# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 19 20:39:47 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1NC(=O)[C@H](O)[C@@H](O)[C@@H]1O[C@@H]2O[C@H](CO)[C@@H](O)[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
 ABL  ABL  '(2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside'  D-saccharide  44  23  .  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_ABL
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
 ABL  C1    C  C     0   0.496  -4.1678   0.0162   0.2517
 ABL  O1    O  O     0  -0.495  -5.3714   0.1135   0.4500
 ABL  C2    C  CH1   0  -0.076  -3.3713   1.2404  -0.1782
 ABL  O2    O  OH1   0  -0.667  -4.1660   2.1007  -0.9425
 ABL  C3    C  CH1   0   0.022  -2.1279   0.8758  -0.9763
 ABL  O3    O  OH1   0  -0.650  -1.3409   2.0018  -1.2388
 ABL  C4    C  CH1   0   0.004  -1.3123  -0.1085  -0.1498
 ABL  O4    O  O2    0  -0.508  -0.1203  -0.4281  -0.8346
 ABL  C5    C  CH1   0  -0.095  -2.1120  -1.3983   0.0554
 ABL  N5    N  NH1   0  -0.638  -3.4795  -1.1124   0.4545
 ABL  C6    C  CH2   0  -0.147  -1.4748  -2.3023   1.0998
 ABL  O6    O  OH1   0  -0.670  -2.2683  -3.4616   1.2051
 ABL  C1A   C  CH1   0   0.286   1.0634  -0.3055  -0.1308
 ABL  C2A   C  CH1   0  -0.032   2.1147  -1.1831  -0.8060
 ABL  O2A   O  OH1   0  -0.663   1.7770  -2.5463  -0.7446
 ABL  C3A   C  CH1   0  -0.011   3.4358  -0.9987  -0.0730
 ABL  O3A   O  OH1   0  -0.672   4.4969  -1.6666  -0.7114
 ABL  C4A   C  CH1   0   0.033   3.8050   0.4787   0.0024
 ABL  O4A   O  OH1   0  -0.672   4.9343   0.6795   0.8149
 ABL  C5A   C  CH1   0  -0.020   2.6398   1.2737   0.5965
 ABL  O5A   O  O2    0  -0.476   1.4692   1.0324  -0.1572
 ABL  C6A   C  CH2   0  -0.153   2.9078   2.7632   0.5748
 ABL  O6A   O  OH1   0  -0.667   1.8648   3.4269   1.2461
 ABL  H2    H  HCH1  0   0.246  -3.0407   1.7279   0.7553
 ABL  HO2   H  HOH1  0   0.453  -5.0378   2.1412  -0.5305
 ABL  H3    H  HCH1  0   0.225  -2.4400   0.3789  -1.9093
 ABL  HO3   H  HOH1  0   0.453  -1.8512   2.6020  -1.7924
 ABL  H4    H  HCH1  0   0.248  -1.0895   0.3475   0.8250
 ABL  H5    H  HCH1  0   0.262  -2.1242  -1.9346  -0.9025
 ABL  HN5   H  HNH1  0   0.400  -4.0167  -1.9102   0.7673
 ABL  H6    H  HCH2  0   0.210  -0.4539  -2.5472   0.7905
 ABL  H6A   H  HCH2  0   0.208  -1.4158  -1.7586   2.0515
 ABL  HO6   H  HOH1  0   0.464  -1.9320  -3.9953   1.9306
 ABL  H1A   H  HCH1  0   0.190   0.9363  -0.6346   0.9178
 ABL  H2A   H  HCH1  0   0.229   2.2318  -0.8429  -1.8457
 ABL  HO2A  H  HOH1  0   0.458   1.0727  -2.7192  -1.3769
 ABL  H3A   H  HCH1  0   0.217   3.3078  -1.3656   0.9586
 ABL  HO3A  H  HOH1  0   0.458   4.3780  -2.6147  -0.5975
 ABL  H4A   H  HCH1  0   0.212   3.9840   0.8435  -1.0221
 ABL  HO4A  H  HOH1  0   0.454   5.6560   0.1501   0.4598
 ABL  H5A   H  HCH1  0   0.222   2.4947   0.9500   1.6409
 ABL  H6AA  H  HCH2  0   0.212   3.8766   2.9474   1.0508
 ABL  H6AB  H  HCH2  0   0.195   2.9955   3.0901  -0.4711
 ABL  HO6A  H  HOH1  0   0.455   2.0897   4.3604   1.2897

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
 ABL  C1   O1    double  1.224  0.020  1.224
 ABL  C1   C2    single  1.522  0.020  1.522
 ABL  C1   N5    single  1.337  0.020  1.337
 ABL  C2   O2    single  1.398  0.020  1.398
 ABL  C2   C3    single  1.522  0.020  1.522
 ABL  C3   O3    single  1.399  0.020  1.399
 ABL  C3   C4    single  1.522  0.020  1.522
 ABL  C4   O4    single  1.411  0.020  1.411
 ABL  C4   C5    single  1.531  0.020  1.531
 ABL  O4   C1A   single  1.383  0.020  1.383
 ABL  C5   N5    single  1.453  0.020  1.453
 ABL  C5   C6    single  1.521  0.020  1.521
 ABL  C6   O6    single  1.409  0.020  1.409
 ABL  C1A  C2A   single  1.527  0.020  1.527
 ABL  C1A  O5A   single  1.398  0.020  1.398
 ABL  C2A  O2A   single  1.406  0.020  1.406
 ABL  C2A  C3A   single  1.522  0.020  1.522
 ABL  C3A  O3A   single  1.407  0.020  1.407
 ABL  C3A  C4A   single  1.525  0.020  1.525
 ABL  C4A  O4A   single  1.406  0.020  1.406
 ABL  C4A  C5A   single  1.531  0.020  1.531
 ABL  C5A  O5A   single  1.413  0.020  1.413
 ABL  C5A  C6A   single  1.514  0.020  1.514
 ABL  C6A  O6A   single  1.407  0.020  1.407
 ABL  C2   H2    single  0.970  0.020  1.090
 ABL  O2   HO2   single  0.850  0.020  0.980
 ABL  C3   H3    single  0.970  0.020  1.090
 ABL  O3   HO3   single  0.850  0.020  0.980
 ABL  C4   H4    single  0.970  0.020  1.090
 ABL  C5   H5    single  0.970  0.020  1.090
 ABL  N5   HN5   single  0.860  0.020  1.020
 ABL  C6   H6    single  0.970  0.020  1.090
 ABL  C6   H6A   single  0.970  0.020  1.090
 ABL  O6   HO6   single  0.850  0.020  0.980
 ABL  C1A  H1A   single  0.970  0.020  1.090
 ABL  C2A  H2A   single  0.970  0.020  1.090
 ABL  O2A  HO2A  single  0.850  0.020  0.980
 ABL  C3A  H3A   single  0.970  0.020  1.090
 ABL  O3A  HO3A  single  0.850  0.020  0.980
 ABL  C4A  H4A   single  0.970  0.020  1.090
 ABL  O4A  HO4A  single  0.850  0.020  0.980
 ABL  C5A  H5A   single  0.970  0.020  1.090
 ABL  C6A  H6AA  single  0.970  0.020  1.090
 ABL  C6A  H6AB  single  0.970  0.020  1.090
 ABL  O6A  HO6A  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
 ABL  N5    C1   C2    116.88  3.000
 ABL  N5    C1   O1    123.28  3.000
 ABL  C2    C1   O1    119.76  3.000
 ABL  H2    C2   C3    107.73  3.000
 ABL  H2    C2   O2    111.14  3.000
 ABL  C3    C2   O2    108.97  3.000
 ABL  H2    C2   C1    105.84  3.000
 ABL  C3    C2   C1    112.51  3.000
 ABL  O2    C2   C1    110.60  3.000
 ABL  HO2   O2   C2    107.80  3.000
 ABL  H3    C3   C4    108.65  3.000
 ABL  H3    C3   O3    111.31  3.000
 ABL  C4    C3   O3    108.72  3.000
 ABL  H3    C3   C2    108.70  3.000
 ABL  C4    C3   C2    107.94  3.000
 ABL  O3    C3   C2    111.42  3.000
 ABL  HO3   O3   C3    108.15  3.000
 ABL  H4    C4   C5    109.66  3.000
 ABL  H4    C4   O4    110.68  3.000
 ABL  C5    C4   O4    108.38  3.000
 ABL  H4    C4   C3    108.78  3.000
 ABL  C5    C4   C3    109.73  3.000
 ABL  O4    C4   C3    109.61  3.000
 ABL  C1A   O4   C4    117.13  3.000
 ABL  H5    C5   C6    108.27  3.000
 ABL  H5    C5   N5    108.98  3.000
 ABL  C6    C5   N5    108.82  3.000
 ABL  H5    C5   C4    107.48  3.000
 ABL  C6    C5   C4    111.95  3.000
 ABL  N5    C5   C4    111.25  3.000
 ABL  HN5   N5   C5    115.45  3.000
 ABL  HN5   N5   C1    116.05  3.000
 ABL  C5    N5   C1    127.50  3.000
 ABL  H6A   C6   H6    107.80  3.000
 ABL  H6A   C6   O6    111.90  3.000
 ABL  H6    C6   O6    111.24  3.000
 ABL  H6A   C6   C5    108.88  3.000
 ABL  H6    C6   C5    109.25  3.000
 ABL  O6    C6   C5    107.73  3.000
 ABL  HO6   O6   C6    108.44  3.000
 ABL  H1A   C1A  O5A   109.62  3.000
 ABL  H1A   C1A  C2A   109.10  3.000
 ABL  O5A   C1A  C2A   109.98  3.000
 ABL  H1A   C1A  O4    110.96  3.000
 ABL  O5A   C1A  O4    108.89  3.000
 ABL  C2A   C1A  O4    108.27  3.000
 ABL  H2A   C2A  C3A   108.98  3.000
 ABL  H2A   C2A  O2A   111.51  3.000
 ABL  C3A   C2A  O2A   107.76  3.000
 ABL  H2A   C2A  C1A   108.27  3.000
 ABL  C3A   C2A  C1A   108.36  3.000
 ABL  O2A   C2A  C1A   111.88  3.000
 ABL  HO2A  O2A  C2A   108.75  3.000
 ABL  H3A   C3A  C4A   107.72  3.000
 ABL  H3A   C3A  O3A   110.74  3.000
 ABL  C4A   C3A  O3A   107.45  3.000
 ABL  H3A   C3A  C2A   108.04  3.000
 ABL  C4A   C3A  C2A   110.57  3.000
 ABL  O3A   C3A  C2A   112.24  3.000
 ABL  HO3A  O3A  C3A   108.71  3.000
 ABL  H4A   C4A  C5A   108.21  3.000
 ABL  H4A   C4A  O4A   111.07  3.000
 ABL  C5A   C4A  O4A   108.25  3.000
 ABL  H4A   C4A  C3A   108.31  3.000
 ABL  C5A   C4A  C3A   109.76  3.000
 ABL  O4A   C4A  C3A   111.20  3.000
 ABL  HO4A  O4A  C4A   108.09  3.000
 ABL  H5A   C5A  C6A   109.01  3.000
 ABL  H5A   C5A  O5A   110.24  3.000
 ABL  C6A   C5A  O5A   107.89  3.000
 ABL  H5A   C5A  C4A   108.37  3.000
 ABL  C6A   C5A  C4A   111.76  3.000
 ABL  O5A   C5A  C4A   109.57  3.000
 ABL  C5A   O5A  C1A   113.19  3.000
 ABL  H6AB  C6A  H6AA  107.04  3.000
 ABL  H6AB  C6A  O6A   111.89  3.000
 ABL  H6AA  C6A  O6A   111.67  3.000
 ABL  H6AB  C6A  C5A   108.69  3.000
 ABL  H6AA  C6A  C5A   108.42  3.000
 ABL  O6A   C6A  C5A   109.03  3.000
 ABL  HO6A  O6A  C6A   107.84  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
 ABL  CONST_01  C5   N5  C1  C2    0.00  0.0  0
 ABL  CONST_02  C5   N5  C1  O1  180.00  0.0  0
 ABL  CONST_03  HN5  N5  C1  C2  180.00  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
 ABL  chir_01  C2   C1   O2   C3   positiv
 ABL  chir_02  C3   O3   C2   C4   positiv
 ABL  chir_03  C4   O4   C5   C3   positiv
 ABL  chir_04  C5   N5   C4   C6   negativ
 ABL  chir_05  C1A  O4   O5A  C2A  positiv
 ABL  chir_06  C2A  O2A  C1A  C3A  negativ
 ABL  chir_07  C3A  O3A  C2A  C4A  positiv
 ABL  chir_08  C4A  O4A  C5A  C3A  positiv
 ABL  chir_09  C5A  O5A  C4A  C6A  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
 ABL  plan-1  C1   0.020
 ABL  plan-1  O1   0.020
 ABL  plan-1  C2   0.020
 ABL  plan-1  C5   0.020
 ABL  plan-1  N5   0.020
 ABL  plan-1  HN5  0.020

