# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:56:22 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N-[(biphenyl-4-yloxy)acetyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)COc2ccc(cc2)c3ccccc3)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 26M  26M  N-[(biphenyl-4-yloxy)acetyl]-beta-D-glucopyranosylamine  saccharide  51  28  .  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_26M
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
 26M  C17  C  CR16  0  -0.316   -7.1483   0.1190   1.5170
 26M  C16  C  CR16  0  -0.239   -8.5054   0.2309   1.7816
 26M  C15  C  CR16  0  -0.269   -9.4213   0.2629   0.7381
 26M  C14  C  CR16  0  -0.239   -8.9659   0.1829  -0.5714
 26M  C13  C  CR16  0  -0.317   -7.6081   0.0757  -0.8353
 26M  C12  C  CR6   0   0.097   -6.6762   0.0421   0.2048
 26M  C9   C  CR6   0   0.068   -5.2310  -0.0694  -0.0745
 26M  C8   C  CR16  0  -0.294   -4.7547  -0.8319  -1.1456
 26M  C7   C  CR16  0  -0.331   -3.4036  -0.9375  -1.4113
 26M  C10  C  CR16  0  -0.299   -4.2901   0.5823   0.7173
 26M  C11  C  CR16  0  -0.361   -2.9277   0.4878   0.4652
 26M  C6   C  CR6   0   0.376   -2.4754  -0.2767  -0.6058
 26M  O5   O  O2    0  -0.462   -1.1770  -0.4359  -0.9379
 26M  C4   C  CH2   0  -0.313   -0.2124   0.2188  -0.1639
 26M  C2   C  C     0   0.525    1.1553  -0.1145  -0.7334
 26M  O3   O  O     0  -0.456    1.3125  -0.8220  -1.7051
 26M  N1   N  NH1   0  -0.692    2.1605   0.4813  -0.0496
 26M  C1'  C  CH1   0   0.211    3.5444   0.2705  -0.3216
 26M  O5'  O  O2    0  -0.488    4.0316  -0.6943   0.5802
 26M  C5'  C  CH1   0  -0.016    5.3806  -1.0491   0.3545
 26M  C6'  C  CH2   0  -0.156    5.7334  -2.1567   1.3246
 26M  O6'  O  OH1   0  -0.670    4.9321  -3.2791   1.0436
 26M  C4'  C  CH1   0   0.035    6.2768   0.1768   0.5416
 26M  O4'  O  OH1   0  -0.672    7.5985  -0.2011   0.2488
 26M  C3'  C  CH1   0  -0.006    5.8067   1.3005  -0.3744
 26M  O3'  O  OH1   0  -0.671    6.5989   2.4300  -0.0988
 26M  C2'  C  CH1   0  -0.027    4.3253   1.5780  -0.1642
 26M  O2'  O  OH1   0  -0.663    3.9297   2.5298  -1.1174
 26M  H1   H  HCR6  0   0.253   -6.4510   0.0702   2.3440
 26M  H2   H  HCR6  0   0.256   -8.8474   0.2849   2.8072
 26M  H3   H  HCR6  0   0.256  -10.4806   0.3473   0.9428
 26M  H4   H  HCR6  0   0.257   -9.6696   0.2128  -1.3930
 26M  H5   H  HCR6  0   0.252   -7.2706   0.0355  -1.8638
 26M  H6   H  HCR6  0   0.257   -5.4497  -1.3723  -1.7762
 26M  H7   H  HCR6  0   0.266   -3.0576  -1.5394  -2.2424
 26M  H8   H  HCR6  0   0.259   -4.6140   1.1980   1.5471
 26M  H9   H  HCR6  0   0.284   -2.2450   1.0250   1.1093
 26M  H10  H  HCH2  0   0.270   -0.3502   1.3072  -0.1775
 26M  H11  H  HCH2  0   0.269   -0.2481  -0.0990   0.8857
 26M  H12  H  HNH1  0   0.411    1.9277   0.9819   0.7973
 26M  H13  H  HCH1  0   0.236    3.6428  -0.0831  -1.3557
 26M  H14  H  HCH1  0   0.225    5.5048  -1.4174  -0.6774
 26M  H15  H  HCH2  0   0.213    6.7992  -2.3831   1.2185
 26M  H16  H  HCH2  0   0.197    5.5801  -1.7913   2.3498
 26M  H17  H  HOH1  0   0.457    5.1917  -3.9854   1.6417
 26M  H18  H  HCH1  0   0.214    6.1825   0.5177   1.5852
 26M  H19  H  HOH1  0   0.455    8.1665   0.5659   0.3758
 26M  H20  H  HCH1  0   0.218    5.9486   0.9683  -1.4156
 26M  H21  H  HOH1  0   0.457    6.4346   3.0942  -0.7756
 26M  H22  H  HCH1  0   0.227    4.1787   1.9474   0.8629
 26M  H23  H  HOH1  0   0.457    3.0579   2.8635  -0.8842

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
 26M  O3'  C3'  single    1.407  0.020  1.407
 26M  O4'  C4'  single    1.406  0.020  1.406
 26M  C3'  C4'  single    1.524  0.020  1.524
 26M  C3'  C2'  single    1.522  0.020  1.522
 26M  C4'  C5'  single    1.530  0.020  1.530
 26M  O2'  C2'  single    1.404  0.020  1.404
 26M  C2'  C1'  single    1.531  0.020  1.531
 26M  O6'  C6'  single    1.407  0.020  1.407
 26M  C5'  C6'  single    1.514  0.020  1.514
 26M  C5'  O5'  single    1.413  0.020  1.413
 26M  C1'  O5'  single    1.408  0.020  1.408
 26M  C1'  N1   single    1.426  0.020  1.426
 26M  N1   C2   single    1.354  0.020  1.354
 26M  C2   O3   double    1.212  0.020  1.212
 26M  C2   C4   single    1.519  0.020  1.519
 26M  C4   O5   single    1.399  0.020  1.399
 26M  O5   C6   single    1.350  0.020  1.350
 26M  C7   C6   aromatic  1.395  0.020  1.395
 26M  C7   C8   aromatic  1.381  0.020  1.381
 26M  C6   C11  aromatic  1.391  0.020  1.391
 26M  C8   C9   aromatic  1.398  0.020  1.398
 26M  C11  C10  aromatic  1.389  0.020  1.389
 26M  C9   C10  aromatic  1.392  0.020  1.392
 26M  C9   C12  single    1.476  0.020  1.476
 26M  C13  C12  aromatic  1.397  0.020  1.397
 26M  C13  C14  aromatic  1.387  0.020  1.387
 26M  C12  C17  aromatic  1.397  0.020  1.397
 26M  C14  C15  aromatic  1.389  0.020  1.389
 26M  C17  C16  aromatic  1.387  0.020  1.387
 26M  C15  C16  aromatic  1.389  0.020  1.389
 26M  C17  H1   single    0.930  0.020  1.080
 26M  C16  H2   single    0.930  0.020  1.080
 26M  C15  H3   single    0.930  0.020  1.080
 26M  C14  H4   single    0.930  0.020  1.080
 26M  C13  H5   single    0.930  0.020  1.080
 26M  C8   H6   single    0.930  0.020  1.080
 26M  C7   H7   single    0.930  0.020  1.080
 26M  C10  H8   single    0.930  0.020  1.080
 26M  C11  H9   single    0.930  0.020  1.080
 26M  C4   H10  single    0.970  0.020  1.090
 26M  C4   H11  single    0.970  0.020  1.090
 26M  N1   H12  single    0.860  0.020  1.020
 26M  C1'  H13  single    0.970  0.020  1.090
 26M  C5'  H14  single    0.970  0.020  1.090
 26M  C6'  H15  single    0.970  0.020  1.090
 26M  C6'  H16  single    0.970  0.020  1.090
 26M  O6'  H17  single    0.850  0.020  0.980
 26M  C4'  H18  single    0.970  0.020  1.090
 26M  O4'  H19  single    0.850  0.020  0.980
 26M  C3'  H20  single    0.970  0.020  1.090
 26M  O3'  H21  single    0.850  0.020  0.980
 26M  C2'  H22  single    0.970  0.020  1.090
 26M  O2'  H23  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
 26M  H1   C17  C12  119.83  3.000
 26M  H1   C17  C16  119.21  3.000
 26M  C12  C17  C16  120.95  3.000
 26M  H2   C16  C15  120.16  3.000
 26M  H2   C16  C17  119.59  3.000
 26M  C15  C16  C17  120.25  3.000
 26M  H3   C15  C14  120.25  3.000
 26M  H3   C15  C16  120.35  3.000
 26M  C14  C15  C16  119.40  3.000
 26M  H4   C14  C13  119.62  3.000
 26M  H4   C14  C15  120.07  3.000
 26M  C13  C14  C15  120.32  3.000
 26M  H5   C13  C12  119.89  3.000
 26M  H5   C13  C14  119.23  3.000
 26M  C12  C13  C14  120.87  3.000
 26M  C9   C12  C13  120.94  3.000
 26M  C13  C12  C17  118.21  3.000
 26M  C9   C12  C17  120.85  3.000
 26M  C10  C9   C8   117.44  3.000
 26M  C10  C9   C12  121.26  3.000
 26M  C8   C9   C12  121.30  3.000
 26M  H6   C8   C7   118.54  3.000
 26M  H6   C8   C9   119.97  3.000
 26M  C7   C8   C9   121.48  3.000
 26M  H7   C7   C6   119.59  3.000
 26M  H7   C7   C8   120.18  3.000
 26M  C6   C7   C8   120.23  3.000
 26M  H8   C10  C11  118.12  3.000
 26M  H8   C10  C9   120.00  3.000
 26M  C11  C10  C9   121.88  3.000
 26M  H9   C11  C6   121.74  3.000
 26M  H9   C11  C10  118.52  3.000
 26M  C6   C11  C10  119.74  3.000
 26M  O5   C6   C11  124.54  3.000
 26M  C11  C6   C7   119.23  3.000
 26M  O5   C6   C7   116.23  3.000
 26M  C4   O5   C6   118.15  3.000
 26M  H11  C4   H10  107.17  3.000
 26M  H11  C4   C2   108.94  3.000
 26M  H10  C4   C2   109.04  3.000
 26M  H11  C4   O5   111.79  3.000
 26M  H10  C4   O5   111.76  3.000
 26M  C2   C4   O5   108.10  3.000
 26M  N1   C2   O3   124.43  3.000
 26M  O3   C2   C4   123.06  3.000
 26M  N1   C2   C4   112.50  3.000
 26M  H12  N1   C1'  117.15  3.000
 26M  H12  N1   C2   118.04  3.000
 26M  C1'  N1   C2   124.00  3.000
 26M  H13  C1'  C2'  109.05  3.000
 26M  H13  C1'  O5'  110.60  3.000
 26M  C2'  C1'  O5'  110.06  3.000
 26M  H13  C1'  N1   108.32  3.000
 26M  O5'  C1'  N1   108.36  3.000
 26M  C2'  C1'  N1   110.43  3.000
 26M  C5'  O5'  C1'  113.59  3.000
 26M  H14  C5'  C4'  108.42  3.000
 26M  H14  C5'  C6'  109.21  3.000
 26M  C4'  C5'  C6'  111.80  3.000
 26M  H14  C5'  O5'  109.93  3.000
 26M  C6'  C5'  O5'  107.69  3.000
 26M  C4'  C5'  O5'  109.79  3.000
 26M  H16  C6'  H15  107.15  3.000
 26M  H16  C6'  O6'  111.83  3.000
 26M  H15  C6'  O6'  111.72  3.000
 26M  H16  C6'  C5'  108.78  3.000
 26M  H15  C6'  C5'  108.43  3.000
 26M  O6'  C6'  C5'  108.83  3.000
 26M  H17  O6'  C6'  107.94  3.000
 26M  H18  C4'  C3'  108.34  3.000
 26M  H18  C4'  O4'  111.15  3.000
 26M  C3'  C4'  O4'  111.29  3.000
 26M  H18  C4'  C5'  108.27  3.000
 26M  C3'  C4'  C5'  109.67  3.000
 26M  O4'  C4'  C5'  108.06  3.000
 26M  H19  O4'  C4'  108.25  3.000
 26M  H20  C3'  C2'  108.11  3.000
 26M  H20  C3'  O3'  110.76  3.000
 26M  C2'  C3'  O3'  112.00  3.000
 26M  H20  C3'  C4'  107.81  3.000
 26M  C2'  C3'  C4'  110.59  3.000
 26M  O3'  C3'  C4'  107.49  3.000
 26M  H21  O3'  C3'  108.67  3.000
 26M  H22  C2'  O2'  111.61  3.000
 26M  H22  C2'  C3'  108.64  3.000
 26M  O2'  C2'  C3'  107.71  3.000
 26M  H22  C2'  C1'  108.33  3.000
 26M  O2'  C2'  C1'  111.44  3.000
 26M  C3'  C2'  C1'  109.06  3.000
 26M  H23  O2'  C2'  109.02  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
 26M  CONST_03  C14  C13  C12  C17     0.00   0.0  0
 26M  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 26M  CONST_05  C9   C12  C17  C16   180.00   0.0  0
 26M  CONST_06  C13  C12  C17  C16     0.00   0.0  0
 26M  CONST_07  C13  C14  C15  C16     0.00   0.0  0
 26M  CONST_08  C12  C13  C14  C15     0.00   0.0  0
 26M  CONST_09  C12  C17  C16  C15     0.00   0.0  0
 26M  CONST_10  C9   C12  C13  C14   180.00   0.0  0
 26M  CONST_13  C7   C8   C9   C12   180.00   0.0  0
 26M  CONST_14  C11  C10  C9   C12   180.00   0.0  0
 26M  CONST_15  C6   C7   C8   C9      0.00   0.0  0
 26M  CONST_16  C6   C11  C10  C9      0.00   0.0  0
 26M  CONST_17  C11  C6   C7   C8      0.00   0.0  0
 26M  CONST_18  C11  C10  C9   C8      0.00   0.0  0
 26M  CONST_19  C10  C11  C6   C7      0.00   0.0  0
 26M  CONST_20  C10  C9   C8   C7      0.00   0.0  0
 26M  CONST_21  O5   C6   C7   C8    180.00   0.0  0
 26M  CONST_22  O5   C6   C11  C10   180.00   0.0  0
 26M  CONST_23  H5   C13  C12  C17   180.00   0.0  0
 26M  CONST_24  H3   C15  C16  C17   180.00   0.0  0
 26M  CONST_25  H4   C14  C15  C16   180.00   0.0  0
 26M  CONST_26  H1   C17  C16  C15   180.00   0.0  0
 26M  CONST_27  H2   C16  C15  C14   180.00   0.0  0
 26M  CONST_28  H6   C8   C9   C12     0.00   0.0  0
 26M  CONST_29  H8   C10  C9   C12     0.00   0.0  0
 26M  CONST_30  H7   C7   C8   C9    180.00   0.0  0
 26M  CONST_31  H9   C11  C10  C9    180.00   0.0  0
 26M  CONST_32  C1'  N1   C2   C4    180.00   0.0  0
 26M  CONST_33  C1'  N1   C2   O3      0.00   0.0  0
 26M  CONST_34  H12  N1   C2   C4      0.00   0.0  0
 26M  Var_01    C2   C4   O5   C6   -179.98  30.0  1
 26M  Var_02    N1   C2   C4   O5    179.76  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
 26M  chir_01  C1'  C2'  O5'  N1   negativ
 26M  chir_02  C5'  O5'  C6'  C4'  positiv
 26M  chir_03  C4'  O4'  C5'  C3'  positiv
 26M  chir_04  C3'  O3'  C4'  C2'  negativ
 26M  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
 26M  plan-1  C17  0.020
 26M  plan-1  C16  0.020
 26M  plan-1  C15  0.020
 26M  plan-1  C14  0.020
 26M  plan-1  C13  0.020
 26M  plan-1  C12  0.020
 26M  plan-1  C9   0.020
 26M  plan-1  H1   0.020
 26M  plan-1  H2   0.020
 26M  plan-1  H3   0.020
 26M  plan-1  H4   0.020
 26M  plan-1  H5   0.020
 26M  plan-2  C12  0.020
 26M  plan-2  C9   0.020
 26M  plan-2  C8   0.020
 26M  plan-2  C7   0.020
 26M  plan-2  C10  0.020
 26M  plan-2  C11  0.020
 26M  plan-2  C6   0.020
 26M  plan-2  O5   0.020
 26M  plan-2  H6   0.020
 26M  plan-2  H7   0.020
 26M  plan-2  H8   0.020
 26M  plan-2  H9   0.020
 26M  plan-3  C4   0.020
 26M  plan-3  C2   0.020
 26M  plan-3  O3   0.020
 26M  plan-3  N1   0.020
 26M  plan-3  C1'  0.020
 26M  plan-3  H12  0.020

