# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 16:36:01 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-[(1R,2S,3R,4R,5R)-2-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-3-hydroxy-6,8-dioxabicyclo[3.2.1]oct-4-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2NC(C)=O)[C@H]3CO[C@@H]1O3
#
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
 3QL  3QL  'N-[(1R,2S,3R,4R,5R)-2-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-3-hydroxy-6,8-dioxabicyclo[3.2.1]oct-4-yl]acetamide (non-preferred name)'  ligand  54  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3QL
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
 3QL  O7A  O  O     0  -0.510  -0.4224   2.7888   0.1413
 3QL  C7A  C  C     0   0.558  -0.0455   2.5488  -1.0003
 3QL  C8A  C  CH3   0  -0.776  -0.7463   3.1297  -2.2001
 3QL  N2A  N  NH1   0  -0.630   1.0306   1.7901  -1.2721
 3QL  C2A  C  CH1   0  -0.160   1.8020   1.0933  -0.2755
 3QL  C3A  C  CH1   0   0.035   3.2882   1.1498  -0.6008
 3QL  O3A  O  OH1   0  -0.662   3.6975   2.4898  -0.5496
 3QL  C4A  C  CH1   0  -0.000   4.0816   0.2724   0.3643
 3QL  O4A  O  OH1   0  -0.673   5.4181   0.2745  -0.0857
 3QL  C5A  C  CH1   0  -0.026   3.4925  -1.1432   0.3896
 3QL  C6A  C  CH2   0  -0.159   4.1876  -2.0325   1.3964
 3QL  O6A  O  OH1   0  -0.668   3.6597  -3.3325   1.2986
 3QL  O5A  O  O2    0  -0.489   2.1259  -1.0694   0.7443
 3QL  C1A  C  CH1   0   0.343   1.3537  -0.3677  -0.1887
 3QL  O1A  O  O2    0  -0.499   0.0458  -0.3908   0.2400
 3QL  C4B  C  CH1   0   0.032  -0.7626  -1.4591  -0.2156
 3QL  C3B  C  CH1   0   0.016  -1.9104  -1.5933   0.7989
 3QL  O3B  O  OH1   0  -0.660  -2.3588  -2.9239   0.7325
 3QL  C5B  C  CH1   0  -0.128  -1.2841  -1.1382  -1.6179
 3QL  O5B  O  O2    0  -0.472  -2.0544   0.0521  -1.5628
 3QL  C1B  C  CH1   0   0.262  -3.2516  -0.3949  -0.9928
 3QL  O1B  O  O2    0  -0.502  -3.5441  -1.6163  -1.6213
 3QL  C6B  C  CH2   0  -0.165  -2.3208  -2.1361  -2.1301
 3QL  C2B  C  CH1   0  -0.168  -3.0437  -0.5773   0.5146
 3QL  N2B  N  NH1   0  -0.650  -2.7641   0.7111   1.1022
 3QL  C7B  C  C     0   0.522  -3.4821   1.2431   2.1102
 3QL  O7B  O  O     0  -0.508  -4.4347   0.6758   2.6296
 3QL  C8B  C  CH3   0  -0.791  -3.0316   2.6071   2.5698
 3QL  H1   H  HCH3  0   0.265  -0.6181   4.2125  -2.2021
 3QL  H2   H  HCH3  0   0.247  -0.3853   2.7385  -3.1490
 3QL  H3   H  HCH3  0   0.265  -1.8125   2.9245  -2.1245
 3QL  H4   H  HNH1  0   0.401   1.2734   1.6358  -2.2382
 3QL  H5   H  HCH1  0   0.275   1.6238   1.5633   0.6950
 3QL  H6   H  HCH1  0   0.212   3.4355   0.7355  -1.6138
 3QL  H7   H  HOH1  0   0.452   4.6366   2.5206  -0.7616
 3QL  H8   H  HCH1  0   0.230   4.0036   0.7026   1.3730
 3QL  H9   H  HOH1  0   0.464   6.0069   0.1955   0.6698
 3QL  H10  H  HCH1  0   0.225   3.6026  -1.5857  -0.6144
 3QL  H11  H  HCH2  0   0.204   5.2630  -2.0178   1.1845
 3QL  H12  H  HCH2  0   0.200   4.0492  -1.6093   2.4011
 3QL  H13  H  HOH1  0   0.457   4.1205  -3.8886   1.9330
 3QL  H14  H  HCH1  0   0.190   1.4691  -0.8351  -1.1838
 3QL  H15  H  HCH1  0   0.260  -0.1990  -2.4007  -0.2345
 3QL  H16  H  HCH1  0   0.242  -1.5078  -1.3690   1.7956
 3QL  H17  H  HOH1  0   0.457  -3.1185  -3.0229   1.3148
 3QL  H18  H  HCH1  0   0.270  -0.4638  -0.9979  -2.3236
 3QL  H19  H  HCH1  0   0.259  -4.0421   0.3335  -1.1946
 3QL  H20  H  HCH2  0   0.238  -2.3452  -2.1424  -3.2230
 3QL  H21  H  HCH2  0   0.241  -2.1563  -3.1551  -1.7812
 3QL  H22  H  HCH1  0   0.276  -3.9693  -0.9435   0.9647
 3QL  H23  H  HNH1  0   0.418  -1.9766   1.2364   0.7452
 3QL  H24  H  HCH3  0   0.263  -3.8771   3.2936   2.5365
 3QL  H25  H  HCH3  0   0.264  -2.7041   2.5475   3.6081
 3QL  H26  H  HCH3  0   0.253  -2.2230   3.0237   1.9744

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
 3QL  C8A  C7A  single  1.506  0.020  1.506
 3QL  C7A  O7A  double  1.226  0.020  1.226
 3QL  C7A  N2A  single  1.344  0.020  1.344
 3QL  N2A  C2A  single  1.440  0.020  1.440
 3QL  O3A  C3A  single  1.402  0.020  1.402
 3QL  C3A  C2A  single  1.522  0.020  1.522
 3QL  C3A  C4A  single  1.527  0.020  1.527
 3QL  C2A  C1A  single  1.531  0.020  1.531
 3QL  C5B  C6B  single  1.527  0.020  1.527
 3QL  C5B  O5B  single  1.419  0.020  1.419
 3QL  C5B  C4B  single  1.530  0.020  1.530
 3QL  C6B  O1B  single  1.423  0.020  1.423
 3QL  C1A  O1A  single  1.377  0.020  1.377
 3QL  C1A  O5A  single  1.400  0.020  1.400
 3QL  O5B  C1B  single  1.399  0.020  1.399
 3QL  O1A  C4B  single  1.415  0.020  1.415
 3QL  O4A  C4A  single  1.410  0.020  1.410
 3QL  C4A  C5A  single  1.533  0.020  1.533
 3QL  O1B  C1B  single  1.404  0.020  1.404
 3QL  C4B  C3B  single  1.538  0.020  1.538
 3QL  C1B  C2B  single  1.533  0.020  1.533
 3QL  O5A  C5A  single  1.414  0.020  1.414
 3QL  C5A  C6A  single  1.513  0.020  1.513
 3QL  C3B  C2B  single  1.548  0.020  1.548
 3QL  C3B  O3B  single  1.406  0.020  1.406
 3QL  C2B  N2B  single  1.443  0.020  1.443
 3QL  C6A  O6A  single  1.407  0.020  1.407
 3QL  N2B  C7B  single  1.347  0.020  1.347
 3QL  C7B  O7B  double  1.224  0.020  1.224
 3QL  C7B  C8B  single  1.508  0.020  1.508
 3QL  C8A  H1   single  0.970  0.020  1.090
 3QL  C8A  H2   single  0.970  0.020  1.090
 3QL  C8A  H3   single  0.970  0.020  1.090
 3QL  N2A  H4   single  0.860  0.020  1.020
 3QL  C2A  H5   single  0.970  0.020  1.090
 3QL  C3A  H6   single  0.970  0.020  1.090
 3QL  O3A  H7   single  0.850  0.020  0.980
 3QL  C4A  H8   single  0.970  0.020  1.090
 3QL  O4A  H9   single  0.850  0.020  0.980
 3QL  C5A  H10  single  0.970  0.020  1.090
 3QL  C6A  H11  single  0.970  0.020  1.090
 3QL  C6A  H12  single  0.970  0.020  1.090
 3QL  O6A  H13  single  0.850  0.020  0.980
 3QL  C1A  H14  single  0.970  0.020  1.090
 3QL  C4B  H15  single  0.970  0.020  1.090
 3QL  C3B  H16  single  0.970  0.020  1.090
 3QL  O3B  H17  single  0.850  0.020  0.980
 3QL  C5B  H18  single  0.970  0.020  1.090
 3QL  C1B  H19  single  0.970  0.020  1.090
 3QL  C6B  H20  single  0.970  0.020  1.090
 3QL  C6B  H21  single  0.970  0.020  1.090
 3QL  C2B  H22  single  0.970  0.020  1.090
 3QL  N2B  H23  single  0.860  0.020  1.020
 3QL  C8B  H24  single  0.970  0.020  1.090
 3QL  C8B  H25  single  0.970  0.020  1.090
 3QL  C8B  H26  single  0.970  0.020  1.090

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
 3QL  N2A  C7A  C8A  115.41  3.000
 3QL  N2A  C7A  O7A  123.01  3.000
 3QL  C8A  C7A  O7A  121.56  3.000
 3QL  H3   C8A  H2   108.53  3.000
 3QL  H3   C8A  H1   107.61  3.000
 3QL  H2   C8A  H1   108.44  3.000
 3QL  H3   C8A  C7A  109.14  3.000
 3QL  H2   C8A  C7A  113.68  3.000
 3QL  H1   C8A  C7A  109.26  3.000
 3QL  H4   N2A  C2A  117.40  3.000
 3QL  H4   N2A  C7A  118.23  3.000
 3QL  C2A  N2A  C7A  124.19  3.000
 3QL  H5   C2A  C1A  108.20  3.000
 3QL  H5   C2A  C3A  109.45  3.000
 3QL  C1A  C2A  C3A  109.48  3.000
 3QL  H5   C2A  N2A  108.61  3.000
 3QL  C1A  C2A  N2A  110.13  3.000
 3QL  C3A  C2A  N2A  110.92  3.000
 3QL  H6   C3A  C4A  107.15  3.000
 3QL  H6   C3A  O3A  110.68  3.000
 3QL  C4A  C3A  O3A  112.00  3.000
 3QL  H6   C3A  C2A  108.20  3.000
 3QL  C4A  C3A  C2A  110.54  3.000
 3QL  O3A  C3A  C2A  108.22  3.000
 3QL  H7   O3A  C3A  107.89  3.000
 3QL  H8   C4A  C5A  108.60  3.000
 3QL  H8   C4A  O4A  111.07  3.000
 3QL  C5A  C4A  O4A  111.76  3.000
 3QL  H8   C4A  C3A  108.55  3.000
 3QL  C5A  C4A  C3A  109.96  3.000
 3QL  O4A  C4A  C3A  106.85  3.000
 3QL  H9   O4A  C4A  109.24  3.000
 3QL  H10  C5A  O5A  110.24  3.000
 3QL  H10  C5A  C6A  108.92  3.000
 3QL  O5A  C5A  C6A  107.93  3.000
 3QL  H10  C5A  C4A  108.48  3.000
 3QL  C6A  C5A  C4A  112.16  3.000
 3QL  O5A  C5A  C4A  109.11  3.000
 3QL  H12  C6A  H11  107.17  3.000
 3QL  H12  C6A  O6A  111.86  3.000
 3QL  H11  C6A  O6A  111.54  3.000
 3QL  H12  C6A  C5A  108.92  3.000
 3QL  H11  C6A  C5A  108.32  3.000
 3QL  O6A  C6A  C5A  108.94  3.000
 3QL  H13  O6A  C6A  107.99  3.000
 3QL  C1A  O5A  C5A  113.09  3.000
 3QL  H14  C1A  O1A  111.87  3.000
 3QL  H14  C1A  O5A  109.30  3.000
 3QL  O1A  C1A  O5A  107.95  3.000
 3QL  H14  C1A  C2A  108.78  3.000
 3QL  O5A  C1A  C2A  110.78  3.000
 3QL  O1A  C1A  C2A  108.18  3.000
 3QL  C4B  O1A  C1A  117.07  3.000
 3QL  H15  C4B  C5B  109.83  3.000
 3QL  H15  C4B  C3B  108.65  3.000
 3QL  C5B  C4B  C3B  111.62  3.000
 3QL  H15  C4B  O1A  111.09  3.000
 3QL  C3B  C4B  O1A  106.25  3.000
 3QL  C5B  C4B  O1A  109.36  3.000
 3QL  H16  C3B  C2B  107.52  3.000
 3QL  H16  C3B  O3B  110.68  3.000
 3QL  C2B  C3B  O3B  112.27  3.000
 3QL  H16  C3B  C4B  107.90  3.000
 3QL  O3B  C3B  C4B  106.83  3.000
 3QL  C2B  C3B  C4B  111.59  3.000
 3QL  H17  O3B  C3B  108.70  3.000
 3QL  H18  C5B  C6B  112.18  3.000
 3QL  H18  C5B  O5B  108.99  3.000
 3QL  C6B  C5B  O5B  101.11  3.000
 3QL  H18  C5B  C4B  111.31  3.000
 3QL  O5B  C5B  C4B  108.99  3.000
 3QL  C6B  C5B  C4B  113.68  3.000
 3QL  C1B  O5B  C5B  102.26  3.000
 3QL  H19  C1B  C2B  111.03  3.000
 3QL  H19  C1B  O1B  110.25  3.000
 3QL  C2B  C1B  O1B  111.40  3.000
 3QL  H19  C1B  O5B  109.30  3.000
 3QL  C2B  C1B  O5B  108.82  3.000
 3QL  O1B  C1B  O5B  105.88  3.000
 3QL  C6B  O1B  C1B  107.37  3.000
 3QL  H21  C6B  H20  108.55  3.000
 3QL  H21  C6B  O1B  110.90  3.000
 3QL  H20  C6B  O1B  109.90  3.000
 3QL  H21  C6B  C5B  113.65  3.000
 3QL  H20  C6B  C5B  110.75  3.000
 3QL  O1B  C6B  C5B  103.00  3.000
 3QL  H22  C2B  N2B  107.19  3.000
 3QL  H22  C2B  C1B  109.28  3.000
 3QL  N2B  C2B  C1B  108.69  3.000
 3QL  H22  C2B  C3B  108.94  3.000
 3QL  N2B  C2B  C3B  111.66  3.000
 3QL  C1B  C2B  C3B  110.98  3.000
 3QL  H23  N2B  C7B  118.29  3.000
 3QL  H23  N2B  C2B  118.07  3.000
 3QL  C7B  N2B  C2B  123.64  3.000
 3QL  C8B  C7B  O7B  121.48  3.000
 3QL  C8B  C7B  N2B  115.22  3.000
 3QL  O7B  C7B  N2B  123.31  3.000
 3QL  H26  C8B  H25  108.61  3.000
 3QL  H26  C8B  H24  108.61  3.000
 3QL  H25  C8B  H24  107.25  3.000
 3QL  H26  C8B  C7B  113.69  3.000
 3QL  H25  C8B  C7B  109.30  3.000
 3QL  H24  C8B  C7B  109.19  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
 3QL  CONST_01  C2A  N2A  C7A  O7A     0.00   0.0  0
 3QL  CONST_02  C2A  N2A  C7A  C8A   180.00   0.0  0
 3QL  CONST_03  O7B  C7B  N2B  C2B     0.00   0.0  0
 3QL  CONST_04  C8B  C7B  N2B  C2B   180.00   0.0  0
 3QL  CONST_05  H4   N2A  C7A  O7A   180.00   0.0  0
 3QL  CONST_06  H23  N2B  C7B  O7B   180.00   0.0  0
 3QL  Var_01    H20  C6B  O1B  C1B  -113.34  30.0  3
 3QL  Var_02    H1   C8A  C7A  O7A    65.85  30.0  3
 3QL  Var_03    H24  C8B  C7B  N2B   125.78  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
 3QL  chir_01  C2A  N2A  C3A  C1A  positiv
 3QL  chir_02  C3A  O3A  C2A  C4A  positiv
 3QL  chir_03  C4A  O4A  C3A  C5A  negativ
 3QL  chir_04  C5A  O5A  C4A  C6A  negativ
 3QL  chir_05  C1A  O1A  O5A  C2A  positiv
 3QL  chir_06  C4B  O1A  C3B  C5B  negativ
 3QL  chir_07  C3B  O3B  C4B  C2B  negativ
 3QL  chir_08  C5B  O5B  C4B  C6B  negativ
 3QL  chir_09  C1B  O1B  O5B  C2B  positiv
 3QL  chir_10  C2B  N2B  C3B  C1B  positiv

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
 3QL  plan-1  O7A  0.020
 3QL  plan-1  C7A  0.020
 3QL  plan-1  C8A  0.020
 3QL  plan-1  N2A  0.020
 3QL  plan-1  C2A  0.020
 3QL  plan-1  H4   0.020
 3QL  plan-2  C2B  0.020
 3QL  plan-2  N2B  0.020
 3QL  plan-2  C7B  0.020
 3QL  plan-2  O7B  0.020
 3QL  plan-2  C8B  0.020
 3QL  plan-2  H23  0.020

