# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 23:24:44 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: N,N'-(dihydroxy-lambda~5~-phosphanediyl)bis(phosphoramidic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[PH](O)(N[P](O)(O)=O)N[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
 XE1  XE1  'N,N'-(dihydroxy-lambda~5~-phosphanediyl)bis(phosphoramidic acid)'  ligand  18  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XE1
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
 XE1  N3A   N  NH1    0  -0.868  6.2574   -8.2163  -19.3718
 XE1  N3B   N  NH1    0  -0.952  6.2302   -6.2907  -20.9791
 XE1  O1A   O  OP    -1  -0.814  3.8975   -8.9884  -20.3274
 XE1  O1B   O  OH1    0  -0.612  6.9804   -6.6964  -17.5726
 XE1  O1G   O  O      0  -0.998  5.3049   -5.1323  -23.0818
 XE1  O2A   O  O      0  -0.956  5.9192   -8.9334  -21.9080
 XE1  O2B   O  OH1    0  -0.739  8.2329   -6.1696  -19.5674
 XE1  O2G   O  OP    -1  -0.841  3.9730   -4.8898  -20.9008
 XE1  O3G   O  OP    -1  -1.009  6.2072   -3.6763  -21.1521
 XE1  O4A   O  OP    -1  -0.831  5.8207  -10.6613  -20.0052
 XE1  PA    P  P      0   1.077  5.3795   -9.2934  -20.5167
 XE1  PB    P  P      0   1.070  6.6360   -6.5863  -19.3524
 XE1  PG    P  P      0   1.112  5.3587   -4.8863  -21.5682
 XE1  H3A1  H  HNH1   0   0.361  6.3202   -8.6578  -18.4676
 XE1  H3B1  H  HNH1   0   0.302  6.1666   -7.1270  -21.5618
 XE1  H1B1  H  HOH1   0   0.227  7.5576   -7.4294  -17.3304
 XE1  H2B1  H  HOH1   0   0.452  8.6653   -6.1346  -18.7072
 XE1  HB1   H  H      0   0.021  5.8075   -5.5401  -18.8934

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
 XE1  O1G  PG    deloc   1.534  0.020  1.534
 XE1  O2A  PA    deloc   1.535  0.020  1.535
 XE1  O3G  PG    deloc   1.535  0.020  1.535
 XE1  PG   N3B   single  1.755  0.020  1.755
 XE1  PG   O2G   deloc   1.538  0.020  1.538
 XE1  N3B  PB    single  1.702  0.020  1.702
 XE1  PA   O4A   deloc   1.526  0.020  1.526
 XE1  PA   N3A   single  1.800  0.020  1.800
 XE1  PA   O1A   deloc   1.525  0.020  1.525
 XE1  N3A  PB    single  1.673  0.020  1.673
 XE1  PB   O2B   single  1.664  0.020  1.664
 XE1  PB   O1B   single  1.816  0.020  1.816
 XE1  N3A  H3A1  single  0.868  0.020  1.013
 XE1  N3B  H3B1  single  0.868  0.020  1.013
 XE1  O1B  H1B1  single  0.832  0.020  0.971
 XE1  O2B  H2B1  single  0.832  0.020  0.971
 XE1  PB   HB1   single  1.214  0.020  1.417

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
 XE1  H3A1  N3A  PB   113.70  3.000
 XE1  H3A1  N3A  PA   109.80  3.000
 XE1  PB    N3A  PA   134.46  3.000
 XE1  H3B1  N3B  PG   115.66  3.000
 XE1  H3B1  N3B  PB   114.70  3.000
 XE1  PG    N3B  PB   125.32  3.000
 XE1  H1B1  O1B  PB   113.95  3.000
 XE1  H2B1  O2B  PB   108.92  3.000
 XE1  O4A   PA   O2A  114.36  3.000
 XE1  O4A   PA   O1A  114.76  3.000
 XE1  O2A   PA   O1A  114.03  3.000
 XE1  O1A   PA   N3A  105.98  3.000
 XE1  O4A   PA   N3A  100.50  3.000
 XE1  O2A   PA   N3A  105.34  3.000
 XE1  HB1   PB   O2B  114.81  3.000
 XE1  HB1   PB   O1B   80.65  3.000
 XE1  O2B   PB   O1B   87.70  3.000
 XE1  HB1   PB   N3B   92.41  3.000
 XE1  O1B   PB   N3B  172.81  3.000
 XE1  O2B   PB   N3B   93.54  3.000
 XE1  HB1   PB   N3A  126.38  3.000
 XE1  O1B   PB   N3A   89.73  3.000
 XE1  O2B   PB   N3A  117.35  3.000
 XE1  N3B   PB   N3A   95.97  3.000
 XE1  O3G   PG   O2G  112.47  3.000
 XE1  O2G   PG   O1G  113.33  3.000
 XE1  O3G   PG   O1G  114.40  3.000
 XE1  O2G   PG   N3B  107.46  3.000
 XE1  O3G   PG   N3B  105.39  3.000
 XE1  O1G   PG   N3B  102.72  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
 XE1  Var_01  PG  N3B  PB  N3A  138.01  30.0  2
 XE1  Var_02  PA  N3A  PB  N3B  -12.58  30.0  2
 XE1  Var_03  PB  N3A  PA  O1A  -75.72  30.0  3
 XE1  Var_04  PB  N3B  PG  O1G  178.91  30.0  3

