# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 17 12:40:46 2022
#   Inital geometry file: a 35 line input string
#   Ligand name: dihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P]([O-])(=O)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
 POP  POP  "PYROPHOSPHATE 2-"  ligand  11  9  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_POP
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
 POP  P1   P  P      0   1.323  -3.4952  58.4366  16.9066
 POP  O1   O  O      0  -0.804  -3.2870  59.4653  17.9720
 POP  O2   O  OH1    0  -0.789  -3.5033  59.2593  15.4853
 POP  O3   O  OP    -1  -0.804  -4.6400  57.4730  16.9425
 POP  O    O  O2     0  -0.751  -2.1023  57.5781  16.6608
 POP  P2   P  P      0   1.315  -1.2674  56.7138  17.7733
 POP  O4   O  O      0  -0.795  -0.6236  55.5687  17.0530
 POP  O5   O  OH1    0  -0.796  -0.1380  57.8728  18.0887
 POP  O6   O  OP    -1  -0.808  -2.0972  56.4622  18.9961
 POP  HO2  H  HOH1   0   0.455  -3.8464  58.7319  14.7561
 POP  HO5  H  HOH1   0   0.455   0.4779  57.5813  18.7696

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
 POP  P1  O1   double  1.496  0.020  1.496
 POP  P1  O2   single  1.642  0.020  1.642
 POP  P1  O3   single  1.497  0.020  1.497
 POP  P1  O    single  1.655  0.020  1.655
 POP  O2  HO2  single  0.850  0.020  0.980
 POP  O   P2   single  1.638  0.020  1.638
 POP  P2  O4   double  1.498  0.020  1.498
 POP  P2  O5   single  1.649  0.020  1.649
 POP  P2  O6   single  1.499  0.020  1.499
 POP  O5  HO5  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
 POP  O    P1  O3  108.26  3.000
 POP  O    P1  O2   97.79  3.000
 POP  O3   P1  O2  109.85  3.000
 POP  O    P1  O1  110.22  3.000
 POP  O3   P1  O1  122.15  3.000
 POP  O2   P1  O1  105.82  3.000
 POP  HO2  O2  P1  112.50  3.000
 POP  P2   O   P1  127.02  3.000
 POP  O6   P2  O5  109.95  3.000
 POP  O6   P2  O4  120.12  3.000
 POP  O5   P2  O4  109.56  3.000
 POP  O6   P2  O   111.14  3.000
 POP  O5   P2  O    96.21  3.000
 POP  O4   P2  O   107.21  3.000
 POP  HO5  O5  P2  111.13  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
 POP  Var_01  O4  P2  O   P1  148.70  30.0  3
 POP  Var_02  O5  P2  O   P1  -98.58  30.0  3
 POP  Var_03  O6  P2  O   P1   15.63  30.0  3
 POP  Var_04  P2  O   P1  O1   57.73  30.0  3
 POP  Var_05  P2  O   P1  O2  167.83  30.0  3
 POP  Var_06  P2  O   P1  O3  -78.22  30.0  3

