# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 09:00:28 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (1R,2r,3S,4R,6S)-4,6-diaminocyclohexane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C[C@H](N)[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
 CYY  CYY  (1R,2r,3S,4R,6S)-4,6-diaminocyclohexane-1,2,3-triol  ligand  25  11  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CYY
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
 CYY  C1    C  CH1   0  -0.120   1.0602  -0.2862   1.2653
 CYY  C2    C  CH2   0  -0.462   1.7152   0.1164  -0.0580
 CYY  C3    C  CH1   0  -0.100   0.9273  -0.3213  -1.2864
 CYY  C4    C  CH1   0   0.059  -0.4751   0.2607  -1.2052
 CYY  C5    C  CH1   0  -0.026  -1.1502  -0.1806   0.0901
 CYY  C6    C  CH1   0   0.073  -0.3597   0.2649   1.3181
 CYY  N1    N  NH2   0  -0.785   1.8084   0.1396   2.4377
 CYY  N3    N  NH2   0  -0.805   1.5927   0.1525  -2.4904
 CYY  O4    O  OH1   0  -0.680  -1.2072  -0.1684  -2.3321
 CYY  O5    O  OH1   0  -0.685  -2.4517   0.3755   0.1852
 CYY  O6    O  OH1   0  -0.673  -0.9883  -0.1678   2.4993
 CYY  H1    H  HCH1  0   0.223   0.9965  -1.3808   1.3029
 CYY  H21   H  HCH2  0   0.218   1.8361   1.2061  -0.0859
 CYY  H22   H  HCH2  0   0.243   2.7224  -0.3086  -0.1003
 CYY  H3    H  HCH1  0   0.201   0.8343  -1.4205  -1.2603
 CYY  H4    H  HCH1  0   0.196  -0.3844   1.3589  -1.2001
 CYY  H5    H  HCH1  0   0.219  -1.2058  -1.2788   0.0981
 CYY  H6    H  HCH1  0   0.188  -0.2943   1.3677   1.2985
 CYY  HN11  H  HNH2  0   0.345   2.7397  -0.2566   2.3937
 CYY  HN12  H  HNH2  0   0.334   1.9426   1.1444   2.4012
 CYY  HN31  H  HNH2  0   0.344   2.5174  -0.2575  -2.5405
 CYY  HN32  H  HNH2  0   0.344   1.0993  -0.1876  -3.3059
 CYY  HO4   H  HOH1  0   0.448  -2.0500   0.2960  -2.3371
 CYY  HO5   H  HOH1  0   0.462  -3.0987  -0.2939  -0.0514
 CYY  HO6   H  HOH1  0   0.441  -1.9173   0.0795   2.4310

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
 CYY  C1  C2    single  1.530  0.020  1.530
 CYY  C1  C6    single  1.524  0.020  1.524
 CYY  C1  N1    single  1.454  0.020  1.454
 CYY  C1  H1    single  0.970  0.020  1.090
 CYY  C2  C3    single  1.524  0.020  1.524
 CYY  C2  H21   single  0.970  0.020  1.090
 CYY  C2  H22   single  0.970  0.020  1.090
 CYY  C3  C4    single  1.521  0.020  1.521
 CYY  C3  N3    single  1.455  0.020  1.455
 CYY  C3  H3    single  0.970  0.020  1.090
 CYY  C4  C5    single  1.526  0.020  1.526
 CYY  C4  O4    single  1.411  0.020  1.411
 CYY  C4  H4    single  0.970  0.020  1.090
 CYY  C5  C6    single  1.527  0.020  1.527
 CYY  C5  O5    single  1.418  0.020  1.418
 CYY  C5  H5    single  0.970  0.020  1.090
 CYY  C6  O6    single  1.406  0.020  1.406
 CYY  C6  H6    single  0.970  0.020  1.090
 CYY  N1  HN11  single  0.890  0.020  1.040
 CYY  N1  HN12  single  0.890  0.020  1.040
 CYY  N3  HN31  single  0.890  0.020  1.040
 CYY  N3  HN32  single  0.890  0.020  1.040
 CYY  O4  HO4   single  0.850  0.020  0.980
 CYY  O5  HO5   single  0.850  0.020  0.980
 CYY  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
 CYY  H1    C1  N1    107.12  3.000
 CYY  H1    C1  C6    107.79  3.000
 CYY  N1    C1  C6    110.21  3.000
 CYY  H1    C1  C2    108.48  3.000
 CYY  N1    C1  C2    113.57  3.000
 CYY  C6    C1  C2    109.48  3.000
 CYY  H22   C2  H21   106.47  3.000
 CYY  H22   C2  C3    109.47  3.000
 CYY  H21   C2  C3    108.78  3.000
 CYY  H22   C2  C1    108.98  3.000
 CYY  H21   C2  C1    109.30  3.000
 CYY  C3    C2  C1    113.59  3.000
 CYY  H3    C3  N3    112.49  3.000
 CYY  H3    C3  C4    107.59  3.000
 CYY  N3    C3  C4    109.96  3.000
 CYY  H3    C3  C2    108.10  3.000
 CYY  N3    C3  C2    109.70  3.000
 CYY  C4    C3  C2    108.90  3.000
 CYY  H4    C4  O4    110.46  3.000
 CYY  H4    C4  C5    108.71  3.000
 CYY  O4    C4  C5    111.14  3.000
 CYY  H4    C4  C3    107.80  3.000
 CYY  O4    C4  C3    108.63  3.000
 CYY  C5    C4  C3    110.04  3.000
 CYY  H5    C5  O5    110.16  3.000
 CYY  H5    C5  C6    108.16  3.000
 CYY  O5    C5  C6    107.86  3.000
 CYY  H5    C5  C4    108.51  3.000
 CYY  O5    C5  C4    110.46  3.000
 CYY  C6    C5  C4    111.67  3.000
 CYY  H6    C6  O6    110.39  3.000
 CYY  H6    C6  C5    107.91  3.000
 CYY  O6    C6  C5    110.75  3.000
 CYY  H6    C6  C1    107.77  3.000
 CYY  O6    C6  C1    109.53  3.000
 CYY  C5    C6  C1    110.43  3.000
 CYY  HN12  N1  HN11  105.32  3.000
 CYY  HN12  N1  C1    109.21  3.000
 CYY  HN11  N1  C1    108.87  3.000
 CYY  HN32  N3  HN31  105.62  3.000
 CYY  HN32  N3  C3    109.54  3.000
 CYY  HN31  N3  C3    109.07  3.000
 CYY  HO4   O4  C4    108.17  3.000
 CYY  HO5   O5  C5    109.17  3.000
 CYY  HO6   O6  C6    107.00  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
 CYY  chir_01  C1  C2  C6  N1  positiv
 CYY  chir_02  C3  N3  C4  C2  positiv
 CYY  chir_03  C4  O4  C3  C5  positiv
 CYY  chir_04  C5  O5  C4  C6  negativ
 CYY  chir_05  C6  O6  C5  C1  positiv

