# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 10:13:56 2020
#   Inital geometry file: a 38 line input string
#   Ligand name: (hydroxy-oxido-phosphinimyl) hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P@@]([O-])(=N)O[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
 PON  PON  '(hydroxy-oxido-phosphinimyl) hydrogen phosphate'  ligand  12  9  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PON
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
 PON  P1   P  P      0   1.248   1.3825   0.1692   0.1542
 PON  O1   O  O      0  -0.831   1.5225   1.6489  -0.0510
 PON  O2   O  OH1    0  -0.688   2.3557  -0.6295  -0.9054
 PON  O3   O  O2     0  -0.738   0.0056  -0.3678  -0.5599
 PON  O4   O  OP    -1  -0.917   1.5303  -0.4141   1.5254
 PON  P2   P  P      0   1.176  -1.5288  -0.2039   0.0150
 PON  O5   O  OH1    0  -0.723  -1.3688   1.1022   1.0158
 PON  O6   O  OP    -1  -0.923  -1.8699  -1.3291   0.9477
 PON  N7   N  N      0  -0.897  -2.3379   0.1149  -1.3010
 PON  HO2  H  HOH1   0   0.510   3.2771  -0.3730  -0.7906
 PON  HO5  H  HOH1   0   0.436  -1.1786   1.9073   0.5217
 PON  H7   H  H      0   0.348  -3.3354   0.0503  -1.1312

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
 PON  P1  O1   double  1.500  0.020  1.500
 PON  P1  O2   single  1.646  0.020  1.646
 PON  P1  O3   single  1.641  0.020  1.641
 PON  P1  O4   single  1.497  0.020  1.497
 PON  O2  HO2  single  0.850  0.020  0.980
 PON  O3  P2   single  1.647  0.020  1.647
 PON  P2  O5   single  1.653  0.020  1.653
 PON  P2  O6   single  1.501  0.020  1.501
 PON  P2  N7   double  1.577  0.020  1.577
 PON  O5  HO5  single  0.850  0.020  0.980
 PON  N7  H7   single  0.890  0.020  1.040

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
 PON  O4   P1  O3  110.72  3.000
 PON  O4   P1  O2  110.01  3.000
 PON  O3   P1  O2   93.28  3.000
 PON  O4   P1  O1  120.01  3.000
 PON  O3   P1  O1  109.97  3.000
 PON  O2   P1  O1  109.60  3.000
 PON  HO2  O2  P1  111.08  3.000
 PON  P2   O3  P1  126.67  3.000
 PON  N7   P2  O6  123.60  3.000
 PON  N7   P2  O5  113.27  3.000
 PON  O6   P2  O5  103.78  3.000
 PON  N7   P2  O3  101.93  3.000
 PON  O6   P2  O3  110.74  3.000
 PON  O5   P2  O3  101.52  3.000
 PON  HO5  O5  P2  111.64  3.000
 PON  H7   N7  P2  110.61  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
 PON  Var_01  O5  P2  O3  P1  23.20  30.0  3

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
 PON  chir_01  P2  O5  O6  N7  both

