# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 17:01:20 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (2-hydroxyethoxy)acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCC(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
 VKC  VKC  '(2-hydroxyethoxy)acetate '  ligand  16  8  .  2021-08-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VKC
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
 VKC  C     C  C     0   0.494  -1.9649  -0.2127  -0.0312
 VKC  O     O  O     0  -0.431  -1.8547  -1.3771   0.2451
 VKC  CA    C  CH2   0  -0.238  -0.8201   0.7607  -0.1513
 VKC  CD    C  CH2   0  -0.185   2.7347   0.1894   0.4259
 VKC  CG    C  CH2   0  -0.166   1.4886   0.9472   0.0482
 VKC  OAD   O  O2    0  -0.479   0.3689   0.0951   0.1290
 VKC  OE1   O  OH1   0  -0.671   2.9774  -0.8260  -0.5198
 VKC  OXT   O  OH1   0  -0.595  -3.1206   0.3930  -0.2717
 VKC  HA    H  HCH2  0   0.251  -0.8301   1.1897  -1.1645
 VKC  HAA   H  HCH2  0   0.250  -1.0006   1.5991   0.5378
 VKC  HD    H  HCH2  0   0.205   3.5546   0.9171   0.4672
 VKC  HDA   H  HCH2  0   0.202   2.6192  -0.2156   1.4397
 VKC  HG    H  HCH2  0   0.211   1.3848   1.7968   0.7363
 VKC  HGA   H  HCH2  0   0.210   1.5899   1.3636  -0.9640
 VKC  HOE1  H  HOH1  0   0.456   3.7950  -1.2682  -0.2759
 VKC  HXT   H  HOH1  0   0.486  -3.8522  -0.2370  -0.1891

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
 VKC  C    O     double  1.202  0.020  1.202
 VKC  C    CA    single  1.508  0.020  1.508
 VKC  C    OXT   single  1.327  0.020  1.327
 VKC  CA   OAD   single  1.391  0.020  1.391
 VKC  CD   CG    single  1.507  0.020  1.507
 VKC  CD   OE1   single  1.409  0.020  1.409
 VKC  CG   OAD   single  1.409  0.020  1.409
 VKC  CA   HA    single  0.970  0.020  1.090
 VKC  CA   HAA   single  0.970  0.020  1.090
 VKC  CD   HD    single  0.970  0.020  1.090
 VKC  CD   HDA   single  0.970  0.020  1.090
 VKC  CG   HG    single  0.970  0.020  1.090
 VKC  CG   HGA   single  0.970  0.020  1.090
 VKC  OE1  HOE1  single  0.850  0.020  0.980
 VKC  OXT  HXT   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
 VKC  OXT   C    CA   110.63  3.000
 VKC  OXT   C    O    124.32  3.000
 VKC  CA    C    O    125.05  3.000
 VKC  HAA   CA   HA   106.15  3.000
 VKC  HAA   CA   OAD  112.25  3.000
 VKC  HA    CA   OAD  112.33  3.000
 VKC  HAA   CA   C    108.52  3.000
 VKC  HA    CA   C    108.55  3.000
 VKC  OAD   CA   C    108.91  3.000
 VKC  HDA   CD   HD   106.78  3.000
 VKC  HDA   CD   OE1  111.85  3.000
 VKC  HD    CD   OE1  112.00  3.000
 VKC  HDA   CD   CG   109.27  3.000
 VKC  HD    CD   CG   107.10  3.000
 VKC  OE1   CD   CG   109.68  3.000
 VKC  HGA   CG   HG   107.02  3.000
 VKC  HGA   CG   OAD  110.80  3.000
 VKC  HG    CG   OAD  110.89  3.000
 VKC  HGA   CG   CD   110.19  3.000
 VKC  HG    CG   CD   108.08  3.000
 VKC  OAD   CG   CD   109.80  3.000
 VKC  CG    OAD  CA   112.22  3.000
 VKC  HOE1  OE1  CD   107.94  3.000
 VKC  HXT   OXT  C    110.21  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
 VKC  CONST_01  HXT  OXT  C    O      0.00   0.0  0
 VKC  Var_01    OAD  CA   C    O     -0.90  30.0  3
 VKC  Var_02    CD   CG   OAD  CA   177.26  30.0  1
 VKC  Var_03    OE1  CD   CG   OAD   65.00  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
 VKC  plan-1  C    0.020
 VKC  plan-1  O    0.020
 VKC  plan-1  CA   0.020
 VKC  plan-1  OXT  0.020
 VKC  plan-1  HXT  0.020

