# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 09:08:02 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  23  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  -0.105  -0.5839  -0.6933   0.7756
 DG2  C4   C  CH2   0  -0.190   0.8319  -0.3185   1.1560
 DG2  O2   O  O2    0  -0.587  -1.1863   0.4270   0.1625
 DG2  O5   O  O2    0  -0.589   1.5700  -0.1217  -0.0463
 DG2  O9   O  OH1   0  -0.729  -3.1770   1.7352   1.0883
 DG2  O10  O  OH1   0  -0.727  -2.8925   1.1392  -1.3874
 DG2  O11  O  O     0  -0.706  -3.5341  -0.6677   0.4269
 DG2  P1   P  P     0   1.457  -2.7841   0.5549   0.0891
 DG2  C7   C  C     0   0.533  -0.6127  -1.8704  -0.1912
 DG2  P6   P  P     0   1.462   2.9540   0.6820  -0.0188
 DG2  O15  O  O     0  -0.703   2.9072   2.0513   0.5234
 DG2  O14  O  OH1   0  -0.741   3.9766  -0.1997   0.8332
 DG2  O13  O  OH1   0  -0.728   3.2979   0.4973  -1.5614
 DG2  H1   H  HCH1  0   0.311  -1.1005  -0.9832   1.6976
 DG2  H2   H  HCH2  0   0.275   0.8083   0.5879   1.7655
 DG2  H3   H  HCH2  0   0.268   1.2744  -1.1173   1.7530
 DG2  H4   H  HOH1  0   0.492  -0.0854  -3.6882  -0.2572
 DG2  H5   H  HOH1  0   0.497  -2.7721   2.5951   0.9115
 DG2  H6   H  HOH1  0   0.504  -3.7886   1.3910  -1.6507
 DG2  H7   H  HOH1  0   0.497   4.1315  -1.0987   0.5132
 DG2  H8   H  HOH1  0   0.506   4.0413   1.0341  -1.8677
 DG2  O7   O  O     0  -0.414  -1.0700  -1.8198  -1.2991
 DG2  O8   O  OH1   0  -0.586  -0.0709  -2.9411   0.3609

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   double  1.473  0.020  1.473
 DG2  O13  P6   single  1.591  0.020  1.591
 DG2  P6   O14  single  1.597  0.020  1.597
 DG2  P6   O5   single  1.601  0.020  1.601
 DG2  O5   C4   single  1.425  0.020  1.425
 DG2  C4   C3   single  1.513  0.020  1.513
 DG2  O7   C7   double  1.200  0.020  1.200
 DG2  C3   C7   single  1.524  0.020  1.524
 DG2  C3   O2   single  1.412  0.020  1.412
 DG2  C7   O8   single  1.321  0.020  1.321
 DG2  O2   P1   single  1.605  0.020  1.605
 DG2  O11  P1   double  1.474  0.020  1.474
 DG2  P1   O9   single  1.595  0.020  1.595
 DG2  P1   O10  single  1.592  0.020  1.592
 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
 DG2  O8   H4   single  0.850  0.020  0.980
 DG2  O9   H5   single  0.850  0.020  0.980
 DG2  O10  H6   single  0.850  0.020  0.980
 DG2  O14  H7   single  0.850  0.020  0.980
 DG2  O13  H8   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
 DG2  H1   C3   C7   108.70  3.000
 DG2  H1   C3   O2   111.97  3.000
 DG2  C7   C3   O2   109.23  3.000
 DG2  H1   C3   C4   107.16  3.000
 DG2  O2   C3   C4   108.17  3.000
 DG2  C7   C3   C4   111.63  3.000
 DG2  H3   C4   H2   108.12  3.000
 DG2  H3   C4   O5   110.66  3.000
 DG2  H2   C4   O5   111.55  3.000
 DG2  H3   C4   C3   109.62  3.000
 DG2  H2   C4   C3   109.00  3.000
 DG2  O5   C4   C3   107.87  3.000
 DG2  P1   O2   C3   120.52  3.000
 DG2  P6   O5   C4   120.19  3.000
 DG2  H5   O9   P1   116.13  3.000
 DG2  H6   O10  P1   114.28  3.000
 DG2  O11  P1   O10  118.85  3.000
 DG2  O10  P1   O9   107.01  3.000
 DG2  O11  P1   O9   110.18  3.000
 DG2  O10  P1   O2    98.02  3.000
 DG2  O9   P1   O2   105.99  3.000
 DG2  O11  P1   O2   115.48  3.000
 DG2  O8   C7   O7   125.21  3.000
 DG2  O8   C7   C3   110.69  3.000
 DG2  O7   C7   C3   124.10  3.000
 DG2  O13  P6   O14  108.35  3.000
 DG2  O14  P6   O15  109.71  3.000
 DG2  O13  P6   O15  118.13  3.000
 DG2  O14  P6   O5   106.60  3.000
 DG2  O13  P6   O5    96.42  3.000
 DG2  O15  P6   O5   116.45  3.000
 DG2  H7   O14  P6   116.07  3.000
 DG2  H8   O13  P6   114.13  3.000
 DG2  H4   O8   C7   110.61  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  CONST_01  H4   O8  C7  C3  180.00   0.0  0
 DG2  Var_01    O11  P1  O2  C3  -12.50  30.0  3
 DG2  Var_02    O15  P6  O5  C4  -56.90  30.0  2
 DG2  Var_03    H2   C4  O5  P6   42.55  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  H4  0.020
 DG2  plan-1  O7  0.020
 DG2  plan-1  O8  0.020

