# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 03:54:02 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-(acetylamino)-4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-2-deoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2NC(C)=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
 CBS  CBS  2-(acetylamino)-4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-2-deoxy-beta-D-glucopyranose  D-saccharide  57  29  .  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_CBS
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
 CBS  C1A   C  CH1   0   0.332  -0.3180   0.1945  -1.5330
 CBS  C2A   C  CH1   0  -0.158   0.1620  -0.4534  -2.8377
 CBS  C3A   C  CH1   0   0.034  -0.6244   0.1161  -4.0123
 CBS  C4A   C  CH1   0   0.000  -2.1245   0.0439  -3.7442
 CBS  C5A   C  CH1   0  -0.028  -2.4399   0.6957  -2.3938
 CBS  C6A   C  CH2   0  -0.154  -3.9069   0.5966  -2.0389
 CBS  C8A   C  CH3   0  -0.788   3.9405  -0.5988  -2.7932
 CBS  N2A   N  NH1   0  -0.632   1.5731  -0.2367  -3.0236
 CBS  O1A   O  O2    0  -0.499   0.3148  -0.4427  -0.4880
 CBS  O3A   O  OH1   0  -0.662  -0.2636  -0.5969  -5.1646
 CBS  O4A   O  OH1   0  -0.672  -2.7594   0.7061  -4.8154
 CBS  O5A   O  O2    0  -0.473  -1.6989   0.0403  -1.3856
 CBS  O6A   O  OH1   0  -0.665  -4.1484   1.3376  -0.8690
 CBS  O7A   O  O     0  -0.492   2.2901  -2.2729  -2.3443
 CBS  C1B   C  CH1   0   0.306   1.5444   0.2519   3.3966
 CBS  C2B   C  CH1   0  -0.172   0.0712  -0.1063   3.2236
 CBS  C3B   C  CH1   0   0.033  -0.1638  -0.7073   1.8331
 CBS  C4B   C  CH1   0   0.018   0.3709   0.2280   0.7553
 CBS  C5B   C  CH1   0  -0.005   1.8323   0.5798   1.0749
 CBS  C6B   C  CH2   0  -0.165   2.4234   1.5849   0.1099
 CBS  C8B   C  CH3   0  -0.782  -1.4489  -1.7797   6.2628
 CBS  N2B   N  NH1   0  -0.647  -0.3750  -1.0229   4.2410
 CBS  O3B   O  OH1   0  -0.644  -1.5232  -0.9420   1.6031
 CBS  O5B   O  O2    0  -0.495   1.9198   1.1360   2.3685
 CBS  O6B   O  OH1   0  -0.669   3.8112   1.6597   0.3360
 CBS  O7B   O  O     0  -0.495  -1.7467   0.4035   5.3405
 CBS  H1A   H  HCH1  0   0.183  -0.0704   1.2734  -1.5539
 CBS  H2A   H  HCH1  0   0.273  -0.0184  -1.5297  -2.7707
 CBS  H3A   H  HCH1  0   0.211  -0.3635   1.1845  -4.1171
 CBS  H4A   H  HCH1  0   0.228  -2.4207  -1.0141  -3.7000
 CBS  H5A   H  HCH1  0   0.222  -2.1562   1.7604  -2.4460
 CBS  H61A  H  HCH2  0   0.198  -4.4932   0.9800  -2.8829
 CBS  H62A  H  HCH2  0   0.200  -4.1726  -0.4629  -1.9179
 CBS  H81A  H  HCH3  0   0.265   4.6197  -1.3879  -3.1093
 CBS  H82A  H  HCH3  0   0.253   4.0367   0.2457  -3.4739
 CBS  H83A  H  HCH3  0   0.266   4.2577  -0.2651  -1.8027
 CBS  HN2A  H  HNH1  0   0.401   1.8630   0.6810  -3.3253
 CBS  HO3A  H  HOH1  0   0.452  -0.7649  -0.2351  -5.9032
 CBS  HO4A  H  HOH1  0   0.463  -3.6236   0.3129  -4.9641
 CBS  HO6A  H  HOH1  0   0.456  -5.0853   1.2718  -0.6649
 CBS  H1B   H  HCH1  0   0.188   2.1585  -0.6635   3.3278
 CBS  H2B   H  HCH1  0   0.273  -0.5177   0.8094   3.3157
 CBS  H3B   H  HCH1  0   0.209   0.4138  -1.6455   1.7656
 CBS  H4B   H  HCH1  0   0.244  -0.2360   1.1434   0.7428
 CBS  H5B   H  HCH1  0   0.225   2.4222  -0.3506   1.0193
 CBS  H61B  H  HCH2  0   0.199   2.2076   1.2660  -0.9137
 CBS  H62B  H  HCH2  0   0.211   1.9314   2.5557   0.2583
 CBS  H81B  H  HCH3  0   0.265  -2.5177  -1.8877   6.4408
 CBS  H82B  H  HCH3  0   0.249  -1.0441  -2.7463   5.9693
 CBS  H83B  H  HCH3  0   0.270  -0.9899  -1.4902   7.2089
 CBS  HN2B  H  HNH1  0   0.402   0.0589  -1.9330   4.2709
 CBS  HO3B  H  HOH1  0   0.449  -1.8223  -1.5875   2.2524
 CBS  HO6B  H  HOH1  0   0.458   4.1759   2.3155  -0.2649
 CBS  O1B   O  OH1   0  -0.647   1.7146   0.8851   4.6053
 CBS  C7A   C  C     0   0.519   2.5317  -1.1310  -2.7020
 CBS  C7B   C  C     0   0.526  -1.2122  -0.6904   5.2470
 CBS  HO1B  H  HOH1  0   0.466   2.6450   0.8563   4.8523

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
 CBS  C1A  C2A   single  1.534  0.020  1.534
 CBS  C1A  O1A   single  1.378  0.020  1.378
 CBS  C1A  O5A   single  1.397  0.020  1.397
 CBS  C1A  H1A   single  0.970  0.020  1.090
 CBS  C2A  C3A   single  1.524  0.020  1.524
 CBS  C2A  N2A   single  1.440  0.020  1.440
 CBS  C2A  H2A   single  0.970  0.020  1.090
 CBS  C3A  C4A   single  1.526  0.020  1.526
 CBS  C3A  O3A   single  1.402  0.020  1.402
 CBS  C3A  H3A   single  0.970  0.020  1.090
 CBS  C4A  C5A   single  1.532  0.020  1.532
 CBS  C4A  O4A   single  1.410  0.020  1.410
 CBS  C4A  H4A   single  0.970  0.020  1.090
 CBS  C5A  C6A   single  1.513  0.020  1.513
 CBS  C5A  O5A   single  1.413  0.020  1.413
 CBS  C5A  H5A   single  0.970  0.020  1.090
 CBS  C6A  O6A   single  1.406  0.020  1.406
 CBS  C6A  H61A  single  0.970  0.020  1.090
 CBS  C6A  H62A  single  0.970  0.020  1.090
 CBS  C7A  C8A   single  1.509  0.020  1.509
 CBS  C7A  N2A   single  1.350  0.020  1.350
 CBS  C7A  O7A   double  1.221  0.020  1.221
 CBS  C8A  H81A  single  0.970  0.020  1.090
 CBS  C8A  H82A  single  0.970  0.020  1.090
 CBS  C8A  H83A  single  0.970  0.020  1.090
 CBS  N2A  HN2A  single  0.860  0.020  1.020
 CBS  O1A  C4B   single  1.414  0.020  1.414
 CBS  O3A  HO3A  single  0.850  0.020  0.980
 CBS  O4A  HO4A  single  0.850  0.020  0.980
 CBS  O6A  HO6A  single  0.850  0.020  0.980
 CBS  C1B  C2B   single  1.526  0.020  1.526
 CBS  C1B  O1B   single  1.375  0.020  1.375
 CBS  C1B  O5B   single  1.407  0.020  1.407
 CBS  C1B  H1B   single  0.970  0.020  1.090
 CBS  C2B  C3B   single  1.533  0.020  1.533
 CBS  C2B  N2B   single  1.440  0.020  1.440
 CBS  C2B  H2B   single  0.970  0.020  1.090
 CBS  C3B  C4B   single  1.524  0.020  1.524
 CBS  C3B  O3B   single  1.399  0.020  1.399
 CBS  C3B  H3B   single  0.970  0.020  1.090
 CBS  C4B  C5B   single  1.537  0.020  1.537
 CBS  C4B  H4B   single  0.970  0.020  1.090
 CBS  C5B  C6B   single  1.514  0.020  1.514
 CBS  C5B  O5B   single  1.411  0.020  1.411
 CBS  C5B  H5B   single  0.970  0.020  1.090
 CBS  C6B  O6B   single  1.408  0.020  1.408
 CBS  C6B  H61B  single  0.970  0.020  1.090
 CBS  C6B  H62B  single  0.970  0.020  1.090
 CBS  C7B  C8B   single  1.508  0.020  1.508
 CBS  C7B  N2B   single  1.350  0.020  1.350
 CBS  C7B  O7B   double  1.221  0.020  1.221
 CBS  C8B  H81B  single  0.970  0.020  1.090
 CBS  C8B  H82B  single  0.970  0.020  1.090
 CBS  C8B  H83B  single  0.970  0.020  1.090
 CBS  N2B  HN2B  single  0.860  0.020  1.020
 CBS  O1B  HO1B  single  0.850  0.020  0.980
 CBS  O3B  HO3B  single  0.850  0.020  0.980
 CBS  O6B  HO6B  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
 CBS  H1A   C1A  O5A   109.31  3.000
 CBS  H1A   C1A  O1A   111.24  3.000
 CBS  O5A   C1A  O1A   108.84  3.000
 CBS  H1A   C1A  C2A   109.00  3.000
 CBS  O5A   C1A  C2A   110.64  3.000
 CBS  O1A   C1A  C2A   107.82  3.000
 CBS  H2A   C2A  N2A   108.53  3.000
 CBS  H2A   C2A  C3A   109.27  3.000
 CBS  N2A   C2A  C3A   110.49  3.000
 CBS  H2A   C2A  C1A   108.18  3.000
 CBS  N2A   C2A  C1A   110.67  3.000
 CBS  C3A   C2A  C1A   109.65  3.000
 CBS  H3A   C3A  O3A   110.67  3.000
 CBS  H3A   C3A  C4A   107.14  3.000
 CBS  O3A   C3A  C4A   111.93  3.000
 CBS  H3A   C3A  C2A   108.21  3.000
 CBS  O3A   C3A  C2A   108.09  3.000
 CBS  C4A   C3A  C2A   110.75  3.000
 CBS  H4A   C4A  O4A   111.16  3.000
 CBS  H4A   C4A  C5A   108.57  3.000
 CBS  O4A   C4A  C5A   112.15  3.000
 CBS  H4A   C4A  C3A   108.51  3.000
 CBS  O4A   C4A  C3A   106.67  3.000
 CBS  C5A   C4A  C3A   109.71  3.000
 CBS  H5A   C5A  O5A   110.29  3.000
 CBS  H5A   C5A  C6A   108.90  3.000
 CBS  O5A   C5A  C6A   108.12  3.000
 CBS  H5A   C5A  C4A   108.42  3.000
 CBS  O5A   C5A  C4A   108.88  3.000
 CBS  C6A   C5A  C4A   112.24  3.000
 CBS  H62A  C6A  H61A  107.01  3.000
 CBS  H62A  C6A  O6A   112.03  3.000
 CBS  H61A  C6A  O6A   111.36  3.000
 CBS  H62A  C6A  C5A   108.87  3.000
 CBS  H61A  C6A  C5A   108.36  3.000
 CBS  O6A   C6A  C5A   109.11  3.000
 CBS  H83A  C8A  H82A  107.71  3.000
 CBS  H83A  C8A  H81A  107.68  3.000
 CBS  H82A  C8A  H81A  109.01  3.000
 CBS  H83A  C8A  C7A   108.91  3.000
 CBS  H82A  C8A  C7A   113.20  3.000
 CBS  H81A  C8A  C7A   110.16  3.000
 CBS  HN2A  N2A  C7A   118.04  3.000
 CBS  HN2A  N2A  C2A   117.21  3.000
 CBS  C7A   N2A  C2A   124.44  3.000
 CBS  C4B   O1A  C1A   117.76  3.000
 CBS  HO3A  O3A  C3A   107.77  3.000
 CBS  HO4A  O4A  C4A   109.29  3.000
 CBS  C5A   O5A  C1A   113.08  3.000
 CBS  HO6A  O6A  C6A   107.94  3.000
 CBS  H1B   C1B  O5B   109.08  3.000
 CBS  H1B   C1B  O1B   111.57  3.000
 CBS  O5B   C1B  O1B   108.66  3.000
 CBS  H1B   C1B  C2B   109.58  3.000
 CBS  O5B   C1B  C2B   108.80  3.000
 CBS  O1B   C1B  C2B   109.11  3.000
 CBS  H2B   C2B  N2B   107.87  3.000
 CBS  H2B   C2B  C3B   108.81  3.000
 CBS  N2B   C2B  C3B   110.11  3.000
 CBS  H2B   C2B  C1B   108.30  3.000
 CBS  N2B   C2B  C1B   111.62  3.000
 CBS  C3B   C2B  C1B   110.05  3.000
 CBS  H3B   C3B  O3B   110.85  3.000
 CBS  H3B   C3B  C4B   107.15  3.000
 CBS  O3B   C3B  C4B   109.13  3.000
 CBS  H3B   C3B  C2B   107.97  3.000
 CBS  O3B   C3B  C2B   111.34  3.000
 CBS  C4B   C3B  C2B   110.31  3.000
 CBS  H4B   C4B  C5B   109.70  3.000
 CBS  H4B   C4B  C3B   109.01  3.000
 CBS  C5B   C4B  C3B   109.09  3.000
 CBS  H4B   C4B  O1A   111.31  3.000
 CBS  C5B   C4B  O1A   109.22  3.000
 CBS  C3B   C4B  O1A   108.48  3.000
 CBS  H5B   C5B  O5B   110.22  3.000
 CBS  H5B   C5B  C6B   108.61  3.000
 CBS  O5B   C5B  C6B   107.37  3.000
 CBS  H5B   C5B  C4B   107.76  3.000
 CBS  O5B   C5B  C4B   109.87  3.000
 CBS  C6B   C5B  C4B   113.01  3.000
 CBS  H62B  C6B  H61B  107.20  3.000
 CBS  H62B  C6B  O6B   111.89  3.000
 CBS  H61B  C6B  O6B   111.12  3.000
 CBS  H62B  C6B  C5B   109.02  3.000
 CBS  H61B  C6B  C5B   109.03  3.000
 CBS  O6B   C6B  C5B   108.53  3.000
 CBS  H83B  C8B  H82B  108.26  3.000
 CBS  H83B  C8B  H81B  107.31  3.000
 CBS  H82B  C8B  H81B  108.73  3.000
 CBS  H83B  C8B  C7B   109.06  3.000
 CBS  H82B  C8B  C7B   113.67  3.000
 CBS  H81B  C8B  C7B   109.62  3.000
 CBS  HN2B  N2B  C7B   117.82  3.000
 CBS  HN2B  N2B  C2B   117.51  3.000
 CBS  C7B   N2B  C2B   124.17  3.000
 CBS  HO3B  O3B  C3B   107.66  3.000
 CBS  C5B   O5B  C1B   113.94  3.000
 CBS  HO6B  O6B  C6B   108.05  3.000
 CBS  HO1B  O1B  C1B   109.35  3.000
 CBS  O7A   C7A  N2A   123.30  3.000
 CBS  O7A   C7A  C8A   122.18  3.000
 CBS  N2A   C7A  C8A   114.51  3.000
 CBS  O7B   C7B  N2B   123.29  3.000
 CBS  O7B   C7B  C8B   121.79  3.000
 CBS  N2B   C7B  C8B   114.91  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
 CBS  CONST_01  C8A   C7A  N2A  C2A   180.00   0.0  0
 CBS  CONST_02  O7A   C7A  N2A  C2A     0.00   0.0  0
 CBS  CONST_03  C8B   C7B  N2B  C2B   180.00   0.0  0
 CBS  CONST_04  O7B   C7B  N2B  C2B     0.00   0.0  0
 CBS  CONST_05  HN2A  N2A  C7A  C8A     0.00   0.0  0
 CBS  CONST_06  HN2B  N2B  C7B  C8B     0.00   0.0  0
 CBS  Var_01    H81A  C8A  C7A  N2A  -146.42  30.0  3
 CBS  Var_02    H81B  C8B  C7B  N2B  -131.36  30.0  3

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
 CBS  chir_01  C1A  C2A  O1A  O5A  positiv
 CBS  chir_02  C2A  N2A  C3A  C1A  positiv
 CBS  chir_03  C3A  O3A  C2A  C4A  positiv
 CBS  chir_04  C4A  O4A  C5A  C3A  positiv
 CBS  chir_05  C5A  O5A  C4A  C6A  negativ
 CBS  chir_06  C1B  C2B  O1B  O5B  positiv
 CBS  chir_07  C2B  N2B  C3B  C1B  positiv
 CBS  chir_08  C3B  O3B  C2B  C4B  positiv
 CBS  chir_09  C4B  O1A  C5B  C3B  positiv
 CBS  chir_10  C5B  O5B  C4B  C6B  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
 CBS  plan-1  C2A   0.020
 CBS  plan-1  C8A   0.020
 CBS  plan-1  N2A   0.020
 CBS  plan-1  O7A   0.020
 CBS  plan-1  HN2A  0.020
 CBS  plan-1  C7A   0.020
 CBS  plan-2  C2B   0.020
 CBS  plan-2  C8B   0.020
 CBS  plan-2  N2B   0.020
 CBS  plan-2  O7B   0.020
 CBS  plan-2  HN2B  0.020
 CBS  plan-2  C7B   0.020

