# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 08:05:41 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3S,6S)-3-(3,4-dihydroxybenzyl)-6-(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)c(O)c3)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
 1G7  1G7  (3S,6S)-3-(3,4-dihydroxybenzyl)-6-(4-hydroxybenzyl)piperazine-2,5-dione  ligand  43  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1G7
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
 1G7  OB   O  O     0  -0.483   0.7459  -3.0661   1.1387
 1G7  CB   C  C     0   0.532   0.5206  -1.8699   1.2306
 1G7  CAB  C  CH1   0  -0.195  -0.8954  -1.3478   1.1027
 1G7  CBB  C  CH2   0  -0.532  -1.3366  -1.4111  -0.3742
 1G7  CGB  C  CR6   0   0.118  -2.7355  -0.8988  -0.5598
 1G7  CD4  C  CR16  0  -0.428  -2.9580   0.4107  -0.9816
 1G7  CE4  C  CR6   0   0.274  -4.2435   0.9109  -1.1157
 1G7  OH4  O  OH1   0  -0.645  -4.5246   2.1705  -1.5214
 1G7  CZB  C  CR6   0   0.279  -5.3446   0.0970  -0.8213
 1G7  OHB  O  OH1   0  -0.635  -6.6124   0.5478  -0.9393
 1G7  CE3  C  CR16  0  -0.328  -5.1252  -1.2048  -0.3995
 1G7  CD3  C  CR16  0  -0.313  -3.8334  -1.6983  -0.2684
 1G7  NB   N  NH1   0  -0.625  -1.0539  -0.0321   1.6770
 1G7  CA   C  C     0   0.532  -0.1026   0.9014   1.7977
 1G7  OA   O  O     0  -0.484  -0.3215   2.0410   2.1766
 1G7  NA   N  NH1   0  -0.625   1.4749  -0.9517   1.4245
 1G7  CAA  C  CH1   0  -0.195   1.3010   0.4826   1.4116
 1G7  CBA  C  CH2   0  -0.530   1.6730   1.1150   0.0550
 1G7  CGA  C  CR6   0   0.106   3.0692   0.7585  -0.3651
 1G7  CD1  C  CR16  0  -0.297   3.3136  -0.3019  -1.2341
 1G7  CE1  C  CR16  0  -0.324   4.6022  -0.6584  -1.5993
 1G7  CZA  C  CR6   0   0.342   5.6878   0.0499  -1.0904
 1G7  OHA  O  OH1   0  -0.633   6.9247  -0.3271  -1.4728
 1G7  CE2  C  CR16  0  -0.368   5.4618   1.1125  -0.2187
 1G7  CD2  C  CR16  0  -0.285   4.1658   1.4545   0.1353
 1G7  H1   H  HCH1  0   0.308  -1.5288  -2.0296   1.6738
 1G7  H2   H  HCH2  0   0.262  -0.6414  -0.8347  -0.9892
 1G7  H3   H  HCH2  0   0.275  -1.2636  -2.4502  -0.7004
 1G7  H4   H  HCR6  0   0.263  -2.1144   1.0527  -1.2170
 1G7  H5   H  HOH1  0   0.482  -3.7160   2.6577  -1.7135
 1G7  H6   H  HOH1  0   0.472  -6.6183   1.4561  -1.2625
 1G7  H7   H  HCR6  0   0.264  -5.9770  -1.8358  -0.1771
 1G7  H8   H  HCR6  0   0.249  -3.6889  -2.7211   0.0588
 1G7  H9   H  HNH1  0   0.408  -1.9978   0.2524   1.9001
 1G7  H10  H  HNH1  0   0.408   2.4244  -1.2927   1.4862
 1G7  H11  H  HCH1  0   0.309   1.9661   0.8973   2.1723
 1G7  H12  H  HCH2  0   0.260   0.9588   0.7933  -0.7079
 1G7  H13  H  HCH2  0   0.274   1.5686   2.1970   0.1512
 1G7  H14  H  HCR6  0   0.248   2.4804  -0.8606  -1.6443
 1G7  H15  H  HCR6  0   0.263   4.7675  -1.4834  -2.2809
 1G7  H16  H  HOH1  0   0.474   7.5883   0.2429  -1.0687
 1G7  H17  H  HCR6  0   0.271   6.2963   1.6786   0.1797
 1G7  H18  H  HCR6  0   0.255   4.0114   2.2865   0.8129

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
 1G7  OHA  CZA  single    1.348  0.020  1.348
 1G7  CZA  CE2  aromatic  1.393  0.020  1.393
 1G7  CZA  CE1  aromatic  1.393  0.020  1.393
 1G7  CE2  CD2  aromatic  1.386  0.020  1.386
 1G7  OH4  CE4  single    1.353  0.020  1.353
 1G7  OHB  CZB  single    1.351  0.020  1.351
 1G7  CE1  CD1  aromatic  1.386  0.020  1.386
 1G7  CZB  CE4  aromatic  1.401  0.020  1.401
 1G7  CZB  CE3  aromatic  1.386  0.020  1.386
 1G7  CE4  CD4  aromatic  1.386  0.020  1.386
 1G7  CE3  CD3  aromatic  1.389  0.020  1.389
 1G7  CD4  CGB  aromatic  1.394  0.020  1.394
 1G7  CD3  CGB  aromatic  1.389  0.020  1.389
 1G7  CGB  CBB  single    1.501  0.020  1.501
 1G7  CD2  CGA  aromatic  1.392  0.020  1.392
 1G7  CD1  CGA  aromatic  1.393  0.020  1.393
 1G7  CBB  CAB  single    1.543  0.020  1.543
 1G7  CGA  CBA  single    1.501  0.020  1.501
 1G7  CAB  NB   single    1.444  0.020  1.444
 1G7  CAB  CB   single    1.515  0.020  1.515
 1G7  NB   CA   single    1.338  0.020  1.338
 1G7  OB   CB   double    1.221  0.020  1.221
 1G7  CBA  CAA  single    1.542  0.020  1.542
 1G7  CB   NA   single    1.338  0.020  1.338
 1G7  CA   OA   double    1.221  0.020  1.221
 1G7  CA   CAA  single    1.515  0.020  1.515
 1G7  NA   CAA  single    1.445  0.020  1.445
 1G7  CAB  H1   single    0.970  0.020  1.090
 1G7  CBB  H2   single    0.970  0.020  1.090
 1G7  CBB  H3   single    0.970  0.020  1.090
 1G7  CD4  H4   single    0.930  0.020  1.080
 1G7  OH4  H5   single    0.850  0.020  0.980
 1G7  OHB  H6   single    0.850  0.020  0.980
 1G7  CE3  H7   single    0.930  0.020  1.080
 1G7  CD3  H8   single    0.930  0.020  1.080
 1G7  NB   H9   single    0.860  0.020  1.020
 1G7  NA   H10  single    0.860  0.020  1.020
 1G7  CAA  H11  single    0.970  0.020  1.090
 1G7  CBA  H12  single    0.970  0.020  1.090
 1G7  CBA  H13  single    0.970  0.020  1.090
 1G7  CD1  H14  single    0.930  0.020  1.080
 1G7  CE1  H15  single    0.930  0.020  1.080
 1G7  OHA  H16  single    0.850  0.020  0.980
 1G7  CE2  H17  single    0.930  0.020  1.080
 1G7  CD2  H18  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
 1G7  NA   CB   CAB  116.25  3.000
 1G7  NA   CB   OB   123.48  3.000
 1G7  CAB  CB   OB   120.26  3.000
 1G7  H1   CAB  NB   107.29  3.000
 1G7  H1   CAB  CBB  108.01  3.000
 1G7  NB   CAB  CBB  112.75  3.000
 1G7  H1   CAB  CB   106.43  3.000
 1G7  NB   CAB  CB   112.52  3.000
 1G7  CBB  CAB  CB   109.52  3.000
 1G7  H3   CBB  H2   106.94  3.000
 1G7  H3   CBB  CGB  110.50  3.000
 1G7  H2   CBB  CGB  110.08  3.000
 1G7  H3   CBB  CAB  107.82  3.000
 1G7  H2   CBB  CAB  109.59  3.000
 1G7  CGB  CBB  CAB  111.77  3.000
 1G7  CD3  CGB  CD4  118.56  3.000
 1G7  CD3  CGB  CBB  120.94  3.000
 1G7  CD4  CGB  CBB  120.45  3.000
 1G7  H4   CD4  CE4  119.10  3.000
 1G7  H4   CD4  CGB  119.80  3.000
 1G7  CE4  CD4  CGB  121.10  3.000
 1G7  CZB  CE4  OH4  116.15  3.000
 1G7  CZB  CE4  CD4  119.95  3.000
 1G7  OH4  CE4  CD4  123.90  3.000
 1G7  H5   OH4  CE4  110.87  3.000
 1G7  CE3  CZB  OHB  119.26  3.000
 1G7  CE3  CZB  CE4  119.03  3.000
 1G7  OHB  CZB  CE4  121.71  3.000
 1G7  H6   OHB  CZB  110.46  3.000
 1G7  H7   CE3  CD3  120.33  3.000
 1G7  H7   CE3  CZB  119.02  3.000
 1G7  CD3  CE3  CZB  120.65  3.000
 1G7  H8   CD3  CE3  119.20  3.000
 1G7  H8   CD3  CGB  120.09  3.000
 1G7  CE3  CD3  CGB  120.71  3.000
 1G7  H9   NB   CA   116.59  3.000
 1G7  H9   NB   CAB  116.54  3.000
 1G7  CA   NB   CAB  126.39  3.000
 1G7  CAA  CA   OA   120.22  3.000
 1G7  CAA  CA   NB   116.29  3.000
 1G7  OA   CA   NB   123.48  3.000
 1G7  H10  NA   CAA  116.65  3.000
 1G7  H10  NA   CB   116.56  3.000
 1G7  CAA  NA   CB   126.44  3.000
 1G7  H11  CAA  CBA  108.07  3.000
 1G7  H11  CAA  NA   107.30  3.000
 1G7  CBA  CAA  NA   112.70  3.000
 1G7  H11  CAA  CA   106.36  3.000
 1G7  NA   CAA  CA   112.56  3.000
 1G7  CBA  CAA  CA   109.53  3.000
 1G7  H13  CBA  H12  106.90  3.000
 1G7  H13  CBA  CGA  110.43  3.000
 1G7  H12  CBA  CGA  110.02  3.000
 1G7  H13  CBA  CAA  107.81  3.000
 1G7  H12  CBA  CAA  109.61  3.000
 1G7  CGA  CBA  CAA  111.91  3.000
 1G7  CD2  CGA  CD1  117.83  3.000
 1G7  CD1  CGA  CBA  121.24  3.000
 1G7  CD2  CGA  CBA  120.90  3.000
 1G7  H14  CD1  CE1  118.84  3.000
 1G7  H14  CD1  CGA  119.60  3.000
 1G7  CE1  CD1  CGA  121.56  3.000
 1G7  H15  CE1  CZA  119.90  3.000
 1G7  H15  CE1  CD1  120.25  3.000
 1G7  CZA  CE1  CD1  119.85  3.000
 1G7  CE2  CZA  OHA  122.65  3.000
 1G7  CE2  CZA  CE1  119.36  3.000
 1G7  OHA  CZA  CE1  117.99  3.000
 1G7  H16  OHA  CZA  110.32  3.000
 1G7  H17  CE2  CD2  119.79  3.000
 1G7  H17  CE2  CZA  120.23  3.000
 1G7  CD2  CE2  CZA  119.98  3.000
 1G7  H18  CD2  CE2  118.82  3.000
 1G7  H18  CD2  CGA  119.76  3.000
 1G7  CE2  CD2  CGA  121.42  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
 1G7  CONST_01  CZB  CE4  CD4  CGB    0.00   0.0  0
 1G7  CONST_02  CZB  CE3  CD3  CGB    0.00   0.0  0
 1G7  CONST_03  CE3  CZB  CE4  CD4    0.00   0.0  0
 1G7  CONST_04  CE3  CD3  CGB  CD4    0.00   0.0  0
 1G7  CONST_05  CD3  CE3  CZB  CE4    0.00   0.0  0
 1G7  CONST_06  CD3  CGB  CD4  CE4    0.00   0.0  0
 1G7  CONST_07  CZA  CE2  CD2  CGA    0.00   0.0  0
 1G7  CONST_08  CZA  CE1  CD1  CGA    0.00   0.0  0
 1G7  CONST_09  CE2  CZA  CE1  CD1    0.00   0.0  0
 1G7  CONST_10  CE2  CD2  CGA  CD1    0.00   0.0  0
 1G7  CONST_11  CD2  CE2  CZA  CE1    0.00   0.0  0
 1G7  CONST_12  CD2  CGA  CD1  CE1    0.00   0.0  0
 1G7  CONST_13  CAA  CA   NB   CAB    0.00   0.0  0
 1G7  CONST_14  CAA  NA   CB   CAB    0.00   0.0  0
 1G7  CONST_15  CE4  CD4  CGB  CBB  180.00   0.0  0
 1G7  CONST_16  CE3  CD3  CGB  CBB  180.00   0.0  0
 1G7  CONST_17  OH4  CE4  CD4  CGB  180.00   0.0  0
 1G7  CONST_18  OHB  CZB  CE4  CD4  180.00   0.0  0
 1G7  CONST_19  CE3  CZB  CE4  OH4  180.00   0.0  0
 1G7  CONST_20  CD3  CE3  CZB  OHB  180.00   0.0  0
 1G7  CONST_21  CE2  CD2  CGA  CBA  180.00   0.0  0
 1G7  CONST_22  CE1  CD1  CGA  CBA  180.00   0.0  0
 1G7  CONST_23  OHA  CZA  CE1  CD1  180.00   0.0  0
 1G7  CONST_24  CD2  CE2  CZA  OHA  180.00   0.0  0
 1G7  CONST_25  CAA  NA   CB   OB   180.00   0.0  0
 1G7  CONST_26  OA   CA   NB   CAB  180.00   0.0  0
 1G7  CONST_27  H7   CE3  CD3  CGB  180.00   0.0  0
 1G7  CONST_28  H8   CD3  CGB  CD4  180.00   0.0  0
 1G7  CONST_29  H4   CD4  CE4  CZB  180.00   0.0  0
 1G7  CONST_30  H17  CE2  CD2  CGA  180.00   0.0  0
 1G7  CONST_31  H15  CE1  CD1  CGA  180.00   0.0  0
 1G7  CONST_32  H18  CD2  CGA  CD1  180.00   0.0  0
 1G7  CONST_33  H14  CD1  CE1  CZA  180.00   0.0  0
 1G7  CONST_34  H10  NA   CB   CAB  180.00   0.0  0
 1G7  CONST_35  H9   NB   CA   CAA  180.00   0.0  0
 1G7  Var_01    CD4  CGB  CBB  CAB   97.81  30.0  2
 1G7  Var_02    CD2  CGA  CBA  CAA  -81.85  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
 1G7  chir_01  CAB  CBB  NB   CB  positiv
 1G7  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
 1G7  plan-1  CBB  0.020
 1G7  plan-1  CGB  0.020
 1G7  plan-1  CD4  0.020
 1G7  plan-1  CE4  0.020
 1G7  plan-1  OH4  0.020
 1G7  plan-1  CZB  0.020
 1G7  plan-1  OHB  0.020
 1G7  plan-1  CE3  0.020
 1G7  plan-1  CD3  0.020
 1G7  plan-1  H4   0.020
 1G7  plan-1  H7   0.020
 1G7  plan-1  H8   0.020
 1G7  plan-2  CBA  0.020
 1G7  plan-2  CGA  0.020
 1G7  plan-2  CD1  0.020
 1G7  plan-2  CE1  0.020
 1G7  plan-2  CZA  0.020
 1G7  plan-2  OHA  0.020
 1G7  plan-2  CE2  0.020
 1G7  plan-2  CD2  0.020
 1G7  plan-2  H14  0.020
 1G7  plan-2  H15  0.020
 1G7  plan-2  H17  0.020
 1G7  plan-2  H18  0.020
 1G7  plan-3  OB   0.020
 1G7  plan-3  CB   0.020
 1G7  plan-3  CAB  0.020
 1G7  plan-3  NA   0.020
 1G7  plan-3  CAA  0.020
 1G7  plan-3  H10  0.020
 1G7  plan-4  CAB  0.020
 1G7  plan-4  NB   0.020
 1G7  plan-4  CA   0.020
 1G7  plan-4  OA   0.020
 1G7  plan-4  CAA  0.020
 1G7  plan-4  H9   0.020

