# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 08:31:04 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (1~{R},2~{R},3~{R},4~{S},5~{R})-4-(hydroxymethyl)cyclohexane-1,2,3,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1[C@H](O)C[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 UKT  UKT  (1~{R},2~{R},3~{R},4~{S},5~{R})-4-(hydroxymethyl)cyclohexane-1,2,3,5-tetrol  ligand  26  12  .  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_UKT
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
 UKT  C4   C  CH1   0   0.062  18.9461  2.4209  18.4850
 UKT  C2   C  CH1   0  -0.366  17.7601  3.7581  20.2709
 UKT  C6   C  CH2   0  -0.519  17.0472  1.4060  19.7074
 UKT  C5   C  CH1   0   0.001  17.7707  1.4660  18.3686
 UKT  O10  O  OH1   0  -0.678  19.6765  4.6003  19.0070
 UKT  C3   C  CH1   0   0.022  18.4990  3.8140  18.9270
 UKT  C1   C  CH2   0  -0.141  17.3004  5.1581  20.6613
 UKT  O8   O  OH1   0  -0.672  16.7184  5.1267  21.9557
 UKT  O11  O  OH1   0  -0.673  19.6309  2.4655  17.2595
 UKT  O12  O  OH1   0  -0.667  16.9331  1.9149  17.3244
 UKT  C7   C  CH1   0   0.118  16.5831  2.7744  20.1847
 UKT  O13  O  OH1   0  -0.695  15.9339  2.5885  21.4233
 UKT  H1   H  HCH1  0   0.201  19.5952  2.0179  19.2805
 UKT  H2   H  HCH1  0   0.233  18.4652  3.3880  21.0282
 UKT  H3   H  HCH2  0   0.248  16.1907  0.7279  19.6359
 UKT  H4   H  HCH2  0   0.231  17.7213  0.9753  20.4552
 UKT  H5   H  HCH1  0   0.225  18.1645  0.4647  18.1406
 UKT  H6   H  HOH1  0   0.458  19.4833  5.4934  18.7103
 UKT  H7   H  HCH1  0   0.219  17.8243  4.2264  18.1649
 UKT  H8   H  HCH2  0   0.213  18.1491  5.8498  20.6477
 UKT  H9   H  HCH2  0   0.203  16.5773  5.5132  19.9148
 UKT  H10  H  HOH1  0   0.464  16.2552  5.9565  22.1057
 UKT  H11  H  HOH1  0   0.441  20.3049  3.1494  17.3404
 UKT  H12  H  HOH1  0   0.449  16.1612  1.3410  17.2933
 UKT  H13  H  HCH1  0   0.179  15.8743  3.1820  19.4456
 UKT  H14  H  HOH1  0   0.443  15.8882  3.4550  21.8537

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
 UKT  O11  C4   single  1.405  0.020  1.405
 UKT  O12  C5   single  1.412  0.020  1.412
 UKT  C4   C5   single  1.519  0.020  1.519
 UKT  C4   C3   single  1.528  0.020  1.528
 UKT  C5   C6   single  1.523  0.020  1.523
 UKT  C3   O10  single  1.418  0.020  1.418
 UKT  C3   C2   single  1.535  0.020  1.535
 UKT  C6   C7   single  1.522  0.020  1.522
 UKT  C7   C2   single  1.536  0.020  1.536
 UKT  C7   O13  single  1.411  0.020  1.411
 UKT  C2   C1   single  1.524  0.020  1.524
 UKT  C1   O8   single  1.420  0.020  1.420
 UKT  C4   H1   single  0.970  0.020  1.090
 UKT  C2   H2   single  0.970  0.020  1.090
 UKT  C6   H3   single  0.970  0.020  1.090
 UKT  C6   H4   single  0.970  0.020  1.090
 UKT  C5   H5   single  0.970  0.020  1.090
 UKT  O10  H6   single  0.850  0.020  0.980
 UKT  C3   H7   single  0.970  0.020  1.090
 UKT  C1   H8   single  0.970  0.020  1.090
 UKT  C1   H9   single  0.970  0.020  1.090
 UKT  O8   H10  single  0.850  0.020  0.980
 UKT  O11  H11  single  0.850  0.020  0.980
 UKT  O12  H12  single  0.850  0.020  0.980
 UKT  C7   H13  single  0.970  0.020  1.090
 UKT  O13  H14  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
 UKT  H1   C4   O11  110.73  3.000
 UKT  H1   C4   C3   107.25  3.000
 UKT  O11  C4   C3   111.47  3.000
 UKT  H1   C4   C5   106.32  3.000
 UKT  C3   C4   C5   111.64  3.000
 UKT  O11  C4   C5   109.30  3.000
 UKT  H2   C2   C7   108.33  3.000
 UKT  H2   C2   C1   109.04  3.000
 UKT  C7   C2   C1   111.80  3.000
 UKT  H2   C2   C3   107.87  3.000
 UKT  C1   C2   C3   109.64  3.000
 UKT  C7   C2   C3   110.06  3.000
 UKT  H4   C6   H3   106.42  3.000
 UKT  H4   C6   C7   109.10  3.000
 UKT  H3   C6   C7   109.80  3.000
 UKT  H4   C6   C5   108.87  3.000
 UKT  H3   C6   C5   109.80  3.000
 UKT  C7   C6   C5   112.66  3.000
 UKT  H5   C5   O12  110.40  3.000
 UKT  H5   C5   C6   108.45  3.000
 UKT  O12  C5   C6   112.39  3.000
 UKT  H5   C5   C4   108.13  3.000
 UKT  C6   C5   C4   108.97  3.000
 UKT  O12  C5   C4   108.41  3.000
 UKT  H6   O10  C3   109.33  3.000
 UKT  H7   C3   O10  109.93  3.000
 UKT  H7   C3   C2   109.00  3.000
 UKT  O10  C3   C2   111.75  3.000
 UKT  H7   C3   C4   108.74  3.000
 UKT  C2   C3   C4   111.16  3.000
 UKT  O10  C3   C4   106.19  3.000
 UKT  H9   C1   H8   107.32  3.000
 UKT  H9   C1   O8   110.92  3.000
 UKT  H8   C1   O8   110.06  3.000
 UKT  H9   C1   C2   108.74  3.000
 UKT  H8   C1   C2   110.07  3.000
 UKT  O8   C1   C2   109.68  3.000
 UKT  H10  O8   C1   108.69  3.000
 UKT  H11  O11  C4   106.88  3.000
 UKT  H12  O12  C5   108.06  3.000
 UKT  H13  C7   O13  109.98  3.000
 UKT  H13  C7   C6   108.56  3.000
 UKT  O13  C7   C6   107.29  3.000
 UKT  H13  C7   C2   107.07  3.000
 UKT  O13  C7   C2   112.81  3.000
 UKT  C6   C7   C2   111.08  3.000
 UKT  H14  O13  C7   107.09  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
 UKT  chir_01  C4  O11  C5  C3  positiv
 UKT  chir_02  C2  C3   C7  C1  positiv
 UKT  chir_03  C5  O12  C4  C6  negativ
 UKT  chir_04  C3  O10  C4  C2  negativ
 UKT  chir_05  C7  O13  C2  C6  negativ

