# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:46:19 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1R,2S,3R,4R,5S)-5-amino-2,3,4-trihydroxycyclohexanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[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
 NEB  NEB  (1R,2S,3R,4R,5S)-5-amino-2,3,4-trihydroxycyclohexanaminium  ligand  26  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 OK
;

data_comp_NEB
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
 NEB  C1   C  CH1   0  -0.159  -1.2072   0.8924   0.3253
 NEB  N1   N  NT3   1  -0.786  -2.4976   1.5075  -0.0909
 NEB  C2   C  CH2   0  -0.452  -0.0395   1.7356  -0.1503
 NEB  C3   C  CH1   0  -0.123   1.2929   1.1081   0.2524
 NEB  N3   N  NH2   0  -0.786   2.3729   1.9650  -0.1991
 NEB  C4   C  CH1   0   0.052   1.3743  -0.3345  -0.2536
 NEB  O4   O  OH1   0  -0.672   2.5817  -0.8876   0.2072
 NEB  C5   C  CH1   0  -0.012   0.1808  -1.1600   0.2200
 NEB  O5   O  OH1   0  -0.676   0.2992  -2.4569  -0.3227
 NEB  C6   C  CH1   0   0.047  -1.1357  -0.5232  -0.2209
 NEB  O6   O  OH1   0  -0.672  -2.2538  -1.2278   0.2615
 NEB  H1   H  HCH1  0   0.311  -1.2404   0.8669   1.4169
 NEB  H11  H  HNT3  0   0.466  -2.5505   1.6532  -1.0997
 NEB  H12  H  HNT3  0   0.471  -3.2848   0.9104   0.1686
 NEB  H13  H  HNT3  0   0.477  -2.6480   2.4142   0.3511
 NEB  H21  H  HCH2  0   0.250  -0.0835   1.8372  -1.2408
 NEB  H22  H  HCH2  0   0.282  -0.1037   2.7406   0.2697
 NEB  H3   H  HCH1  0   0.240   1.3389   1.0819   1.3482
 NEB  H31  H  HNH2  0   0.352   3.2587   1.5899   0.1147
 NEB  H32  H  HNH2  0   0.340   2.4128   1.9589  -1.2125
 NEB  H4   H  HCH1  0   0.201   1.3553  -0.3064  -1.3570
 NEB  HO4  H  HOH1  0   0.450   2.6614  -1.7753  -0.1573
 NEB  H5   H  HCH1  0   0.230   0.1983  -1.1975   1.3190
 NEB  HO5  H  HOH1  0   0.463  -0.0062  -3.0981   0.3245
 NEB  H6   H  HCH1  0   0.239  -1.1485  -0.4755  -1.3203
 NEB  HO6  H  HOH1  0   0.466  -2.4506  -1.9514  -0.3409

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
 NEB  C1  N1   single  1.489  0.020  1.489
 NEB  C1  C2   single  1.517  0.020  1.517
 NEB  C1  C6   single  1.519  0.020  1.519
 NEB  C1  H1   single  0.970  0.020  1.090
 NEB  N1  H11  single  0.890  0.020  1.040
 NEB  N1  H12  single  0.890  0.020  1.040
 NEB  N1  H13  single  0.890  0.020  1.040
 NEB  C2  C3   single  1.527  0.020  1.527
 NEB  C2  H21  single  0.970  0.020  1.090
 NEB  C2  H22  single  0.970  0.020  1.090
 NEB  C3  N3   single  1.451  0.020  1.451
 NEB  C3  C4   single  1.531  0.020  1.531
 NEB  C3  H3   single  0.970  0.020  1.090
 NEB  N3  H31  single  0.890  0.020  1.040
 NEB  N3  H32  single  0.890  0.020  1.040
 NEB  C4  O4   single  1.406  0.020  1.406
 NEB  C4  C5   single  1.527  0.020  1.527
 NEB  C4  H4   single  0.970  0.020  1.090
 NEB  O4  HO4  single  0.850  0.020  0.980
 NEB  C5  O5   single  1.411  0.020  1.411
 NEB  C5  C6   single  1.527  0.020  1.527
 NEB  C5  H5   single  0.970  0.020  1.090
 NEB  O5  HO5  single  0.850  0.020  0.980
 NEB  C6  O6   single  1.407  0.020  1.407
 NEB  C6  H6   single  0.970  0.020  1.090
 NEB  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
 NEB  H1   C1  C6   109.82  3.000
 NEB  H1   C1  C2   110.47  3.000
 NEB  C6   C1  C2   111.66  3.000
 NEB  H1   C1  N1   105.23  3.000
 NEB  C6   C1  N1   108.98  3.000
 NEB  C2   C1  N1   110.48  3.000
 NEB  H13  N1  H12  107.21  3.000
 NEB  H13  N1  H11  107.09  3.000
 NEB  H12  N1  H11  107.13  3.000
 NEB  H13  N1  C1   111.96  3.000
 NEB  H12  N1  C1   110.82  3.000
 NEB  H11  N1  C1   112.35  3.000
 NEB  H22  C2  H21  107.17  3.000
 NEB  H22  C2  C3   109.17  3.000
 NEB  H21  C2  C3   109.60  3.000
 NEB  H22  C2  C1   110.25  3.000
 NEB  H21  C2  C1   109.43  3.000
 NEB  C3   C2  C1   111.14  3.000
 NEB  H3   C3  C4   107.78  3.000
 NEB  H3   C3  N3   107.09  3.000
 NEB  C4   C3  N3   114.46  3.000
 NEB  H3   C3  C2   108.05  3.000
 NEB  C4   C3  C2   110.27  3.000
 NEB  N3   C3  C2   108.96  3.000
 NEB  H32  N3  H31  105.85  3.000
 NEB  H32  N3  C3   109.68  3.000
 NEB  H31  N3  C3   109.65  3.000
 NEB  H4   C4  C5   108.08  3.000
 NEB  H4   C4  O4   110.64  3.000
 NEB  C5   C4  O4   110.92  3.000
 NEB  H4   C4  C3   107.79  3.000
 NEB  C5   C4  C3   111.43  3.000
 NEB  O4   C4  C3   107.94  3.000
 NEB  HO4  O4  C4   108.04  3.000
 NEB  H5   C5  C6   108.44  3.000
 NEB  H5   C5  O5   110.59  3.000
 NEB  C6   C5  O5   110.16  3.000
 NEB  H5   C5  C4   108.42  3.000
 NEB  C6   C5  C4   111.03  3.000
 NEB  O5   C5  C4   108.19  3.000
 NEB  HO5  O5  C5   109.13  3.000
 NEB  H6   C6  O6   110.79  3.000
 NEB  H6   C6  C5   108.44  3.000
 NEB  O6   C6  C5   112.16  3.000
 NEB  H6   C6  C1   108.56  3.000
 NEB  O6   C6  C1   107.82  3.000
 NEB  C5   C6  C1   108.98  3.000
 NEB  HO6  O6  C6   108.95  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
 NEB  chir_01  C1  N1  C2  C6  positiv
 NEB  chir_02  C3  N3  C4  C2  positiv
 NEB  chir_03  C4  O4  C3  C5  positiv
 NEB  chir_04  C5  O5  C4  C6  negativ
 NEB  chir_05  C6  O6  C5  C1  positiv

