# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:13:51 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-{(2E)-3-[4-(propan-2-yl)phenyl]prop-2-enoyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ccc(/C=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
 26Y  26Y  N-{(2E)-3-[4-(propan-2-yl)phenyl]prop-2-enoyl}-beta-D-glucopyranosylamine  saccharide  50  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_26Y
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
 26Y  C14  C  CH3   0  -0.644   8.4391   1.0253   0.3276
 26Y  C13  C  CH1   0  -0.328   7.6794   0.2217  -0.7289
 26Y  C15  C  CH3   0  -0.645   8.3457  -1.1312  -0.9774
 26Y  C10  C  CR6   0   0.164   6.2252   0.0667  -0.3553
 26Y  C9   C  CR16  0  -0.297   5.8403  -0.6213   0.7939
 26Y  C8   C  CR16  0  -0.289   4.5045  -0.7357   1.1396
 26Y  C11  C  CR16  0  -0.307   5.2224   0.6249  -1.1482
 26Y  C12  C  CR16  0  -0.294   3.8858   0.5107  -0.8093
 26Y  C7   C  CR6   0   0.130   3.5004  -0.1715   0.3474
 26Y  C6   C  C1    0  -0.221   2.1131  -0.3098   0.7736
 26Y  C4   C  C1    0  -0.436   1.0262   0.1410   0.1381
 26Y  C2   C  C     0   0.587  -0.3209  -0.0546   0.7133
 26Y  O3   O  O     0  -0.484  -0.5198  -0.5841   1.7959
 26Y  N1   N  NH1   0  -0.721  -1.3250   0.4300  -0.0635
 26Y  C1'  C  CH1   0   0.218  -2.7036   0.3308   0.2770
 26Y  O5'  O  O2    0  -0.489  -3.2330  -0.8388  -0.3038
 26Y  C5'  C  CH1   0  -0.014  -4.5754  -1.0833   0.0593
 26Y  C6'  C  CH2   0  -0.157  -4.9778  -2.4248  -0.5158
 26Y  O6'  O  OH1   0  -0.670  -4.1900  -3.4274   0.0803
 26Y  C4'  C  CH1   0   0.036  -5.4607   0.0515  -0.4589
 26Y  O4'  O  OH1   0  -0.672  -6.7803  -0.1947  -0.0413
 26Y  C3'  C  CH1   0  -0.004  -4.9490   1.3823   0.0798
 26Y  O3'  O  OH1   0  -0.672  -5.7310   2.4015  -0.4939
 26Y  C2'  C  CH1   0  -0.035  -3.4684   1.5567  -0.2293
 26Y  O2'  O  OH1   0  -0.663  -3.0380   2.7325   0.4081
 26Y  H1   H  HCH3  0   0.220   8.4844   0.4932   1.2797
 26Y  H2   H  HCH3  0   0.232   9.4645   1.2081   0.0027
 26Y  H3   H  HCH3  0   0.233   7.9676   1.9918   0.5084
 26Y  H4   H  HCH1  0   0.243   7.7146   0.7886  -1.6640
 26Y  H5   H  HCH3  0   0.222   8.3315  -1.7550  -0.0822
 26Y  H6   H  HCH3  0   0.233   7.8445  -1.6811  -1.7749
 26Y  H7   H  HCH3  0   0.232   9.3888  -0.9963  -1.2681
 26Y  H8   H  HCR6  0   0.251   6.5887  -1.0729   1.4342
 26Y  H9   H  HCR6  0   0.257   4.2311  -1.2699   2.0421
 26Y  H10  H  HCR6  0   0.254   5.4962   1.1636  -2.0479
 26Y  H11  H  HCR6  0   0.250   3.1439   0.9648  -1.4538
 26Y  H12  H  H     0   0.262   1.9662  -0.8339   1.7133
 26Y  H13  H  H     0   0.269   1.0965   0.6675  -0.8073
 26Y  H14  H  HNH1  0   0.406  -1.0921   0.7693  -0.9855
 26Y  H15  H  HCH1  0   0.230  -2.7879   0.2825   1.3700
 26Y  H16  H  HCH1  0   0.222  -4.6680  -1.1245   1.1575
 26Y  H17  H  HCH2  0   0.213  -6.0442  -2.5765  -0.3207
 26Y  H18  H  HCH2  0   0.196  -4.8488  -2.3981  -1.6069
 26Y  H19  H  HOH1  0   0.456  -4.4992  -4.2787  -0.2416
 26Y  H20  H  HCH1  0   0.213  -5.3899   0.0694  -1.5584
 26Y  H21  H  HOH1  0   0.455  -7.3382   0.5171  -0.3716
 26Y  H22  H  HCH1  0   0.217  -5.0673   1.3688   1.1756
 26Y  H23  H  HOH1  0   0.457  -5.5336   3.2293  -0.0446
 26Y  H24  H  HCH1  0   0.228  -3.3405   1.6212  -1.3214
 26Y  H25  H  HOH1  0   0.456  -2.1735   2.9774   0.0642

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
 26Y  O3'  C3'  single    1.407  0.020  1.407
 26Y  O4'  C4'  single    1.406  0.020  1.406
 26Y  C3'  C4'  single    1.524  0.020  1.524
 26Y  C3'  C2'  single    1.523  0.020  1.523
 26Y  C4'  C5'  single    1.530  0.020  1.530
 26Y  O2'  C2'  single    1.405  0.020  1.405
 26Y  C2'  C1'  single    1.531  0.020  1.531
 26Y  O6'  C6'  single    1.407  0.020  1.407
 26Y  C5'  C6'  single    1.514  0.020  1.514
 26Y  C5'  O5'  single    1.412  0.020  1.412
 26Y  C1'  O5'  single    1.409  0.020  1.409
 26Y  C1'  N1   single    1.424  0.020  1.424
 26Y  N1   C2   single    1.359  0.020  1.359
 26Y  C2   O3   double    1.221  0.020  1.221
 26Y  C2   C4   single    1.478  0.020  1.478
 26Y  C4   C6   double    1.337  0.020  1.337
 26Y  C8   C9   aromatic  1.385  0.020  1.385
 26Y  C8   C7   aromatic  1.398  0.020  1.398
 26Y  C6   C7   single    1.458  0.020  1.458
 26Y  C9   C10  aromatic  1.394  0.020  1.394
 26Y  C7   C12  aromatic  1.397  0.020  1.397
 26Y  C10  C13  single    1.509  0.020  1.509
 26Y  C10  C11  aromatic  1.395  0.020  1.395
 26Y  C12  C11  aromatic  1.384  0.020  1.384
 26Y  C13  C14  single    1.529  0.020  1.529
 26Y  C13  C15  single    1.528  0.020  1.528
 26Y  C14  H1   single    0.970  0.020  1.090
 26Y  C14  H2   single    0.970  0.020  1.090
 26Y  C14  H3   single    0.970  0.020  1.090
 26Y  C13  H4   single    0.970  0.020  1.090
 26Y  C15  H5   single    0.970  0.020  1.090
 26Y  C15  H6   single    0.970  0.020  1.090
 26Y  C15  H7   single    0.970  0.020  1.090
 26Y  C9   H8   single    0.930  0.020  1.080
 26Y  C8   H9   single    0.930  0.020  1.080
 26Y  C11  H10  single    0.930  0.020  1.080
 26Y  C12  H11  single    0.930  0.020  1.080
 26Y  C6   H12  single    0.930  0.020  1.080
 26Y  C4   H13  single    0.930  0.020  1.080
 26Y  N1   H14  single    0.860  0.020  1.020
 26Y  C1'  H15  single    0.970  0.020  1.090
 26Y  C5'  H16  single    0.970  0.020  1.090
 26Y  C6'  H17  single    0.970  0.020  1.090
 26Y  C6'  H18  single    0.970  0.020  1.090
 26Y  O6'  H19  single    0.850  0.020  0.980
 26Y  C4'  H20  single    0.970  0.020  1.090
 26Y  O4'  H21  single    0.850  0.020  0.980
 26Y  C3'  H22  single    0.970  0.020  1.090
 26Y  O3'  H23  single    0.850  0.020  0.980
 26Y  C2'  H24  single    0.970  0.020  1.090
 26Y  O2'  H25  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
 26Y  H3   C14  H2   107.89  3.000
 26Y  H3   C14  H1   107.78  3.000
 26Y  H2   C14  H1   107.60  3.000
 26Y  H3   C14  C13  111.43  3.000
 26Y  H2   C14  C13  110.44  3.000
 26Y  H1   C14  C13  111.53  3.000
 26Y  H4   C13  C10  107.20  3.000
 26Y  H4   C13  C15  107.79  3.000
 26Y  C10  C13  C15  111.68  3.000
 26Y  H4   C13  C14  107.59  3.000
 26Y  C15  C13  C14  111.15  3.000
 26Y  C10  C13  C14  111.20  3.000
 26Y  H7   C15  H6   107.87  3.000
 26Y  H7   C15  H5   107.55  3.000
 26Y  H6   C15  H5   107.80  3.000
 26Y  H7   C15  C13  110.53  3.000
 26Y  H6   C15  C13  111.40  3.000
 26Y  H5   C15  C13  111.52  3.000
 26Y  C11  C10  C9   117.89  3.000
 26Y  C11  C10  C13  120.72  3.000
 26Y  C9   C10  C13  121.39  3.000
 26Y  H8   C9   C8   118.97  3.000
 26Y  H8   C9   C10  120.15  3.000
 26Y  C8   C9   C10  120.88  3.000
 26Y  H9   C8   C7   119.32  3.000
 26Y  H9   C8   C9   119.47  3.000
 26Y  C7   C8   C9   121.20  3.000
 26Y  H10  C11  C12  119.24  3.000
 26Y  H10  C11  C10  119.29  3.000
 26Y  C12  C11  C10  121.48  3.000
 26Y  H11  C12  C7   120.58  3.000
 26Y  H11  C12  C11  118.79  3.000
 26Y  C7   C12  C11  120.64  3.000
 26Y  C6   C7   C12  123.42  3.000
 26Y  C12  C7   C8   117.92  3.000
 26Y  C6   C7   C8   118.66  3.000
 26Y  H12  C6   C4   117.64  3.000
 26Y  H12  C6   C7   115.31  3.000
 26Y  C4   C6   C7   127.05  3.000
 26Y  H13  C4   C2   117.56  3.000
 26Y  H13  C4   C6   121.68  3.000
 26Y  C2   C4   C6   120.75  3.000
 26Y  N1   C2   O3   122.75  3.000
 26Y  O3   C2   C4   123.42  3.000
 26Y  N1   C2   C4   113.82  3.000
 26Y  H14  N1   C1'  117.73  3.000
 26Y  H14  N1   C2   118.13  3.000
 26Y  C1'  N1   C2   123.64  3.000
 26Y  H15  C1'  C2'  109.04  3.000
 26Y  H15  C1'  O5'  110.20  3.000
 26Y  C2'  C1'  O5'  109.91  3.000
 26Y  H15  C1'  N1   108.40  3.000
 26Y  O5'  C1'  N1   108.85  3.000
 26Y  C2'  C1'  N1   110.42  3.000
 26Y  C5'  O5'  C1'  113.26  3.000
 26Y  H16  C5'  C4'  108.45  3.000
 26Y  H16  C5'  C6'  108.83  3.000
 26Y  C4'  C5'  C6'  112.01  3.000
 26Y  H16  C5'  O5'  110.02  3.000
 26Y  C6'  C5'  O5'  107.97  3.000
 26Y  C4'  C5'  O5'  109.55  3.000
 26Y  H18  C6'  H17  107.13  3.000
 26Y  H18  C6'  O6'  111.85  3.000
 26Y  H17  C6'  O6'  111.78  3.000
 26Y  H18  C6'  C5'  108.92  3.000
 26Y  H17  C6'  C5'  108.30  3.000
 26Y  O6'  C6'  C5'  108.76  3.000
 26Y  H19  O6'  C6'  108.00  3.000
 26Y  H20  C4'  C3'  108.48  3.000
 26Y  H20  C4'  O4'  111.08  3.000
 26Y  C3'  C4'  O4'  111.29  3.000
 26Y  H20  C4'  C5'  108.23  3.000
 26Y  C3'  C4'  C5'  109.49  3.000
 26Y  O4'  C4'  C5'  108.22  3.000
 26Y  H21  O4'  C4'  108.21  3.000
 26Y  H22  C3'  C2'  107.91  3.000
 26Y  H22  C3'  O3'  110.77  3.000
 26Y  C2'  C3'  O3'  112.01  3.000
 26Y  H22  C3'  C4'  107.73  3.000
 26Y  C2'  C3'  C4'  110.78  3.000
 26Y  O3'  C3'  C4'  107.56  3.000
 26Y  H23  O3'  C3'  108.59  3.000
 26Y  H24  C2'  O2'  111.42  3.000
 26Y  H24  C2'  C3'  108.72  3.000
 26Y  O2'  C2'  C3'  107.56  3.000
 26Y  H24  C2'  C1'  108.47  3.000
 26Y  O2'  C2'  C1'  111.53  3.000
 26Y  C3'  C2'  C1'  109.08  3.000
 26Y  H25  O2'  C2'  109.03  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
 26Y  CONST_01  C7   C8   C9   C10     0.00   0.0  0
 26Y  CONST_02  C7   C12  C11  C10     0.00   0.0  0
 26Y  CONST_03  C12  C7   C8   C9      0.00   0.0  0
 26Y  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 26Y  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 26Y  CONST_06  C11  C12  C7   C8      0.00   0.0  0
 26Y  CONST_07  C8   C9   C10  C13   180.00   0.0  0
 26Y  CONST_08  C12  C11  C10  C13   180.00   0.0  0
 26Y  CONST_09  C6   C7   C8   C9    180.00   0.0  0
 26Y  CONST_10  C6   C7   C12  C11   180.00   0.0  0
 26Y  CONST_11  H9   C8   C9   C10   180.00   0.0  0
 26Y  CONST_12  H11  C12  C11  C10   180.00   0.0  0
 26Y  CONST_13  H10  C11  C10  C9    180.00   0.0  0
 26Y  CONST_14  H8   C9   C10  C11   180.00   0.0  0
 26Y  CONST_15  C1'  N1   C2   C4    180.00   0.0  0
 26Y  CONST_16  C1'  N1   C2   O3      0.00   0.0  0
 26Y  CONST_17  H14  N1   C2   C4      0.00   0.0  0
 26Y  Var_01    C9   C10  C13  C14   -63.00  30.0  2
 26Y  Var_02    C4   C6   C7   C8   -178.81  30.0  2
 26Y  Var_03    C2   C4   C6   C7   -178.76   0.0  2
 26Y  Var_04    H1   C14  C13  C10    65.58  30.0  3
 26Y  Var_05    H5   C15  C13  C10   -61.70  30.0  3
 26Y  Var_06    N1   C2   C4   C6   -178.52  30.0  2

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
 26Y  chir_01  C1'  C2'  O5'  N1   negativ
 26Y  chir_02  C5'  O5'  C6'  C4'  positiv
 26Y  chir_03  C4'  O4'  C5'  C3'  positiv
 26Y  chir_04  C3'  O3'  C4'  C2'  negativ
 26Y  chir_05  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
 26Y  plan-1  C13  0.020
 26Y  plan-1  C10  0.020
 26Y  plan-1  C9   0.020
 26Y  plan-1  C8   0.020
 26Y  plan-1  C11  0.020
 26Y  plan-1  C12  0.020
 26Y  plan-1  C7   0.020
 26Y  plan-1  C6   0.020
 26Y  plan-1  H8   0.020
 26Y  plan-1  H9   0.020
 26Y  plan-1  H10  0.020
 26Y  plan-1  H11  0.020
 26Y  plan-2  C4   0.020
 26Y  plan-2  C2   0.020
 26Y  plan-2  O3   0.020
 26Y  plan-2  N1   0.020
 26Y  plan-2  C1'  0.020
 26Y  plan-2  H14  0.020
 26Y  plan-3  C7   0.020
 26Y  plan-3  C6   0.020
 26Y  plan-3  C4   0.020
 26Y  plan-3  C2   0.020
 26Y  plan-3  H12  0.020
 26Y  plan-3  H13  0.020

