# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 08:02:28 2020
#   Inital geometry file: a 32 line input string
#   Ligand name: (R)-P-methylphosphonamidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P@](N)(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
 PNO  PNO  '(R)-P-methylphosphonamidic acid'  ligand  11  5  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PNO
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
 PNO  N1   N  NH2   0  -0.956  -1.1387  -0.5903  -0.9561
 PNO  P1   P  P     0   1.282   0.0377   0.1234  -0.0209
 PNO  O1   O  OH1   0  -0.756   1.5006  -0.4935  -0.3603
 PNO  O2   O  O     0  -0.731   0.1107   1.5979  -0.2105
 PNO  C1   C  CH3   0  -0.950  -0.3414  -0.4424   1.6432
 PNO  HN1  H  HNH2  0   0.398  -1.3031  -1.5792  -0.8259
 PNO  HN2  H  HNH2  0   0.400  -1.1252  -0.3565  -1.9398
 PNO  HO1  H  HOH1  0   0.480   1.5576  -1.4561  -0.3203
 PNO  H1   H  HCH3  0   0.280   0.4215  -0.0832   2.3331
 PNO  H2   H  HCH3  0   0.278  -1.3076  -0.0512   1.9570
 PNO  H3   H  HCH3  0   0.274  -0.3719  -1.5304   1.7025

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
 PNO  N1  P1   single  1.664  0.020  1.664
 PNO  N1  HN1  single  0.890  0.020  1.040
 PNO  N1  HN2  single  0.890  0.020  1.040
 PNO  P1  O1   single  1.624  0.020  1.624
 PNO  P1  O2   double  1.488  0.020  1.488
 PNO  P1  C1   single  1.798  0.020  1.798
 PNO  O1  HO1  single  0.850  0.020  0.980
 PNO  C1  H1   single  0.970  0.020  1.090
 PNO  C1  H2   single  0.970  0.020  1.090
 PNO  C1  H3   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
 PNO  HN2  N1  HN1  110.70  3.000
 PNO  HN2  N1  P1   115.99  3.000
 PNO  HN1  N1  P1   117.54  3.000
 PNO  C1   P1  O2   116.10  3.000
 PNO  C1   P1  O1   105.30  3.000
 PNO  O2   P1  O1   107.79  3.000
 PNO  C1   P1  N1   103.66  3.000
 PNO  O2   P1  N1   112.84  3.000
 PNO  O1   P1  N1   110.89  3.000
 PNO  HO1  O1  P1   115.06  3.000
 PNO  H3   C1  H2   108.55  3.000
 PNO  H3   C1  H1   108.31  3.000
 PNO  H2   C1  H1   108.70  3.000
 PNO  H3   C1  P1   111.74  3.000
 PNO  H2   C1  P1   109.92  3.000
 PNO  H1   C1  P1   109.56  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
 PNO  Var_01  H1   C1  P1  N1  176.03  30.0  3
 PNO  Var_02  HN1  N1  P1  O1   64.00  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
 PNO  chir_01  P1  O1  O2  C1  both

