# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:43:32 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1R,3S,4R,5r,6S)-4,5,6-trihydroxycyclohexane-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)[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
 2TB  2TB  (1R,3S,4R,5r,6S)-4,5,6-trihydroxycyclohexane-1,3-diaminium  ligand  27  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2TB
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
 2TB  C1    C  CH1   0  -0.164  -1.2086   0.9847   0.3031
 2TB  C2    C  CH2   0  -0.463   0.0409   1.7153  -0.1593
 2TB  C3    C  CH1   0  -0.164   1.2626   0.9345   0.2960
 2TB  C4    C  CH1   0   0.059   1.2589  -0.4920  -0.2328
 2TB  C5    C  CH1   0  -0.007  -0.0149  -1.1988   0.2270
 2TB  C6    C  CH1   0   0.044  -1.2598  -0.4377  -0.2358
 2TB  N1    N  NT3   1  -0.786  -2.4237   1.7179  -0.1346
 2TB  N3    N  NT3   1  -0.786   2.5023   1.6170  -0.1573
 2TB  O5    O  OH1   0  -0.667   0.0057  -2.4923  -0.3181
 2TB  O4    O  OH1   0  -0.665   2.4149  -1.1132   0.2567
 2TB  O6    O  OH1   0  -0.668  -2.4387  -1.0297   0.2452
 2TB  H1    H  HCH1  0   0.328  -1.2564   0.9715   1.3943
 2TB  H21   H  HCH2  0   0.285   0.0391   1.8073  -1.2496
 2TB  H22   H  HCH2  0   0.315   0.0653   2.7235   0.2574
 2TB  H3    H  HCH1  0   0.330   1.3189   0.9246   1.3866
 2TB  H4    H  HCH1  0   0.247   1.2621  -0.4586  -1.3337
 2TB  H5    H  HCH1  0   0.244  -0.0145  -1.2317   1.3261
 2TB  H6    H  HCH1  0   0.253  -1.2585  -0.3978  -1.3345
 2TB  HN11  H  HNT3  0   0.471  -2.4540   1.8623  -1.1449
 2TB  HN12  H  HNT3  0   0.482  -2.4929   2.6370   0.3032
 2TB  HN13  H  HNT3  0   0.475  -3.2670   1.1993   0.1198
 2TB  HN31  H  HNT3  0   0.483   2.6023   2.5426   0.2602
 2TB  HN32  H  HNT3  0   0.477   3.3295   1.0788   0.1075
 2TB  HN33  H  HNT3  0   0.472   2.5363   1.7388  -1.1706
 2TB  HO5   H  HOH1  0   0.467  -0.4501  -3.0926   0.2787
 2TB  HO4   H  HOH1  0   0.467   2.5215  -1.9640  -0.1816
 2TB  HO6   H  HOH1  0   0.471  -2.7328  -1.7014  -0.3776

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
 2TB  C1  C2    single  1.520  0.020  1.520
 2TB  C1  C6    single  1.522  0.020  1.522
 2TB  C1  N1    single  1.485  0.020  1.485
 2TB  C1  H1    single  0.970  0.020  1.090
 2TB  C2  C3    single  1.520  0.020  1.520
 2TB  C2  H21   single  0.970  0.020  1.090
 2TB  C2  H22   single  0.970  0.020  1.090
 2TB  C3  C4    single  1.521  0.020  1.521
 2TB  C3  N3    single  1.486  0.020  1.486
 2TB  C3  H3    single  0.970  0.020  1.090
 2TB  C4  C5    single  1.528  0.020  1.528
 2TB  C4  O4    single  1.401  0.020  1.401
 2TB  C4  H4    single  0.970  0.020  1.090
 2TB  C5  C6    single  1.531  0.020  1.531
 2TB  C5  O5    single  1.404  0.020  1.404
 2TB  C5  H5    single  0.970  0.020  1.090
 2TB  C6  O6    single  1.404  0.020  1.404
 2TB  C6  H6    single  0.970  0.020  1.090
 2TB  N1  HN11  single  0.890  0.020  1.040
 2TB  N1  HN12  single  0.890  0.020  1.040
 2TB  N1  HN13  single  0.890  0.020  1.040
 2TB  N3  HN31  single  0.890  0.020  1.040
 2TB  N3  HN32  single  0.890  0.020  1.040
 2TB  N3  HN33  single  0.890  0.020  1.040
 2TB  O5  HO5   single  0.850  0.020  0.980
 2TB  O4  HO4   single  0.850  0.020  0.980
 2TB  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
 2TB  H1    C1  N1    105.34  3.000
 2TB  H1    C1  C6    109.94  3.000
 2TB  N1    C1  C6    109.24  3.000
 2TB  H1    C1  C2    110.23  3.000
 2TB  N1    C1  C2    110.23  3.000
 2TB  C6    C1  C2    111.67  3.000
 2TB  H22   C2  H21   107.63  3.000
 2TB  H22   C2  C3    110.02  3.000
 2TB  H21   C2  C3    110.06  3.000
 2TB  H22   C2  C1    110.27  3.000
 2TB  H21   C2  C1    110.02  3.000
 2TB  C3    C2  C1    108.83  3.000
 2TB  H3    C3  N3    105.41  3.000
 2TB  H3    C3  C4    109.80  3.000
 2TB  N3    C3  C4    109.07  3.000
 2TB  H3    C3  C2    110.20  3.000
 2TB  N3    C3  C2    110.08  3.000
 2TB  C4    C3  C2    112.07  3.000
 2TB  H4    C4  O4    111.12  3.000
 2TB  H4    C4  C5    108.50  3.000
 2TB  O4    C4  C5    112.20  3.000
 2TB  H4    C4  C3    108.60  3.000
 2TB  O4    C4  C3    107.00  3.000
 2TB  C5    C4  C3    109.35  3.000
 2TB  H5    C5  O5    111.13  3.000
 2TB  H5    C5  C6    108.50  3.000
 2TB  O5    C5  C6    110.65  3.000
 2TB  H5    C5  C4    108.33  3.000
 2TB  O5    C5  C4    107.29  3.000
 2TB  C6    C5  C4    110.92  3.000
 2TB  H6    C6  O6    111.01  3.000
 2TB  H6    C6  C5    108.62  3.000
 2TB  O6    C6  C5    111.69  3.000
 2TB  H6    C6  C1    108.66  3.000
 2TB  O6    C6  C1    107.51  3.000
 2TB  C5    C6  C1    109.29  3.000
 2TB  HN13  N1  HN12  107.11  3.000
 2TB  HN13  N1  HN11  107.07  3.000
 2TB  HN12  N1  HN11  107.16  3.000
 2TB  HN13  N1  C1    110.56  3.000
 2TB  HN12  N1  C1    111.95  3.000
 2TB  HN11  N1  C1    112.69  3.000
 2TB  HN33  N3  HN32  107.04  3.000
 2TB  HN33  N3  HN31  107.13  3.000
 2TB  HN32  N3  HN31  107.00  3.000
 2TB  HN33  N3  C3    112.66  3.000
 2TB  HN32  N3  C3    110.76  3.000
 2TB  HN31  N3  C3    111.94  3.000
 2TB  HO5   O5  C5    109.11  3.000
 2TB  HO4   O4  C4    108.92  3.000
 2TB  HO6   O6  C6    109.22  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
 2TB  chir_01  C1  C2  C6  N1  positiv
 2TB  chir_02  C3  N3  C2  C4  negativ
 2TB  chir_03  C4  O4  C3  C5  positiv
 2TB  chir_04  C5  O5  C4  C6  negativ
 2TB  chir_05  C6  O6  C5  C1  positiv

