# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:27:37 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1~{H}-imidazol-2-yl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1c2[nH]cc(n2)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
 9LE  9LE  (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1~{H}-imidazol-2-yl)oxane-3,4-diol  ligand  47  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9LE
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
 9LE  O6'  O  OH1   0  -0.669   3.9469   0.2081   3.3974
 9LE  C6'  C  CH2   0  -0.162   4.1373   1.0901   2.3179
 9LE  C5'  C  CH1   0  -0.020   3.9765   0.3288   1.0209
 9LE  C4'  C  CH1   0   0.002   4.2778   1.2021  -0.2021
 9LE  O4'  O  OH1   0  -0.675   5.6239   1.6269  -0.2287
 9LE  C3'  C  CH1   0   0.038   4.0273   0.3986  -1.4722
 9LE  O3'  O  OH1   0  -0.670   4.1880   1.1838  -2.6268
 9LE  O5'  O  O2    0  -0.494   2.6416  -0.1312   0.9542
 9LE  C1'  C  CH1   0  -0.034   2.3817  -0.9385  -0.1703
 9LE  C2'  C  CH1   0  -0.142   2.6128  -0.1759  -1.4781
 9LE  N2'  N  NH2   0  -0.788   2.3156  -1.0565  -2.5885
 9LE  C1   C  CR5   0   0.495   0.9695  -1.4050  -0.0705
 9LE  N2   N  NR15  0  -0.622   0.6203  -2.7032   0.0321
 9LE  C3   C  CR15  0  -0.115  -0.7363  -2.7699   0.0991
 9LE  C4   C  CR5   0   0.134  -1.1663  -1.4665   0.0385
 9LE  N5   N  N     0  -0.464  -0.0856  -0.6345  -0.0672
 9LE  C6   C  CR6   0   0.040  -2.5353  -0.9609   0.0741
 9LE  C11  C  CR16  0  -0.330  -3.6292  -1.8622   0.1575
 9LE  C10  C  CR16  0  -0.293  -4.9155  -1.4096   0.1900
 9LE  C9   C  CR66  0   0.095  -5.2021  -0.0242   0.1407
 9LE  C15  C  CR16  0  -0.308  -6.5237   0.4747   0.1713
 9LE  C14  C  CR16  0  -0.263  -6.7620   1.8223   0.1226
 9LE  C13  C  CR16  0  -0.257  -5.6849   2.7300   0.0414
 9LE  C12  C  CR16  0  -0.320  -4.3950   2.2736   0.0096
 9LE  C8   C  CR66  0   0.151  -4.1173   0.8862   0.0581
 9LE  C7   C  CR16  0  -0.396  -2.7956   0.3886   0.0261
 9LE  H1   H  HOH1  0   0.457   4.0607   0.7074   4.2109
 9LE  H2   H  HCH2  0   0.200   3.4167   1.9196   2.3348
 9LE  H3   H  HCH2  0   0.203   5.1393   1.5344   2.3354
 9LE  H4   H  HCH1  0   0.218   4.6708  -0.5285   1.0177
 9LE  H5   H  HCH1  0   0.223   3.5925   2.0626  -0.1939
 9LE  H6   H  HOH1  0   0.462   5.7012   2.4516   0.2588
 9LE  H7   H  HCH1  0   0.197   4.7341  -0.4504  -1.4762
 9LE  H8   H  HOH1  0   0.450   5.0839   1.5368  -2.6240
 9LE  H9   H  HCH1  0   0.236   3.0462  -1.8194  -0.1646
 9LE  H10  H  HCH1  0   0.246   1.8984   0.6546  -1.5067
 9LE  H11  H  HNH2  0   0.356   2.3437  -0.5384  -3.4566
 9LE  H12  H  HNH2  0   0.341   3.0269  -1.7750  -2.6674
 9LE  H14  H  HNR5  0   0.422   1.2505  -3.4901   0.0519
 9LE  H15  H  HCR5  0   0.289  -1.2574  -3.7083   0.1852
 9LE  H17  H  HCR6  0   0.244  -3.4469  -2.9288   0.1944
 9LE  H18  H  HCR6  0   0.255  -5.7353  -2.1149   0.2520
 9LE  H19  H  HCR6  0   0.255  -7.3479  -0.2261   0.2338
 9LE  H20  H  HCR6  0   0.257  -7.7774   2.1962   0.1459
 9LE  H21  H  HCR6  0   0.257  -5.8831   3.7934   0.0045
 9LE  H22  H  HCR6  0   0.253  -3.5694   2.9723  -0.0520
 9LE  H23  H  HCR6  0   0.246  -1.9750   1.0931  -0.0360

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
 9LE  O3'  C3'  single    1.405  0.020  1.405
 9LE  O4'  C4'  single    1.412  0.020  1.412
 9LE  C3'  C4'  single    1.524  0.020  1.524
 9LE  C3'  C2'  single    1.527  0.020  1.527
 9LE  C4'  C5'  single    1.533  0.020  1.533
 9LE  N2'  C2'  single    1.448  0.020  1.448
 9LE  C2'  C1'  single    1.531  0.020  1.531
 9LE  O6'  C6'  single    1.407  0.020  1.407
 9LE  C5'  C6'  single    1.513  0.020  1.513
 9LE  C5'  O5'  single    1.414  0.020  1.414
 9LE  C1'  O5'  single    1.409  0.020  1.409
 9LE  C1'  C1   single    1.491  0.020  1.491
 9LE  N2   C1   aromatic  1.348  0.020  1.348
 9LE  N2   C3   aromatic  1.360  0.020  1.360
 9LE  C1   N5   aromatic  1.306  0.020  1.306
 9LE  C3   C4   aromatic  1.374  0.020  1.374
 9LE  N5   C4   aromatic  1.368  0.020  1.368
 9LE  C4   C6   single    1.460  0.020  1.460
 9LE  C6   C7   aromatic  1.375  0.020  1.375
 9LE  C6   C11  aromatic  1.420  0.020  1.420
 9LE  C7   C8   aromatic  1.413  0.020  1.413
 9LE  C11  C10  aromatic  1.364  0.020  1.364
 9LE  C8   C12  aromatic  1.416  0.020  1.416
 9LE  C8   C9   aromatic  1.419  0.020  1.419
 9LE  C12  C13  aromatic  1.369  0.020  1.369
 9LE  C10  C9   aromatic  1.416  0.020  1.416
 9LE  C9   C15  aromatic  1.413  0.020  1.413
 9LE  C13  C14  aromatic  1.411  0.020  1.411
 9LE  C15  C14  aromatic  1.369  0.020  1.369
 9LE  O6'  H1   single    0.850  0.020  0.980
 9LE  C6'  H2   single    0.970  0.020  1.090
 9LE  C6'  H3   single    0.970  0.020  1.090
 9LE  C5'  H4   single    0.970  0.020  1.090
 9LE  C4'  H5   single    0.970  0.020  1.090
 9LE  O4'  H6   single    0.850  0.020  0.980
 9LE  C3'  H7   single    0.970  0.020  1.090
 9LE  O3'  H8   single    0.850  0.020  0.980
 9LE  C1'  H9   single    0.970  0.020  1.090
 9LE  C2'  H10  single    0.970  0.020  1.090
 9LE  N2'  H11  single    0.890  0.020  1.040
 9LE  N2'  H12  single    0.890  0.020  1.040
 9LE  N2   H14  single    0.860  0.020  1.020
 9LE  C3   H15  single    0.930  0.020  1.080
 9LE  C11  H17  single    0.930  0.020  1.080
 9LE  C10  H18  single    0.930  0.020  1.080
 9LE  C15  H19  single    0.930  0.020  1.080
 9LE  C14  H20  single    0.930  0.020  1.080
 9LE  C13  H21  single    0.930  0.020  1.080
 9LE  C12  H22  single    0.930  0.020  1.080
 9LE  C7   H23  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
 9LE  H1   O6'  C6'  107.92  3.000
 9LE  H3   C6'  H2   107.04  3.000
 9LE  H3   C6'  C5'  108.35  3.000
 9LE  H2   C6'  C5'  108.87  3.000
 9LE  H3   C6'  O6'  111.44  3.000
 9LE  H2   C6'  O6'  111.88  3.000
 9LE  C5'  C6'  O6'  109.15  3.000
 9LE  H4   C5'  O5'  109.96  3.000
 9LE  H4   C5'  C4'  108.47  3.000
 9LE  O5'  C5'  C4'  109.48  3.000
 9LE  H4   C5'  C6'  109.07  3.000
 9LE  O5'  C5'  C6'  107.73  3.000
 9LE  C4'  C5'  C6'  112.12  3.000
 9LE  H5   C4'  C3'  108.44  3.000
 9LE  H5   C4'  O4'  111.02  3.000
 9LE  C3'  C4'  O4'  107.44  3.000
 9LE  H5   C4'  C5'  108.50  3.000
 9LE  C3'  C4'  C5'  109.41  3.000
 9LE  O4'  C4'  C5'  111.96  3.000
 9LE  H6   O4'  C4'  108.99  3.000
 9LE  H7   C3'  C2'  107.68  3.000
 9LE  H7   C3'  O3'  110.68  3.000
 9LE  C2'  C3'  O3'  108.24  3.000
 9LE  H7   C3'  C4'  107.64  3.000
 9LE  C2'  C3'  C4'  110.73  3.000
 9LE  O3'  C3'  C4'  111.80  3.000
 9LE  H8   O3'  C3'  107.99  3.000
 9LE  C1'  O5'  C5'  113.48  3.000
 9LE  H9   C1'  C1   108.68  3.000
 9LE  H9   C1'  C2'  108.13  3.000
 9LE  C1   C1'  C2'  110.85  3.000
 9LE  H9   C1'  O5'  110.02  3.000
 9LE  C1   C1'  O5'  107.50  3.000
 9LE  C2'  C1'  O5'  111.62  3.000
 9LE  H10  C2'  N2'  107.88  3.000
 9LE  H10  C2'  C1'  107.54  3.000
 9LE  N2'  C2'  C1'  108.73  3.000
 9LE  H10  C2'  C3'  108.60  3.000
 9LE  C1'  C2'  C3'  108.89  3.000
 9LE  N2'  C2'  C3'  114.96  3.000
 9LE  H12  N2'  H11  106.06  3.000
 9LE  H12  N2'  C2'  110.28  3.000
 9LE  H11  N2'  C2'  109.93  3.000
 9LE  N5   C1   N2   111.01  3.000
 9LE  N5   C1   C1'  125.50  3.000
 9LE  N2   C1   C1'  123.49  3.000
 9LE  H14  N2   C3   125.75  3.000
 9LE  H14  N2   C1   126.23  3.000
 9LE  C3   N2   C1   108.02  3.000
 9LE  H15  C3   C4   132.75  3.000
 9LE  H15  C3   N2   121.97  3.000
 9LE  C4   C3   N2   105.28  3.000
 9LE  C6   C4   N5   122.15  3.000
 9LE  C6   C4   C3   128.39  3.000
 9LE  N5   C4   C3   109.46  3.000
 9LE  C4   N5   C1   106.23  3.000
 9LE  C7   C6   C11  118.63  3.000
 9LE  C11  C6   C4   120.27  3.000
 9LE  C7   C6   C4   121.10  3.000
 9LE  H17  C11  C10  119.00  3.000
 9LE  H17  C11  C6   119.85  3.000
 9LE  C10  C11  C6   121.15  3.000
 9LE  H18  C10  C9   119.08  3.000
 9LE  H18  C10  C11  119.94  3.000
 9LE  C9   C10  C11  120.98  3.000
 9LE  C8   C9   C15  119.33  3.000
 9LE  C15  C9   C10  122.29  3.000
 9LE  C8   C9   C10  118.38  3.000
 9LE  H19  C15  C14  120.40  3.000
 9LE  H19  C15  C9   118.97  3.000
 9LE  C14  C15  C9   120.63  3.000
 9LE  H20  C14  C13  119.68  3.000
 9LE  H20  C14  C15  120.16  3.000
 9LE  C13  C14  C15  120.16  3.000
 9LE  H21  C13  C12  119.96  3.000
 9LE  H21  C13  C14  119.62  3.000
 9LE  C12  C13  C14  120.41  3.000
 9LE  H22  C12  C8   118.98  3.000
 9LE  H22  C12  C13  120.29  3.000
 9LE  C8   C12  C13  120.72  3.000
 9LE  C7   C8   C12  121.86  3.000
 9LE  C12  C8   C9   118.75  3.000
 9LE  C7   C8   C9   119.39  3.000
 9LE  H23  C7   C8   118.75  3.000
 9LE  H23  C7   C6   119.79  3.000
 9LE  C8   C7   C6   121.46  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
 9LE  CONST_01  C4   C3   N2   C1     0.00  0.0  0
 9LE  CONST_02  C3   C4   N5   C1     0.00  0.0  0
 9LE  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 9LE  CONST_04  C4   N5   C1   N2     0.00  0.0  0
 9LE  CONST_05  N5   C4   C3   N2     0.00  0.0  0
 9LE  CONST_06  C6   C4   C3   N2   180.00  0.0  0
 9LE  CONST_07  N5   C1   N2   C3     0.00  0.0  0
 9LE  CONST_08  C7   C6   C4   C3   180.00  0.0  0
 9LE  CONST_09  C11  C6   C4   C3     0.00  0.0  0
 9LE  CONST_10  C8   C7   C6   C4   180.00  0.0  0
 9LE  CONST_11  C10  C11  C6   C4   180.00  0.0  0
 9LE  CONST_12  C7   C6   C4   N5     0.00  0.0  0
 9LE  CONST_13  C11  C6   C4   N5   180.00  0.0  0
 9LE  CONST_14  C12  C8   C7   C6   180.00  0.0  0
 9LE  CONST_15  C9   C8   C7   C6     0.00  0.0  0
 9LE  CONST_16  C9   C10  C11  C6     0.00  0.0  0
 9LE  CONST_17  C8   C7   C6   C11    0.00  0.0  0
 9LE  CONST_18  C8   C9   C10  C11    0.00  0.0  0
 9LE  CONST_19  C15  C9   C10  C11  180.00  0.0  0
 9LE  CONST_20  C7   C6   C11  C10    0.00  0.0  0
 9LE  CONST_21  C7   C8   C9   C10    0.00  0.0  0
 9LE  CONST_22  C12  C8   C9   C10  180.00  0.0  0
 9LE  CONST_23  C14  C15  C9   C10  180.00  0.0  0
 9LE  CONST_24  C13  C12  C8   C9     0.00  0.0  0
 9LE  CONST_25  C13  C14  C15  C9     0.00  0.0  0
 9LE  CONST_26  C7   C8   C9   C15  180.00  0.0  0
 9LE  CONST_27  C12  C8   C9   C15    0.00  0.0  0
 9LE  CONST_28  C12  C13  C14  C15    0.00  0.0  0
 9LE  CONST_29  C8   C12  C13  C14    0.00  0.0  0
 9LE  CONST_30  C8   C9   C15  C14    0.00  0.0  0
 9LE  CONST_31  C7   C8   C12  C13  180.00  0.0  0
 9LE  CONST_32  C3   N2   C1   C1'  180.00  0.0  0
 9LE  CONST_33  C4   N5   C1   C1'  180.00  0.0  0
 9LE  CONST_34  H14  N2   C1   C1'    0.00  0.0  0
 9LE  CONST_35  H15  C3   N2   C1   180.00  0.0  0
 9LE  CONST_36  H23  C7   C6   C4     0.00  0.0  0
 9LE  CONST_37  H17  C11  C6   C4     0.00  0.0  0
 9LE  CONST_38  H18  C10  C11  C6   180.00  0.0  0
 9LE  CONST_39  H19  C15  C9   C10    0.00  0.0  0
 9LE  CONST_40  H22  C12  C8   C9   180.00  0.0  0
 9LE  CONST_41  H20  C14  C15  C9   180.00  0.0  0
 9LE  CONST_42  H21  C13  C14  C15  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
 9LE  chir_01  C5'  C4'  C6'  O5'  negativ
 9LE  chir_02  C4'  O4'  C5'  C3'  positiv
 9LE  chir_03  C3'  O3'  C4'  C2'  negativ
 9LE  chir_04  C1'  O5'  C1   C2'  negativ
 9LE  chir_05  C2'  N2'  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
 9LE  plan-1  C1'  0.020
 9LE  plan-1  C1   0.020
 9LE  plan-1  N2   0.020
 9LE  plan-1  C3   0.020
 9LE  plan-1  C4   0.020
 9LE  plan-1  N5   0.020
 9LE  plan-1  C6   0.020
 9LE  plan-1  H14  0.020
 9LE  plan-1  H15  0.020
 9LE  plan-2  C4   0.020
 9LE  plan-2  C6   0.020
 9LE  plan-2  C11  0.020
 9LE  plan-2  C10  0.020
 9LE  plan-2  C9   0.020
 9LE  plan-2  C15  0.020
 9LE  plan-2  C14  0.020
 9LE  plan-2  C13  0.020
 9LE  plan-2  C12  0.020
 9LE  plan-2  C8   0.020
 9LE  plan-2  C7   0.020
 9LE  plan-2  H17  0.020
 9LE  plan-2  H18  0.020
 9LE  plan-2  H19  0.020
 9LE  plan-2  H20  0.020
 9LE  plan-2  H21  0.020
 9LE  plan-2  H22  0.020
 9LE  plan-2  H23  0.020

