# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:57:43 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: (3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(4-methoxyphenyl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@@H]2NC(=O)[C@H](Cc3ccc(O)cc3)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
 KEQ  KEQ  (3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(4-methoxyphenyl)methyl]piperazine-2,5-dione  ligand  45  25  .  2022-03-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KEQ
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
 KEQ  CA   C  CR6   0   0.539   -8.8710  20.3859   0.4971
 KEQ  CB   C  CR6   0   0.540   -8.2716  17.5493   0.3728
 KEQ  NB   N  NR16  0  -0.631   -7.7465  19.9229  -0.0580
 KEQ  OB   O  O     0  -0.490   -8.0142  16.3595   0.2621
 KEQ  CD1  C  CR16  0  -0.298  -10.6303  17.5325   3.8485
 KEQ  CD2  C  CR16  0  -0.285  -12.4021  18.9296   3.0797
 KEQ  CD3  C  CR16  0  -0.286   -6.3120  20.0340   2.8610
 KEQ  CE1  C  CR16  0  -0.371  -11.5524  16.6438   4.3835
 KEQ  CE2  C  CR16  0  -0.322  -13.3369  18.0552   3.6077
 KEQ  CE3  C  CR16  0  -0.373   -6.6279  20.3022   4.1886
 KEQ  CAA  C  CR16  0  -0.177   -9.8276  19.3701   1.0827
 KEQ  CAB  C  CR16  0  -0.187   -7.2295  18.5763  -0.0123
 KEQ  CBA  C  CH2   0  -0.518  -10.0304  19.6309   2.5862
 KEQ  CBB  C  CH2   0  -0.523   -6.0013  18.4645   0.9120
 KEQ  CD4  C  CR16  0  -0.274   -6.6250  17.7016   3.2327
 KEQ  CE4  C  CR16  0  -0.339   -6.9350  17.9462   4.5577
 KEQ  CGA  C  CR6   0   0.083  -11.0329  18.6897   3.1908
 KEQ  CGB  C  CR6   0   0.085   -6.3100  18.7402   2.3544
 KEQ  CZA  C  CR6   0   0.342  -12.9146  16.9012   4.2659
 KEQ  CZB  C  CR6   0   0.370   -6.9481  19.2541   5.0473
 KEQ  NA   N  NR16  0  -0.630   -9.4468  18.0028   0.8171
 KEQ  OA   O  O     0  -0.490   -9.1621  21.5724   0.5220
 KEQ  OAX  O  OH1   0  -0.633  -13.8586  16.0789   4.7675
 KEQ  OAY  O  O2    0  -0.470   -7.2711  19.4035   6.3460
 KEQ  H1   H  HNR6  0   0.405   -7.1344  20.6175  -0.4642
 KEQ  H3   H  HCR6  0   0.252  -12.7503  19.8252   2.5779
 KEQ  H4   H  HCR6  0   0.252   -6.0552  20.8654   2.2153
 KEQ  H5   H  HCR6  0   0.269  -11.2058  15.7508   4.8913
 KEQ  H6   H  HCR6  0   0.262  -14.3952  18.2667   3.5170
 KEQ  H7   H  HCR6  0   0.278   -6.6161  21.3287   4.5293
 KEQ  H8   H  HCR6  0   0.299  -10.7836  19.5504   0.5808
 KEQ  H9   H  HCR6  0   0.305   -6.9045  18.3106  -1.0217
 KEQ  H10  H  HCH3  0   0.259   -7.6381  20.6065   7.9180
 KEQ  H11  H  HCH3  0   0.228   -6.3669  21.2167   6.8462
 KEQ  H12  H  HCH3  0   0.227   -8.0734  21.3283   6.3593
 KEQ  H13  H  HCH2  0   0.274   -9.0711  19.5434   3.0994
 KEQ  H14  H  HCH2  0   0.264  -10.3651  20.6626   2.7034
 KEQ  H15  H  HCH2  0   0.268   -5.5857  17.4633   0.7916
 KEQ  H16  H  HCH2  0   0.271   -5.2454  19.1605   0.5411
 KEQ  H17  H  HCR6  0   0.252   -6.6230  16.6782   2.8764
 KEQ  H18  H  HCR6  0   0.265   -7.1686  17.1246   5.2239
 KEQ  H19  H  HNR6  0   0.405  -10.1289  17.2980   1.0646
 KEQ  H20  H  HOH1  0   0.474  -13.4474  15.3276   5.2091
 KEQ  H2   H  HCR6  0   0.264   -9.5733  17.3203   3.9552
 KEQ  CAY  C  CH3   0  -0.436   -7.3356  20.7108   6.8789

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
 KEQ  CAB  NB   single    1.443  0.020  1.443
 KEQ  CAB  CB   single    1.513  0.020  1.513
 KEQ  CAB  CBB  single    1.541  0.020  1.541
 KEQ  NB   CA   single    1.337  0.020  1.337
 KEQ  OB   CB   double    1.222  0.020  1.222
 KEQ  CB   NA   single    1.336  0.020  1.336
 KEQ  CA   OA   double    1.222  0.020  1.222
 KEQ  CA   CAA  single    1.513  0.020  1.513
 KEQ  NA   CAA  single    1.444  0.020  1.444
 KEQ  CBB  CGB  single    1.501  0.020  1.501
 KEQ  CAA  CBA  single    1.539  0.020  1.539
 KEQ  CGB  CD3  aromatic  1.390  0.020  1.390
 KEQ  CGB  CD4  aromatic  1.396  0.020  1.396
 KEQ  CBA  CGA  single    1.502  0.020  1.502
 KEQ  CD3  CE3  aromatic  1.391  0.020  1.391
 KEQ  CGA  CD2  aromatic  1.394  0.020  1.394
 KEQ  CGA  CD1  aromatic  1.391  0.020  1.391
 KEQ  CD2  CE2  aromatic  1.385  0.020  1.385
 KEQ  CD4  CE4  aromatic  1.383  0.020  1.383
 KEQ  CD1  CE1  aromatic  1.388  0.020  1.388
 KEQ  CE2  CZA  aromatic  1.394  0.020  1.394
 KEQ  CE1  CZA  aromatic  1.391  0.020  1.391
 KEQ  CZA  OAX  single    1.349  0.020  1.349
 KEQ  CE3  CZB  aromatic  1.392  0.020  1.392
 KEQ  CE4  CZB  aromatic  1.397  0.020  1.397
 KEQ  CZB  OAY  single    1.347  0.020  1.347
 KEQ  OAY  CAY  single    1.413  0.020  1.413
 KEQ  NB   H1   single    0.860  0.020  1.020
 KEQ  CD1  H2   single    0.930  0.020  1.080
 KEQ  CD2  H3   single    0.930  0.020  1.080
 KEQ  CD3  H4   single    0.930  0.020  1.080
 KEQ  CE1  H5   single    0.930  0.020  1.080
 KEQ  CE2  H6   single    0.930  0.020  1.080
 KEQ  CE3  H7   single    0.930  0.020  1.080
 KEQ  CAA  H8   single    0.970  0.020  1.090
 KEQ  CAB  H9   single    0.970  0.020  1.090
 KEQ  CAY  H10  single    0.970  0.020  1.090
 KEQ  CAY  H11  single    0.970  0.020  1.090
 KEQ  CAY  H12  single    0.970  0.020  1.090
 KEQ  CBA  H13  single    0.970  0.020  1.090
 KEQ  CBA  H14  single    0.970  0.020  1.090
 KEQ  CBB  H15  single    0.970  0.020  1.090
 KEQ  CBB  H16  single    0.970  0.020  1.090
 KEQ  CD4  H17  single    0.930  0.020  1.080
 KEQ  CE4  H18  single    0.930  0.020  1.080
 KEQ  NA   H19  single    0.860  0.020  1.020
 KEQ  OAX  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
 KEQ  OA   CA   CAA  119.56  3.000
 KEQ  CAA  CA   NB   117.38  3.000
 KEQ  OA   CA   NB   123.04  3.000
 KEQ  NA   CB   CAB  117.40  3.000
 KEQ  NA   CB   OB   123.08  3.000
 KEQ  CAB  CB   OB   119.51  3.000
 KEQ  H1   NB   CAB  115.91  3.000
 KEQ  H1   NB   CA   115.98  3.000
 KEQ  CAB  NB   CA   127.69  3.000
 KEQ  H2   CD1  CGA  119.48  3.000
 KEQ  H2   CD1  CE1  119.00  3.000
 KEQ  CGA  CD1  CE1  121.52  3.000
 KEQ  H3   CD2  CGA  119.63  3.000
 KEQ  H3   CD2  CE2  118.78  3.000
 KEQ  CGA  CD2  CE2  121.59  3.000
 KEQ  H4   CD3  CGB  119.79  3.000
 KEQ  H4   CD3  CE3  118.34  3.000
 KEQ  CGB  CD3  CE3  121.87  3.000
 KEQ  H5   CE1  CZA  120.33  3.000
 KEQ  H5   CE1  CD1  119.71  3.000
 KEQ  CZA  CE1  CD1  119.96  3.000
 KEQ  H6   CE2  CZA  119.82  3.000
 KEQ  H6   CE2  CD2  120.30  3.000
 KEQ  CZA  CE2  CD2  119.89  3.000
 KEQ  H7   CE3  CZB  121.51  3.000
 KEQ  H7   CE3  CD3  118.77  3.000
 KEQ  CZB  CE3  CD3  119.72  3.000
 KEQ  H8   CAA  NA   107.58  3.000
 KEQ  H8   CAA  CBA  107.75  3.000
 KEQ  NA   CAA  CBA  112.02  3.000
 KEQ  H8   CAA  CA   105.31  3.000
 KEQ  CBA  CAA  CA   110.34  3.000
 KEQ  NA   CAA  CA   113.43  3.000
 KEQ  H9   CAB  CBB  107.41  3.000
 KEQ  H9   CAB  NB   107.70  3.000
 KEQ  CBB  CAB  NB   111.85  3.000
 KEQ  H9   CAB  CB   105.95  3.000
 KEQ  CBB  CAB  CB   110.31  3.000
 KEQ  NB   CAB  CB   113.24  3.000
 KEQ  H14  CBA  H13  107.15  3.000
 KEQ  H14  CBA  CGA  110.15  3.000
 KEQ  H13  CBA  CGA  110.31  3.000
 KEQ  H14  CBA  CAA  107.80  3.000
 KEQ  H13  CBA  CAA  109.26  3.000
 KEQ  CGA  CBA  CAA  112.02  3.000
 KEQ  H16  CBB  H15  106.49  3.000
 KEQ  H16  CBB  CGB  110.59  3.000
 KEQ  H15  CBB  CGB  110.68  3.000
 KEQ  H16  CBB  CAB  107.55  3.000
 KEQ  H15  CBB  CAB  107.70  3.000
 KEQ  CGB  CBB  CAB  113.53  3.000
 KEQ  H17  CD4  CGB  119.68  3.000
 KEQ  H17  CD4  CE4  118.86  3.000
 KEQ  CGB  CD4  CE4  121.46  3.000
 KEQ  H18  CE4  CZB  119.51  3.000
 KEQ  H18  CE4  CD4  120.24  3.000
 KEQ  CZB  CE4  CD4  120.25  3.000
 KEQ  CBA  CGA  CD2  121.03  3.000
 KEQ  CD2  CGA  CD1  117.72  3.000
 KEQ  CBA  CGA  CD1  121.23  3.000
 KEQ  CD4  CGB  CBB  120.96  3.000
 KEQ  CD4  CGB  CD3  117.58  3.000
 KEQ  CBB  CGB  CD3  121.45  3.000
 KEQ  OAX  CZA  CE2  117.93  3.000
 KEQ  OAX  CZA  CE1  122.75  3.000
 KEQ  CE2  CZA  CE1  119.32  3.000
 KEQ  OAY  CZB  CE4  116.38  3.000
 KEQ  OAY  CZB  CE3  124.50  3.000
 KEQ  CE4  CZB  CE3  119.11  3.000
 KEQ  H19  NA   CAA  115.90  3.000
 KEQ  H19  NA   CB   115.98  3.000
 KEQ  CAA  NA   CB   127.93  3.000
 KEQ  H20  OAX  CZA  110.31  3.000
 KEQ  CZB  OAY  CAY  118.51  3.000
 KEQ  H12  CAY  H11  108.80  3.000
 KEQ  H12  CAY  H10  108.70  3.000
 KEQ  H11  CAY  H10  108.63  3.000
 KEQ  H12  CAY  OAY  111.97  3.000
 KEQ  H11  CAY  OAY  112.10  3.000
 KEQ  H10  CAY  OAY  106.52  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
 KEQ  CONST_01  CE2  CD2  CGA  CD1     0.00   0.0  0
 KEQ  CONST_02  CE2  CZA  CE1  CD1     0.00   0.0  0
 KEQ  CONST_03  CE1  CD1  CGA  CD2     0.00   0.0  0
 KEQ  CONST_04  CE1  CZA  CE2  CD2     0.00   0.0  0
 KEQ  CONST_05  CE4  CD4  CGB  CD3     0.00   0.0  0
 KEQ  CONST_06  CE4  CZB  CE3  CD3     0.00   0.0  0
 KEQ  CONST_07  CD4  CGB  CD3  CE3     0.00   0.0  0
 KEQ  CONST_08  CD4  CE4  CZB  CE3     0.00   0.0  0
 KEQ  CONST_09  CZA  CE2  CD2  CGA     0.00   0.0  0
 KEQ  CONST_10  CZA  CE1  CD1  CGA     0.00   0.0  0
 KEQ  CONST_11  CZB  CE3  CD3  CGB     0.00   0.0  0
 KEQ  CONST_12  CZB  CE4  CD4  CGB     0.00   0.0  0
 KEQ  CONST_13  CAB  NB   CA   CAA     0.00   0.0  0
 KEQ  CONST_14  CAB  CB   NA   CAA     0.00   0.0  0
 KEQ  CONST_15  OAX  CZA  CE1  CD1   180.00   0.0  0
 KEQ  CONST_16  OAX  CZA  CE2  CD2   180.00   0.0  0
 KEQ  CONST_17  OAY  CZB  CE3  CD3   180.00   0.0  0
 KEQ  CONST_18  CBA  CGA  CD1  CE1   180.00   0.0  0
 KEQ  CONST_19  CBA  CGA  CD2  CE2   180.00   0.0  0
 KEQ  CONST_20  CBB  CGB  CD3  CE3   180.00   0.0  0
 KEQ  CONST_21  CE4  CD4  CGB  CBB   180.00   0.0  0
 KEQ  CONST_22  OAY  CZB  CE4  CD4   180.00   0.0  0
 KEQ  CONST_23  CAA  NA   CB   OB    180.00   0.0  0
 KEQ  CONST_24  OA   CA   NB   CAB   180.00   0.0  0
 KEQ  CONST_25  H3   CD2  CGA  CD1   180.00   0.0  0
 KEQ  CONST_26  H2   CD1  CGA  CD2   180.00   0.0  0
 KEQ  CONST_27  H17  CD4  CGB  CD3   180.00   0.0  0
 KEQ  CONST_28  H6   CE2  CZA  CE1   180.00   0.0  0
 KEQ  CONST_29  H5   CE1  CZA  CE2   180.00   0.0  0
 KEQ  CONST_30  H18  CE4  CZB  CE3   180.00   0.0  0
 KEQ  CONST_31  H4   CD3  CGB  CD4   180.00   0.0  0
 KEQ  CONST_32  H7   CE3  CZB  CE4   180.00   0.0  0
 KEQ  CONST_33  H1   NB   CA   CAA   180.00   0.0  0
 KEQ  CONST_34  H19  NA   CB   CAB   180.00   0.0  0
 KEQ  Var_01    CAA  CBA  CGA  CD1    96.41  30.0  2
 KEQ  Var_02    CAB  CBB  CGB  CD3   -85.72  30.0  2
 KEQ  Var_03    CE4  CZB  OAY  CAY  -178.21  30.0  1
 KEQ  Var_04    H10  CAY  OAY  CZB   178.30  30.0  3

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
 KEQ  chir_01  CAA  CA  NA   CBA  negativ
 KEQ  chir_02  CAB  NB  CBB  CB   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
 KEQ  plan-1  CD1  0.020
 KEQ  plan-1  CD2  0.020
 KEQ  plan-1  CE1  0.020
 KEQ  plan-1  CE2  0.020
 KEQ  plan-1  CBA  0.020
 KEQ  plan-1  CGA  0.020
 KEQ  plan-1  CZA  0.020
 KEQ  plan-1  OAX  0.020
 KEQ  plan-1  H3   0.020
 KEQ  plan-1  H5   0.020
 KEQ  plan-1  H6   0.020
 KEQ  plan-1  H2   0.020
 KEQ  plan-2  CD3  0.020
 KEQ  plan-2  CE3  0.020
 KEQ  plan-2  CBB  0.020
 KEQ  plan-2  CD4  0.020
 KEQ  plan-2  CE4  0.020
 KEQ  plan-2  CGB  0.020
 KEQ  plan-2  CZB  0.020
 KEQ  plan-2  OAY  0.020
 KEQ  plan-2  H4   0.020
 KEQ  plan-2  H7   0.020
 KEQ  plan-2  H17  0.020
 KEQ  plan-2  H18  0.020
 KEQ  plan-3  CB   0.020
 KEQ  plan-3  OB   0.020
 KEQ  plan-3  CAA  0.020
 KEQ  plan-3  CAB  0.020
 KEQ  plan-3  NA   0.020
 KEQ  plan-3  H19  0.020
 KEQ  plan-4  CA   0.020
 KEQ  plan-4  NB   0.020
 KEQ  plan-4  CAA  0.020
 KEQ  plan-4  CAB  0.020
 KEQ  plan-4  OA   0.020
 KEQ  plan-4  H1   0.020

