# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 21:48:38 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C[C@H]2CN[C@@H](Cc3ccc(O)cc3)C(=O)N2)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
 1G4  1G4  (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazin-2-one  ligand  43  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 PERFECT
;

data_comp_1G4
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
 1G4  OB   O  O     0  -0.507   0.2145  -2.6865   0.4869
 1G4  CB   C  C     0   0.532   0.1706  -1.4918   0.7587
 1G4  CAB  C  CH1   0  -0.195  -1.1584  -0.7365   0.7432
 1G4  CBB  C  CH2   0  -0.555  -1.9462  -1.0794  -0.5248
 1G4  CGB  C  CR6   0   0.141  -3.3432  -0.5271  -0.5009
 1G4  CD4  C  CR16  0  -0.307  -3.6821   0.6264  -1.1980
 1G4  CE4  C  CR16  0  -0.371  -4.9691   1.1455  -1.1638
 1G4  CZB  C  CR6   0   0.336  -5.9548   0.5099  -0.4156
 1G4  OHB  O  OH1   0  -0.636  -7.2242   0.9652  -0.3444
 1G4  CE3  C  CR16  0  -0.323  -5.6342  -0.6477   0.2903
 1G4  CD3  C  CR16  0  -0.294  -4.3449  -1.1519   0.2400
 1G4  NB   N  NH1   0  -0.585  -1.0646   0.6998   0.9047
 1G4  CA   C  CH2   0  -0.340  -0.0485   1.0851   1.8588
 1G4  CAA  C  CH1   0  -0.081   1.3416   0.6045   1.4593
 1G4  NA   N  NH1   0  -0.623   1.2634  -0.8080   1.1298
 1G4  CBA  C  CH2   0  -0.513   1.9307   1.4195   0.2987
 1G4  CGA  C  CR6   0   0.106   3.2675   0.9023  -0.1510
 1G4  CD2  C  CR16  0  -0.298   3.3830   0.0419  -1.2404
 1G4  CE2  C  CR16  0  -0.324   4.6077  -0.4769  -1.6314
 1G4  CZA  C  CR6   0   0.338   5.7603  -0.1414  -0.9263
 1G4  OHA  O  OH1   0  -0.634   6.9325  -0.6649  -1.3424
 1G4  CE1  C  CR16  0  -0.369   5.6653   0.7169   0.1664
 1G4  CD1  C  CR16  0  -0.288   4.4311   1.2267   0.5412
 1G4  H1   H  HCH1  0   0.275  -1.7138  -1.1389   1.6024
 1G4  H2   H  HCH2  0   0.252  -1.4081  -0.6883  -1.3943
 1G4  H3   H  HCH2  0   0.267  -1.9726  -2.1631  -0.6354
 1G4  H4   H  HCR6  0   0.247  -2.9320   1.1342  -1.7931
 1G4  H5   H  HCR6  0   0.267  -5.2003   2.0465  -1.7211
 1G4  H6   H  HOH1  0   0.472  -7.3232   1.7572  -0.8840
 1G4  H7   H  HCR6  0   0.260  -6.3959  -1.1519   0.8721
 1G4  H8   H  HCR6  0   0.248  -4.1176  -2.0585   0.7898
 1G4  H9   H  HNH1  0   0.351  -0.8938   1.1462   0.0113
 1G4  H11  H  HCH2  0   0.256  -0.0443   2.1708   1.9684
 1G4  H12  H  HCH2  0   0.252  -0.3100   0.6667   2.8350
 1G4  H13  H  HCH1  0   0.262   2.0103   0.7019   2.3193
 1G4  H14  H  HNH1  0   0.393   2.1288  -1.3298   1.1250
 1G4  H15  H  HCH2  0   0.239   1.2313   1.4124  -0.5425
 1G4  H16  H  HCH2  0   0.253   2.0195   2.4575   0.6299
 1G4  H17  H  HCR6  0   0.247   2.4978  -0.2282  -1.8046
 1G4  H18  H  HCR6  0   0.261   4.6727  -1.1416  -2.4840
 1G4  H19  H  HOH1  0   0.473   7.6521  -0.3645  -0.7766
 1G4  H20  H  HCR6  0   0.268   6.5534   0.9915   0.7250
 1G4  H21  H  HCR6  0   0.251   4.3810   1.8977   1.3911

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
 1G4  OHB  CZB  single    1.350  0.020  1.350
 1G4  CE1  CD1  aromatic  1.387  0.020  1.387
 1G4  CE1  CZA  aromatic  1.393  0.020  1.393
 1G4  CZB  CE3  aromatic  1.393  0.020  1.393
 1G4  CZB  CE4  aromatic  1.391  0.020  1.391
 1G4  CE3  CD3  aromatic  1.385  0.020  1.385
 1G4  CE4  CD4  aromatic  1.388  0.020  1.388
 1G4  CD3  CGB  aromatic  1.394  0.020  1.394
 1G4  CD1  CGA  aromatic  1.392  0.020  1.392
 1G4  CD4  CGB  aromatic  1.390  0.020  1.390
 1G4  OHA  CZA  single    1.350  0.020  1.350
 1G4  CGB  CBB  single    1.502  0.020  1.502
 1G4  CZA  CE2  aromatic  1.392  0.020  1.392
 1G4  CBB  CAB  single    1.532  0.020  1.532
 1G4  CGA  CBA  single    1.502  0.020  1.502
 1G4  CGA  CD2  aromatic  1.393  0.020  1.393
 1G4  CE2  CD2  aromatic  1.386  0.020  1.386
 1G4  CBA  CAA  single    1.536  0.020  1.536
 1G4  CAB  CB   single    1.529  0.020  1.529
 1G4  CAB  NB   single    1.448  0.020  1.448
 1G4  CA   NB   single    1.446  0.020  1.446
 1G4  CA   CAA  single    1.524  0.020  1.524
 1G4  CB   OB   double    1.226  0.020  1.226
 1G4  CB   NA   single    1.342  0.020  1.342
 1G4  CAA  NA   single    1.452  0.020  1.452
 1G4  CAB  H1   single    0.970  0.020  1.090
 1G4  CBB  H2   single    0.970  0.020  1.090
 1G4  CBB  H3   single    0.970  0.020  1.090
 1G4  CD4  H4   single    0.930  0.020  1.080
 1G4  CE4  H5   single    0.930  0.020  1.080
 1G4  OHB  H6   single    0.850  0.020  0.980
 1G4  CE3  H7   single    0.930  0.020  1.080
 1G4  CD3  H8   single    0.930  0.020  1.080
 1G4  NB   H9   single    0.890  0.020  1.040
 1G4  CA   H11  single    0.970  0.020  1.090
 1G4  CA   H12  single    0.970  0.020  1.090
 1G4  CAA  H13  single    0.970  0.020  1.090
 1G4  NA   H14  single    0.860  0.020  1.020
 1G4  CBA  H15  single    0.970  0.020  1.090
 1G4  CBA  H16  single    0.970  0.020  1.090
 1G4  CD2  H17  single    0.930  0.020  1.080
 1G4  CE2  H18  single    0.930  0.020  1.080
 1G4  OHA  H19  single    0.850  0.020  0.980
 1G4  CE1  H20  single    0.930  0.020  1.080
 1G4  CD1  H21  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
 1G4  NA   CB   CAB  117.33  3.000
 1G4  NA   CB   OB   121.93  3.000
 1G4  CAB  CB   OB   120.69  3.000
 1G4  H1   CAB  NB   107.97  3.000
 1G4  H1   CAB  CBB  107.77  3.000
 1G4  NB   CAB  CBB  110.34  3.000
 1G4  H1   CAB  CB   104.51  3.000
 1G4  NB   CAB  CB   115.63  3.000
 1G4  CBB  CAB  CB   110.17  3.000
 1G4  H3   CBB  H2   106.65  3.000
 1G4  H3   CBB  CGB  110.16  3.000
 1G4  H2   CBB  CGB  109.77  3.000
 1G4  H3   CBB  CAB  108.61  3.000
 1G4  H2   CBB  CAB  108.95  3.000
 1G4  CGB  CBB  CAB  112.51  3.000
 1G4  CD3  CGB  CD4  117.62  3.000
 1G4  CD4  CGB  CBB  121.59  3.000
 1G4  CD3  CGB  CBB  120.79  3.000
 1G4  H4   CD4  CE4  118.68  3.000
 1G4  H4   CD4  CGB  119.71  3.000
 1G4  CE4  CD4  CGB  121.61  3.000
 1G4  H5   CE4  CZB  120.33  3.000
 1G4  H5   CE4  CD4  119.72  3.000
 1G4  CZB  CE4  CD4  119.95  3.000
 1G4  CE3  CZB  OHB  118.02  3.000
 1G4  CE3  CZB  CE4  119.28  3.000
 1G4  OHB  CZB  CE4  122.71  3.000
 1G4  H6   OHB  CZB  110.13  3.000
 1G4  H7   CE3  CD3  120.31  3.000
 1G4  H7   CE3  CZB  119.81  3.000
 1G4  CD3  CE3  CZB  119.88  3.000
 1G4  H8   CD3  CE3  118.75  3.000
 1G4  H8   CD3  CGB  119.59  3.000
 1G4  CE3  CD3  CGB  121.67  3.000
 1G4  H9   NB   CA   110.24  3.000
 1G4  H9   NB   CAB  110.46  3.000
 1G4  CA   NB   CAB  112.54  3.000
 1G4  H12  CA   H11  106.97  3.000
 1G4  H12  CA   CAA  109.34  3.000
 1G4  H11  CA   CAA  109.66  3.000
 1G4  H12  CA   NB   108.60  3.000
 1G4  H11  CA   NB   109.52  3.000
 1G4  CAA  CA   NB   112.58  3.000
 1G4  H13  CAA  CBA  108.21  3.000
 1G4  H13  CAA  NA   107.33  3.000
 1G4  CBA  CAA  NA   111.43  3.000
 1G4  H13  CAA  CA   108.87  3.000
 1G4  NA   CAA  CA   108.48  3.000
 1G4  CBA  CAA  CA   112.37  3.000
 1G4  H14  NA   CAA  117.20  3.000
 1G4  H14  NA   CB   115.66  3.000
 1G4  CAA  NA   CB   127.03  3.000
 1G4  H16  CBA  H15  106.92  3.000
 1G4  H16  CBA  CGA  110.20  3.000
 1G4  H15  CBA  CGA  109.66  3.000
 1G4  H16  CBA  CAA  107.83  3.000
 1G4  H15  CBA  CAA  109.42  3.000
 1G4  CGA  CBA  CAA  112.64  3.000
 1G4  CD1  CGA  CD2  117.61  3.000
 1G4  CD2  CGA  CBA  121.37  3.000
 1G4  CD1  CGA  CBA  120.98  3.000
 1G4  H17  CD2  CE2  118.78  3.000
 1G4  H17  CD2  CGA  119.55  3.000
 1G4  CE2  CD2  CGA  121.66  3.000
 1G4  H18  CE2  CZA  119.80  3.000
 1G4  H18  CE2  CD2  120.31  3.000
 1G4  CZA  CE2  CD2  119.89  3.000
 1G4  CE1  CZA  OHA  122.70  3.000
 1G4  OHA  CZA  CE2  118.00  3.000
 1G4  CE1  CZA  CE2  119.31  3.000
 1G4  H19  OHA  CZA  110.29  3.000
 1G4  H20  CE1  CD1  119.76  3.000
 1G4  H20  CE1  CZA  120.29  3.000
 1G4  CD1  CE1  CZA  119.95  3.000
 1G4  H21  CD1  CE1  118.72  3.000
 1G4  H21  CD1  CGA  119.69  3.000
 1G4  CE1  CD1  CGA  121.58  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
 1G4  CONST_01  CZB  CE3  CD3  CGB    0.00   0.0  0
 1G4  CONST_02  CZB  CE4  CD4  CGB    0.00   0.0  0
 1G4  CONST_03  CE3  CZB  CE4  CD4    0.00   0.0  0
 1G4  CONST_04  CE3  CD3  CGB  CD4    0.00   0.0  0
 1G4  CONST_05  CD3  CE3  CZB  CE4    0.00   0.0  0
 1G4  CONST_06  CD3  CGB  CD4  CE4    0.00   0.0  0
 1G4  CONST_07  CZA  CE1  CD1  CGA    0.00   0.0  0
 1G4  CONST_08  CZA  CE2  CD2  CGA    0.00   0.0  0
 1G4  CONST_09  CE1  CD1  CGA  CD2    0.00   0.0  0
 1G4  CONST_10  CE1  CZA  CE2  CD2    0.00   0.0  0
 1G4  CONST_11  CD1  CE1  CZA  CE2    0.00   0.0  0
 1G4  CONST_12  CD1  CGA  CD2  CE2    0.00   0.0  0
 1G4  CONST_13  CAA  NA   CB   CAB    0.00   0.0  0
 1G4  CONST_14  CE3  CD3  CGB  CBB  180.00   0.0  0
 1G4  CONST_15  CE4  CD4  CGB  CBB  180.00   0.0  0
 1G4  CONST_16  OHB  CZB  CE4  CD4  180.00   0.0  0
 1G4  CONST_17  CD3  CE3  CZB  OHB  180.00   0.0  0
 1G4  CONST_18  CE1  CD1  CGA  CBA  180.00   0.0  0
 1G4  CONST_19  CE2  CD2  CGA  CBA  180.00   0.0  0
 1G4  CONST_20  OHA  CZA  CE2  CD2  180.00   0.0  0
 1G4  CONST_21  CD1  CE1  CZA  OHA  180.00   0.0  0
 1G4  CONST_22  CAA  NA   CB   OB   180.00   0.0  0
 1G4  CONST_23  H7   CE3  CD3  CGB  180.00   0.0  0
 1G4  CONST_24  H5   CE4  CD4  CGB  180.00   0.0  0
 1G4  CONST_25  H8   CD3  CGB  CD4  180.00   0.0  0
 1G4  CONST_26  H4   CD4  CE4  CZB  180.00   0.0  0
 1G4  CONST_27  H20  CE1  CD1  CGA  180.00   0.0  0
 1G4  CONST_28  H18  CE2  CD2  CGA  180.00   0.0  0
 1G4  CONST_29  H21  CD1  CGA  CD2  180.00   0.0  0
 1G4  CONST_30  H17  CD2  CE2  CZA  180.00   0.0  0
 1G4  CONST_31  H14  NA   CB   CAB  180.00   0.0  0
 1G4  Var_01    CAA  CA   NB   CAB   59.72  30.0  1
 1G4  Var_02    CD3  CGB  CBB  CAB  -77.93  30.0  3
 1G4  Var_03    CD1  CGA  CBA  CAA  -80.57  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
 1G4  chir_01  CAB  CBB  CB   NB  negativ
 1G4  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
 1G4  plan-1  CBB  0.020
 1G4  plan-1  CGB  0.020
 1G4  plan-1  CD4  0.020
 1G4  plan-1  CE4  0.020
 1G4  plan-1  CZB  0.020
 1G4  plan-1  OHB  0.020
 1G4  plan-1  CE3  0.020
 1G4  plan-1  CD3  0.020
 1G4  plan-1  H4   0.020
 1G4  plan-1  H5   0.020
 1G4  plan-1  H7   0.020
 1G4  plan-1  H8   0.020
 1G4  plan-2  CBA  0.020
 1G4  plan-2  CGA  0.020
 1G4  plan-2  CD2  0.020
 1G4  plan-2  CE2  0.020
 1G4  plan-2  CZA  0.020
 1G4  plan-2  OHA  0.020
 1G4  plan-2  CE1  0.020
 1G4  plan-2  CD1  0.020
 1G4  plan-2  H17  0.020
 1G4  plan-2  H18  0.020
 1G4  plan-2  H20  0.020
 1G4  plan-2  H21  0.020
 1G4  plan-3  OB   0.020
 1G4  plan-3  CB   0.020
 1G4  plan-3  CAB  0.020
 1G4  plan-3  CAA  0.020
 1G4  plan-3  NA   0.020
 1G4  plan-3  H14  0.020

