# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 21:36:24 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{R})-2-methyl-6-[2-(1,2,3-triazol-1-yl)ethoxy]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](OCCn2ccnn2)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 KBA  KBA  (2~{S},3~{S},4~{R},5~{S},6~{R})-2-methyl-6-[2-(1,2,3-triazol-1-yl)ethoxy]oxane-3,4,5-triol  L-saccharide  35  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KBA
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
 KBA  C04  C  CH2   0  -0.135  -1.2826  -0.2204   0.2958
 KBA  C05  C  CH2   0  -0.343  -2.2544  -0.9306  -0.6350
 KBA  C06  C  CR15  0  -0.055  -4.2566   0.5223  -1.0764
 KBA  C07  C  CR15  0  -0.186  -5.4677   0.5915  -0.4414
 KBA  C1   C  CH1   0   0.251   0.9956  -0.4062   0.8985
 KBA  C2   C  CH1   0  -0.025   2.2722  -1.1380   0.4690
 KBA  C3   C  CH1   0   0.023   2.8377  -0.5032  -0.7975
 KBA  C4   C  CH1   0  -0.004   3.0549   0.9870  -0.5760
 KBA  C5   C  CH1   0   0.014   1.7350   1.6155  -0.1227
 KBA  C6   C  CH3   0  -0.708   1.8600   3.0878   0.2097
 KBA  N01  N  NR5   0  -0.248  -3.6068  -0.4595  -0.4285
 KBA  N02  N  N     0  -0.295  -5.4793  -0.3339   0.5411
 KBA  N03  N  N     0  -0.102  -4.3527  -0.9588   0.5429
 KBA  O03  O  O2    0  -0.496   0.0023  -0.6856  -0.0388
 KBA  O2   O  OH1   0  -0.670   2.0382  -2.4989   0.2065
 KBA  O3   O  OH1   0  -0.672   4.0542  -1.0915  -1.1811
 KBA  O4   O  OH1   0  -0.672   4.0859   1.1485   0.3683
 KBA  O5   O  O2    0  -0.501   1.2306   0.9628   1.0384
 KBA  H1   H  HCH2  0   0.225  -1.3715   0.8641   0.1650
 KBA  H2   H  HCH2  0   0.223  -1.5289  -0.4511   1.3398
 KBA  H3   H  HCH2  0   0.281  -1.9914  -0.7455  -1.6757
 KBA  H4   H  HCH2  0   0.285  -2.2391  -2.0062  -0.4653
 KBA  H5   H  HCR5  0   0.312  -3.8299   1.0643  -1.9027
 KBA  H6   H  HCR5  0   0.277  -6.3072   1.2359  -0.6412
 KBA  H7   H  HCH1  0   0.234   0.6797  -0.7460   1.8954
 KBA  H8   H  HCH1  0   0.234   2.9997  -1.0123   1.2806
 KBA  H9   H  HCH1  0   0.219   2.0905  -0.6023  -1.5989
 KBA  H10  H  HCH1  0   0.233   3.3232   1.4478  -1.5377
 KBA  H11  H  HCH1  0   0.222   1.0264   1.5085  -0.9545
 KBA  H12  H  HCH3  0   0.237   2.2374   3.6381  -0.6528
 KBA  H13  H  HCH3  0   0.250   0.8889   3.5092   0.4688
 KBA  H14  H  HCH3  0   0.229   2.5342   3.2627   1.0493
 KBA  H15  H  HOH1  0   0.458   1.9765  -2.9715   1.0418
 KBA  H16  H  HOH1  0   0.448   3.8926  -2.0286  -1.3309
 KBA  H17  H  HOH1  0   0.457   4.3575   2.0709   0.3729

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
 KBA  O2   C2   single    1.406  0.020  1.406
 KBA  O3   C3   single    1.405  0.020  1.405
 KBA  C2   C3   single    1.525  0.020  1.525
 KBA  C2   C1   single    1.533  0.020  1.533
 KBA  O4   C4   single    1.407  0.020  1.407
 KBA  C3   C4   single    1.522  0.020  1.522
 KBA  C1   O5   single    1.396  0.020  1.396
 KBA  C1   O03  single    1.394  0.020  1.394
 KBA  C4   C5   single    1.531  0.020  1.531
 KBA  O5   C5   single    1.424  0.020  1.424
 KBA  O03  C04  single    1.407  0.020  1.407
 KBA  C5   C6   single    1.514  0.020  1.514
 KBA  C04  C05  single    1.522  0.020  1.522
 KBA  C05  N01  single    1.447  0.020  1.447
 KBA  C06  N01  aromatic  1.344  0.020  1.344
 KBA  C06  C07  aromatic  1.369  0.020  1.369
 KBA  N01  N03  aromatic  1.323  0.020  1.323
 KBA  C07  N02  aromatic  1.350  0.020  1.350
 KBA  N03  N02  aromatic  1.288  0.020  1.288
 KBA  C04  H1   single    0.970  0.020  1.090
 KBA  C04  H2   single    0.970  0.020  1.090
 KBA  C05  H3   single    0.970  0.020  1.090
 KBA  C05  H4   single    0.970  0.020  1.090
 KBA  C06  H5   single    0.930  0.020  1.080
 KBA  C07  H6   single    0.930  0.020  1.080
 KBA  C1   H7   single    0.970  0.020  1.090
 KBA  C2   H8   single    0.970  0.020  1.090
 KBA  C3   H9   single    0.970  0.020  1.090
 KBA  C4   H10  single    0.970  0.020  1.090
 KBA  C5   H11  single    0.970  0.020  1.090
 KBA  C6   H12  single    0.970  0.020  1.090
 KBA  C6   H13  single    0.970  0.020  1.090
 KBA  C6   H14  single    0.970  0.020  1.090
 KBA  O2   H15  single    0.850  0.020  0.980
 KBA  O3   H16  single    0.850  0.020  0.980
 KBA  O4   H17  single    0.850  0.020  0.980

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
 KBA  H2   C04  H1   107.66  3.000
 KBA  H2   C04  O03  111.21  3.000
 KBA  H1   C04  O03  111.90  3.000
 KBA  H2   C04  C05  109.91  3.000
 KBA  H1   C04  C05  109.70  3.000
 KBA  O03  C04  C05  106.47  3.000
 KBA  H4   C05  H3   108.26  3.000
 KBA  H4   C05  N01  108.21  3.000
 KBA  H3   C05  N01  107.86  3.000
 KBA  H4   C05  C04  110.90  3.000
 KBA  H3   C05  C04  110.54  3.000
 KBA  N01  C05  C04  110.96  3.000
 KBA  H5   C06  N01  123.11  3.000
 KBA  H5   C06  C07  132.94  3.000
 KBA  N01  C06  C07  103.95  3.000
 KBA  H6   C07  N02  122.59  3.000
 KBA  H6   C07  C06  129.32  3.000
 KBA  N02  C07  C06  108.09  3.000
 KBA  H7   C1   O5   105.10  3.000
 KBA  H7   C1   O03  110.05  3.000
 KBA  O5   C1   O03  112.57  3.000
 KBA  H7   C1   C2   110.23  3.000
 KBA  O03  C1   C2   108.02  3.000
 KBA  O5   C1   C2   110.86  3.000
 KBA  H8   C2   O2   111.07  3.000
 KBA  H8   C2   C3   108.70  3.000
 KBA  O2   C2   C3   108.03  3.000
 KBA  H8   C2   C1   106.87  3.000
 KBA  C3   C2   C1   110.04  3.000
 KBA  O2   C2   C1   112.08  3.000
 KBA  H9   C3   O3   110.58  3.000
 KBA  H9   C3   C4   106.93  3.000
 KBA  O3   C3   C4   109.04  3.000
 KBA  H9   C3   C2   108.39  3.000
 KBA  C4   C3   C2   109.85  3.000
 KBA  O3   C3   C2   111.93  3.000
 KBA  H10  C4   O4   111.10  3.000
 KBA  H10  C4   C5   107.30  3.000
 KBA  O4   C4   C5   112.69  3.000
 KBA  H10  C4   C3   108.53  3.000
 KBA  C5   C4   C3   108.79  3.000
 KBA  O4   C4   C3   108.34  3.000
 KBA  H11  C5   O5   110.15  3.000
 KBA  H11  C5   C6   108.32  3.000
 KBA  O5   C5   C6   107.21  3.000
 KBA  H11  C5   C4   106.98  3.000
 KBA  C6   C5   C4   113.14  3.000
 KBA  O5   C5   C4   111.02  3.000
 KBA  H14  C6   H13  107.80  3.000
 KBA  H14  C6   H12  108.30  3.000
 KBA  H13  C6   H12  107.54  3.000
 KBA  H14  C6   C5   112.07  3.000
 KBA  H13  C6   C5   110.77  3.000
 KBA  H12  C6   C5   110.22  3.000
 KBA  N03  N01  C06  110.93  3.000
 KBA  N03  N01  C05  120.60  3.000
 KBA  C06  N01  C05  128.39  3.000
 KBA  N03  N02  C07  109.03  3.000
 KBA  N02  N03  N01  108.00  3.000
 KBA  C1   O03  C04  115.13  3.000
 KBA  H15  O2   C2   108.92  3.000
 KBA  H16  O3   C3   107.74  3.000
 KBA  H17  O4   C4   108.68  3.000
 KBA  C5   O5   C1   115.30  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
 KBA  CONST_01  N02  N03  N01  C06     0.00   0.0  0
 KBA  CONST_02  N03  N02  C07  C06     0.00   0.0  0
 KBA  CONST_03  N03  N01  C06  C07     0.00   0.0  0
 KBA  CONST_04  N01  N03  N02  C07     0.00   0.0  0
 KBA  CONST_05  N02  C07  C06  N01     0.00   0.0  0
 KBA  CONST_06  C07  C06  N01  C05   180.00   0.0  0
 KBA  CONST_07  N02  N03  N01  C05   180.00   0.0  0
 KBA  CONST_08  H6   C07  C06  N01   180.00   0.0  0
 KBA  CONST_09  H5   C06  C07  N02   180.00   0.0  0
 KBA  Var_01    C06  N01  C05  C04    93.18  30.0  2
 KBA  Var_02    O03  C04  C05  N01  -176.48  30.0  2
 KBA  Var_03    H1   C04  O03  C1     74.91  30.0  3

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
 KBA  chir_01  C1  C2  O5  O03  negativ
 KBA  chir_02  C2  O2  C1  C3   positiv
 KBA  chir_03  C3  O3  C2  C4   negativ
 KBA  chir_04  C4  O4  C3  C5   negativ
 KBA  chir_05  C5  O5  C4  C6   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
 KBA  plan-1  C05  0.020
 KBA  plan-1  C06  0.020
 KBA  plan-1  C07  0.020
 KBA  plan-1  N01  0.020
 KBA  plan-1  N02  0.020
 KBA  plan-1  N03  0.020
 KBA  plan-1  H5   0.020
 KBA  plan-1  H6   0.020

