# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:32:35 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: (3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(3-methyl-4-oxidanyl-phenyl)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)ccc1O
#
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
 KE2  KE2  (3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(3-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 PERFECT
;

data_comp_KE2
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
 KE2  C01  C  CH3   0  -0.770  -11.3917  15.1492   4.5171
 KE2  C02  C  CR6   0   0.011  -11.7693  16.5203   4.0344
 KE2  C03  C  CR16  0  -0.358  -10.7992  17.4436   3.6579
 KE2  C04  C  CR6   0   0.102  -11.1138  18.7227   3.2100
 KE2  C05  C  CH2   0  -0.518  -10.0407  19.6805   2.7772
 KE2  C06  C  CH1   0  -0.181   -9.8538  19.6819   1.2489
 KE2  C08  C  C     0   0.540   -8.3808  17.9385   0.2348
 KE2  C10  C  CH1   0  -0.185   -7.2865  18.9642   0.0380
 KE2  C11  C  CH2   0  -0.523   -6.0719  18.6416   0.9291
 KE2  C12  C  CR6   0   0.084   -6.3732  18.6802   2.3990
 KE2  C13  C  CR16  0  -0.287   -6.2894  19.8643   3.1260
 KE2  C14  C  CR16  0  -0.375   -6.5872  19.9058   4.4806
 KE2  C15  C  CR6   0   0.345   -6.9792  18.7458   5.1432
 KE2  C17  C  CR16  0  -0.336   -7.0619  17.5502   4.4330
 KE2  C18  C  CR16  0  -0.275   -6.7630  17.5280   3.0807
 KE2  C20  C  C     0   0.539   -8.8466  20.7367   0.8442
 KE2  C22  C  CR16  0  -0.305  -12.4590  19.0735   3.1365
 KE2  C23  C  CR16  0  -0.318  -13.4494  18.1784   3.5037
 KE2  C24  C  CR6   0   0.297  -13.1113  16.9048   3.9520
 KE2  N07  N  NH1   0  -0.629   -9.5384  18.3650   0.7466
 KE2  N19  N  NH1   0  -0.631   -7.7380  20.3224   0.2230
 KE2  O09  O  O     0  -0.491   -8.1795  16.7751  -0.0825
 KE2  O16  O  OH1   0  -0.632   -7.2769  18.7221   6.4578
 KE2  O21  O  O     0  -0.490   -9.0835  21.9139   1.0710
 KE2  O25  O  OH1   0  -0.630  -14.1248  16.0806   4.2969
 KE2  H1   H  HCH3  0   0.252  -11.7345  14.9625   5.5380
 KE2  H2   H  HCH3  0   0.254  -11.8079  14.3613   3.8843
 KE2  H3   H  HCH3  0   0.263  -10.3106  15.0223   4.5160
 KE2  H4   H  HCR6  0   0.251   -9.7562  17.1530   3.7244
 KE2  H5   H  HCH2  0   0.272   -9.0911  19.4227   3.2489
 KE2  H6   H  HCH2  0   0.264  -10.2946  20.6956   3.0858
 KE2  H7   H  HCH1  0   0.300  -10.7995  19.9911   0.7928
 KE2  H8   H  HCH1  0   0.304   -6.9644  18.8596  -1.0016
 KE2  H9   H  HCH2  0   0.267   -5.6953  17.6592   0.6404
 KE2  H10  H  HCH2  0   0.271   -5.2875  19.3607   0.6819
 KE2  H11  H  HCR6  0   0.253   -5.9735  20.7769   2.6353
 KE2  H12  H  HCR6  0   0.271   -6.5074  20.8430   5.0203
 KE2  H13  H  HCR6  0   0.265   -7.3528  16.6401   4.9436
 KE2  H14  H  HCR6  0   0.253   -6.8289  16.5880   2.5459
 KE2  H15  H  HCR6  0   0.249  -12.7418  20.0612   2.7911
 KE2  H16  H  HCR6  0   0.259  -14.4928  18.4637   3.4480
 KE2  H17  H  HNH1  0   0.406  -10.2587  17.6641   0.8603
 KE2  H18  H  HNH1  0   0.406   -7.0842  21.0449  -0.0483
 KE2  H19  H  HOH1  0   0.474   -7.1760  19.6014   6.8386
 KE2  H20  H  HOH1  0   0.480  -13.7930  15.2340   4.6151

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
 KE2  C10  N19  single    1.443  0.020  1.443
 KE2  C10  C08  single    1.513  0.020  1.513
 KE2  C10  C11  single    1.541  0.020  1.541
 KE2  N19  C20  single    1.337  0.020  1.337
 KE2  O09  C08  double    1.223  0.020  1.223
 KE2  C08  N07  single    1.336  0.020  1.336
 KE2  C20  O21  double    1.222  0.020  1.222
 KE2  C20  C06  single    1.514  0.020  1.514
 KE2  N07  C06  single    1.444  0.020  1.444
 KE2  C11  C12  single    1.501  0.020  1.501
 KE2  C06  C05  single    1.540  0.020  1.540
 KE2  C12  C18  aromatic  1.394  0.020  1.394
 KE2  C12  C13  aromatic  1.392  0.020  1.392
 KE2  C05  C04  single    1.502  0.020  1.502
 KE2  C18  C17  aromatic  1.385  0.020  1.385
 KE2  C13  C14  aromatic  1.388  0.020  1.388
 KE2  C04  C22  aromatic  1.392  0.020  1.392
 KE2  C04  C03  aromatic  1.391  0.020  1.391
 KE2  C22  C23  aromatic  1.385  0.020  1.385
 KE2  C03  C02  aromatic  1.391  0.020  1.391
 KE2  C23  C24  aromatic  1.392  0.020  1.392
 KE2  C02  C24  aromatic  1.398  0.020  1.398
 KE2  C02  C01  single    1.502  0.020  1.502
 KE2  C24  O25  single    1.351  0.020  1.351
 KE2  C17  C15  aromatic  1.393  0.020  1.393
 KE2  C14  C15  aromatic  1.392  0.020  1.392
 KE2  C15  O16  single    1.348  0.020  1.348
 KE2  C01  H1   single    0.970  0.020  1.090
 KE2  C01  H2   single    0.970  0.020  1.090
 KE2  C01  H3   single    0.970  0.020  1.090
 KE2  C03  H4   single    0.930  0.020  1.080
 KE2  C05  H5   single    0.970  0.020  1.090
 KE2  C05  H6   single    0.970  0.020  1.090
 KE2  C06  H7   single    0.970  0.020  1.090
 KE2  C10  H8   single    0.970  0.020  1.090
 KE2  C11  H9   single    0.970  0.020  1.090
 KE2  C11  H10  single    0.970  0.020  1.090
 KE2  C13  H11  single    0.930  0.020  1.080
 KE2  C14  H12  single    0.930  0.020  1.080
 KE2  C17  H13  single    0.930  0.020  1.080
 KE2  C18  H14  single    0.930  0.020  1.080
 KE2  C22  H15  single    0.930  0.020  1.080
 KE2  C23  H16  single    0.930  0.020  1.080
 KE2  N07  H17  single    0.860  0.020  1.020
 KE2  N19  H18  single    0.860  0.020  1.020
 KE2  O16  H19  single    0.850  0.020  0.980
 KE2  O25  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
 KE2  H3   C01  H2   107.07  3.000
 KE2  H3   C01  H1   107.01  3.000
 KE2  H2   C01  H1   107.35  3.000
 KE2  H3   C01  C02  110.84  3.000
 KE2  H2   C01  C02  112.11  3.000
 KE2  H1   C01  C02  112.17  3.000
 KE2  C24  C02  C03  118.08  3.000
 KE2  C24  C02  C01  120.74  3.000
 KE2  C03  C02  C01  121.17  3.000
 KE2  H4   C03  C04  118.91  3.000
 KE2  H4   C03  C02  118.43  3.000
 KE2  C04  C03  C02  122.66  3.000
 KE2  C22  C04  C05  120.96  3.000
 KE2  C22  C04  C03  117.85  3.000
 KE2  C05  C04  C03  121.16  3.000
 KE2  H6   C05  H5   107.46  3.000
 KE2  H6   C05  C06  107.95  3.000
 KE2  H5   C05  C06  108.89  3.000
 KE2  H6   C05  C04  110.21  3.000
 KE2  H5   C05  C04  110.27  3.000
 KE2  C06  C05  C04  111.92  3.000
 KE2  H7   C06  N07  107.54  3.000
 KE2  H7   C06  C20  105.47  3.000
 KE2  N07  C06  C20  113.40  3.000
 KE2  H7   C06  C05  108.00  3.000
 KE2  N07  C06  C05  111.77  3.000
 KE2  C20  C06  C05  110.29  3.000
 KE2  O09  C08  N07  123.10  3.000
 KE2  N07  C08  C10  117.40  3.000
 KE2  O09  C08  C10  119.50  3.000
 KE2  H8   C10  N19  107.70  3.000
 KE2  H8   C10  C11  107.32  3.000
 KE2  N19  C10  C11  111.69  3.000
 KE2  H8   C10  C08  105.78  3.000
 KE2  C11  C10  C08  110.68  3.000
 KE2  N19  C10  C08  113.28  3.000
 KE2  H10  C11  H9   106.56  3.000
 KE2  H10  C11  C12  110.42  3.000
 KE2  H9   C11  C12  110.58  3.000
 KE2  H10  C11  C10  107.30  3.000
 KE2  H9   C11  C10  107.91  3.000
 KE2  C12  C11  C10  113.75  3.000
 KE2  C18  C12  C13  117.67  3.000
 KE2  C13  C12  C11  121.42  3.000
 KE2  C18  C12  C11  120.91  3.000
 KE2  H11  C13  C14  118.66  3.000
 KE2  H11  C13  C12  119.84  3.000
 KE2  C14  C13  C12  121.50  3.000
 KE2  H12  C14  C15  120.26  3.000
 KE2  H12  C14  C13  119.73  3.000
 KE2  C15  C14  C13  120.01  3.000
 KE2  O16  C15  C17  117.96  3.000
 KE2  O16  C15  C14  122.75  3.000
 KE2  C17  C15  C14  119.29  3.000
 KE2  H13  C17  C18  120.31  3.000
 KE2  H13  C17  C15  119.78  3.000
 KE2  C18  C17  C15  119.91  3.000
 KE2  H14  C18  C17  118.85  3.000
 KE2  H14  C18  C12  119.51  3.000
 KE2  C17  C18  C12  121.63  3.000
 KE2  O21  C20  N19  123.07  3.000
 KE2  O21  C20  C06  119.52  3.000
 KE2  N19  C20  C06  117.40  3.000
 KE2  H15  C22  C23  119.14  3.000
 KE2  H15  C22  C04  119.91  3.000
 KE2  C23  C22  C04  120.95  3.000
 KE2  H16  C23  C24  119.44  3.000
 KE2  H16  C23  C22  120.34  3.000
 KE2  C24  C23  C22  120.22  3.000
 KE2  O25  C24  C23  117.27  3.000
 KE2  O25  C24  C02  122.49  3.000
 KE2  C23  C24  C02  120.24  3.000
 KE2  H17  N07  C08  116.04  3.000
 KE2  H17  N07  C06  115.93  3.000
 KE2  C08  N07  C06  127.86  3.000
 KE2  H18  N19  C20  116.06  3.000
 KE2  H18  N19  C10  115.83  3.000
 KE2  C20  N19  C10  127.64  3.000
 KE2  H19  O16  C15  110.25  3.000
 KE2  H20  O25  C24  111.22  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
 KE2  CONST_01  C22  C04  C03  C02    0.00   0.0  0
 KE2  CONST_02  C22  C23  C24  C02    0.00   0.0  0
 KE2  CONST_03  C23  C22  C04  C03    0.00   0.0  0
 KE2  CONST_04  C23  C24  C02  C03    0.00   0.0  0
 KE2  CONST_05  C24  C23  C22  C04    0.00   0.0  0
 KE2  CONST_06  C24  C02  C03  C04    0.00   0.0  0
 KE2  CONST_07  C15  C17  C18  C12    0.00   0.0  0
 KE2  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 KE2  CONST_09  C17  C18  C12  C13    0.00   0.0  0
 KE2  CONST_10  C17  C15  C14  C13    0.00   0.0  0
 KE2  CONST_11  C18  C12  C13  C14    0.00   0.0  0
 KE2  CONST_12  C18  C17  C15  C14    0.00   0.0  0
 KE2  CONST_13  C10  N19  C20  C06    0.00   0.0  0
 KE2  CONST_14  C10  C08  N07  C06    0.00   0.0  0
 KE2  CONST_15  C04  C03  C02  C01  180.00   0.0  0
 KE2  CONST_16  C23  C24  C02  C01  180.00   0.0  0
 KE2  CONST_17  C05  C04  C03  C02  180.00   0.0  0
 KE2  CONST_18  O25  C24  C02  C03  180.00   0.0  0
 KE2  CONST_19  C23  C22  C04  C05  180.00   0.0  0
 KE2  CONST_20  C17  C18  C12  C11  180.00   0.0  0
 KE2  CONST_21  C14  C13  C12  C11  180.00   0.0  0
 KE2  CONST_22  O16  C15  C14  C13  180.00   0.0  0
 KE2  CONST_23  O16  C15  C17  C18  180.00   0.0  0
 KE2  CONST_24  O25  C24  C23  C22  180.00   0.0  0
 KE2  CONST_25  O09  C08  N07  C06  180.00   0.0  0
 KE2  CONST_26  O21  C20  N19  C10  180.00   0.0  0
 KE2  CONST_27  H16  C23  C24  C02  180.00   0.0  0
 KE2  CONST_28  H15  C22  C04  C03  180.00   0.0  0
 KE2  CONST_29  H13  C17  C18  C12  180.00   0.0  0
 KE2  CONST_30  H12  C14  C13  C12  180.00   0.0  0
 KE2  CONST_31  H14  C18  C12  C13  180.00   0.0  0
 KE2  CONST_32  H11  C13  C14  C15  180.00   0.0  0
 KE2  CONST_33  H4   C03  C04  C22  180.00   0.0  0
 KE2  CONST_34  H18  N19  C20  C06  180.00   0.0  0
 KE2  CONST_35  H17  N07  C08  C10  180.00   0.0  0
 KE2  Var_01    C06  C05  C04  C03   97.22  30.0  2
 KE2  Var_02    C18  C12  C11  C10   92.08  30.0  2
 KE2  Var_03    H1   C01  C02  C03  119.45  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
 KE2  chir_01  C06  C20  N07  C05  negativ
 KE2  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
 KE2  plan-1  C01  0.020
 KE2  plan-1  C02  0.020
 KE2  plan-1  C03  0.020
 KE2  plan-1  C04  0.020
 KE2  plan-1  C05  0.020
 KE2  plan-1  C22  0.020
 KE2  plan-1  C23  0.020
 KE2  plan-1  C24  0.020
 KE2  plan-1  O25  0.020
 KE2  plan-1  H4   0.020
 KE2  plan-1  H15  0.020
 KE2  plan-1  H16  0.020
 KE2  plan-2  C11  0.020
 KE2  plan-2  C12  0.020
 KE2  plan-2  C13  0.020
 KE2  plan-2  C14  0.020
 KE2  plan-2  C15  0.020
 KE2  plan-2  C17  0.020
 KE2  plan-2  C18  0.020
 KE2  plan-2  O16  0.020
 KE2  plan-2  H11  0.020
 KE2  plan-2  H12  0.020
 KE2  plan-2  H13  0.020
 KE2  plan-2  H14  0.020
 KE2  plan-3  C06  0.020
 KE2  plan-3  C10  0.020
 KE2  plan-3  C20  0.020
 KE2  plan-3  N19  0.020
 KE2  plan-3  O21  0.020
 KE2  plan-3  H18  0.020
 KE2  plan-4  C06  0.020
 KE2  plan-4  C08  0.020
 KE2  plan-4  C10  0.020
 KE2  plan-4  N07  0.020
 KE2  plan-4  O09  0.020
 KE2  plan-4  H17  0.020

