# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:32:22 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: (2-oxopropyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)C[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
 7VD  7VD  '(2-oxopropyl)phosphonic acid'  ligand  15  8  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7VD
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
 7VD  P1  P  P     0   1.378  -1.0238  -0.0433   0.1374
 7VD  C1  C  CH2   0  -0.886   0.5366   0.8589  -0.0018
 7VD  O2  O  OH1   0  -0.748  -1.1078  -1.0513  -1.1097
 7VD  O3  O  O     0  -0.710  -1.2582  -0.7819   1.3980
 7VD  O4  O  OH1   0  -0.745  -2.0463   1.1583  -0.1730
 7VD  C6  C  C     0   0.410   1.7622  -0.0168   0.0701
 7VD  O7  O  O     0  -0.389   1.6877  -1.2076   0.2627
 7VD  C8  C  CH3   0  -0.764   3.0760   0.6832  -0.1350
 7VD  H1  H  HCH2  0   0.326   0.5649   1.4465  -0.9263
 7VD  H2  H  HCH2  0   0.332   0.5901   1.5965   0.8060
 7VD  H3  H  HOH1  0   0.491  -1.0489  -0.6450  -1.9841
 7VD  H4  H  HOH1  0   0.494  -2.9755   0.9354  -0.0229
 7VD  H5  H  HCH3  0   0.258   2.9997   1.7611  -0.0100
 7VD  H6  H  HCH3  0   0.273   3.8307   0.2902   0.5447
 7VD  H7  H  HCH3  0   0.280   3.4160   0.4894  -1.1552

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
 7VD  O7  C6  double  1.209  0.020  1.209
 7VD  C6  C8  single  1.503  0.020  1.503
 7VD  C6  C1  single  1.508  0.020  1.508
 7VD  O3  P1  double  1.480  0.020  1.480
 7VD  C1  P1  single  1.808  0.020  1.808
 7VD  O2  P1  single  1.606  0.020  1.606
 7VD  P1  O4  single  1.608  0.020  1.608
 7VD  C1  H1  single  0.970  0.020  1.090
 7VD  C1  H2  single  0.970  0.020  1.090
 7VD  O2  H3  single  0.850  0.020  0.980
 7VD  O4  H4  single  0.850  0.020  0.980
 7VD  C8  H5  single  0.970  0.020  1.090
 7VD  C8  H6  single  0.970  0.020  1.090
 7VD  C8  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
 7VD  O4  P1  O3  115.89  3.000
 7VD  O4  P1  O2  106.61  3.000
 7VD  O3  P1  O2  109.88  3.000
 7VD  O4  P1  C1   99.27  3.000
 7VD  O2  P1  C1  107.38  3.000
 7VD  O3  P1  C1  116.84  3.000
 7VD  H2  C1  H1  105.06  3.000
 7VD  H2  C1  C6  108.43  3.000
 7VD  H1  C1  C6  109.31  3.000
 7VD  H2  C1  P1  108.76  3.000
 7VD  H1  C1  P1  110.78  3.000
 7VD  C6  C1  P1  114.08  3.000
 7VD  H3  O2  P1  115.83  3.000
 7VD  H4  O4  P1  114.12  3.000
 7VD  C8  C6  O7  122.31  3.000
 7VD  C8  C6  C1  115.69  3.000
 7VD  O7  C6  C1  121.98  3.000
 7VD  H7  C8  H6  107.64  3.000
 7VD  H7  C8  H5  107.75  3.000
 7VD  H6  C8  H5  109.54  3.000
 7VD  H7  C8  C6  108.48  3.000
 7VD  H6  C8  C6  110.65  3.000
 7VD  H5  C8  C6  112.62  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
 7VD  Var_01  O7  C6  C1  P1   -3.04  30.0  1
 7VD  Var_02  C6  C1  P1  O2  -62.16  30.0  2
 7VD  Var_03  H5  C8  C6  C1   17.42  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
 7VD  plan-1  C1  0.020
 7VD  plan-1  C6  0.020
 7VD  plan-1  O7  0.020
 7VD  plan-1  C8  0.020

