# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 15:31:59 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (1~{R},3~{R},4~{S},5~{R})-3-methyl-1,3,4,5-tetrakis(oxidanyl)cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(O)C[C@](O)(C[C@@H](O)[C@@H]1O)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
 VAU  VAU  '(1~{R},3~{R},4~{S},5~{R})-3-methyl-1,3,4,5-tetrakis(oxidanyl)cyclohexane-1-carboxylic acid'  ligand  28  14  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VAU
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
 VAU  CAJ  C  CH3   0  -0.671  -1.8325   2.3117   0.6992
 VAU  CAR  C  CT    0   0.169  -1.1745   1.1336  -0.0225
 VAU  OAG  O  OH1   0  -0.669  -1.3894   1.2416  -1.4150
 VAU  CAL  C  CH2   0  -0.431   0.3314   1.1848   0.2434
 VAU  CAQ  C  CT    0   0.101   1.1312  -0.0380  -0.2229
 VAU  CAN  C  C     0   0.536   2.5270   0.0539   0.4113
 VAU  OAC  O  OH1   0  -0.577   3.5059   0.0568  -0.4774
 VAU  OAB  O  O     0  -0.444   2.7108   0.1051   1.6026
 VAU  OAF  O  OH1   0  -0.652   1.1967  -0.0115  -1.6210
 VAU  CAK  C  CH2   0  -0.520   0.4710  -1.3259   0.2898
 VAU  CAO  C  CH1   0   0.039  -1.0027  -1.3874  -0.0891
 VAU  OAD  O  OH1   0  -0.681  -1.6171  -2.5484   0.4394
 VAU  CAP  C  CH1   0   0.059  -1.7420  -0.1945   0.5005
 VAU  OAE  O  OH1   0  -0.683  -3.1137  -0.2319   0.1850
 VAU  H1   H  HCH3  0   0.235  -1.3988   3.2528   0.3572
 VAU  H2   H  HCH3  0   0.238  -2.9060   2.3485   0.5094
 VAU  H3   H  HOH1  0   0.439  -2.3341   1.1260  -1.5686
 VAU  H4   H  HCH2  0   0.264   0.7434   2.0889  -0.2154
 VAU  H5   H  HCH2  0   0.256   0.4709   1.2955   1.3200
 VAU  H6   H  HOH1  0   0.484   4.3605   0.0930  -0.0207
 VAU  H7   H  HOH1  0   0.448   1.5639  -0.8440  -1.9382
 VAU  H8   H  HCH2  0   0.262   0.9970  -2.1977  -0.1150
 VAU  H9   H  HCH2  0   0.250   0.5629  -1.3834   1.3772
 VAU  H10  H  HCH1  0   0.218  -1.1069  -1.3670  -1.1800
 VAU  H11  H  HOH1  0   0.458  -1.4137  -3.2921  -0.1356
 VAU  H12  H  HCH1  0   0.198  -1.5939  -0.2164   1.5934
 VAU  H13  H  HOH1  0   0.450  -3.4176  -1.1396   0.2970
 VAU  H14  H  HCH3  0   0.223  -1.6899   2.2487   1.7788

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
 VAU  OAE  CAP  single  1.408  0.020  1.408
 VAU  OAD  CAO  single  1.416  0.020  1.416
 VAU  CAP  CAR  single  1.536  0.020  1.536
 VAU  CAP  CAO  single  1.522  0.020  1.522
 VAU  CAJ  CAR  single  1.530  0.020  1.530
 VAU  OAG  CAR  single  1.413  0.020  1.413
 VAU  CAR  CAL  single  1.530  0.020  1.530
 VAU  CAO  CAK  single  1.523  0.020  1.523
 VAU  CAL  CAQ  single  1.534  0.020  1.534
 VAU  CAK  CAQ  single  1.535  0.020  1.535
 VAU  OAF  CAQ  single  1.400  0.020  1.400
 VAU  CAQ  CAN  single  1.536  0.020  1.536
 VAU  CAN  OAB  double  1.206  0.020  1.206
 VAU  CAN  OAC  single  1.322  0.020  1.322
 VAU  CAJ  H1   single  0.970  0.020  1.090
 VAU  CAJ  H2   single  0.970  0.020  1.090
 VAU  OAG  H3   single  0.850  0.020  0.980
 VAU  CAL  H4   single  0.970  0.020  1.090
 VAU  CAL  H5   single  0.970  0.020  1.090
 VAU  OAC  H6   single  0.850  0.020  0.980
 VAU  OAF  H7   single  0.850  0.020  0.980
 VAU  CAK  H8   single  0.970  0.020  1.090
 VAU  CAK  H9   single  0.970  0.020  1.090
 VAU  CAO  H10  single  0.970  0.020  1.090
 VAU  OAD  H11  single  0.850  0.020  0.980
 VAU  CAP  H12  single  0.970  0.020  1.090
 VAU  OAE  H13  single  0.850  0.020  0.980
 VAU  CAJ  H14  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
 VAU  H14  CAJ  H2   107.63  3.000
 VAU  H14  CAJ  H1   107.94  3.000
 VAU  H2   CAJ  H1   107.91  3.000
 VAU  H14  CAJ  CAR  111.47  3.000
 VAU  H2   CAJ  CAR  111.53  3.000
 VAU  H1   CAJ  CAR  110.20  3.000
 VAU  CAP  CAR  CAL  109.47  3.000
 VAU  CAL  CAR  OAG  108.57  3.000
 VAU  CAP  CAR  OAG  110.21  3.000
 VAU  CAL  CAR  CAJ  108.39  3.000
 VAU  OAG  CAR  CAJ  109.91  3.000
 VAU  CAP  CAR  CAJ  110.25  3.000
 VAU  H3   OAG  CAR  107.26  3.000
 VAU  H5   CAL  H4   106.36  3.000
 VAU  H5   CAL  CAQ  108.31  3.000
 VAU  H4   CAL  CAQ  109.56  3.000
 VAU  H5   CAL  CAR  107.50  3.000
 VAU  H4   CAL  CAR  108.98  3.000
 VAU  CAQ  CAL  CAR  115.71  3.000
 VAU  CAK  CAQ  OAF  111.68  3.000
 VAU  OAF  CAQ  CAN  111.64  3.000
 VAU  CAK  CAQ  CAN  107.64  3.000
 VAU  CAN  CAQ  CAL  107.50  3.000
 VAU  OAF  CAQ  CAL  108.24  3.000
 VAU  CAK  CAQ  CAL  110.06  3.000
 VAU  OAB  CAN  OAC  123.42  3.000
 VAU  OAC  CAN  CAQ  113.29  3.000
 VAU  OAB  CAN  CAQ  123.28  3.000
 VAU  H6   OAC  CAN  109.64  3.000
 VAU  H7   OAF  CAQ  109.29  3.000
 VAU  H9   CAK  H8   106.58  3.000
 VAU  H9   CAK  CAO  109.08  3.000
 VAU  H8   CAK  CAO  109.91  3.000
 VAU  H9   CAK  CAQ  109.89  3.000
 VAU  H8   CAK  CAQ  109.73  3.000
 VAU  CAO  CAK  CAQ  111.53  3.000
 VAU  H10  CAO  CAP  108.95  3.000
 VAU  H10  CAO  OAD  110.21  3.000
 VAU  CAP  CAO  OAD  106.70  3.000
 VAU  H10  CAO  CAK  109.81  3.000
 VAU  CAP  CAO  CAK  110.00  3.000
 VAU  OAD  CAO  CAK  111.11  3.000
 VAU  H11  OAD  CAO  108.61  3.000
 VAU  H12  CAP  OAE  110.63  3.000
 VAU  H12  CAP  CAO  107.64  3.000
 VAU  OAE  CAP  CAO  111.44  3.000
 VAU  H12  CAP  CAR  107.75  3.000
 VAU  CAO  CAP  CAR  111.48  3.000
 VAU  OAE  CAP  CAR  107.85  3.000
 VAU  H13  OAE  CAP  107.83  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
 VAU  CONST_01  H6  OAC  CAN  CAQ  180.00  0.0  0

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
 VAU  chir_01  CAR  CAP  OAG  CAL  positiv
 VAU  chir_02  CAQ  CAL  CAK  CAN  positiv
 VAU  chir_03  CAO  OAD  CAP  CAK  negativ
 VAU  chir_04  CAP  OAE  CAO  CAR  negativ

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
 VAU  plan-1  CAQ  0.020
 VAU  plan-1  CAN  0.020
 VAU  plan-1  OAC  0.020
 VAU  plan-1  OAB  0.020
 VAU  plan-1  H6   0.020

