# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 17:31:01 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1,3-thiazol-2-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)c2scc(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
 KVE  KVE  (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1,3-thiazol-2-yl)oxane-3,4,5-triol  ligand  45  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KVE
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
 KVE  C1   C  CR5   0   0.037   0.9166  -0.7536  -0.2352
 KVE  C3   C  CR15  0  -0.613  -0.9681  -1.9971   0.5902
 KVE  C4   C  CR5   0   0.423  -1.2749  -0.7861   0.0392
 KVE  C6   C  CR6   0   0.056  -2.6127  -0.1958  -0.0942
 KVE  C10  C  CR16  0  -0.296  -3.9975   1.6563  -0.8160
 KVE  C14  C  CR16  0  -0.259  -7.5586   0.8517  -0.0965
 KVE  C7   C  CR16  0  -0.418  -3.7364  -0.8649   0.3309
 KVE  C8   C  CR66  0   0.159  -5.0233  -0.3034   0.1981
 KVE  C12  C  CR16  0  -0.313  -6.1833  -0.9907   0.6313
 KVE  C13  C  CR16  0  -0.257  -7.4208  -0.4267   0.4862
 KVE  C15  C  CR16  0  -0.306  -6.4551   1.5398  -0.5228
 KVE  C9   C  CR66  0   0.099  -5.1632   0.9815  -0.3870
 KVE  C11  C  CR16  0  -0.297  -2.7629   1.0891  -0.6757
 KVE  N5   N  N     0  -0.470  -0.1816  -0.0985  -0.4212
 KVE  S2   S  S2    0   0.297   0.7174  -2.2760   0.5356
 KVE  C1'  C  CH1   0  -0.014   2.2680  -0.2634  -0.6398
 KVE  O5'  O  O2    0  -0.497   3.2017  -1.0570   0.0373
 KVE  C5'  C  CH1   0  -0.011   4.5416  -0.7817  -0.3264
 KVE  C6'  C  CH2   0  -0.156   5.4280  -1.7717   0.3968
 KVE  O6'  O  OH1   0  -0.667   5.1005  -3.0716  -0.0304
 KVE  C4'  C  CH1   0   0.036   4.8760   0.6651   0.0420
 KVE  O4'  O  OH1   0  -0.671   6.1943   0.9254  -0.3695
 KVE  C3'  C  CH1   0  -0.007   3.8884   1.6107  -0.6344
 KVE  O3'  O  OH1   0  -0.671   4.1981   2.9157  -0.2101
 KVE  C2'  C  CH1   0   0.008   2.4562   1.2217  -0.2942
 KVE  O2'  O  OH1   0  -0.682   1.5914   2.0405  -1.0349
 KVE  H1   H  HCR5  0   0.309  -1.6306  -2.7268   1.0278
 KVE  H2   H  HCR6  0   0.257  -4.0921   2.6380  -1.2648
 KVE  H3   H  HCR6  0   0.260  -8.5439   1.2853  -0.2065
 KVE  H4   H  HCR6  0   0.249  -3.6576  -1.8478   0.7802
 KVE  H5   H  HCR6  0   0.255  -6.0766  -1.9714   1.0797
 KVE  H6   H  HCR6  0   0.260  -8.3024  -0.9597   0.8173
 KVE  H7   H  HCR6  0   0.256  -6.5607   2.5198  -0.9725
 KVE  H8   H  HCR6  0   0.260  -1.8867   1.6258  -1.0124
 KVE  H9   H  HCH1  0   0.261   2.3703  -0.3820  -1.7314
 KVE  H10  H  HCH1  0   0.228   4.6655  -0.9087  -1.4141
 KVE  H11  H  HCH2  0   0.216   6.4705  -1.5229   0.1760
 KVE  H12  H  HCH2  0   0.197   5.2893  -1.6484   1.4804
 KVE  H13  H  HOH1  0   0.457   5.7494  -3.6759   0.3404
 KVE  H14  H  HCH1  0   0.216   4.7726   0.7731   1.1338
 KVE  H15  H  HOH1  0   0.456   6.4143   1.8284  -0.1183
 KVE  H16  H  HCH1  0   0.215   4.0171   1.5114  -1.7246
 KVE  H17  H  HOH1  0   0.458   3.6923   3.5404  -0.7394
 KVE  H18  H  HCH1  0   0.220   2.3013   1.3403   0.7894
 KVE  H19  H  HOH1  0   0.463   0.6878   1.7316  -0.8706

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
 KVE  O3'  C3'  single    1.407  0.020  1.407
 KVE  O4'  C4'  single    1.405  0.020  1.405
 KVE  C3'  C4'  single    1.525  0.020  1.525
 KVE  C3'  C2'  single    1.523  0.020  1.523
 KVE  C4'  C5'  single    1.530  0.020  1.530
 KVE  O2'  C2'  single    1.402  0.020  1.402
 KVE  C2'  C1'  single    1.536  0.020  1.536
 KVE  O6'  C6'  single    1.407  0.020  1.407
 KVE  C5'  C6'  single    1.513  0.020  1.513
 KVE  C5'  O5'  single    1.415  0.020  1.415
 KVE  C1'  O5'  single    1.400  0.020  1.400
 KVE  C1'  C1   single    1.493  0.020  1.493
 KVE  S2   C1   aromatic  1.718  0.020  1.718
 KVE  S2   C3   aromatic  1.709  0.020  1.709
 KVE  C1   N5   aromatic  1.292  0.020  1.292
 KVE  C3   C4   aromatic  1.365  0.020  1.365
 KVE  N5   C4   aromatic  1.371  0.020  1.371
 KVE  C4   C6   single    1.468  0.020  1.468
 KVE  C6   C7   aromatic  1.375  0.020  1.375
 KVE  C6   C11  aromatic  1.418  0.020  1.418
 KVE  C7   C8   aromatic  1.410  0.020  1.410
 KVE  C11  C10  aromatic  1.366  0.020  1.366
 KVE  C8   C12  aromatic  1.416  0.020  1.416
 KVE  C8   C9   aromatic  1.419  0.020  1.419
 KVE  C12  C13  aromatic  1.368  0.020  1.368
 KVE  C10  C9   aromatic  1.414  0.020  1.414
 KVE  C9   C15  aromatic  1.414  0.020  1.414
 KVE  C13  C14  aromatic  1.412  0.020  1.412
 KVE  C15  C14  aromatic  1.369  0.020  1.369
 KVE  C3   H1   single    0.930  0.020  1.080
 KVE  C10  H2   single    0.930  0.020  1.080
 KVE  C14  H3   single    0.930  0.020  1.080
 KVE  C7   H4   single    0.930  0.020  1.080
 KVE  C12  H5   single    0.930  0.020  1.080
 KVE  C13  H6   single    0.930  0.020  1.080
 KVE  C15  H7   single    0.930  0.020  1.080
 KVE  C11  H8   single    0.930  0.020  1.080
 KVE  C1'  H9   single    0.970  0.020  1.090
 KVE  C5'  H10  single    0.970  0.020  1.090
 KVE  C6'  H11  single    0.970  0.020  1.090
 KVE  C6'  H12  single    0.970  0.020  1.090
 KVE  O6'  H13  single    0.850  0.020  0.980
 KVE  C4'  H14  single    0.970  0.020  1.090
 KVE  O4'  H15  single    0.850  0.020  0.980
 KVE  C3'  H16  single    0.970  0.020  1.090
 KVE  O3'  H17  single    0.850  0.020  0.980
 KVE  C2'  H18  single    0.970  0.020  1.090
 KVE  O2'  H19  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
 KVE  C1'  C1   S2   121.16  3.000
 KVE  S2   C1   N5   114.54  3.000
 KVE  C1'  C1   N5   124.31  3.000
 KVE  H1   C3   S2   120.56  3.000
 KVE  H1   C3   C4   128.74  3.000
 KVE  S2   C3   C4   110.70  3.000
 KVE  N5   C4   C6   119.63  3.000
 KVE  C6   C4   C3   126.73  3.000
 KVE  N5   C4   C3   113.64  3.000
 KVE  C11  C6   C7   118.75  3.000
 KVE  C11  C6   C4   119.86  3.000
 KVE  C7   C6   C4   121.39  3.000
 KVE  H2   C10  C11  119.85  3.000
 KVE  H2   C10  C9   119.09  3.000
 KVE  C11  C10  C9   121.06  3.000
 KVE  H3   C14  C15  120.07  3.000
 KVE  H3   C14  C13  119.58  3.000
 KVE  C15  C14  C13  120.34  3.000
 KVE  H4   C7   C8   117.81  3.000
 KVE  H4   C7   C6   120.67  3.000
 KVE  C8   C7   C6   121.52  3.000
 KVE  C9   C8   C12  119.00  3.000
 KVE  C9   C8   C7   119.30  3.000
 KVE  C12  C8   C7   121.69  3.000
 KVE  H5   C12  C13  120.41  3.000
 KVE  H5   C12  C8   119.02  3.000
 KVE  C13  C12  C8   120.56  3.000
 KVE  H6   C13  C12  120.11  3.000
 KVE  H6   C13  C14  119.52  3.000
 KVE  C12  C13  C14  120.37  3.000
 KVE  H7   C15  C9   119.08  3.000
 KVE  H7   C15  C14  120.37  3.000
 KVE  C9   C15  C14  120.55  3.000
 KVE  C15  C9   C8   119.17  3.000
 KVE  C15  C9   C10  122.40  3.000
 KVE  C8   C9   C10  118.43  3.000
 KVE  H8   C11  C10  119.63  3.000
 KVE  H8   C11  C6   119.44  3.000
 KVE  C10  C11  C6   120.93  3.000
 KVE  C4   N5   C1   112.03  3.000
 KVE  C3   S2   C1    89.09  3.000
 KVE  H9   C1'  C2'  108.38  3.000
 KVE  H9   C1'  O5'  110.85  3.000
 KVE  C2'  C1'  O5'  110.95  3.000
 KVE  H9   C1'  C1   108.47  3.000
 KVE  O5'  C1'  C1   106.64  3.000
 KVE  C2'  C1'  C1   111.54  3.000
 KVE  C5'  O5'  C1'  113.38  3.000
 KVE  H10  C5'  C4'  108.79  3.000
 KVE  H10  C5'  C6'  109.30  3.000
 KVE  C4'  C5'  C6'  112.06  3.000
 KVE  H10  C5'  O5'  109.73  3.000
 KVE  C6'  C5'  O5'  107.73  3.000
 KVE  C4'  C5'  O5'  109.21  3.000
 KVE  H12  C6'  H11  107.08  3.000
 KVE  H12  C6'  O6'  111.93  3.000
 KVE  H11  C6'  O6'  111.75  3.000
 KVE  H12  C6'  C5'  108.90  3.000
 KVE  H11  C6'  C5'  108.23  3.000
 KVE  O6'  C6'  C5'  108.85  3.000
 KVE  H13  O6'  C6'  107.86  3.000
 KVE  H14  C4'  C3'  108.53  3.000
 KVE  H14  C4'  O4'  111.10  3.000
 KVE  C3'  C4'  O4'  111.27  3.000
 KVE  H14  C4'  C5'  108.10  3.000
 KVE  C3'  C4'  C5'  109.75  3.000
 KVE  O4'  C4'  C5'  108.04  3.000
 KVE  H15  O4'  C4'  108.15  3.000
 KVE  H16  C3'  C2'  107.92  3.000
 KVE  H16  C3'  O3'  110.87  3.000
 KVE  C2'  C3'  O3'  112.13  3.000
 KVE  H16  C3'  C4'  107.88  3.000
 KVE  C2'  C3'  C4'  110.59  3.000
 KVE  O3'  C3'  C4'  107.39  3.000
 KVE  H17  O3'  C3'  108.70  3.000
 KVE  H18  C2'  O2'  111.72  3.000
 KVE  H18  C2'  C3'  108.94  3.000
 KVE  O2'  C2'  C3'  108.23  3.000
 KVE  H18  C2'  C1'  107.95  3.000
 KVE  O2'  C2'  C1'  111.72  3.000
 KVE  C3'  C2'  C1'  108.17  3.000
 KVE  H19  O2'  C2'  107.42  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
 KVE  CONST_01  C4   C3   S2   C1     0.00  0.0  0
 KVE  CONST_02  C3   C4   N5   C1     0.00  0.0  0
 KVE  CONST_03  C6   C4   N5   C1   180.00  0.0  0
 KVE  CONST_04  N5   C1   S2   C3     0.00  0.0  0
 KVE  CONST_05  C7   C6   C4   C3     0.00  0.0  0
 KVE  CONST_06  C11  C6   C4   C3   180.00  0.0  0
 KVE  CONST_07  S2   C1   N5   C4     0.00  0.0  0
 KVE  CONST_08  C8   C7   C6   C4   180.00  0.0  0
 KVE  CONST_09  C10  C11  C6   C4   180.00  0.0  0
 KVE  CONST_10  S2   C3   C4   C6   180.00  0.0  0
 KVE  CONST_11  C12  C8   C7   C6   180.00  0.0  0
 KVE  CONST_12  C9   C8   C7   C6     0.00  0.0  0
 KVE  CONST_13  C9   C10  C11  C6     0.00  0.0  0
 KVE  CONST_14  C7   C6   C11  C10    0.00  0.0  0
 KVE  CONST_15  C7   C8   C9   C10    0.00  0.0  0
 KVE  CONST_16  C12  C8   C9   C10  180.00  0.0  0
 KVE  CONST_17  C14  C15  C9   C10  180.00  0.0  0
 KVE  CONST_18  C8   C12  C13  C14    0.00  0.0  0
 KVE  CONST_19  C8   C9   C15  C14    0.00  0.0  0
 KVE  CONST_20  N5   C4   C6   C7   180.00  0.0  0
 KVE  CONST_21  C13  C12  C8   C7   180.00  0.0  0
 KVE  CONST_22  C15  C9   C8   C7   180.00  0.0  0
 KVE  CONST_23  C11  C6   C7   C8     0.00  0.0  0
 KVE  CONST_24  C11  C10  C9   C8     0.00  0.0  0
 KVE  CONST_25  C15  C9   C8   C12    0.00  0.0  0
 KVE  CONST_26  C15  C14  C13  C12    0.00  0.0  0
 KVE  CONST_27  C9   C8   C12  C13    0.00  0.0  0
 KVE  CONST_28  C9   C15  C14  C13    0.00  0.0  0
 KVE  CONST_29  C11  C10  C9   C15  180.00  0.0  0
 KVE  CONST_30  N5   C4   C6   C11    0.00  0.0  0
 KVE  CONST_31  S2   C3   C4   N5     0.00  0.0  0
 KVE  CONST_32  C1'  C1   S2   C3   180.00  0.0  0
 KVE  CONST_33  C1'  C1   N5   C4   180.00  0.0  0
 KVE  CONST_34  H1   C3   S2   C1   180.00  0.0  0
 KVE  CONST_35  H4   C7   C6   C4     0.00  0.0  0
 KVE  CONST_36  H8   C11  C6   C4     0.00  0.0  0
 KVE  CONST_37  H2   C10  C11  C6   180.00  0.0  0
 KVE  CONST_38  H7   C15  C9   C10    0.00  0.0  0
 KVE  CONST_39  H5   C12  C13  C14  180.00  0.0  0
 KVE  CONST_40  H6   C13  C12  C8   180.00  0.0  0
 KVE  CONST_41  H3   C14  C13  C12  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
 KVE  chir_01  C1'  C2'  O5'  C1   negativ
 KVE  chir_02  C5'  O5'  C6'  C4'  positiv
 KVE  chir_03  C4'  O4'  C5'  C3'  positiv
 KVE  chir_04  C3'  O3'  C4'  C2'  negativ
 KVE  chir_05  C2'  O2'  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
 KVE  plan-1  C1   0.020
 KVE  plan-1  C3   0.020
 KVE  plan-1  C4   0.020
 KVE  plan-1  C6   0.020
 KVE  plan-1  N5   0.020
 KVE  plan-1  S2   0.020
 KVE  plan-1  C1'  0.020
 KVE  plan-1  H1   0.020
 KVE  plan-2  C4   0.020
 KVE  plan-2  C6   0.020
 KVE  plan-2  C10  0.020
 KVE  plan-2  C14  0.020
 KVE  plan-2  C7   0.020
 KVE  plan-2  C8   0.020
 KVE  plan-2  C12  0.020
 KVE  plan-2  C13  0.020
 KVE  plan-2  C15  0.020
 KVE  plan-2  C9   0.020
 KVE  plan-2  C11  0.020
 KVE  plan-2  H2   0.020
 KVE  plan-2  H3   0.020
 KVE  plan-2  H4   0.020
 KVE  plan-2  H5   0.020
 KVE  plan-2  H6   0.020
 KVE  plan-2  H7   0.020
 KVE  plan-2  H8   0.020

