# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 16:52:13 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (1S)-1,5-anhydro-1-[5-(naphthalen-2-yl)-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)c3ccc4ccccc4c3
#
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
 6NE  6NE  (1S)-1,5-anhydro-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]-D-glucitol  ligand  46  26  .  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_6NE
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
 6NE  C6   C  CR6   0   0.069   2.6533  -0.1462  -0.0091
 6NE  C8   C  CR66  0   0.152   5.0070   0.1571   0.5168
 6NE  N5   N  NR15  0  -0.676   0.1863  -0.1009  -0.3839
 6NE  C9   C  CR66  0   0.099   5.3367   0.0776  -0.8612
 6NE  C5'  C  CH1   0  -0.015  -4.2177   1.1728  -0.1107
 6NE  C4'  C  CH1   0   0.038  -5.1453  -0.0276   0.0885
 6NE  O4'  O  OH1   0  -0.673  -6.3867   0.2747  -0.4981
 6NE  O5'  O  O2    0  -0.493  -2.9387   0.8825   0.4160
 6NE  C1'  C  CH1   0  -0.068  -2.3010  -0.2000  -0.2212
 6NE  C2'  C  CH1   0   0.016  -3.1060  -1.4801  -0.0077
 6NE  O2'  O  OH1   0  -0.671  -2.4405  -2.5182  -0.6851
 6NE  C3'  C  CH1   0  -0.019  -4.5188  -1.2665  -0.5408
 6NE  O3'  O  OH1   0  -0.675  -5.3606  -2.3628  -0.2576
 6NE  C1   C  CR5   0   0.460  -0.9271  -0.3228   0.3417
 6NE  N2   N  N     0  -0.440  -0.6282  -0.6456   1.5762
 6NE  C3   C  CR15  0  -0.259   0.7293  -0.6225   1.6459
 6NE  C4   C  CR5   0   0.312   1.2723  -0.2824   0.4294
 6NE  C7   C  CR16  0  -0.414   3.6572   0.0488   0.9119
 6NE  C12  C  CR16  0  -0.316   6.0463   0.3523   1.4587
 6NE  C13  C  CR16  0  -0.256   7.3468   0.4594   1.0484
 6NE  C14  C  CR16  0  -0.260   7.6733   0.3780  -0.3226
 6NE  C15  C  CR16  0  -0.306   6.6896   0.1918  -1.2556
 6NE  C10  C  CR16  0  -0.296   4.2919  -0.1151  -1.7941
 6NE  C11  C  CR16  0  -0.310   2.9942  -0.2281  -1.3843
 6NE  H1   H  HNR5  0   0.423   0.2026   0.1945  -1.3482
 6NE  H2   H  HOH1  0   0.457  -4.2252   4.2714   0.7334
 6NE  H6   H  HCH1  0   0.211  -5.2528  -0.2037   1.1714
 6NE  H7   H  HOH1  0   0.453  -6.9509  -0.5020  -0.4188
 6NE  H8   H  HCH1  0   0.244  -2.2193  -0.0149  -1.3049
 6NE  H9   H  HCH1  0   0.226  -3.1536  -1.6750   1.0720
 6NE  H10  H  HOH1  0   0.460  -2.6720  -3.3556  -0.2740
 6NE  H11  H  HCH1  0   0.218  -4.4537  -1.0987  -1.6271
 6NE  H12  H  HOH1  0   0.459  -5.2227  -3.0420  -0.9242
 6NE  H14  H  HCR5  0   0.259   1.2561  -0.8718   2.5548
 6NE  H15  H  HCR6  0   0.251   3.4205   0.1351   1.9660
 6NE  H16  H  HCR6  0   0.255   5.7983   0.4145   2.5115
 6NE  H17  H  HCR6  0   0.260   8.1337   0.6069   1.7764
 6NE  H18  H  HCR6  0   0.259   8.7070   0.4641  -0.6314
 6NE  H19  H  HCR6  0   0.256   6.9361   0.1296  -2.3089
 6NE  H20  H  HCR6  0   0.259   4.5307  -0.1817  -2.8486
 6NE  H21  H  HCR6  0   0.249   2.2251  -0.3975  -2.1273
 6NE  H5   H  HCH1  0   0.221  -4.1403   1.3770  -1.1914
 6NE  C6'  C  CH2   0  -0.157  -4.7349   2.4113   0.5898
 6NE  H3   H  HCH2  0   0.198  -4.7695   2.2209   1.6714
 6NE  O6'  O  OH1   0  -0.671  -3.8919   3.4943   0.2764
 6NE  H4   H  HCH2  0   0.212  -5.7637   2.5895   0.2603

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
 6NE  O3'  C3'  single    1.411  0.020  1.411
 6NE  O4'  C4'  single    1.406  0.020  1.406
 6NE  C3'  C4'  single    1.524  0.020  1.524
 6NE  C3'  C2'  single    1.525  0.020  1.525
 6NE  C4'  C5'  single    1.530  0.020  1.530
 6NE  O2'  C2'  single    1.407  0.020  1.407
 6NE  C2'  C1'  single    1.527  0.020  1.527
 6NE  O6'  C6'  single    1.408  0.020  1.408
 6NE  C5'  C6'  single    1.514  0.020  1.514
 6NE  C5'  O5'  single    1.413  0.020  1.413
 6NE  C1'  O5'  single    1.409  0.020  1.409
 6NE  C1'  C1   single    1.490  0.020  1.490
 6NE  N2   C1   aromatic  1.311  0.020  1.311
 6NE  N2   C3   aromatic  1.359  0.020  1.359
 6NE  C1   N5   aromatic  1.347  0.020  1.347
 6NE  C3   C4   aromatic  1.375  0.020  1.375
 6NE  N5   C4   aromatic  1.369  0.020  1.369
 6NE  C4   C6   single    1.455  0.020  1.455
 6NE  C6   C7   aromatic  1.376  0.020  1.376
 6NE  C6   C11  aromatic  1.419  0.020  1.419
 6NE  C7   C8   aromatic  1.411  0.020  1.411
 6NE  C11  C10  aromatic  1.365  0.020  1.365
 6NE  C8   C12  aromatic  1.416  0.020  1.416
 6NE  C8   C9   aromatic  1.419  0.020  1.419
 6NE  C12  C13  aromatic  1.368  0.020  1.368
 6NE  C10  C9   aromatic  1.414  0.020  1.414
 6NE  C9   C15  aromatic  1.414  0.020  1.414
 6NE  C13  C14  aromatic  1.412  0.020  1.412
 6NE  C15  C14  aromatic  1.369  0.020  1.369
 6NE  N5   H1   single    0.860  0.020  1.020
 6NE  O6'  H2   single    0.850  0.020  0.980
 6NE  C6'  H3   single    0.970  0.020  1.090
 6NE  C6'  H4   single    0.970  0.020  1.090
 6NE  C5'  H5   single    0.970  0.020  1.090
 6NE  C4'  H6   single    0.970  0.020  1.090
 6NE  O4'  H7   single    0.850  0.020  0.980
 6NE  C1'  H8   single    0.970  0.020  1.090
 6NE  C2'  H9   single    0.970  0.020  1.090
 6NE  O2'  H10  single    0.850  0.020  0.980
 6NE  C3'  H11  single    0.970  0.020  1.090
 6NE  O3'  H12  single    0.850  0.020  0.980
 6NE  C3   H14  single    0.930  0.020  1.080
 6NE  C7   H15  single    0.930  0.020  1.080
 6NE  C12  H16  single    0.930  0.020  1.080
 6NE  C13  H17  single    0.930  0.020  1.080
 6NE  C14  H18  single    0.930  0.020  1.080
 6NE  C15  H19  single    0.930  0.020  1.080
 6NE  C10  H20  single    0.930  0.020  1.080
 6NE  C11  H21  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
 6NE  C11  C6   C7   118.77  3.000
 6NE  C11  C6   C4   120.96  3.000
 6NE  C7   C6   C4   120.26  3.000
 6NE  C12  C8   C7   121.77  3.000
 6NE  C12  C8   C9   118.89  3.000
 6NE  C7   C8   C9   119.34  3.000
 6NE  H1   N5   C4   126.44  3.000
 6NE  H1   N5   C1   125.20  3.000
 6NE  C4   N5   C1   108.29  3.000
 6NE  C10  C9   C15  122.28  3.000
 6NE  C15  C9   C8   119.25  3.000
 6NE  C10  C9   C8   118.46  3.000
 6NE  H5   C5'  O5'  109.87  3.000
 6NE  H5   C5'  C4'  108.38  3.000
 6NE  O5'  C5'  C4'  109.81  3.000
 6NE  H5   C5'  C6'  109.03  3.000
 6NE  O5'  C5'  C6'  107.75  3.000
 6NE  C4'  C5'  C6'  111.99  3.000
 6NE  H6   C4'  C3'  108.41  3.000
 6NE  H6   C4'  O4'  110.98  3.000
 6NE  C3'  C4'  O4'  111.43  3.000
 6NE  H6   C4'  C5'  108.20  3.000
 6NE  C3'  C4'  C5'  109.56  3.000
 6NE  O4'  C4'  C5'  108.20  3.000
 6NE  H7   O4'  C4'  108.03  3.000
 6NE  C1'  O5'  C5'  113.51  3.000
 6NE  H8   C1'  C1   108.48  3.000
 6NE  H8   C1'  C2'  108.49  3.000
 6NE  C1   C1'  C2'  111.36  3.000
 6NE  H8   C1'  O5'  110.44  3.000
 6NE  C1   C1'  O5'  108.05  3.000
 6NE  C2'  C1'  O5'  110.01  3.000
 6NE  H9   C2'  C3'  109.17  3.000
 6NE  H9   C2'  O2'  111.28  3.000
 6NE  C3'  C2'  O2'  111.92  3.000
 6NE  H9   C2'  C1'  108.00  3.000
 6NE  O2'  C2'  C1'  107.57  3.000
 6NE  C3'  C2'  C1'  108.79  3.000
 6NE  H10  O2'  C2'  108.84  3.000
 6NE  H11  C3'  O3'  110.59  3.000
 6NE  H11  C3'  C2'  108.14  3.000
 6NE  O3'  C3'  C2'  111.95  3.000
 6NE  H11  C3'  C4'  107.93  3.000
 6NE  C2'  C3'  C4'  110.50  3.000
 6NE  O3'  C3'  C4'  107.66  3.000
 6NE  H12  O3'  C3'  108.91  3.000
 6NE  N2   C1   C1'  125.91  3.000
 6NE  N2   C1   N5   111.06  3.000
 6NE  C1'  C1   N5   123.02  3.000
 6NE  C3   N2   C1   105.78  3.000
 6NE  H14  C3   C4   127.53  3.000
 6NE  H14  C3   N2   121.77  3.000
 6NE  C4   C3   N2   110.68  3.000
 6NE  C3   C4   N5   104.19  3.000
 6NE  N5   C4   C6   124.15  3.000
 6NE  C3   C4   C6   131.64  3.000
 6NE  H15  C7   C8   118.38  3.000
 6NE  H15  C7   C6   120.18  3.000
 6NE  C8   C7   C6   121.43  3.000
 6NE  H16  C12  C13  120.31  3.000
 6NE  H16  C12  C8   119.09  3.000
 6NE  C13  C12  C8   120.60  3.000
 6NE  H17  C13  C14  119.54  3.000
 6NE  H17  C13  C12  120.01  3.000
 6NE  C14  C13  C12  120.45  3.000
 6NE  H18  C14  C15  120.19  3.000
 6NE  H18  C14  C13  119.56  3.000
 6NE  C15  C14  C13  120.24  3.000
 6NE  H19  C15  C14  120.47  3.000
 6NE  H19  C15  C9   118.96  3.000
 6NE  C14  C15  C9   120.57  3.000
 6NE  H20  C10  C11  119.78  3.000
 6NE  H20  C10  C9   119.19  3.000
 6NE  C11  C10  C9   121.03  3.000
 6NE  H21  C11  C10  118.82  3.000
 6NE  H21  C11  C6   120.22  3.000
 6NE  C10  C11  C6   120.95  3.000
 6NE  H4   C6'  H3   107.14  3.000
 6NE  H4   C6'  C5'  108.36  3.000
 6NE  H3   C6'  C5'  108.93  3.000
 6NE  H4   C6'  O6'  111.74  3.000
 6NE  H3   C6'  O6'  111.80  3.000
 6NE  C5'  C6'  O6'  108.77  3.000
 6NE  H2   O6'  C6'  107.97  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
 6NE  CONST_01  N2   C3   C4   C6   180.00  0.0  0
 6NE  CONST_02  C1   N5   C4   C6   180.00  0.0  0
 6NE  CONST_03  C12  C8   C7   C6   180.00  0.0  0
 6NE  CONST_04  C9   C8   C7   C6     0.00  0.0  0
 6NE  CONST_05  C9   C10  C11  C6     0.00  0.0  0
 6NE  CONST_06  C4   C6   C7   C8   180.00  0.0  0
 6NE  CONST_07  C11  C6   C7   C8     0.00  0.0  0
 6NE  CONST_08  C14  C13  C12  C8     0.00  0.0  0
 6NE  CONST_09  C11  C10  C9   C8     0.00  0.0  0
 6NE  CONST_10  C14  C15  C9   C8     0.00  0.0  0
 6NE  CONST_11  C3   N2   C1   N5     0.00  0.0  0
 6NE  CONST_12  N2   C3   C4   N5     0.00  0.0  0
 6NE  CONST_15  C13  C12  C8   C9     0.00  0.0  0
 6NE  CONST_16  C13  C14  C15  C9     0.00  0.0  0
 6NE  CONST_17  C4   C3   N2   C1     0.00  0.0  0
 6NE  CONST_18  C3   C4   N5   C1     0.00  0.0  0
 6NE  CONST_19  C4   N5   C1   N2     0.00  0.0  0
 6NE  CONST_22  C10  C11  C6   C4   180.00  0.0  0
 6NE  CONST_23  C10  C11  C6   C7     0.00  0.0  0
 6NE  CONST_24  C13  C12  C8   C7   180.00  0.0  0
 6NE  CONST_25  C10  C9   C8   C7     0.00  0.0  0
 6NE  CONST_26  C15  C9   C8   C7   180.00  0.0  0
 6NE  CONST_27  C10  C9   C8   C12  180.00  0.0  0
 6NE  CONST_28  C15  C9   C8   C12    0.00  0.0  0
 6NE  CONST_29  C15  C14  C13  C12    0.00  0.0  0
 6NE  CONST_30  C10  C9   C15  C14  180.00  0.0  0
 6NE  CONST_31  C11  C10  C9   C15  180.00  0.0  0
 6NE  CONST_32  C3   N2   C1   C1'  180.00  0.0  0
 6NE  CONST_33  C4   N5   C1   C1'  180.00  0.0  0
 6NE  CONST_34  H14  C3   C4   C6     0.00  0.0  0
 6NE  CONST_35  H1   N5   C4   C6     0.00  0.0  0
 6NE  CONST_36  H20  C10  C11  C6   180.00  0.0  0
 6NE  CONST_37  H17  C13  C12  C8   180.00  0.0  0
 6NE  CONST_38  H19  C15  C9   C8   180.00  0.0  0
 6NE  CONST_39  H15  C7   C8   C9   180.00  0.0  0
 6NE  CONST_40  H16  C12  C8   C9   180.00  0.0  0
 6NE  CONST_41  H21  C11  C10  C9   180.00  0.0  0
 6NE  CONST_42  H18  C14  C15  C9   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
 6NE  chir_01  C5'  C4'  C6'  O5'  negativ
 6NE  chir_02  C4'  O4'  C5'  C3'  positiv
 6NE  chir_03  C1'  O5'  C2'  C1   positiv
 6NE  chir_04  C2'  O2'  C1'  C3'  negativ
 6NE  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
 6NE  plan-1  C6   0.020
 6NE  plan-1  N5   0.020
 6NE  plan-1  C1'  0.020
 6NE  plan-1  C1   0.020
 6NE  plan-1  N2   0.020
 6NE  plan-1  C3   0.020
 6NE  plan-1  C4   0.020
 6NE  plan-1  H1   0.020
 6NE  plan-1  H14  0.020
 6NE  plan-2  C6   0.020
 6NE  plan-2  C8   0.020
 6NE  plan-2  C9   0.020
 6NE  plan-2  C4   0.020
 6NE  plan-2  C7   0.020
 6NE  plan-2  C12  0.020
 6NE  plan-2  C13  0.020
 6NE  plan-2  C14  0.020
 6NE  plan-2  C15  0.020
 6NE  plan-2  C10  0.020
 6NE  plan-2  C11  0.020
 6NE  plan-2  H15  0.020
 6NE  plan-2  H16  0.020
 6NE  plan-2  H17  0.020
 6NE  plan-2  H18  0.020
 6NE  plan-2  H19  0.020
 6NE  plan-2  H20  0.020
 6NE  plan-2  H21  0.020

