# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:58:54 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (3S,6S)-3,6-bis(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](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
 YTT  YTT  (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione  ligand  42  24  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YTT
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
 YTT  OB    O  O     0  -0.484  -0.3958  -2.7531  -1.4114
 YTT  CB    C  C     0   0.532  -0.2331  -1.5449  -1.3480
 YTT  CAB   C  CH1   0  -0.193   1.1512  -0.9724  -1.1246
 YTT  CBB   C  CH2   0  -0.531   1.5740  -1.2066   0.3404
 YTT  CGB   C  CR6   0   0.105   2.9376  -0.6487   0.6274
 YTT  CD3   C  CR16  0  -0.295   3.0963   0.6242   1.1707
 YTT  CE3   C  CR16  0  -0.324   4.3520   1.1621   1.4030
 YTT  CZB   C  CR6   0   0.342   5.4908   0.4259   1.0860
 YTT  OHB   O  OH1   0  -0.633   6.6926   0.9880   1.3278
 YTT  CE4   C  CR16  0  -0.368   5.3511  -0.8482   0.5410
 YTT  CD4   C  CR16  0  -0.285   4.0863  -1.3704   0.3167
 YTT  NB    N  NH1   0  -0.626   1.2472   0.4138  -1.5198
 YTT  NA    N  NH1   0  -0.626  -1.2328  -0.6596  -1.4438
 YTT  CAA   C  CH1   0  -0.195  -1.1361   0.7686  -1.2458
 YTT  CA    C  C     0   0.531   0.2488   1.3041  -1.5450
 YTT  OA    O  O     0  -0.484   0.4118   2.4919  -1.7754
 YTT  CBA   C  CH2   0  -0.528  -1.5639   1.2014   0.1702
 YTT  CGA   C  CR6   0   0.104  -2.9624   0.7601   0.4911
 YTT  CD2   C  CR16  0  -0.297  -3.2072  -0.4157   1.1923
 YTT  CE2   C  CR16  0  -0.370  -4.5000  -0.8411   1.4635
 YTT  CZA   C  CR6   0   0.342  -5.5848  -0.0864   1.0278
 YTT  OHA   O  OH1   0  -0.633  -6.8634  -0.4421   1.2656
 YTT  CE1   C  CR16  0  -0.322  -5.3578   1.0924   0.3193
 YTT  CD1   C  CR16  0  -0.284  -4.0611   1.5012   0.0584
 YTT  HAB   H  HCH1  0   0.308   1.8283  -1.5406  -1.7656
 YTT  HBB   H  HCH2  0   0.262   0.8373  -0.7569   1.0109
 YTT  HBBA  H  HCH2  0   0.274   1.5556  -2.2823   0.5245
 YTT  HD3   H  HCR6  0   0.247   2.2213   1.2093   1.4300
 YTT  HE3   H  HCR6  0   0.263   4.4525   2.1506   1.8340
 YTT  HOHB  H  HOH1  0   0.474   7.4012   0.3756   1.1010
 YTT  HE4   H  HCR6  0   0.271   6.2287  -1.4361   0.2955
 YTT  HD4   H  HCR6  0   0.254   3.9993  -2.3657  -0.1044
 YTT  HNB   H  HNH1  0   0.408   2.1771   0.7710  -1.6925
 YTT  HNA   H  HNH1  0   0.408  -2.1621  -1.0382  -1.5662
 YTT  HAA   H  HCH1  0   0.309  -1.8099   1.2432  -1.9621
 YTT  HBA   H  HCH2  0   0.261  -0.8643   0.7933   0.9045
 YTT  HBAA  H  HCH2  0   0.274  -1.4878   2.2889   0.2268
 YTT  HD2   H  HCR6  0   0.251  -2.3744  -1.0139   1.5442
 YTT  HE2   H  HCR6  0   0.271  -4.6602  -1.7592   2.0174
 YTT  HOHA  H  HOH1  0   0.474  -6.8943  -1.2637   1.7684
 YTT  HE1   H  HCR6  0   0.263  -6.1977   1.6877  -0.0176
 YTT  HD1   H  HCR6  0   0.252  -3.9027   2.4225  -0.4909

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
 YTT  OB   CB    double    1.221  0.020  1.221
 YTT  CB   CAB   single    1.515  0.020  1.515
 YTT  CB   NA    single    1.339  0.020  1.339
 YTT  CAB  CBB   single    1.543  0.020  1.543
 YTT  CAB  NB    single    1.445  0.020  1.445
 YTT  CBB  CGB   single    1.501  0.020  1.501
 YTT  CGB  CD3   aromatic  1.393  0.020  1.393
 YTT  CGB  CD4   aromatic  1.392  0.020  1.392
 YTT  CD3  CE3   aromatic  1.386  0.020  1.386
 YTT  CE3  CZB   aromatic  1.393  0.020  1.393
 YTT  CZB  OHB   single    1.349  0.020  1.349
 YTT  CZB  CE4   aromatic  1.393  0.020  1.393
 YTT  CE4  CD4   aromatic  1.387  0.020  1.387
 YTT  NB   CA    single    1.338  0.020  1.338
 YTT  NA   CAA   single    1.445  0.020  1.445
 YTT  CAA  CA    single    1.515  0.020  1.515
 YTT  CAA  CBA   single    1.541  0.020  1.541
 YTT  CA   OA    double    1.221  0.020  1.221
 YTT  CBA  CGA   single    1.501  0.020  1.501
 YTT  CGA  CD2   aromatic  1.391  0.020  1.391
 YTT  CGA  CD1   aromatic  1.394  0.020  1.394
 YTT  CD2  CE2   aromatic  1.388  0.020  1.388
 YTT  CE2  CZA   aromatic  1.391  0.020  1.391
 YTT  CZA  OHA   single    1.348  0.020  1.348
 YTT  CZA  CE1   aromatic  1.394  0.020  1.394
 YTT  CE1  CD1   aromatic  1.384  0.020  1.384
 YTT  CAB  HAB   single    0.970  0.020  1.090
 YTT  CBB  HBB   single    0.970  0.020  1.090
 YTT  CBB  HBBA  single    0.970  0.020  1.090
 YTT  CD3  HD3   single    0.930  0.020  1.080
 YTT  CE3  HE3   single    0.930  0.020  1.080
 YTT  OHB  HOHB  single    0.850  0.020  0.980
 YTT  CE4  HE4   single    0.930  0.020  1.080
 YTT  CD4  HD4   single    0.930  0.020  1.080
 YTT  NB   HNB   single    0.860  0.020  1.020
 YTT  NA   HNA   single    0.860  0.020  1.020
 YTT  CAA  HAA   single    0.970  0.020  1.090
 YTT  CBA  HBA   single    0.970  0.020  1.090
 YTT  CBA  HBAA  single    0.970  0.020  1.090
 YTT  CD2  HD2   single    0.930  0.020  1.080
 YTT  CE2  HE2   single    0.930  0.020  1.080
 YTT  OHA  HOHA  single    0.850  0.020  0.980
 YTT  CE1  HE1   single    0.930  0.020  1.080
 YTT  CD1  HD1   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
 YTT  NA    CB   CAB  116.30  3.000
 YTT  NA    CB   OB   123.45  3.000
 YTT  CAB   CB   OB   120.24  3.000
 YTT  HAB   CAB  NB   107.32  3.000
 YTT  HAB   CAB  CBB  107.97  3.000
 YTT  NB    CAB  CBB  112.79  3.000
 YTT  HAB   CAB  CB   106.47  3.000
 YTT  NB    CAB  CB   112.53  3.000
 YTT  CBB   CAB  CB   109.46  3.000
 YTT  HBBA  CBB  HBB  106.90  3.000
 YTT  HBBA  CBB  CGB  110.45  3.000
 YTT  HBB   CBB  CGB  110.01  3.000
 YTT  HBBA  CBB  CAB  107.77  3.000
 YTT  HBB   CBB  CAB  109.60  3.000
 YTT  CGB   CBB  CAB  111.97  3.000
 YTT  CD4   CGB  CD3  117.83  3.000
 YTT  CD4   CGB  CBB  120.96  3.000
 YTT  CD3   CGB  CBB  121.18  3.000
 YTT  HD3   CD3  CE3  118.80  3.000
 YTT  HD3   CD3  CGB  119.63  3.000
 YTT  CE3   CD3  CGB  121.56  3.000
 YTT  HE3   CE3  CZB  119.81  3.000
 YTT  HE3   CE3  CD3  120.34  3.000
 YTT  CZB   CE3  CD3  119.85  3.000
 YTT  CE4   CZB  OHB  122.74  3.000
 YTT  CE4   CZB  CE3  119.38  3.000
 YTT  OHB   CZB  CE3  117.88  3.000
 YTT  HOHB  OHB  CZB  110.38  3.000
 YTT  HE4   CE4  CD4  119.82  3.000
 YTT  HE4   CE4  CZB  120.22  3.000
 YTT  CD4   CE4  CZB  119.95  3.000
 YTT  HD4   CD4  CE4  118.80  3.000
 YTT  HD4   CD4  CGB  119.77  3.000
 YTT  CE4   CD4  CGB  121.43  3.000
 YTT  HNB   NB   CA   116.62  3.000
 YTT  HNB   NB   CAB  116.54  3.000
 YTT  CA    NB   CAB  126.45  3.000
 YTT  HNA   NA   CAA  116.63  3.000
 YTT  HNA   NA   CB   116.58  3.000
 YTT  CAA   NA   CB   126.43  3.000
 YTT  HAA   CAA  CBA  108.02  3.000
 YTT  HAA   CAA  CA   106.32  3.000
 YTT  CBA   CAA  CA   109.63  3.000
 YTT  HAA   CAA  NA   107.36  3.000
 YTT  CBA   CAA  NA   112.64  3.000
 YTT  CA    CAA  NA   112.55  3.000
 YTT  OA    CA   CAA  120.22  3.000
 YTT  OA    CA   NB   123.46  3.000
 YTT  CAA   CA   NB   116.32  3.000
 YTT  HBAA  CBA  HBA  107.01  3.000
 YTT  HBAA  CBA  CGA  110.28  3.000
 YTT  HBA   CBA  CGA  110.05  3.000
 YTT  HBAA  CBA  CAA  107.94  3.000
 YTT  HBA   CBA  CAA  109.55  3.000
 YTT  CGA   CBA  CAA  111.86  3.000
 YTT  CD1   CGA  CD2  117.86  3.000
 YTT  CD1   CGA  CBA  120.77  3.000
 YTT  CD2   CGA  CBA  121.35  3.000
 YTT  HD2   CD2  CE2  118.88  3.000
 YTT  HD2   CD2  CGA  119.67  3.000
 YTT  CE2   CD2  CGA  121.44  3.000
 YTT  HE2   CE2  CZA  120.27  3.000
 YTT  HE2   CE2  CD2  119.81  3.000
 YTT  CZA   CE2  CD2  119.92  3.000
 YTT  CE1   CZA  OHA  117.85  3.000
 YTT  CE1   CZA  CE2  119.40  3.000
 YTT  OHA   CZA  CE2  122.75  3.000
 YTT  HOHA  OHA  CZA  110.32  3.000
 YTT  HE1   CE1  CD1  120.36  3.000
 YTT  HE1   CE1  CZA  119.77  3.000
 YTT  CD1   CE1  CZA  119.87  3.000
 YTT  HD1   CD1  CE1  118.89  3.000
 YTT  HD1   CD1  CGA  119.59  3.000
 YTT  CE1   CD1  CGA  121.51  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
 YTT  CONST_01  CZB  CE3  CD3  CGB    0.00   0.0  0
 YTT  CONST_02  CZB  CE4  CD4  CGB    0.00   0.0  0
 YTT  CONST_03  CE4  CD4  CGB  CD3    0.00   0.0  0
 YTT  CONST_04  CE4  CZB  CE3  CD3    0.00   0.0  0
 YTT  CONST_05  CD4  CGB  CD3  CE3    0.00   0.0  0
 YTT  CONST_06  CD4  CE4  CZB  CE3    0.00   0.0  0
 YTT  CONST_07  CZA  CE2  CD2  CGA    0.00   0.0  0
 YTT  CONST_08  CZA  CE1  CD1  CGA    0.00   0.0  0
 YTT  CONST_09  CE1  CD1  CGA  CD2    0.00   0.0  0
 YTT  CONST_10  CE1  CZA  CE2  CD2    0.00   0.0  0
 YTT  CONST_11  CD1  CGA  CD2  CE2    0.00   0.0  0
 YTT  CONST_12  CD1  CE1  CZA  CE2    0.00   0.0  0
 YTT  CONST_13  CAA  NA   CB   CAB    0.00   0.0  0
 YTT  CONST_14  CAA  CA   NB   CAB    0.00   0.0  0
 YTT  CONST_15  CE3  CD3  CGB  CBB  180.00   0.0  0
 YTT  CONST_16  CE4  CD4  CGB  CBB  180.00   0.0  0
 YTT  CONST_17  OHB  CZB  CE3  CD3  180.00   0.0  0
 YTT  CONST_18  CD4  CE4  CZB  OHB  180.00   0.0  0
 YTT  CONST_19  CE2  CD2  CGA  CBA  180.00   0.0  0
 YTT  CONST_20  CE1  CD1  CGA  CBA  180.00   0.0  0
 YTT  CONST_21  OHA  CZA  CE2  CD2  180.00   0.0  0
 YTT  CONST_22  CD1  CE1  CZA  OHA  180.00   0.0  0
 YTT  CONST_23  CAA  NA   CB   OB   180.00   0.0  0
 YTT  CONST_24  OA   CA   NB   CAB  180.00   0.0  0
 YTT  CONST_25  HE3  CE3  CD3  CGB  180.00   0.0  0
 YTT  CONST_26  HE4  CE4  CD4  CGB  180.00   0.0  0
 YTT  CONST_27  HD4  CD4  CGB  CD3  180.00   0.0  0
 YTT  CONST_28  HD3  CD3  CE3  CZB  180.00   0.0  0
 YTT  CONST_29  HE2  CE2  CD2  CGA  180.00   0.0  0
 YTT  CONST_30  HE1  CE1  CD1  CGA  180.00   0.0  0
 YTT  CONST_31  HD1  CD1  CGA  CD2  180.00   0.0  0
 YTT  CONST_32  HD2  CD2  CE2  CZA  180.00   0.0  0
 YTT  CONST_33  HNA  NA   CB   CAB  180.00   0.0  0
 YTT  CONST_34  HNB  NB   CA   CAA  180.00   0.0  0
 YTT  Var_01    CD3  CGB  CBB  CAB   95.00  30.0  2
 YTT  Var_02    CD2  CGA  CBA  CAA   95.86  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
 YTT  chir_01  CAB  CB  CBB  NB   positiv
 YTT  chir_02  CAA  NA  CA   CBA  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
 YTT  plan-1  CBB  0.020
 YTT  plan-1  CGB  0.020
 YTT  plan-1  CD3  0.020
 YTT  plan-1  CE3  0.020
 YTT  plan-1  CZB  0.020
 YTT  plan-1  OHB  0.020
 YTT  plan-1  CE4  0.020
 YTT  plan-1  CD4  0.020
 YTT  plan-1  HD3  0.020
 YTT  plan-1  HE3  0.020
 YTT  plan-1  HE4  0.020
 YTT  plan-1  HD4  0.020
 YTT  plan-2  CBA  0.020
 YTT  plan-2  CGA  0.020
 YTT  plan-2  CD2  0.020
 YTT  plan-2  CE2  0.020
 YTT  plan-2  CZA  0.020
 YTT  plan-2  OHA  0.020
 YTT  plan-2  CE1  0.020
 YTT  plan-2  CD1  0.020
 YTT  plan-2  HD2  0.020
 YTT  plan-2  HE2  0.020
 YTT  plan-2  HE1  0.020
 YTT  plan-2  HD1  0.020
 YTT  plan-3  OB   0.020
 YTT  plan-3  CB   0.020
 YTT  plan-3  CAB  0.020
 YTT  plan-3  NA   0.020
 YTT  plan-3  CAA  0.020
 YTT  plan-3  HNA  0.020
 YTT  plan-4  CAB  0.020
 YTT  plan-4  NB   0.020
 YTT  plan-4  CAA  0.020
 YTT  plan-4  CA   0.020
 YTT  plan-4  OA   0.020
 YTT  plan-4  HNB  0.020

