# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:15:53 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 3-oxopentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC(=O)CC(O)=O
#
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
 6JN  6JN  '3-oxopentanedioic acid   '  ligand  16  10  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6JN
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
 6JN  CAA  C  CH2   0  -0.698  -1.2533  -0.9977  -0.1925
 6JN  CAB  C  C     0   0.580  -2.4612  -0.1054  -0.0902
 6JN  CAC  C  C     0   0.438   0.0254  -0.2019  -0.0444
 6JN  CAD  C  CH2   0  -0.635   1.2846  -0.9387  -0.4398
 6JN  CAE  C  C     0   0.489   2.5094  -0.1253  -0.1148
 6JN  OAF  O  OH1   0  -0.690   2.8025  -0.1831   1.1756
 6JN  OAG  O  O     0  -0.201   3.1395   0.5068  -0.9220
 6JN  OAH  O  O     0  -0.422   0.0377   0.9321   0.3603
 6JN  OAI  O  OH1   0  -0.604  -3.1442  -0.3011   1.0250
 6JN  OAJ  O  O     0  -0.413  -2.7599   0.7034  -0.9307
 6JN  H1   H  HCH2  0   0.331  -1.2542  -1.7764   0.5749
 6JN  H2   H  HCH2  0   0.306  -1.2556  -1.5033  -1.1606
 6JN  H3   H  HCH2  0   0.315   1.3063  -1.9069   0.0672
 6JN  H4   H  HCH2  0   0.338   1.2389  -1.1406  -1.5114
 6JN  H5   H  HOH1  0   0.402   3.5698   0.3751   1.3708
 6JN  H6   H  HOH1  0   0.464  -3.9059   0.2969   1.0599

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
 6JN  OAG  CAE  double  1.203  0.020  1.203
 6JN  CAD  CAE  single  1.506  0.020  1.506
 6JN  CAD  CAC  single  1.512  0.020  1.512
 6JN  CAE  OAF  single  1.325  0.020  1.325
 6JN  OAH  CAC  double  1.204  0.020  1.204
 6JN  CAC  CAA  single  1.513  0.020  1.513
 6JN  CAA  CAB  single  1.505  0.020  1.505
 6JN  CAB  OAJ  double  1.204  0.020  1.204
 6JN  CAB  OAI  single  1.322  0.020  1.322
 6JN  CAA  H1   single  0.970  0.020  1.090
 6JN  CAA  H2   single  0.970  0.020  1.090
 6JN  CAD  H3   single  0.970  0.020  1.090
 6JN  CAD  H4   single  0.970  0.020  1.090
 6JN  OAF  H5   single  0.850  0.020  0.980
 6JN  OAI  H6   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
 6JN  H2   CAA  H1   107.00  3.000
 6JN  H2   CAA  CAC  109.39  3.000
 6JN  H1   CAA  CAC  107.85  3.000
 6JN  H2   CAA  CAB  109.46  3.000
 6JN  H1   CAA  CAB  111.95  3.000
 6JN  CAC  CAA  CAB  111.08  3.000
 6JN  OAJ  CAB  OAI  124.05  3.000
 6JN  OAI  CAB  CAA  112.59  3.000
 6JN  OAJ  CAB  CAA  123.35  3.000
 6JN  OAH  CAC  CAD  122.58  3.000
 6JN  OAH  CAC  CAA  122.47  3.000
 6JN  CAD  CAC  CAA  114.96  3.000
 6JN  H4   CAD  H3   107.00  3.000
 6JN  H4   CAD  CAE  110.23  3.000
 6JN  H3   CAD  CAE  111.24  3.000
 6JN  H4   CAD  CAC  108.19  3.000
 6JN  H3   CAD  CAC  109.08  3.000
 6JN  CAE  CAD  CAC  110.97  3.000
 6JN  OAG  CAE  OAF  124.09  3.000
 6JN  OAF  CAE  CAD  111.51  3.000
 6JN  OAG  CAE  CAD  124.40  3.000
 6JN  H5   OAF  CAE  110.27  3.000
 6JN  H6   OAI  CAB  110.19  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
 6JN  CONST_01  H6   OAI  CAB  CAA   180.00   0.0  0
 6JN  CONST_02  H5   OAF  CAE  CAD   180.00   0.0  0
 6JN  Var_01    CAE  CAD  CAC  CAA  -173.69  30.0  2
 6JN  Var_02    CAD  CAC  CAA  CAB  -166.77  30.0  2
 6JN  Var_03    OAG  CAE  CAD  CAC  -101.49  30.0  3
 6JN  Var_04    OAJ  CAB  CAA  CAC    69.50  30.0  3

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
 6JN  plan-1  CAA  0.020
 6JN  plan-1  CAC  0.020
 6JN  plan-1  CAD  0.020
 6JN  plan-1  OAH  0.020
 6JN  plan-2  CAA  0.020
 6JN  plan-2  CAB  0.020
 6JN  plan-2  OAI  0.020
 6JN  plan-2  OAJ  0.020
 6JN  plan-2  H6   0.020
 6JN  plan-3  CAD  0.020
 6JN  plan-3  CAE  0.020
 6JN  plan-3  OAF  0.020
 6JN  plan-3  OAG  0.020
 6JN  plan-3  H5   0.020

