# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 17 13:05:42 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: 2-(hydroxyamino)-2-oxoethyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=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
 PGH  PGH  "PHOSPHOGLYCOLOHYDROXAMIC ACID"  ligand  16  10  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PGH
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
 PGH  C1    C  C     0   0.483  23.4925  30.0911  19.5220
 PGH  C2    C  CH2   0  -0.280  24.8052  30.8467  19.6578
 PGH  N2    N  NH1   0  -0.372  23.2537  29.6984  18.2604
 PGH  O2    O  OH1   0  -0.535  22.1028  29.0395  17.9576
 PGH  O1    O  O     0  -0.449  22.7870  29.8328  20.4742
 PGH  O1P   O  O2    0  -0.573  24.6261  31.7961  20.6929
 PGH  O2P   O  O     0  -0.695  26.9895  31.9722  21.8137
 PGH  O3P   O  OH1   0  -0.741  26.2408  33.5795  19.9267
 PGH  O4P   O  OH1   0  -0.723  24.9929  33.6494  22.1246
 PGH  P     P  P     0   1.445  25.8549  32.6854  21.1980
 PGH  H21   H  HCH2  0   0.277  25.5882  30.1248  19.9117
 PGH  H22   H  HCH2  0   0.266  25.0930  31.3337  18.7222
 PGH  HN    H  HNH1  0   0.421  23.7693  30.0478  17.4645
 PGH  HO2   H  HOH1  0   0.478  22.3178  28.0970  17.9738
 PGH  HOP3  H  HOH1  0   0.498  27.1536  33.4685  19.6292
 PGH  HOP4  H  HOH1  0   0.502  25.5187  34.1622  22.7534

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
 PGH  C1   C2    single  1.521  0.020  1.521
 PGH  C1   N2    single  1.343  0.020  1.343
 PGH  C1   O1    double  1.213  0.020  1.213
 PGH  C2   O1P   single  1.416  0.020  1.416
 PGH  C2   H21   single  0.970  0.020  1.090
 PGH  C2   H22   single  0.970  0.020  1.090
 PGH  N2   O2    single  1.360  0.020  1.360
 PGH  N2   HN    single  0.860  0.020  1.020
 PGH  O2   HO2   single  0.850  0.020  0.980
 PGH  O1P  P     single  1.599  0.020  1.599
 PGH  O2P  P     double  1.475  0.020  1.475
 PGH  O3P  P     single  1.601  0.020  1.601
 PGH  O3P  HOP3  single  0.850  0.020  0.980
 PGH  O4P  P     single  1.591  0.020  1.591
 PGH  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
 PGH  O1    C1   N2   124.88  3.000
 PGH  O1    C1   C2   122.53  3.000
 PGH  N2    C1   C2   112.51  3.000
 PGH  H22   C2   H21  107.69  3.000
 PGH  H22   C2   O1P  111.12  3.000
 PGH  H21   C2   O1P  111.29  3.000
 PGH  H22   C2   C1   111.84  3.000
 PGH  H21   C2   C1   108.08  3.000
 PGH  O1P   C2   C1   106.82  3.000
 PGH  HN    N2   O2   115.08  3.000
 PGH  HN    N2   C1   123.24  3.000
 PGH  O2    N2   C1   120.08  3.000
 PGH  HO2   O2   N2   106.28  3.000
 PGH  P     O1P  C2   120.45  3.000
 PGH  HOP3  O3P  P    114.07  3.000
 PGH  HOP4  O4P  P    113.93  3.000
 PGH  O4P   P    O3P  104.75  3.000
 PGH  O4P   P    O2P  117.82  3.000
 PGH  O3P   P    O2P  114.58  3.000
 PGH  O4P   P    O1P   96.00  3.000
 PGH  O3P   P    O1P  104.18  3.000
 PGH  O2P   P    O1P  117.01  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
 PGH  CONST_01  O2   N2   C1   C2   180.00   0.0  0
 PGH  CONST_02  O1   C1   N2   O2     0.00   0.0  0
 PGH  CONST_03  HN   N2   C1   C2     0.00   0.0  0
 PGH  CONST_04  HN   N2   C1   O1   180.00   0.0  0
 PGH  Var_01    P    O1P  C2   C1   174.54  30.0  3
 PGH  Var_02    O2P  P    O1P  C2   -63.18  30.0  3
 PGH  Var_03    O3P  P    O1P  C2    64.44  30.0  3
 PGH  Var_04    O4P  P    O1P  C2   171.34  30.0  3
 PGH  Var_05    O1P  C2   C1   N2   147.97  30.0  3
 PGH  Var_06    O1P  C2   C1   O1   -35.10  30.0  3
 PGH  Var_07    H21  C2   C1   N2   -92.18  30.0  3
 PGH  Var_08    H22  C2   C1   N2    26.19  30.0  3
 PGH  Var_09    H21  C2   C1   O1    84.75  30.0  3
 PGH  Var_10    H22  C2   C1   O1  -156.88  30.0  3
 PGH  Var_11    H21  C2   O1P  P     56.78  30.0  1
 PGH  Var_12    H22  C2   O1P  P    -63.23  30.0  1

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
 PGH  plan-1  C1  0.020
 PGH  plan-1  C2  0.020
 PGH  plan-1  N2  0.020
 PGH  plan-1  O2  0.020
 PGH  plan-1  O1  0.020
 PGH  plan-1  HN  0.020

