# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:32:26 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-{[(2E)-2-(3-chlorobenzylidene)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/c2cccc(Cl)c2)[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
 23V  23V  N-{[(2E)-2-(3-chlorobenzylidene)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 OK
;

data_comp_23V
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
 23V  C1   C   CH1   0   0.223  -2.4174  -0.2044   0.5583
 23V  N1   N   NH1   0  -0.674  -1.0394  -0.5635   0.6305
 23V  S1   S   S1    0  -0.391  -1.5310  -3.0726   1.4455
 23V  CL1  CL  CL    0  -0.121   7.6760   0.1476  -0.5344
 23V  C2   C   CH1   0  -0.027  -2.6270   1.2295   1.0499
 23V  N2   N   NH1   0  -0.479   0.7515  -1.9512   0.8551
 23V  O2   O   OH1   0  -0.662  -2.3088   1.3591   2.4113
 23V  C3   C   CH1   0  -0.006  -4.0970   1.5912   0.8817
 23V  N3   N   N     0  -0.214   1.5471  -0.9568   0.4383
 23V  O3   O   OH1   0  -0.668  -4.3120  -1.7167  -2.6920
 23V  C4   C   CH1   0   0.035  -4.5554   1.3412  -0.5507
 23V  O4   O   OH1   0  -0.671  -5.9446   1.5164  -0.6768
 23V  C5   C   CH1   0  -0.012  -4.2145  -0.0926  -0.9588
 23V  O5   O   O2    0  -0.485  -2.8316  -0.3204  -0.7798
 23V  C6   C   CH2   0  -0.157  -4.5454  -0.3576  -2.4123
 23V  O6   O   OH1   0  -0.671  -4.3437   2.9445   1.1755
 23V  C7   C   C     0   0.430  -0.5877  -1.7851   0.9454
 23V  C8   C   C1    0  -0.051   2.7995  -1.1708   0.3809
 23V  C9   C   CR6   0   0.057   3.7217  -0.1344  -0.0718
 23V  C10  C   CR16  0  -0.262   5.0830  -0.4317  -0.0909
 23V  C11  C   CR6   0  -0.023   5.9862   0.5292  -0.5148
 23V  C12  C   CR16  0  -0.217   5.5654   1.7843  -0.9218
 23V  C13  C   CR16  0  -0.243   4.2054   2.0730  -0.8997
 23V  C14  C   CR16  0  -0.275   3.2866   1.1284  -0.4809
 23V  H1   H   HCH1  0   0.235  -2.9772  -0.8955   1.2005
 23V  HN1  H   HNH1  0   0.419  -0.3536   0.0973   0.2843
 23V  H2   H   HCH1  0   0.229  -2.0237   1.9085   0.4277
 23V  HN2  H   HNH1  0   0.417   1.1312  -2.8565   1.1101
 23V  HO2  H   HOH1  0   0.458  -1.3519   1.3519   2.5128
 23V  H3   H   HCH1  0   0.219  -4.6858   0.9347   1.5421
 23V  HO3  H   HOH1  0   0.456  -4.5568  -1.8762  -3.6078
 23V  H4   H   HCH1  0   0.213  -4.0087   2.0288  -1.2160
 23V  HO4  H   HOH1  0   0.455  -6.1565   2.4207  -0.4230
 23V  H5   H   HCH1  0   0.224  -4.7938  -0.7852  -0.3262
 23V  H6   H   HCH2  0   0.197  -3.9307   0.3009  -3.0415
 23V  H6A  H   HCH2  0   0.213  -5.5909  -0.0815  -2.5822
 23V  HO6  H   HOH1  0   0.458  -4.2515   3.0750   2.1244
 23V  H8   H   H     0   0.263   3.2335  -2.1302   0.6675
 23V  H10  H   HCR6  0   0.283   5.4323  -1.4062   0.2257
 23V  H12  H   HCR6  0   0.286   6.2801   2.5262  -1.2510
 23V  H13  H   HCR6  0   0.275   3.8674   3.0499  -1.2181
 23V  H14  H   HCR6  0   0.268   2.2318   1.3674  -0.4722

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
 23V  O5   C1   single    1.406  0.020  1.406
 23V  C2   C1   single    1.530  0.020  1.530
 23V  N1   C1   single    1.426  0.020  1.426
 23V  C1   H1   single    0.970  0.020  1.090
 23V  N1   C7   single    1.340  0.020  1.340
 23V  N1   HN1  single    0.860  0.020  1.020
 23V  C7   S1   double    1.673  0.020  1.673
 23V  CL1  C11  single    1.732  0.020  1.732
 23V  C2   C3   single    1.523  0.020  1.523
 23V  C2   O2   single    1.404  0.020  1.404
 23V  C2   H2   single    0.970  0.020  1.090
 23V  N3   N2   single    1.340  0.020  1.340
 23V  N2   C7   single    1.352  0.020  1.352
 23V  N2   HN2  single    0.860  0.020  1.020
 23V  O2   HO2  single    0.850  0.020  0.980
 23V  O6   C3   single    1.407  0.020  1.407
 23V  C4   C3   single    1.525  0.020  1.525
 23V  C3   H3   single    0.970  0.020  1.090
 23V  C8   N3   double    1.272  0.020  1.272
 23V  O3   C6   single    1.407  0.020  1.407
 23V  O3   HO3  single    0.850  0.020  0.980
 23V  C4   O4   single    1.406  0.020  1.406
 23V  C4   C5   single    1.529  0.020  1.529
 23V  C4   H4   single    0.970  0.020  1.090
 23V  O4   HO4  single    0.850  0.020  0.980
 23V  C6   C5   single    1.514  0.020  1.514
 23V  O5   C5   single    1.413  0.020  1.413
 23V  C5   H5   single    0.970  0.020  1.090
 23V  C6   H6   single    0.970  0.020  1.090
 23V  C6   H6A  single    0.970  0.020  1.090
 23V  O6   HO6  single    0.850  0.020  0.980
 23V  C9   C8   single    1.459  0.020  1.459
 23V  C8   H8   single    0.930  0.020  1.080
 23V  C10  C9   aromatic  1.394  0.020  1.394
 23V  C14  C9   aromatic  1.397  0.020  1.397
 23V  C11  C10  aromatic  1.385  0.020  1.385
 23V  C10  H10  single    0.930  0.020  1.080
 23V  C12  C11  aromatic  1.385  0.020  1.385
 23V  C12  C13  aromatic  1.391  0.020  1.391
 23V  C12  H12  single    0.930  0.020  1.080
 23V  C13  C14  aromatic  1.383  0.020  1.383
 23V  C13  H13  single    0.930  0.020  1.080
 23V  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
 23V  H1   C1   O5   110.80  3.000
 23V  H1   C1   C2   109.41  3.000
 23V  O5   C1   C2   110.05  3.000
 23V  H1   C1   N1   107.75  3.000
 23V  C2   C1   N1   110.62  3.000
 23V  O5   C1   N1   108.19  3.000
 23V  HN1  N1   C7   116.53  3.000
 23V  HN1  N1   C1   118.19  3.000
 23V  C7   N1   C1   124.57  3.000
 23V  H2   C2   C3   108.66  3.000
 23V  H2   C2   O2   111.52  3.000
 23V  C3   C2   O2   107.69  3.000
 23V  H2   C2   C1   108.75  3.000
 23V  O2   C2   C1   111.52  3.000
 23V  C3   C2   C1   108.61  3.000
 23V  HN2  N2   C7   117.61  3.000
 23V  HN2  N2   N3   121.22  3.000
 23V  C7   N2   N3   121.17  3.000
 23V  HO2  O2   C2   109.07  3.000
 23V  H3   C3   O6   110.75  3.000
 23V  H3   C3   C4   107.74  3.000
 23V  O6   C3   C4   107.53  3.000
 23V  H3   C3   C2   107.95  3.000
 23V  C4   C3   C2   110.79  3.000
 23V  O6   C3   C2   112.00  3.000
 23V  C8   N3   N2   118.28  3.000
 23V  HO3  O3   C6   107.91  3.000
 23V  H4   C4   C5   108.26  3.000
 23V  H4   C4   O4   111.00  3.000
 23V  C5   C4   O4   108.25  3.000
 23V  H4   C4   C3   108.40  3.000
 23V  C5   C4   C3   109.72  3.000
 23V  O4   C4   C3   111.16  3.000
 23V  HO4  O4   C4   108.11  3.000
 23V  H5   C5   C6   109.03  3.000
 23V  H5   C5   O5   109.90  3.000
 23V  C6   C5   O5   107.90  3.000
 23V  H5   C5   C4   108.59  3.000
 23V  O5   C5   C4   109.60  3.000
 23V  C6   C5   C4   111.81  3.000
 23V  C5   O5   C1   113.31  3.000
 23V  H6A  C6   H6   107.11  3.000
 23V  H6A  C6   C5   108.28  3.000
 23V  H6   C6   C5   108.82  3.000
 23V  H6A  C6   O3   111.79  3.000
 23V  H6   C6   O3   111.85  3.000
 23V  C5   C6   O3   108.88  3.000
 23V  HO6  O6   C3   108.64  3.000
 23V  N2   C7   S1   118.94  3.000
 23V  N2   C7   N1   115.47  3.000
 23V  S1   C7   N1   125.58  3.000
 23V  H8   C8   C9   117.03  3.000
 23V  H8   C8   N3   121.85  3.000
 23V  C9   C8   N3   121.12  3.000
 23V  C14  C9   C10  119.55  3.000
 23V  C14  C9   C8   122.42  3.000
 23V  C10  C9   C8   118.04  3.000
 23V  H10  C10  C11  120.23  3.000
 23V  H10  C10  C9   120.22  3.000
 23V  C11  C10  C9   119.55  3.000
 23V  C12  C11  C10  121.36  3.000
 23V  C12  C11  CL1  119.52  3.000
 23V  C10  C11  CL1  119.12  3.000
 23V  H12  C12  C13  120.58  3.000
 23V  H12  C12  C11  120.69  3.000
 23V  C13  C12  C11  118.73  3.000
 23V  H13  C13  C14  119.90  3.000
 23V  H13  C13  C12  119.24  3.000
 23V  C14  C13  C12  120.85  3.000
 23V  H14  C14  C13  119.96  3.000
 23V  H14  C14  C9   120.08  3.000
 23V  C13  C14  C9   119.96  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
 23V  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 23V  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 23V  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 23V  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 23V  CONST_05  C14  C9   C10  C11    0.00   0.0  0
 23V  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 23V  CONST_07  C9   C10  C11  CL1  180.00   0.0  0
 23V  CONST_08  C13  C12  C11  CL1  180.00   0.0  0
 23V  CONST_09  C11  C10  C9   C8   180.00   0.0  0
 23V  CONST_10  C13  C14  C9   C8   180.00   0.0  0
 23V  CONST_11  H13  C13  C14  C9   180.00   0.0  0
 23V  CONST_12  H14  C14  C9   C10  180.00   0.0  0
 23V  CONST_13  H12  C12  C11  C10  180.00   0.0  0
 23V  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 23V  CONST_15  S1   C7   N1   C1     0.00   0.0  0
 23V  CONST_16  N2   C7   N1   C1   180.00   0.0  0
 23V  CONST_17  N3   N2   C7   N1     0.00   0.0  0
 23V  CONST_18  N3   N2   C7   S1   180.00   0.0  0
 23V  CONST_19  HN2  N2   C7   N1   180.00   0.0  0
 23V  CONST_20  HN1  N1   C7   S1   180.00   0.0  0
 23V  Var_01    C10  C9   C8   N3   179.08  30.0  2
 23V  Var_02    C9   C8   N3   N2   179.62   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
 23V  chir_01  C1  O5  C2  N1  positiv
 23V  chir_02  C2  O2  C1  C3  negativ
 23V  chir_03  C3  O6  C2  C4  positiv
 23V  chir_04  C4  O4  C5  C3  positiv
 23V  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
 23V  plan-1  CL1  0.020
 23V  plan-1  C8   0.020
 23V  plan-1  C9   0.020
 23V  plan-1  C10  0.020
 23V  plan-1  C11  0.020
 23V  plan-1  C12  0.020
 23V  plan-1  C13  0.020
 23V  plan-1  C14  0.020
 23V  plan-1  H10  0.020
 23V  plan-1  H12  0.020
 23V  plan-1  H13  0.020
 23V  plan-1  H14  0.020
 23V  plan-2  C1   0.020
 23V  plan-2  N1   0.020
 23V  plan-2  S1   0.020
 23V  plan-2  N2   0.020
 23V  plan-2  N3   0.020
 23V  plan-2  C7   0.020
 23V  plan-2  HN1  0.020
 23V  plan-2  HN2  0.020
 23V  plan-3  N2   0.020
 23V  plan-3  N3   0.020
 23V  plan-3  C8   0.020
 23V  plan-3  C9   0.020
 23V  plan-3  H8   0.020

