# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 15:11:47 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: N-[(1Z)-2-phenylethanimidoyl]-5-thio-alpha-D-mannopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1S[C@H](NC(=N)Cc2ccccc2)[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
 LKS  LKS  N-[(1Z)-2-phenylethanimidoyl]-5-thio-alpha-D-mannopyranosylamine  D-saccharide  41  21  .  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_LKS
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
 LKS  C5   C  CH1   0  -0.463  -0.3365  -1.5955   1.7029
 LKS  S1   S  S2    0   0.032  -0.6897  -2.7499   0.3341
 LKS  C1   C  CH1   0  -0.313   0.8750  -3.6517   0.2765
 LKS  N1   N  NH1   0  -0.609   1.0246  -4.5035   1.4281
 LKS  C2   C  CH1   0   0.020   2.0660  -2.6919   0.1074
 LKS  O2   O  OH1   0  -0.662   1.9823  -1.9807  -1.1003
 LKS  C3   C  CH1   0  -0.003   2.1626  -1.6729   1.2393
 LKS  O3   O  OH1   0  -0.663   3.3053  -0.8627   1.0756
 LKS  C4   C  CH1   0   0.096   0.9181  -0.7878   1.3925
 LKS  O4   O  OH1   0  -0.673   1.1134   0.1138   2.4575
 LKS  C6   C  CH2   0  -0.143  -1.5655  -0.6986   1.8626
 LKS  O6   O  OH1   0  -0.661  -2.7259  -1.4056   2.2216
 LKS  C7   C  C     0   0.414   1.9486  -5.5121   1.5047
 LKS  C8   C  CH2   0  -0.599   2.3108  -5.8798   2.9256
 LKS  C9   C  CR6   0   0.092   2.9480  -4.6933   3.6049
 LKS  C10  C  CR16  0  -0.273   4.2004  -4.2449   3.1876
 LKS  C11  C  CR16  0  -0.233   4.7584  -3.0989   3.7332
 LKS  C14  C  CR16  0  -0.327   2.2730  -3.9760   4.5878
 LKS  C13  C  CR16  0  -0.237   2.8296  -2.8256   5.1359
 LKS  C12  C  CR16  0  -0.262   4.0721  -2.3827   4.7071
 LKS  N2   N  N     0  -0.649   2.5155  -6.1175   0.5365
 LKS  H5   H  HCH1  0   0.269  -0.2005  -2.1585   2.6339
 LKS  H1   H  HCH1  0   0.308   0.7926  -4.2710  -0.6221
 LKS  HN1  H  HNH1  0   0.396   0.7235  -4.1134   2.3068
 LKS  H2   H  HCH1  0   0.250   2.9813  -3.3005   0.1376
 LKS  HO2  H  HOH1  0   0.464   2.2479  -2.5554  -1.8246
 LKS  H3   H  HCH1  0   0.253   2.3184  -2.2115   2.1805
 LKS  HO3  H  HOH1  0   0.445   3.2847  -0.4967   0.1825
 LKS  H4   H  HCH1  0   0.210   0.7421  -0.2443   0.4508
 LKS  HO4  H  HOH1  0   0.448   2.0004   0.4802   2.3641
 LKS  H61  H  HCH2  0   0.212  -1.7028  -0.1141   0.9427
 LKS  H62  H  HCH2  0   0.251  -1.3724   0.0088   2.6685
 LKS  HO6  H  HOH1  0   0.451  -3.0329  -1.9199   1.4690
 LKS  H81  H  HCH2  0   0.282   1.4169  -6.1940   3.4705
 LKS  H82  H  HCH2  0   0.277   2.9930  -6.7282   2.8909
 LKS  H10  H  HCR6  0   0.251   4.7359  -4.7924   2.4206
 LKS  H11  H  HCR6  0   0.255   5.7294  -2.7610   3.3951
 LKS  H14  H  HCR6  0   0.258   1.3004  -4.3150   4.9266
 LKS  H13  H  HCR6  0   0.256   2.2881  -2.2762   5.8950
 LKS  H12  H  HCR6  0   0.255   4.5053  -1.4847   5.1282
 LKS  HN2  H  H     0   0.325   2.2061  -5.7856  -0.3729

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
 LKS  C5   S1   single    1.825  0.020  1.825
 LKS  C5   C4   single    1.524  0.020  1.524
 LKS  C5   C6   single    1.530  0.020  1.530
 LKS  C5   H5   single    0.970  0.020  1.090
 LKS  S1   C1   single    1.807  0.020  1.807
 LKS  C1   N1   single    1.440  0.020  1.440
 LKS  C1   C2   single    1.539  0.020  1.539
 LKS  C1   H1   single    0.970  0.020  1.090
 LKS  N1   C7   single    1.370  0.020  1.370
 LKS  N1   HN1  single    0.890  0.020  1.040
 LKS  C2   O2   single    1.404  0.020  1.404
 LKS  C2   C3   single    1.526  0.020  1.526
 LKS  C2   H2   single    0.970  0.020  1.090
 LKS  O2   HO2  single    0.850  0.020  0.980
 LKS  C3   O3   single    1.410  0.020  1.410
 LKS  C3   C4   single    1.535  0.020  1.535
 LKS  C3   H3   single    0.970  0.020  1.090
 LKS  O3   HO3  single    0.850  0.020  0.980
 LKS  C4   O4   single    1.409  0.020  1.409
 LKS  C4   H4   single    0.970  0.020  1.090
 LKS  O4   HO4  single    0.850  0.020  0.980
 LKS  C6   O6   single    1.405  0.020  1.405
 LKS  C6   H61  single    0.970  0.020  1.090
 LKS  C6   H62  single    0.970  0.020  1.090
 LKS  O6   HO6  single    0.850  0.020  0.980
 LKS  C7   C8   single    1.512  0.020  1.512
 LKS  C7   N2   double    1.275  0.020  1.275
 LKS  C8   C9   single    1.508  0.020  1.508
 LKS  C8   H81  single    0.970  0.020  1.090
 LKS  C8   H82  single    0.970  0.020  1.090
 LKS  C9   C10  aromatic  1.394  0.020  1.394
 LKS  C9   C14  aromatic  1.392  0.020  1.392
 LKS  C10  C11  aromatic  1.387  0.020  1.387
 LKS  C10  H10  single    0.930  0.020  1.080
 LKS  C11  C12  aromatic  1.390  0.020  1.390
 LKS  C11  H11  single    0.930  0.020  1.080
 LKS  C14  C13  aromatic  1.391  0.020  1.391
 LKS  C14  H14  single    0.930  0.020  1.080
 LKS  C13  C12  aromatic  1.387  0.020  1.387
 LKS  C13  H13  single    0.930  0.020  1.080
 LKS  C12  H12  single    0.930  0.020  1.080
 LKS  HN2  N2   single    0.890  0.020  1.040

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
 LKS  H5   C5   C6   108.18  3.000
 LKS  H5   C5   C4   110.06  3.000
 LKS  C6   C5   C4   111.84  3.000
 LKS  H5   C5   S1   109.63  3.000
 LKS  C6   C5   S1   107.07  3.000
 LKS  C4   C5   S1   109.99  3.000
 LKS  C1   S1   C5    99.90  3.000
 LKS  H1   C1   C2   108.72  3.000
 LKS  H1   C1   N1   109.24  3.000
 LKS  C2   C1   N1   112.11  3.000
 LKS  H1   C1   S1   104.09  3.000
 LKS  C2   C1   S1   111.25  3.000
 LKS  N1   C1   S1   111.08  3.000
 LKS  HN1  N1   C7   115.96  3.000
 LKS  HN1  N1   C1   115.94  3.000
 LKS  C7   N1   C1   123.39  3.000
 LKS  H2   C2   C3   107.25  3.000
 LKS  H2   C2   O2   110.71  3.000
 LKS  C3   C2   O2   107.67  3.000
 LKS  H2   C2   C1   107.22  3.000
 LKS  C3   C2   C1   112.58  3.000
 LKS  O2   C2   C1   111.36  3.000
 LKS  HO2  O2   C2   109.18  3.000
 LKS  H3   C3   C4   108.24  3.000
 LKS  H3   C3   O3   105.48  3.000
 LKS  C4   C3   O3   109.72  3.000
 LKS  H3   C3   C2   108.53  3.000
 LKS  C4   C3   C2   114.06  3.000
 LKS  O3   C3   C2   110.41  3.000
 LKS  HO3  O3   C3   107.93  3.000
 LKS  H4   C4   O4   110.65  3.000
 LKS  H4   C4   C3   109.19  3.000
 LKS  O4   C4   C3   109.40  3.000
 LKS  H4   C4   C5   107.71  3.000
 LKS  O4   C4   C5   107.41  3.000
 LKS  C3   C4   C5   112.47  3.000
 LKS  HO4  O4   C4   107.30  3.000
 LKS  H62  C6   H61  107.23  3.000
 LKS  H62  C6   O6   106.50  3.000
 LKS  H61  C6   O6   112.23  3.000
 LKS  H62  C6   C5   108.38  3.000
 LKS  H61  C6   C5   108.96  3.000
 LKS  O6   C6   C5   113.27  3.000
 LKS  HO6  O6   C6   109.43  3.000
 LKS  N2   C7   C8   119.46  3.000
 LKS  N2   C7   N1   127.37  3.000
 LKS  C8   C7   N1   113.16  3.000
 LKS  H82  C8   H81  107.71  3.000
 LKS  H82  C8   C9   111.25  3.000
 LKS  H81  C8   C9   110.31  3.000
 LKS  H82  C8   C7   108.03  3.000
 LKS  H81  C8   C7   110.03  3.000
 LKS  C9   C8   C7   109.46  3.000
 LKS  C14  C9   C10  118.78  3.000
 LKS  C14  C9   C8   121.24  3.000
 LKS  C10  C9   C8   119.85  3.000
 LKS  H10  C10  C11  119.81  3.000
 LKS  H10  C10  C9   119.55  3.000
 LKS  C11  C10  C9   120.63  3.000
 LKS  H11  C11  C12  120.07  3.000
 LKS  H11  C11  C10  119.74  3.000
 LKS  C12  C11  C10  120.19  3.000
 LKS  H14  C14  C13  119.64  3.000
 LKS  H14  C14  C9   119.65  3.000
 LKS  C13  C14  C9   120.71  3.000
 LKS  H13  C13  C12  120.19  3.000
 LKS  H13  C13  C14  119.75  3.000
 LKS  C12  C13  C14  120.06  3.000
 LKS  H12  C12  C13  120.21  3.000
 LKS  H12  C12  C11  120.16  3.000
 LKS  C13  C12  C11  119.63  3.000
 LKS  HN2  N2   C7   112.90  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 LKS  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 LKS  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 LKS  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 LKS  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 LKS  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 LKS  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 LKS  CONST_07  C11  C10  C9   C8   180.00   0.0  0
 LKS  CONST_08  C13  C14  C9   C8   180.00   0.0  0
 LKS  CONST_09  H11  C11  C10  C9   180.00   0.0  0
 LKS  CONST_10  H13  C13  C14  C9   180.00   0.0  0
 LKS  CONST_11  H14  C14  C9   C10  180.00   0.0  0
 LKS  CONST_12  H12  C12  C11  C10  180.00   0.0  0
 LKS  CONST_13  H10  C10  C9   C14  180.00   0.0  0
 LKS  CONST_16  HN2  N2   C7   N1     0.00   0.0  0
 LKS  CONST_17  HN1  N1   C7   C8     0.00   0.0  0
 LKS  Var_01    C10  C9   C8   C7   -67.71  30.0  2
 LKS  Var_02    C9   C8   C7   N1   -62.52  30.0  3

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
 LKS  chir_01  C5  S1  C4  C6  negativ
 LKS  chir_02  C1  S1  N1  C2  positiv
 LKS  chir_03  C2  O2  C1  C3  positiv
 LKS  chir_04  C3  O3  C2  C4  positiv
 LKS  chir_05  C4  O4  C5  C3  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 LKS  plan-1  C8   0.020
 LKS  plan-1  C9   0.020
 LKS  plan-1  C10  0.020
 LKS  plan-1  C11  0.020
 LKS  plan-1  C14  0.020
 LKS  plan-1  C13  0.020
 LKS  plan-1  C12  0.020
 LKS  plan-1  H10  0.020
 LKS  plan-1  H11  0.020
 LKS  plan-1  H14  0.020
 LKS  plan-1  H13  0.020
 LKS  plan-1  H12  0.020
 LKS  plan-2  C1   0.020
 LKS  plan-2  N1   0.020
 LKS  plan-2  C7   0.020
 LKS  plan-2  C8   0.020
 LKS  plan-2  N2   0.020
 LKS  plan-2  HN1  0.020
 LKS  plan-2  HN2  0.020

