# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:28:58 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  17  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  -0.362  -4.1145  -0.2923  -0.4066
 G3H  C1    C  C1    0   0.144  -3.1304  -0.7061   0.1486
 G3H  C2    C  CH1   0  -0.103  -1.9443   0.1677   0.4817
 G3H  O2    O  OH1   0  -0.646  -2.1581   1.5114   0.1897
 G3H  C3    C  CH2   0  -0.182  -0.7105  -0.4089  -0.2014
 G3H  O1P   O  O2    0  -0.584   0.4232   0.3110   0.2798
 G3H  O2P   O  O     0  -0.709   2.1059  -0.4130  -1.5858
 G3H  O3P   O  OH1   0  -0.730   2.6772   1.0459   0.5266
 G3H  O4P   O  OH1   0  -0.741   2.2084  -1.4876   0.6822
 G3H  P     P  P     0   1.458   1.8886  -0.1612  -0.1495
 G3H  H11   H  H     0   0.215  -3.0321  -1.7617   0.4515
 G3H  H2    H  HCH1  0   0.282  -1.7974   0.0751   1.5663
 G3H  HO2   H  HOH1  0   0.450  -2.6348   1.5795  -0.6460
 G3H  H31   H  HCH2  0   0.249  -0.6222  -1.4744   0.0308
 G3H  H32   H  HCH2  0   0.257  -0.7943  -0.3027  -1.2864
 G3H  HOP3  H  HOH1  0   0.505   3.6200   1.0678   0.3132
 G3H  HOP4  H  HOH1  0   0.496   2.1283  -1.4101   1.6425

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  1.203  0.020  1.203
 G3H  C1   C2    single  1.510  0.020  1.510
 G3H  C1   H11   single  0.930  0.020  1.080
 G3H  C2   O2    single  1.392  0.020  1.392
 G3H  C2   C3    single  1.524  0.020  1.524
 G3H  C2   H2    single  0.970  0.020  1.090
 G3H  O2   HO2   single  0.850  0.020  0.980
 G3H  C3   O1P   single  1.427  0.020  1.427
 G3H  C3   H31   single  0.970  0.020  1.090
 G3H  C3   H32   single  0.970  0.020  1.090
 G3H  O1P  P     single  1.598  0.020  1.598
 G3H  O2P  P     double  1.474  0.020  1.474
 G3H  O3P  P     single  1.593  0.020  1.593
 G3H  O3P  HOP3  single  0.850  0.020  0.980
 G3H  O4P  P     single  1.598  0.020  1.598
 G3H  O4P  HOP4  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
 G3H  H11   C1   C2   115.05  3.000
 G3H  H11   C1   O1   121.93  3.000
 G3H  C2    C1   O1   123.03  3.000
 G3H  H2    C2   C3   107.61  3.000
 G3H  H2    C2   O2   108.01  3.000
 G3H  C3    C2   O2   113.31  3.000
 G3H  H2    C2   C1   105.91  3.000
 G3H  C3    C2   C1   108.54  3.000
 G3H  O2    C2   C1   113.06  3.000
 G3H  HO2   O2   C2   109.02  3.000
 G3H  H32   C3   H31  108.14  3.000
 G3H  H32   C3   O1P  110.28  3.000
 G3H  H31   C3   O1P  110.84  3.000
 G3H  H32   C3   C2   110.25  3.000
 G3H  H31   C3   C2   109.80  3.000
 G3H  O1P   C3   C2   107.54  3.000
 G3H  P     O1P  C3   119.27  3.000
 G3H  HOP3  O3P  P    113.98  3.000
 G3H  HOP4  O4P  P    115.71  3.000
 G3H  O4P   P    O3P  108.00  3.000
 G3H  O4P   P    O2P  109.62  3.000
 G3H  O3P   P    O2P  118.04  3.000
 G3H  O4P   P    O1P  106.79  3.000
 G3H  O3P   P    O1P   96.67  3.000
 G3H  O2P   P    O1P  116.57  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  48.56  30.0  3
 G3H  Var_02  H31  C3  O1P  P   54.05  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

