# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 08:02:04 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (3S,6S)-3-(4-hydroxybenzyl)-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C[C@@H]2NC(=O)[C@H](Cc3c[nH]c4ccccc34)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
 1GB  1GB  (3S,6S)-3-(4-hydroxybenzyl)-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione  ligand  45  26  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1GB
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
 1GB  OB   O  O     0  -0.482   0.4479  -1.3739   2.6435
 1GB  CB   C  C     0   0.530   0.1761  -0.3568   2.0261
 1GB  CAB  C  CH1   0  -0.196  -1.2379  -0.1084   1.5409
 1GB  CBB  C  CH2   0  -0.548  -1.5120  -0.9861   0.3014
 1GB  CGB  C  CR6   0   0.120  -2.9033  -0.7971  -0.2278
 1GB  CD4  C  CR16  0  -0.296  -3.1756   0.1357  -1.2258
 1GB  CE4  C  CR16  0  -0.323  -4.4635   0.3446  -1.6924
 1GB  CZB  C  CR6   0   0.341  -5.5216  -0.3871  -1.1591
 1GB  OHB  O  OH1   0  -0.632  -6.7582  -0.1548  -1.6436
 1GB  CE3  C  CR16  0  -0.368  -5.2675  -1.3251  -0.1613
 1GB  CD3  C  CR16  0  -0.288  -3.9723  -1.5190   0.2941
 1GB  NB   N  NH1   0  -0.625  -1.4953   1.2933   1.3050
 1GB  CA   C  C     0   0.527  -0.5928   2.2027   0.9156
 1GB  OA   O  O     0  -0.482  -0.8826   3.3444   0.5955
 1GB  NA   N  NH1   0  -0.623   1.0776   0.5802   1.7077
 1GB  CAA  C  CH1   0  -0.198   0.8485   1.7367   0.8710
 1GB  CBA  C  CH2   0  -0.555   1.2845   1.5122  -0.5927
 1GB  CGA  C  CR5   0   0.008   2.7118   1.0925  -0.7032
 1GB  CD2  C  CR56  0   0.024   3.2314  -0.2432  -0.6721
 1GB  CE2  C  CR16  0  -0.366   2.6481  -1.5129  -0.5817
 1GB  CZ3  C  CR16  0  -0.269   3.4623  -2.6278  -0.5932
 1GB  CH2  C  CR16  0  -0.285   4.8587  -2.5038  -0.6915
 1GB  CZ2  C  CR16  0  -0.303   5.4640  -1.2657  -0.7834
 1GB  CE1  C  CR56  0   0.355   4.6371  -0.1431  -0.7735
 1GB  NE1  N  NR15  0  -0.684   4.9449   1.1831  -0.8556
 1GB  CD1  C  CR15  0  -0.070   3.7964   1.9182  -0.8163
 1GB  H1   H  HCH1  0   0.309  -1.9061  -0.4327   2.3410
 1GB  H2   H  HCH2  0   0.262  -0.7806  -0.7548  -0.4780
 1GB  H3   H  HCH2  0   0.276  -1.3505  -2.0277   0.5858
 1GB  H4   H  HCR6  0   0.248  -2.3653   0.7094  -1.6602
 1GB  H5   H  HCR6  0   0.263  -4.6482   1.0717  -2.4733
 1GB  H6   H  HOH1  0   0.474  -7.4002  -0.7294  -1.2120
 1GB  H7   H  HCR6  0   0.271  -6.0782  -1.9101   0.2581
 1GB  H8   H  HCR6  0   0.255  -3.7976  -2.2568   1.0688
 1GB  H9   H  HNH1  0   0.408  -2.4622   1.5874   1.3115
 1GB  H10  H  HNH1  0   0.408   2.0342   0.4014   1.9806
 1GB  H11  H  HCH1  0   0.307   1.4508   2.5532   1.2743
 1GB  H12  H  HCH2  0   0.254   0.6360   0.7638  -1.0590
 1GB  H13  H  HCH2  0   0.274   1.1218   2.4445  -1.1363
 1GB  H14  H  HCR6  0   0.233   1.5732  -1.6262  -0.5117
 1GB  H15  H  HCR6  0   0.246   3.0224  -3.6145  -0.5249
 1GB  H16  H  HCR6  0   0.249   5.4725  -3.3953  -0.6977
 1GB  H17  H  HCR6  0   0.259   6.5398  -1.1711  -0.8603
 1GB  H18  H  HNR5  0   0.410   5.8700   1.5653  -0.9592
 1GB  H19  H  HCR5  0   0.284   3.8314   2.9949  -0.8777

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
 1GB  CH2  CZ2  aromatic  1.381  0.020  1.381
 1GB  CH2  CZ3  aromatic  1.405  0.020  1.405
 1GB  CZ2  CE1  aromatic  1.394  0.020  1.394
 1GB  CZ3  CE2  aromatic  1.381  0.020  1.381
 1GB  CE1  NE1  aromatic  1.364  0.020  1.364
 1GB  CE1  CD2  aromatic  1.413  0.020  1.413
 1GB  NE1  CD1  aromatic  1.364  0.020  1.364
 1GB  OHB  CZB  single    1.348  0.020  1.348
 1GB  CE2  CD2  aromatic  1.400  0.020  1.400
 1GB  CE4  CZB  aromatic  1.393  0.020  1.393
 1GB  CE4  CD4  aromatic  1.386  0.020  1.386
 1GB  CZB  CE3  aromatic  1.393  0.020  1.393
 1GB  CD2  CGA  aromatic  1.434  0.020  1.434
 1GB  CE3  CD3  aromatic  1.387  0.020  1.387
 1GB  CD4  CGB  aromatic  1.393  0.020  1.393
 1GB  CD3  CGB  aromatic  1.392  0.020  1.392
 1GB  CGB  CBB  single    1.501  0.020  1.501
 1GB  CBB  CAB  single    1.543  0.020  1.543
 1GB  CD1  CGA  aromatic  1.368  0.020  1.368
 1GB  CGA  CBA  single    1.492  0.020  1.492
 1GB  CAB  NB   single    1.445  0.020  1.445
 1GB  CAB  CB   single    1.515  0.020  1.515
 1GB  CBA  CAA  single    1.544  0.020  1.544
 1GB  OB   CB   double    1.220  0.020  1.220
 1GB  NB   CA   single    1.339  0.020  1.339
 1GB  CB   NA   single    1.339  0.020  1.339
 1GB  CA   CAA  single    1.515  0.020  1.515
 1GB  CA   OA   double    1.221  0.020  1.221
 1GB  NA   CAA  single    1.446  0.020  1.446
 1GB  CAB  H1   single    0.970  0.020  1.090
 1GB  CBB  H2   single    0.970  0.020  1.090
 1GB  CBB  H3   single    0.970  0.020  1.090
 1GB  CD4  H4   single    0.930  0.020  1.080
 1GB  CE4  H5   single    0.930  0.020  1.080
 1GB  OHB  H6   single    0.850  0.020  0.980
 1GB  CE3  H7   single    0.930  0.020  1.080
 1GB  CD3  H8   single    0.930  0.020  1.080
 1GB  NB   H9   single    0.860  0.020  1.020
 1GB  NA   H10  single    0.860  0.020  1.020
 1GB  CAA  H11  single    0.970  0.020  1.090
 1GB  CBA  H12  single    0.970  0.020  1.090
 1GB  CBA  H13  single    0.970  0.020  1.090
 1GB  CE2  H14  single    0.930  0.020  1.080
 1GB  CZ3  H15  single    0.930  0.020  1.080
 1GB  CH2  H16  single    0.930  0.020  1.080
 1GB  CZ2  H17  single    0.930  0.020  1.080
 1GB  NE1  H18  single    0.860  0.020  1.020
 1GB  CD1  H19  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
 1GB  NA   CB   CAB  115.95  3.000
 1GB  NA   CB   OB   123.62  3.000
 1GB  CAB  CB   OB   120.42  3.000
 1GB  H1   CAB  NB   107.38  3.000
 1GB  H1   CAB  CBB  108.12  3.000
 1GB  NB   CAB  CBB  112.90  3.000
 1GB  H1   CAB  CB   106.72  3.000
 1GB  NB   CAB  CB   112.18  3.000
 1GB  CBB  CAB  CB   109.25  3.000
 1GB  H3   CBB  H2   106.77  3.000
 1GB  H3   CBB  CGB  110.44  3.000
 1GB  H2   CBB  CGB  110.00  3.000
 1GB  H3   CBB  CAB  107.89  3.000
 1GB  H2   CBB  CAB  109.47  3.000
 1GB  CGB  CBB  CAB  112.10  3.000
 1GB  CD3  CGB  CD4  117.77  3.000
 1GB  CD3  CGB  CBB  120.97  3.000
 1GB  CD4  CGB  CBB  121.22  3.000
 1GB  H4   CD4  CE4  118.69  3.000
 1GB  H4   CD4  CGB  119.70  3.000
 1GB  CE4  CD4  CGB  121.60  3.000
 1GB  H5   CE4  CZB  119.96  3.000
 1GB  H5   CE4  CD4  120.17  3.000
 1GB  CZB  CE4  CD4  119.86  3.000
 1GB  CE3  CZB  OHB  122.74  3.000
 1GB  CE3  CZB  CE4  119.32  3.000
 1GB  OHB  CZB  CE4  117.95  3.000
 1GB  H6   OHB  CZB  110.33  3.000
 1GB  H7   CE3  CD3  119.74  3.000
 1GB  H7   CE3  CZB  120.27  3.000
 1GB  CD3  CE3  CZB  119.99  3.000
 1GB  H8   CD3  CE3  118.72  3.000
 1GB  H8   CD3  CGB  119.82  3.000
 1GB  CE3  CD3  CGB  121.46  3.000
 1GB  H9   NB   CA   116.68  3.000
 1GB  H9   NB   CAB  116.87  3.000
 1GB  CA   NB   CAB  125.90  3.000
 1GB  CAA  CA   OA   120.38  3.000
 1GB  OA   CA   NB   123.46  3.000
 1GB  CAA  CA   NB   116.15  3.000
 1GB  H10  NA   CAA  116.60  3.000
 1GB  H10  NA   CB   116.70  3.000
 1GB  CAA  NA   CB   126.22  3.000
 1GB  H11  CAA  CBA  107.65  3.000
 1GB  H11  CAA  NA   107.28  3.000
 1GB  CBA  CAA  NA   112.81  3.000
 1GB  H11  CAA  CA   106.49  3.000
 1GB  NA   CAA  CA   112.31  3.000
 1GB  CBA  CAA  CA   109.96  3.000
 1GB  H13  CBA  H12  106.47  3.000
 1GB  H13  CBA  CGA  110.25  3.000
 1GB  H12  CBA  CGA  110.06  3.000
 1GB  H13  CBA  CAA  107.81  3.000
 1GB  H12  CBA  CAA  109.63  3.000
 1GB  CGA  CBA  CAA  112.42  3.000
 1GB  CD1  CGA  CD2  106.07  3.000
 1GB  CD1  CGA  CBA  126.51  3.000
 1GB  CD2  CGA  CBA  127.39  3.000
 1GB  CE1  CD2  CE2  118.90  3.000
 1GB  CE2  CD2  CGA  134.06  3.000
 1GB  CE1  CD2  CGA  107.04  3.000
 1GB  H14  CE2  CZ3  120.09  3.000
 1GB  H14  CE2  CD2  120.83  3.000
 1GB  CZ3  CE2  CD2  119.08  3.000
 1GB  H15  CZ3  CH2  119.25  3.000
 1GB  H15  CZ3  CE2  119.73  3.000
 1GB  CH2  CZ3  CE2  121.02  3.000
 1GB  H16  CH2  CZ2  119.30  3.000
 1GB  H16  CH2  CZ3  119.42  3.000
 1GB  CZ2  CH2  CZ3  121.28  3.000
 1GB  H17  CZ2  CE1  121.30  3.000
 1GB  H17  CZ2  CH2  121.23  3.000
 1GB  CE1  CZ2  CH2  117.47  3.000
 1GB  NE1  CE1  CZ2  130.43  3.000
 1GB  NE1  CE1  CD2  107.32  3.000
 1GB  CZ2  CE1  CD2  122.24  3.000
 1GB  H18  NE1  CD1  124.90  3.000
 1GB  H18  NE1  CE1  125.66  3.000
 1GB  CD1  NE1  CE1  109.40  3.000
 1GB  H19  CD1  NE1  120.58  3.000
 1GB  H19  CD1  CGA  129.26  3.000
 1GB  NE1  CD1  CGA  110.16  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
 1GB  CONST_01  CZB  CE4  CD4  CGB    0.00   0.0  0
 1GB  CONST_02  CZB  CE3  CD3  CGB    0.00   0.0  0
 1GB  CONST_03  CE3  CZB  CE4  CD4    0.00   0.0  0
 1GB  CONST_04  CE3  CD3  CGB  CD4    0.00   0.0  0
 1GB  CONST_05  CD3  CE3  CZB  CE4    0.00   0.0  0
 1GB  CONST_06  CD3  CGB  CD4  CE4    0.00   0.0  0
 1GB  CONST_07  CZ2  CE1  CD2  CGA  180.00   0.0  0
 1GB  CONST_08  NE1  CE1  CD2  CGA    0.00   0.0  0
 1GB  CONST_09  CZ3  CE2  CD2  CGA  180.00   0.0  0
 1GB  CONST_10  CE1  NE1  CD1  CGA    0.00   0.0  0
 1GB  CONST_11  CH2  CZ2  CE1  CD2    0.00   0.0  0
 1GB  CONST_12  CD1  NE1  CE1  CD2    0.00   0.0  0
 1GB  CONST_13  CH2  CZ3  CE2  CD2    0.00   0.0  0
 1GB  CONST_14  NE1  CD1  CGA  CD2    0.00   0.0  0
 1GB  CONST_15  CZ2  CH2  CZ3  CE2    0.00   0.0  0
 1GB  CONST_16  CZ2  CE1  CD2  CE2    0.00   0.0  0
 1GB  CONST_17  NE1  CE1  CD2  CE2  180.00   0.0  0
 1GB  CONST_18  CD1  CGA  CD2  CE2  180.00   0.0  0
 1GB  CONST_19  CE1  CZ2  CH2  CZ3    0.00   0.0  0
 1GB  CONST_20  CE1  CD2  CE2  CZ3    0.00   0.0  0
 1GB  CONST_21  NE1  CE1  CZ2  CH2  180.00   0.0  0
 1GB  CONST_22  CD1  NE1  CE1  CZ2  180.00   0.0  0
 1GB  CONST_23  CD1  CGA  CD2  CE1    0.00   0.0  0
 1GB  CONST_24  CAA  CA   NB   CAB    0.00   0.0  0
 1GB  CONST_25  CAA  NA   CB   CAB    0.00   0.0  0
 1GB  CONST_26  CE4  CD4  CGB  CBB  180.00   0.0  0
 1GB  CONST_27  CE3  CD3  CGB  CBB  180.00   0.0  0
 1GB  CONST_28  OHB  CZB  CE4  CD4  180.00   0.0  0
 1GB  CONST_29  CD3  CE3  CZB  OHB  180.00   0.0  0
 1GB  CONST_30  CE1  CD2  CGA  CBA  180.00   0.0  0
 1GB  CONST_31  CE2  CD2  CGA  CBA    0.00   0.0  0
 1GB  CONST_32  NE1  CD1  CGA  CBA  180.00   0.0  0
 1GB  CONST_33  CAA  NA   CB   OB   180.00   0.0  0
 1GB  CONST_34  OA   CA   NB   CAB  180.00   0.0  0
 1GB  CONST_35  H5   CE4  CD4  CGB  180.00   0.0  0
 1GB  CONST_36  H7   CE3  CD3  CGB  180.00   0.0  0
 1GB  CONST_37  H8   CD3  CGB  CD4  180.00   0.0  0
 1GB  CONST_38  H4   CD4  CE4  CZB  180.00   0.0  0
 1GB  CONST_39  H14  CE2  CD2  CGA    0.00   0.0  0
 1GB  CONST_40  H18  NE1  CD1  CGA  180.00   0.0  0
 1GB  CONST_41  H17  CZ2  CE1  CD2  180.00   0.0  0
 1GB  CONST_42  H15  CZ3  CE2  CD2  180.00   0.0  0
 1GB  CONST_43  H19  CD1  CGA  CD2  180.00   0.0  0
 1GB  CONST_44  H16  CH2  CZ3  CE2  180.00   0.0  0
 1GB  CONST_45  H10  NA   CB   CAB  180.00   0.0  0
 1GB  CONST_46  H9   NB   CA   CAA  180.00   0.0  0
 1GB  Var_01    CD4  CGB  CBB  CAB   92.48  30.0  3
 1GB  Var_02    CD2  CGA  CBA  CAA   88.89  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
 1GB  chir_01  CAB  CBB  NB   CB  positiv
 1GB  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
 1GB  plan-1  CBB  0.020
 1GB  plan-1  CGB  0.020
 1GB  plan-1  CD4  0.020
 1GB  plan-1  CE4  0.020
 1GB  plan-1  CZB  0.020
 1GB  plan-1  OHB  0.020
 1GB  plan-1  CE3  0.020
 1GB  plan-1  CD3  0.020
 1GB  plan-1  H4   0.020
 1GB  plan-1  H5   0.020
 1GB  plan-1  H7   0.020
 1GB  plan-1  H8   0.020
 1GB  plan-2  CBA  0.020
 1GB  plan-2  CGA  0.020
 1GB  plan-2  CD2  0.020
 1GB  plan-2  CE2  0.020
 1GB  plan-2  CZ3  0.020
 1GB  plan-2  CH2  0.020
 1GB  plan-2  CZ2  0.020
 1GB  plan-2  CE1  0.020
 1GB  plan-2  NE1  0.020
 1GB  plan-2  CD1  0.020
 1GB  plan-2  H14  0.020
 1GB  plan-2  H15  0.020
 1GB  plan-2  H16  0.020
 1GB  plan-2  H17  0.020
 1GB  plan-2  H18  0.020
 1GB  plan-2  H19  0.020
 1GB  plan-3  OB   0.020
 1GB  plan-3  CB   0.020
 1GB  plan-3  CAB  0.020
 1GB  plan-3  NA   0.020
 1GB  plan-3  CAA  0.020
 1GB  plan-3  H10  0.020
 1GB  plan-4  CAB  0.020
 1GB  plan-4  NB   0.020
 1GB  plan-4  CA   0.020
 1GB  plan-4  OA   0.020
 1GB  plan-4  CAA  0.020
 1GB  plan-4  H9   0.020

