# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 12:45:44 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (3S,6S)-3-(4-hydroxybenzyl)-6-methylpiperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1NC(=O)[C@H](Cc2ccc(O)cc2)NC1=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
 1G9  1G9  (3S,6S)-3-(4-hydroxybenzyl)-6-methylpiperazine-2,5-dione  ligand  31  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1G9
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
 1G9  OB   O  O     0  -0.489   2.4610  -2.7440  -0.0671
 1G9  CB   C  C     0   0.534   2.3145  -1.5408   0.0857
 1G9  NA   N  NH1   0  -0.623   3.3081  -0.6546  -0.0348
 1G9  CAA  C  CH1   0  -0.206   3.1780   0.7876  -0.0382
 1G9  CBA  C  CH3   0  -0.652   3.1405   1.3576  -1.4564
 1G9  CAB  C  CH1   0  -0.195   0.9479  -0.9799   0.4204
 1G9  NB   N  NH1   0  -0.625   1.0126   0.3549   0.9690
 1G9  CA   C  C     0   0.530   1.9736   1.2602   0.7492
 1G9  OA   O  O     0  -0.487   1.9088   2.4157   1.1385
 1G9  CBB  C  CH2   0  -0.525   0.0308  -1.0634  -0.8161
 1G9  CGB  C  CR6   0   0.101  -1.3578  -0.5817  -0.5104
 1G9  CD4  C  CR16  0  -0.299  -1.7617   0.7109  -0.8260
 1G9  CE4  C  CR16  0  -0.369  -3.0323   1.1711  -0.5088
 1G9  CZB  C  CR6   0   0.341  -3.9310   0.3338   0.1447
 1G9  OHB  O  OH1   0  -0.633  -5.1794   0.7200   0.4779
 1G9  CE3  C  CR16  0  -0.322  -3.5423  -0.9648   0.4704
 1G9  CD3  C  CR16  0  -0.284  -2.2718  -1.4068   0.1436
 1G9  H1   H  HNH1  0   0.408   4.2127  -1.0228  -0.2955
 1G9  H2   H  HCH1  0   0.299   4.0531   1.1918   0.4738
 1G9  H3   H  HCH3  0   0.234   2.2683   1.0011  -2.0050
 1G9  H4   H  HCH3  0   0.249   3.1163   2.4461  -1.4339
 1G9  H5   H  HCH3  0   0.255   4.0323   1.0512  -2.0021
 1G9  H6   H  HCH1  0   0.305   0.5338  -1.6289   1.1957
 1G9  H7   H  HNH1  0   0.406   0.1951   0.6770   1.4689
 1G9  H8   H  HCH2  0   0.263   0.4627  -0.4743  -1.6294
 1G9  H9   H  HCH2  0   0.271   0.0091  -2.1023  -1.1501
 1G9  H10  H  HCR6  0   0.253  -1.0787   1.3764  -1.3409
 1G9  H11  H  HCR6  0   0.270  -3.3191   2.1818  -0.7760
 1G9  H12  H  HOH1  0   0.474  -5.3308   1.6334   0.2108
 1G9  H13  H  HCR6  0   0.263  -4.2383  -1.6237   0.9749
 1G9  H14  H  HCR6  0   0.252  -1.9896  -2.4211   0.4022

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
 1G9  OHB  CZB  single    1.349  0.020  1.349
 1G9  CZB  CE3  aromatic  1.394  0.020  1.394
 1G9  CZB  CE4  aromatic  1.391  0.020  1.391
 1G9  CE3  CD3  aromatic  1.384  0.020  1.384
 1G9  CE4  CD4  aromatic  1.388  0.020  1.388
 1G9  CD3  CGB  aromatic  1.394  0.020  1.394
 1G9  CD4  CGB  aromatic  1.390  0.020  1.390
 1G9  CGB  CBB  single    1.501  0.020  1.501
 1G9  CBB  CAB  single    1.542  0.020  1.542
 1G9  CBA  CAA  single    1.529  0.020  1.529
 1G9  CAB  NB   single    1.445  0.020  1.445
 1G9  CAB  CB   single    1.515  0.020  1.515
 1G9  NB   CA   single    1.338  0.020  1.338
 1G9  CB   OB   double    1.222  0.020  1.222
 1G9  CB   NA   single    1.337  0.020  1.337
 1G9  CA   CAA  single    1.515  0.020  1.515
 1G9  CA   OA   double    1.221  0.020  1.221
 1G9  CAA  NA   single    1.448  0.020  1.448
 1G9  NA   H1   single    0.860  0.020  1.020
 1G9  CAA  H2   single    0.970  0.020  1.090
 1G9  CBA  H3   single    0.970  0.020  1.090
 1G9  CBA  H4   single    0.970  0.020  1.090
 1G9  CBA  H5   single    0.970  0.020  1.090
 1G9  CAB  H6   single    0.970  0.020  1.090
 1G9  NB   H7   single    0.860  0.020  1.020
 1G9  CBB  H8   single    0.970  0.020  1.090
 1G9  CBB  H9   single    0.970  0.020  1.090
 1G9  CD4  H10  single    0.930  0.020  1.080
 1G9  CE4  H11  single    0.930  0.020  1.080
 1G9  OHB  H12  single    0.850  0.020  0.980
 1G9  CE3  H13  single    0.930  0.020  1.080
 1G9  CD3  H14  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
 1G9  CAB  CB   NA   116.43  3.000
 1G9  NA   CB   OB   123.54  3.000
 1G9  CAB  CB   OB   120.03  3.000
 1G9  H1   NA   CAA  116.27  3.000
 1G9  H1   NA   CB   116.55  3.000
 1G9  CAA  NA   CB   126.42  3.000
 1G9  H2   CAA  CA   106.15  3.000
 1G9  H2   CAA  CBA  108.47  3.000
 1G9  CA   CAA  CBA  110.26  3.000
 1G9  H2   CAA  NA   107.20  3.000
 1G9  CA   CAA  NA   112.40  3.000
 1G9  CBA  CAA  NA   112.07  3.000
 1G9  H5   CBA  H4   108.04  3.000
 1G9  H5   CBA  H3   108.11  3.000
 1G9  H4   CBA  H3   108.63  3.000
 1G9  H5   CBA  CAA  109.86  3.000
 1G9  H4   CBA  CAA  110.73  3.000
 1G9  H3   CBA  CAA  111.37  3.000
 1G9  H6   CAB  CBB  108.15  3.000
 1G9  H6   CAB  NB   107.24  3.000
 1G9  CBB  CAB  NB   112.41  3.000
 1G9  H6   CAB  CB   106.19  3.000
 1G9  NB   CAB  CB   112.69  3.000
 1G9  CBB  CAB  CB   109.84  3.000
 1G9  H7   NB   CA   116.51  3.000
 1G9  H7   NB   CAB  116.49  3.000
 1G9  CA   NB   CAB  126.49  3.000
 1G9  OA   CA   NB   123.34  3.000
 1G9  OA   CA   CAA  120.21  3.000
 1G9  NB   CA   CAA  116.44  3.000
 1G9  H9   CBB  H8   107.04  3.000
 1G9  H9   CBB  CGB  110.45  3.000
 1G9  H8   CBB  CGB  110.12  3.000
 1G9  H9   CBB  CAB  107.99  3.000
 1G9  H8   CBB  CAB  109.42  3.000
 1G9  CGB  CBB  CAB  111.69  3.000
 1G9  CD3  CGB  CD4  117.79  3.000
 1G9  CD4  CGB  CBB  121.38  3.000
 1G9  CD3  CGB  CBB  120.79  3.000
 1G9  H10  CD4  CE4  118.81  3.000
 1G9  H10  CD4  CGB  119.71  3.000
 1G9  CE4  CD4  CGB  121.48  3.000
 1G9  H11  CE4  CZB  120.40  3.000
 1G9  H11  CE4  CD4  119.67  3.000
 1G9  CZB  CE4  CD4  119.94  3.000
 1G9  CE3  CZB  OHB  117.85  3.000
 1G9  CE3  CZB  CE4  119.36  3.000
 1G9  OHB  CZB  CE4  122.80  3.000
 1G9  H12  OHB  CZB  110.39  3.000
 1G9  H13  CE3  CD3  120.37  3.000
 1G9  H13  CE3  CZB  119.76  3.000
 1G9  CD3  CE3  CZB  119.87  3.000
 1G9  H14  CD3  CE3  118.77  3.000
 1G9  H14  CD3  CGB  119.67  3.000
 1G9  CE3  CD3  CGB  121.56  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
 1G9  CONST_01  CZB  CE3  CD3  CGB    0.00   0.0  0
 1G9  CONST_02  CZB  CE4  CD4  CGB    0.00   0.0  0
 1G9  CONST_03  CE3  CZB  CE4  CD4    0.00   0.0  0
 1G9  CONST_04  CE3  CD3  CGB  CD4    0.00   0.0  0
 1G9  CONST_05  CD3  CE3  CZB  CE4    0.00   0.0  0
 1G9  CONST_06  CD3  CGB  CD4  CE4    0.00   0.0  0
 1G9  CONST_07  CAB  NB   CA   CAA    0.00   0.0  0
 1G9  CONST_08  CAB  CB   NA   CAA    0.00   0.0  0
 1G9  CONST_09  CE3  CD3  CGB  CBB  180.00   0.0  0
 1G9  CONST_10  CE4  CD4  CGB  CBB  180.00   0.0  0
 1G9  CONST_11  OHB  CZB  CE4  CD4  180.00   0.0  0
 1G9  CONST_12  CD3  CE3  CZB  OHB  180.00   0.0  0
 1G9  CONST_13  CAA  NA   CB   OB   180.00   0.0  0
 1G9  CONST_14  OA   CA   NB   CAB  180.00   0.0  0
 1G9  CONST_15  H13  CE3  CD3  CGB  180.00   0.0  0
 1G9  CONST_16  H11  CE4  CD4  CGB  180.00   0.0  0
 1G9  CONST_17  H14  CD3  CGB  CD4  180.00   0.0  0
 1G9  CONST_18  H10  CD4  CE4  CZB  180.00   0.0  0
 1G9  CONST_19  H7   NB   CA   CAA  180.00   0.0  0
 1G9  CONST_20  H1   NA   CB   CAB  180.00   0.0  0
 1G9  Var_01    CD3  CGB  CBB  CAB  -79.65  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
 1G9  chir_01  CAA  CBA  CA  NA   negativ
 1G9  chir_02  CAB  NB   CB  CBB  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
 1G9  plan-1  CBB  0.020
 1G9  plan-1  CGB  0.020
 1G9  plan-1  CD4  0.020
 1G9  plan-1  CE4  0.020
 1G9  plan-1  CZB  0.020
 1G9  plan-1  OHB  0.020
 1G9  plan-1  CE3  0.020
 1G9  plan-1  CD3  0.020
 1G9  plan-1  H10  0.020
 1G9  plan-1  H11  0.020
 1G9  plan-1  H13  0.020
 1G9  plan-1  H14  0.020
 1G9  plan-2  CAA  0.020
 1G9  plan-2  CAB  0.020
 1G9  plan-2  NB   0.020
 1G9  plan-2  CA   0.020
 1G9  plan-2  OA   0.020
 1G9  plan-2  H7   0.020
 1G9  plan-3  OB   0.020
 1G9  plan-3  CB   0.020
 1G9  plan-3  NA   0.020
 1G9  plan-3  CAA  0.020
 1G9  plan-3  CAB  0.020
 1G9  plan-3  H1   0.020

