# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:31:00 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,3R,4S,5S)-4,5-dihydroxycyclohexane-1,3-diaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@H]1C[C@@H]([NH3+])[C@H](O)[C@@H](O)C1
#
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
 TOB  TOB  (1S,3R,4S,5S)-4,5-dihydroxycyclohexane-1,3-diaminium  ligand  26  10  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TOB
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
 TOB  C1    C  CH1   0  -0.165   0.4307  -1.1878   0.2835
 TOB  C2    C  CH2   0  -0.456  -1.0257  -1.2603  -0.1444
 TOB  C3    C  CH1   0  -0.137  -1.7401  -0.0057   0.3341
 TOB  C4    C  CH2   0  -0.491  -1.0786   1.2582  -0.1867
 TOB  C5    C  CH1   0   0.027   0.3874   1.2980   0.2405
 TOB  C6    C  CH1   0   0.068   1.1268   0.0556  -0.2499
 TOB  N1    N  NT3   1  -0.786   1.1573  -2.3958  -0.1886
 TOB  N3    N  NT3   1  -0.784  -3.1611  -0.0517  -0.1029
 TOB  O5    O  OH1   0  -0.666   1.0544   2.4062  -0.3069
 TOB  O6    O  OH1   0  -0.668   2.4514   0.0081   0.2043
 TOB  H1    H  HCH1  0   0.326   0.5047  -1.2128   1.3729
 TOB  H21   H  HCH2  0   0.308  -1.4946  -2.1502   0.2806
 TOB  H22   H  HCH2  0   0.281  -1.0938  -1.3372  -1.2341
 TOB  H3    H  HCH1  0   0.323  -1.7729   0.0074   1.4246
 TOB  H41   H  HCH2  0   0.263  -1.1435   1.2931  -1.2789
 TOB  H42   H  HCH2  0   0.287  -1.5941   2.1396   0.2024
 TOB  H5    H  HCH1  0   0.235   0.4394   1.3127   1.3385
 TOB  H6    H  HCH1  0   0.241   1.0775   0.0396  -1.3508
 TOB  HN11  H  HNT3  0   0.471   1.1059  -2.5129  -1.2016
 TOB  HN12  H  HNT3  0   0.477   2.1477  -2.3475   0.0577
 TOB  HN13  H  HNT3  0   0.482   0.7863  -3.2485   0.2315
 TOB  HN31  H  HNT3  0   0.480  -3.6458  -0.8741   0.2588
 TOB  HN32  H  HNT3  0   0.471  -3.2559  -0.0708  -1.1194
 TOB  HN33  H  HNT3  0   0.481  -3.6810   0.7618   0.2287
 TOB  HO5   H  HOH1  0   0.464   0.8420   3.1857   0.2154
 TOB  HO6   H  HOH1  0   0.466   2.9455   0.7281  -0.2017

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
 TOB  C1  C2    single  1.520  0.020  1.520
 TOB  C1  C6    single  1.522  0.020  1.522
 TOB  C1  N1    single  1.487  0.020  1.487
 TOB  C1  H1    single  0.970  0.020  1.090
 TOB  C2  C3    single  1.521  0.020  1.521
 TOB  C2  H21   single  0.970  0.020  1.090
 TOB  C2  H22   single  0.970  0.020  1.090
 TOB  C3  C4    single  1.519  0.020  1.519
 TOB  C3  N3    single  1.487  0.020  1.487
 TOB  C3  H3    single  0.970  0.020  1.090
 TOB  C4  C5    single  1.527  0.020  1.527
 TOB  C4  H41   single  0.970  0.020  1.090
 TOB  C4  H42   single  0.970  0.020  1.090
 TOB  C5  C6    single  1.527  0.020  1.527
 TOB  C5  O5    single  1.405  0.020  1.405
 TOB  C5  H5    single  0.970  0.020  1.090
 TOB  C6  O6    single  1.401  0.020  1.401
 TOB  C6  H6    single  0.970  0.020  1.090
 TOB  N1  HN11  single  0.890  0.020  1.040
 TOB  N1  HN12  single  0.890  0.020  1.040
 TOB  N1  HN13  single  0.890  0.020  1.040
 TOB  N3  HN31  single  0.890  0.020  1.040
 TOB  N3  HN32  single  0.890  0.020  1.040
 TOB  N3  HN33  single  0.890  0.020  1.040
 TOB  O5  HO5   single  0.850  0.020  0.980
 TOB  O6  HO6   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
 TOB  H1    C1  N1    105.37  3.000
 TOB  H1    C1  C6    109.72  3.000
 TOB  N1    C1  C6    109.21  3.000
 TOB  H1    C1  C2    110.17  3.000
 TOB  N1    C1  C2    109.89  3.000
 TOB  C6    C1  C2    112.26  3.000
 TOB  H22   C2  H21   107.67  3.000
 TOB  H22   C2  C3    110.00  3.000
 TOB  H21   C2  C3    110.36  3.000
 TOB  H22   C2  C1    110.08  3.000
 TOB  H21   C2  C1    109.93  3.000
 TOB  C3    C2  C1    108.80  3.000
 TOB  H3    C3  N3    105.39  3.000
 TOB  H3    C3  C4    110.23  3.000
 TOB  N3    C3  C4    109.94  3.000
 TOB  H3    C3  C2    109.79  3.000
 TOB  N3    C3  C2    109.32  3.000
 TOB  C4    C3  C2    111.96  3.000
 TOB  H42   C4  H41   107.56  3.000
 TOB  H42   C4  C5    109.40  3.000
 TOB  H41   C4  C5    109.58  3.000
 TOB  H42   C4  C3    110.10  3.000
 TOB  H41   C4  C3    110.05  3.000
 TOB  C5    C4  C3    110.11  3.000
 TOB  H5    C5  O5    110.87  3.000
 TOB  H5    C5  C6    107.99  3.000
 TOB  O5    C5  C6    106.67  3.000
 TOB  H5    C5  C4    108.97  3.000
 TOB  O5    C5  C4    111.55  3.000
 TOB  C6    C5  C4    110.72  3.000
 TOB  H6    C6  O6    111.45  3.000
 TOB  H6    C6  C5    108.12  3.000
 TOB  O6    C6  C5    112.42  3.000
 TOB  H6    C6  C1    108.53  3.000
 TOB  O6    C6  C1    106.93  3.000
 TOB  C5    C6  C1    109.31  3.000
 TOB  HN13  N1  HN12  107.02  3.000
 TOB  HN13  N1  HN11  107.12  3.000
 TOB  HN12  N1  HN11  107.07  3.000
 TOB  HN13  N1  C1    111.75  3.000
 TOB  HN12  N1  C1    111.02  3.000
 TOB  HN11  N1  C1    112.56  3.000
 TOB  HN33  N3  HN32  106.92  3.000
 TOB  HN33  N3  HN31  106.56  3.000
 TOB  HN32  N3  HN31  107.07  3.000
 TOB  HN33  N3  C3    111.50  3.000
 TOB  HN32  N3  C3    112.45  3.000
 TOB  HN31  N3  C3    111.99  3.000
 TOB  HO5   O5  C5    108.84  3.000
 TOB  HO6   O6  C6    108.85  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
 TOB  chir_01  C1  C2  C6  N1  positiv
 TOB  chir_02  C3  N3  C2  C4  negativ
 TOB  chir_03  C5  O5  C4  C6  negativ
 TOB  chir_04  C6  O6  C5  C1  positiv

