# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:20:25 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 3-(phosphonooxy)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCO[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
 48X  48X  '3-(phosphonooxy)propanoic acid'  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_48X
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
 48X  P    P  P     0   1.456  -1.9812  -0.1066  -0.0808
 48X  O1   O  OH1   0  -0.590   4.1608   0.7374   0.2005
 48X  O2   O  O     0  -0.439   3.2212  -1.2280  -0.2851
 48X  O4P  O  OH1   0  -0.731  -2.8326   1.2394  -0.0689
 48X  O2P  O  OH1   0  -0.740  -2.2018  -0.8421   1.3198
 48X  O3P  O  O     0  -0.709  -2.2036  -1.0611  -1.1822
 48X  O1P  O  O2    0  -0.589  -0.5424   0.5863  -0.0200
 48X  C3   C  CH2   0  -0.139   0.6318  -0.2237  -0.1342
 48X  C2   C  CH2   0  -0.596   1.8198   0.6872   0.0860
 48X  C1   C  C     0   0.554   3.1226  -0.0555  -0.0240
 48X  H1   H  HOH1  0   0.483   4.9863   0.2355   0.1229
 48X  H2   H  HOH1  0   0.505  -3.7841   1.1077  -0.1764
 48X  H3   H  HOH1  0   0.497  -2.1237  -0.2793   2.1018
 48X  H4   H  HCH2  0   0.237   0.6192  -1.0219   0.6119
 48X  H5   H  HCH2  0   0.239   0.6711  -0.6841  -1.1227
 48X  H6   H  HCH2  0   0.281   1.8193   1.5000  -0.6456
 48X  H7   H  HCH2  0   0.279   1.7646   1.1595   1.0703

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
 48X  O3P  P    double  1.474  0.020  1.474
 48X  O4P  P    single  1.593  0.020  1.593
 48X  P    O2P  single  1.597  0.020  1.597
 48X  P    O1P  single  1.598  0.020  1.598
 48X  O1P  C3   single  1.431  0.020  1.431
 48X  C3   C2   single  1.513  0.020  1.513
 48X  C2   C1   single  1.504  0.020  1.504
 48X  C1   O2   double  1.205  0.020  1.205
 48X  C1   O1   single  1.326  0.020  1.326
 48X  O1   H1   single  0.850  0.020  0.980
 48X  O4P  H2   single  0.850  0.020  0.980
 48X  O2P  H3   single  0.850  0.020  0.980
 48X  C3   H4   single  0.970  0.020  1.090
 48X  C3   H5   single  0.970  0.020  1.090
 48X  C2   H6   single  0.970  0.020  1.090
 48X  C2   H7   single  0.970  0.020  1.090

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
 48X  O1P  P    O3P  116.42  3.000
 48X  O1P  P    O2P  106.90  3.000
 48X  O3P  P    O2P  109.64  3.000
 48X  O1P  P    O4P   96.58  3.000
 48X  O2P  P    O4P  107.99  3.000
 48X  O3P  P    O4P  118.16  3.000
 48X  H1   O1   C1   110.11  3.000
 48X  H2   O4P  P    114.22  3.000
 48X  H3   O2P  P    115.48  3.000
 48X  C3   O1P  P    119.36  3.000
 48X  H5   C3   H4   108.11  3.000
 48X  H5   C3   C2   110.95  3.000
 48X  H4   C3   C2   110.45  3.000
 48X  H5   C3   O1P  109.92  3.000
 48X  H4   C3   O1P  110.46  3.000
 48X  C2   C3   O1P  106.97  3.000
 48X  H7   C2   H6   106.34  3.000
 48X  H7   C2   C1   108.85  3.000
 48X  H6   C2   C1   108.58  3.000
 48X  H7   C2   C3   110.58  3.000
 48X  H6   C2   C3   110.47  3.000
 48X  C1   C2   C3   111.85  3.000
 48X  C2   C1   O2   124.56  3.000
 48X  O2   C1   O1   123.67  3.000
 48X  C2   C1   O1   111.77  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
 48X  CONST_01  H1  O1  C1   O2      0.00   0.0  0
 48X  Var_01    C2  C3  O1P  P    -174.90  30.0  3
 48X  Var_02    C1  C2  C3   O1P  -179.46  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
 48X  plan-1  O1  0.020
 48X  plan-1  O2  0.020
 48X  plan-1  C2  0.020
 48X  plan-1  C1  0.020
 48X  plan-1  H1  0.020

