3  118.75  3.000
 KE5  CGB  CD3  CE3  121.52  3.000
 KE5  H8   CE1  CZA  120.30  3.000
 KE5  H8   CE1  CD1  120.62  3.000
 KE5  CZA  CE1  CD1  119.08  3.000
 KE5  H9   CE2  CZA  119.51  3.000
 KE5  H9   CE2  CD2  119.03  3.000
 KE5  CZA  CE2  CD2  121.46  3.000
 KE5  H10  CE3  CZB  120.29  3.000
 KE5  H10  CE3  CD3  119.71  3.000
 KE5  CZB  CE3  CD3  120.00  3.000
 KE5  H11  CAA  NA   107.60  3.000
 KE5  H11  CAA  CBA  108.53  3.000
 KE5  NA   CAA  CBA  111.60  3.000
 KE5  H11  CAA  CA   105.03  3.000
 KE5  NA   CAA  CA   113.40  3.000
 KE5  CBA  CAA  CA   110.33  3.000
 KE5  H13  CBA  H12  106.87  3.000
 KE5  H13  CBA  CGA  109.62  3.000
 KE5  H12  CBA  CGA  111.20  3.000
 KE5  H13  CBA  CAA  108.34  3.000
 KE5  H12  CBA  CAA  108.26  3.000
 KE5  CGA  CBA  CAA  112.36  3.000
 KE5  H15  CBB  H14  106.40  3.000
 KE5  H15  CBB  CGB  110.62  3.000
 KE5  H14  CBB  CGB  110.33  3.000
 KE5  H15  CBB  CAB  107.89  3.000
 KE5  H14  CBB  CAB  107.51  3.000
 KE5  CGB  CBB  CAB  113.76  3.000
 KE5  H16  CD4  CGB  119.72  3.000
 KE5  H16  CD4  CE4  118.66  3.000
 KE5  CGB  CD4  CE4  121.62  3.000
 KE5  H17  CE4  CZB  119.78  3.000
 KE5  H17  CE4  CD4  120.30  3.000
 KE5  CZB  CE4  CD4  119.91  3.000
 KE5  CBA  CGA  CD2  122.30  3.000
 KE5  CD2  CGA  CD1  118.37  3.000
 KE5  CBA  CGA  CD1  119.30  3.000
 KE5  CD4  CGB  CBB  121.24  3.000
 KE5  CBB  CGB  CD3  121.11  3.000
 KE5  CD4  CGB  CD3  117.65  3.000
 KE5  OHA  CZA  CE2  122.56  3.000
 KE5  OHA  CZA  CE1  118.05  3.000
 KE5  CE2  CZA  CE1  119.39  3.000
 KE5  OHB  CZB  CE4  117.94  3.000
 KE5  CE4  CZB  CE3  119.29  3.000
 KE5  OHB  CZB  CE3  122.77  3.000
 KE5  H18  NA   CAA  115.87  3.000
 KE5  H18  NA   CB   115.96  3.000
 KE5  CAA  NA   CB   127.89  3.000
 KE5  H19  OHA  CZA  110.39  3.000
 KE5  H20  OHB  CZB  110.39  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
 KE5  CONST_01  CE2  CD2  CGA  CD1    0.00   0.0  0
 KE5  CONST_02  CE2  CZA  CE1  CD1    0.00   0.0  0
 KE5  CONST_03  CE1  CD1  CGA  CD2    0.00   0.0  0
 KE5  CONST_04  CE1  CZA  CE2  CD2    0.00   0.0  0
 KE5  CONST_05  CE4  CZB  CE3  CD3    0.00   0.0  0
 KE5  CONST_06  CE4  CD4  CGB  CD3    0.00   0.0  0
 KE5  CONST_07  CD4  CE4  CZB  CE3    0.00   0.0  0
 KE5  CONST_08  CD4  CGB  CD3  CE3    0.00   0.0  0
 KE5  CONST_09  CZA  CE1  CD1  CGA    0.00   0.0  0
 KE5  CONST_10  CZA  CE2  CD2  CGA    0.00   0.0  0
 KE5  CONST_11  CZB  CE4  CD4  CGB    0.00   0.0  0
 KE5  CONST_12  CZB  CE3  CD3  CGB    0.00   0.0  0
 KE5  CONST_13  CAA  CA   NB   CAB    0.00   0.0  0
 KE5  CONST_14  CAA  NA   CB   CAB    0.00   0.0  0
 KE5  CONST_15  CD1  CGA  CD2  CAX  180.00   0.0  0
 KE5  CONST_16  CZA  CE2  CD2  CAX  180.00   0.0  0
 KE5  CONST_17  OHA  CZA  CE1  CD1  180.00   0.0  0
 KE5  CONST_18  OHA  CZA  CE2  CD2  180.00   0.0  0
 KE5  CONST_19  OHB  CZB  CE3  CD3  180.00   0.0  0
 KE5  CONST_20  CBA  CGA  CD1  CE1  180.00   0.0  0
 KE5  CONST_21  CBA  CGA  CD2  CE2  180.00   0.0  0
 KE5  CONST_22  CBB  CGB  CD3  CE3  180.00   0.0  0
 KE5  CONST_23  CE4  CD4  CGB  CBB  180.00   0.0  0
 KE5  CONST_24  OHB  CZB  CE4  CD4  180.00   0.0  0
 KE5  CONST_25  OA   CA   NB   CAB  180.00   0.0  0
 KE5  CONST_26  CAA  NA   CB   OB   180.00   0.0  0
 KE5  CONST_27  H6   CD1  CGA  CD2  180.00   0.0  0
 KE5  CONST_28  H16  CD4  CGB  CD3  180.00   0.0  0
 KE5  CONST_29  H9   CE2  CZA  CE1  180.00   0.0  0
 KE5  CONST_30  H8   CE1  CZA  CE2  180.00   0.0  0
 KE5  CONST_31  H17  CE4  CZB  CE3  180.00   0.0  0
 KE5  CONST_32  H7   CD3  CGB  CD4  180.00   0.0  0
 KE5  CONST_33  H10  CE3  CZB  CE4  180.00   0.0  0
 KE5  CONST_34  H18  NA   CB   CAB  180.00   0.0  0
 KE5  CONST_35  H5   NB   CA   CAA  180.00   0.0  0
 KE5  Var_01    CD4  CGB  CBB  CAB  -85.66  30.0  2
 KE5  Var_02    CAA  CBA  CGA  CD1   99.62  30.0  1
 KE5  Var_03    H2   CAX  CD2  CE2  -96.39  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
 KE5  chir_01  CAB  NB  CBB  CB   negativ
 KE5  chir_02  CAA  NA  CA   CBA  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
 KE5  plan-1  CAX  0.020
 KE5  plan-1  CD1  0.020
 KE5  plan-1  CD2  0.020
 KE5  plan-1  CE1  0.020
 KE5  plan-1  CE2  0.020
 KE5  plan-1  CBA  0.020
 KE5  plan-1  CGA  0.020
 KE5  plan-1  CZA  0.020
 KE5  plan-1  OHA  0.020
 KE5  plan-1  H8   0.020
 KE5  plan-1  H9   0.020
 KE5  plan-1  H6   0.020
 KE5  plan-2  CD3  0.020
 KE5  plan-2  CE3  0.020
 KE5  plan-2  CBB  0.020
 KE5  plan-2  CD4  0.020
 KE5  plan-2  CE4  0.020
 KE5  plan-2  CGB  0.020
 KE5  plan-2  CZB  0.020
 KE5  plan-2  OHB  0.020
 KE5  plan-2  H7   0.020
 KE5  plan-2  H10  0.020
 KE5  plan-2  H16  0.020
 KE5  plan-2  H17  0.020
 KE5  plan-3  CAB  0.020
 KE5  plan-3  CB   0.020
 KE5  plan-3  OB   0.020
 KE5  plan-3  CAA  0.020
 KE5  plan-3  NA   0.020
 KE5  plan-3  H18  0.020
 KE5  plan-4  CAB  0.020
 KE5  plan-4  CA   0.020
 KE5  plan-4  NB   0.020
 KE5  plan-4  CAA  0.020
 KE5  plan-4  OA   0.020
 KE5  plan-4  H5   0.020

