# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:25:57 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (2R)-2-hydroxy-3-oxopropyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](CO[P](O)(O)=O)C=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
 G3H  G3H  '(2R)-2-hydroxy-3-oxopropyl dihydrogen phosphate'  ligand  15  10  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G3H
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
 G3H  O1   O  O      0  -0.376  -4.0652  -0.5092  -0.5496
 G3H  C1   C  C1     0   0.148  -3.1346  -0.7682   0.1707
 G3H  C2   C  CH1    0  -0.113  -2.0005   0.1775   0.4664
 G3H  O2   O  OH1    0  -0.652  -2.2160   1.4576  -0.0503
 G3H  C3   C  CH2    0  -0.133  -0.6834  -0.4593   0.0207
 G3H  O1P  O  O2     0  -0.652   0.3805   0.2786   0.5235
 G3H  O2P  O  O      0  -0.902   1.8319   0.3892  -1.5923
 G3H  O3P  O  OP    -1  -0.896   2.8001   0.8238   0.7486
 G3H  O4P  O  OP    -1  -0.905   2.1076  -1.5556   0.0497
 G3H  P    P  P      0   1.222   1.9262  -0.0531  -0.1366
 G3H  H11  H  H      0   0.192  -3.0511  -1.7500   0.6709
 G3H  H2   H  HCH1   0   0.258  -1.9688   0.2732   1.5602
 G3H  HO2  H  HOH1   0   0.445  -2.2851   1.3957  -1.0091
 G3H  H31  H  HCH2   0   0.181  -0.6626  -1.5025   0.3688
 G3H  H32  H  HCH2   0   0.182  -0.6768  -0.5029  -1.0796

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
 G3H  O1   C1   double  1.205  0.020  1.205
 G3H  C1   C2   single  1.506  0.020  1.506
 G3H  C1   H11  single  0.930  0.020  1.080
 G3H  C2   O2   single  1.397  0.020  1.397
 G3H  C2   C3   single  1.529  0.020  1.529
 G3H  C2   H2   single  0.970  0.020  1.090
 G3H  O2   HO2  single  0.850  0.020  0.980
 G3H  C3   O1P  single  1.389  0.020  1.389
 G3H  C3   H31  single  0.970  0.020  1.090
 G3H  C3   H32  single  0.970  0.020  1.090
 G3H  O1P  P    single  1.713  0.020  1.713
 G3H  O2P  P    deloc   1.524  0.020  1.524
 G3H  O3P  P    deloc   1.522  0.020  1.522
 G3H  O4P  P    deloc   1.525  0.020  1.525

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
 G3H  H11  C1   C2   114.34  3.000
 G3H  H11  C1   O1   121.33  3.000
 G3H  C2   C1   O1   124.33  3.000
 G3H  H2   C2   C3   107.56  3.000
 G3H  H2   C2   O2   107.03  3.000
 G3H  C3   C2   O2   113.99  3.000
 G3H  H2   C2   C1   105.78  3.000
 G3H  C3   C2   C1   109.26  3.000
 G3H  O2   C2   C1   112.74  3.000
 G3H  HO2  O2   C2   108.67  3.000
 G3H  H32  C3   H31  106.17  3.000
 G3H  H32  C3   O1P  112.22  3.000
 G3H  H31  C3   O1P  112.01  3.000
 G3H  H32  C3   C2   108.23  3.000
 G3H  H31  C3   C2   108.60  3.000
 G3H  O1P  C3   C2   109.45  3.000
 G3H  P    O1P  C3   116.66  3.000
 G3H  O4P  P    O3P  115.36  3.000
 G3H  O4P  P    O2P  114.20  3.000
 G3H  O3P  P    O2P  115.07  3.000
 G3H  O4P  P    O1P  104.54  3.000
 G3H  O3P  P    O1P  100.51  3.000
 G3H  O2P  P    O1P  104.83  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
 G3H  Var_01  O2P  P   O1P  C3  65.83  30.0  3
 G3H  Var_02  H31  C3  O1P  P   72.66  30.0  1

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
 G3H  chir_01  C2  C1  O2  C3  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
 G3H  plan-1  O1   0.020
 G3H  plan-1  C1   0.020
 G3H  plan-1  C2   0.020
 G3H  plan-1  H11  0.020

