# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:21:17 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: N-[4-(5,6,7,8-tetrahydronaphthalen-2-yl)butanoyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)CCCc2ccc3CCCCc3c2)[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
 26V  26V  N-[4-(5,6,7,8-tetrahydronaphthalen-2-yl)butanoyl]-beta-D-glucopyranosylamine  saccharide  56  27  .  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_26V
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
 26V  C12  C  CR16  0  -0.362  -4.7205   0.8702   0.2745
 26V  C11  C  CR6   0   0.094  -5.9240   0.3984  -0.2475
 26V  C16  C  CH2   0  -0.498  -6.6909   1.2487  -1.2301
 26V  C15  C  CH2   0  -0.444  -7.7084   0.4514  -2.0335
 26V  C14  C  CH2   0  -0.444  -8.5542  -0.4021  -1.0990
 26V  C13  C  CH2   0  -0.495  -7.6825  -1.4281  -0.3860
 26V  C10  C  CR6   0   0.049  -6.4049  -0.8466   0.1678
 26V  C9   C  CR16  0  -0.281  -5.6610  -1.5728   1.0967
 26V  C8   C  CR16  0  -0.328  -4.4658  -1.0911   1.6048
 26V  C7   C  CR6   0   0.141  -3.9746   0.1469   1.1970
 26V  C6   C  CH2   0  -0.508  -2.6533   0.6656   1.6927
 26V  C5   C  CH2   0  -0.412  -1.5346   0.4337   0.6758
 26V  C4   C  CH2   0  -0.594  -0.1956   0.9448   1.1854
 26V  C2   C  C     0   0.574   0.9328   0.7615   0.1951
 26V  O3   O  O     0  -0.480   0.7543   0.7111  -1.0087
 26V  N1   N  NH1   0  -0.695   2.1664   0.7017   0.7582
 26V  C1'  C  CH1   0   0.210   3.3728   0.5297   0.0209
 26V  O5'  O  O2    0  -0.490   3.7217  -0.8357   0.0424
 26V  C5'  C  CH1   0  -0.014   4.8611  -1.1409  -0.7352
 26V  C6'  C  CH2   0  -0.156   5.0527  -2.6424  -0.6999
 26V  O6'  O  OH1   0  -0.670   3.9436  -3.2570  -1.3111
 26V  C4'  C  CH1   0   0.035   6.0784  -0.3987  -0.1808
 26V  O4'  O  OH1   0  -0.672   7.1786  -0.6763  -1.0103
 26V  C3'  C  CH1   0  -0.006   5.7870   1.0966  -0.1328
 26V  O3'  O  OH1   0  -0.672   6.8977   1.7240   0.4613
 26V  C2'  C  CH1   0  -0.030   4.4996   1.3666   0.6316
 26V  O2'  O  OH1   0  -0.663   4.2263   2.7409   0.5350
 26V  H1   H  HCR6  0   0.232  -4.3549   1.8389  -0.0550
 26V  H2   H  HCH2  0   0.239  -7.2131   2.0394  -0.6796
 26V  H3   H  HCH2  0   0.244  -5.9910   1.7622  -1.8939
 26V  H4   H  HCH2  0   0.235  -8.3360   1.1315  -2.6125
 26V  H5   H  HCH2  0   0.220  -7.1947  -0.1931  -2.7541
 26V  H6   H  HCH2  0   0.220  -9.0463   0.2459  -0.3667
 26V  H7   H  HCH2  0   0.234  -9.3478  -0.9129  -1.6476
 26V  H8   H  HCH2  0   0.243  -8.2435  -1.9125   0.4170
 26V  H9   H  HCH2  0   0.238  -7.4273  -2.2268  -1.0911
 26V  H10  H  HCR6  0   0.239  -6.0279  -2.5384   1.4277
 26V  H11  H  HCR6  0   0.239  -3.9103  -1.6812   2.3249
 26V  H12  H  HCH2  0   0.238  -2.7288   1.7362   1.9044
 26V  H13  H  HCH2  0   0.238  -2.3944   0.1798   2.6373
 26V  H14  H  HCH2  0   0.234  -1.4636  -0.6344   0.4548
 26V  H15  H  HCH2  0   0.235  -1.7935   0.9302  -0.2615
 26V  H16  H  HCH2  0   0.278  -0.2645   2.0161   1.4048
 26V  H17  H  HCH2  0   0.258   0.0580   0.4628   2.1334
 26V  H18  H  HNH1  0   0.404   2.2268   0.6621   1.7653
 26V  H19  H  HCH1  0   0.231   3.1985   0.8635  -1.0098
 26V  H20  H  HCH1  0   0.223   4.7036  -0.8212  -1.7789
 26V  H21  H  HCH2  0   0.213   5.9863  -2.8868  -1.2168
 26V  H22  H  HCH2  0   0.196   5.1702  -2.9592   0.3461
 26V  H23  H  HOH1  0   0.457   4.0990  -4.2055  -1.3204
 26V  H24  H  HCH1  0   0.212   6.2586  -0.7511   0.8479
 26V  H25  H  HOH1  0   0.454   7.9354  -0.1822  -0.6782
 26V  H26  H  HCH1  0   0.218   5.6468   1.4462  -1.1687
 26V  H27  H  HOH1  0   0.458   6.8209   2.6745   0.3326
 26V  H28  H  HCH1  0   0.226   4.6382   1.0548   1.6787
 26V  H29  H  HOH1  0   0.456   3.5206   2.9618   1.1508

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
 26V  O3'  C3'  single    1.407  0.020  1.407
 26V  O4'  C4'  single    1.406  0.020  1.406
 26V  C3'  C4'  single    1.524  0.020  1.524
 26V  C3'  C2'  single    1.521  0.020  1.521
 26V  C4'  C5'  single    1.530  0.020  1.530
 26V  O2'  C2'  single    1.405  0.020  1.405
 26V  C2'  C1'  single    1.531  0.020  1.531
 26V  O6'  C6'  single    1.408  0.020  1.408
 26V  C5'  C6'  single    1.514  0.020  1.514
 26V  C5'  O5'  single    1.413  0.020  1.413
 26V  C1'  O5'  single    1.409  0.020  1.409
 26V  C1'  N1   single    1.424  0.020  1.424
 26V  N1   C2   single    1.357  0.020  1.357
 26V  C2   C4   single    1.512  0.020  1.512
 26V  C2   O3   double    1.218  0.020  1.218
 26V  C4   C5   single    1.521  0.020  1.521
 26V  C5   C6   single    1.529  0.020  1.529
 26V  C6   C7   single    1.504  0.020  1.504
 26V  C7   C8   aromatic  1.393  0.020  1.393
 26V  C7   C12  aromatic  1.389  0.020  1.389
 26V  C8   C9   aromatic  1.385  0.020  1.385
 26V  C12  C11  aromatic  1.394  0.020  1.394
 26V  C9   C10  aromatic  1.394  0.020  1.394
 26V  C11  C10  aromatic  1.398  0.020  1.398
 26V  C11  C16  single    1.509  0.020  1.509
 26V  C10  C13  single    1.509  0.020  1.509
 26V  C16  C15  single    1.522  0.020  1.522
 26V  C13  C14  single    1.523  0.020  1.523
 26V  C15  C14  single    1.522  0.020  1.522
 26V  C12  H1   single    0.930  0.020  1.080
 26V  C16  H2   single    0.970  0.020  1.090
 26V  C16  H3   single    0.970  0.020  1.090
 26V  C15  H4   single    0.970  0.020  1.090
 26V  C15  H5   single    0.970  0.020  1.090
 26V  C14  H6   single    0.970  0.020  1.090
 26V  C14  H7   single    0.970  0.020  1.090
 26V  C13  H8   single    0.970  0.020  1.090
 26V  C13  H9   single    0.970  0.020  1.090
 26V  C9   H10  single    0.930  0.020  1.080
 26V  C8   H11  single    0.930  0.020  1.080
 26V  C6   H12  single    0.970  0.020  1.090
 26V  C6   H13  single    0.970  0.020  1.090
 26V  C5   H14  single    0.970  0.020  1.090
 26V  C5   H15  single    0.970  0.020  1.090
 26V  C4   H16  single    0.970  0.020  1.090
 26V  C4   H17  single    0.970  0.020  1.090
 26V  N1   H18  single    0.860  0.020  1.020
 26V  C1'  H19  single    0.970  0.020  1.090
 26V  C5'  H20  single    0.970  0.020  1.090
 26V  C6'  H21  single    0.970  0.020  1.090
 26V  C6'  H22  single    0.970  0.020  1.090
 26V  O6'  H23  single    0.850  0.020  0.980
 26V  C4'  H24  single    0.970  0.020  1.090
 26V  O4'  H25  single    0.850  0.020  0.980
 26V  C3'  H26  single    0.970  0.020  1.090
 26V  O3'  H27  single    0.850  0.020  0.980
 26V  C2'  H28  single    0.970  0.020  1.090
 26V  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
 26V  H1   C12  C7   119.00  3.000
 26V  H1   C12  C11  118.60  3.000
 26V  C7   C12  C11  122.40  3.000
 26V  C10  C11  C16  121.37  3.000
 26V  C16  C11  C12  119.47  3.000
 26V  C10  C11  C12  119.16  3.000
 26V  H3   C16  H2   105.75  3.000
 26V  H3   C16  C15  110.71  3.000
 26V  H2   C16  C15  108.94  3.000
 26V  H3   C16  C11  109.56  3.000
 26V  H2   C16  C11  108.76  3.000
 26V  C15  C16  C11  112.85  3.000
 26V  H5   C15  H4   106.70  3.000
 26V  H5   C15  C14  109.55  3.000
 26V  H4   C15  C14  110.82  3.000
 26V  H5   C15  C16  110.01  3.000
 26V  H4   C15  C16  109.75  3.000
 26V  C14  C15  C16  109.95  3.000
 26V  H7   C14  H6   106.64  3.000
 26V  H7   C14  C13  109.63  3.000
 26V  H6   C14  C13  110.05  3.000
 26V  H7   C14  C15  110.96  3.000
 26V  H6   C14  C15  109.18  3.000
 26V  C13  C14  C15  110.31  3.000
 26V  H9   C13  H8   105.63  3.000
 26V  H9   C13  C10  108.65  3.000
 26V  H8   C13  C10  109.62  3.000
 26V  H9   C13  C14  108.85  3.000
 26V  H8   C13  C14  110.41  3.000
 26V  C10  C13  C14  113.37  3.000
 26V  C9   C10  C13  119.71  3.000
 26V  C13  C10  C11  121.70  3.000
 26V  C9   C10  C11  118.58  3.000
 26V  H10  C9   C8   119.31  3.000
 26V  H10  C9   C10  119.11  3.000
 26V  C8   C9   C10  121.58  3.000
 26V  H11  C8   C7   119.84  3.000
 26V  H11  C8   C9   119.76  3.000
 26V  C7   C8   C9   120.39  3.000
 26V  C6   C7   C8   121.33  3.000
 26V  C8   C7   C12  117.89  3.000
 26V  C6   C7   C12  120.74  3.000
 26V  H13  C6   H12  106.50  3.000
 26V  H13  C6   C5   109.50  3.000
 26V  H12  C6   C5   109.12  3.000
 26V  H13  C6   C7   109.86  3.000
 26V  H12  C6   C7   109.92  3.000
 26V  C5   C6   C7   111.80  3.000
 26V  H15  C5   H14  106.63  3.000
 26V  H15  C5   C4   110.10  3.000
 26V  H14  C5   C4   109.81  3.000
 26V  H15  C5   C6   109.17  3.000
 26V  H14  C5   C6   109.27  3.000
 26V  C4   C5   C6   111.73  3.000
 26V  H17  C4   H16  105.78  3.000
 26V  H17  C4   C2   109.95  3.000
 26V  H16  C4   C2   107.24  3.000
 26V  H17  C4   C5   110.28  3.000
 26V  H16  C4   C5   109.89  3.000
 26V  C2   C4   C5   113.37  3.000
 26V  N1   C2   O3   122.78  3.000
 26V  O3   C2   C4   122.87  3.000
 26V  N1   C2   C4   114.32  3.000
 26V  H18  N1   C1'  117.45  3.000
 26V  H18  N1   C2   118.02  3.000
 26V  C1'  N1   C2   124.08  3.000
 26V  H19  C1'  C2'  108.98  3.000
 26V  H19  C1'  O5'  110.39  3.000
 26V  C2'  C1'  O5'  109.96  3.000
 26V  H19  C1'  N1   108.36  3.000
 26V  O5'  C1'  N1   108.59  3.000
 26V  C2'  C1'  N1   110.55  3.000
 26V  C5'  O5'  C1'  113.62  3.000
 26V  H20  C5'  C4'  108.43  3.000
 26V  H20  C5'  C6'  109.12  3.000
 26V  C4'  C5'  C6'  111.84  3.000
 26V  H20  C5'  O5'  110.06  3.000
 26V  C6'  C5'  O5'  107.66  3.000
 26V  C4'  C5'  O5'  109.72  3.000
 26V  H22  C6'  H21  107.09  3.000
 26V  H22  C6'  O6'  111.81  3.000
 26V  H21  C6'  O6'  111.68  3.000
 26V  H22  C6'  C5'  108.76  3.000
 26V  H21  C6'  C5'  108.56  3.000
 26V  O6'  C6'  C5'  108.85  3.000
 26V  H23  O6'  C6'  107.92  3.000
 26V  H24  C4'  C3'  108.40  3.000
 26V  H24  C4'  O4'  111.08  3.000
 26V  C3'  C4'  O4'  111.22  3.000
 26V  H24  C4'  C5'  108.25  3.000
 26V  C3'  C4'  C5'  109.59  3.000
 26V  O4'  C4'  C5'  108.25  3.000
 26V  H25  O4'  C4'  108.08  3.000
 26V  H26  C3'  C2'  107.95  3.000
 26V  H26  C3'  O3'  110.84  3.000
 26V  C2'  C3'  O3'  112.13  3.000
 26V  H26  C3'  C4'  107.82  3.000
 26V  C2'  C3'  C4'  110.59  3.000
 26V  O3'  C3'  C4'  107.45  3.000
 26V  H27  O3'  C3'  108.72  3.000
 26V  H28  C2'  O2'  111.52  3.000
 26V  H28  C2'  C3'  108.72  3.000
 26V  O2'  C2'  C3'  107.68  3.000
 26V  H28  C2'  C1'  108.49  3.000
 26V  O2'  C2'  C1'  111.37  3.000
 26V  C3'  C2'  C1'  108.99  3.000
 26V  H29  O2'  C2'  108.86  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
 26V  CONST_01  C9   C8   C7   C12     0.00   0.0  0
 26V  CONST_02  C9   C10  C11  C12     0.00   0.0  0
 26V  CONST_03  C8   C7   C12  C11     0.00   0.0  0
 26V  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 26V  CONST_05  C7   C8   C9   C10     0.00   0.0  0
 26V  CONST_06  C7   C12  C11  C10     0.00   0.0  0
 26V  CONST_07  C6   C7   C12  C11   180.00   0.0  0
 26V  CONST_08  C6   C7   C8   C9    180.00   0.0  0
 26V  CONST_09  H11  C8   C7   C12   180.00   0.0  0
 26V  CONST_10  H10  C9   C10  C11   180.00   0.0  0
 26V  CONST_11  H1   C12  C11  C16     0.00   0.0  0
 26V  CONST_12  C1'  N1   C2   C4    180.00   0.0  0
 26V  CONST_13  C1'  N1   C2   O3      0.00   0.0  0
 26V  CONST_14  H18  N1   C2   C4      0.00   0.0  0
 26V  Var_01    C15  C16  C11  C12   161.54  30.0  1
 26V  Var_02    C14  C13  C10  C11   -16.06  30.0  1
 26V  Var_03    C14  C15  C16  C11    49.22  30.0  1
 26V  Var_04    C13  C14  C15  C16   -63.37  30.0  1
 26V  Var_05    C10  C13  C14  C15    45.93  30.0  1
 26V  Var_06    C5   C6   C7   C12   -78.46  30.0  2
 26V  Var_07    C4   C5   C6   C7   -179.35  30.0  1
 26V  Var_08    C2   C4   C5   C6   -178.73  30.0  2
 26V  Var_09    N1   C2   C4   C5   -155.44  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
 26V  chir_01  C1'  C2'  O5'  N1   negativ
 26V  chir_02  C5'  O5'  C6'  C4'  positiv
 26V  chir_03  C4'  O4'  C5'  C3'  positiv
 26V  chir_04  C3'  O3'  C4'  C2'  negativ
 26V  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
 26V  plan-1  C4   0.020
 26V  plan-1  C2   0.020
 26V  plan-1  O3   0.020
 26V  plan-1  N1   0.020
 26V  plan-1  C1'  0.020
 26V  plan-1  H18  0.020
 26V  plan-2  C12  0.020
 26V  plan-2  C11  0.020
 26V  plan-2  C16  0.020
 26V  plan-2  C13  0.020
 26V  plan-2  C10  0.020
 26V  plan-2  C9   0.020
 26V  plan-2  C8   0.020
 26V  plan-2  C7   0.020
 26V  plan-2  C6   0.020
 26V  plan-2  H1   0.020
 26V  plan-2  H10  0.020
 26V  plan-2  H11  0.020

