# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 20:01:52 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (4~{S},5~{S})-4,5-bis(oxidanyl)-2,6-bis(oxidanylidene)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CC(=O)C(O)=O)[C@H](O)C=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
 V4W  V4W  '(4~{S},5~{S})-4,5-bis(oxidanyl)-2,6-bis(oxidanylidene)hexanoic acid'  ligand  19  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V4W
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
 V4W  O1   O  O      0  -0.360   4.4009   -6.3611  19.3616
 V4W  O2   O  OH1    0  -0.650   7.2419   -8.1928  19.6599
 V4W  C1   C  C1     0   0.169   5.5416   -6.5263  19.7062
 V4W  C2   C  CH1    0  -0.074   6.0792   -7.7934  20.3417
 V4W  C3   C  CH1    0   0.035   6.4826   -7.5093  21.7854
 V4W  C4   C  CH2    0  -0.577   6.8617   -8.7992  22.5174
 V4W  C5   C  C      0   0.261   8.0579   -9.5362  21.9577
 V4W  C6   C  C      0   0.339   9.4140   -8.7847  21.9178
 V4W  O3   O  OH1    0  -0.663   5.3746   -6.8797  22.3857
 V4W  O5   O  O      0  -0.404   7.9853  -10.7012  21.6368
 V4W  O6A  O  OC    -1  -0.580   9.5096   -7.8361  22.7181
 V4W  O6B  O  O      0  -0.579  10.2563   -9.2232  21.1237
 V4W  H2   H  H      0   0.186   6.3127   -5.7473  19.5510
 V4W  H3   H  HCH1   0   0.237   5.2935   -8.5595  20.3207
 V4W  H4   H  HCH1   0   0.225   7.3510   -6.8401  21.7708
 V4W  H5   H  HCH2   0   0.266   7.0989   -8.5342  23.5528
 V4W  H6   H  HCH2   0   0.244   5.9988   -9.4691  22.5335
 V4W  H7   H  HOH1   0   0.458   5.6451   -6.5402  23.2446
 V4W  H1   H  HOH1   0   0.467   6.9958   -8.7255  18.8970

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
 V4W  O2   C2   single  1.406  0.020  1.406
 V4W  C1   O1   double  1.203  0.020  1.203
 V4W  C1   C2   single  1.516  0.020  1.516
 V4W  C2   C3   single  1.526  0.020  1.526
 V4W  O6B  C6   deloc   1.238  0.020  1.238
 V4W  O5   C5   double  1.211  0.020  1.211
 V4W  C6   C5   single  1.551  0.020  1.551
 V4W  C6   O6A  deloc   1.245  0.020  1.245
 V4W  C3   C4   single  1.531  0.020  1.531
 V4W  C3   O3   single  1.409  0.020  1.409
 V4W  C5   C4   single  1.512  0.020  1.512
 V4W  O2   H1   single  0.850  0.020  0.980
 V4W  C1   H2   single  0.930  0.020  1.080
 V4W  C2   H3   single  0.970  0.020  1.090
 V4W  C3   H4   single  0.970  0.020  1.090
 V4W  C4   H5   single  0.970  0.020  1.090
 V4W  C4   H6   single  0.970  0.020  1.090
 V4W  O3   H7   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
 V4W  H1   O2  C2   109.27  3.000
 V4W  H2   C1  C2   113.57  3.000
 V4W  H2   C1  O1   121.58  3.000
 V4W  C2   C1  O1   124.83  3.000
 V4W  H3   C2  C3   109.71  3.000
 V4W  H3   C2  C1   108.75  3.000
 V4W  C3   C2  C1   109.56  3.000
 V4W  H3   C2  O2   112.62  3.000
 V4W  C3   C2  O2   107.05  3.000
 V4W  C1   C2  O2   109.11  3.000
 V4W  H4   C3  O3   110.84  3.000
 V4W  H4   C3  C4   108.94  3.000
 V4W  O3   C3  C4   111.57  3.000
 V4W  H4   C3  C2   108.09  3.000
 V4W  O3   C3  C2   106.17  3.000
 V4W  C4   C3  C2   111.17  3.000
 V4W  H6   C4  H5   107.79  3.000
 V4W  H6   C4  C5   109.35  3.000
 V4W  H5   C4  C5   107.25  3.000
 V4W  H6   C4  C3   109.16  3.000
 V4W  H5   C4  C3   107.57  3.000
 V4W  C5   C4  C3   115.44  3.000
 V4W  O5   C5  C6   120.79  3.000
 V4W  C6   C5  C4   117.71  3.000
 V4W  O5   C5  C4   121.31  3.000
 V4W  O6B  C6  O6A  129.06  3.000
 V4W  O6A  C6  C5   114.83  3.000
 V4W  O6B  C6  C5   116.09  3.000
 V4W  H7   O3  C3   108.48  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
 V4W  Var_01  O5   C5  C4  C3  -125.32  30.0  2
 V4W  Var_02  O6B  C6  C5  C4  -159.28  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 V4W  chir_01  C2  O2  C1  C3  positiv
 V4W  chir_02  C3  O3  C2  C4  positiv

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
 V4W  plan-1  C4   0.020
 V4W  plan-1  C5   0.020
 V4W  plan-1  C6   0.020
 V4W  plan-1  O5   0.020
 V4W  plan-2  C5   0.020
 V4W  plan-2  C6   0.020
 V4W  plan-2  O6A  0.020
 V4W  plan-2  O6B  0.020
 V4W  plan-3  O1   0.020
 V4W  plan-3  C1   0.020
 V4W  plan-3  C2   0.020
 V4W  plan-3  H2   0.020

