# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:52:47 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-[(3R)-3-(4-ethylphenyl)butanoyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(cc1)[C@H](C)CC(=O)N[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
 26W  26W  N-[(3R)-3-(4-ethylphenyl)butanoyl]-beta-D-glucopyranosylamine  saccharide  52  25  .  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_26W
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
 26W  C14  C  CH3   0  -0.655  -8.1250   1.4810   1.0080
 26W  C13  C  CH2   0  -0.503  -7.8164   0.0172   0.6987
 26W  C10  C  CR6   0   0.111  -6.3751  -0.1890   0.3233
 26W  C11  C  CR16  0  -0.289  -5.3927  -0.3243   1.3031
 26W  C12  C  CR16  0  -0.298  -4.0561  -0.4692   0.9642
 26W  C9   C  CR16  0  -0.295  -5.9705  -0.2055  -1.0076
 26W  C8   C  CR16  0  -0.314  -4.6312  -0.3518  -1.3475
 26W  C7   C  CR6   0   0.159  -3.6512  -0.4864  -0.3697
 26W  C5   C  CH1   0  -0.337  -2.1961  -0.6215  -0.7517
 26W  C6   C  CH3   0  -0.656  -1.5374  -1.8363  -0.0998
 26W  C4   C  CH2   0  -0.556  -1.4433   0.6755  -0.4137
 26W  C2   C  C     0   0.555  -0.0236   0.6323  -0.9304
 26W  O3   O  O     0  -0.483   0.2228   0.4660  -2.1130
 26W  N1   N  NH1   0  -0.682   0.9394   0.7906   0.0094
 26W  C1'  C  CH1   0   0.204   2.3326   0.6438  -0.2556
 26W  O5'  O  O2    0  -0.483   2.7156  -0.6596   0.1135
 26W  C5'  C  CH1   0  -0.014   4.0605  -0.9612  -0.1941
 26W  C6'  C  CH2   0  -0.156   4.3016  -2.4125   0.1652
 26W  O6'  O  OH1   0  -0.668   3.4733  -3.2234  -0.6328
 26W  C4'  C  CH1   0   0.036   4.9910  -0.0239   0.5777
 26W  O4'  O  OH1   0  -0.672   6.3143  -0.3117   0.2014
 26W  C3'  C  CH1   0  -0.007   4.6295   1.4244   0.2688
 26W  O3'  O  OH1   0  -0.672   5.4526   2.2429   1.0644
 26W  C2'  C  CH1   0  -0.025   3.1500   1.6713   0.5301
 26W  O2'  O  OH1   0  -0.664   2.8546   2.9825   0.1226
 26W  H1   H  HCH3  0   0.230  -9.1724   1.6095   1.2835
 26W  H2   H  HCH3  0   0.225  -7.5146   1.8451   1.8357
 26W  H3   H  HCH3  0   0.225  -7.9255   2.1158   0.1437
 26W  H4   H  HCH2  0   0.238  -8.0637  -0.5943   1.5698
 26W  H5   H  HCH2  0   0.238  -8.4609  -0.3251  -0.1141
 26W  H6   H  HCR6  0   0.243  -5.6772  -0.3173   2.3495
 26W  H7   H  HCR6  0   0.243  -3.3235  -0.5719   1.7563
 26W  H8   H  HCR6  0   0.243  -6.7113  -0.1073  -1.7930
 26W  H9   H  HCR6  0   0.244  -4.3465  -0.3653  -2.3936
 26W  H10  H  HCH1  0   0.254  -2.1516  -0.7516  -1.8366
 26W  H11  H  HCH3  0   0.224  -1.4908  -1.7370   0.9858
 26W  H12  H  HCH3  0   0.241  -2.0917  -2.7464  -0.3290
 26W  H13  H  HCH3  0   0.236  -0.5162  -1.9777  -0.4581
 26W  H14  H  HCH2  0   0.282  -1.9453   1.5222  -0.8889
 26W  H15  H  HCH2  0   0.254  -1.4731   0.8534   0.6644
 26W  H16  H  HNH1  0   0.404   0.6521   0.8408   0.9759
 26W  H17  H  HCH1  0   0.232   2.4927   0.8046  -1.3291
 26W  H18  H  HCH1  0   0.222   4.2408  -0.8223  -1.2730
 26W  H19  H  HCH2  0   0.213   5.3615  -2.6360   0.0064
 26W  H20  H  HCH2  0   0.195   4.0995  -2.5494   1.2370
 26W  H21  H  HOH1  0   0.456   3.6964  -4.1409  -0.4530
 26W  H22  H  HCH1  0   0.212   4.8397  -0.1967   1.6558
 26W  H23  H  HOH1  0   0.454   6.8961   0.3052   0.6578
 26W  H24  H  HCH1  0   0.218   4.8214   1.5996  -0.8022
 26W  H25  H  HOH1  0   0.458   5.3738   3.1514   0.7572
 26W  H26  H  HCH1  0   0.225   2.9518   1.5288   1.6041
 26W  H27  H  HOH1  0   0.457   1.9765   3.2162   0.4399

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
 26W  O3'  C3'  single    1.407  0.020  1.407
 26W  O4'  C4'  single    1.406  0.020  1.406
 26W  C3'  C4'  single    1.524  0.020  1.524
 26W  C3'  C2'  single    1.523  0.020  1.523
 26W  C4'  C5'  single    1.530  0.020  1.530
 26W  O2'  C2'  single    1.404  0.020  1.404
 26W  C2'  C1'  single    1.530  0.020  1.530
 26W  O6'  C6'  single    1.407  0.020  1.407
 26W  C5'  C6'  single    1.514  0.020  1.514
 26W  C5'  O5'  single    1.412  0.020  1.412
 26W  C1'  O5'  single    1.408  0.020  1.408
 26W  C1'  N1   single    1.426  0.020  1.426
 26W  N1   C2   single    1.355  0.020  1.355
 26W  C2   O3   double    1.219  0.020  1.219
 26W  C2   C4   single    1.511  0.020  1.511
 26W  C4   C5   single    1.537  0.020  1.537
 26W  C6   C5   single    1.528  0.020  1.528
 26W  C5   C7   single    1.510  0.020  1.510
 26W  C8   C7   aromatic  1.391  0.020  1.391
 26W  C8   C9   aromatic  1.389  0.020  1.389
 26W  C7   C12  aromatic  1.394  0.020  1.394
 26W  C9   C10  aromatic  1.391  0.020  1.391
 26W  C12  C11  aromatic  1.386  0.020  1.386
 26W  C10  C11  aromatic  1.394  0.020  1.394
 26W  C10  C13  single    1.504  0.020  1.504
 26W  C13  C14  single    1.528  0.020  1.528
 26W  C14  H1   single    0.970  0.020  1.090
 26W  C14  H2   single    0.970  0.020  1.090
 26W  C14  H3   single    0.970  0.020  1.090
 26W  C13  H4   single    0.970  0.020  1.090
 26W  C13  H5   single    0.970  0.020  1.090
 26W  C11  H6   single    0.930  0.020  1.080
 26W  C12  H7   single    0.930  0.020  1.080
 26W  C9   H8   single    0.930  0.020  1.080
 26W  C8   H9   single    0.930  0.020  1.080
 26W  C5   H10  single    0.970  0.020  1.090
 26W  C6   H11  single    0.970  0.020  1.090
 26W  C6   H12  single    0.970  0.020  1.090
 26W  C6   H13  single    0.970  0.020  1.090
 26W  C4   H14  single    0.970  0.020  1.090
 26W  C4   H15  single    0.970  0.020  1.090
 26W  N1   H16  single    0.860  0.020  1.020
 26W  C1'  H17  single    0.970  0.020  1.090
 26W  C5'  H18  single    0.970  0.020  1.090
 26W  C6'  H19  single    0.970  0.020  1.090
 26W  C6'  H20  single    0.970  0.020  1.090
 26W  O6'  H21  single    0.850  0.020  0.980
 26W  C4'  H22  single    0.970  0.020  1.090
 26W  O4'  H23  single    0.850  0.020  0.980
 26W  C3'  H24  single    0.970  0.020  1.090
 26W  O3'  H25  single    0.850  0.020  0.980
 26W  C2'  H26  single    0.970  0.020  1.090
 26W  O2'  H27  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
 26W  H3   C14  H2   107.74  3.000
 26W  H3   C14  H1   107.89  3.000
 26W  H2   C14  H1   107.84  3.000
 26W  H3   C14  C13  111.12  3.000
 26W  H2   C14  C13  111.12  3.000
 26W  H1   C14  C13  110.98  3.000
 26W  H5   C13  H4   106.52  3.000
 26W  H5   C13  C10  109.69  3.000
 26W  H4   C13  C10  109.83  3.000
 26W  H5   C13  C14  109.37  3.000
 26W  H4   C13  C14  109.21  3.000
 26W  C10  C13  C14  112.06  3.000
 26W  C9   C10  C11  117.80  3.000
 26W  C11  C10  C13  120.89  3.000
 26W  C9   C10  C13  121.28  3.000
 26W  H6   C11  C12  119.31  3.000
 26W  H6   C11  C10  119.52  3.000
 26W  C12  C11  C10  121.18  3.000
 26W  H7   C12  C7   120.12  3.000
 26W  H7   C12  C11  118.87  3.000
 26W  C7   C12  C11  121.01  3.000
 26W  H8   C9   C8   119.40  3.000
 26W  H8   C9   C10  119.57  3.000
 26W  C8   C9   C10  121.04  3.000
 26W  H9   C8   C7   119.47  3.000
 26W  H9   C8   C9   119.37  3.000
 26W  C7   C8   C9   121.15  3.000
 26W  C5   C7   C8   120.64  3.000
 26W  C8   C7   C12  117.83  3.000
 26W  C5   C7   C12  121.52  3.000
 26W  H10  C5   C4   107.38  3.000
 26W  H10  C5   C6   108.12  3.000
 26W  C4   C5   C6   111.46  3.000
 26W  H10  C5   C7   107.50  3.000
 26W  C6   C5   C7   112.24  3.000
 26W  C4   C5   C7   109.92  3.000
 26W  H13  C6   H12  107.37  3.000
 26W  H13  C6   H11  107.37  3.000
 26W  H12  C6   H11  107.87  3.000
 26W  H13  C6   C5   111.49  3.000
 26W  H12  C6   C5   110.79  3.000
 26W  H11  C6   C5   111.75  3.000
 26W  H15  C4   H14  106.87  3.000
 26W  H15  C4   C2   111.56  3.000
 26W  H14  C4   C2   107.76  3.000
 26W  H15  C4   C5   109.93  3.000
 26W  H14  C4   C5   109.45  3.000
 26W  C2   C4   C5   111.14  3.000
 26W  N1   C2   O3   123.03  3.000
 26W  O3   C2   C4   121.69  3.000
 26W  N1   C2   C4   115.29  3.000
 26W  H16  N1   C1'  117.46  3.000
 26W  H16  N1   C2   117.88  3.000
 26W  C1'  N1   C2   123.62  3.000
 26W  H17  C1'  C2'  109.03  3.000
 26W  H17  C1'  O5'  110.64  3.000
 26W  C2'  C1'  O5'  109.99  3.000
 26W  H17  C1'  N1   108.02  3.000
 26W  O5'  C1'  N1   108.20  3.000
 26W  C2'  C1'  N1   110.95  3.000
 26W  C5'  O5'  C1'  113.56  3.000
 26W  H18  C5'  C4'  108.48  3.000
 26W  H18  C5'  C6'  109.08  3.000
 26W  C4'  C5'  C6'  111.75  3.000
 26W  H18  C5'  O5'  110.00  3.000
 26W  C6'  C5'  O5'  107.74  3.000
 26W  C4'  C5'  O5'  109.78  3.000
 26W  H20  C6'  H19  107.10  3.000
 26W  H20  C6'  O6'  111.89  3.000
 26W  H19  C6'  O6'  111.71  3.000
 26W  H20  C6'  C5'  108.75  3.000
 26W  H19  C6'  C5'  108.39  3.000
 26W  O6'  C6'  C5'  108.90  3.000
 26W  H21  O6'  C6'  107.90  3.000
 26W  H22  C4'  C3'  108.33  3.000
 26W  H22  C4'  O4'  111.03  3.000
 26W  C3'  C4'  O4'  111.32  3.000
 26W  H22  C4'  C5'  108.30  3.000
 26W  C3'  C4'  C5'  109.61  3.000
 26W  O4'  C4'  C5'  108.19  3.000
 26W  H23  O4'  C4'  108.11  3.000
 26W  H24  C3'  C2'  108.07  3.000
 26W  H24  C3'  O3'  110.80  3.000
 26W  C2'  C3'  O3'  112.15  3.000
 26W  H24  C3'  C4'  107.85  3.000
 26W  C2'  C3'  C4'  110.47  3.000
 26W  O3'  C3'  C4'  107.42  3.000
 26W  H25  O3'  C3'  108.71  3.000
 26W  H26  C2'  O2'  111.46  3.000
 26W  H26  C2'  C3'  108.74  3.000
 26W  O2'  C2'  C3'  107.82  3.000
 26W  H26  C2'  C1'  108.52  3.000
 26W  O2'  C2'  C1'  111.44  3.000
 26W  C3'  C2'  C1'  108.79  3.000
 26W  H27  O2'  C2'  108.84  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
 26W  CONST_01  C7   C8   C9   C10     0.00   0.0  0
 26W  CONST_02  C7   C12  C11  C10     0.00   0.0  0
 26W  CONST_03  C8   C7   C12  C11     0.00   0.0  0
 26W  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 26W  CONST_05  C9   C8   C7   C12     0.00   0.0  0
 26W  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 26W  CONST_07  C8   C9   C10  C13   180.00   0.0  0
 26W  CONST_08  C12  C11  C10  C13   180.00   0.0  0
 26W  CONST_09  C5   C7   C12  C11   180.00   0.0  0
 26W  CONST_10  C5   C7   C8   C9    180.00   0.0  0
 26W  CONST_11  H9   C8   C9   C10   180.00   0.0  0
 26W  CONST_12  H7   C12  C11  C10   180.00   0.0  0
 26W  CONST_13  H8   C9   C10  C11   180.00   0.0  0
 26W  CONST_14  H6   C11  C10  C9    180.00   0.0  0
 26W  CONST_15  C1'  N1   C2   C4    180.00   0.0  0
 26W  CONST_16  C1'  N1   C2   O3      0.00   0.0  0
 26W  CONST_17  H16  N1   C2   C4      0.00   0.0  0
 26W  Var_01    C9   C10  C13  C14   -94.98  30.0  2
 26W  Var_02    H1   C14  C13  C10  -179.67  30.0  3
 26W  Var_03    N1   C2   C4   C5   -121.86  30.0  1

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
 26W  chir_01  C5   C4   C6   C7   negativ
 26W  chir_02  C1'  O5'  N1   C2'  negativ
 26W  chir_03  C5'  O5'  C6'  C4'  positiv
 26W  chir_04  C4'  O4'  C5'  C3'  positiv
 26W  chir_05  C3'  O3'  C4'  C2'  negativ
 26W  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
 26W  plan-1  C13  0.020
 26W  plan-1  C10  0.020
 26W  plan-1  C11  0.020
 26W  plan-1  C12  0.020
 26W  plan-1  C9   0.020
 26W  plan-1  C8   0.020
 26W  plan-1  C7   0.020
 26W  plan-1  C5   0.020
 26W  plan-1  H6   0.020
 26W  plan-1  H7   0.020
 26W  plan-1  H8   0.020
 26W  plan-1  H9   0.020
 26W  plan-2  C4   0.020
 26W  plan-2  C2   0.020
 26W  plan-2  O3   0.020
 26W  plan-2  N1   0.020
 26W  plan-2  C1'  0.020
 26W  plan-2  H16  0.020

