# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 17:56:07 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2~{R},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H](O)[C@@H](O)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
 TK8  TK8  '(2~{R},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentanoic acid'  ligand  20  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TK8
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
 TK8  C02   C  CH2    0  -0.173  -19.4030  5.8390  -2.9363
 TK8  C03   C  CH1    0   0.008  -20.7862  5.2368  -3.1367
 TK8  C04   C  CH1    0   0.001  -20.7136  3.9400  -3.9434
 TK8  C05   C  CH1    0  -0.085  -22.0658  3.2397  -4.1685
 TK8  C06   C  C      0   0.390  -22.7329  2.7691  -2.8470
 TK8  O01   O  OH1    0  -0.673  -19.5484  6.9809  -2.1161
 TK8  O07   O  OC    -1  -0.574  -23.1670  3.6173  -2.0550
 TK8  O08   O  O      0  -0.605  -22.7752  1.5223  -2.7206
 TK8  O09   O  OH1    0  -0.693  -21.8746  2.1108  -4.9828
 TK8  O10   O  OH1    0  -0.676  -20.1534  4.1737  -5.2239
 TK8  O11   O  OH1    0  -0.677  -21.6406  6.1448  -3.7966
 TK8  H1    H  HCH2   0   0.190  -18.7483  5.0876  -2.4737
 TK8  H2    H  HCH2   0   0.195  -18.9654  6.1063  -3.9055
 TK8  H031  H  HCH1   0   0.204  -21.1785  4.9823  -2.1444
 TK8  H041  H  HCH1   0   0.206  -20.0788  3.2465  -3.3713
 TK8  H051  H  HCH1   0   0.198  -22.7456  3.9464  -4.6641
 TK8  H3    H  HOH1   0   0.455  -18.7275  7.4804  -2.1385
 TK8  H5    H  HOH1   0   0.421  -22.1199  1.3909  -4.3667
 TK8  H6    H  HOH1   0   0.447  -19.1989  4.0868  -5.1628
 TK8  H7    H  HOH1   0   0.441  -21.5986  6.9803  -3.3204

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
 TK8  O10  C04   single  1.417  0.020  1.417
 TK8  O09  C05   single  1.405  0.020  1.405
 TK8  C05  C04   single  1.539  0.020  1.539
 TK8  C05  C06   single  1.553  0.020  1.553
 TK8  O11  C03   single  1.411  0.020  1.411
 TK8  C04  C03   single  1.529  0.020  1.529
 TK8  C03  C02   single  1.522  0.020  1.522
 TK8  C06  O08   deloc   1.254  0.020  1.254
 TK8  C06  O07   deloc   1.239  0.020  1.239
 TK8  C02  O01   single  1.413  0.020  1.413
 TK8  C02  H1    single  0.970  0.020  1.090
 TK8  C02  H2    single  0.970  0.020  1.090
 TK8  C03  H031  single  0.970  0.020  1.090
 TK8  C04  H041  single  0.970  0.020  1.090
 TK8  C05  H051  single  0.970  0.020  1.090
 TK8  O01  H3    single  0.850  0.020  0.980
 TK8  O09  H5    single  0.850  0.020  0.980
 TK8  O10  H6    single  0.850  0.020  0.980
 TK8  O11  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
 TK8  H2    C02  H1   107.52  3.000
 TK8  H2    C02  O01  110.92  3.000
 TK8  H1    C02  O01  111.69  3.000
 TK8  H2    C02  C03  110.05  3.000
 TK8  H1    C02  C03  109.05  3.000
 TK8  O01   C02  C03  107.61  3.000
 TK8  H031  C03  O11  110.85  3.000
 TK8  H031  C03  C04  107.30  3.000
 TK8  O11   C03  C04  109.14  3.000
 TK8  H031  C03  C02  107.32  3.000
 TK8  C04   C03  C02  111.22  3.000
 TK8  O11   C03  C02  110.94  3.000
 TK8  H041  C04  O10  110.22  3.000
 TK8  H041  C04  C05  107.22  3.000
 TK8  O10   C04  C05  106.87  3.000
 TK8  H041  C04  C03  106.72  3.000
 TK8  C05   C04  C03  114.92  3.000
 TK8  O10   C04  C03  110.84  3.000
 TK8  H051  C05  O09  109.85  3.000
 TK8  H051  C05  C06  108.24  3.000
 TK8  O09   C05  C06  107.94  3.000
 TK8  H051  C05  C04  108.47  3.000
 TK8  C06   C05  C04  112.99  3.000
 TK8  O09   C05  C04  109.31  3.000
 TK8  O08   C06  O07  127.19  3.000
 TK8  O07   C06  C05  119.13  3.000
 TK8  O08   C06  C05  113.68  3.000
 TK8  H3    O01  C02  108.57  3.000
 TK8  H5    O09  C05  101.07  3.000
 TK8  H6    O10  C04  108.69  3.000
 TK8  H7    O11  C03  107.51  3.000

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
 TK8  chir_01  C03  O11  C04  C02  negativ
 TK8  chir_02  C04  O10  C03  C05  negativ
 TK8  chir_03  C05  O09  C04  C06  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
 TK8  plan-1  C05  0.020
 TK8  plan-1  C06  0.020
 TK8  plan-1  O07  0.020
 TK8  plan-1  O08  0.020

