# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  1 09:39:56 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (2R,3R,4R,5S,6Z)-4,5-dihydroxy-6-(hydroxyimino)-2-(hydroxymethyl)piperidin-3-yl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1NC(=N\O)/[C@H](O)[C@@H](O)[C@@H]1O[C@H]2O[C@H](CO)[C@@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@H](O)[C@H]2O
#
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
 LAG  LAG  '(2R,3R,4R,5S,6Z)-4,5-dihydroxy-6-(hydroxyimino)-2-(hydroxymethyl)piperidin-3-yl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside'  saccharide  67  35  .  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 (reasonable std)
;

data_comp_LAG
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
 LAG  CA1   C  C     0   0.419  -4.5418  -1.1331  -1.0108
 LAG  NA1   N  N     0  -0.236  -5.3493  -1.7222  -1.8101
 LAG  OA7   O  OH1   0  -0.588  -5.1275  -3.0900  -1.8478
 LAG  CA2   C  CH1   0  -0.044  -4.6453   0.3697  -0.9801
 LAG  OA2   O  OH1   0  -0.664  -3.7159   0.9419  -1.8778
 LAG  CA3   C  CH1   0  -0.007  -4.3867   0.9026   0.4298
 LAG  OA3   O  OH1   0  -0.659  -5.4504   0.5483   1.2752
 LAG  CA4   C  CH1   0   0.004  -3.1186   0.3017   1.0384
 LAG  OA4   O  O2    0  -0.508  -1.9978   0.7891   0.3288
 LAG  CA5   C  CH1   0  -0.150  -3.0855  -1.2222   0.9765
 LAG  NA5   N  NH1   0  -0.645  -3.5280  -1.7188  -0.3169
 LAG  CA6   C  CH2   0  -0.146  -3.8460  -1.8893   2.1203
 LAG  OA6   O  OH1   0  -0.671  -3.5517  -3.2694   2.0692
 LAG  CB1   C  CH1   0   0.230  -1.4211   1.9640   0.8084
 LAG  CB2   C  CH1   0  -0.025  -0.7848   2.6731  -0.3838
 LAG  CB3   C  CH1   0   0.009   0.3912   1.8478  -0.9008
 LAG  CB4   C  CH1   0   0.015   1.3645   1.5589   0.2351
 LAG  CB5   C  CH1   0  -0.007   0.6276   0.9078   1.4146
 LAG  CB6   C  CH2   0  -0.193   1.5116   0.7638   2.6348
 LAG  OB2   O  OH1   0  -0.691  -1.7155   2.9706  -1.3880
 LAG  OB3   O  OH1   0  -0.672   1.0980   2.5395  -1.9078
 LAG  OB4   O  O2    0  -0.517   2.3597   0.6975  -0.2719
 LAG  OB5   O  O2    0  -0.494  -0.4743   1.7156   1.8014
 LAG  OB6   O  OH1   0  -0.668   0.7823   0.1082   3.6466
 LAG  CD1   C  CH1   0   0.219   3.7134   1.0157  -0.1153
 LAG  CD2   C  CH1   0  -0.010   4.3966   0.9139  -1.4804
 LAG  CD3   C  CH1   0  -0.011   4.3933  -0.5378  -1.9523
 LAG  CD4   C  CH1   0   0.035   5.0338  -1.4224  -0.8893
 LAG  CD5   C  CH1   0  -0.015   4.3245  -1.2145   0.4493
 LAG  CD6   C  CH2   0  -0.160   5.0025  -1.9629   1.5771
 LAG  OD2   O  OH1   0  -0.690   3.8467   1.7878  -2.4297
 LAG  OD3   O  OH1   0  -0.677   5.1360  -0.6985  -3.1396
 LAG  OD4   O  OH1   0  -0.673   4.9439  -2.7871  -1.2191
 LAG  OD5   O  O2    0  -0.496   4.3363   0.1637   0.7945
 LAG  OD6   O  OH1   0  -0.663   4.2431  -1.7988   2.7514
 LAG  HA7   H  HOH1  0   0.471  -5.8088  -3.4169  -2.4423
 LAG  HA2   H  HCH1  0   0.256  -5.6669   0.6420  -1.2713
 LAG  H8    H  HOH1  0   0.467  -4.0088   0.7623  -2.7774
 LAG  HA3   H  HCH1  0   0.249  -4.2714   1.9943   0.3736
 LAG  H7    H  HOH1  0   0.463  -6.2517   0.9870   0.9713
 LAG  HA4   H  HCH1  0   0.262  -3.0616   0.6005   2.0930
 LAG  H1    H  HCH1  0   0.268  -2.0347  -1.5084   1.0942
 LAG  HA5   H  HNH1  0   0.386  -3.4928  -2.7255  -0.3860
 LAG  HA61  H  HCH2  0   0.199  -3.5207  -1.4491   3.0722
 LAG  HA62  H  HCH2  0   0.220  -4.9175  -1.7055   2.0205
 LAG  HA6   H  HOH1  0   0.459  -4.2755  -3.7502   2.4782
 LAG  HB1   H  HCH1  0   0.249  -2.1715   2.6137   1.2761
 LAG  HB2   H  HCH1  0   0.247  -0.3952   3.6317  -0.0232
 LAG  HB3   H  HCH1  0   0.227   0.0202   0.8880  -1.2891
 LAG  HB4   H  HCH1  0   0.238   1.8078   2.5088   0.5713
 LAG  HB5   H  HCH1  0   0.233   0.2839  -0.0889   1.1057
 LAG  HB61  H  HCH2  0   0.237   2.4045   0.1980   2.3608
 LAG  HB62  H  HCH2  0   0.191   1.8455   1.7624   2.9529
 LAG  H6    H  HOH1  0   0.455  -2.2731   2.1929  -1.5595
 LAG  H5    H  HOH1  0   0.463   0.5133   2.6572  -2.6643
 LAG  HB6   H  HOH1  0   0.454   1.3952  -0.1042   4.3556
 LAG  HD1   H  HCH1  0   0.254   3.8308   2.0282   0.2888
 LAG  HD2   H  HCH1  0   0.236   5.4398   1.2210  -1.3403
 LAG  HD3   H  HCH1  0   0.211   3.3538  -0.8688  -2.1013
 LAG  HD4   H  HCH1  0   0.210   6.0852  -1.1116  -0.7742
 LAG  HD5   H  HCH1  0   0.229   3.2906  -1.5752   0.3610
 LAG  HD61  H  HCH2  0   0.212   5.0809  -3.0167   1.2909
 LAG  HD62  H  HCH2  0   0.194   6.0270  -1.5826   1.6968
 LAG  H4    H  HOH1  0   0.449   2.8802   1.8124  -2.3371
 LAG  H3    H  HOH1  0   0.453   4.7114  -0.1797  -3.8305
 LAG  H2    H  HOH1  0   0.455   5.3748  -2.9189  -2.0699
 LAG  HD6   H  HOH1  0   0.456   4.6275  -2.3556   3.4341

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
 LAG  CA1  NA1   double  1.280  0.020  1.280
 LAG  CA1  CA2   single  1.507  0.020  1.507
 LAG  CA1  NA5   single  1.361  0.020  1.361
 LAG  NA1  OA7   single  1.386  0.020  1.386
 LAG  OA7  HA7   single  0.850  0.020  0.980
 LAG  CA2  OA2   single  1.413  0.020  1.413
 LAG  CA2  CA3   single  1.529  0.020  1.529
 LAG  CA2  HA2   single  0.970  0.020  1.090
 LAG  OA2  H8    single  0.850  0.020  0.980
 LAG  CA3  OA3   single  1.404  0.020  1.404
 LAG  CA3  CA4   single  1.530  0.020  1.530
 LAG  CA3  HA3   single  0.970  0.020  1.090
 LAG  OA3  H7    single  0.850  0.020  0.980
 LAG  CA4  OA4   single  1.413  0.020  1.413
 LAG  CA4  CA5   single  1.526  0.020  1.526
 LAG  CA4  HA4   single  0.970  0.020  1.090
 LAG  OA4  CB1   single  1.394  0.020  1.394
 LAG  CA5  NA5   single  1.454  0.020  1.454
 LAG  CA5  CA6   single  1.527  0.020  1.527
 LAG  CA5  H1    single  0.970  0.020  1.090
 LAG  NA5  HA5   single  0.890  0.020  1.040
 LAG  CA6  OA6   single  1.412  0.020  1.412
 LAG  CA6  HA61  single  0.970  0.020  1.090
 LAG  CA6  HA62  single  0.970  0.020  1.090
 LAG  OA6  HA6   single  0.850  0.020  0.980
 LAG  CB1  CB2   single  1.526  0.020  1.526
 LAG  CB1  OB5   single  1.394  0.020  1.394
 LAG  CB1  HB1   single  0.970  0.020  1.090
 LAG  CB2  CB3   single  1.527  0.020  1.527
 LAG  CB2  OB2   single  1.401  0.020  1.401
 LAG  CB2  HB2   single  0.970  0.020  1.090
 LAG  CB3  CB4   single  1.523  0.020  1.523
 LAG  CB3  OB3   single  1.411  0.020  1.411
 LAG  CB3  HB3   single  0.970  0.020  1.090
 LAG  CB4  CB5   single  1.536  0.020  1.536
 LAG  CB4  OB4   single  1.410  0.020  1.410
 LAG  CB4  HB4   single  0.970  0.020  1.090
 LAG  CB5  CB6   single  1.514  0.020  1.514
 LAG  CB5  OB5   single  1.420  0.020  1.420
 LAG  CB5  HB5   single  0.970  0.020  1.090
 LAG  CB6  OB6   single  1.409  0.020  1.409
 LAG  CB6  HB61  single  0.970  0.020  1.090
 LAG  CB6  HB62  single  0.970  0.020  1.090
 LAG  OB2  H6    single  0.850  0.020  0.980
 LAG  OB3  H5    single  0.850  0.020  0.980
 LAG  OB4  CD1   single  1.399  0.020  1.399
 LAG  OB6  HB6   single  0.850  0.020  0.980
 LAG  CD1  CD2   single  1.530  0.020  1.530
 LAG  CD1  OD5   single  1.393  0.020  1.393
 LAG  CD1  HD1   single  0.970  0.020  1.090
 LAG  CD2  CD3   single  1.527  0.020  1.527
 LAG  CD2  OD2   single  1.403  0.020  1.403
 LAG  CD2  HD2   single  0.970  0.020  1.090
 LAG  CD3  CD4   single  1.524  0.020  1.524
 LAG  CD3  OD3   single  1.410  0.020  1.410
 LAG  CD3  HD3   single  0.970  0.020  1.090
 LAG  CD4  CD5   single  1.529  0.020  1.529
 LAG  CD4  OD4   single  1.407  0.020  1.407
 LAG  CD4  HD4   single  0.970  0.020  1.090
 LAG  CD5  CD6   single  1.514  0.020  1.514
 LAG  CD5  OD5   single  1.421  0.020  1.421
 LAG  CD5  HD5   single  0.970  0.020  1.090
 LAG  CD6  OD6   single  1.408  0.020  1.408
 LAG  CD6  HD61  single  0.970  0.020  1.090
 LAG  CD6  HD62  single  0.970  0.020  1.090
 LAG  OD2  H4    single  0.850  0.020  0.980
 LAG  OD3  H3    single  0.850  0.020  0.980
 LAG  OD4  H2    single  0.850  0.020  0.980
 LAG  OD6  HD6   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
 LAG  NA5   CA1  CA2   118.04  3.000
 LAG  NA5   CA1  NA1   126.18  3.000
 LAG  CA2   CA1  NA1   115.37  3.000
 LAG  OA7   NA1  CA1   111.73  3.000
 LAG  HA7   OA7  NA1   103.82  3.000
 LAG  HA2   CA2  CA3   108.41  3.000
 LAG  HA2   CA2  OA2   110.09  3.000
 LAG  CA3   CA2  OA2   109.48  3.000
 LAG  HA2   CA2  CA1   107.83  3.000
 LAG  CA3   CA2  CA1   110.78  3.000
 LAG  OA2   CA2  CA1   110.23  3.000
 LAG  H8    OA2  CA2   108.54  3.000
 LAG  HA3   CA3  CA4   108.88  3.000
 LAG  HA3   CA3  OA3   111.15  3.000
 LAG  CA4   CA3  OA3   106.82  3.000
 LAG  HA3   CA3  CA2   108.47  3.000
 LAG  CA4   CA3  CA2   111.72  3.000
 LAG  OA3   CA3  CA2   109.82  3.000
 LAG  H7    OA3  CA3   109.00  3.000
 LAG  HA4   CA4  CA5   108.04  3.000
 LAG  HA4   CA4  OA4   110.32  3.000
 LAG  CA5   CA4  OA4   107.88  3.000
 LAG  HA4   CA4  CA3   108.57  3.000
 LAG  CA5   CA4  CA3   113.22  3.000
 LAG  OA4   CA4  CA3   108.80  3.000
 LAG  CB1   OA4  CA4   116.49  3.000
 LAG  H1    CA5  CA6   106.45  3.000
 LAG  H1    CA5  NA5   107.35  3.000
 LAG  CA6   CA5  NA5   111.44  3.000
 LAG  H1    CA5  CA4   106.11  3.000
 LAG  CA6   CA5  CA4   113.28  3.000
 LAG  NA5   CA5  CA4   111.75  3.000
 LAG  HA5   NA5  CA5   113.00  3.000
 LAG  HA5   NA5  CA1   114.85  3.000
 LAG  CA5   NA5  CA1   122.21  3.000
 LAG  HA62  CA6  HA61  107.61  3.000
 LAG  HA62  CA6  OA6   111.46  3.000
 LAG  HA61  CA6  OA6   111.19  3.000
 LAG  HA62  CA6  CA5   110.29  3.000
 LAG  HA61  CA6  CA5   109.07  3.000
 LAG  OA6   CA6  CA5   107.22  3.000
 LAG  HA6   OA6  CA6   108.47  3.000
 LAG  HB1   CB1  OB5   105.44  3.000
 LAG  HB1   CB1  CB2   110.06  3.000
 LAG  OB5   CB1  CB2   110.86  3.000
 LAG  HB1   CB1  OA4   111.27  3.000
 LAG  OB5   CB1  OA4   112.08  3.000
 LAG  CB2   CB1  OA4   107.18  3.000
 LAG  HB2   CB2  OB2   106.63  3.000
 LAG  HB2   CB2  CB3   108.08  3.000
 LAG  OB2   CB2  CB3   112.56  3.000
 LAG  HB2   CB2  CB1   107.32  3.000
 LAG  OB2   CB2  CB1   112.44  3.000
 LAG  CB3   CB2  CB1   109.54  3.000
 LAG  HB3   CB3  OB3   110.16  3.000
 LAG  HB3   CB3  CB4   108.26  3.000
 LAG  OB3   CB3  CB4   107.76  3.000
 LAG  HB3   CB3  CB2   109.35  3.000
 LAG  OB3   CB3  CB2   111.25  3.000
 LAG  CB4   CB3  CB2   110.00  3.000
 LAG  HB4   CB4  OB4   110.65  3.000
 LAG  HB4   CB4  CB5   108.94  3.000
 LAG  OB4   CB4  CB5   110.84  3.000
 LAG  HB4   CB4  CB3   108.74  3.000
 LAG  OB4   CB4  CB3   107.37  3.000
 LAG  CB5   CB4  CB3   110.27  3.000
 LAG  HB5   CB5  OB5   110.49  3.000
 LAG  HB5   CB5  CB6   108.85  3.000
 LAG  OB5   CB5  CB6   106.72  3.000
 LAG  HB5   CB5  CB4   108.59  3.000
 LAG  OB5   CB5  CB4   109.90  3.000
 LAG  CB6   CB5  CB4   112.29  3.000
 LAG  HB62  CB6  HB61  107.15  3.000
 LAG  HB62  CB6  OB6   111.83  3.000
 LAG  HB61  CB6  OB6   111.25  3.000
 LAG  HB62  CB6  CB5   108.90  3.000
 LAG  HB61  CB6  CB5   108.94  3.000
 LAG  OB6   CB6  CB5   108.71  3.000
 LAG  H6    OB2  CB2   109.73  3.000
 LAG  H5    OB3  CB3   108.44  3.000
 LAG  CD1   OB4  CB4   120.23  3.000
 LAG  CB5   OB5  CB1   115.74  3.000
 LAG  HB6   OB6  CB6   107.60  3.000
 LAG  HD1   CD1  OD5   106.03  3.000
 LAG  HD1   CD1  CD2   110.03  3.000
 LAG  OD5   CD1  CD2   110.01  3.000
 LAG  HD1   CD1  OB4   110.78  3.000
 LAG  OD5   CD1  OB4   111.50  3.000
 LAG  CD2   CD1  OB4   108.48  3.000
 LAG  HD2   CD2  OD2   106.56  3.000
 LAG  HD2   CD2  CD3   107.93  3.000
 LAG  OD2   CD2  CD3   112.49  3.000
 LAG  HD2   CD2  CD1   106.99  3.000
 LAG  OD2   CD2  CD1   112.79  3.000
 LAG  CD3   CD2  CD1   109.76  3.000
 LAG  HD3   CD3  OD3   110.44  3.000
 LAG  HD3   CD3  CD4   108.46  3.000
 LAG  OD3   CD3  CD4   107.45  3.000
 LAG  HD3   CD3  CD2   109.25  3.000
 LAG  OD3   CD3  CD2   111.57  3.000
 LAG  CD4   CD3  CD2   109.60  3.000
 LAG  HD4   CD4  OD4   111.03  3.000
 LAG  HD4   CD4  CD5   108.22  3.000
 LAG  OD4   CD4  CD5   107.91  3.000
 LAG  HD4   CD4  CD3   108.06  3.000
 LAG  OD4   CD4  CD3   111.88  3.000
 LAG  CD5   CD4  CD3   109.68  3.000
 LAG  HD5   CD5  OD5   110.24  3.000
 LAG  HD5   CD5  CD6   108.60  3.000
 LAG  OD5   CD5  CD6   107.15  3.000
 LAG  HD5   CD5  CD4   108.76  3.000
 LAG  OD5   CD5  CD4   109.92  3.000
 LAG  CD6   CD5  CD4   112.16  3.000
 LAG  HD62  CD6  HD61  107.14  3.000
 LAG  HD62  CD6  OD6   111.81  3.000
 LAG  HD61  CD6  OD6   111.64  3.000
 LAG  HD62  CD6  CD5   109.12  3.000
 LAG  HD61  CD6  CD5   108.25  3.000
 LAG  OD6   CD6  CD5   108.79  3.000
 LAG  H4    OD2  CD2   109.96  3.000
 LAG  H3    OD3  CD3   108.10  3.000
 LAG  H2    OD4  CD4   108.14  3.000
 LAG  CD5   OD5  CD1   115.52  3.000
 LAG  HD6   OD6  CD6   108.01  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
 LAG  CONST_03  HA5  NA5  CA1  CA2  180.00  0.0  0
 LAG  CONST_04  CA2  CA1  NA1  OA7  180.00  0.0  0
 LAG  CONST_05  NA5  CA1  NA1  OA7    0.00  0.0  0

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
 LAG  chir_01  CA2  CA1  OA2  CA3  positiv
 LAG  chir_02  CA3  OA3  CA2  CA4  positiv
 LAG  chir_03  CA4  OA4  CA5  CA3  positiv
 LAG  chir_04  CA5  NA5  CA4  CA6  negativ
 LAG  chir_05  CB1  OA4  OB5  CB2  negativ
 LAG  chir_06  CB2  OB2  CB1  CB3  negativ
 LAG  chir_07  CB3  OB3  CB2  CB4  positiv
 LAG  chir_08  CB4  OB4  CB5  CB3  positiv
 LAG  chir_09  CB5  OB5  CB4  CB6  negativ
 LAG  chir_10  CD1  OB4  OD5  CD2  negativ
 LAG  chir_11  CD2  OD2  CD1  CD3  negativ
 LAG  chir_12  CD3  OD3  CD2  CD4  positiv
 LAG  chir_13  CD4  OD4  CD3  CD5  negativ
 LAG  chir_14  CD5  OD5  CD4  CD6  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
 LAG  plan-1  CA1  0.020
 LAG  plan-1  NA1  0.020
 LAG  plan-1  OA7  0.020
 LAG  plan-1  CA2  0.020
 LAG  plan-1  CA5  0.020
 LAG  plan-1  NA5  0.020
 LAG  plan-1  HA5  0.020

