# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 00:12:54 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 3-hydroxypropyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCO[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
 PDI  PDI  '3-hydroxypropyl dihydrogen phosphate'  ligand  18  9  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PDI
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
 PDI  O3P   O  OH1   0  -0.731  -1.0915   0.6195  -2.5686
 PDI  P     P  P     0   1.451   0.0506  -0.1501  -1.7657
 PDI  O1P   O  O     0  -0.709   0.1917  -1.5999  -1.9973
 PDI  O2P   O  OH1   0  -0.745   1.4442   0.5725  -2.0698
 PDI  OA    O  O2    0  -0.588  -0.4070   0.3055  -0.3080
 PDI  CA    C  CH2   0  -0.165   0.3973  -0.0338   0.8325
 PDI  CB    C  CH2   0  -0.496  -0.4511   0.1089   2.0770
 PDI  CG    C  CH2   0  -0.144   0.3715  -0.1800   3.3196
 PDI  OG    O  OH1   0  -0.671  -0.4552  -0.0260   4.4513
 PDI  HOP3  H  HOH1  0   0.504  -1.1449   0.3795  -3.5033
 PDI  HOP2  H  HOH1  0   0.495   1.4483   1.5354  -1.9865
 PDI  HA1   H  HCH2  0   0.237   1.2593   0.6371   0.8744
 PDI  HA2   H  HCH2  0   0.234   0.7720  -1.0571   0.7418
 PDI  HB1   H  HCH2  0   0.241  -1.2968  -0.5818   2.0264
 PDI  HB2   H  HCH2  0   0.241  -0.8519   1.1246   2.1328
 PDI  HG1   H  HCH2  0   0.196   1.2290   0.5045   3.3547
 PDI  HG2   H  HCH2  0   0.196   0.7818  -1.1968   3.2583
 PDI  HGT   H  HOH1  0   0.455   0.0817  -0.1791   5.2338

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
 PDI  O3P  P     single  1.594  0.020  1.594
 PDI  O3P  HOP3  single  0.850  0.020  0.980
 PDI  P    O1P   double  1.475  0.020  1.475
 PDI  P    O2P   single  1.599  0.020  1.599
 PDI  P    OA    single  1.594  0.020  1.594
 PDI  O2P  HOP2  single  0.850  0.020  0.980
 PDI  OA   CA    single  1.436  0.020  1.436
 PDI  CA   CB    single  1.513  0.020  1.513
 PDI  CA   HA1   single  0.970  0.020  1.090
 PDI  CA   HA2   single  0.970  0.020  1.090
 PDI  CB   CG    single  1.518  0.020  1.518
 PDI  CB   HB1   single  0.970  0.020  1.090
 PDI  CB   HB2   single  0.970  0.020  1.090
 PDI  CG   OG    single  1.410  0.020  1.410
 PDI  CG   HG1   single  0.970  0.020  1.090
 PDI  CG   HG2   single  0.970  0.020  1.090
 PDI  OG   HGT   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
 PDI  HOP3  O3P  P    114.01  3.000
 PDI  OA    P    O2P  107.15  3.000
 PDI  OA    P    O1P  116.87  3.000
 PDI  O2P   P    O1P  109.32  3.000
 PDI  OA    P    O3P   96.72  3.000
 PDI  O2P   P    O3P  108.09  3.000
 PDI  O1P   P    O3P  117.64  3.000
 PDI  HOP2  O2P  P    115.94  3.000
 PDI  CA    OA   P    119.86  3.000
 PDI  HA2   CA   HA1  107.89  3.000
 PDI  HA2   CA   CB   110.40  3.000
 PDI  HA1   CA   CB   110.66  3.000
 PDI  HA2   CA   OA   110.31  3.000
 PDI  HA1   CA   OA   109.09  3.000
 PDI  CB    CA   OA   108.48  3.000
 PDI  HB2   CB   HB1  107.80  3.000
 PDI  HB2   CB   CG   109.50  3.000
 PDI  HB1   CB   CG   109.69  3.000
 PDI  HB2   CB   CA   109.58  3.000
 PDI  HB1   CB   CA   109.64  3.000
 PDI  CG    CB   CA   110.58  3.000
 PDI  HG2   CG   HG1  106.70  3.000
 PDI  HG2   CG   OG   111.41  3.000
 PDI  HG1   CG   OG   111.36  3.000
 PDI  HG2   CG   CB   109.46  3.000
 PDI  HG1   CG   CB   109.31  3.000
 PDI  OG    CG   CB   108.57  3.000
 PDI  HGT   OG   CG   107.97  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
 PDI  Var_01  CB  CA  OA  P   -161.98  30.0  3
 PDI  Var_02  CG  CB  CA  OA  -177.51  30.0  3
 PDI  Var_03  OG  CG  CB  CA   179.58  30.0  3

