# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 15:56:38 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3S,6S)-3-benzyl-6-(4-hydroxybenzyl)piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C[C@@H]2NC(=O)[C@H](Cc3ccccc3)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
 1ED  1ED  (3S,6S)-3-benzyl-6-(4-hydroxybenzyl)piperazine-2,5-dione  ligand  41  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1ED
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
 1ED  OB   O  O     0  -0.483   0.6902  -2.7550   1.3459
 1ED  CB   C  C     0   0.533   0.5797  -1.5420   1.2678
 1ED  CAB  C  CH1   0  -0.196  -0.7858  -0.9104   1.0891
 1ED  CBB  C  CH2   0  -0.531  -1.2818  -1.1408  -0.3527
 1ED  CGB  C  CR6   0   0.105  -2.6574  -0.5789  -0.5665
 1ED  CD4  C  CR16  0  -0.297  -2.8436   0.6962  -1.0951
 1ED  CE4  C  CR16  0  -0.323  -4.1099   1.2344  -1.2603
 1ED  CZB  C  CR6   0   0.342  -5.2310   0.4960  -0.8902
 1ED  OHB  O  OH1   0  -0.633  -6.4438   1.0571  -1.0697
 1ED  CE3  C  CR16  0  -0.369  -5.0635  -0.7807  -0.3591
 1ED  CD3  C  CR16  0  -0.284  -3.7888  -1.3028  -0.2013
 1ED  NB   N  NH1   0  -0.625  -0.8038   0.4837   1.4679
 1ED  CA   C  C     0   0.532   0.2323   1.3292   1.4295
 1ED  OA   O  O     0  -0.483   0.1334   2.5271   1.6414
 1ED  NA   N  NH1   0  -0.626   1.6203  -0.7010   1.3169
 1ED  CAA  C  CH1   0  -0.197   1.5792   0.7247   1.0870
 1ED  CBA  C  CH2   0  -0.531   1.9679   1.1059  -0.3552
 1ED  CGA  C  CR6   0   0.127   3.3428   0.6127  -0.7037
 1ED  CD1  C  CR16  0  -0.310   3.5208  -0.5939  -1.3756
 1ED  CE1  C  CR16  0  -0.239   4.7955  -1.0663  -1.6616
 1ED  CZA  C  CR16  0  -0.269   5.9110  -0.3365  -1.2748
 1ED  CE2  C  CR16  0  -0.239   5.7446   0.8687  -0.6033
 1ED  CD2  C  CR16  0  -0.297   4.4697   1.3371  -0.3192
 1ED  H1   H  HCH1  0   0.309  -1.4591  -1.4401   1.7660
 1ED  H2   H  HCH2  0   0.262  -0.5786  -0.6889  -1.0572
 1ED  H3   H  HCH2  0   0.274  -1.2768  -2.2156  -0.5423
 1ED  H4   H  HCR6  0   0.249  -1.9831   1.2832  -1.3956
 1ED  H5   H  HCR6  0   0.263  -4.2327   2.2250  -1.6805
 1ED  H6   H  HOH1  0   0.474  -7.1391   0.4415  -0.8126
 1ED  H7   H  HCR6  0   0.270  -5.9271  -1.3708  -0.0725
 1ED  H8   H  HCR6  0   0.254  -3.6801  -2.3000   0.2104
 1ED  H9   H  HNH1  0   0.409  -1.7082   0.8855   1.6731
 1ED  H10  H  HNH1  0   0.409   2.5354  -1.1188   1.4170
 1ED  H11  H  HCH1  0   0.310   2.3013   1.1843   1.7648
 1ED  H12  H  HCH2  0   0.264   1.2340   0.6954  -1.0533
 1ED  H13  H  HCH2  0   0.277   1.9234   2.1930  -0.4420
 1ED  H14  H  HCR6  0   0.248   2.6544  -1.1668  -1.6856
 1ED  H15  H  HCR6  0   0.256   4.9159  -2.0038  -2.1893
 1ED  H16  H  HCR6  0   0.257   6.9049  -0.7024  -1.4971
 1ED  H17  H  HCR6  0   0.256   6.6096   1.4472  -0.3050
 1ED  H18  H  HCR6  0   0.251   4.3494   2.2801   0.2026

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
 1ED  CZA  CE2  aromatic  1.390  0.020  1.390
 1ED  CZA  CE1  aromatic  1.388  0.020  1.388
 1ED  CE2  CD2  aromatic  1.388  0.020  1.388
 1ED  CE1  CD1  aromatic  1.389  0.020  1.389
 1ED  OHB  CZB  single    1.348  0.020  1.348
 1ED  CZB  CE4  aromatic  1.393  0.020  1.393
 1ED  CZB  CE3  aromatic  1.393  0.020  1.393
 1ED  CD2  CGA  aromatic  1.394  0.020  1.394
 1ED  CE4  CD4  aromatic  1.386  0.020  1.386
 1ED  CE3  CD3  aromatic  1.387  0.020  1.387
 1ED  CD1  CGA  aromatic  1.392  0.020  1.392
 1ED  CD4  CGB  aromatic  1.393  0.020  1.393
 1ED  CD3  CGB  aromatic  1.392  0.020  1.392
 1ED  CGB  CBB  single    1.501  0.020  1.501
 1ED  CGA  CBA  single    1.502  0.020  1.502
 1ED  CBB  CAB  single    1.542  0.020  1.542
 1ED  CBA  CAA  single    1.541  0.020  1.541
 1ED  CAB  NB   single    1.445  0.020  1.445
 1ED  CAB  CB   single    1.515  0.020  1.515
 1ED  NB   CA   single    1.338  0.020  1.338
 1ED  CB   OB   double    1.220  0.020  1.220
 1ED  CB   NA   single    1.339  0.020  1.339
 1ED  CA   CAA  single    1.515  0.020  1.515
 1ED  CA   OA   double    1.221  0.020  1.221
 1ED  NA   CAA  single    1.445  0.020  1.445
 1ED  CAB  H1   single    0.970  0.020  1.090
 1ED  CBB  H2   single    0.970  0.020  1.090
 1ED  CBB  H3   single    0.970  0.020  1.090
 1ED  CD4  H4   single    0.930  0.020  1.080
 1ED  CE4  H5   single    0.930  0.020  1.080
 1ED  OHB  H6   single    0.850  0.020  0.980
 1ED  CE3  H7   single    0.930  0.020  1.080
 1ED  CD3  H8   single    0.930  0.020  1.080
 1ED  NB   H9   single    0.860  0.020  1.020
 1ED  NA   H10  single    0.860  0.020  1.020
 1ED  CAA  H11  single    0.970  0.020  1.090
 1ED  CBA  H12  single    0.970  0.020  1.090
 1ED  CBA  H13  single    0.970  0.020  1.090
 1ED  CD1  H14  single    0.930  0.020  1.080
 1ED  CE1  H15  single    0.930  0.020  1.080
 1ED  CZA  H16  single    0.930  0.020  1.080
 1ED  CE2  H17  single    0.930  0.020  1.080
 1ED  CD2  H18  single    0.930  0.020  1.080

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
 1ED  NA   CB   CAB  116.29  3.000
 1ED  NA   CB   OB   123.47  3.000
 1ED  CAB  CB   OB   120.24  3.000
 1ED  H1   CAB  NB   107.33  3.000
 1ED  H1   CAB  CBB  107.99  3.000
 1ED  NB   CAB  CBB  112.66  3.000
 1ED  H1   CAB  CB   106.29  3.000
 1ED  NB   CAB  CB   112.50  3.000
 1ED  CBB  CAB  CB   109.75  3.000
 1ED  H3   CBB  H2   106.99  3.000
 1ED  H3   CBB  CGB  110.36  3.000
 1ED  H2   CBB  CGB  110.05  3.000
 1ED  H3   CBB  CAB  107.95  3.000
 1ED  H2   CBB  CAB  109.51  3.000
 1ED  CGB  CBB  CAB  111.84  3.000
 1ED  CD3  CGB  CD4  117.84  3.000
 1ED  CD3  CGB  CBB  120.85  3.000
 1ED  CD4  CGB  CBB  121.28  3.000
 1ED  H4   CD4  CE4  118.81  3.000
 1ED  H4   CD4  CGB  119.66  3.000
 1ED  CE4  CD4  CGB  121.53  3.000
 1ED  H5   CE4  CZB  119.79  3.000
 1ED  H5   CE4  CD4  120.34  3.000
 1ED  CZB  CE4  CD4  119.87  3.000
 1ED  CE3  CZB  OHB  122.71  3.000
 1ED  CE3  CZB  CE4  119.38  3.000
 1ED  OHB  CZB  CE4  117.91  3.000
 1ED  H6   OHB  CZB  110.34  3.000
 1ED  H7   CE3  CD3  119.81  3.000
 1ED  H7   CE3  CZB  120.25  3.000
 1ED  CD3  CE3  CZB  119.94  3.000
 1ED  H8   CD3  CE3  118.79  3.000
 1ED  H8   CD3  CGB  119.76  3.000
 1ED  CE3  CD3  CGB  121.44  3.000
 1ED  H9   NB   CA   116.59  3.000
 1ED  H9   NB   CAB  116.62  3.000
 1ED  CA   NB   CAB  126.34  3.000
 1ED  CAA  CA   OA   120.18  3.000
 1ED  OA   CA   NB   123.53  3.000
 1ED  CAA  CA   NB   116.28  3.000
 1ED  H10  NA   CAA  116.70  3.000
 1ED  H10  NA   CB   116.59  3.000
 1ED  CAA  NA   CB   126.29  3.000
 1ED  H11  CAA  CBA  108.05  3.000
 1ED  H11  CAA  NA   107.33  3.000
 1ED  CBA  CAA  NA   112.69  3.000
 1ED  H11  CAA  CA   106.23  3.000
 1ED  NA   CAA  CA   112.52  3.000
 1ED  CBA  CAA  CA   109.69  3.000
 1ED  H13  CBA  H12  107.21  3.000
 1ED  H13  CBA  CGA  110.24  3.000
 1ED  H12  CBA  CGA  110.07  3.000
 1ED  H13  CBA  CAA  108.09  3.000
 1ED  H12  CBA  CAA  109.60  3.000
 1ED  CGA  CBA  CAA  111.52  3.000
 1ED  CD2  CGA  CD1  118.70  3.000
 1ED  CD1  CGA  CBA  120.91  3.000
 1ED  CD2  CGA  CBA  120.36  3.000
 1ED  H14  CD1  CE1  119.66  3.000
 1ED  H14  CD1  CGA  119.59  3.000
 1ED  CE1  CD1  CGA  120.75  3.000
 1ED  H15  CE1  CZA  120.12  3.000
 1ED  H15  CE1  CD1  119.80  3.000
 1ED  CZA  CE1  CD1  120.08  3.000
 1ED  H16  CZA  CE2  120.16  3.000
 1ED  H16  CZA  CE1  120.20  3.000
 1ED  CE2  CZA  CE1  119.63  3.000
 1ED  H17  CE2  CD2  119.82  3.000
 1ED  H17  CE2  CZA  120.06  3.000
 1ED  CD2  CE2  CZA  120.11  3.000
 1ED  H18  CD2  CE2  119.60  3.000
 1ED  H18  CD2  CGA  119.67  3.000
 1ED  CE2  CD2  CGA  120.72  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
 1ED  CONST_01  CZB  CE4  CD4  CGB    0.00   0.0  0
 1ED  CONST_02  CZB  CE3  CD3  CGB    0.00   0.0  0
 1ED  CONST_03  CE3  CZB  CE4  CD4    0.00   0.0  0
 1ED  CONST_04  CE3  CD3  CGB  CD4    0.00   0.0  0
 1ED  CONST_05  CD3  CE3  CZB  CE4    0.00   0.0  0
 1ED  CONST_06  CD3  CGB  CD4  CE4    0.00   0.0  0
 1ED  CONST_07  CZA  CE2  CD2  CGA    0.00   0.0  0
 1ED  CONST_08  CZA  CE1  CD1  CGA    0.00   0.0  0
 1ED  CONST_09  CE2  CZA  CE1  CD1    0.00   0.0  0
 1ED  CONST_10  CE2  CD2  CGA  CD1    0.00   0.0  0
 1ED  CONST_11  CD2  CE2  CZA  CE1    0.00   0.0  0
 1ED  CONST_12  CD2  CGA  CD1  CE1    0.00   0.0  0
 1ED  CONST_13  CAA  CA   NB   CAB    0.00   0.0  0
 1ED  CONST_14  CAA  NA   CB   CAB    0.00   0.0  0
 1ED  CONST_15  CE4  CD4  CGB  CBB  180.00   0.0  0
 1ED  CONST_16  CE3  CD3  CGB  CBB  180.00   0.0  0
 1ED  CONST_17  OHB  CZB  CE4  CD4  180.00   0.0  0
 1ED  CONST_18  CD3  CE3  CZB  OHB  180.00   0.0  0
 1ED  CONST_19  CE2  CD2  CGA  CBA  180.00   0.0  0
 1ED  CONST_20  CE1  CD1  CGA  CBA  180.00   0.0  0
 1ED  CONST_21  CAA  NA   CB   OB   180.00   0.0  0
 1ED  CONST_22  OA   CA   NB   CAB  180.00   0.0  0
 1ED  CONST_23  H5   CE4  CD4  CGB  180.00   0.0  0
 1ED  CONST_24  H7   CE3  CD3  CGB  180.00   0.0  0
 1ED  CONST_25  H8   CD3  CGB  CD4  180.00   0.0  0
 1ED  CONST_26  H4   CD4  CE4  CZB  180.00   0.0  0
 1ED  CONST_27  H17  CE2  CD2  CGA  180.00   0.0  0
 1ED  CONST_28  H15  CE1  CD1  CGA  180.00   0.0  0
 1ED  CONST_29  H16  CZA  CE1  CD1  180.00   0.0  0
 1ED  CONST_30  H18  CD2  CGA  CD1  180.00   0.0  0
 1ED  CONST_31  H14  CD1  CE1  CZA  180.00   0.0  0
 1ED  CONST_32  H10  NA   CB   CAB  180.00   0.0  0
 1ED  CONST_33  H9   NB   CA   CAA  180.00   0.0  0
 1ED  Var_01    CD4  CGB  CBB  CAB   94.91  30.0  2
 1ED  Var_02    CD2  CGA  CBA  CAA  -82.04  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
 1ED  chir_01  CAB  CBB  NB   CB  positiv
 1ED  chir_02  CAA  NA   CBA  CA  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
 1ED  plan-1  CBB  0.020
 1ED  plan-1  CGB  0.020
 1ED  plan-1  CD4  0.020
 1ED  plan-1  CE4  0.020
 1ED  plan-1  CZB  0.020
 1ED  plan-1  OHB  0.020
 1ED  plan-1  CE3  0.020
 1ED  plan-1  CD3  0.020
 1ED  plan-1  H4   0.020
 1ED  plan-1  H5   0.020
 1ED  plan-1  H7   0.020
 1ED  plan-1  H8   0.020
 1ED  plan-2  CBA  0.020
 1ED  plan-2  CGA  0.020
 1ED  plan-2  CD1  0.020
 1ED  plan-2  CE1  0.020
 1ED  plan-2  CZA  0.020
 1ED  plan-2  CE2  0.020
 1ED  plan-2  CD2  0.020
 1ED  plan-2  H14  0.020
 1ED  plan-2  H15  0.020
 1ED  plan-2  H16  0.020
 1ED  plan-2  H17  0.020
 1ED  plan-2  H18  0.020
 1ED  plan-3  OB   0.020
 1ED  plan-3  CB   0.020
 1ED  plan-3  CAB  0.020
 1ED  plan-3  NA   0.020
 1ED  plan-3  CAA  0.020
 1ED  plan-3  H10  0.020
 1ED  plan-4  CAB  0.020
 1ED  plan-4  NB   0.020
 1ED  plan-4  CA   0.020
 1ED  plan-4  OA   0.020
 1ED  plan-4  CAA  0.020
 1ED  plan-4  H9   0.020

