# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:41:23 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: ethyl hydrogen (S)-methylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P@](C)(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
 VX  VX  'ethyl hydrogen (S)-methylphosphonate'  ligand  15  7  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VX
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
 VX  P1   P  P      0   1.259   0.4348   1.1182  -3.2485
 VX  O1   O  O      0  -0.808  -0.8307   1.8217  -2.8401
 VX  O2   O  O2     0  -0.625  -0.0640  -0.3648  -3.7895
 VX  C1   C  CH3    0  -0.964   1.0871   1.8799  -4.7734
 VX  C2   C  CH2    0  -0.152   0.8932  -1.3684  -4.0763
 VX  C3   C  CH3    0  -0.683   0.2044  -2.5278  -4.7634
 VX  H1   H  HCH3   0   0.244   1.4286   2.8935  -4.5572
 VX  H2   H  HCH3   0   0.238   1.9378   1.3312  -5.1794
 VX  H3   H  HCH3   0   0.239   0.3221   1.9450  -5.5476
 VX  H21  H  HCH2   0   0.194   1.6896  -0.9829  -4.7249
 VX  H22  H  HCH2   0   0.202   1.3762  -1.7139  -3.1567
 VX  H31  H  HCH3   0   0.224   0.9263  -3.3170  -4.9755
 VX  H32  H  HCH3   0   0.225  -0.5784  -2.9531  -4.1340
 VX  H33  H  HCH3   0   0.224  -0.2452  -2.2218  -5.7088
 VX  O3   O  OP    -1  -0.816   1.5600   0.9365  -2.2635

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
 VX  P1  O1   deloc   1.504  0.020  1.504
 VX  P1  O2   single  1.655  0.020  1.655
 VX  P1  C1   single  1.825  0.020  1.825
 VX  O2  C2   single  1.416  0.020  1.416
 VX  C1  H1   single  0.970  0.020  1.090
 VX  C1  H2   single  0.970  0.020  1.090
 VX  C1  H3   single  0.970  0.020  1.090
 VX  C2  C3   single  1.514  0.020  1.514
 VX  C2  H21  single  0.970  0.020  1.090
 VX  C2  H22  single  0.970  0.020  1.090
 VX  C3  H31  single  0.970  0.020  1.090
 VX  C3  H32  single  0.970  0.020  1.090
 VX  C3  H33  single  0.970  0.020  1.090
 VX  P1  O3   deloc   1.506  0.020  1.506

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
 VX  O3   P1  C1   109.25  3.000
 VX  O3   P1  O2   109.31  3.000
 VX  C1   P1  O2   102.04  3.000
 VX  O3   P1  O1   120.48  3.000
 VX  C1   P1  O1   109.41  3.000
 VX  O2   P1  O1   104.73  3.000
 VX  C2   O2  P1   119.83  3.000
 VX  H3   C1  H2   108.24  3.000
 VX  H3   C1  H1   107.75  3.000
 VX  H2   C1  H1   107.28  3.000
 VX  H3   C1  P1   111.55  3.000
 VX  H2   C1  P1   112.32  3.000
 VX  H1   C1  P1   109.51  3.000
 VX  H22  C2  H21  106.70  3.000
 VX  H22  C2  C3   109.90  3.000
 VX  H21  C2  C3   109.34  3.000
 VX  H22  C2  O2   110.59  3.000
 VX  H21  C2  O2   111.19  3.000
 VX  C3   C2  O2   109.10  3.000
 VX  H33  C3  H32  108.29  3.000
 VX  H33  C3  H31  107.90  3.000
 VX  H32  C3  H31  107.77  3.000
 VX  H33  C3  C2   111.48  3.000
 VX  H32  C3  C2   111.31  3.000
 VX  H31  C3  C2   109.96  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
 VX  Var_01  C3   C2  O2  P1  -170.66  30.0  3
 VX  Var_02  O3   P1  O2  C2   -40.53  30.0  1
 VX  Var_03  H1   C1  P1  O1    67.80  30.0  3
 VX  Var_04  H31  C3  C2  O2  -179.03  30.0  3

