# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:24:17 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(5-phenyl-1H-imidazol-2-yl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2[nH]c(cn2)c3ccccc3
#
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
 6MY  6MY  (1S)-1,5-anhydro-1-(5-phenyl-1H-imidazol-2-yl)-D-glucitol  ligand  40  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6MY
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
 6MY  C6   C  CR6   0   0.069   3.7991   0.0729   0.0677
 6MY  C8   C  CR16  0  -0.236   6.1237   0.4381   0.6281
 6MY  N5   N  NR15  0  -0.676   1.3374  -0.0069  -0.3423
 6MY  C9   C  CR16  0  -0.269   6.4783   0.3317  -0.7117
 6MY  C5'  C  CH1   0  -0.015  -3.1317   1.0956  -0.2137
 6MY  C4'  C  CH1   0   0.037  -4.0024  -0.1348   0.0469
 6MY  O4'  O  OH1   0  -0.673  -5.2448   0.0665  -0.5794
 6MY  O5'  O  O2    0  -0.494  -1.8498   0.9052   0.3507
 6MY  C1'  C  CH1   0  -0.066  -1.1469  -0.1816  -0.2050
 6MY  C2'  C  CH1   0   0.015  -1.8920  -1.4842   0.0787
 6MY  O2'  O  OH1   0  -0.671  -1.1642  -2.5303  -0.5175
 6MY  C3'  C  CH1   0  -0.018  -3.3026  -1.3781  -0.4908
 6MY  O3'  O  OH1   0  -0.675  -4.0949  -2.4949  -0.1519
 6MY  C1   C  CR5   0   0.460   0.2205  -0.1977   0.3861
 6MY  N2   N  N     0  -0.440   0.5085  -0.3861   1.6503
 6MY  C3   C  CR15  0  -0.261   1.8637  -0.3069   1.7355
 6MY  C4   C  CR5   0   0.308   2.4155  -0.0701   0.4986
 6MY  C7   C  CR16  0  -0.329   4.7992   0.3153   1.0139
 6MY  C10  C  CR16  0  -0.237   5.4925   0.0972  -1.6602
 6MY  C11  C  CR16  0  -0.318   4.1661  -0.0355  -1.2758
 6MY  H1   H  HCR6  0   0.260   6.8822   0.6252   1.3771
 6MY  H2   H  HNR5  0   0.422   1.3605   0.1786  -1.3333
 6MY  H3   H  HCR6  0   0.258   7.5131   0.4322  -1.0116
 6MY  H4   H  HOH1  0   0.457  -3.3225   4.2408   0.4037
 6MY  H8   H  HCH1  0   0.212  -4.1222  -0.2477   1.1369
 6MY  H9   H  HOH1  0   0.453  -5.7808  -0.7210  -0.4375
 6MY  H10  H  HCH1  0   0.244  -1.0545  -0.0619  -1.2970
 6MY  H11  H  HCH1  0   0.227  -1.9510  -1.6110   1.1681
 6MY  H12  H  HOH1  0   0.460  -1.3581  -3.3478  -0.0507
 6MY  H13  H  HCH1  0   0.217  -3.2233  -1.2765  -1.5844
 6MY  H14  H  HOH1  0   0.459  -3.9014  -3.2118  -0.7632
 6MY  H16  H  HCR5  0   0.258   2.3814  -0.4390   2.6738
 6MY  H17  H  HCR6  0   0.253   4.5393   0.4196   2.0598
 6MY  H18  H  HCR6  0   0.260   5.7536   0.0103  -2.7069
 6MY  H19  H  HCR6  0   0.246   3.4226  -0.2363  -2.0374
 6MY  H7   H  HCH1  0   0.221  -3.0437   1.2365  -1.3038
 6MY  C6'  C  CH2   0  -0.157  -3.7207   2.3480   0.3997
 6MY  H5   H  HCH2  0   0.197  -3.7758   2.2187   1.4896
 6MY  O6'  O  OH1   0  -0.671  -2.9162   3.4474   0.0438
 6MY  H6   H  HCH2  0   0.213  -4.7470   2.4631   0.0363

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
 6MY  O3'  C3'  single    1.411  0.020  1.411
 6MY  O4'  C4'  single    1.406  0.020  1.406
 6MY  C3'  C4'  single    1.525  0.020  1.525
 6MY  C3'  C2'  single    1.525  0.020  1.525
 6MY  C4'  C5'  single    1.530  0.020  1.530
 6MY  O2'  C2'  single    1.407  0.020  1.407
 6MY  C2'  C1'  single    1.527  0.020  1.527
 6MY  O6'  C6'  single    1.408  0.020  1.408
 6MY  C5'  C6'  single    1.514  0.020  1.514
 6MY  C5'  O5'  single    1.414  0.020  1.414
 6MY  C1'  O5'  single    1.409  0.020  1.409
 6MY  C1'  C1   single    1.490  0.020  1.490
 6MY  N2   C1   aromatic  1.310  0.020  1.310
 6MY  N2   C3   aromatic  1.360  0.020  1.360
 6MY  C1   N5   aromatic  1.347  0.020  1.347
 6MY  C3   C4   aromatic  1.375  0.020  1.375
 6MY  N5   C4   aromatic  1.369  0.020  1.369
 6MY  C4   C6   single    1.456  0.020  1.456
 6MY  C6   C7   aromatic  1.398  0.020  1.398
 6MY  C6   C11  aromatic  1.397  0.020  1.397
 6MY  C7   C8   aromatic  1.385  0.020  1.385
 6MY  C11  C10  aromatic  1.387  0.020  1.387
 6MY  C8   C9   aromatic  1.390  0.020  1.390
 6MY  C10  C9   aromatic  1.388  0.020  1.388
 6MY  C8   H1   single    0.930  0.020  1.080
 6MY  N5   H2   single    0.860  0.020  1.020
 6MY  C9   H3   single    0.930  0.020  1.080
 6MY  O6'  H4   single    0.850  0.020  0.980
 6MY  C6'  H5   single    0.970  0.020  1.090
 6MY  C6'  H6   single    0.970  0.020  1.090
 6MY  C5'  H7   single    0.970  0.020  1.090
 6MY  C4'  H8   single    0.970  0.020  1.090
 6MY  O4'  H9   single    0.850  0.020  0.980
 6MY  C1'  H10  single    0.970  0.020  1.090
 6MY  C2'  H11  single    0.970  0.020  1.090
 6MY  O2'  H12  single    0.850  0.020  0.980
 6MY  C3'  H13  single    0.970  0.020  1.090
 6MY  O3'  H14  single    0.850  0.020  0.980
 6MY  C3   H16  single    0.930  0.020  1.080
 6MY  C7   H17  single    0.930  0.020  1.080
 6MY  C10  H18  single    0.930  0.020  1.080
 6MY  C11  H19  single    0.930  0.020  1.080

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
 6MY  C11  C6   C7   118.46  3.000
 6MY  C11  C6   C4   121.77  3.000
 6MY  C7   C6   C4   119.76  3.000
 6MY  H1   C8   C7   119.52  3.000
 6MY  H1   C8   C9   120.10  3.000
 6MY  C7   C8   C9   120.38  3.000
 6MY  H2   N5   C4   126.46  3.000
 6MY  H2   N5   C1   125.20  3.000
 6MY  C4   N5   C1   108.32  3.000
 6MY  H3   C9   C10  120.37  3.000
 6MY  H3   C9   C8   120.26  3.000
 6MY  C10  C9   C8   119.37  3.000
 6MY  H7   C5'  O5'  109.85  3.000
 6MY  H7   C5'  C4'  108.46  3.000
 6MY  O5'  C5'  C4'  109.87  3.000
 6MY  H7   C5'  C6'  109.02  3.000
 6MY  O5'  C5'  C6'  107.60  3.000
 6MY  C4'  C5'  C6'  112.03  3.000
 6MY  H8   C4'  C3'  108.37  3.000
 6MY  H8   C4'  O4'  111.05  3.000
 6MY  C3'  C4'  O4'  111.42  3.000
 6MY  H8   C4'  C5'  108.22  3.000
 6MY  C3'  C4'  C5'  109.55  3.000
 6MY  O4'  C4'  C5'  108.17  3.000
 6MY  H9   O4'  C4'  108.00  3.000
 6MY  C1'  O5'  C5'  113.51  3.000
 6MY  H10  C1'  C1   108.50  3.000
 6MY  H10  C1'  C2'  108.51  3.000
 6MY  C1   C1'  C2'  111.40  3.000
 6MY  H10  C1'  O5'  110.42  3.000
 6MY  C1   C1'  O5'  108.05  3.000
 6MY  C2'  C1'  O5'  109.96  3.000
 6MY  H11  C2'  C3'  109.20  3.000
 6MY  H11  C2'  O2'  111.24  3.000
 6MY  C3'  C2'  O2'  111.84  3.000
 6MY  H11  C2'  C1'  107.99  3.000
 6MY  O2'  C2'  C1'  107.64  3.000
 6MY  C3'  C2'  C1'  108.82  3.000
 6MY  H12  O2'  C2'  108.79  3.000
 6MY  H13  C3'  O3'  110.62  3.000
 6MY  H13  C3'  C2'  108.10  3.000
 6MY  O3'  C3'  C2'  112.01  3.000
 6MY  H13  C3'  C4'  107.94  3.000
 6MY  C2'  C3'  C4'  110.46  3.000
 6MY  O3'  C3'  C4'  107.64  3.000
 6MY  H14  O3'  C3'  108.93  3.000
 6MY  N2   C1   C1'  125.89  3.000
 6MY  N2   C1   N5   111.09  3.000
 6MY  C1'  C1   N5   123.02  3.000
 6MY  C3   N2   C1   105.73  3.000
 6MY  H16  C3   C4   127.62  3.000
 6MY  H16  C3   N2   121.67  3.000
 6MY  C4   C3   N2   110.70  3.000
 6MY  C3   C4   N5   104.16  3.000
 6MY  N5   C4   C6   124.20  3.000
 6MY  C3   C4   C6   131.64  3.000
 6MY  H17  C7   C8   119.35  3.000
 6MY  H17  C7   C6   119.92  3.000
 6MY  C8   C7   C6   120.72  3.000
 6MY  H18  C10  C11  119.40  3.000
 6MY  H18  C10  C9   120.21  3.000
 6MY  C11  C10  C9   120.39  3.000
 6MY  H19  C11  C10  118.63  3.000
 6MY  H19  C11  C6   120.69  3.000
 6MY  C10  C11  C6   120.68  3.000
 6MY  H6   C6'  H5   107.13  3.000
 6MY  H6   C6'  C5'  108.49  3.000
 6MY  H5   C6'  C5'  108.91  3.000
 6MY  H6   C6'  O6'  111.69  3.000
 6MY  H5   C6'  O6'  111.79  3.000
 6MY  C5'  C6'  O6'  108.74  3.000
 6MY  H4   O6'  C6'  107.96  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
 6MY  CONST_01  N2   C3   C4   C6   180.00  0.0  0
 6MY  CONST_02  C1   N5   C4   C6   180.00  0.0  0
 6MY  CONST_03  C9   C8   C7   C6     0.00  0.0  0
 6MY  CONST_04  C9   C10  C11  C6     0.00  0.0  0
 6MY  CONST_05  C4   C6   C7   C8   180.00  0.0  0
 6MY  CONST_06  C11  C6   C7   C8     0.00  0.0  0
 6MY  CONST_07  C11  C10  C9   C8     0.00  0.0  0
 6MY  CONST_08  C3   N2   C1   N5     0.00  0.0  0
 6MY  CONST_09  N2   C3   C4   N5     0.00  0.0  0
 6MY  CONST_12  C4   C3   N2   C1     0.00  0.0  0
 6MY  CONST_13  C3   C4   N5   C1     0.00  0.0  0
 6MY  CONST_14  C4   N5   C1   N2     0.00  0.0  0
 6MY  CONST_17  C10  C11  C6   C4   180.00  0.0  0
 6MY  CONST_18  C10  C11  C6   C7     0.00  0.0  0
 6MY  CONST_19  C10  C9   C8   C7     0.00  0.0  0
 6MY  CONST_20  C3   N2   C1   C1'  180.00  0.0  0
 6MY  CONST_21  C4   N5   C1   C1'  180.00  0.0  0
 6MY  CONST_22  H16  C3   C4   C6     0.00  0.0  0
 6MY  CONST_23  H2   N5   C4   C6     0.00  0.0  0
 6MY  CONST_24  H1   C8   C7   C6   180.00  0.0  0
 6MY  CONST_25  H18  C10  C11  C6   180.00  0.0  0
 6MY  CONST_26  H17  C7   C8   C9   180.00  0.0  0
 6MY  CONST_27  H19  C11  C10  C9   180.00  0.0  0
 6MY  CONST_28  H3   C9   C8   C7   180.00  0.0  0

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
 6MY  chir_01  C5'  C4'  C6'  O5'  negativ
 6MY  chir_02  C4'  O4'  C5'  C3'  positiv
 6MY  chir_03  C1'  O5'  C2'  C1   positiv
 6MY  chir_04  C2'  O2'  C1'  C3'  negativ
 6MY  chir_05  C3'  O3'  C2'  C4'  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
 6MY  plan-1  C6   0.020
 6MY  plan-1  N5   0.020
 6MY  plan-1  C1'  0.020
 6MY  plan-1  C1   0.020
 6MY  plan-1  N2   0.020
 6MY  plan-1  C3   0.020
 6MY  plan-1  C4   0.020
 6MY  plan-1  H2   0.020
 6MY  plan-1  H16  0.020
 6MY  plan-2  C6   0.020
 6MY  plan-2  C8   0.020
 6MY  plan-2  C9   0.020
 6MY  plan-2  C4   0.020
 6MY  plan-2  C7   0.020
 6MY  plan-2  C10  0.020
 6MY  plan-2  C11  0.020
 6MY  plan-2  H1   0.020
 6MY  plan-2  H3   0.020
 6MY  plan-2  H17  0.020
 6MY  plan-2  H18  0.020
 6MY  plan-2  H19  0.020

