# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:44:31 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: (3S,6S)-3-{[4-(hydroxymethoxy)phenyl]methyl}-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCOc1ccc(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
 QFD  QFD  (3S,6S)-3-{[4-(hydroxymethoxy)phenyl]methyl}-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione  ligand  46  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QFD
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
 QFD  C13  C  CR16  0  -0.341   -6.5051  17.8519   4.5828
 QFD  C15  C  CR6   0   0.541   -7.9427  17.6006   0.4475
 QFD  C20  C  CR6   0   0.085  -10.6213  18.7256   3.3617
 QFD  C21  C  CR16  0  -0.296  -10.2337  17.5551   4.0044
 QFD  C22  C  CR16  0  -0.372  -11.1670  16.6716   4.5285
 QFD  C26  C  CR16  0  -0.285  -11.9871  18.9851   3.2545
 QFD  C02  C  CR6   0   0.541   -8.4729  20.4445   0.6715
 QFD  C04  C  CR16  0  -0.188   -6.8911  18.6150   0.0550
 QFD  C05  C  CH2   0  -0.523   -5.6349  18.4477   0.9331
 QFD  C06  C  CR6   0   0.085   -5.8977  18.6866   2.3905
 QFD  C07  C  CR16  0  -0.284   -5.8728  19.9680   2.9291
 QFD  C08  C  CR16  0  -0.390   -6.1734  20.2081   4.2639
 QFD  C09  C  CR6   0   0.381   -6.5014  19.1455   5.1021
 QFD  C11  C  CH2   0   0.009   -7.1718  20.5403   6.9162
 QFD  C14  C  CR16  0  -0.273   -6.2088  17.6322   3.2490
 QFD  C18  C  CR16  0  -0.177   -9.4378  19.4339   1.2524
 QFD  C19  C  CH2   0  -0.518   -9.6057  19.6584   2.7660
 QFD  C23  C  CR6   0   0.342  -12.5258  16.9479   4.4140
 QFD  C25  C  CR16  0  -0.322  -12.9330  18.1159   3.7713
 QFD  N03  N  NR16  0  -0.631   -7.3766  19.9738   0.0687
 QFD  N17  N  NR16  0  -0.630   -9.0911  18.0660   0.9461
 QFD  O10  O  O2    0  -0.490   -6.8077  19.2684   6.4147
 QFD  O12  O  OH1   0  -0.651   -8.3791  20.9867   6.4111
 QFD  O16  O  O     0  -0.490   -7.7149  16.4092   0.2965
 QFD  O24  O  OH1   0  -0.633  -13.4804  16.1309   4.9040
 QFD  H1   H  HCR6  0   0.269   -6.7431  17.0178   5.2317
 QFD  H2   H  HCR6  0   0.263   -9.1796  17.3278   4.1076
 QFD  H3   H  HCR6  0   0.269  -10.8316  15.7679   5.0249
 QFD  H4   H  HCR6  0   0.252  -12.3244  19.8914   2.7644
 QFD  H5   H  HCR6  0   0.306   -6.6070  18.3724  -0.9724
 QFD  H6   H  HCH2  0   0.270   -5.2455  17.4422   0.7703
 QFD  H7   H  HCH2  0   0.272   -4.8764  19.1394   0.5598
 QFD  H8   H  HCR6  0   0.254   -5.6102  20.8121   2.3028
 QFD  H9   H  HCR6  0   0.281   -6.1190  21.2282   4.6218
 QFD  H10  H  HCH2  0   0.249   -7.2914  20.3829   7.9863
 QFD  H11  H  HCH2  0   0.219   -6.3624  21.2603   6.7538
 QFD  H12  H  HCR6  0   0.254   -6.2233  16.6171   2.8701
 QFD  H13  H  HCR6  0   0.299  -10.3990  19.6471   0.7734
 QFD  H14  H  HCH2  0   0.272   -8.6398  19.5255   3.2548
 QFD  H15  H  HCH2  0   0.264   -9.9087  20.6953   2.9197
 QFD  H16  H  HCR6  0   0.262  -13.9885  18.3418   3.6829
 QFD  H17  H  HNR6  0   0.406   -6.7629  20.6664  -0.3387
 QFD  H18  H  HNR6  0   0.406   -9.7794  17.3686   1.1978
 QFD  H19  H  HOH1  0   0.463   -8.2390  21.4729   5.5928
 QFD  H20  H  HOH1  0   0.473  -13.0794  15.3692   5.3369
 QFD  O01  O  O     0  -0.489   -8.7352  21.6361   0.7407

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
 QFD  O16  C15  double    1.222  0.020  1.222
 QFD  C04  N03  single    1.443  0.020  1.443
 QFD  C04  C15  single    1.513  0.020  1.513
 QFD  C04  C05  single    1.542  0.020  1.542
 QFD  N03  C02  single    1.337  0.020  1.337
 QFD  C15  N17  single    1.336  0.020  1.336
 QFD  C02  O01  double    1.222  0.020  1.222
 QFD  C02  C18  single    1.513  0.020  1.513
 QFD  N17  C18  single    1.444  0.020  1.444
 QFD  C05  C06  single    1.500  0.020  1.500
 QFD  C18  C19  single    1.539  0.020  1.539
 QFD  C06  C07  aromatic  1.390  0.020  1.390
 QFD  C06  C14  aromatic  1.395  0.020  1.395
 QFD  C19  C20  single    1.502  0.020  1.502
 QFD  C07  C08  aromatic  1.389  0.020  1.389
 QFD  C26  C20  aromatic  1.394  0.020  1.394
 QFD  C26  C25  aromatic  1.385  0.020  1.385
 QFD  C20  C21  aromatic  1.390  0.020  1.390
 QFD  C25  C23  aromatic  1.394  0.020  1.394
 QFD  C21  C22  aromatic  1.388  0.020  1.388
 QFD  C14  C13  aromatic  1.384  0.020  1.384
 QFD  C23  C22  aromatic  1.391  0.020  1.391
 QFD  C23  O24  single    1.349  0.020  1.349
 QFD  C08  C09  aromatic  1.393  0.020  1.393
 QFD  C13  C09  aromatic  1.394  0.020  1.394
 QFD  C09  O10  single    1.353  0.020  1.353
 QFD  O10  C11  single    1.415  0.020  1.415
 QFD  C11  O12  single    1.383  0.020  1.383
 QFD  C13  H1   single    0.930  0.020  1.080
 QFD  C21  H2   single    0.930  0.020  1.080
 QFD  C22  H3   single    0.930  0.020  1.080
 QFD  C26  H4   single    0.930  0.020  1.080
 QFD  C04  H5   single    0.970  0.020  1.090
 QFD  C05  H6   single    0.970  0.020  1.090
 QFD  C05  H7   single    0.970  0.020  1.090
 QFD  C07  H8   single    0.930  0.020  1.080
 QFD  C08  H9   single    0.930  0.020  1.080
 QFD  C11  H10  single    0.970  0.020  1.090
 QFD  C11  H11  single    0.970  0.020  1.090
 QFD  C14  H12  single    0.930  0.020  1.080
 QFD  C18  H13  single    0.970  0.020  1.090
 QFD  C19  H14  single    0.970  0.020  1.090
 QFD  C19  H15  single    0.970  0.020  1.090
 QFD  C25  H16  single    0.930  0.020  1.080
 QFD  N03  H17  single    0.860  0.020  1.020
 QFD  N17  H18  single    0.860  0.020  1.020
 QFD  O12  H19  single    0.850  0.020  0.980
 QFD  O24  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
 QFD  H1   C13  C14  120.14  3.000
 QFD  H1   C13  C09  119.48  3.000
 QFD  C14  C13  C09  120.38  3.000
 QFD  O16  C15  N17  123.09  3.000
 QFD  N17  C15  C04  117.44  3.000
 QFD  O16  C15  C04  119.47  3.000
 QFD  C19  C20  C26  121.08  3.000
 QFD  C26  C20  C21  117.72  3.000
 QFD  C19  C20  C21  121.17  3.000
 QFD  H2   C21  C22  119.00  3.000
 QFD  H2   C21  C20  119.47  3.000
 QFD  C22  C21  C20  121.54  3.000
 QFD  H3   C22  C23  120.35  3.000
 QFD  H3   C22  C21  119.70  3.000
 QFD  C23  C22  C21  119.95  3.000
 QFD  H4   C26  C25  118.75  3.000
 QFD  H4   C26  C20  119.67  3.000
 QFD  C25  C26  C20  121.58  3.000
 QFD  O01  C02  N03  123.02  3.000
 QFD  O01  C02  C18  119.51  3.000
 QFD  N03  C02  C18  117.44  3.000
 QFD  H5   C04  N03  107.78  3.000
 QFD  H5   C04  C05  107.42  3.000
 QFD  N03  C04  C05  111.77  3.000
 QFD  H5   C04  C15  106.00  3.000
 QFD  C05  C04  C15  110.23  3.000
 QFD  N03  C04  C15  113.27  3.000
 QFD  H7   C05  H6   106.55  3.000
 QFD  H7   C05  C06  110.66  3.000
 QFD  H6   C05  C06  110.76  3.000
 QFD  H7   C05  C04  107.60  3.000
 QFD  H6   C05  C04  107.82  3.000
 QFD  C06  C05  C04  113.16  3.000
 QFD  C14  C06  C07  117.54  3.000
 QFD  C14  C06  C05  121.11  3.000
 QFD  C07  C06  C05  121.33  3.000
 QFD  H8   C07  C08  118.24  3.000
 QFD  H8   C07  C06  119.91  3.000
 QFD  C08  C07  C06  121.85  3.000
 QFD  H9   C08  C09  122.14  3.000
 QFD  H9   C08  C07  118.02  3.000
 QFD  C09  C08  C07  119.83  3.000
 QFD  O10  C09  C08  124.59  3.000
 QFD  O10  C09  C13  116.42  3.000
 QFD  C08  C09  C13  118.98  3.000
 QFD  H11  C11  H10  108.79  3.000
 QFD  H11  C11  O12  112.26  3.000
 QFD  H10  C11  O12  108.06  3.000
 QFD  H11  C11  O10  110.38  3.000
 QFD  H10  C11  O10  104.29  3.000
 QFD  O12  C11  O10  112.67  3.000
 QFD  H12  C14  C06  119.73  3.000
 QFD  H12  C14  C13  118.87  3.000
 QFD  C06  C14  C13  121.40  3.000
 QFD  H13  C18  N17  107.61  3.000
 QFD  H13  C18  C19  107.82  3.000
 QFD  N17  C18  C19  111.89  3.000
 QFD  H13  C18  C02  105.18  3.000
 QFD  C19  C18  C02  110.46  3.000
 QFD  N17  C18  C02  113.46  3.000
 QFD  H15  C19  H14  107.37  3.000
 QFD  H15  C19  C18  107.90  3.000
 QFD  H14  C19  C18  109.04  3.000
 QFD  H15  C19  C20  110.27  3.000
 QFD  H14  C19  C20  110.20  3.000
 QFD  C18  C19  C20  111.91  3.000
 QFD  O24  C23  C25  117.92  3.000
 QFD  O24  C23  C22  122.76  3.000
 QFD  C25  C23  C22  119.32  3.000
 QFD  H16  C25  C23  119.81  3.000
 QFD  H16  C25  C26  120.29  3.000
 QFD  C23  C25  C26  119.90  3.000
 QFD  H17  N03  C04  115.92  3.000
 QFD  H17  N03  C02  115.99  3.000
 QFD  C04  N03  C02  127.72  3.000
 QFD  H18  N17  C18  115.90  3.000
 QFD  H18  N17  C15  115.96  3.000
 QFD  C18  N17  C15  128.00  3.000
 QFD  C11  O10  C09  118.92  3.000
 QFD  H19  O12  C11  110.28  3.000
 QFD  H20  O24  C23  110.33  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
 QFD  CONST_01  C07  C06  C14  C13    0.00   0.0  0
 QFD  CONST_02  C07  C08  C09  C13    0.00   0.0  0
 QFD  CONST_03  C23  C25  C26  C20    0.00   0.0  0
 QFD  CONST_04  C23  C22  C21  C20    0.00   0.0  0
 QFD  CONST_05  C25  C26  C20  C21    0.00   0.0  0
 QFD  CONST_06  C25  C23  C22  C21    0.00   0.0  0
 QFD  CONST_07  C26  C20  C21  C22    0.00   0.0  0
 QFD  CONST_08  C26  C25  C23  C22    0.00   0.0  0
 QFD  CONST_09  C09  C08  C07  C06    0.00   0.0  0
 QFD  CONST_10  C09  C13  C14  C06    0.00   0.0  0
 QFD  CONST_11  C14  C06  C07  C08    0.00   0.0  0
 QFD  CONST_12  C14  C13  C09  C08    0.00   0.0  0
 QFD  CONST_13  C18  C02  N03  C04    0.00   0.0  0
 QFD  CONST_14  C18  N17  C15  C04    0.00   0.0  0
 QFD  CONST_15  C05  C06  C14  C13  180.00   0.0  0
 QFD  CONST_16  O24  C23  C22  C21  180.00   0.0  0
 QFD  CONST_17  C19  C20  C21  C22  180.00   0.0  0
 QFD  CONST_18  O24  C23  C25  C26  180.00   0.0  0
 QFD  CONST_19  C08  C07  C06  C05  180.00   0.0  0
 QFD  CONST_20  O10  C09  C08  C07  180.00   0.0  0
 QFD  CONST_21  O10  C09  C13  C14  180.00   0.0  0
 QFD  CONST_22  C25  C26  C20  C19  180.00   0.0  0
 QFD  CONST_23  O01  C02  N03  C04  180.00   0.0  0
 QFD  CONST_24  O16  C15  N17  C18  180.00   0.0  0
 QFD  CONST_25  H9   C08  C09  C13  180.00   0.0  0
 QFD  CONST_26  H16  C25  C26  C20  180.00   0.0  0
 QFD  CONST_27  H3   C22  C21  C20  180.00   0.0  0
 QFD  CONST_28  H4   C26  C20  C21  180.00   0.0  0
 QFD  CONST_29  H2   C21  C20  C26  180.00   0.0  0
 QFD  CONST_30  H1   C13  C14  C06  180.00   0.0  0
 QFD  CONST_31  H12  C14  C06  C07  180.00   0.0  0
 QFD  CONST_32  H8   C07  C08  C09  180.00   0.0  0
 QFD  CONST_33  H18  N17  C15  C04  180.00   0.0  0
 QFD  CONST_34  H17  N03  C02  C18  180.00   0.0  0
 QFD  Var_01    C18  C19  C20  C21   97.83  30.0  2
 QFD  Var_02    C07  C06  C05  C04  -84.93  30.0  2
 QFD  Var_03    O12  C11  O10  C09   67.14  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
 QFD  chir_01  C04  N03  C15  C05  positiv
 QFD  chir_02  C18  N17  C19  C02  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
 QFD  plan-1  C20  0.020
 QFD  plan-1  C21  0.020
 QFD  plan-1  C22  0.020
 QFD  plan-1  C26  0.020
 QFD  plan-1  C19  0.020
 QFD  plan-1  C23  0.020
 QFD  plan-1  C25  0.020
 QFD  plan-1  O24  0.020
 QFD  plan-1  H2   0.020
 QFD  plan-1  H3   0.020
 QFD  plan-1  H4   0.020
 QFD  plan-1  H16  0.020
 QFD  plan-2  C13  0.020
 QFD  plan-2  C05  0.020
 QFD  plan-2  C06  0.020
 QFD  plan-2  C07  0.020
 QFD  plan-2  C08  0.020
 QFD  plan-2  C09  0.020
 QFD  plan-2  C14  0.020
 QFD  plan-2  O10  0.020
 QFD  plan-2  H1   0.020
 QFD  plan-2  H8   0.020
 QFD  plan-2  H9   0.020
 QFD  plan-2  H12  0.020
 QFD  plan-3  C15  0.020
 QFD  plan-3  C04  0.020
 QFD  plan-3  C18  0.020
 QFD  plan-3  N17  0.020
 QFD  plan-3  O16  0.020
 QFD  plan-3  H18  0.020
 QFD  plan-4  C02  0.020
 QFD  plan-4  C04  0.020
 QFD  plan-4  C18  0.020
 QFD  plan-4  N03  0.020
 QFD  plan-4  H17  0.020
 QFD  plan-4  O01  0.020

