# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:43:21 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  13  8  .  2021-08-05  2021-08-05  
;
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   1.176  -0.7448   0.0409  -0.3781
 7VD  C1  C  CH2    0  -0.839   0.5922   1.1388   0.4388
 7VD  O2  O  OP    -1  -0.883  -0.1510  -0.3525  -1.7335
 7VD  O3  O  O      0  -0.889  -0.9198  -1.1223   0.5959
 7VD  O4  O  OP    -1  -0.892  -1.9466   0.9810  -0.4730
 7VD  C6  C  C      0   0.389   1.8218   0.3684   0.7153
 7VD  O7  O  O      0  -0.458   2.0383  -0.1809   1.7834
 7VD  C8  C  CH3    0  -0.780   2.7946   0.2542  -0.4303
 7VD  H1  H  HCH2   0   0.218   0.7934   1.9694  -0.2413
 7VD  H2  H  HCH2   0   0.223   0.1737   1.5319   1.3678
 7VD  H5  H  HCH3   0   0.245   3.2530   1.2272  -0.6228
 7VD  H6  H  HCH3   0   0.233   3.5825  -0.4690  -0.2254
 7VD  H7  H  HCH3   0   0.255   2.2479  -0.0277  -1.3307

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  1.221  0.020  1.221
 7VD  C6  C8  single  1.507  0.020  1.507
 7VD  C6  C1  single  1.477  0.020  1.477
 7VD  O3  P1  deloc   1.527  0.020  1.527
 7VD  C1  P1  single  1.913  0.020  1.913
 7VD  O2  P1  deloc   1.531  0.020  1.531
 7VD  P1  O4  deloc   1.529  0.020  1.529
 7VD  C1  H1  single  0.970  0.020  1.090
 7VD  C1  H2  single  0.970  0.020  1.090
 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  114.70  3.000
 7VD  O4  P1  O2  114.07  3.000
 7VD  O3  P1  O2  114.41  3.000
 7VD  O4  P1  C1  102.88  3.000
 7VD  O2  P1  C1  104.74  3.000
 7VD  O3  P1  C1  104.18  3.000
 7VD  H2  C1  H1  109.07  3.000
 7VD  H2  C1  C6  110.33  3.000
 7VD  H1  C1  C6  111.08  3.000
 7VD  H2  C1  P1  107.58  3.000
 7VD  H1  C1  P1  107.41  3.000
 7VD  C6  C1  P1  111.24  3.000
 7VD  C8  C6  O7  121.10  3.000
 7VD  C8  C6  C1  115.76  3.000
 7VD  O7  C6  C1  123.11  3.000
 7VD  H7  C8  H6  110.27  3.000
 7VD  H7  C8  H5  107.16  3.000
 7VD  H6  C8  H5  108.72  3.000
 7VD  H7  C8  C6  108.88  3.000
 7VD  H6  C8  C6  111.98  3.000
 7VD  H5  C8  C6  109.71  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  -93.04  30.0  1
 7VD  Var_02  C6  C1  P1  O2  -64.83  30.0  3
 7VD  Var_03  H5  C8  C6  C1   69.66  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

