# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 08:53:38 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (3S,8aS)-3-(4-hydroxybenzyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C[C@@H]2NC(=O)[C@@H]3CCCN3C2=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
 TYP  TYP  (3S,8aS)-3-(4-hydroxybenzyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione  ligand  35  19  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TYP
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
 TYP  N     N  NH1   0  -0.642   0.7037   0.2220  -0.4115
 TYP  CA    C  CH1   0  -0.193  -0.7161  -0.0813  -0.3900
 TYP  C     C  C     0   0.595  -1.3318   0.2256  -1.7518
 TYP  O     O  O     0  -0.495  -2.4618   0.6743  -1.8759
 TYP  CB    C  CH2   0  -0.524  -1.4057   0.7013   0.7272
 TYP  CG    C  CR6   0   0.075  -0.8354   0.3798   2.0814
 TYP  CD1   C  CR16  0  -0.308   0.0179   1.2609   2.7370
 TYP  CE1   C  CR16  0  -0.371   0.5720   0.9518   3.9728
 TYP  CE2   C  CR16  0  -0.322  -0.5818  -1.1564   3.9414
 TYP  CD2   C  CR16  0  -0.280  -1.1237  -0.8318   2.7107
 TYP  CZ    C  CR6   0   0.343   0.2763  -0.2625   4.5820
 TYP  OH    O  OH1   0  -0.632   0.7807  -0.6228   5.7792
 TYP  NP    N  NT    0  -0.498  -0.5348  -0.0550  -2.7838
 TYP  CAP   C  CH1   0  -0.192   0.8037  -0.6144  -2.6498
 TYP  CP    C  C     0   0.554   1.5196  -0.0738  -1.4334
 TYP  OP    O  O     0  -0.481   2.7320   0.0573  -1.4000
 TYP  CBP   C  CH2   0  -0.456   1.4517  -0.2778  -3.9859
 TYP  CGP   C  CH2   0  -0.498   0.2771  -0.3870  -4.9541
 TYP  CDP   C  CH2   0  -0.256  -0.8986   0.1975  -4.1739
 TYP  H     H  HNH1  0   0.405   1.1357   0.4917   0.4623
 TYP  HA    H  HCH1  0   0.296  -0.8683  -1.1549  -0.2052
 TYP  HBC1  H  HCH2  0   0.272  -2.4679   0.4578   0.6994
 TYP  HBC2  H  HCH2  0   0.264  -1.3192   1.7715   0.5269
 TYP  HD1   H  HCR6  0   0.262   0.2567   2.2163   2.2835
 TYP  HE1   H  HCR6  0   0.272   1.2324   1.6616   4.4575
 TYP  HE2   H  HCR6  0   0.264  -0.8228  -2.1016   4.4120
 TYP  HD2   H  HCR6  0   0.254  -1.7905  -1.5392   2.2310
 TYP  HH    H  HOH1  0   0.474   1.3626   0.0660   6.1191
 TYP  HAP   H  HCH1  0   0.299   0.7463  -1.7064  -2.5313
 TYP  HBP1  H  HCH2  0   0.249   1.8420   0.7419  -3.9684
 TYP  HBP2  H  HCH2  0   0.262   2.2717  -0.9510  -4.2267
 TYP  HGP1  H  HCH2  0   0.262   0.4511   0.1408  -5.8903
 TYP  HGP2  H  HCH2  0   0.246   0.0834  -1.4341  -5.1939
 TYP  HDP1  H  HCH2  0   0.247  -1.0049   1.2716  -4.3426
 TYP  HDP2  H  HCH2  0   0.255  -1.8477  -0.2765  -4.4243

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
 TYP  N    CA    single    1.452  0.020  1.452
 TYP  N    CP    single    1.341  0.020  1.341
 TYP  N    H     single    0.860  0.020  1.020
 TYP  CA   C     single    1.526  0.020  1.526
 TYP  CA   CB    single    1.528  0.020  1.528
 TYP  CA   HA    single    0.970  0.020  1.090
 TYP  C    O     double    1.222  0.020  1.222
 TYP  C    NP    single    1.334  0.020  1.334
 TYP  CB   CG    single    1.504  0.020  1.504
 TYP  CB   HBC1  single    0.970  0.020  1.090
 TYP  CB   HBC2  single    0.970  0.020  1.090
 TYP  CG   CD1   aromatic  1.391  0.020  1.391
 TYP  CG   CD2   aromatic  1.395  0.020  1.395
 TYP  CD1  CE1   aromatic  1.389  0.020  1.389
 TYP  CD1  HD1   single    0.930  0.020  1.080
 TYP  CE1  CZ    aromatic  1.390  0.020  1.390
 TYP  CE1  HE1   single    0.930  0.020  1.080
 TYP  CE2  CD2   aromatic  1.383  0.020  1.383
 TYP  CE2  CZ    aromatic  1.395  0.020  1.395
 TYP  CE2  HE2   single    0.930  0.020  1.080
 TYP  CD2  HD2   single    0.930  0.020  1.080
 TYP  CZ   OH    single    1.348  0.020  1.348
 TYP  OH   HH    single    0.850  0.020  0.980
 TYP  NP   CAP   single    1.457  0.020  1.457
 TYP  NP   CDP   single    1.459  0.020  1.459
 TYP  CAP  CP    single    1.511  0.020  1.511
 TYP  CAP  CBP   single    1.523  0.020  1.523
 TYP  CAP  HAP   single    0.970  0.020  1.090
 TYP  CP   OP    double    1.220  0.020  1.220
 TYP  CBP  CGP   single    1.526  0.020  1.526
 TYP  CBP  HBP1  single    0.970  0.020  1.090
 TYP  CBP  HBP2  single    0.970  0.020  1.090
 TYP  CGP  CDP   single    1.527  0.020  1.527
 TYP  CGP  HGP1  single    0.970  0.020  1.090
 TYP  CGP  HGP2  single    0.970  0.020  1.090
 TYP  CDP  HDP1  single    0.970  0.020  1.090
 TYP  CDP  HDP2  single    0.970  0.020  1.090

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
 TYP  H     N    CP    117.22  3.000
 TYP  H     N    CA    117.43  3.000
 TYP  CP    N    CA    124.07  3.000
 TYP  HA    CA   CB    108.33  3.000
 TYP  HA    CA   C     106.89  3.000
 TYP  CB    CA   C     111.55  3.000
 TYP  HA    CA   N     109.98  3.000
 TYP  CB    CA   N     110.18  3.000
 TYP  C     CA   N     109.84  3.000
 TYP  NP    C    O     123.45  3.000
 TYP  NP    C    CA    114.03  3.000
 TYP  O     C    CA    122.52  3.000
 TYP  HBC2  CB   HBC1  106.94  3.000
 TYP  HBC2  CB   CG    110.15  3.000
 TYP  HBC1  CB   CG    110.16  3.000
 TYP  HBC2  CB   CA    109.39  3.000
 TYP  HBC1  CB   CA    107.86  3.000
 TYP  CG    CB   CA    112.18  3.000
 TYP  CD2   CG   CD1   117.67  3.000
 TYP  CD2   CG   CB    120.88  3.000
 TYP  CD1   CG   CB    121.44  3.000
 TYP  HD1   CD1  CE1   118.71  3.000
 TYP  HD1   CD1  CG    119.75  3.000
 TYP  CE1   CD1  CG    121.54  3.000
 TYP  HE1   CE1  CZ    120.37  3.000
 TYP  HE1   CE1  CD1   119.68  3.000
 TYP  CZ    CE1  CD1   119.95  3.000
 TYP  HE2   CE2  CZ    119.78  3.000
 TYP  HE2   CE2  CD2   120.28  3.000
 TYP  CZ    CE2  CD2   119.94  3.000
 TYP  HD2   CD2  CE2   118.78  3.000
 TYP  HD2   CD2  CG    119.62  3.000
 TYP  CE2   CD2  CG    121.60  3.000
 TYP  OH    CZ   CE2   117.82  3.000
 TYP  OH    CZ   CE1   122.89  3.000
 TYP  CE2   CZ   CE1   119.29  3.000
 TYP  HH    OH   CZ    110.37  3.000
 TYP  CDP   NP   CAP   112.53  3.000
 TYP  CDP   NP   C     123.49  3.000
 TYP  CAP   NP   C     123.97  3.000
 TYP  HAP   CAP  CBP   109.65  3.000
 TYP  HAP   CAP  CP    107.04  3.000
 TYP  CBP   CAP  CP    115.19  3.000
 TYP  HAP   CAP  NP    110.07  3.000
 TYP  CBP   CAP  NP    103.03  3.000
 TYP  CP    CAP  NP    111.83  3.000
 TYP  OP    CP   CAP   122.09  3.000
 TYP  OP    CP   N     124.07  3.000
 TYP  CAP   CP   N     113.83  3.000
 TYP  HBP2  CBP  HBP1  108.18  3.000
 TYP  HBP2  CBP  CGP   113.30  3.000
 TYP  HBP1  CBP  CGP   110.61  3.000
 TYP  HBP2  CBP  CAP   112.22  3.000
 TYP  HBP1  CBP  CAP   110.15  3.000
 TYP  CGP   CBP  CAP   102.31  3.000
 TYP  HGP2  CGP  HGP1  107.73  3.000
 TYP  HGP2  CGP  CDP   110.04  3.000
 TYP  HGP1  CGP  CDP   112.14  3.000
 TYP  HGP2  CGP  CBP   110.15  3.000
 TYP  HGP1  CGP  CBP   112.82  3.000
 TYP  CDP   CGP  CBP   103.95  3.000
 TYP  HDP2  CDP  HDP1  107.91  3.000
 TYP  HDP2  CDP  CGP   112.74  3.000
 TYP  HDP1  CDP  CGP   111.85  3.000
 TYP  HDP2  CDP  NP    111.14  3.000
 TYP  HDP1  CDP  NP    109.97  3.000
 TYP  CGP   CDP  NP    103.21  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
 TYP  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 TYP  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 TYP  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 TYP  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 TYP  CONST_05  CD2  CG   CD1  CE1     0.00   0.0  0
 TYP  CONST_06  CD2  CE2  CZ   CE1     0.00   0.0  0
 TYP  CONST_07  CAP  CP   N    CA      0.00   0.0  0
 TYP  CONST_08  CAP  NP   C    CA      0.00   0.0  0
 TYP  CONST_09  CDP  NP   C    CA    180.00   0.0  0
 TYP  CONST_10  CE1  CD1  CG   CB    180.00   0.0  0
 TYP  CONST_11  CE2  CD2  CG   CB    180.00   0.0  0
 TYP  CONST_12  OH   CZ   CE1  CD1   180.00   0.0  0
 TYP  CONST_13  OH   CZ   CE2  CD2   180.00   0.0  0
 TYP  CONST_14  OP   CP   N    CA    180.00   0.0  0
 TYP  CONST_15  CAP  NP   C    O     180.00   0.0  0
 TYP  CONST_16  CDP  NP   C    O       0.00   0.0  0
 TYP  CONST_17  HE1  CE1  CD1  CG    180.00   0.0  0
 TYP  CONST_18  HE2  CE2  CD2  CG    180.00   0.0  0
 TYP  CONST_19  HD2  CD2  CG   CD1   180.00   0.0  0
 TYP  CONST_20  HD1  CD1  CG   CD2   180.00   0.0  0
 TYP  CONST_21  H    N    CP   CAP   180.00   0.0  0
 TYP  Var_01    CGP  CDP  NP   C    -175.74  30.0  1
 TYP  Var_02    CBP  CGP  CDP  NP    -27.36  30.0  1
 TYP  Var_03    CDP  CGP  CBP  CAP    38.43  30.0  1
 TYP  Var_04    CD1  CG   CB   CA    104.30  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
 TYP  chir_01  CA   N   C   CB   positiv
 TYP  chir_02  CAP  NP  CP  CBP  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
 TYP  plan-1  CB   0.020
 TYP  plan-1  CG   0.020
 TYP  plan-1  CD1  0.020
 TYP  plan-1  CE1  0.020
 TYP  plan-1  CE2  0.020
 TYP  plan-1  CD2  0.020
 TYP  plan-1  CZ   0.020
 TYP  plan-1  OH   0.020
 TYP  plan-1  HD1  0.020
 TYP  plan-1  HE1  0.020
 TYP  plan-1  HE2  0.020
 TYP  plan-1  HD2  0.020
 TYP  plan-2  N    0.020
 TYP  plan-2  CA   0.020
 TYP  plan-2  CAP  0.020
 TYP  plan-2  CP   0.020
 TYP  plan-2  OP   0.020
 TYP  plan-2  H    0.020
 TYP  plan-3  CA   0.020
 TYP  plan-3  C    0.020
 TYP  plan-3  O    0.020
 TYP  plan-3  NP   0.020
 TYP  plan-3  CAP  0.020
 TYP  plan-3  CDP  0.020

