# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:36:29 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{[(2E)-2-(4-bromobenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=S)N/N=C/c2ccc(Br)cc2)[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
 16O  16O  N-{[(2E)-2-(4-bromobenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  D-saccharide  42  24  .  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_16O
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
 16O  C1   C   CH1   0   0.226  -3.2032  -0.2225   0.4813
 16O  N1   N   NH1   0  -0.675  -1.9353  -0.8736   0.4836
 16O  S1   S   S1    0  -0.392  -2.9851  -3.3330   0.6963
 16O  BR1  BR  BR    0  -0.033   6.6626   1.3132  -0.3559
 16O  C2   C   CH1   0  -0.029  -3.1222   1.1084   1.2332
 16O  N2   N   NH1   0  -0.480  -0.4866  -2.6291   0.4159
 16O  O2   O   OH1   0  -0.662  -2.8345   0.9172   2.5942
 16O  C3   C   CH1   0  -0.009  -4.4761   1.7988   1.1430
 16O  N3   N   N     0  -0.213   0.5283  -1.7624   0.2884
 16O  O3   O   OH1   0  -0.671  -4.4433   3.0982   1.6817
 16O  C4   C   CH1   0   0.038  -4.9307   1.9172  -0.3073
 16O  O4   O   OH1   0  -0.672  -6.2467   2.4045  -0.3886
 16O  C5   C   CH1   0  -0.013  -4.8841   0.5426  -0.9759
 16O  O5   O   O2    0  -0.484  -3.5845   0.0020  -0.8532
 16O  C6   C   CH2   0  -0.157  -5.2170   0.6231  -2.4503
 16O  O6   O   OH1   0  -0.668  -5.2334  -0.6786  -2.9850
 16O  C7   C   C     0   0.430  -1.7651  -2.2025   0.5193
 16O  C8   C   C1    0  -0.055   1.7074  -2.2317   0.1983
 16O  C9   C   CR6   0   0.065   2.8652  -1.3563   0.0662
 16O  C10  C   CR16  0  -0.296   4.1274  -1.9335  -0.0580
 16O  C11  C   CR16  0  -0.212   5.2634  -1.1489  -0.1845
 16O  C12  C   CR6   0  -0.118   5.1288   0.2306  -0.1850
 16O  C13  C   CR16  0  -0.209   3.8803   0.8312  -0.0610
 16O  C14  C   CR16  0  -0.277   2.7562   0.0363   0.0636
 16O  H1   H   HCH1  0   0.234  -3.9230  -0.8820   0.9814
 16O  HN1  H   HNH1  0   0.417  -1.1112  -0.3158   0.2930
 16O  H2   H   HCH1  0   0.230  -2.3670   1.7431   0.7442
 16O  HN2  H   HNH1  0   0.417  -0.3227  -3.6298   0.4471
 16O  HO2  H   HOH1  0   0.458  -1.9013   0.7056   2.6936
 16O  H3   H   HCH1  0   0.220  -5.2101   1.1736   1.6770
 16O  HO3  H   HOH1  0   0.458  -4.3408   3.0318   2.6362
 16O  H4   H   HCH1  0   0.212  -4.2294   2.5820  -0.8377
 16O  HO4  H   HOH1  0   0.454  -6.2831   3.2431   0.0837
 16O  H5   H   HCH1  0   0.224  -5.6147  -0.1166  -0.4786
 16O  H6   H   HCH2  0   0.214  -6.1886   1.1163  -2.5579
 16O  H6A  H   HCH2  0   0.196  -4.4736   1.2614  -2.9485
 16O  HO6  H   HOH1  0   0.456  -5.5292  -0.6177  -3.8975
 16O  H8   H   H     0   0.261   1.9000  -3.3059   0.2174
 16O  H10  H   HCR6  0   0.273   4.2309  -3.0116  -0.0566
 16O  H11  H   HCR6  0   0.286   6.2331  -1.6180  -0.2809
 16O  H13  H   HCR6  0   0.285   3.7782   1.9079  -0.0605
 16O  H14  H   HCR6  0   0.272   1.7867   0.5061   0.1630

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
 16O  C2   C1   single    1.531  0.020  1.531
 16O  N1   C1   single    1.425  0.020  1.425
 16O  O5   C1   single    1.406  0.020  1.406
 16O  C1   H1   single    0.970  0.020  1.090
 16O  N1   C7   single    1.340  0.020  1.340
 16O  N1   HN1  single    0.860  0.020  1.020
 16O  C7   S1   double    1.673  0.020  1.673
 16O  BR1  C12  single    1.885  0.020  1.885
 16O  C2   C3   single    1.522  0.020  1.522
 16O  C2   O2   single    1.404  0.020  1.404
 16O  C2   H2   single    0.970  0.020  1.090
 16O  N3   N2   single    1.341  0.020  1.341
 16O  N2   C7   single    1.352  0.020  1.352
 16O  N2   HN2  single    0.860  0.020  1.020
 16O  O2   HO2  single    0.850  0.020  0.980
 16O  O3   C3   single    1.407  0.020  1.407
 16O  C4   C3   single    1.524  0.020  1.524
 16O  C3   H3   single    0.970  0.020  1.090
 16O  C8   N3   double    1.272  0.020  1.272
 16O  O3   HO3  single    0.850  0.020  0.980
 16O  C4   O4   single    1.406  0.020  1.406
 16O  C4   C5   single    1.529  0.020  1.529
 16O  C4   H4   single    0.970  0.020  1.090
 16O  O4   HO4  single    0.850  0.020  0.980
 16O  O5   C5   single    1.413  0.020  1.413
 16O  C6   C5   single    1.514  0.020  1.514
 16O  C5   H5   single    0.970  0.020  1.090
 16O  O6   C6   single    1.407  0.020  1.407
 16O  C6   H6   single    0.970  0.020  1.090
 16O  C6   H6A  single    0.970  0.020  1.090
 16O  O6   HO6  single    0.850  0.020  0.980
 16O  C9   C8   single    1.457  0.020  1.457
 16O  C8   H8   single    0.930  0.020  1.080
 16O  C14  C9   aromatic  1.397  0.020  1.397
 16O  C10  C9   aromatic  1.393  0.020  1.393
 16O  C11  C10  aromatic  1.386  0.020  1.386
 16O  C10  H10  single    0.930  0.020  1.080
 16O  C12  C11  aromatic  1.386  0.020  1.386
 16O  C11  H11  single    0.930  0.020  1.080
 16O  C12  C13  aromatic  1.391  0.020  1.391
 16O  C13  C14  aromatic  1.382  0.020  1.382
 16O  C13  H13  single    0.930  0.020  1.080
 16O  C14  H14  single    0.930  0.020  1.080

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
 16O  H1   C1   O5   110.53  3.000
 16O  H1   C1   C2   109.48  3.000
 16O  O5   C1   C2   109.98  3.000
 16O  H1   C1   N1   107.96  3.000
 16O  O5   C1   N1   108.41  3.000
 16O  C2   C1   N1   110.45  3.000
 16O  HN1  N1   C7   116.59  3.000
 16O  HN1  N1   C1   118.14  3.000
 16O  C7   N1   C1   124.47  3.000
 16O  H2   C2   C3   108.80  3.000
 16O  H2   C2   O2   111.61  3.000
 16O  C3   C2   O2   107.54  3.000
 16O  H2   C2   C1   108.63  3.000
 16O  O2   C2   C1   111.62  3.000
 16O  C3   C2   C1   108.55  3.000
 16O  HN2  N2   C7   117.50  3.000
 16O  HN2  N2   N3   121.22  3.000
 16O  C7   N2   N3   121.28  3.000
 16O  HO2  O2   C2   109.21  3.000
 16O  H3   C3   C4   107.84  3.000
 16O  H3   C3   O3   110.73  3.000
 16O  C4   C3   O3   107.42  3.000
 16O  H3   C3   C2   107.83  3.000
 16O  C4   C3   C2   110.90  3.000
 16O  O3   C3   C2   112.05  3.000
 16O  C8   N3   N2   118.03  3.000
 16O  HO3  O3   C3   108.57  3.000
 16O  H4   C4   C5   108.20  3.000
 16O  H4   C4   O4   111.02  3.000
 16O  C5   C4   O4   108.35  3.000
 16O  H4   C4   C3   108.36  3.000
 16O  C5   C4   C3   109.70  3.000
 16O  O4   C4   C3   111.17  3.000
 16O  HO4  O4   C4   107.99  3.000
 16O  H5   C5   C6   108.99  3.000
 16O  H5   C5   O5   109.97  3.000
 16O  C6   C5   O5   107.89  3.000
 16O  H5   C5   C4   108.67  3.000
 16O  C6   C5   C4   111.80  3.000
 16O  O5   C5   C4   109.51  3.000
 16O  C5   O5   C1   113.14  3.000
 16O  H6A  C6   H6   107.10  3.000
 16O  H6A  C6   O6   111.89  3.000
 16O  H6   C6   O6   111.65  3.000
 16O  H6A  C6   C5   108.88  3.000
 16O  H6   C6   C5   108.35  3.000
 16O  O6   C6   C5   108.88  3.000
 16O  HO6  O6   C6   107.80  3.000
 16O  N2   C7   S1   118.99  3.000
 16O  N2   C7   N1   115.53  3.000
 16O  S1   C7   N1   125.48  3.000
 16O  H8   C8   C9   116.91  3.000
 16O  H8   C8   N3   121.69  3.000
 16O  C9   C8   N3   121.40  3.000
 16O  C14  C9   C10  118.91  3.000
 16O  C10  C9   C8   118.61  3.000
 16O  C14  C9   C8   122.48  3.000
 16O  H10  C10  C11  119.02  3.000
 16O  H10  C10  C9   119.92  3.000
 16O  C11  C10  C9   121.06  3.000
 16O  H11  C11  C12  121.25  3.000
 16O  H11  C11  C10  119.83  3.000
 16O  C12  C11  C10  118.93  3.000
 16O  C13  C12  C11  121.12  3.000
 16O  C13  C12  BR1  119.37  3.000
 16O  C11  C12  BR1  119.51  3.000
 16O  H13  C13  C14  119.71  3.000
 16O  H13  C13  C12  120.97  3.000
 16O  C14  C13  C12  119.32  3.000
 16O  H14  C14  C13  119.17  3.000
 16O  H14  C14  C9   120.17  3.000
 16O  C13  C14  C9   120.66  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
 16O  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 16O  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 16O  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 16O  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 16O  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 16O  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 16O  CONST_07  C10  C11  C12  BR1   180.00   0.0  0
 16O  CONST_08  C14  C13  C12  BR1   180.00   0.0  0
 16O  CONST_09  C13  C14  C9   C8    180.00   0.0  0
 16O  CONST_10  C11  C10  C9   C8    180.00   0.0  0
 16O  CONST_11  H13  C13  C14  C9    180.00   0.0  0
 16O  CONST_12  H11  C11  C10  C9    180.00   0.0  0
 16O  CONST_13  H14  C14  C9   C10   180.00   0.0  0
 16O  CONST_14  H10  C10  C11  C12   180.00   0.0  0
 16O  CONST_15  S1   C7   N1   C1      0.00   0.0  0
 16O  CONST_16  N2   C7   N1   C1    180.00   0.0  0
 16O  CONST_17  N3   N2   C7   N1      0.00   0.0  0
 16O  CONST_18  N3   N2   C7   S1    180.00   0.0  0
 16O  CONST_19  HN2  N2   C7   N1    180.00   0.0  0
 16O  CONST_20  HN1  N1   C7   S1    180.00   0.0  0
 16O  Var_01    C14  C9   C8   N3      1.61  30.0  2
 16O  Var_02    C9   C8   N3   N2   -179.59   0.0  2

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
 16O  chir_01  C1  C2  N1  O5  positiv
 16O  chir_02  C2  O2  C1  C3  negativ
 16O  chir_03  C3  O3  C2  C4  positiv
 16O  chir_04  C4  O4  C5  C3  positiv
 16O  chir_05  C5  O5  C4  C6  negativ

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
 16O  plan-1  BR1  0.020
 16O  plan-1  C8   0.020
 16O  plan-1  C9   0.020
 16O  plan-1  C10  0.020
 16O  plan-1  C11  0.020
 16O  plan-1  C12  0.020
 16O  plan-1  C13  0.020
 16O  plan-1  C14  0.020
 16O  plan-1  H10  0.020
 16O  plan-1  H11  0.020
 16O  plan-1  H13  0.020
 16O  plan-1  H14  0.020
 16O  plan-2  C1   0.020
 16O  plan-2  N1   0.020
 16O  plan-2  S1   0.020
 16O  plan-2  N2   0.020
 16O  plan-2  N3   0.020
 16O  plan-2  C7   0.020
 16O  plan-2  HN1  0.020
 16O  plan-2  HN2  0.020
 16O  plan-3  N2   0.020
 16O  plan-3  N3   0.020
 16O  plan-3  C8   0.020
 16O  plan-3  C9   0.020
 16O  plan-3  H8   0.020

