# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 02:02:50 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methylphenyl)-4~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2[nH]c(nn2)[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O
#
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
 KS2  KS2  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methylphenyl)-4~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol  ligand  42  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KS2
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
 KS2  O3'  O  OH1   0  -0.674  -4.3339   2.4994   0.2425
 KS2  C3'  C  CH1   0  -0.024  -3.5852   1.3444   0.5512
 KS2  C4'  C  CH1   0   0.038  -4.3363   0.1407  -0.0074
 KS2  O4'  O  OH1   0  -0.673  -5.5821  -0.0231   0.6215
 KS2  C2'  C  CH1   0   0.017  -2.1790   1.4051  -0.0347
 KS2  O2'  O  OH1   0  -0.669  -1.3940   2.4061   0.5628
 KS2  C1'  C  CH1   0  -0.057  -1.4873   0.0673   0.2264
 KS2  O5'  O  O2    0  -0.492  -2.2271  -0.9811  -0.3439
 KS2  C5'  C  CH1   0  -0.017  -3.5152  -1.1294   0.2236
 KS2  C6'  C  CH2   0  -0.158  -4.1576  -2.3435  -0.4118
 KS2  O6'  O  OH1   0  -0.670  -3.3932  -3.4813  -0.0916
 KS2  C1   C  CR5   0   0.429  -0.1197   0.0461  -0.3647
 KS2  N5   N  NR15  0  -0.675   1.0154  -0.0172   0.3620
 KS2  C4   C  CR5   0   0.437   2.0307   0.0040  -0.5347
 KS2  N3   N  N     0  -0.335   1.5254   0.0733  -1.7401
 KS2  N2   N  N     0  -0.319   0.1780   0.1024  -1.6314
 KS2  C6   C  CR6   0   0.010   3.4486  -0.0426  -0.1984
 KS2  C11  C  CR16  0  -0.290   3.8879  -0.0027   1.1231
 KS2  C10  C  CR16  0  -0.281   5.2416  -0.0464   1.4170
 KS2  C9   C  CR6   0   0.093   6.1962  -0.1322   0.4071
 KS2  C12  C  CH3   0  -0.721   7.6588  -0.2153   0.7268
 KS2  C8   C  CR16  0  -0.281   5.7485  -0.1656  -0.9137
 KS2  C7   C  CR16  0  -0.270   4.3995  -0.1223  -1.2168
 KS2  H1   H  HOH1  0   0.461  -4.1533   3.1762   0.9011
 KS2  H2   H  HCH1  0   0.223  -3.4978   1.2174   1.6411
 KS2  H3   H  HCH1  0   0.212  -4.4566   0.2806  -1.0943
 KS2  H4   H  HOH1  0   0.453  -6.0717   0.8013   0.5287
 KS2  H5   H  HCH1  0   0.230  -2.2475   1.5469  -1.1221
 KS2  H6   H  HOH1  0   0.462  -1.6017   3.2505   0.1524
 KS2  H7   H  HCH1  0   0.253  -1.3942  -0.0687   1.3162
 KS2  H8   H  HCH1  0   0.224  -3.4266  -1.2950   1.3098
 KS2  H9   H  HCH2  0   0.215  -5.1834  -2.4267  -0.0387
 KS2  H10  H  HCH2  0   0.197  -4.2203  -2.1865  -1.4978
 KS2  H11  H  HOH1  0   0.457  -3.8625  -4.2544  -0.4168
 KS2  H12  H  HNR5  0   0.437   1.0778  -0.0821   1.3668
 KS2  H13  H  HCR6  0   0.246   3.1847   0.0683   1.9435
 KS2  H14  H  HCR6  0   0.256   5.5563  -0.0098   2.4529
 KS2  H15  H  HCH3  0   0.253   7.9840  -1.2567   0.7788
 KS2  H16  H  HCH3  0   0.247   8.2638   0.2729  -0.0366
 KS2  H17  H  HCH3  0   0.246   7.8872   0.2437   1.6878
 KS2  H18  H  HCR6  0   0.255   6.4691  -0.2266  -1.7204
 KS2  H19  H  HCR6  0   0.255   4.0798  -0.1505  -2.2502

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
 KS2  O3'  C3'  single    1.411  0.020  1.411
 KS2  O4'  C4'  single    1.405  0.020  1.405
 KS2  C3'  C4'  single    1.525  0.020  1.525
 KS2  C3'  C2'  single    1.525  0.020  1.525
 KS2  C4'  C5'  single    1.530  0.020  1.530
 KS2  O2'  C2'  single    1.405  0.020  1.405
 KS2  C2'  C1'  single    1.529  0.020  1.529
 KS2  O6'  C6'  single    1.408  0.020  1.408
 KS2  C5'  C6'  single    1.513  0.020  1.513
 KS2  C5'  O5'  single    1.415  0.020  1.415
 KS2  C1'  O5'  single    1.404  0.020  1.404
 KS2  C1'  C1   single    1.490  0.020  1.490
 KS2  N2   C1   aromatic  1.302  0.020  1.302
 KS2  N2   N3   aromatic  1.352  0.020  1.352
 KS2  C1   N5   aromatic  1.349  0.020  1.349
 KS2  N3   C4   aromatic  1.309  0.020  1.309
 KS2  N5   C4   aromatic  1.355  0.020  1.355
 KS2  C4   C6   single    1.458  0.020  1.458
 KS2  C6   C7   aromatic  1.395  0.020  1.395
 KS2  C6   C11  aromatic  1.393  0.020  1.393
 KS2  C7   C8   aromatic  1.383  0.020  1.383
 KS2  C11  C10  aromatic  1.386  0.020  1.386
 KS2  C8   C9   aromatic  1.395  0.020  1.395
 KS2  C10  C9   aromatic  1.392  0.020  1.392
 KS2  C9   C12  single    1.499  0.020  1.499
 KS2  O3'  H1   single    0.850  0.020  0.980
 KS2  C3'  H2   single    0.970  0.020  1.090
 KS2  C4'  H3   single    0.970  0.020  1.090
 KS2  O4'  H4   single    0.850  0.020  0.980
 KS2  C2'  H5   single    0.970  0.020  1.090
 KS2  O2'  H6   single    0.850  0.020  0.980
 KS2  C1'  H7   single    0.970  0.020  1.090
 KS2  C5'  H8   single    0.970  0.020  1.090
 KS2  C6'  H9   single    0.970  0.020  1.090
 KS2  C6'  H10  single    0.970  0.020  1.090
 KS2  O6'  H11  single    0.850  0.020  0.980
 KS2  N5   H12  single    0.860  0.020  1.020
 KS2  C11  H13  single    0.930  0.020  1.080
 KS2  C10  H14  single    0.930  0.020  1.080
 KS2  C12  H15  single    0.970  0.020  1.090
 KS2  C12  H16  single    0.970  0.020  1.090
 KS2  C12  H17  single    0.970  0.020  1.090
 KS2  C8   H18  single    0.930  0.020  1.080
 KS2  C7   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
 KS2  H1   O3'  C3'  109.07  3.000
 KS2  H2   C3'  C2'  108.17  3.000
 KS2  H2   C3'  C4'  108.10  3.000
 KS2  C2'  C3'  C4'  110.18  3.000
 KS2  H2   C3'  O3'  110.69  3.000
 KS2  C2'  C3'  O3'  111.89  3.000
 KS2  C4'  C3'  O3'  107.74  3.000
 KS2  H3   C4'  C5'  108.23  3.000
 KS2  H3   C4'  O4'  111.06  3.000
 KS2  C5'  C4'  O4'  108.15  3.000
 KS2  H3   C4'  C3'  108.34  3.000
 KS2  C5'  C4'  C3'  109.61  3.000
 KS2  O4'  C4'  C3'  111.40  3.000
 KS2  H4   O4'  C4'  107.93  3.000
 KS2  H5   C2'  C1'  108.07  3.000
 KS2  H5   C2'  O2'  111.33  3.000
 KS2  C1'  C2'  O2'  107.34  3.000
 KS2  H5   C2'  C3'  109.14  3.000
 KS2  C1'  C2'  C3'  108.47  3.000
 KS2  O2'  C2'  C3'  112.34  3.000
 KS2  H6   O2'  C2'  108.87  3.000
 KS2  H7   C1'  C1   108.24  3.000
 KS2  H7   C1'  O5'  110.73  3.000
 KS2  C1   C1'  O5'  108.17  3.000
 KS2  H7   C1'  C2'  108.37  3.000
 KS2  C1   C1'  C2'  111.10  3.000
 KS2  O5'  C1'  C2'  110.22  3.000
 KS2  C5'  O5'  C1'  113.26  3.000
 KS2  H8   C5'  C6'  109.10  3.000
 KS2  H8   C5'  O5'  109.74  3.000
 KS2  C6'  C5'  O5'  107.57  3.000
 KS2  H8   C5'  C4'  108.46  3.000
 KS2  O5'  C5'  C4'  109.93  3.000
 KS2  C6'  C5'  C4'  112.01  3.000
 KS2  H10  C6'  H9   107.10  3.000
 KS2  H10  C6'  O6'  111.79  3.000
 KS2  H9   C6'  O6'  111.71  3.000
 KS2  H10  C6'  C5'  108.93  3.000
 KS2  H9   C6'  C5'  108.40  3.000
 KS2  O6'  C6'  C5'  108.81  3.000
 KS2  H11  O6'  C6'  107.94  3.000
 KS2  N2   C1   N5   109.48  3.000
 KS2  N5   C1   C1'  124.00  3.000
 KS2  N2   C1   C1'  126.51  3.000
 KS2  H12  N5   C4   127.88  3.000
 KS2  H12  N5   C1   126.26  3.000
 KS2  C4   N5   C1   105.86  3.000
 KS2  C6   C4   N3   126.12  3.000
 KS2  C6   C4   N5   125.15  3.000
 KS2  N3   C4   N5   108.73  3.000
 KS2  N2   N3   C4   108.17  3.000
 KS2  N3   N2   C1   107.76  3.000
 KS2  C7   C6   C11  118.62  3.000
 KS2  C11  C6   C4   121.63  3.000
 KS2  C7   C6   C4   119.75  3.000
 KS2  H13  C11  C10  118.40  3.000
 KS2  H13  C11  C6   121.05  3.000
 KS2  C10  C11  C6   120.55  3.000
 KS2  H14  C10  C9   119.77  3.000
 KS2  H14  C10  C11  119.04  3.000
 KS2  C9   C10  C11  121.19  3.000
 KS2  C8   C9   C12  120.91  3.000
 KS2  C12  C9   C10  121.17  3.000
 KS2  C8   C9   C10  117.92  3.000
 KS2  H17  C12  H16  108.23  3.000
 KS2  H17  C12  H15  107.30  3.000
 KS2  H16  C12  H15  107.17  3.000
 KS2  H17  C12  C9   111.67  3.000
 KS2  H16  C12  C9   111.55  3.000
 KS2  H15  C12  C9   110.70  3.000
 KS2  H18  C8   C7   119.16  3.000
 KS2  H18  C8   C9   119.53  3.000
 KS2  C7   C8   C9   121.31  3.000
 KS2  H19  C7   C8   119.77  3.000
 KS2  H19  C7   C6   119.81  3.000
 KS2  C8   C7   C6   120.42  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
 KS2  CONST_01  C4   N3   N2   C1     0.00   0.0  0
 KS2  CONST_02  N3   C4   N5   C1     0.00   0.0  0
 KS2  CONST_03  C6   C4   N5   C1   180.00   0.0  0
 KS2  CONST_04  N3   N2   C1   N5     0.00   0.0  0
 KS2  CONST_05  N2   N3   C4   N5     0.00   0.0  0
 KS2  CONST_06  C7   C6   C4   N5   180.00   0.0  0
 KS2  CONST_07  C11  C6   C4   N5     0.00   0.0  0
 KS2  CONST_08  N2   C1   N5   C4     0.00   0.0  0
 KS2  CONST_09  C8   C7   C6   C4   180.00   0.0  0
 KS2  CONST_10  C10  C11  C6   C4   180.00   0.0  0
 KS2  CONST_11  C7   C6   C4   N3     0.00   0.0  0
 KS2  CONST_12  C11  C6   C4   N3   180.00   0.0  0
 KS2  CONST_13  C6   C4   N3   N2   180.00   0.0  0
 KS2  CONST_14  C9   C8   C7   C6     0.00   0.0  0
 KS2  CONST_15  C9   C10  C11  C6     0.00   0.0  0
 KS2  CONST_16  C8   C7   C6   C11    0.00   0.0  0
 KS2  CONST_17  C8   C9   C10  C11    0.00   0.0  0
 KS2  CONST_18  C7   C6   C11  C10    0.00   0.0  0
 KS2  CONST_19  C7   C8   C9   C10    0.00   0.0  0
 KS2  CONST_20  N3   N2   C1   C1'  180.00   0.0  0
 KS2  CONST_21  C4   N5   C1   C1'  180.00   0.0  0
 KS2  CONST_22  C12  C9   C10  C11  180.00   0.0  0
 KS2  CONST_23  C7   C8   C9   C12  180.00   0.0  0
 KS2  CONST_24  H12  N5   C1   C1'    0.00   0.0  0
 KS2  CONST_25  H19  C7   C6   C4     0.00   0.0  0
 KS2  CONST_26  H13  C11  C6   C4     0.00   0.0  0
 KS2  CONST_27  H18  C8   C7   C6   180.00   0.0  0
 KS2  CONST_28  H14  C10  C11  C6   180.00   0.0  0
 KS2  Var_01    H15  C12  C9   C10   93.26  30.0  2

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
 KS2  chir_01  C3'  O3'  C4'  C2'  negativ
 KS2  chir_02  C4'  O4'  C5'  C3'  positiv
 KS2  chir_03  C2'  O2'  C3'  C1'  positiv
 KS2  chir_04  C1'  O5'  C2'  C1   positiv
 KS2  chir_05  C5'  O5'  C6'  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
 KS2  plan-1  C1'  0.020
 KS2  plan-1  C1   0.020
 KS2  plan-1  N5   0.020
 KS2  plan-1  C4   0.020
 KS2  plan-1  N3   0.020
 KS2  plan-1  N2   0.020
 KS2  plan-1  C6   0.020
 KS2  plan-1  H12  0.020
 KS2  plan-2  C4   0.020
 KS2  plan-2  C6   0.020
 KS2  plan-2  C11  0.020
 KS2  plan-2  C10  0.020
 KS2  plan-2  C9   0.020
 KS2  plan-2  C12  0.020
 KS2  plan-2  C8   0.020
 KS2  plan-2  C7   0.020
 KS2  plan-2  H13  0.020
 KS2  plan-2  H14  0.020
 KS2  plan-2  H18  0.020
 KS2  plan-2  H19  0.020

