# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:09:43 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 3-hydroxy-2-oxopropyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(=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
 13P  13P  '3-hydroxy-2-oxopropyl dihydrogen phosphate'  ligand  17  10  .  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_13P
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
 13P  P     P  P     0   1.461   0.2060  -0.0742  -1.9657
 13P  O1P   O  O     0  -0.706   1.0458  -1.2460  -2.2712
 13P  O2P   O  OH1   0  -0.729  -1.2172   0.0376  -2.6688
 13P  O3P   O  OH1   0  -0.741   1.0168   1.2668  -2.2716
 13P  O1    O  O2    0  -0.577  -0.3275   0.0396  -0.4607
 13P  C1    C  CH2   0  -0.263   0.5965  -0.0479   0.6049
 13P  C2    C  C     0   0.322  -0.1544   0.0631   1.9120
 13P  O2    O  O     0  -0.371  -1.3341   0.2884   1.9634
 13P  C3    C  CH2   0  -0.249   0.7080  -0.1341   3.1312
 13P  O3    O  OH1   0  -0.656  -0.0537   0.0746   4.2797
 13P  HOP2  H  HOH1  0   0.506  -1.2014  -0.1287  -3.6210
 13P  HOP3  H  HOH1  0   0.498   0.5236   2.0920  -2.1689
 13P  H11   H  HCH2  0   0.278   1.3386   0.7574   0.5626
 13P  H12   H  HCH2  0   0.276   1.1478  -0.9940   0.5844
 13P  H31   H  HCH2  0   0.241   1.5659   0.5494   3.0535
 13P  H32   H  HCH2  0   0.245   1.1284  -1.1490   3.0725
 13P  HO3   H  HOH1  0   0.465   0.5179  -0.0604   5.0409

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
 13P  P    O1P   double  1.474  0.020  1.474
 13P  P    O2P   single  1.591  0.020  1.591
 13P  P    O3P   single  1.597  0.020  1.597
 13P  P    O1    single  1.601  0.020  1.601
 13P  O2P  HOP2  single  0.850  0.020  0.980
 13P  O3P  HOP3  single  0.850  0.020  0.980
 13P  O1   C1    single  1.413  0.020  1.413
 13P  C1   C2    single  1.512  0.020  1.512
 13P  C1   H11   single  0.970  0.020  1.090
 13P  C1   H12   single  0.970  0.020  1.090
 13P  C2   O2    double  1.202  0.020  1.202
 13P  C2   C3    single  1.506  0.020  1.506
 13P  C3   O3    single  1.394  0.020  1.394
 13P  C3   H31   single  0.970  0.020  1.090
 13P  C3   H32   single  0.970  0.020  1.090
 13P  O3   HO3   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
 13P  O1    P    O3P  106.84  3.000
 13P  O1    P    O2P   96.45  3.000
 13P  O3P   P    O2P  108.09  3.000
 13P  O1    P    O1P  116.19  3.000
 13P  O3P   P    O1P  109.80  3.000
 13P  O2P   P    O1P  118.29  3.000
 13P  HOP2  O2P  P    114.11  3.000
 13P  HOP3  O3P  P    115.94  3.000
 13P  C1    O1   P    119.12  3.000
 13P  H12   C1   H11  107.05  3.000
 13P  H12   C1   C2   109.25  3.000
 13P  H11   C1   C2   108.41  3.000
 13P  H12   C1   O1   111.63  3.000
 13P  H11   C1   O1   111.60  3.000
 13P  C2    C1   O1   108.83  3.000
 13P  C3    C2   O2   123.49  3.000
 13P  C3    C2   C1   113.94  3.000
 13P  O2    C2   C1   122.57  3.000
 13P  H32   C3   H31  105.75  3.000
 13P  H32   C3   O3   113.02  3.000
 13P  H31   C3   O3   113.05  3.000
 13P  H32   C3   C2   107.24  3.000
 13P  H31   C3   C2   107.94  3.000
 13P  O3    C3   C2   109.54  3.000
 13P  HO3   O3   C3   107.85  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
 13P  Var_01  C2  C1  O1  P   -179.01  30.0  3
 13P  Var_02  O2  C2  C1  O1    -4.93  30.0  3
 13P  Var_03  O3  C3  C2  C1   176.08  30.0  3

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
 13P  plan-1  C1  0.020
 13P  plan-1  C2  0.020
 13P  plan-1  O2  0.020
 13P  plan-1  C3  0.020

