# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:09:19 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-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]nc(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
 9L8  9L8  (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4-diol  ligand  46  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_9L8
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
 9L8  N2'  N  NH2   0  -0.789  -2.4664   2.6415   0.9610
 9L8  C2'  C  CH1   0  -0.150  -2.8317   1.4927   0.1589
 9L8  C3'  C  CH1   0   0.037  -4.3086   1.4053  -0.2156
 9L8  O3'  O  OH1   0  -0.669  -4.6183   2.5171  -1.0171
 9L8  C4'  C  CH1   0   0.003  -4.6121   0.0912  -0.9271
 9L8  O4'  O  OH1   0  -0.674  -6.0044   0.0482  -1.1519
 9L8  C5'  C  CH1   0  -0.021  -4.1388  -1.0788  -0.0577
 9L8  C6'  C  CH2   0  -0.161  -4.3385  -2.4167  -0.7351
 9L8  O6'  O  OH1   0  -0.669  -3.9827  -3.4397   0.1633
 9L8  O5'  O  O2    0  -0.494  -2.7563  -0.9417   0.2061
 9L8  C1'  C  CH1   0  -0.027  -2.4290   0.2239   0.9180
 9L8  C1   C  CR5   0   0.514  -0.9526   0.1973   1.1226
 9L8  N5   N  N     0  -0.475  -0.0486   0.1118   0.1743
 9L8  C4   C  CR5   0   0.305   1.1233   0.1164   0.8486
 9L8  C6   C  CR6   0   0.013   2.4236   0.0251   0.1836
 9L8  C7   C  CR16  0  -0.372   3.5932  -0.0024   0.9037
 9L8  C8   C  CR66  0   0.150   4.8446  -0.0950   0.2577
 9L8  C9   C  CR66  0   0.106   4.8910  -0.1608  -1.1590
 9L8  C15  C  CR16  0  -0.308   6.1459  -0.2549  -1.8035
 9L8  C14  C  CR16  0  -0.257   7.3033  -0.2829  -1.0737
 9L8  C13  C  CR16  0  -0.257   7.2585  -0.2174   0.3357
 9L8  C12  C  CR16  0  -0.315   6.0584  -0.1261   0.9857
 9L8  C10  C  CR16  0  -0.298   3.6743  -0.1304  -1.8792
 9L8  C11  C  CR16  0  -0.297   2.4761  -0.0409  -1.2304
 9L8  N3   N  N     0  -0.269   0.9816   0.2030   2.1556
 9L8  N2   N  NR15  0  -0.472  -0.3401   0.2480   2.3054
 9L8  H1   H  HNH2  0   0.359  -2.5502   3.4870   0.4128
 9L8  H2   H  HNH2  0   0.344  -3.1102   2.7438   1.7374
 9L8  H4   H  HCH1  0   0.254  -2.2422   1.5242  -0.7637
 9L8  H5   H  HCH1  0   0.200  -4.8981   1.4210   0.7182
 9L8  H6   H  HOH1  0   0.451  -5.5534   2.4705  -1.2425
 9L8  H7   H  HCH1  0   0.224  -4.0567   0.0711  -1.8760
 9L8  H8   H  HOH1  0   0.462  -6.1804  -0.4718  -1.9406
 9L8  H9   H  HCH1  0   0.221  -4.7101  -1.0670   0.8854
 9L8  H10  H  HCH2  0   0.204  -5.3878  -2.4998  -1.0409
 9L8  H11  H  HCH2  0   0.201  -3.7299  -2.4454  -1.6495
 9L8  H12  H  HOH1  0   0.457  -4.1195  -4.2828  -0.2776
 9L8  H13  H  HCH1  0   0.246  -2.9266   0.2303   1.9013
 9L8  H15  H  HCR6  0   0.251   3.5689   0.0437   1.9860
 9L8  H16  H  HCR6  0   0.257   6.1787  -0.3042  -2.8852
 9L8  H17  H  HCR6  0   0.260   8.2595  -0.3568  -1.5752
 9L8  H18  H  HCR6  0   0.260   8.1807  -0.2404   0.9016
 9L8  H19  H  HCR6  0   0.256   6.0232  -0.0779   2.0674
 9L8  H20  H  HCR6  0   0.257   3.7020  -0.1790  -2.9610
 9L8  H21  H  HCR6  0   0.255   1.5554  -0.0196  -1.7975
 9L8  H3   H  HNR5  0   0.432  -0.7498   0.3159   3.2255

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
 9L8  O3'  C3'  single    1.405  0.020  1.405
 9L8  O4'  C4'  single    1.411  0.020  1.411
 9L8  C3'  C4'  single    1.525  0.020  1.525
 9L8  C3'  C2'  single    1.526  0.020  1.526
 9L8  C4'  C5'  single    1.533  0.020  1.533
 9L8  N2'  C2'  single    1.448  0.020  1.448
 9L8  C2'  C1'  single    1.532  0.020  1.532
 9L8  O6'  C6'  single    1.407  0.020  1.407
 9L8  C5'  C6'  single    1.513  0.020  1.513
 9L8  C5'  O5'  single    1.414  0.020  1.414
 9L8  C1'  O5'  single    1.404  0.020  1.404
 9L8  C1'  C1   single    1.491  0.020  1.491
 9L8  N2   C1   aromatic  1.333  0.020  1.333
 9L8  N2   N3   aromatic  1.331  0.020  1.331
 9L8  C1   N5   aromatic  1.313  0.020  1.313
 9L8  N3   C4   aromatic  1.318  0.020  1.318
 9L8  N5   C4   aromatic  1.352  0.020  1.352
 9L8  C4   C6   single    1.463  0.020  1.463
 9L8  C6   C7   aromatic  1.374  0.020  1.374
 9L8  C6   C11  aromatic  1.417  0.020  1.417
 9L8  C7   C8   aromatic  1.411  0.020  1.411
 9L8  C11  C10  aromatic  1.365  0.020  1.365
 9L8  C8   C12  aromatic  1.416  0.020  1.416
 9L8  C8   C9   aromatic  1.419  0.020  1.419
 9L8  C12  C13  aromatic  1.368  0.020  1.368
 9L8  C10  C9   aromatic  1.414  0.020  1.414
 9L8  C9   C15  aromatic  1.414  0.020  1.414
 9L8  C13  C14  aromatic  1.412  0.020  1.412
 9L8  C15  C14  aromatic  1.368  0.020  1.368
 9L8  N2'  H1   single    0.890  0.020  1.040
 9L8  N2'  H2   single    0.890  0.020  1.040
 9L8  C2'  H4   single    0.970  0.020  1.090
 9L8  C3'  H5   single    0.970  0.020  1.090
 9L8  O3'  H6   single    0.850  0.020  0.980
 9L8  C4'  H7   single    0.970  0.020  1.090
 9L8  O4'  H8   single    0.850  0.020  0.980
 9L8  C5'  H9   single    0.970  0.020  1.090
 9L8  C6'  H10  single    0.970  0.020  1.090
 9L8  C6'  H11  single    0.970  0.020  1.090
 9L8  O6'  H12  single    0.850  0.020  0.980
 9L8  C1'  H13  single    0.970  0.020  1.090
 9L8  C7   H15  single    0.930  0.020  1.080
 9L8  C15  H16  single    0.930  0.020  1.080
 9L8  C14  H17  single    0.930  0.020  1.080
 9L8  C13  H18  single    0.930  0.020  1.080
 9L8  C12  H19  single    0.930  0.020  1.080
 9L8  C10  H20  single    0.930  0.020  1.080
 9L8  C11  H21  single    0.930  0.020  1.080
 9L8  N2   H3   single    0.860  0.020  1.020

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
 9L8  H2   N2'  H1   106.15  3.000
 9L8  H2   N2'  C2'  110.13  3.000
 9L8  H1   N2'  C2'  110.01  3.000
 9L8  H4   C2'  C1'  107.43  3.000
 9L8  H4   C2'  C3'  108.41  3.000
 9L8  C1'  C2'  C3'  109.17  3.000
 9L8  H4   C2'  N2'  107.94  3.000
 9L8  C1'  C2'  N2'  108.43  3.000
 9L8  C3'  C2'  N2'  115.19  3.000
 9L8  H5   C3'  C4'  107.49  3.000
 9L8  H5   C3'  O3'  110.69  3.000
 9L8  C4'  C3'  O3'  111.83  3.000
 9L8  H5   C3'  C2'  107.95  3.000
 9L8  C4'  C3'  C2'  110.88  3.000
 9L8  O3'  C3'  C2'  107.94  3.000
 9L8  H6   O3'  C3'  108.01  3.000
 9L8  H7   C4'  C5'  108.63  3.000
 9L8  H7   C4'  O4'  111.12  3.000
 9L8  C5'  C4'  O4'  111.83  3.000
 9L8  H7   C4'  C3'  108.54  3.000
 9L8  C5'  C4'  C3'  109.38  3.000
 9L8  O4'  C4'  C3'  107.28  3.000
 9L8  H8   O4'  C4'  109.14  3.000
 9L8  H9   C5'  O5'  110.24  3.000
 9L8  H9   C5'  C6'  108.91  3.000
 9L8  O5'  C5'  C6'  107.36  3.000
 9L8  H9   C5'  C4'  108.48  3.000
 9L8  O5'  C5'  C4'  109.49  3.000
 9L8  C6'  C5'  C4'  112.36  3.000
 9L8  H11  C6'  H10  107.22  3.000
 9L8  H11  C6'  O6'  111.86  3.000
 9L8  H10  C6'  O6'  111.41  3.000
 9L8  H11  C6'  C5'  108.83  3.000
 9L8  H10  C6'  C5'  108.56  3.000
 9L8  O6'  C6'  C5'  108.88  3.000
 9L8  H12  O6'  C6'  107.99  3.000
 9L8  C1'  O5'  C5'  113.76  3.000
 9L8  H13  C1'  C1   108.95  3.000
 9L8  H13  C1'  O5'  110.60  3.000
 9L8  C1   C1'  O5'  106.59  3.000
 9L8  H13  C1'  C2'  108.57  3.000
 9L8  C1   C1'  C2'  110.06  3.000
 9L8  O5'  C1'  C2'  112.01  3.000
 9L8  N2   C1   N5   109.09  3.000
 9L8  N5   C1   C1'  125.73  3.000
 9L8  N2   C1   C1'  125.18  3.000
 9L8  C4   N5   C1   103.67  3.000
 9L8  N3   C4   C6   123.40  3.000
 9L8  C6   C4   N5   122.91  3.000
 9L8  N3   C4   N5   113.69  3.000
 9L8  C11  C6   C7   119.39  3.000
 9L8  C11  C6   C4   119.31  3.000
 9L8  C7   C6   C4   121.31  3.000
 9L8  H15  C7   C8   118.68  3.000
 9L8  H15  C7   C6   120.24  3.000
 9L8  C8   C7   C6   121.08  3.000
 9L8  C12  C8   C9   118.97  3.000
 9L8  C9   C8   C7   119.28  3.000
 9L8  C12  C8   C7   121.75  3.000
 9L8  C10  C9   C15  122.21  3.000
 9L8  C15  C9   C8   119.16  3.000
 9L8  C10  C9   C8   118.64  3.000
 9L8  H16  C15  C14  120.39  3.000
 9L8  H16  C15  C9   119.01  3.000
 9L8  C14  C15  C9   120.59  3.000
 9L8  H17  C14  C13  119.60  3.000
 9L8  H17  C14  C15  120.10  3.000
 9L8  C13  C14  C15  120.31  3.000
 9L8  H18  C13  C12  120.03  3.000
 9L8  H18  C13  C14  119.61  3.000
 9L8  C12  C13  C14  120.36  3.000
 9L8  H19  C12  C13  120.40  3.000
 9L8  H19  C12  C8   118.99  3.000
 9L8  C13  C12  C8   120.61  3.000
 9L8  H20  C10  C11  119.99  3.000
 9L8  H20  C10  C9   119.05  3.000
 9L8  C11  C10  C9   120.96  3.000
 9L8  H21  C11  C10  119.94  3.000
 9L8  H21  C11  C6   119.40  3.000
 9L8  C10  C11  C6   120.66  3.000
 9L8  N2   N3   C4   102.75  3.000
 9L8  H3   N2   N3   120.52  3.000
 9L8  H3   N2   C1   128.67  3.000
 9L8  N3   N2   C1   110.81  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
 9L8  CONST_01  C4   N3   N2   C1     0.00  0.0  0
 9L8  CONST_02  N3   C4   N5   C1     0.00  0.0  0
 9L8  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 9L8  CONST_04  N3   N2   C1   N5     0.00  0.0  0
 9L8  CONST_05  N2   N3   C4   N5     0.00  0.0  0
 9L8  CONST_06  C7   C6   C4   N5   180.00  0.0  0
 9L8  CONST_07  C11  C6   C4   N5     0.00  0.0  0
 9L8  CONST_08  N2   C1   N5   C4     0.00  0.0  0
 9L8  CONST_09  C8   C7   C6   C4   180.00  0.0  0
 9L8  CONST_10  C10  C11  C6   C4   180.00  0.0  0
 9L8  CONST_11  N2   N3   C4   C6   180.00  0.0  0
 9L8  CONST_12  C12  C8   C7   C6   180.00  0.0  0
 9L8  CONST_13  C9   C8   C7   C6     0.00  0.0  0
 9L8  CONST_14  C9   C10  C11  C6     0.00  0.0  0
 9L8  CONST_15  N3   C4   C6   C7     0.00  0.0  0
 9L8  CONST_16  C10  C11  C6   C7     0.00  0.0  0
 9L8  CONST_17  C13  C12  C8   C7   180.00  0.0  0
 9L8  CONST_18  C10  C9   C8   C7     0.00  0.0  0
 9L8  CONST_19  C15  C9   C8   C7   180.00  0.0  0
 9L8  CONST_20  C11  C6   C7   C8     0.00  0.0  0
 9L8  CONST_21  C14  C13  C12  C8     0.00  0.0  0
 9L8  CONST_22  C11  C10  C9   C8     0.00  0.0  0
 9L8  CONST_23  C14  C15  C9   C8     0.00  0.0  0
 9L8  CONST_24  C13  C12  C8   C9     0.00  0.0  0
 9L8  CONST_25  C13  C14  C15  C9     0.00  0.0  0
 9L8  CONST_26  C12  C8   C9   C15    0.00  0.0  0
 9L8  CONST_27  C11  C10  C9   C15  180.00  0.0  0
 9L8  CONST_28  C12  C13  C14  C15    0.00  0.0  0
 9L8  CONST_29  C10  C9   C15  C14  180.00  0.0  0
 9L8  CONST_30  C10  C9   C8   C12  180.00  0.0  0
 9L8  CONST_31  N3   C4   C6   C11  180.00  0.0  0
 9L8  CONST_32  N3   N2   C1   C1'  180.00  0.0  0
 9L8  CONST_33  C4   N5   C1   C1'  180.00  0.0  0
 9L8  CONST_34  H3   N2   C1   C1'    0.00  0.0  0
 9L8  CONST_35  H15  C7   C6   C4     0.00  0.0  0
 9L8  CONST_36  H21  C11  C6   C4     0.00  0.0  0
 9L8  CONST_37  H20  C10  C11  C6   180.00  0.0  0
 9L8  CONST_38  H19  C12  C8   C7     0.00  0.0  0
 9L8  CONST_39  H18  C13  C12  C8   180.00  0.0  0
 9L8  CONST_40  H16  C15  C9   C8   180.00  0.0  0
 9L8  CONST_41  H17  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
 9L8  chir_01  C2'  C3'  N2'  C1'  negativ
 9L8  chir_02  C3'  O3'  C2'  C4'  positiv
 9L8  chir_03  C4'  O4'  C5'  C3'  positiv
 9L8  chir_04  C5'  O5'  C6'  C4'  positiv
 9L8  chir_05  C1'  O5'  C1   C2'  negativ

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
 9L8  plan-1  C1'  0.020
 9L8  plan-1  C1   0.020
 9L8  plan-1  N5   0.020
 9L8  plan-1  C4   0.020
 9L8  plan-1  C6   0.020
 9L8  plan-1  N3   0.020
 9L8  plan-1  N2   0.020
 9L8  plan-1  H3   0.020
 9L8  plan-2  C4   0.020
 9L8  plan-2  C6   0.020
 9L8  plan-2  C7   0.020
 9L8  plan-2  C8   0.020
 9L8  plan-2  C9   0.020
 9L8  plan-2  C15  0.020
 9L8  plan-2  C14  0.020
 9L8  plan-2  C13  0.020
 9L8  plan-2  C12  0.020
 9L8  plan-2  C10  0.020
 9L8  plan-2  C11  0.020
 9L8  plan-2  H15  0.020
 9L8  plan-2  H16  0.020
 9L8  plan-2  H17  0.020
 9L8  plan-2  H18  0.020
 9L8  plan-2  H19  0.020
 9L8  plan-2  H20  0.020
 9L8  plan-2  H21  0.020

