# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:15:26 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 5-thio-alpha-D-mannopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1S[C@H](CO)[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
 LKA  LKA  5-thio-alpha-D-mannopyranosylamine  D-saccharide  25  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LKA
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
 LKA  C5    C  CH1   0  -0.426   1.0555   0.1934   0.5813
 LKA  S0    S  S2    0   0.001   0.3880   1.6378  -0.3034
 LKA  C1    C  CH1   0  -0.271  -1.3766   1.3850   0.0342
 LKA  N1    N  NH2   0  -0.775  -1.6591   1.5385   1.4440
 LKA  C2    C  CH1   0   0.028  -1.8277   0.0006  -0.4470
 LKA  O2    O  OH1   0  -0.659  -1.6634  -0.1504  -1.8305
 LKA  C3    C  CH1   0   0.017  -1.0677  -1.1215   0.2563
 LKA  O3    O  OH1   0  -0.681  -1.5161  -2.3880  -0.1855
 LKA  C4    C  CH1   0   0.097   0.4458  -1.0892   0.0215
 LKA  O4    O  OH1   0  -0.683   1.0498  -2.1742   0.6922
 LKA  C6    C  CH2   0  -0.151   2.5695   0.2477   0.5028
 LKA  O6    O  OH1   0  -0.667   2.9706   0.2108  -0.8458
 LKA  H5    H  HCH1  0   0.278   0.7823   0.2890   1.6362
 LKA  H1    H  HCH1  0   0.267  -1.8705   2.1422  -0.5931
 LKA  HN11  H  HNH2  0   0.358  -1.4316   2.4804   1.7352
 LKA  HN12  H  HNH2  0   0.354  -2.6540   1.4233   1.6033
 LKA  H2    H  HCH1  0   0.227  -2.8917  -0.0982  -0.1707
 LKA  HO2   H  HOH1  0   0.451  -2.1329   0.5623  -2.2755
 LKA  H3    H  HCH1  0   0.227  -1.2373  -1.0081   1.3339
 LKA  HO3   H  HOH1  0   0.458  -2.3016  -2.6296   0.3137
 LKA  H4    H  HCH1  0   0.211   0.6481  -1.1401  -1.0566
 LKA  HO4   H  HOH1  0   0.446   0.5280  -2.9589   0.4886
 LKA  H61   H  HCH2  0   0.214   2.9089   1.1658   1.0000
 LKA  H62   H  HCH2  0   0.223   2.9780  -0.5924   1.0752
 LKA  HO6   H  HOH1  0   0.457   3.9314   0.1931  -0.8721

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
 LKA  C5  S0    single  1.821  0.020  1.821
 LKA  C5  C4    single  1.527  0.020  1.527
 LKA  C5  C6    single  1.517  0.020  1.517
 LKA  C5  H5    single  0.970  0.020  1.090
 LKA  S0  C1    single  1.814  0.020  1.814
 LKA  C1  N1    single  1.446  0.020  1.446
 LKA  C1  C2    single  1.533  0.020  1.533
 LKA  C1  H1    single  0.970  0.020  1.090
 LKA  N1  HN11  single  0.890  0.020  1.040
 LKA  N1  HN12  single  0.890  0.020  1.040
 LKA  C2  O2    single  1.401  0.020  1.401
 LKA  C2  C3    single  1.527  0.020  1.527
 LKA  C2  H2    single  0.970  0.020  1.090
 LKA  O2  HO2   single  0.850  0.020  0.980
 LKA  C3  O3    single  1.414  0.020  1.414
 LKA  C3  C4    single  1.532  0.020  1.532
 LKA  C3  H3    single  0.970  0.020  1.090
 LKA  O3  HO3   single  0.850  0.020  0.980
 LKA  C4  O4    single  1.411  0.020  1.411
 LKA  C4  H4    single  0.970  0.020  1.090
 LKA  O4  HO4   single  0.850  0.020  0.980
 LKA  C6  O6    single  1.408  0.020  1.408
 LKA  C6  H61   single  0.970  0.020  1.090
 LKA  C6  H62   single  0.970  0.020  1.090
 LKA  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
 LKA  H5    C5  C6    107.22  3.000
 LKA  H5    C5  C4    109.10  3.000
 LKA  C6    C5  C4    114.19  3.000
 LKA  H5    C5  S0    107.92  3.000
 LKA  C6    C5  S0    108.20  3.000
 LKA  C4    C5  S0    110.00  3.000
 LKA  C1    S0  C5     98.95  3.000
 LKA  H1    C1  C2    108.08  3.000
 LKA  H1    C1  N1    113.27  3.000
 LKA  C2    C1  N1    110.14  3.000
 LKA  H1    C1  S0    103.57  3.000
 LKA  C2    C1  S0    110.71  3.000
 LKA  N1    C1  S0    110.89  3.000
 LKA  HN12  N1  HN11  106.32  3.000
 LKA  HN12  N1  C1    109.44  3.000
 LKA  HN11  N1  C1    109.61  3.000
 LKA  H2    C2  C3    107.38  3.000
 LKA  H2    C2  O2    110.52  3.000
 LKA  C3    C2  O2    108.50  3.000
 LKA  H2    C2  C1    106.61  3.000
 LKA  C3    C2  C1    111.87  3.000
 LKA  O2    C2  C1    111.87  3.000
 LKA  HO2   O2  C2    108.63  3.000
 LKA  H3    C3  C4    107.53  3.000
 LKA  H3    C3  O3    110.52  3.000
 LKA  C4    C3  O3    106.51  3.000
 LKA  H3    C3  C2    107.44  3.000
 LKA  C4    C3  C2    113.94  3.000
 LKA  O3    C3  C2    110.88  3.000
 LKA  HO3   O3  C3    108.77  3.000
 LKA  H4    C4  O4    110.62  3.000
 LKA  H4    C4  C3    109.36  3.000
 LKA  O4    C4  C3    109.50  3.000
 LKA  H4    C4  C5    108.99  3.000
 LKA  O4    C4  C5    107.51  3.000
 LKA  C3    C4  C5    110.86  3.000
 LKA  HO4   O4  C4    107.08  3.000
 LKA  H62   C6  H61   106.82  3.000
 LKA  H62   C6  O6    111.98  3.000
 LKA  H61   C6  O6    111.58  3.000
 LKA  H62   C6  C5    108.52  3.000
 LKA  H61   C6  C5    108.36  3.000
 LKA  O6    C6  C5    109.45  3.000
 LKA  HO6   O6  C6    108.15  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
 LKA  chir_01  C5  S0  C4  C6  negativ
 LKA  chir_02  C1  S0  N1  C2  positiv
 LKA  chir_03  C2  O2  C1  C3  positiv
 LKA  chir_04  C3  O3  C2  C4  positiv
 LKA  chir_05  C4  O4  C5  C3  positiv

