# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:14:26 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-{[(2Z)-2-(2-nitrobenzylidene)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/c2ccccc2[N+]([O-])=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
 24S  24S  N-{[(2Z)-2-(2-nitrobenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  D-saccharide  44  26  .  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_24S
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
 24S  C1    C  CH1    0   0.227   2.3901  -0.3084   0.3467
 24S  C2    C  CH1    0  -0.032   2.9835  -1.6797   0.0151
 24S  O2    O  OH1    0  -0.662   2.5065  -2.6742   0.8852
 24S  C3    C  CH1    0  -0.004   4.4958  -1.6109   0.1841
 24S  O3    O  OH1    0  -0.671   5.1279  -2.7876  -0.2570
 24S  C4    C  CH1    0   0.035   5.0831  -0.4504  -0.6117
 24S  O4    O  OH1    0  -0.671   6.4487  -0.2782  -0.3263
 24S  C5    C  CH1    0  -0.012   4.3516   0.8434  -0.2525
 24S  O5    O  O2     0  -0.484   2.9662   0.6767  -0.4738
 24S  C6    C  CH2    0  -0.158   4.8198   2.0113  -1.0940
 24S  O6    O  OH1    0  -0.668   4.1866   3.1818  -0.6368
 24S  NAL   N  NH1    0  -0.674   0.9816  -0.3088   0.1226
 24S  CAM   C  C      0   0.432   0.1018   0.4081   0.8324
 24S  NAN   N  NH1    0  -0.489  -1.1810   0.3540   0.4022
 24S  SAO   S  S1     0  -0.391   0.4624   1.3291   2.1803
 24S  NAP   N  N      0  -0.184  -1.5186  -0.4048  -0.6557
 24S  CAQ   C  C1     0  -0.049  -2.7241  -0.4421  -1.0517
 24S  CAR   C  CR6    0  -0.050  -3.8389   0.3908  -0.5428
 24S  CAS   C  CR6    0   0.245  -5.0184  -0.1178   0.0038
 24S  CAT   C  CR16   0  -0.268  -6.0621   0.7049   0.3971
 24S  CAU   C  CR16   0  -0.251  -5.9344   2.0761   0.2545
 24S  CAV   C  CR16   0  -0.215  -4.7766   2.6091  -0.2909
 24S  CAW   C  CR16   0  -0.268  -3.7449   1.7725  -0.6903
 24S  NAX   N  N      1   0.333  -5.1712  -1.5516   0.2009
 24S  OAY   O  O      0  -0.371  -4.1716  -2.2312   0.2014
 24S  OAZ   O  O     -1  -0.366  -6.2854  -1.9867   0.3604
 24S  H1    H  HCH1   0   0.234   2.5655  -0.0797   1.4053
 24S  H2    H  HCH1   0   0.231   2.7560  -1.9179  -1.0355
 24S  HO2   H  HOH1   0   0.458   1.6032  -2.9005   0.6436
 24S  H3    H  HCH1   0   0.218   4.7085  -1.4291   1.2500
 24S  HO3   H  HOH1   0   0.457   4.9127  -3.5000   0.3532
 24S  H4    H  HCH1   0   0.214   4.9253  -0.6477  -1.6842
 24S  HO4   H  HOH1   0   0.455   6.9114  -1.0840  -0.5782
 24S  H5    H  HCH1   0   0.224   4.5381   1.0696   0.8103
 24S  H6    H  HCH2   0   0.211   5.9096   2.0814  -1.0119
 24S  H6A   H  HCH2   0   0.198   4.5889   1.8064  -2.1486
 24S  HO6   H  HOH1   0   0.456   4.4767   3.9104  -1.1922
 24S  HNAL  H  HNH1   0   0.418   0.6299  -0.7636  -0.7117
 24S  HNAN  H  HNH1   0   0.417  -1.8693   0.8610   0.9469
 24S  HAQ   H  H      0   0.296  -2.9159  -1.0994  -1.8918
 24S  HAT   H  HCR6   0   0.306  -6.9620   0.2887   0.8254
 24S  HAU   H  HCR6   0   0.287  -6.7406   2.7228   0.5712
 24S  HAV   H  HCR6   0   0.287  -4.6738   3.6785  -0.4137
 24S  HAW   H  HCR6   0   0.298  -2.8578   2.1990  -1.1406

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
 24S  C1   C2    single    1.530  0.020  1.530
 24S  C1   O5    single    1.405  0.020  1.405
 24S  C2   C3    single    1.523  0.020  1.523
 24S  O2   C2    single    1.405  0.020  1.405
 24S  C3   O3    single    1.407  0.020  1.407
 24S  C3   C4    single    1.525  0.020  1.525
 24S  C4   O4    single    1.406  0.020  1.406
 24S  C5   C4    single    1.529  0.020  1.529
 24S  C5   C6    single    1.514  0.020  1.514
 24S  O5   C5    single    1.413  0.020  1.413
 24S  O6   C6    single    1.407  0.020  1.407
 24S  NAL  C1    single    1.426  0.020  1.426
 24S  CAM  NAL   single    1.339  0.020  1.339
 24S  CAM  SAO   double    1.672  0.020  1.672
 24S  NAN  CAM   single    1.354  0.020  1.354
 24S  NAP  NAN   single    1.345  0.020  1.345
 24S  CAQ  NAP   double    1.269  0.020  1.269
 24S  CAR  CAQ   single    1.482  0.020  1.482
 24S  CAR  CAS   aromatic  1.396  0.020  1.396
 24S  CAS  NAX   single    1.455  0.020  1.455
 24S  CAT  CAS   aromatic  1.386  0.020  1.386
 24S  CAU  CAT   aromatic  1.385  0.020  1.385
 24S  CAV  CAU   aromatic  1.386  0.020  1.386
 24S  CAV  CAW   aromatic  1.387  0.020  1.387
 24S  CAW  CAR   aromatic  1.393  0.020  1.393
 24S  NAX  OAZ   single    1.207  0.020  1.207
 24S  NAX  OAY   double    1.209  0.020  1.209
 24S  C1   H1    single    0.970  0.020  1.090
 24S  C2   H2    single    0.970  0.020  1.090
 24S  O2   HO2   single    0.850  0.020  0.980
 24S  C3   H3    single    0.970  0.020  1.090
 24S  O3   HO3   single    0.850  0.020  0.980
 24S  C4   H4    single    0.970  0.020  1.090
 24S  O4   HO4   single    0.850  0.020  0.980
 24S  C5   H5    single    0.970  0.020  1.090
 24S  C6   H6    single    0.970  0.020  1.090
 24S  C6   H6A   single    0.970  0.020  1.090
 24S  O6   HO6   single    0.850  0.020  0.980
 24S  NAL  HNAL  single    0.860  0.020  1.020
 24S  NAN  HNAN  single    0.860  0.020  1.020
 24S  CAQ  HAQ   single    0.930  0.020  1.080
 24S  CAT  HAT   single    0.930  0.020  1.080
 24S  CAU  HAU   single    0.930  0.020  1.080
 24S  CAV  HAV   single    0.930  0.020  1.080
 24S  CAW  HAW   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
 24S  H1    C1   NAL  108.03  3.000
 24S  H1    C1   O5   110.58  3.000
 24S  NAL   C1   O5   108.26  3.000
 24S  H1    C1   C2   109.51  3.000
 24S  NAL   C1   C2   110.40  3.000
 24S  O5    C1   C2   110.03  3.000
 24S  H2    C2   C3   108.71  3.000
 24S  H2    C2   O2   111.57  3.000
 24S  C3    C2   O2   107.47  3.000
 24S  H2    C2   C1   108.70  3.000
 24S  O2    C2   C1   111.62  3.000
 24S  C3    C2   C1   108.69  3.000
 24S  HO2   O2   C2   109.25  3.000
 24S  H3    C3   C4   107.75  3.000
 24S  H3    C3   O3   110.77  3.000
 24S  C4    C3   O3   107.45  3.000
 24S  H3    C3   C2   107.84  3.000
 24S  C4    C3   C2   111.03  3.000
 24S  O3    C3   C2   111.94  3.000
 24S  HO3   O3   C3   108.66  3.000
 24S  H4    C4   C5   108.16  3.000
 24S  H4    C4   O4   111.02  3.000
 24S  C5    C4   O4   108.26  3.000
 24S  H4    C4   C3   108.45  3.000
 24S  C5    C4   C3   109.70  3.000
 24S  O4    C4   C3   111.19  3.000
 24S  HO4   O4   C4   108.13  3.000
 24S  H5    C5   C6   108.99  3.000
 24S  H5    C5   O5   109.94  3.000
 24S  C6    C5   O5   107.89  3.000
 24S  H5    C5   C4   108.61  3.000
 24S  O5    C5   C4   109.42  3.000
 24S  C6    C5   C4   111.98  3.000
 24S  C5    O5   C1   113.15  3.000
 24S  H6A   C6   H6   107.04  3.000
 24S  H6A   C6   O6   111.86  3.000
 24S  H6    C6   O6   111.73  3.000
 24S  H6A   C6   C5   108.95  3.000
 24S  H6    C6   C5   108.39  3.000
 24S  O6    C6   C5   108.78  3.000
 24S  HO6   O6   C6   107.88  3.000
 24S  HNAL  NAL  CAM  116.67  3.000
 24S  HNAL  NAL  C1   118.18  3.000
 24S  CAM   NAL  C1   124.45  3.000
 24S  SAO   CAM  NAN  118.85  3.000
 24S  NAN   CAM  NAL  115.65  3.000
 24S  SAO   CAM  NAL  125.51  3.000
 24S  HNAN  NAN  NAP  122.30  3.000
 24S  HNAN  NAN  CAM  116.91  3.000
 24S  NAP   NAN  CAM  120.68  3.000
 24S  CAQ   NAP  NAN  120.02  3.000
 24S  HAQ   CAQ  CAR  118.29  3.000
 24S  HAQ   CAQ  NAP  115.32  3.000
 24S  CAR   CAQ  NAP  126.22  3.000
 24S  CAW   CAR  CAS  117.38  3.000
 24S  CAW   CAR  CAQ  118.07  3.000
 24S  CAS   CAR  CAQ  124.43  3.000
 24S  NAX   CAS  CAT  117.86  3.000
 24S  CAT   CAS  CAR  122.09  3.000
 24S  NAX   CAS  CAR  120.04  3.000
 24S  HAT   CAT  CAU  119.95  3.000
 24S  HAT   CAT  CAS  120.75  3.000
 24S  CAU   CAT  CAS  119.29  3.000
 24S  HAU   CAU  CAV  120.54  3.000
 24S  HAU   CAU  CAT  119.58  3.000
 24S  CAV   CAU  CAT  119.88  3.000
 24S  HAV   CAV  CAW  119.54  3.000
 24S  HAV   CAV  CAU  120.28  3.000
 24S  CAW   CAV  CAU  120.18  3.000
 24S  HAW   CAW  CAV  119.46  3.000
 24S  HAW   CAW  CAR  119.36  3.000
 24S  CAV   CAW  CAR  121.17  3.000
 24S  OAZ   NAX  OAY  124.11  3.000
 24S  OAY   NAX  CAS  117.85  3.000
 24S  OAZ   NAX  CAS  118.04  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
 24S  CONST_01  CAU   CAT  CAS  CAR     0.00   0.0  0
 24S  CONST_02  CAU   CAV  CAW  CAR     0.00   0.0  0
 24S  CONST_03  CAV   CAW  CAR  CAS     0.00   0.0  0
 24S  CONST_04  CAV   CAU  CAT  CAS     0.00   0.0  0
 24S  CONST_05  CAW   CAR  CAS  CAT     0.00   0.0  0
 24S  CONST_06  CAW   CAV  CAU  CAT     0.00   0.0  0
 24S  CONST_07  CAT   CAS  CAR  CAQ   180.00   0.0  0
 24S  CONST_08  CAV   CAW  CAR  CAQ   180.00   0.0  0
 24S  CONST_09  NAX   CAS  CAT  CAU   180.00   0.0  0
 24S  CONST_10  NAX   CAS  CAR  CAW   180.00   0.0  0
 24S  CONST_11  HAT   CAT  CAS  CAR   180.00   0.0  0
 24S  CONST_12  HAV   CAV  CAW  CAR   180.00   0.0  0
 24S  CONST_13  HAW   CAW  CAR  CAS   180.00   0.0  0
 24S  CONST_14  HAU   CAU  CAT  CAS   180.00   0.0  0
 24S  CONST_19  SAO   CAM  NAL  C1      0.00   0.0  0
 24S  CONST_20  NAN   CAM  NAL  C1    180.00   0.0  0
 24S  CONST_21  NAP   NAN  CAM  NAL     0.00   0.0  0
 24S  CONST_22  NAP   NAN  CAM  SAO   180.00   0.0  0
 24S  CONST_23  HNAN  NAN  CAM  NAL   180.00   0.0  0
 24S  CONST_24  HNAL  NAL  CAM  NAN     0.00   0.0  0
 24S  Var_01    CAS   CAR  CAQ  NAP  -122.43  30.0  2
 24S  Var_02    CAR   CAQ  NAP  NAN     6.52   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
 24S  chir_01  C1  C2  O5  NAL  negativ
 24S  chir_02  C2  O2  C1  C3   negativ
 24S  chir_03  C3  O3  C2  C4   positiv
 24S  chir_04  C4  O4  C5  C3   positiv
 24S  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
 24S  plan-1  CAQ   0.020
 24S  plan-1  CAR   0.020
 24S  plan-1  CAS   0.020
 24S  plan-1  CAT   0.020
 24S  plan-1  CAU   0.020
 24S  plan-1  CAV   0.020
 24S  plan-1  CAW   0.020
 24S  plan-1  NAX   0.020
 24S  plan-1  HAT   0.020
 24S  plan-1  HAU   0.020
 24S  plan-1  HAV   0.020
 24S  plan-1  HAW   0.020
 24S  plan-2  CAS   0.020
 24S  plan-2  NAX   0.020
 24S  plan-2  OAY   0.020
 24S  plan-2  OAZ   0.020
 24S  plan-3  C1    0.020
 24S  plan-3  NAL   0.020
 24S  plan-3  CAM   0.020
 24S  plan-3  NAN   0.020
 24S  plan-3  SAO   0.020
 24S  plan-3  NAP   0.020
 24S  plan-3  HNAL  0.020
 24S  plan-3  HNAN  0.020
 24S  plan-4  NAN   0.020
 24S  plan-4  NAP   0.020
 24S  plan-4  CAQ   0.020
 24S  plan-4  CAR   0.020
 24S  plan-4  HAQ   0.020

