# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:11:46 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: N-{[(2E)-2-(2-hydroxybenzylidene)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/c2ccccc2O)[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
 26O  26O  N-{[(2E)-2-(2-hydroxybenzylidene)hydrazinyl]carbothioyl}-beta-D-glucopyranosylamine  D-saccharide  43  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_26O
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
 26O  C1    C  CH1   0   0.215   1.7650  -0.2040  -0.5703
 26O  C2    C  CH1   0  -0.027   1.9962   1.2368  -1.0298
 26O  O2    O  OH1   0  -0.660   1.6319   1.4117  -2.3743
 26O  C3    C  CH1   0  -0.008   3.4807   1.5546  -0.9101
 26O  O3    O  OH1   0  -0.670   3.7526   2.9088  -1.1760
 26O  C4    C  CH1   0   0.036   3.9865   1.2514   0.4955
 26O  O4    O  OH1   0  -0.671   5.3830   1.3910   0.5731
 26O  C5    C  CH1   0  -0.012   3.6276  -0.1863   0.8731
 26O  O5    O  O2    0  -0.483   2.2331  -0.3768   0.7427
 26O  C6    C  CH2   0  -0.157   4.0074  -0.5039   2.3037
 26O  O6    O  OH1   0  -0.668   3.7474  -1.8641   2.5530
 26O  NAL   N  NH1   0  -0.676   0.3716  -0.5152  -0.5888
 26O  CAM   C  C     0   0.431  -0.1281  -1.7258  -0.8890
 26O  NAN   N  NH1   0  -0.475  -1.4600  -1.8723  -0.7400
 26O  SAO   S  S1    0  -0.388   0.7671  -3.0276  -1.4401
 26O  NAP   N  N     0  -0.317  -2.2686  -0.8615  -0.3648
 26O  CAQ   C  C1    0   0.032  -3.5025  -1.1336  -0.1663
 26O  CAR   C  CR6   0  -0.083  -4.4735  -0.1229   0.2015
 26O  CAS   C  CR6   0   0.348  -4.1581   1.2473   0.2863
 26O  CAT   C  CR16  0  -0.336  -5.1524   2.1602   0.6320
 26O  CAU   C  CR16  0  -0.241  -6.4391   1.7250   0.8955
 26O  CAV   C  CR16  0  -0.269  -6.7657   0.3734   0.8161
 26O  CAW   C  CR16  0  -0.301  -5.7846  -0.5334   0.4688
 26O  OAX   O  OH1   0  -0.629  -2.9320   1.7185   0.0356
 26O  H1    H  HCH1  0   0.238   2.2691  -0.8915  -1.2603
 26O  H2    H  HCH1  0   0.228   1.4374   1.9157  -0.3666
 26O  HO2   H  HOH1  0   0.455   0.6727   1.3960  -2.4480
 26O  H3    H  HCH1  0   0.220   4.0252   0.9020  -1.6112
 26O  HO3   H  HOH1  0   0.458   3.6445   3.0648  -2.1193
 26O  H4    H  HCH1  0   0.214   3.4816   1.9307   1.2015
 26O  HO4   H  HOH1  0   0.455   5.6083   2.2914   0.3163
 26O  H5    H  HCH1  0   0.224   4.1651  -0.8719   0.1978
 26O  H6    H  HCH2  0   0.214   5.0663  -0.2617   2.4398
 26O  H6A   H  HCH2  0   0.197   3.4369   0.1515   2.9766
 26O  HO6   H  HOH1  0   0.456   4.0412  -2.0619   3.4466
 26O  HNAL  H  HNH1  0   0.413  -0.2425   0.1295  -0.1107
 26O  HNAN  H  HNH1  0   0.422  -1.8519  -2.7839  -0.9485
 26O  HAQ   H  H     0   0.277  -3.8766  -2.1528  -0.2754
 26O  HAT   H  HCR6  0   0.271  -4.9040   3.2124   0.6908
 26O  HAU   H  HCR6  0   0.266  -7.1970   2.4498   1.1635
 26O  HAV   H  HCR6  0   0.261  -7.7725   0.0382   1.0227
 26O  HAW   H  HCR6  0   0.266  -6.0231  -1.5884   0.4016
 26O  HOAX  H  HOH1  0   0.477  -2.3502   0.9760  -0.2080

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
 26O  NAL  C1    single    1.428  0.020  1.428
 26O  C2   C1    single    1.530  0.020  1.530
 26O  O5   C1    single    1.405  0.020  1.405
 26O  C1   H1    single    0.970  0.020  1.090
 26O  C2   C3    single    1.523  0.020  1.523
 26O  C2   O2    single    1.404  0.020  1.404
 26O  C2   H2    single    0.970  0.020  1.090
 26O  O2   HO2   single    0.850  0.020  0.980
 26O  C4   C3    single    1.524  0.020  1.524
 26O  O3   C3    single    1.407  0.020  1.407
 26O  C3   H3    single    0.970  0.020  1.090
 26O  O3   HO3   single    0.850  0.020  0.980
 26O  C4   O4    single    1.406  0.020  1.406
 26O  C4   C5    single    1.529  0.020  1.529
 26O  C4   H4    single    0.970  0.020  1.090
 26O  O4   HO4   single    0.850  0.020  0.980
 26O  C6   C5    single    1.514  0.020  1.514
 26O  O5   C5    single    1.413  0.020  1.413
 26O  C5   H5    single    0.970  0.020  1.090
 26O  O6   C6    single    1.407  0.020  1.407
 26O  C6   H6    single    0.970  0.020  1.090
 26O  C6   H6A   single    0.970  0.020  1.090
 26O  O6   HO6   single    0.850  0.020  0.980
 26O  NAL  CAM   single    1.344  0.020  1.344
 26O  NAL  HNAL  single    0.860  0.020  1.020
 26O  NAN  CAM   single    1.348  0.020  1.348
 26O  CAM  SAO   double    1.673  0.020  1.673
 26O  NAP  NAN   single    1.348  0.020  1.348
 26O  NAN  HNAN  single    0.860  0.020  1.020
 26O  CAQ  NAP   double    1.279  0.020  1.279
 26O  CAR  CAQ   single    1.449  0.020  1.449
 26O  CAQ  HAQ   single    0.930  0.020  1.080
 26O  CAS  CAR   aromatic  1.409  0.020  1.409
 26O  CAW  CAR   aromatic  1.400  0.020  1.400
 26O  CAT  CAS   aromatic  1.393  0.020  1.393
 26O  CAS  OAX   single    1.337  0.020  1.337
 26O  CAU  CAT   aromatic  1.384  0.020  1.384
 26O  CAT  HAT   single    0.930  0.020  1.080
 26O  CAU  CAV   aromatic  1.393  0.020  1.393
 26O  CAU  HAU   single    0.930  0.020  1.080
 26O  CAV  CAW   aromatic  1.380  0.020  1.380
 26O  CAV  HAV   single    0.930  0.020  1.080
 26O  CAW  HAW   single    0.930  0.020  1.080
 26O  OAX  HOAX  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
 26O  H1    C1   NAL  107.68  3.000
 26O  H1    C1   O5   110.97  3.000
 26O  NAL   C1   O5   108.09  3.000
 26O  H1    C1   C2   109.38  3.000
 26O  O5    C1   C2   110.26  3.000
 26O  NAL   C1   C2   110.42  3.000
 26O  H2    C2   C3   108.58  3.000
 26O  H2    C2   O2   111.61  3.000
 26O  C3    C2   O2   107.59  3.000
 26O  H2    C2   C1   108.84  3.000
 26O  O2    C2   C1   111.45  3.000
 26O  C3    C2   C1   108.67  3.000
 26O  HO2   O2   C2   109.27  3.000
 26O  H3    C3   C4   107.76  3.000
 26O  H3    C3   O3   110.76  3.000
 26O  C4    C3   O3   107.56  3.000
 26O  H3    C3   C2   107.95  3.000
 26O  O3    C3   C2   111.99  3.000
 26O  C4    C3   C2   110.76  3.000
 26O  HO3   O3   C3   108.64  3.000
 26O  H4    C4   C5   108.28  3.000
 26O  H4    C4   O4   111.01  3.000
 26O  C5    C4   O4   108.24  3.000
 26O  H4    C4   C3   108.43  3.000
 26O  C5    C4   C3   109.68  3.000
 26O  O4    C4   C3   111.15  3.000
 26O  HO4   O4   C4   108.10  3.000
 26O  H5    C5   C6   109.03  3.000
 26O  H5    C5   O5   109.92  3.000
 26O  C6    C5   O5   107.84  3.000
 26O  H5    C5   C4   108.61  3.000
 26O  O5    C5   C4   109.60  3.000
 26O  C6    C5   C4   111.82  3.000
 26O  C5    O5   C1   113.48  3.000
 26O  H6A   C6   H6   107.10  3.000
 26O  H6A   C6   O6   111.84  3.000
 26O  H6    C6   O6   111.75  3.000
 26O  H6A   C6   C5   108.86  3.000
 26O  H6    C6   C5   108.29  3.000
 26O  O6    C6   C5   108.90  3.000
 26O  HO6   O6   C6   107.89  3.000
 26O  HNAL  NAL  CAM  117.03  3.000
 26O  HNAL  NAL  C1   116.60  3.000
 26O  CAM   NAL  C1   124.21  3.000
 26O  SAO   CAM  NAN  118.71  3.000
 26O  SAO   CAM  NAL  125.14  3.000
 26O  NAN   CAM  NAL  116.15  3.000
 26O  HNAN  NAN  NAP  119.98  3.000
 26O  HNAN  NAN  CAM  117.18  3.000
 26O  NAP   NAN  CAM  122.82  3.000
 26O  CAQ   NAP  NAN  117.55  3.000
 26O  HAQ   CAQ  CAR  116.56  3.000
 26O  HAQ   CAQ  NAP  120.93  3.000
 26O  CAR   CAQ  NAP  122.51  3.000
 26O  CAW   CAR  CAS  118.92  3.000
 26O  CAW   CAR  CAQ  118.14  3.000
 26O  CAS   CAR  CAQ  122.94  3.000
 26O  OAX   CAS  CAT  118.03  3.000
 26O  OAX   CAS  CAR  122.46  3.000
 26O  CAT   CAS  CAR  119.50  3.000
 26O  HAT   CAT  CAU  120.57  3.000
 26O  HAT   CAT  CAS  119.11  3.000
 26O  CAU   CAT  CAS  120.32  3.000
 26O  HAU   CAU  CAV  119.98  3.000
 26O  HAU   CAU  CAT  119.19  3.000
 26O  CAV   CAU  CAT  120.82  3.000
 26O  HAV   CAV  CAW  120.42  3.000
 26O  HAV   CAV  CAU  120.55  3.000
 26O  CAW   CAV  CAU  119.03  3.000
 26O  HAW   CAW  CAV  119.92  3.000
 26O  HAW   CAW  CAR  118.67  3.000
 26O  CAV   CAW  CAR  121.41  3.000
 26O  HOAX  OAX  CAS  109.01  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
 26O  CONST_01  CAU   CAT  CAS  CAR     0.00   0.0  0
 26O  CONST_02  CAU   CAV  CAW  CAR     0.00   0.0  0
 26O  CONST_03  CAV   CAW  CAR  CAS     0.00   0.0  0
 26O  CONST_04  CAV   CAU  CAT  CAS     0.00   0.0  0
 26O  CONST_05  CAW   CAR  CAS  CAT     0.00   0.0  0
 26O  CONST_06  CAW   CAV  CAU  CAT     0.00   0.0  0
 26O  CONST_07  CAT   CAS  CAR  CAQ   180.00   0.0  0
 26O  CONST_08  CAV   CAW  CAR  CAQ   180.00   0.0  0
 26O  CONST_09  OAX   CAS  CAT  CAU   180.00   0.0  0
 26O  CONST_10  OAX   CAS  CAR  CAW   180.00   0.0  0
 26O  CONST_11  HAT   CAT  CAS  CAR   180.00   0.0  0
 26O  CONST_12  HAV   CAV  CAW  CAR   180.00   0.0  0
 26O  CONST_13  HAW   CAW  CAR  CAS   180.00   0.0  0
 26O  CONST_14  HAU   CAU  CAT  CAS   180.00   0.0  0
 26O  CONST_15  NAN   CAM  NAL  C1    180.00   0.0  0
 26O  CONST_16  SAO   CAM  NAL  C1      0.00   0.0  0
 26O  CONST_17  NAP   NAN  CAM  NAL     0.00   0.0  0
 26O  CONST_18  NAP   NAN  CAM  SAO   180.00   0.0  0
 26O  CONST_19  HNAN  NAN  CAM  NAL   180.00   0.0  0
 26O  CONST_20  HNAL  NAL  CAM  NAN     0.00   0.0  0
 26O  Var_01    CAS   CAR  CAQ  NAP     4.18  30.0  1
 26O  Var_02    CAR   CAQ  NAP  NAN  -178.16   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
 26O  chir_01  C1  NAL  C2  O5  negativ
 26O  chir_02  C2  O2   C1  C3  negativ
 26O  chir_03  C3  O3   C2  C4  positiv
 26O  chir_04  C4  O4   C5  C3  positiv
 26O  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
 26O  plan-1  CAQ   0.020
 26O  plan-1  CAR   0.020
 26O  plan-1  CAS   0.020
 26O  plan-1  CAT   0.020
 26O  plan-1  CAU   0.020
 26O  plan-1  CAV   0.020
 26O  plan-1  CAW   0.020
 26O  plan-1  OAX   0.020
 26O  plan-1  HAT   0.020
 26O  plan-1  HAU   0.020
 26O  plan-1  HAV   0.020
 26O  plan-1  HAW   0.020
 26O  plan-2  C1    0.020
 26O  plan-2  NAL   0.020
 26O  plan-2  CAM   0.020
 26O  plan-2  NAN   0.020
 26O  plan-2  SAO   0.020
 26O  plan-2  NAP   0.020
 26O  plan-2  HNAL  0.020
 26O  plan-2  HNAN  0.020
 26O  plan-3  NAN   0.020
 26O  plan-3  NAP   0.020
 26O  plan-3  CAQ   0.020
 26O  plan-3  CAR   0.020
 26O  plan-3  HAQ   0.020

