# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 21:51:52 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCCC(=O)N1
#
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
 9UZ  9UZ  'piperidine-2,6-dione     '  ligand  15  8  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9UZ
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
 9UZ  O05  O  O     0  -0.417  -2.2308  -1.0655  -0.0256
 9UZ  C04  C  C     0   0.554  -1.2325  -0.3820   0.0267
 9UZ  N03  N  NH1   0  -0.676   0.0128  -0.9726  -0.0456
 9UZ  C06  C  CH2   0  -0.567  -1.2466   1.1109   0.1910
 9UZ  C07  C  CH2   0  -0.465  -0.0047   1.7684  -0.3862
 9UZ  C08  C  CH2   0  -0.566   1.2441   1.1277   0.1951
 9UZ  C02  C  C     0   0.537   1.2498  -0.3656   0.0331
 9UZ  O01  O  O     0  -0.382   2.2574  -1.0359  -0.0128
 9UZ  H1   H  HNH1  0   0.392   0.0198  -1.9822  -0.1382
 9UZ  H2   H  HCH2  0   0.276  -2.1597   1.4944  -0.2631
 9UZ  H3   H  HCH2  0   0.269  -1.3181   1.3163   1.2649
 9UZ  H4   H  HCH2  0   0.242  -0.0021   1.6695  -1.4739
 9UZ  H5   H  HCH2  0   0.255  -0.0124   2.8349  -0.1660
 9UZ  H6   H  HCH2  0   0.284   2.1530   1.5222  -0.2578
 9UZ  H7   H  HCH2  0   0.264   1.3104   1.3355   1.2689

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
 9UZ  O01  C02  double  1.211  0.020  1.211
 9UZ  C02  N03  single  1.380  0.020  1.380
 9UZ  C02  C08  single  1.502  0.020  1.502
 9UZ  N03  C04  single  1.380  0.020  1.380
 9UZ  C08  C07  single  1.519  0.020  1.519
 9UZ  O05  C04  double  1.211  0.020  1.211
 9UZ  C04  C06  single  1.502  0.020  1.502
 9UZ  C07  C06  single  1.519  0.020  1.519
 9UZ  N03  H1   single  0.860  0.020  1.020
 9UZ  C06  H2   single  0.970  0.020  1.090
 9UZ  C06  H3   single  0.970  0.020  1.090
 9UZ  C07  H4   single  0.970  0.020  1.090
 9UZ  C07  H5   single  0.970  0.020  1.090
 9UZ  C08  H6   single  0.970  0.020  1.090
 9UZ  C08  H7   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
 9UZ  C06  C04  N03  116.07  3.000
 9UZ  C06  C04  O05  123.92  3.000
 9UZ  N03  C04  O05  120.00  3.000
 9UZ  H1   N03  C02  115.91  3.000
 9UZ  H1   N03  C04  115.92  3.000
 9UZ  C02  N03  C04  128.13  3.000
 9UZ  H3   C06  H2   106.73  3.000
 9UZ  H3   C06  C07  110.15  3.000
 9UZ  H2   C06  C07  111.99  3.000
 9UZ  H3   C06  C04  107.11  3.000
 9UZ  H2   C06  C04  108.19  3.000
 9UZ  C07  C06  C04  112.40  3.000
 9UZ  H5   C07  H4   106.86  3.000
 9UZ  H5   C07  C08  109.97  3.000
 9UZ  H4   C07  C08  109.93  3.000
 9UZ  H5   C07  C06  109.96  3.000
 9UZ  H4   C07  C06  109.95  3.000
 9UZ  C08  C07  C06  110.13  3.000
 9UZ  H7   C08  H6   106.75  3.000
 9UZ  H7   C08  C02  107.10  3.000
 9UZ  H6   C08  C02  108.18  3.000
 9UZ  H7   C08  C07  110.16  3.000
 9UZ  H6   C08  C07  111.96  3.000
 9UZ  C02  C08  C07  112.41  3.000
 9UZ  O01  C02  C08  123.88  3.000
 9UZ  C08  C02  N03  116.11  3.000
 9UZ  O01  C02  N03  120.01  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
 9UZ  CONST_01  C02  N03  C04  C06    0.00   0.0  0
 9UZ  CONST_02  C02  N03  C04  O05  180.00   0.0  0
 9UZ  CONST_03  H1   N03  C04  C06  180.00   0.0  0
 9UZ  Var_01    C08  C02  N03  C04   -1.11  30.0  1
 9UZ  Var_02    C08  C07  C06  C04  -53.52  30.0  1
 9UZ  Var_03    C07  C08  C02  N03  -26.84  30.0  1
 9UZ  Var_04    C07  C06  C04  N03   27.03  30.0  1

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
 9UZ  plan-1  N03  0.020
 9UZ  plan-1  C08  0.020
 9UZ  plan-1  C02  0.020
 9UZ  plan-1  O01  0.020
 9UZ  plan-2  O05  0.020
 9UZ  plan-2  C04  0.020
 9UZ  plan-2  N03  0.020
 9UZ  plan-2  C06  0.020
 9UZ  plan-2  C02  0.020
 9UZ  plan-2  H1   0.020

