# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:06:01 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: (3~{S},6~{S})-3-[(3-fluoranyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]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(F)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
 R2H  R2H  (3~{S},6~{S})-3-[(3-fluoranyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione  ligand  42  25  .  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_R2H
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
 R2H  CA   C  CR6   0   0.539   -8.8886  20.5270   0.7636
 R2H  CB   C  CR6   0   0.541   -8.3785  17.7350   0.1596
 R2H  NB   N  NR16  0  -0.631   -7.7747  20.1291   0.1404
 R2H  OB   O  O     0  -0.489   -8.1598  16.5746  -0.1553
 R2H  CD1  C  CR16  0  -0.312  -10.7482  17.1903   3.5752
 R2H  CD2  C  CR16  0  -0.448  -12.4263  18.8374   3.1550
 R2H  CD3  C  CR16  0  -0.286   -6.2797  19.7195   3.0211
 R2H  CE1  C  CR16  0  -0.328  -11.7222  16.2806   3.9621
 R2H  CE2  C  CR6   0   0.452  -13.3827  17.9275   3.5430
 R2H  CE3  C  CR16  0  -0.328   -6.5644  19.7757   4.3758
 R2H  CAA  C  CR16  0  -0.181   -9.8723  19.4545   1.1821
 R2H  CAB  C  CR16  0  -0.186   -7.3026  18.7785  -0.0461
 R2H  CBA  C  CH2   0  -0.519  -10.0310  19.4525   2.7140
 R2H  CBB  C  CH2   0  -0.524   -6.0753  18.4760   0.8342
 R2H  CD4  C  CR16  0  -0.275   -6.7363  17.3796   3.0033
 R2H  CE4  C  CR16  0  -0.383   -7.0231  17.4162   4.3602
 R2H  CGA  C  CR6   0   0.100  -11.0797  18.4790   3.1684
 R2H  CGB  C  CR6   0   0.084   -6.3617  18.5252   2.3066
 R2H  CZA  C  CR6   0   0.214  -13.0653  16.6354   3.9524
 R2H  CZB  C  CR6   0   0.343   -6.9422  18.6197   5.0557
 R2H  NA   N  NR16  0  -0.630   -9.5427  18.1446   0.6725
 R2H  OA   O  O     0  -0.489   -9.1464  21.7004   0.9857
 R2H  OAX  O  OH1   0  -0.628  -13.9888  15.7359   4.3364
 R2H  OAY  O  OH1   0  -0.631   -7.2066  18.7204   6.3737
 R2H  H1   H  HNR6  0   0.406   -7.1416  20.8631  -0.1482
 R2H  H2   H  HCR6  0   0.264   -9.7085  16.8885   3.5988
 R2H  H3   H  HCR6  0   0.278  -12.7349  19.8292   2.8457
 R2H  H4   H  HCR6  0   0.251   -5.9732  20.6278   2.5162
 R2H  H5   H  HCR6  0   0.275  -11.4437  15.2842   4.2813
 R2H  H6   H  HCR6  0   0.263   -6.4892  20.7142   4.9111
 R2H  H7   H  HCR6  0   0.303  -10.8302  19.7484   0.7423
 R2H  H8   H  HCR6  0   0.306   -6.9887  18.6768  -1.0886
 R2H  H9   H  HCH2  0   0.277   -9.0703  19.2091   3.1698
 R2H  H10  H  HCH2  0   0.270  -10.2952  20.4632   3.0274
 R2H  H11  H  HCH2  0   0.268   -5.6917  17.4953   0.5491
 R2H  H12  H  HCH2  0   0.271   -5.3002  19.2003   0.5736
 R2H  H13  H  HCR6  0   0.255   -6.8005  16.4321   2.4816
 R2H  H14  H  HCR6  0   0.274   -7.3036  16.5038   4.8748
 R2H  H15  H  HNR6  0   0.406  -10.2548  17.4344   0.7781
 R2H  H16  H  HOH1  0   0.477  -14.8788  16.1028   4.2816
 R2H  H17  H  HOH1  0   0.474   -7.4493  17.8607   6.7350
 R2H  FY   F  F     0  -0.323  -14.6827  18.2855   3.5372

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
 R2H  CAB  NB   single    1.443  0.020  1.443
 R2H  CAB  CB   single    1.513  0.020  1.513
 R2H  CAB  CBB  single    1.540  0.020  1.540
 R2H  OB   CB   double    1.222  0.020  1.222
 R2H  NB   CA   single    1.337  0.020  1.337
 R2H  CB   NA   single    1.336  0.020  1.336
 R2H  CA   OA   double    1.222  0.020  1.222
 R2H  CA   CAA  single    1.514  0.020  1.514
 R2H  NA   CAA  single    1.444  0.020  1.444
 R2H  CBB  CGB  single    1.501  0.020  1.501
 R2H  CAA  CBA  single    1.540  0.020  1.540
 R2H  CGB  CD3  aromatic  1.394  0.020  1.394
 R2H  CGB  CD4  aromatic  1.392  0.020  1.392
 R2H  CBA  CGA  single    1.501  0.020  1.501
 R2H  CD3  CE3  aromatic  1.385  0.020  1.385
 R2H  CD4  CE4  aromatic  1.387  0.020  1.387
 R2H  CGA  CD1  aromatic  1.391  0.020  1.391
 R2H  CGA  CD2  aromatic  1.394  0.020  1.394
 R2H  CD1  CE1  aromatic  1.388  0.020  1.388
 R2H  CD2  CE2  aromatic  1.376  0.020  1.376
 R2H  CE1  CZA  aromatic  1.389  0.020  1.389
 R2H  CE2  CZA  aromatic  1.392  0.020  1.392
 R2H  CE2  FY   single    1.348  0.020  1.348
 R2H  CZA  OAX  single    1.345  0.020  1.345
 R2H  CE3  CZB  aromatic  1.393  0.020  1.393
 R2H  CE4  CZB  aromatic  1.392  0.020  1.392
 R2H  CZB  OAY  single    1.348  0.020  1.348
 R2H  NB   H1   single    0.860  0.020  1.020
 R2H  CD1  H2   single    0.930  0.020  1.080
 R2H  CD2  H3   single    0.930  0.020  1.080
 R2H  CD3  H4   single    0.930  0.020  1.080
 R2H  CE1  H5   single    0.930  0.020  1.080
 R2H  CE3  H6   single    0.930  0.020  1.080
 R2H  CAA  H7   single    0.970  0.020  1.090
 R2H  CAB  H8   single    0.970  0.020  1.090
 R2H  CBA  H9   single    0.970  0.020  1.090
 R2H  CBA  H10  single    0.970  0.020  1.090
 R2H  CBB  H11  single    0.970  0.020  1.090
 R2H  CBB  H12  single    0.970  0.020  1.090
 R2H  CD4  H13  single    0.930  0.020  1.080
 R2H  CE4  H14  single    0.930  0.020  1.080
 R2H  NA   H15  single    0.860  0.020  1.020
 R2H  OAX  H16  single    0.850  0.020  0.980
 R2H  OAY  H17  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
 R2H  OA   CA   CAA  119.53  3.000
 R2H  CAA  CA   NB   117.34  3.000
 R2H  OA   CA   NB   123.12  3.000
 R2H  NA   CB   CAB  117.41  3.000
 R2H  NA   CB   OB   123.08  3.000
 R2H  CAB  CB   OB   119.51  3.000
 R2H  H1   NB   CAB  115.95  3.000
 R2H  H1   NB   CA   116.02  3.000
 R2H  CAB  NB   CA   127.69  3.000
 R2H  H2   CD1  CGA  119.55  3.000
 R2H  H2   CD1  CE1  119.02  3.000
 R2H  CGA  CD1  CE1  121.43  3.000
 R2H  H3   CD2  CGA  120.88  3.000
 R2H  H3   CD2  CE2  119.20  3.000
 R2H  CGA  CD2  CE2  119.93  3.000
 R2H  H4   CD3  CGB  119.73  3.000
 R2H  H4   CD3  CE3  118.68  3.000
 R2H  CGB  CD3  CE3  121.59  3.000
 R2H  H5   CE1  CZA  119.06  3.000
 R2H  H5   CE1  CD1  120.32  3.000
 R2H  CZA  CE1  CD1  120.61  3.000
 R2H  FY   CE2  CZA  117.87  3.000
 R2H  FY   CE2  CD2  119.56  3.000
 R2H  CZA  CE2  CD2  122.56  3.000
 R2H  H6   CE3  CZB  119.78  3.000
 R2H  H6   CE3  CD3  120.27  3.000
 R2H  CZB  CE3  CD3  119.95  3.000
 R2H  H7   CAA  NA   107.56  3.000
 R2H  H7   CAA  CBA  108.06  3.000
 R2H  NA   CAA  CBA  111.93  3.000
 R2H  H7   CAA  CA   105.51  3.000
 R2H  CBA  CAA  CA   110.04  3.000
 R2H  NA   CAA  CA   113.37  3.000
 R2H  H8   CAB  CBB  107.33  3.000
 R2H  H8   CAB  NB   107.71  3.000
 R2H  CBB  CAB  NB   111.76  3.000
 R2H  H8   CAB  CB   105.64  3.000
 R2H  CBB  CAB  CB   110.70  3.000
 R2H  NB   CAB  CB   113.28  3.000
 R2H  H10  CBA  H9   107.46  3.000
 R2H  H10  CBA  CGA  110.16  3.000
 R2H  H9   CBA  CGA  110.12  3.000
 R2H  H10  CBA  CAA  108.04  3.000
 R2H  H9   CBA  CAA  108.97  3.000
 R2H  CGA  CBA  CAA  111.95  3.000
 R2H  H12  CBB  H11  106.51  3.000
 R2H  H12  CBB  CGB  110.34  3.000
 R2H  H11  CBB  CGB  110.67  3.000
 R2H  H12  CBB  CAB  107.38  3.000
 R2H  H11  CBB  CAB  107.90  3.000
 R2H  CGB  CBB  CAB  113.72  3.000
 R2H  H13  CD4  CGB  119.64  3.000
 R2H  H13  CD4  CE4  118.80  3.000
 R2H  CGB  CD4  CE4  121.56  3.000
 R2H  H14  CE4  CZB  120.35  3.000
 R2H  H14  CE4  CD4  119.69  3.000
 R2H  CZB  CE4  CD4  119.96  3.000
 R2H  CBA  CGA  CD2  120.35  3.000
 R2H  CD2  CGA  CD1  118.11  3.000
 R2H  CBA  CGA  CD1  121.51  3.000
 R2H  CD4  CGB  CBB  121.02  3.000
 R2H  CD4  CGB  CD3  117.66  3.000
 R2H  CBB  CGB  CD3  121.31  3.000
 R2H  OAX  CZA  CE2  123.23  3.000
 R2H  OAX  CZA  CE1  119.41  3.000
 R2H  CE2  CZA  CE1  117.36  3.000
 R2H  OAY  CZB  CE4  122.79  3.000
 R2H  OAY  CZB  CE3  117.92  3.000
 R2H  CE4  CZB  CE3  119.29  3.000
 R2H  H15  NA   CAA  116.07  3.000
 R2H  H15  NA   CB   116.00  3.000
 R2H  CAA  NA   CB   127.76  3.000
 R2H  H16  OAX  CZA  111.29  3.000
 R2H  H17  OAY  CZB  110.45  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
 R2H  CONST_01  CE2  CD2  CGA  CD1    0.00   0.0  0
 R2H  CONST_02  CE2  CZA  CE1  CD1    0.00   0.0  0
 R2H  CONST_03  CE1  CD1  CGA  CD2    0.00   0.0  0
 R2H  CONST_04  CE1  CZA  CE2  CD2    0.00   0.0  0
 R2H  CONST_05  CE4  CD4  CGB  CD3    0.00   0.0  0
 R2H  CONST_06  CE4  CZB  CE3  CD3    0.00   0.0  0
 R2H  CONST_07  CD4  CGB  CD3  CE3    0.00   0.0  0
 R2H  CONST_08  CD4  CE4  CZB  CE3    0.00   0.0  0
 R2H  CONST_09  CZA  CE1  CD1  CGA    0.00   0.0  0
 R2H  CONST_10  CZA  CE2  CD2  CGA    0.00   0.0  0
 R2H  CONST_11  CZB  CE3  CD3  CGB    0.00   0.0  0
 R2H  CONST_12  CZB  CE4  CD4  CGB    0.00   0.0  0
 R2H  CONST_13  CAB  NB   CA   CAA    0.00   0.0  0
 R2H  CONST_14  CAB  CB   NA   CAA    0.00   0.0  0
 R2H  CONST_15  OAX  CZA  CE1  CD1  180.00   0.0  0
 R2H  CONST_16  OAX  CZA  CE2  CD2  180.00   0.0  0
 R2H  CONST_17  OAY  CZB  CE3  CD3  180.00   0.0  0
 R2H  CONST_18  CBA  CGA  CD1  CE1  180.00   0.0  0
 R2H  CONST_19  FY   CE2  CZA  CE1  180.00   0.0  0
 R2H  CONST_20  CBA  CGA  CD2  CE2  180.00   0.0  0
 R2H  CONST_21  CBB  CGB  CD3  CE3  180.00   0.0  0
 R2H  CONST_22  CE4  CD4  CGB  CBB  180.00   0.0  0
 R2H  CONST_23  OAY  CZB  CE4  CD4  180.00   0.0  0
 R2H  CONST_24  FY   CE2  CD2  CGA  180.00   0.0  0
 R2H  CONST_25  CAA  NA   CB   OB   180.00   0.0  0
 R2H  CONST_26  OA   CA   NB   CAB  180.00   0.0  0
 R2H  CONST_27  H3   CD2  CGA  CD1  180.00   0.0  0
 R2H  CONST_28  H2   CD1  CGA  CD2  180.00   0.0  0
 R2H  CONST_29  H13  CD4  CGB  CD3  180.00   0.0  0
 R2H  CONST_30  H5   CE1  CZA  CE2  180.00   0.0  0
 R2H  CONST_31  H14  CE4  CZB  CE3  180.00   0.0  0
 R2H  CONST_32  H4   CD3  CGB  CD4  180.00   0.0  0
 R2H  CONST_33  H6   CE3  CZB  CE4  180.00   0.0  0
 R2H  CONST_34  H1   NB   CA   CAA  180.00   0.0  0
 R2H  CONST_35  H15  NA   CB   CAB  180.00   0.0  0
 R2H  Var_01    CAA  CBA  CGA  CD1   95.23  30.0  2
 R2H  Var_02    CAB  CBB  CGB  CD3  -87.25  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
 R2H  chir_01  CAA  CA  NA   CBA  negativ
 R2H  chir_02  CAB  NB  CBB  CB   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
 R2H  plan-1  CD1  0.020
 R2H  plan-1  CD2  0.020
 R2H  plan-1  CE1  0.020
 R2H  plan-1  CE2  0.020
 R2H  plan-1  CBA  0.020
 R2H  plan-1  CGA  0.020
 R2H  plan-1  CZA  0.020
 R2H  plan-1  OAX  0.020
 R2H  plan-1  H2   0.020
 R2H  plan-1  H3   0.020
 R2H  plan-1  H5   0.020
 R2H  plan-1  FY   0.020
 R2H  plan-2  CD3  0.020
 R2H  plan-2  CE3  0.020
 R2H  plan-2  CBB  0.020
 R2H  plan-2  CD4  0.020
 R2H  plan-2  CE4  0.020
 R2H  plan-2  CGB  0.020
 R2H  plan-2  CZB  0.020
 R2H  plan-2  OAY  0.020
 R2H  plan-2  H4   0.020
 R2H  plan-2  H6   0.020
 R2H  plan-2  H13  0.020
 R2H  plan-2  H14  0.020
 R2H  plan-3  CB   0.020
 R2H  plan-3  OB   0.020
 R2H  plan-3  CAA  0.020
 R2H  plan-3  CAB  0.020
 R2H  plan-3  NA   0.020
 R2H  plan-3  H15  0.020
 R2H  plan-4  CA   0.020
 R2H  plan-4  NB   0.020
 R2H  plan-4  CAA  0.020
 R2H  plan-4  CAB  0.020
 R2H  plan-4  OA   0.020
 R2H  plan-4  H1   0.020

