# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:06:12 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: methanediylbis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C[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
 MDN  MDN  'methanediylbis(phosphonic acid)'  ligand  11  9  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MDN
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
 MDN  O3   O  OP    -1  -0.950   0.2303  -1.1165   2.6989
 MDN  P1   P  P      0   1.144   0.1013   0.0037   1.6405
 MDN  O1   O  O      0  -0.933   1.2112   1.0581   1.7857
 MDN  O2   O  OP    -1  -0.927  -1.3130   0.6040   1.6051
 MDN  C4   C  CH2    0  -0.974   0.3847  -0.8554   0.0216
 MDN  P5   P  P      0   1.144   0.0232  -0.0063  -1.5878
 MDN  O6   O  O      0  -0.926   0.6425   1.3983  -1.5265
 MDN  O7   O  OP    -1  -0.950   0.7031  -0.8963  -2.6540
 MDN  O8   O  OP    -1  -0.934  -1.5070   0.0065  -1.7433
 MDN  H41  H  HCH2   0   0.152   1.4334  -1.1834   0.0123
 MDN  H42  H  HCH2   0   0.152  -0.1978  -1.7871   0.0239

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
 MDN  O3  P1   deloc   1.547  0.020  1.547
 MDN  P1  O1   deloc   1.538  0.020  1.538
 MDN  P1  O2   deloc   1.537  0.020  1.537
 MDN  P1  C4   single  1.854  0.020  1.854
 MDN  C4  P5   single  1.855  0.020  1.855
 MDN  C4  H41  single  0.970  0.020  1.090
 MDN  C4  H42  single  0.970  0.020  1.090
 MDN  P5  O6   deloc   1.536  0.020  1.536
 MDN  P5  O7   deloc   1.546  0.020  1.546
 MDN  P5  O8   deloc   1.538  0.020  1.538

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
 MDN  C4   P1  O2   107.55  3.000
 MDN  C4   P1  O1   106.84  3.000
 MDN  O2   P1  O1   113.49  3.000
 MDN  C4   P1  O3   104.43  3.000
 MDN  O2   P1  O3   112.05  3.000
 MDN  O1   P1  O3   111.83  3.000
 MDN  H42  C4  H41  104.64  3.000
 MDN  H42  C4  P5   106.66  3.000
 MDN  H41  C4  P5   108.38  3.000
 MDN  H42  C4  P1   108.05  3.000
 MDN  H41  C4  P1   106.95  3.000
 MDN  P5   C4  P1   121.03  3.000
 MDN  O8   P5  O7   111.87  3.000
 MDN  O8   P5  O6   113.42  3.000
 MDN  O7   P5  O6   112.12  3.000
 MDN  O8   P5  C4   106.58  3.000
 MDN  O7   P5  C4   104.42  3.000
 MDN  O6   P5  C4   107.77  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
 MDN  Var_01  P5  C4  P1  O3  168.44  30.0  3
 MDN  Var_02  O6  P5  C4  P1   47.23  30.0  3

