# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 08:59:29 2020
#   Inital geometry file: a 30 line input string
#   Ligand name: phosphorodiamidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[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
 2PA  2PA  'phosphorodiamidic acid   '  ligand  9  5  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2PA
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
 2PA  N4    N  NH2    0  -0.984   1.0246  -0.5258   1.1579
 2PA  N5    N  NH2    0  -0.983   0.3717  -0.7455  -1.3318
 2PA  O1    O  O      0  -0.834   0.2287   1.6135  -0.0311
 2PA  P2    P  P      0   1.215  -0.0989   0.1407   0.0535
 2PA  O3    O  OP    -1  -0.834  -1.5294  -0.2589   0.3326
 2PA  HN41  H  HNH2   0   0.354   0.8341  -1.4859   1.4134
 2PA  HN42  H  HNH2   0   0.356   1.1077   0.0185   2.0061
 2PA  HN51  H  HNH2   0   0.356  -0.3008  -0.6821  -2.0843
 2PA  HN52  H  HNH2   0   0.353   1.2824  -0.4971  -1.6957

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
 2PA  N4  P2    single  1.711  0.020  1.711
 2PA  N4  HN41  single  0.890  0.020  1.040
 2PA  N4  HN42  single  0.890  0.020  1.040
 2PA  N5  P2    single  1.710  0.020  1.710
 2PA  N5  HN51  single  0.890  0.020  1.040
 2PA  N5  HN52  single  0.890  0.020  1.040
 2PA  O1  P2    deloc   1.511  0.020  1.511
 2PA  P2  O3    deloc   1.511  0.020  1.511

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
 2PA  HN42  N4  HN41  108.33  3.000
 2PA  HN42  N4  P2    112.69  3.000
 2PA  HN41  N4  P2    114.15  3.000
 2PA  HN52  N5  HN51  108.39  3.000
 2PA  HN52  N5  P2    114.31  3.000
 2PA  HN51  N5  P2    112.78  3.000
 2PA  O3    P2  O1    118.25  3.000
 2PA  O3    P2  N5    105.85  3.000
 2PA  O1    P2  N5    113.58  3.000
 2PA  O3    P2  N4    113.54  3.000
 2PA  O1    P2  N4    105.87  3.000
 2PA  N5    P2  N4     98.06  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
 2PA  Var_01  HN51  N5  P2  N4  166.42  30.0  3
 2PA  Var_02  HN41  N4  P2  N5  -71.09  30.0  3

