# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 18:17:27 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (8aS)-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CNC(=O)[C@@H]2CCCN12
#
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
 GIO  GIO  (8aS)-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione  ligand  21  11  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GIO
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
 GIO  OP    O  O     0  -0.484   2.7728   0.2859   0.0004
 GIO  CP    C  C     0   0.555   1.6396   0.0189   0.3672
 GIO  CAP   C  CR15  0  -0.188   0.5771  -0.4552  -0.6006
 GIO  CBP   C  CH2   0  -0.452   0.6908   0.1066  -2.0111
 GIO  CGP   C  CH2   0  -0.501  -0.7360  -0.0345  -2.5359
 GIO  CDP   C  CH2   0  -0.253  -1.6139   0.2895  -1.3279
 GIO  NP    N  NR5   0  -0.478  -0.7607  -0.0445  -0.1933
 GIO  C     C  C     0   0.524  -1.1633   0.0116   1.0769
 GIO  O     O  O     0  -0.499  -2.3022   0.2978   1.4182
 GIO  CA    C  CH2   0  -0.393  -0.0841  -0.3304   2.0838
 GIO  N     N  NH1   0  -0.633   1.2248   0.0939   1.6382
 GIO  HAP   H  HCR5  0   0.298   0.6399  -1.5527  -0.6354
 GIO  HBP1  H  HCH2  0   0.248   0.9873   1.1570  -1.9759
 GIO  HBP2  H  HCH2  0   0.261   1.4215  -0.4318  -2.6107
 GIO  HGP1  H  HCH2  0   0.262  -0.9421   0.6249  -3.3772
 GIO  HGP2  H  HCH2  0   0.246  -0.9137  -1.0597  -2.8662
 GIO  HDP1  H  HCH2  0   0.247  -1.8842   1.3473  -1.2927
 GIO  HDP2  H  HCH2  0   0.254  -2.5354  -0.2931  -1.3110
 GIO  HAC1  H  HCH2  0   0.293  -0.3143   0.1714   3.0209
 GIO  HAC2  H  HCH2  0   0.281  -0.1149  -1.4092   2.2777
 GIO  H     H  HNH1  0   0.410   1.9004   0.3506   2.3433

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
 GIO  OP   CP    double  1.221  0.020  1.221
 GIO  CP   CAP   single  1.513  0.020  1.513
 GIO  CP   N     single  1.339  0.020  1.339
 GIO  CAP  CBP   single  1.523  0.020  1.523
 GIO  CAP  NP    single  1.457  0.020  1.457
 GIO  CAP  HAP   single  0.970  0.020  1.090
 GIO  CBP  CGP   single  1.527  0.020  1.527
 GIO  CBP  HBP1  single  0.970  0.020  1.090
 GIO  CBP  HBP2  single  0.970  0.020  1.090
 GIO  CGP  CDP   single  1.528  0.020  1.528
 GIO  CGP  HGP1  single  0.970  0.020  1.090
 GIO  CGP  HGP2  single  0.970  0.020  1.090
 GIO  CDP  NP    single  1.458  0.020  1.458
 GIO  CDP  HDP1  single  0.970  0.020  1.090
 GIO  CDP  HDP2  single  0.970  0.020  1.090
 GIO  NP   C     single  1.334  0.020  1.334
 GIO  C    O     double  1.223  0.020  1.223
 GIO  C    CA    single  1.515  0.020  1.515
 GIO  CA   N     single  1.446  0.020  1.446
 GIO  CA   HAC1  single  0.970  0.020  1.090
 GIO  CA   HAC2  single  0.970  0.020  1.090
 GIO  N    H     single  0.860  0.020  1.020

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
 GIO  N     CP   CAP   114.02  3.000
 GIO  N     CP   OP    124.10  3.000
 GIO  CAP   CP   OP    121.88  3.000
 GIO  HAP   CAP  NP    110.03  3.000
 GIO  HAP   CAP  CBP   109.55  3.000
 GIO  NP    CAP  CBP   102.91  3.000
 GIO  HAP   CAP  CP    107.02  3.000
 GIO  NP    CAP  CP    112.18  3.000
 GIO  CBP   CAP  CP    115.11  3.000
 GIO  HBP2  CBP  HBP1  108.15  3.000
 GIO  HBP2  CBP  CGP   113.11  3.000
 GIO  HBP1  CBP  CGP   110.71  3.000
 GIO  HBP2  CBP  CAP   112.22  3.000
 GIO  HBP1  CBP  CAP   110.20  3.000
 GIO  CGP   CBP  CAP   102.39  3.000
 GIO  HGP2  CGP  HGP1  107.72  3.000
 GIO  HGP2  CGP  CDP   110.16  3.000
 GIO  HGP1  CGP  CDP   111.94  3.000
 GIO  HGP2  CGP  CBP   110.05  3.000
 GIO  HGP1  CGP  CBP   112.75  3.000
 GIO  CDP   CGP  CBP   104.22  3.000
 GIO  HDP2  CDP  HDP1  107.93  3.000
 GIO  HDP2  CDP  NP    111.10  3.000
 GIO  HDP1  CDP  NP    109.97  3.000
 GIO  HDP2  CDP  CGP   112.61  3.000
 GIO  HDP1  CDP  CGP   111.90  3.000
 GIO  NP    CDP  CGP   103.32  3.000
 GIO  C     NP   CDP   123.69  3.000
 GIO  C     NP   CAP   123.72  3.000
 GIO  CDP   NP   CAP   112.59  3.000
 GIO  CA    C    O     122.06  3.000
 GIO  CA    C    NP    114.11  3.000
 GIO  O     C    NP    123.83  3.000
 GIO  HAC2  CA   HAC1  107.19  3.000
 GIO  HAC2  CA   N     111.63  3.000
 GIO  HAC1  CA   N     108.77  3.000
 GIO  HAC2  CA   C     108.63  3.000
 GIO  HAC1  CA   C     108.52  3.000
 GIO  N     CA   C     111.94  3.000
 GIO  H     N    CA    117.71  3.000
 GIO  H     N    CP    118.02  3.000
 GIO  CA    N    CP    123.80  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
 GIO  CONST_01  CA   N    CP   CAP    0.00   0.0  0
 GIO  CONST_02  CA   C    NP   CAP    0.00   0.0  0
 GIO  CONST_03  CA   C    NP   CDP  180.00   0.0  0
 GIO  CONST_04  CA   N    CP   OP   180.00   0.0  0
 GIO  CONST_05  O    C    NP   CAP  180.00   0.0  0
 GIO  CONST_06  O    C    NP   CDP    0.00   0.0  0
 GIO  CONST_07  H    N    CP   CAP  180.00   0.0  0
 GIO  Var_01    C    CA   N    CP   -38.24  30.0  1
 GIO  Var_02    CDP  CGP  CBP  CAP   37.64  30.0  1
 GIO  Var_03    CGP  CDP  NP   CAP    3.78  30.0  1
 GIO  Var_04    NP   CDP  CGP  CBP  -25.76  30.0  1
 GIO  Var_05    N    CA   C    NP    33.39  30.0  1

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
 GIO  chir_01  CAP  CP  CBP  NP  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
 GIO  plan-1  CAP  0.020
 GIO  plan-1  CDP  0.020
 GIO  plan-1  NP   0.020
 GIO  plan-1  C    0.020
 GIO  plan-1  O    0.020
 GIO  plan-1  CA   0.020
 GIO  plan-2  OP   0.020
 GIO  plan-2  CP   0.020
 GIO  plan-2  CAP  0.020
 GIO  plan-2  CA   0.020
 GIO  plan-2  N    0.020
 GIO  plan-2  H    0.020

