# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:57:42 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (1S,2S,3R,4R)-4-aminocyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1C[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
 YHO  YHO  (1S,2S,3R,4R)-4-aminocyclopentane-1,2,3-triol  ligand  20  9  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YHO
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
 YHO  O3    O  OH1   0  -0.685   1.4905  -1.6867   0.4902
 YHO  C3    C  CH1   0  -0.001   0.6947  -0.5922   0.8573
 YHO  C2    C  CH1   0   0.005  -0.7704  -0.7436   0.4351
 YHO  O2    O  OH1   0  -0.678  -0.8709  -1.2717  -0.8670
 YHO  C1    C  CH1   0  -0.107  -1.2524   0.7022   0.4121
 YHO  N1    N  NH2   0  -0.796  -2.5733   0.8556  -0.1616
 YHO  C5    C  CH2   0  -0.484  -0.0936   1.4409  -0.2744
 YHO  C4    C  CH1   0  -0.001   1.1820   0.7425   0.2031
 YHO  O4    O  OH1   0  -0.674   2.0629   0.4727  -0.8737
 YHO  HO3   H  HOH1  0   0.443   2.0033  -1.3887  -0.2767
 YHO  H3    H  HCH1  0   0.230   0.7267  -0.4803   1.9467
 YHO  H2    H  HCH1  0   0.211  -1.3422  -1.3505   1.1509
 YHO  HO2   H  HOH1  0   0.442  -0.2737  -2.0267  -0.9193
 YHO  H1    H  HCH1  0   0.236  -1.3111   1.0286   1.4562
 YHO  HN1   H  HNH2  0   0.346  -2.8521   1.8273  -0.1045
 YHO  HN1A  H  HNH2  0   0.338  -2.5375   0.6389  -1.1504
 YHO  H5    H  HCH2  0   0.233  -0.1833   1.3221  -1.3575
 YHO  H5A   H  HCH2  0   0.241  -0.0984   2.5110  -0.0627
 YHO  H4    H  HCH1  0   0.238   1.6958   1.3433   0.9570
 YHO  HO4   H  HOH1  0   0.465   2.9553   0.7187  -0.6151

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
 YHO  O3  C3    single  1.402  0.020  1.402
 YHO  O3  HO3   single  0.850  0.020  0.980
 YHO  C4  C3    single  1.564  0.020  1.564
 YHO  C3  C2    single  1.532  0.020  1.532
 YHO  C3  H3    single  0.970  0.020  1.090
 YHO  C1  C2    single  1.524  0.020  1.524
 YHO  C2  O2    single  1.409  0.020  1.409
 YHO  C2  H2    single  0.970  0.020  1.090
 YHO  O2  HO2   single  0.850  0.020  0.980
 YHO  C5  C1    single  1.536  0.020  1.536
 YHO  C1  N1    single  1.448  0.020  1.448
 YHO  C1  H1    single  0.970  0.020  1.090
 YHO  N1  HN1   single  0.890  0.020  1.040
 YHO  N1  HN1A  single  0.890  0.020  1.040
 YHO  C4  C5    single  1.531  0.020  1.531
 YHO  C5  H5    single  0.970  0.020  1.090
 YHO  C5  H5A   single  0.970  0.020  1.090
 YHO  O4  C4    single  1.417  0.020  1.417
 YHO  C4  H4    single  0.970  0.020  1.090
 YHO  O4  HO4   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
 YHO  HO3   O3  C3   105.51  3.000
 YHO  H3    C3  C4   108.64  3.000
 YHO  H3    C3  C2   108.18  3.000
 YHO  C4    C3  C2   105.48  3.000
 YHO  H3    C3  O3   108.88  3.000
 YHO  C2    C3  O3   113.17  3.000
 YHO  C4    C3  O3   112.32  3.000
 YHO  H2    C2  C1   111.67  3.000
 YHO  H2    C2  O2   110.97  3.000
 YHO  C1    C2  O2   108.61  3.000
 YHO  H2    C2  C3   111.88  3.000
 YHO  O2    C2  C3   111.09  3.000
 YHO  C1    C2  C3   102.29  3.000
 YHO  HO2   O2  C2   107.43  3.000
 YHO  H1    C1  C5   108.85  3.000
 YHO  H1    C1  N1   107.28  3.000
 YHO  C5    C1  N1   117.39  3.000
 YHO  H1    C1  C2   106.57  3.000
 YHO  N1    C1  C2   113.26  3.000
 YHO  C5    C1  C2   102.97  3.000
 YHO  HN1A  N1  HN1  105.67  3.000
 YHO  HN1A  N1  C1   109.38  3.000
 YHO  HN1   N1  C1   109.30  3.000
 YHO  H5A   C5  H5   107.37  3.000
 YHO  H5A   C5  C4   113.00  3.000
 YHO  H5    C5  C4   109.14  3.000
 YHO  H5A   C5  C1   112.44  3.000
 YHO  H5    C5  C1   109.18  3.000
 YHO  C4    C5  C1   105.65  3.000
 YHO  H4    C4  O4   109.68  3.000
 YHO  H4    C4  C5   110.87  3.000
 YHO  O4    C4  C5   111.58  3.000
 YHO  H4    C4  C3   109.10  3.000
 YHO  O4    C4  C3   110.43  3.000
 YHO  C5    C4  C3   105.08  3.000
 YHO  HO4   O4  C4   108.90  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
 YHO  chir_01  C3  O3  C4  C2  negativ
 YHO  chir_02  C2  O2  C3  C1  negativ
 YHO  chir_03  C1  N1  C5  C2  positiv
 YHO  chir_04  C4  O4  C5  C3  negativ

