# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 05:20:06 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2~{R})-2,3-diphosphonooxypropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](CO[P](O)(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
 DG2  DG2  '(2~{R})-2,3-diphosphonooxypropanoic acid'  ligand  18  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DG2
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
 DG2  C3   C  CH1    0  -0.079  -0.6969  -0.8393   0.4260
 DG2  C4   C  CH2    0  -0.194   0.6045  -0.1829   0.8634
 DG2  O2   O  O2     0  -0.656  -1.4165  -0.0180  -0.4495
 DG2  O5   O  O2     0  -0.620   1.4913  -0.0827  -0.2181
 DG2  O9   O  OP    -1  -0.829  -2.2523   1.6851   1.2902
 DG2  O10  O  OP    -1  -0.993  -3.2220   1.5594  -1.0874
 DG2  O11  O  O      0  -0.987  -3.7282  -0.2925   0.6232
 DG2  P1   P  P      0   1.198  -2.7639   0.7985   0.1545
 DG2  C7   C  C      0   0.307  -0.4029  -2.2230  -0.1866
 DG2  P6   P  P      0   1.200   2.9374   0.7625   0.0243
 DG2  O15  O  O      0  -0.949   2.5249   2.2045   0.3121
 DG2  O14  O  OP    -1  -0.860   3.6200   0.0716   1.2033
 DG2  O13  O  OP    -1  -1.014   3.6249   0.5541  -1.3216
 DG2  H1   H  HCH1   0   0.215  -1.2654  -1.0254   1.3504
 DG2  H2   H  HCH2   0   0.186   0.3603   0.8042   1.2776
 DG2  H3   H  HCH2   0   0.230   1.0377  -0.7783   1.6772
 DG2  O7   O  O      0  -0.353  -0.6821  -2.4227  -1.3824
 DG2  O8   O  OC    -1  -0.801   0.0949  -3.0577   0.6034

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
 DG2  O15  P6   deloc   1.527  0.020  1.527
 DG2  O13  P6   deloc   1.526  0.020  1.526
 DG2  P6   O14  deloc   1.527  0.020  1.527
 DG2  P6   O5   single  1.692  0.020  1.692
 DG2  O5   C4   single  1.402  0.020  1.402
 DG2  C4   C3   single  1.522  0.020  1.522
 DG2  O7   C7   deloc   1.244  0.020  1.244
 DG2  C3   C7   single  1.542  0.020  1.542
 DG2  C3   O2   single  1.400  0.020  1.400
 DG2  C7   O8   deloc   1.253  0.020  1.253
 DG2  O2   P1   single  1.687  0.020  1.687
 DG2  O11  P1   deloc   1.530  0.020  1.530
 DG2  P1   O9   deloc   1.529  0.020  1.529
 DG2  P1   O10  deloc   1.527  0.020  1.527
 DG2  C3   H1   single  0.970  0.020  1.090
 DG2  C4   H2   single  0.970  0.020  1.090
 DG2  C4   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
 DG2  H1   C3  C7   106.29  3.000
 DG2  H1   C3  O2   111.03  3.000
 DG2  C7   C3  O2   112.10  3.000
 DG2  H1   C3  C4   105.85  3.000
 DG2  O2   C3  C4   111.49  3.000
 DG2  C7   C3  C4   109.77  3.000
 DG2  H3   C4  H2   107.20  3.000
 DG2  H3   C4  O5   111.16  3.000
 DG2  H2   C4  O5   111.55  3.000
 DG2  H3   C4  C3   108.46  3.000
 DG2  H2   C4  C3   107.82  3.000
 DG2  O5   C4  C3   110.49  3.000
 DG2  P1   O2  C3   118.07  3.000
 DG2  P6   O5  C4   117.75  3.000
 DG2  O11  P1  O10  114.55  3.000
 DG2  O10  P1  O9   114.56  3.000
 DG2  O11  P1  O9   113.39  3.000
 DG2  O10  P1  O2   100.93  3.000
 DG2  O9   P1  O2   106.22  3.000
 DG2  O11  P1  O2   105.54  3.000
 DG2  O8   C7  O7   126.05  3.000
 DG2  O8   C7  C3   115.04  3.000
 DG2  O7   C7  C3   118.90  3.000
 DG2  O13  P6  O14  114.70  3.000
 DG2  O14  P6  O15  113.72  3.000
 DG2  O13  P6  O15  114.64  3.000
 DG2  O14  P6  O5   105.46  3.000
 DG2  O13  P6  O5   100.98  3.000
 DG2  O15  P6  O5   105.53  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
 DG2  Var_01  O11  P1  O2  C3  -61.00  30.0  3
 DG2  Var_02  O15  P6  O5  C4  -64.03  30.0  3
 DG2  Var_03  H2   C4  O5  P6   53.98  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
 DG2  chir_01  C3  C4  C7  O2  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 DG2  plan-1  C3  0.020
 DG2  plan-1  C7  0.020
 DG2  plan-1  O7  0.020
 DG2  plan-1  O8  0.020

