# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 09:35:38 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(4-phenyl-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)c3ccccc3
#
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
 KVW  KVW  (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(4-phenyl-1,3-thiazol-2-yl)oxane-3,4,5-triol  ligand  39  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KVW
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
 KVW  C8   C  CR16  0  -0.235  -6.1278   0.1821  -0.1131
 KVW  C6   C  CR6   0   0.055  -3.7197   0.0711   0.0744
 KVW  C10  C  CR16  0  -0.237  -5.0873  -1.8301   0.6756
 KVW  C9   C  CR16  0  -0.265  -6.2367  -1.1236   0.3496
 KVW  C1   C  CR5   0   0.037  -0.2049   0.7171   0.2109
 KVW  S2   S  S2    0   0.292  -0.4362   2.2079  -0.6112
 KVW  C3   C  CR15  0  -0.609  -2.1157   1.8866  -0.6627
 KVW  C4   C  CR5   0   0.409  -2.3957   0.6899  -0.0695
 KVW  C7   C  CR16  0  -0.327  -4.8826   0.7744  -0.2477
 KVW  C11  C  CR16  0  -0.301  -3.8395  -1.2394   0.5396
 KVW  N5   N  N     0  -0.468  -1.2881   0.0435   0.4161
 KVW  C1'  C  CH1   0  -0.014   1.1551   0.2669   0.6335
 KVW  O5'  O  O2    0  -0.497   2.0749   1.0609  -0.0613
 KVW  C5'  C  CH1   0  -0.012   3.4203   0.8150   0.3035
 KVW  C6'  C  CH2   0  -0.156   4.2877   1.8038  -0.4444
 KVW  O6'  O  OH1   0  -0.668   3.9431   3.1071  -0.0413
 KVW  C4'  C  CH1   0   0.038   3.7766  -0.6336  -0.0346
 KVW  O4'  O  OH1   0  -0.672   5.1013  -0.8642   0.3734
 KVW  C3'  C  CH1   0  -0.013   2.8097  -1.5792   0.6705
 KVW  O3'  O  OH1   0  -0.671   3.1401  -2.8891   0.2761
 KVW  C2'  C  CH1   0   0.010   1.3691  -1.2246   0.3286
 KVW  O2'  O  OH1   0  -0.682   0.5215  -2.0357   1.0965
 KVW  H1   H  HCR6  0   0.260  -7.0173   0.7448  -0.3647
 KVW  H2   H  HCR6  0   0.259  -5.1599  -2.8477   1.0373
 KVW  H3   H  HCR6  0   0.259  -7.2098  -1.5843   0.4582
 KVW  H8   H  HCR6  0   0.252  -4.8243   1.7971  -0.5980
 KVW  H9   H  HCR6  0   0.258  -2.9516  -1.8031   0.7923
 KVW  H10  H  HCH1  0   0.260   1.2507   0.4157   1.7219
 KVW  H11  H  HCH1  0   0.228   3.5465   0.9673   1.3877
 KVW  H12  H  HCH2  0   0.217   5.3351   1.5753  -0.2249
 KVW  H13  H  HCH2  0   0.197   4.1448   1.6569  -1.5244
 KVW  H14  H  HOH1  0   0.457   4.5929   3.7114  -0.4102
 KVW  H15  H  HCH1  0   0.215   3.6681  -0.7681  -1.1232
 KVW  H16  H  HOH1  0   0.455   5.3125  -1.7858   0.1907
 KVW  H17  H  HCH1  0   0.217   2.9427  -1.4526   1.7570
 KVW  H18  H  HOH1  0   0.459   2.7197  -3.5088   0.8800
 KVW  H19  H  HCH1  0   0.219   1.2110  -1.3756  -0.7505
 KVW  H20  H  HOH1  0   0.462  -0.3876  -1.7435   0.9312
 KVW  H6   H  HCR5  0   0.309  -2.7936   2.5796  -1.1350

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
 KVW  C8   C9   aromatic  1.390  0.020  1.390
 KVW  C8   C7   aromatic  1.385  0.020  1.385
 KVW  C6   C4   single    1.468  0.020  1.468
 KVW  C6   C7   aromatic  1.397  0.020  1.397
 KVW  C6   C11  aromatic  1.396  0.020  1.396
 KVW  C10  C9   aromatic  1.388  0.020  1.388
 KVW  C10  C11  aromatic  1.387  0.020  1.387
 KVW  C1   S2   aromatic  1.718  0.020  1.718
 KVW  C1   N5   aromatic  1.292  0.020  1.292
 KVW  C1   C1'  single    1.494  0.020  1.494
 KVW  S2   C3   aromatic  1.711  0.020  1.711
 KVW  C3   C4   aromatic  1.365  0.020  1.365
 KVW  C4   N5   aromatic  1.371  0.020  1.371
 KVW  C1'  O5'  single    1.400  0.020  1.400
 KVW  C1'  C2'  single    1.537  0.020  1.537
 KVW  O5'  C5'  single    1.416  0.020  1.416
 KVW  C5'  C6'  single    1.513  0.020  1.513
 KVW  C5'  C4'  single    1.530  0.020  1.530
 KVW  C6'  O6'  single    1.407  0.020  1.407
 KVW  C4'  O4'  single    1.405  0.020  1.405
 KVW  C4'  C3'  single    1.525  0.020  1.525
 KVW  C3'  O3'  single    1.407  0.020  1.407
 KVW  C3'  C2'  single    1.522  0.020  1.522
 KVW  C2'  O2'  single    1.402  0.020  1.402
 KVW  C8   H1   single    0.930  0.020  1.080
 KVW  C10  H2   single    0.930  0.020  1.080
 KVW  C9   H3   single    0.930  0.020  1.080
 KVW  C3   H6   single    0.930  0.020  1.080
 KVW  C7   H8   single    0.930  0.020  1.080
 KVW  C11  H9   single    0.930  0.020  1.080
 KVW  C1'  H10  single    0.970  0.020  1.090
 KVW  C5'  H11  single    0.970  0.020  1.090
 KVW  C6'  H12  single    0.970  0.020  1.090
 KVW  C6'  H13  single    0.970  0.020  1.090
 KVW  O6'  H14  single    0.850  0.020  0.980
 KVW  C4'  H15  single    0.970  0.020  1.090
 KVW  O4'  H16  single    0.850  0.020  0.980
 KVW  C3'  H17  single    0.970  0.020  1.090
 KVW  O3'  H18  single    0.850  0.020  0.980
 KVW  C2'  H19  single    0.970  0.020  1.090
 KVW  O2'  H20  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
 KVW  H1   C8   C7   119.60  3.000
 KVW  H1   C8   C9   120.10  3.000
 KVW  C7   C8   C9   120.30  3.000
 KVW  C11  C6   C7   118.56  3.000
 KVW  C11  C6   C4   120.38  3.000
 KVW  C7   C6   C4   121.06  3.000
 KVW  H2   C10  C11  119.56  3.000
 KVW  H2   C10  C9   120.10  3.000
 KVW  C11  C10  C9   120.34  3.000
 KVW  H3   C9   C10  120.29  3.000
 KVW  H3   C9   C8   120.26  3.000
 KVW  C10  C9   C8   119.44  3.000
 KVW  C1'  C1   N5   124.15  3.000
 KVW  C1'  C1   S2   121.30  3.000
 KVW  N5   C1   S2   114.55  3.000
 KVW  C3   S2   C1    89.06  3.000
 KVW  H6   C3   C4   128.67  3.000
 KVW  H6   C3   S2   120.64  3.000
 KVW  C4   C3   S2   110.68  3.000
 KVW  N5   C4   C3   113.67  3.000
 KVW  N5   C4   C6   119.66  3.000
 KVW  C3   C4   C6   126.66  3.000
 KVW  H8   C7   C6   120.36  3.000
 KVW  H8   C7   C8   118.92  3.000
 KVW  C6   C7   C8   120.71  3.000
 KVW  H9   C11  C10  119.57  3.000
 KVW  H9   C11  C6   119.78  3.000
 KVW  C10  C11  C6   120.65  3.000
 KVW  C4   N5   C1   112.04  3.000
 KVW  H10  C1'  C2'  108.33  3.000
 KVW  H10  C1'  O5'  110.88  3.000
 KVW  C2'  C1'  O5'  111.13  3.000
 KVW  H10  C1'  C1   108.51  3.000
 KVW  C2'  C1'  C1   111.29  3.000
 KVW  O5'  C1'  C1   106.67  3.000
 KVW  C5'  O5'  C1'  113.46  3.000
 KVW  H11  C5'  C4'  108.76  3.000
 KVW  H11  C5'  C6'  109.29  3.000
 KVW  C4'  C5'  C6'  112.09  3.000
 KVW  H11  C5'  O5'  109.78  3.000
 KVW  C4'  C5'  O5'  109.21  3.000
 KVW  C6'  C5'  O5'  107.70  3.000
 KVW  H13  C6'  H12  107.07  3.000
 KVW  H13  C6'  O6'  111.92  3.000
 KVW  H12  C6'  O6'  111.74  3.000
 KVW  H13  C6'  C5'  108.89  3.000
 KVW  H12  C6'  C5'  108.25  3.000
 KVW  O6'  C6'  C5'  108.86  3.000
 KVW  H14  O6'  C6'  107.87  3.000
 KVW  H15  C4'  C3'  108.57  3.000
 KVW  H15  C4'  O4'  111.08  3.000
 KVW  C3'  C4'  O4'  111.20  3.000
 KVW  H15  C4'  C5'  108.12  3.000
 KVW  C3'  C4'  C5'  109.71  3.000
 KVW  O4'  C4'  C5'  108.11  3.000
 KVW  H16  O4'  C4'  107.98  3.000
 KVW  H17  C3'  C2'  107.99  3.000
 KVW  H17  C3'  O3'  110.79  3.000
 KVW  C2'  C3'  O3'  112.09  3.000
 KVW  H17  C3'  C4'  107.95  3.000
 KVW  C2'  C3'  C4'  110.59  3.000
 KVW  O3'  C3'  C4'  107.37  3.000
 KVW  H18  O3'  C3'  108.72  3.000
 KVW  H19  C2'  O2'  111.75  3.000
 KVW  H19  C2'  C3'  108.91  3.000
 KVW  O2'  C2'  C3'  108.32  3.000
 KVW  H19  C2'  C1'  107.90  3.000
 KVW  O2'  C2'  C1'  111.63  3.000
 KVW  C3'  C2'  C1'  108.25  3.000
 KVW  H20  O2'  C2'  107.41  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
 KVW  CONST_01  C11  C10  C9   C8     0.00  0.0  0
 KVW  CONST_02  C4   C6   C7   C8   180.00  0.0  0
 KVW  CONST_03  C11  C6   C7   C8     0.00  0.0  0
 KVW  CONST_04  S2   C3   C4   C6   180.00  0.0  0
 KVW  CONST_05  C1   N5   C4   C6   180.00  0.0  0
 KVW  CONST_06  C9   C8   C7   C6     0.00  0.0  0
 KVW  CONST_07  C9   C10  C11  C6     0.00  0.0  0
 KVW  CONST_08  C7   C8   C9   C10    0.00  0.0  0
 KVW  CONST_09  C4   C6   C11  C10  180.00  0.0  0
 KVW  CONST_10  C7   C6   C11  C10    0.00  0.0  0
 KVW  CONST_11  C4   C3   S2   C1     0.00  0.0  0
 KVW  CONST_12  C3   C4   N5   C1     0.00  0.0  0
 KVW  CONST_13  C4   N5   C1   S2     0.00  0.0  0
 KVW  CONST_14  N5   C4   C3   S2     0.00  0.0  0
 KVW  CONST_15  N5   C1   S2   C3     0.00  0.0  0
 KVW  CONST_16  C7   C6   C4   C3     0.00  0.0  0
 KVW  CONST_17  C11  C6   C4   C3   180.00  0.0  0
 KVW  CONST_18  N5   C4   C6   C7   180.00  0.0  0
 KVW  CONST_19  N5   C4   C6   C11    0.00  0.0  0
 KVW  CONST_20  C1'  C1   S2   C3   180.00  0.0  0
 KVW  CONST_21  C1'  C1   N5   C4   180.00  0.0  0
 KVW  CONST_22  H2   C10  C9   C8   180.00  0.0  0
 KVW  CONST_23  H6   C3   C4   C6     0.00  0.0  0
 KVW  CONST_24  H1   C8   C7   C6   180.00  0.0  0
 KVW  CONST_25  H8   C7   C8   C9   180.00  0.0  0
 KVW  CONST_26  H9   C11  C10  C9   180.00  0.0  0
 KVW  CONST_27  H3   C9   C8   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
 KVW  chir_01  C1'  C1   O5'  C2'  positiv
 KVW  chir_02  C5'  O5'  C6'  C4'  positiv
 KVW  chir_03  C4'  O4'  C5'  C3'  positiv
 KVW  chir_04  C3'  O3'  C4'  C2'  negativ
 KVW  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
 KVW  plan-1  C6   0.020
 KVW  plan-1  C1   0.020
 KVW  plan-1  S2   0.020
 KVW  plan-1  C3   0.020
 KVW  plan-1  C4   0.020
 KVW  plan-1  N5   0.020
 KVW  plan-1  C1'  0.020
 KVW  plan-1  H6   0.020
 KVW  plan-2  C8   0.020
 KVW  plan-2  C6   0.020
 KVW  plan-2  C10  0.020
 KVW  plan-2  C9   0.020
 KVW  plan-2  C4   0.020
 KVW  plan-2  C7   0.020
 KVW  plan-2  C11  0.020
 KVW  plan-2  H1   0.020
 KVW  plan-2  H2   0.020
 KVW  plan-2  H3   0.020
 KVW  plan-2  H8   0.020
 KVW  plan-2  H9   0.020

