# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 13:31:02 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3R)-3-hydroxy-2,4-dioxopentyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@@H](O)C(=O)CO[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
 26T  26T  '(3R)-3-hydroxy-2,4-dioxopentyl dihydrogen phosphate'  ligand  22  13  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_26T
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
 26T  C01  C  CH3   0  -0.796   2.5078   2.0497   0.2286
 26T  C02  C  C     0   0.365   3.1739   0.7232   0.0616
 26T  C03  C  CH1   0  -0.154   2.4471  -0.3482  -0.7579
 26T  C04  C  C     0   0.326   1.1333  -0.6834  -0.0405
 26T  C05  C  CH2   0  -0.272  -0.0950  -0.0331  -0.6148
 26T  O06  O  O2    0  -0.576  -1.1797  -0.2376   0.2610
 26T  P07  P  P     0   1.462  -2.6411   0.2579  -0.1757
 26T  O08  O  OH1   0  -0.737  -3.1810  -0.7882  -1.2522
 26T  O09  O  OH1   0  -0.727  -3.3500  -0.0489   1.2144
 26T  O10  O  O     0  -0.704  -2.7186   1.6241  -0.7217
 26T  O11  O  O     0  -0.344   1.1076  -1.4332   0.8961
 26T  O12  O  OH1   0  -0.650   3.2218  -1.4857  -0.9046
 26T  O13  O  O     0  -0.375   4.2412   0.4402   0.5494
 26T  H1   H  HCH3  0   0.277   2.0594   2.3930  -0.7031
 26T  H2   H  HCH3  0   0.286   1.7047   1.9665   0.9659
 26T  H3   H  HCH3  0   0.292   3.2146   2.7939   0.5878
 26T  H4   H  HCH1  0   0.296   2.2183   0.0879  -1.7408
 26T  H5   H  HCH2  0   0.278   0.0905   1.0315  -0.7938
 26T  H6   H  HCH2  0   0.294  -0.2647  -0.4864  -1.6009
 26T  H7   H  HOH1  0   0.499  -3.2229  -1.7097  -0.9623
 26T  H8   H  HOH1  0   0.507  -4.2809   0.2088   1.2535
 26T  H9   H  HOH1  0   0.453   3.9690  -1.4149  -0.2929

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
 26T  O13  C02  double  1.207  0.020  1.207
 26T  C01  C02  single  1.494  0.020  1.494
 26T  C02  C03  single  1.532  0.020  1.532
 26T  O11  C04  double  1.200  0.020  1.200
 26T  O10  P07  double  1.473  0.020  1.473
 26T  C03  C04  single  1.534  0.020  1.534
 26T  C03  O12  single  1.384  0.020  1.384
 26T  C04  C05  single  1.504  0.020  1.504
 26T  O06  P07  single  1.604  0.020  1.604
 26T  O06  C05  single  1.409  0.020  1.409
 26T  P07  O09  single  1.590  0.020  1.590
 26T  P07  O08  single  1.595  0.020  1.595
 26T  C01  H1   single  0.970  0.020  1.090
 26T  C01  H2   single  0.970  0.020  1.090
 26T  C01  H3   single  0.970  0.020  1.090
 26T  C03  H4   single  0.970  0.020  1.090
 26T  C05  H5   single  0.970  0.020  1.090
 26T  C05  H6   single  0.970  0.020  1.090
 26T  O08  H7   single  0.850  0.020  0.980
 26T  O09  H8   single  0.850  0.020  0.980
 26T  O12  H9   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
 26T  H3   C01  H2   107.87  3.000
 26T  H3   C01  H1   109.53  3.000
 26T  H2   C01  H1   107.36  3.000
 26T  H3   C01  C02  110.78  3.000
 26T  H2   C01  C02  109.59  3.000
 26T  H1   C01  C02  111.57  3.000
 26T  O13  C02  C03  118.14  3.000
 26T  C03  C02  C01  117.99  3.000
 26T  O13  C02  C01  123.87  3.000
 26T  H4   C03  O12  110.35  3.000
 26T  H4   C03  C04  109.06  3.000
 26T  O12  C03  C04  110.45  3.000
 26T  H4   C03  C02  107.43  3.000
 26T  O12  C03  C02  111.46  3.000
 26T  C04  C03  C02  107.99  3.000
 26T  O11  C04  C05  123.42  3.000
 26T  C05  C04  C03  115.25  3.000
 26T  O11  C04  C03  121.32  3.000
 26T  H6   C05  H5   106.29  3.000
 26T  H6   C05  O06  112.28  3.000
 26T  H5   C05  O06  111.90  3.000
 26T  H6   C05  C04  106.89  3.000
 26T  H5   C05  C04  110.14  3.000
 26T  O06  C05  C04  109.19  3.000
 26T  P07  O06  C05  119.17  3.000
 26T  O10  P07  O09  118.64  3.000
 26T  O09  P07  O08  108.21  3.000
 26T  O10  P07  O08  109.89  3.000
 26T  O08  P07  O06  106.84  3.000
 26T  O09  P07  O06   96.23  3.000
 26T  O10  P07  O06  115.80  3.000
 26T  H7   O08  P07  115.93  3.000
 26T  H8   O09  P07  114.41  3.000
 26T  H9   O12  C03  107.76  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
 26T  Var_01  O06  C05  C04  C03  -170.10  30.0  3
 26T  Var_02  O10  P07  O06  C05   -46.96  30.0  3
 26T  Var_03  H1   C01  C02  C03   -42.56  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
 26T  chir_01  C03  C02  C04  O12  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
 26T  plan-1  C01  0.020
 26T  plan-1  C02  0.020
 26T  plan-1  C03  0.020
 26T  plan-1  O13  0.020
 26T  plan-2  C03  0.020
 26T  plan-2  C04  0.020
 26T  plan-2  C05  0.020
 26T  plan-2  O11  0.020

