# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:48:58 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CNCCN1
#
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
 XJJ  XJJ  'piperazin-2-one          '  ligand  15  7  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XJJ
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
 XJJ  O01   O  O     0  -0.504   6.6236  37.8894  -35.4772
 XJJ  C02   C  C     0   0.493   7.5479  37.1886  -35.8714
 XJJ  C03   C  CH2   0  -0.428   8.8710  37.1583  -35.1224
 XJJ  N04   N  NH1   0  -0.579   9.9894  36.5279  -35.7910
 XJJ  C05   C  CH2   0  -0.340   9.5723  35.3046  -36.4480
 XJJ  C06   C  CH2   0  -0.269   8.4999  35.5550  -37.4936
 XJJ  N07   N  NH1   0  -0.618   7.4438  36.3849  -36.9410
 XJJ  H031  H  HCH2  0   0.270   9.1296  38.1859  -34.8634
 XJJ  H032  H  HCH2  0   0.261   8.6775  36.6454  -34.1729
 XJJ  H041  H  HNH1  0   0.352  10.3783  37.1630  -36.4779
 XJJ  H051  H  HCH2  0   0.253  10.4318  34.8256  -36.9182
 XJJ  H052  H  HCH2  0   0.238   9.1968  34.6153  -35.6860
 XJJ  H061  H  HCH2  0   0.233   8.9411  36.0415  -38.3698
 XJJ  H062  H  HCH2  0   0.247   8.0670  34.6121  -37.8315
 XJJ  H071  H  HNH1  0   0.392   6.5729  36.4284  -37.4506

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
 XJJ  C02  O01   double  1.225  0.020  1.225
 XJJ  C03  C02   single  1.521  0.020  1.521
 XJJ  N04  C03   single  1.447  0.020  1.447
 XJJ  C05  N04   single  1.450  0.020  1.450
 XJJ  C06  C05   single  1.519  0.020  1.519
 XJJ  N07  C06   single  1.452  0.020  1.452
 XJJ  C02  N07   single  1.342  0.020  1.342
 XJJ  C03  H031  single  0.970  0.020  1.090
 XJJ  C03  H032  single  0.970  0.020  1.090
 XJJ  N04  H041  single  0.890  0.020  1.040
 XJJ  C05  H051  single  0.970  0.020  1.090
 XJJ  C05  H052  single  0.970  0.020  1.090
 XJJ  C06  H061  single  0.970  0.020  1.090
 XJJ  C06  H062  single  0.970  0.020  1.090
 XJJ  N07  H071  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
 XJJ  N07   C02  C03   116.62  3.000
 XJJ  N07   C02  O01   122.72  3.000
 XJJ  C03   C02  O01   120.63  3.000
 XJJ  H032  C03  H031  106.07  3.000
 XJJ  H032  C03  N04   109.44  3.000
 XJJ  H031  C03  N04   109.68  3.000
 XJJ  H032  C03  C02   106.40  3.000
 XJJ  H031  C03  C02   107.72  3.000
 XJJ  N04   C03  C02   116.97  3.000
 XJJ  H041  N04  C05   109.39  3.000
 XJJ  H041  N04  C03   109.68  3.000
 XJJ  C05   N04  C03   110.76  3.000
 XJJ  H052  C05  H051  107.10  3.000
 XJJ  H052  C05  C06   109.94  3.000
 XJJ  H051  C05  C06   109.40  3.000
 XJJ  H052  C05  N04   108.34  3.000
 XJJ  H051  C05  N04   109.83  3.000
 XJJ  C06   C05  N04   112.09  3.000
 XJJ  H062  C06  H061  107.22  3.000
 XJJ  H062  C06  N07   108.85  3.000
 XJJ  H061  C06  N07   110.09  3.000
 XJJ  H062  C06  C05   110.54  3.000
 XJJ  H061  C06  C05   109.86  3.000
 XJJ  N07   C06  C05   110.22  3.000
 XJJ  H071  N07  C06   117.36  3.000
 XJJ  H071  N07  C02   116.31  3.000
 XJJ  C06   N07  C02   126.09  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
 XJJ  CONST_01  C06   N07  C02  C03    0.00   0.0  0
 XJJ  CONST_02  C06   N07  C02  O01  180.00   0.0  0
 XJJ  CONST_03  H071  N07  C02  C03  180.00   0.0  0
 XJJ  Var_01    C05   N04  C03  C02  -42.20  30.0  1
 XJJ  Var_02    C05   C06  N07  C02   20.87  30.0  1
 XJJ  Var_03    C06   C05  N04  C03   60.04  30.0  1
 XJJ  Var_04    N07   C02  C03  N04   14.26  30.0  1
 XJJ  Var_05    N07   C06  C05  N04  -48.57  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
 XJJ  plan-1  O01   0.020
 XJJ  plan-1  C02   0.020
 XJJ  plan-1  C03   0.020
 XJJ  plan-1  C06   0.020
 XJJ  plan-1  N07   0.020
 XJJ  plan-1  H071  0.020

