# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:52:24 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-{(2R)-2-methyl-3-[4-(propan-2-yl)phenyl]propanoyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ccc(C[C@@H](C)C(=O)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)cc1
#
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
 26R  26R  N-{(2R)-2-methyl-3-[4-(propan-2-yl)phenyl]propanoyl}-beta-D-glucopyranosylamine  saccharide  55  26  .  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_26R
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
 26R  C14  C  CH3   0  -0.646   7.5425  -0.8454   1.9909
 26R  C13  C  CH1   0  -0.327   7.5074  -0.1236   0.6442
 26R  C15  C  CH3   0  -0.641   8.3721  -0.8533  -0.3850
 26R  C10  C  CR6   0   0.158   6.0953   0.0570   0.1384
 26R  C9   C  CR16  0  -0.298   5.2442  -1.0344  -0.0395
 26R  C8   C  CR16  0  -0.289   3.9543  -0.8658  -0.5165
 26R  C11  C  CR16  0  -0.319   5.6043   1.3179  -0.1826
 26R  C12  C  CR16  0  -0.293   4.3107   1.4875  -0.6625
 26R  C7   C  CR6   0   0.109   3.4628   0.3995  -0.8363
 26R  C6   C  CH2   0  -0.497   2.0523   0.5720  -1.3268
 26R  C4   C  CH1   0  -0.393   1.0249   0.4680  -0.1926
 26R  C5   C  CH3   0  -0.651   1.1974   1.5718   0.8529
 26R  C2   C  C     0   0.588  -0.3866   0.5459  -0.7430
 26R  O3   O  O     0  -0.479  -0.7024   1.3157  -1.6327
 26R  N1   N  NH1   0  -0.693  -1.2704  -0.2932  -0.1459
 26R  C1'  C  CH1   0   0.209  -2.6761  -0.2465  -0.3725
 26R  O5'  O  O2    0  -0.488  -3.2529   0.6271   0.5702
 26R  C5'  C  CH1   0  -0.014  -4.6370   0.8299   0.3750
 26R  C6'  C  CH2   0  -0.156  -5.0988   1.8690   1.3746
 26R  O6'  O  OH1   0  -0.670  -4.4283   3.0789   1.1142
 26R  C4'  C  CH1   0   0.034  -5.3796  -0.4962   0.5470
 26R  O4'  O  OH1   0  -0.672  -6.7431  -0.2711   0.2895
 26R  C3'  C  CH1   0  -0.003  -4.7999  -1.5336  -0.4076
 26R  O3'  O  OH1   0  -0.672  -5.4511  -2.7543  -0.1541
 26R  C2'  C  CH1   0  -0.031  -3.2913  -1.6412  -0.2345
 26R  O2'  O  OH1   0  -0.664  -2.8145  -2.5184  -1.2224
 26R  H1   H  HCH3  0   0.218   7.1706  -1.8683   1.9052
 26R  H2   H  HCH3  0   0.230   8.5648  -0.9005   2.3689
 26R  H3   H  HCH3  0   0.231   6.9368  -0.3303   2.7373
 26R  H4   H  HCH1  0   0.237   7.9331   0.8744   0.7905
 26R  H5   H  HCH3  0   0.219   7.9963  -1.8612  -0.5738
 26R  H6   H  HCH3  0   0.230   8.3933  -0.3207  -1.3364
 26R  H7   H  HCH3  0   0.228   9.4000  -0.9451  -0.0297
 26R  H8   H  HCR6  0   0.242   5.5897  -2.0346   0.1952
 26R  H9   H  HCR6  0   0.241   3.3180  -1.7347  -0.6444
 26R  H10  H  HCR6  0   0.243   6.2420   2.1857  -0.0575
 26R  H11  H  HCR6  0   0.244   3.9581   2.4838  -0.9039
 26R  H12  H  HCH2  0   0.249   1.9482   1.5395  -1.8216
 26R  H13  H  HCH2  0   0.255   1.8342  -0.1929  -2.0769
 26R  H14  H  HCH1  0   0.264   1.1559  -0.4983   0.3052
 26R  H15  H  HCH3  0   0.231   1.1265   2.5597   0.3953
 26R  H16  H  HCH3  0   0.241   0.4394   1.5028   1.6340
 26R  H17  H  HCH3  0   0.247   2.1729   1.4935   1.3314
 26R  H18  H  HNH1  0   0.404  -0.9422  -0.8339   0.6413
 26R  H19  H  HCH1  0   0.231  -2.8491   0.1220  -1.3918
 26R  H20  H  HCH1  0   0.223  -4.8222   1.2043  -0.6456
 26R  H21  H  HCH2  0   0.213  -6.1842   1.9788   1.2829
 26R  H22  H  HCH2  0   0.196  -4.8951   1.5004   2.3899
 26R  H23  H  HOH1  0   0.457  -4.7743   3.7441   1.7155
 26R  H24  H  HCH1  0   0.213  -5.2242  -0.8479   1.5797
 26R  H25  H  HOH1  0   0.455  -7.2167  -1.0972   0.4303
 26R  H26  H  HCH1  0   0.216  -4.9968  -1.1899  -1.4363
 26R  H27  H  HOH1  0   0.457  -5.2005  -3.3841  -0.8375
 26R  H28  H  HCH1  0   0.226  -3.0766  -2.0175   0.7782
 26R  H29  H  HOH1  0   0.457  -1.8997  -2.7444  -1.0272

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
 26R  O3'  C3'  single    1.407  0.020  1.407
 26R  O4'  C4'  single    1.406  0.020  1.406
 26R  C3'  C4'  single    1.524  0.020  1.524
 26R  C3'  C2'  single    1.522  0.020  1.522
 26R  C4'  C5'  single    1.530  0.020  1.530
 26R  O2'  C2'  single    1.405  0.020  1.405
 26R  C2'  C1'  single    1.531  0.020  1.531
 26R  O6'  C6'  single    1.408  0.020  1.408
 26R  C5'  C6'  single    1.514  0.020  1.514
 26R  C5'  O5'  single    1.412  0.020  1.412
 26R  C1'  O5'  single    1.409  0.020  1.409
 26R  C1'  N1   single    1.425  0.020  1.425
 26R  N1   C2   single    1.357  0.020  1.357
 26R  C2   C4   single    1.517  0.020  1.517
 26R  C2   O3   double    1.218  0.020  1.218
 26R  C4   C6   single    1.534  0.020  1.534
 26R  C4   C5   single    1.530  0.020  1.530
 26R  C6   C7   single    1.503  0.020  1.503
 26R  C8   C7   aromatic  1.395  0.020  1.395
 26R  C8   C9   aromatic  1.386  0.020  1.386
 26R  C7   C12  aromatic  1.390  0.020  1.390
 26R  C9   C10  aromatic  1.395  0.020  1.395
 26R  C12  C11  aromatic  1.390  0.020  1.390
 26R  C10  C11  aromatic  1.391  0.020  1.391
 26R  C10  C13  single    1.511  0.020  1.511
 26R  C13  C14  single    1.528  0.020  1.528
 26R  C13  C15  single    1.529  0.020  1.529
 26R  C14  H1   single    0.970  0.020  1.090
 26R  C14  H2   single    0.970  0.020  1.090
 26R  C14  H3   single    0.970  0.020  1.090
 26R  C13  H4   single    0.970  0.020  1.090
 26R  C15  H5   single    0.970  0.020  1.090
 26R  C15  H6   single    0.970  0.020  1.090
 26R  C15  H7   single    0.970  0.020  1.090
 26R  C9   H8   single    0.930  0.020  1.080
 26R  C8   H9   single    0.930  0.020  1.080
 26R  C11  H10  single    0.930  0.020  1.080
 26R  C12  H11  single    0.930  0.020  1.080
 26R  C6   H12  single    0.970  0.020  1.090
 26R  C6   H13  single    0.970  0.020  1.090
 26R  C4   H14  single    0.970  0.020  1.090
 26R  C5   H15  single    0.970  0.020  1.090
 26R  C5   H16  single    0.970  0.020  1.090
 26R  C5   H17  single    0.970  0.020  1.090
 26R  N1   H18  single    0.860  0.020  1.020
 26R  C1'  H19  single    0.970  0.020  1.090
 26R  C5'  H20  single    0.970  0.020  1.090
 26R  C6'  H21  single    0.970  0.020  1.090
 26R  C6'  H22  single    0.970  0.020  1.090
 26R  O6'  H23  single    0.850  0.020  0.980
 26R  C4'  H24  single    0.970  0.020  1.090
 26R  O4'  H25  single    0.850  0.020  0.980
 26R  C3'  H26  single    0.970  0.020  1.090
 26R  O3'  H27  single    0.850  0.020  0.980
 26R  C2'  H28  single    0.970  0.020  1.090
 26R  O2'  H29  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
 26R  H3   C14  H2   107.89  3.000
 26R  H3   C14  H1   107.88  3.000
 26R  H2   C14  H1   107.40  3.000
 26R  H3   C14  C13  111.55  3.000
 26R  H2   C14  C13  110.52  3.000
 26R  H1   C14  C13  111.43  3.000
 26R  H4   C13  C10  107.41  3.000
 26R  H4   C13  C15  107.75  3.000
 26R  C10  C13  C15  111.11  3.000
 26R  H4   C13  C14  107.69  3.000
 26R  C15  C13  C14  110.77  3.000
 26R  C10  C13  C14  111.90  3.000
 26R  H7   C15  H6   107.86  3.000
 26R  H7   C15  H5   107.62  3.000
 26R  H6   C15  H5   107.85  3.000
 26R  H7   C15  C13  110.70  3.000
 26R  H6   C15  C13  111.41  3.000
 26R  H5   C15  C13  111.23  3.000
 26R  C11  C10  C9   117.67  3.000
 26R  C11  C10  C13  121.04  3.000
 26R  C9   C10  C13  121.28  3.000
 26R  H8   C9   C8   118.92  3.000
 26R  H8   C9   C10  119.98  3.000
 26R  C8   C9   C10  121.10  3.000
 26R  H9   C8   C7   119.54  3.000
 26R  H9   C8   C9   119.30  3.000
 26R  C7   C8   C9   121.16  3.000
 26R  H10  C11  C12  119.31  3.000
 26R  H10  C11  C10  119.44  3.000
 26R  C12  C11  C10  121.25  3.000
 26R  H11  C12  C7   119.54  3.000
 26R  H11  C12  C11  119.45  3.000
 26R  C7   C12  C11  121.01  3.000
 26R  C6   C7   C12  121.55  3.000
 26R  C12  C7   C8   117.80  3.000
 26R  C6   C7   C8   120.64  3.000
 26R  H13  C6   H12  106.86  3.000
 26R  H13  C6   C4   109.04  3.000
 26R  H12  C6   C4   109.35  3.000
 26R  H13  C6   C7   109.32  3.000
 26R  H12  C6   C7   109.82  3.000
 26R  C4   C6   C7   112.30  3.000
 26R  H14  C4   C2   108.76  3.000
 26R  H14  C4   C5   108.21  3.000
 26R  C2   C4   C5   108.40  3.000
 26R  H14  C4   C6   108.42  3.000
 26R  C5   C4   C6   112.39  3.000
 26R  C2   C4   C6   110.58  3.000
 26R  H17  C5   H16  107.65  3.000
 26R  H17  C5   H15  107.91  3.000
 26R  H16  C5   H15  108.22  3.000
 26R  H17  C5   C4   110.44  3.000
 26R  H16  C5   C4   111.43  3.000
 26R  H15  C5   C4   111.06  3.000
 26R  N1   C2   O3   122.91  3.000
 26R  O3   C2   C4   122.59  3.000
 26R  N1   C2   C4   114.49  3.000
 26R  H18  N1   C1'  117.53  3.000
 26R  H18  N1   C2   117.54  3.000
 26R  C1'  N1   C2   123.53  3.000
 26R  H19  C1'  C2'  109.04  3.000
 26R  H19  C1'  O5'  110.41  3.000
 26R  C2'  C1'  O5'  109.89  3.000
 26R  H19  C1'  N1   108.31  3.000
 26R  O5'  C1'  N1   108.53  3.000
 26R  C2'  C1'  N1   110.64  3.000
 26R  C5'  O5'  C1'  113.44  3.000
 26R  H20  C5'  C4'  108.47  3.000
 26R  H20  C5'  C6'  109.08  3.000
 26R  C4'  C5'  C6'  111.88  3.000
 26R  H20  C5'  O5'  109.95  3.000
 26R  C6'  C5'  O5'  107.83  3.000
 26R  C4'  C5'  O5'  109.62  3.000
 26R  H22  C6'  H21  107.14  3.000
 26R  H22  C6'  O6'  111.77  3.000
 26R  H21  C6'  O6'  111.75  3.000
 26R  H22  C6'  C5'  108.86  3.000
 26R  H21  C6'  C5'  108.42  3.000
 26R  O6'  C6'  C5'  108.82  3.000
 26R  H23  O6'  C6'  107.92  3.000
 26R  H24  C4'  C3'  108.42  3.000
 26R  H24  C4'  O4'  111.07  3.000
 26R  C3'  C4'  O4'  111.29  3.000
 26R  H24  C4'  C5'  108.28  3.000
 26R  C3'  C4'  C5'  109.57  3.000
 26R  O4'  C4'  C5'  108.15  3.000
 26R  H25  O4'  C4'  108.24  3.000
 26R  H26  C3'  C2'  107.77  3.000
 26R  H26  C3'  O3'  110.86  3.000
 26R  C2'  C3'  O3'  112.15  3.000
 26R  H26  C3'  C4'  107.72  3.000
 26R  C2'  C3'  C4'  110.72  3.000
 26R  O3'  C3'  C4'  107.56  3.000
 26R  H27  O3'  C3'  108.62  3.000
 26R  H28  C2'  O2'  111.54  3.000
 26R  H28  C2'  C3'  108.77  3.000
 26R  O2'  C2'  C3'  107.49  3.000
 26R  H28  C2'  C1'  108.41  3.000
 26R  O2'  C2'  C1'  111.67  3.000
 26R  C3'  C2'  C1'  108.89  3.000
 26R  H29  O2'  C2'  109.07  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
 26R  CONST_01  C7   C8   C9   C10    0.00   0.0  0
 26R  CONST_02  C7   C12  C11  C10    0.00   0.0  0
 26R  CONST_03  C12  C7   C8   C9     0.00   0.0  0
 26R  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 26R  CONST_05  C11  C12  C7   C8     0.00   0.0  0
 26R  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 26R  CONST_07  C8   C9   C10  C13  180.00   0.0  0
 26R  CONST_08  C12  C11  C10  C13  180.00   0.0  0
 26R  CONST_09  C6   C7   C8   C9   180.00   0.0  0
 26R  CONST_10  C6   C7   C12  C11  180.00   0.0  0
 26R  CONST_11  H9   C8   C9   C10  180.00   0.0  0
 26R  CONST_12  H11  C12  C11  C10  180.00   0.0  0
 26R  CONST_13  H10  C11  C10  C9   180.00   0.0  0
 26R  CONST_14  H8   C9   C10  C11  180.00   0.0  0
 26R  CONST_15  C1'  N1   C2   C4   180.00   0.0  0
 26R  CONST_16  C1'  N1   C2   O3     0.00   0.0  0
 26R  CONST_17  H18  N1   C2   C4     0.00   0.0  0
 26R  Var_01    C9   C10  C13  C14  -56.58  30.0  2
 26R  Var_02    C4   C6   C7   C8    76.31  30.0  3
 26R  Var_03    H1   C14  C13  C10   64.71  30.0  3
 26R  Var_04    H5   C15  C13  C10  -62.65  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
 26R  chir_01  C4   C2   C6   C5   negativ
 26R  chir_02  C1'  O5'  N1   C2'  negativ
 26R  chir_03  C5'  O5'  C6'  C4'  positiv
 26R  chir_04  C4'  O4'  C5'  C3'  positiv
 26R  chir_05  C3'  O3'  C4'  C2'  negativ
 26R  chir_06  C2'  O2'  C3'  C1'  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
 26R  plan-1  C13  0.020
 26R  plan-1  C10  0.020
 26R  plan-1  C9   0.020
 26R  plan-1  C8   0.020
 26R  plan-1  C11  0.020
 26R  plan-1  C12  0.020
 26R  plan-1  C7   0.020
 26R  plan-1  C6   0.020
 26R  plan-1  H8   0.020
 26R  plan-1  H9   0.020
 26R  plan-1  H10  0.020
 26R  plan-1  H11  0.020
 26R  plan-2  C4   0.020
 26R  plan-2  C2   0.020
 26R  plan-2  O3   0.020
 26R  plan-2  N1   0.020
 26R  plan-2  C1'  0.020
 26R  plan-2  H18  0.020

