# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:32:45 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (1R,2R,3S,4R,5R)-5-aminocyclopentane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@@H](O)[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
 YTB  YTB  (1R,2R,3S,4R,5R)-5-aminocyclopentane-1,2,3,4-tetrol  ligand  21  10  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YTB
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
 YTB  O6    O  OH1   0  -0.674  -2.2485   1.2710  -0.2681
 YTB  C5    C  CH1   0   0.051  -1.0452   0.5608  -0.4420
 YTB  C4    C  CH1   0   0.010   0.2309   1.3266  -0.0479
 YTB  O4    O  OH1   0  -0.688   0.9003   1.8590  -1.1616
 YTB  C3    C  CH1   0  -0.029   1.0993   0.2840   0.7220
 YTB  O3    O  OH1   0  -0.674   2.4344   0.2698   0.2739
 YTB  C1    C  CH1   0  -0.122  -1.0459  -0.6727   0.4548
 YTB  N1    N  NH2   0  -0.804  -1.9340  -1.7097  -0.0260
 YTB  C2    C  CH1   0  -0.005   0.4238  -1.0702   0.4815
 YTB  O2    O  OH1   0  -0.668   0.7823  -1.6152  -0.7637
 YTB  HO6   H  HOH1  0   0.451  -2.3264   1.9220  -0.9715
 YTB  H5    H  HCH1  0   0.206  -0.9323   0.2283  -1.4818
 YTB  H4    H  HCH1  0   0.205  -0.0462   2.1386   0.6376
 YTB  HO4   H  HOH1  0   0.442   1.8166   1.5550  -1.1010
 YTB  H3    H  HCH1  0   0.250   1.0490   0.5064   1.7914
 YTB  HO3   H  HOH1  0   0.472   2.9894   0.7364   0.9053
 YTB  H1    H  HCH1  0   0.217  -1.2876  -0.3370   1.4782
 YTB  HN1   H  HNH2  0   0.345  -1.9529  -2.4749   0.6374
 YTB  HN1A  H  HNH2  0   0.345  -2.8793  -1.3471  -0.0433
 YTB  H2    H  HCH1  0   0.223   0.6413  -1.7746   1.2965
 YTB  HO2   H  HOH1  0   0.448   1.7436  -1.6607  -0.7975

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
 YTB  O6  C5    single  1.408  0.020  1.408
 YTB  O6  HO6   single  0.850  0.020  0.980
 YTB  C4  C5    single  1.540  0.020  1.540
 YTB  C5  C1    single  1.525  0.020  1.525
 YTB  C5  H5    single  0.970  0.020  1.090
 YTB  O4  C4    single  1.404  0.020  1.404
 YTB  C4  C3    single  1.560  0.020  1.560
 YTB  C4  H4    single  0.970  0.020  1.090
 YTB  O4  HO4   single  0.850  0.020  0.980
 YTB  O3  C3    single  1.408  0.020  1.408
 YTB  C3  C2    single  1.532  0.020  1.532
 YTB  C3  H3    single  0.970  0.020  1.090
 YTB  O3  HO3   single  0.850  0.020  0.980
 YTB  C1  C2    single  1.523  0.020  1.523
 YTB  C1  N1    single  1.448  0.020  1.448
 YTB  C1  H1    single  0.970  0.020  1.090
 YTB  N1  HN1   single  0.890  0.020  1.040
 YTB  N1  HN1A  single  0.890  0.020  1.040
 YTB  C2  O2    single  1.406  0.020  1.406
 YTB  C2  H2    single  0.970  0.020  1.090
 YTB  O2  HO2   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
 YTB  HO6   O6  C5   108.69  3.000
 YTB  H5    C5  C1   108.19  3.000
 YTB  H5    C5  C4   107.93  3.000
 YTB  C1    C5  C4   104.60  3.000
 YTB  H5    C5  O6   110.97  3.000
 YTB  C1    C5  O6   109.57  3.000
 YTB  C4    C5  O6   115.20  3.000
 YTB  H4    C4  C3   109.06  3.000
 YTB  H4    C4  O4   109.58  3.000
 YTB  C3    C4  O4   112.30  3.000
 YTB  H4    C4  C5   108.57  3.000
 YTB  C3    C4  C5   104.79  3.000
 YTB  O4    C4  C5   112.38  3.000
 YTB  HO4   O4  C4   106.43  3.000
 YTB  H3    C3  C2   108.24  3.000
 YTB  H3    C3  O3   110.91  3.000
 YTB  C2    C3  O3   111.04  3.000
 YTB  H3    C3  C4   108.73  3.000
 YTB  C2    C3  C4   105.53  3.000
 YTB  O3    C3  C4   112.17  3.000
 YTB  HO3   O3  C3   109.48  3.000
 YTB  H1    C1  C2   105.93  3.000
 YTB  H1    C1  N1   113.04  3.000
 YTB  C2    C1  N1   114.27  3.000
 YTB  H1    C1  C5   107.42  3.000
 YTB  N1    C1  C5   112.60  3.000
 YTB  C2    C1  C5   102.77  3.000
 YTB  HN1A  N1  HN1  105.33  3.000
 YTB  HN1A  N1  C1   108.78  3.000
 YTB  HN1   N1  C1   109.58  3.000
 YTB  H2    C2  O2   110.97  3.000
 YTB  H2    C2  C1   111.80  3.000
 YTB  O2    C2  C1   109.38  3.000
 YTB  H2    C2  C3   111.27  3.000
 YTB  O2    C2  C3   111.67  3.000
 YTB  C1    C2  C3   101.39  3.000
 YTB  HO2   O2  C2   107.70  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
 YTB  chir_01  C5  O6  C4  C1  negativ
 YTB  chir_02  C4  O4  C5  C3  negativ
 YTB  chir_03  C3  O3  C4  C2  negativ
 YTB  chir_04  C1  N1  C2  C5  negativ
 YTB  chir_05  C2  O2  C1  C3  positiv

