# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 19:44:14 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(5-naphthalen-1-yl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4,5-triol
#   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(nn2)c3cccc4ccccc34
#
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
 CNK  CNK  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(5-naphthalen-1-yl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4,5-triol  ligand  45  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CNK
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
 CNK  O5'  O  O2    0  -0.492  -2.6694  -0.8943  -0.4530
 CNK  C5'  C  CH1   0  -0.018  -4.0039  -1.1786  -0.0793
 CNK  C4'  C  CH1   0   0.038  -4.8622   0.0806  -0.2207
 CNK  C3'  C  CH1   0  -0.021  -4.2538   1.2122   0.6010
 CNK  C2'  C  CH1   0   0.014  -2.7903   1.4134   0.2240
 CNK  C1'  C  CH1   0  -0.051  -2.0596   0.0765   0.3567
 CNK  C1   C  CR5   0   0.426  -0.6391   0.2071  -0.0754
 CNK  O2'  O  OH1   0  -0.669  -2.1439   2.3308   1.0706
 CNK  O3'  O  OH1   0  -0.674  -5.0209   2.3716   0.3644
 CNK  O4'  O  OH1   0  -0.672  -6.1630  -0.2268   0.2132
 CNK  C6'  C  CH2   0  -0.157  -4.4990  -2.3022  -0.9645
 CNK  O6'  O  OH1   0  -0.670  -3.7240  -3.4506  -0.7165
 CNK  N5   N  NR15  0  -0.649   0.4227   0.1339   0.7521
 CNK  C4   C  CR5   0   0.369   1.5153   0.3223  -0.0285
 CNK  N3   N  N     0  -0.332   1.1227   0.4990  -1.2646
 CNK  N2   N  N     0  -0.320  -0.2267   0.4269  -1.2916
 CNK  C6   C  CR6   0   0.021   2.8802   0.3742   0.4972
 CNK  C11  C  CR16  0  -0.322   3.0787   0.9606   1.7264
 CNK  C10  C  CR16  0  -0.247   4.3622   1.0674   2.2885
 CNK  C9   C  CR16  0  -0.312   5.4460   0.5886   1.6092
 CNK  C8   C  CR66  0   0.106   5.2892  -0.0286   0.3471
 CNK  C7   C  CR66  0   0.119   3.9941  -0.1477  -0.2288
 CNK  C15  C  CR16  0  -0.308   6.4116  -0.5359  -0.3488
 CNK  C14  C  CR16  0  -0.257   6.2662  -1.1517  -1.5601
 CNK  C13  C  CR16  0  -0.247   4.9826  -1.2917  -2.1228
 CNK  C12  C  CR16  0  -0.334   3.8775  -0.8037  -1.4785
 CNK  H1   H  HCH1  0   0.224  -4.0341  -1.5076   0.9727
 CNK  H2   H  HCH1  0   0.213  -4.8590   0.3824  -1.2806
 CNK  H3   H  HCH1  0   0.221  -4.3008   0.9251   1.6631
 CNK  H4   H  HCH1  0   0.232  -2.7318   1.7290  -0.8266
 CNK  H5   H  HCH1  0   0.253  -2.0813  -0.2290   1.4154
 CNK  H6   H  HOH1  0   0.462  -2.2876   3.2201   0.7351
 CNK  H7   H  HOH1  0   0.460  -4.9363   2.9627   1.1181
 CNK  H8   H  HOH1  0   0.454  -6.6929   0.5759   0.1605
 CNK  H9   H  HCH2  0   0.214  -5.5579  -2.4721  -0.7440
 CNK  H10  H  HCH2  0   0.199  -4.4337  -1.9832  -2.0141
 CNK  H11  H  HOH1  0   0.457  -4.0628  -4.1614  -1.2675
 CNK  H12  H  HNR5  0   0.437   0.4072  -0.0668   1.7413
 CNK  H13  H  HCR6  0   0.266   2.2393   1.3757   2.2699
 CNK  H14  H  HCR6  0   0.266   4.4825   1.5432   3.2522
 CNK  H15  H  HCR6  0   0.262   6.4407   0.6774   2.0286
 CNK  H16  H  HCR6  0   0.259   7.3920  -0.4282   0.0991
 CNK  H17  H  HCR6  0   0.261   7.1308  -1.5356  -2.0853
 CNK  H18  H  HCR6  0   0.261   4.8671  -1.7936  -3.0746
 CNK  H19  H  HCR6  0   0.259   2.9056  -0.9158  -1.9354

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
 CNK  O3'  C3'  single    1.410  0.020  1.410
 CNK  O4'  C4'  single    1.405  0.020  1.405
 CNK  C3'  C4'  single    1.525  0.020  1.525
 CNK  C3'  C2'  single    1.525  0.020  1.525
 CNK  C4'  C5'  single    1.530  0.020  1.530
 CNK  O2'  C2'  single    1.406  0.020  1.406
 CNK  C2'  C1'  single    1.529  0.020  1.529
 CNK  O6'  C6'  single    1.407  0.020  1.407
 CNK  C5'  C6'  single    1.514  0.020  1.514
 CNK  C5'  O5'  single    1.415  0.020  1.415
 CNK  C1'  O5'  single    1.404  0.020  1.404
 CNK  C1'  C1   single    1.490  0.020  1.490
 CNK  N2   C1   aromatic  1.303  0.020  1.303
 CNK  N2   N3   aromatic  1.352  0.020  1.352
 CNK  C1   N5   aromatic  1.348  0.020  1.348
 CNK  N3   C4   aromatic  1.309  0.020  1.309
 CNK  N5   C4   aromatic  1.356  0.020  1.356
 CNK  C4   C6   single    1.464  0.020  1.464
 CNK  C12  C13  aromatic  1.369  0.020  1.369
 CNK  C12  C7   aromatic  1.416  0.020  1.416
 CNK  C6   C7   aromatic  1.428  0.020  1.428
 CNK  C6   C11  aromatic  1.376  0.020  1.376
 CNK  C13  C14  aromatic  1.409  0.020  1.409
 CNK  C7   C8   aromatic  1.422  0.020  1.422
 CNK  C11  C10  aromatic  1.405  0.020  1.405
 CNK  C14  C15  aromatic  1.367  0.020  1.367
 CNK  C8   C15  aromatic  1.415  0.020  1.415
 CNK  C8   C9   aromatic  1.414  0.020  1.414
 CNK  C10  C9   aromatic  1.366  0.020  1.366
 CNK  C5'  H1   single    0.970  0.020  1.090
 CNK  C4'  H2   single    0.970  0.020  1.090
 CNK  C3'  H3   single    0.970  0.020  1.090
 CNK  C2'  H4   single    0.970  0.020  1.090
 CNK  C1'  H5   single    0.970  0.020  1.090
 CNK  O2'  H6   single    0.850  0.020  0.980
 CNK  O3'  H7   single    0.850  0.020  0.980
 CNK  O4'  H8   single    0.850  0.020  0.980
 CNK  C6'  H9   single    0.970  0.020  1.090
 CNK  C6'  H10  single    0.970  0.020  1.090
 CNK  O6'  H11  single    0.850  0.020  0.980
 CNK  N5   H12  single    0.860  0.020  1.020
 CNK  C11  H13  single    0.930  0.020  1.080
 CNK  C10  H14  single    0.930  0.020  1.080
 CNK  C9   H15  single    0.930  0.020  1.080
 CNK  C15  H16  single    0.930  0.020  1.080
 CNK  C14  H17  single    0.930  0.020  1.080
 CNK  C13  H18  single    0.930  0.020  1.080
 CNK  C12  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
 CNK  C1'  O5'  C5'  113.35  3.000
 CNK  H1   C5'  C6'  109.11  3.000
 CNK  H1   C5'  C4'  108.56  3.000
 CNK  C6'  C5'  C4'  111.92  3.000
 CNK  H1   C5'  O5'  109.75  3.000
 CNK  C6'  C5'  O5'  107.65  3.000
 CNK  C4'  C5'  O5'  109.84  3.000
 CNK  H2   C4'  O4'  111.07  3.000
 CNK  H2   C4'  C3'  108.29  3.000
 CNK  O4'  C4'  C3'  111.42  3.000
 CNK  H2   C4'  C5'  108.21  3.000
 CNK  C3'  C4'  C5'  109.69  3.000
 CNK  O4'  C4'  C5'  108.10  3.000
 CNK  H3   C3'  O3'  110.67  3.000
 CNK  H3   C3'  C2'  108.29  3.000
 CNK  O3'  C3'  C2'  111.85  3.000
 CNK  H3   C3'  C4'  108.01  3.000
 CNK  C2'  C3'  C4'  110.34  3.000
 CNK  O3'  C3'  C4'  107.62  3.000
 CNK  H4   C2'  O2'  111.34  3.000
 CNK  H4   C2'  C1'  107.98  3.000
 CNK  O2'  C2'  C1'  107.37  3.000
 CNK  H4   C2'  C3'  109.00  3.000
 CNK  C1'  C2'  C3'  108.77  3.000
 CNK  O2'  C2'  C3'  112.25  3.000
 CNK  H5   C1'  C1   108.76  3.000
 CNK  H5   C1'  C2'  108.43  3.000
 CNK  C1   C1'  C2'  110.71  3.000
 CNK  H5   C1'  O5'  110.73  3.000
 CNK  C1   C1'  O5'  107.90  3.000
 CNK  C2'  C1'  O5'  110.30  3.000
 CNK  N2   C1   N5   109.44  3.000
 CNK  N5   C1   C1'  124.61  3.000
 CNK  N2   C1   C1'  125.95  3.000
 CNK  H6   O2'  C2'  108.95  3.000
 CNK  H7   O3'  C3'  109.03  3.000
 CNK  H8   O4'  C4'  108.06  3.000
 CNK  H10  C6'  H9   107.15  3.000
 CNK  H10  C6'  O6'  111.87  3.000
 CNK  H9   C6'  O6'  111.75  3.000
 CNK  H10  C6'  C5'  108.88  3.000
 CNK  H9   C6'  C5'  108.28  3.000
 CNK  O6'  C6'  C5'  108.81  3.000
 CNK  H11  O6'  C6'  107.96  3.000
 CNK  H12  N5   C4   127.16  3.000
 CNK  H12  N5   C1   126.88  3.000
 CNK  C4   N5   C1   105.89  3.000
 CNK  C6   C4   N3   127.89  3.000
 CNK  C6   C4   N5   123.34  3.000
 CNK  N3   C4   N5   108.71  3.000
 CNK  N2   N3   C4   108.13  3.000
 CNK  N3   N2   C1   107.84  3.000
 CNK  C7   C6   C11  119.81  3.000
 CNK  C11  C6   C4   118.07  3.000
 CNK  C7   C6   C4   122.12  3.000
 CNK  H13  C11  C10  118.56  3.000
 CNK  H13  C11  C6   119.99  3.000
 CNK  C10  C11  C6   121.43  3.000
 CNK  H14  C10  C9   120.61  3.000
 CNK  H14  C10  C11  119.44  3.000
 CNK  C9   C10  C11  119.95  3.000
 CNK  H15  C9   C8   118.90  3.000
 CNK  H15  C9   C10  120.49  3.000
 CNK  C8   C9   C10  120.60  3.000
 CNK  C15  C8   C7   119.55  3.000
 CNK  C15  C8   C9   120.51  3.000
 CNK  C7   C8   C9   119.94  3.000
 CNK  C12  C7   C8   118.10  3.000
 CNK  C8   C7   C6   118.27  3.000
 CNK  C12  C7   C6   123.61  3.000
 CNK  H16  C15  C14  120.50  3.000
 CNK  H16  C15  C8   118.63  3.000
 CNK  C14  C15  C8   120.87  3.000
 CNK  H17  C14  C13  119.94  3.000
 CNK  H17  C14  C15  120.34  3.000
 CNK  C13  C14  C15  119.73  3.000
 CNK  H18  C13  C12  119.54  3.000
 CNK  H18  C13  C14  119.65  3.000
 CNK  C12  C13  C14  120.81  3.000
 CNK  H19  C12  C13  119.36  3.000
 CNK  H19  C12  C7   119.71  3.000
 CNK  C13  C12  C7   120.92  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
 CNK  CONST_01  C4   N3   N2   C1     0.00  0.0  0
 CNK  CONST_02  N3   C4   N5   C1     0.00  0.0  0
 CNK  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 CNK  CONST_04  N3   N2   C1   N5     0.00  0.0  0
 CNK  CONST_05  N2   N3   C4   N5     0.00  0.0  0
 CNK  CONST_08  N2   C1   N5   C4     0.00  0.0  0
 CNK  CONST_09  C12  C7   C6   C4     0.00  0.0  0
 CNK  CONST_10  C8   C7   C6   C4   180.00  0.0  0
 CNK  CONST_11  C10  C11  C6   C4   180.00  0.0  0
 CNK  CONST_14  C6   C4   N3   N2   180.00  0.0  0
 CNK  CONST_15  C13  C12  C7   C6   180.00  0.0  0
 CNK  CONST_16  C15  C8   C7   C6   180.00  0.0  0
 CNK  CONST_17  C9   C8   C7   C6     0.00  0.0  0
 CNK  CONST_18  C9   C10  C11  C6     0.00  0.0  0
 CNK  CONST_19  C12  C7   C6   C11  180.00  0.0  0
 CNK  CONST_20  C8   C7   C6   C11    0.00  0.0  0
 CNK  CONST_21  C8   C9   C10  C11    0.00  0.0  0
 CNK  CONST_22  C7   C6   C11  C10    0.00  0.0  0
 CNK  CONST_23  C7   C8   C9   C10    0.00  0.0  0
 CNK  CONST_24  C15  C8   C9   C10  180.00  0.0  0
 CNK  CONST_25  C12  C7   C8   C9   180.00  0.0  0
 CNK  CONST_26  C14  C15  C8   C9   180.00  0.0  0
 CNK  CONST_27  C13  C12  C7   C8     0.00  0.0  0
 CNK  CONST_28  C13  C14  C15  C8     0.00  0.0  0
 CNK  CONST_29  C14  C13  C12  C7     0.00  0.0  0
 CNK  CONST_30  C14  C15  C8   C7     0.00  0.0  0
 CNK  CONST_31  C12  C13  C14  C15    0.00  0.0  0
 CNK  CONST_32  C12  C7   C8   C15    0.00  0.0  0
 CNK  CONST_33  N3   N2   C1   C1'  180.00  0.0  0
 CNK  CONST_34  C4   N5   C1   C1'  180.00  0.0  0
 CNK  CONST_35  H12  N5   C1   C1'    0.00  0.0  0
 CNK  CONST_36  H13  C11  C6   C4     0.00  0.0  0
 CNK  CONST_37  H19  C12  C7   C6     0.00  0.0  0
 CNK  CONST_38  H14  C10  C11  C6   180.00  0.0  0
 CNK  CONST_39  H15  C9   C10  C11  180.00  0.0  0
 CNK  CONST_40  H16  C15  C8   C9     0.00  0.0  0
 CNK  CONST_41  H17  C14  C15  C8   180.00  0.0  0
 CNK  CONST_42  H18  C13  C12  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
 CNK  chir_01  C5'  C4'  C6'  O5'  negativ
 CNK  chir_02  C4'  O4'  C5'  C3'  positiv
 CNK  chir_03  C3'  O3'  C4'  C2'  negativ
 CNK  chir_04  C2'  O2'  C3'  C1'  positiv
 CNK  chir_05  C1'  O5'  C2'  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
 CNK  plan-1  C1'  0.020
 CNK  plan-1  C1   0.020
 CNK  plan-1  N5   0.020
 CNK  plan-1  C4   0.020
 CNK  plan-1  N3   0.020
 CNK  plan-1  N2   0.020
 CNK  plan-1  C6   0.020
 CNK  plan-1  H12  0.020
 CNK  plan-2  C4   0.020
 CNK  plan-2  C6   0.020
 CNK  plan-2  C11  0.020
 CNK  plan-2  C10  0.020
 CNK  plan-2  C9   0.020
 CNK  plan-2  C8   0.020
 CNK  plan-2  C7   0.020
 CNK  plan-2  C15  0.020
 CNK  plan-2  C14  0.020
 CNK  plan-2  C13  0.020
 CNK  plan-2  C12  0.020
 CNK  plan-2  H13  0.020
 CNK  plan-2  H14  0.020
 CNK  plan-2  H15  0.020
 CNK  plan-2  H16  0.020
 CNK  plan-2  H17  0.020
 CNK  plan-2  H18  0.020
 CNK  plan-2  H19  0.020

