# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:09:05 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 2-oxo-5-phosphonopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)CCC[P](O)(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
 KPA  KPA  '2-oxo-5-phosphonopentanoic acid'  ligand  21  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KPA
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
 KPA  OA   O  O     0  -0.345   2.3824  -1.5463   0.0274
 KPA  CA   C  C     0   0.295   2.4250  -0.3453   0.0201
 KPA  C    C  C     0   0.483   3.7896   0.3660   0.0116
 KPA  OXT  O  OH1   0  -0.570   4.7841  -0.4925   0.0111
 KPA  O    O  O     0  -0.404   3.8933   1.5634   0.0063
 KPA  CB   C  CH2   0  -0.553   1.2311   0.5551   0.0191
 KPA  CG   C  CH2   0  -0.437  -0.0941  -0.1883   0.0405
 KPA  CP   C  CH2   0  -0.761  -1.2570   0.8025   0.0395
 KPA  P    P  P     0   1.376  -2.8540  -0.0252   0.1207
 KPA  O1   O  O     0  -0.719  -3.0570  -0.9276   1.2800
 KPA  O2   O  OH1   0  -0.745  -3.8590   1.2251   0.0126
 KPA  O3   O  OH1   0  -0.752  -3.0197  -0.8751  -1.2376
 KPA  HO   H  HOH1  0   0.494   5.6345  -0.0256   0.0051
 KPA  HB1  H  HCH2  0   0.288   1.3132   1.2291   0.8789
 KPA  HB2  H  HCH2  0   0.288   1.2986   1.2084  -0.8580
 KPA  HG1  H  HCH2  0   0.251  -0.1650  -0.8476  -0.8266
 KPA  HG2  H  HCH2  0   0.252  -0.1505  -0.8228   0.9270
 KPA  HP1  H  HCH2  0   0.289  -1.1883   1.4693   0.9028
 KPA  HP2  H  HCH2  0   0.286  -1.2244   1.4353  -0.8513
 KPA  HO2  H  HOH1  0   0.493  -4.7911   0.9958   0.1301
 KPA  HO3  H  HOH1  0   0.489  -2.9601  -0.3640  -2.0554

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
 KPA  OA   CA   double  1.202  0.020  1.202
 KPA  CA   C    single  1.539  0.020  1.539
 KPA  CA   CB   single  1.495  0.020  1.495
 KPA  C    OXT  single  1.314  0.020  1.314
 KPA  C    O    double  1.202  0.020  1.202
 KPA  OXT  HO   single  0.850  0.020  0.980
 KPA  CB   CG   single  1.520  0.020  1.520
 KPA  CB   HB1  single  0.970  0.020  1.090
 KPA  CB   HB2  single  0.970  0.020  1.090
 KPA  CG   CP   single  1.528  0.020  1.528
 KPA  CG   HG1  single  0.970  0.020  1.090
 KPA  CG   HG2  single  0.970  0.020  1.090
 KPA  CP   P    single  1.801  0.020  1.801
 KPA  CP   HP1  single  0.970  0.020  1.090
 KPA  CP   HP2  single  0.970  0.020  1.090
 KPA  P    O1   double  1.483  0.020  1.483
 KPA  P    O2   single  1.608  0.020  1.608
 KPA  P    O3   single  1.611  0.020  1.611
 KPA  O2   HO2  single  0.850  0.020  0.980
 KPA  O3   HO3  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
 KPA  CB   CA   C    115.44  3.000
 KPA  CB   CA   OA   124.99  3.000
 KPA  C    CA   OA   119.57  3.000
 KPA  O    C    OXT  125.85  3.000
 KPA  O    C    CA   122.48  3.000
 KPA  OXT  C    CA   111.66  3.000
 KPA  HO   OXT  C    110.43  3.000
 KPA  HB2  CB   HB1  104.88  3.000
 KPA  HB2  CB   CG   110.90  3.000
 KPA  HB1  CB   CG   110.81  3.000
 KPA  HB2  CB   CA   108.08  3.000
 KPA  HB1  CB   CA   108.06  3.000
 KPA  CG   CB   CA   113.68  3.000
 KPA  HG2  CG   HG1  106.89  3.000
 KPA  HG2  CG   CP   109.77  3.000
 KPA  HG1  CG   CP   109.98  3.000
 KPA  HG2  CG   CB   109.93  3.000
 KPA  HG1  CG   CB   109.93  3.000
 KPA  CP   CG   CB   110.28  3.000
 KPA  HP2  CP   HP1  106.77  3.000
 KPA  HP2  CP   P    109.22  3.000
 KPA  HP1  CP   P    107.49  3.000
 KPA  HP2  CP   CG   110.69  3.000
 KPA  HP1  CP   CG   110.32  3.000
 KPA  P    CP   CG   112.15  3.000
 KPA  O3   P    O2   106.81  3.000
 KPA  O3   P    O1   108.91  3.000
 KPA  O2   P    O1   116.11  3.000
 KPA  O3   P    CP   107.20  3.000
 KPA  O2   P    CP   101.18  3.000
 KPA  O1   P    CP   115.87  3.000
 KPA  HO2  O2   P    114.20  3.000
 KPA  HO3  O3   P    115.36  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
 KPA  CONST_01  HO   OXT  C   CA   180.00   0.0  0
 KPA  Var_01    OXT  C    CA  OA     0.11  30.0  2
 KPA  Var_02    CG   CB   CA  OA     0.51  30.0  3
 KPA  Var_03    CP   CG   CB  CA   179.94  30.0  3
 KPA  Var_04    P    CP   CG  CB  -178.07  30.0  3
 KPA  Var_05    O1   P    CP  CG    56.88  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
 KPA  plan-1  OA   0.020
 KPA  plan-1  CA   0.020
 KPA  plan-1  C    0.020
 KPA  plan-1  CB   0.020
 KPA  plan-2  CA   0.020
 KPA  plan-2  C    0.020
 KPA  plan-2  OXT  0.020
 KPA  plan-2  O    0.020
 KPA  plan-2  HO   0.020

