# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 08:25:56 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-phenyl-1,3-thiazol-4-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)c2csc(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
 KVQ  KVQ  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-phenyl-1,3-thiazol-4-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 PERFECT
;

data_comp_KVQ
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
 KVQ  C11  C  CR16  0  -0.288  -3.1501   0.3337   1.7255
 KVQ  C10  C  CR16  0  -0.236  -4.2285   0.4687   2.5842
 KVQ  C8   C  CR16  0  -0.237  -5.7287  -0.1155   0.8021
 KVQ  C7   C  CR16  0  -0.321  -4.6519  -0.2529  -0.0599
 KVQ  C4   C  CR5   0   0.006  -2.1951  -0.1676  -0.4943
 KVQ  C9   C  CR16  0  -0.258  -5.5216   0.2457   2.1266
 KVQ  C6   C  CR6   0   0.093  -3.3511  -0.0288   0.3919
 KVQ  N5   N  N     0  -0.403  -0.9674   0.0129  -0.1190
 KVQ  S3   S  S2    0   0.240  -2.3515  -0.5988  -2.1674
 KVQ  C2   C  CR15  0  -0.573  -0.6501  -0.5303  -2.3266
 KVQ  C1   C  CR5   0   0.381  -0.0871  -0.1896  -1.1382
 KVQ  C1'  C  CH1   0  -0.041   1.3769  -0.0212  -0.8974
 KVQ  O5'  O  O2    0  -0.495   1.7440  -0.8877   0.1507
 KVQ  C5'  C  CH1   0  -0.013   3.1321  -0.9136   0.4118
 KVQ  C6'  C  CH2   0  -0.157   3.3791  -1.9509   1.4863
 KVQ  O6'  O  OH1   0  -0.671   2.9980  -3.2145   0.9973
 KVQ  C4'  C  CH1   0   0.036   3.6022   0.4759   0.8446
 KVQ  O4'  O  OH1   0  -0.673   4.9927   0.4313   1.0466
 KVQ  C3'  C  CH1   0  -0.028   3.2284   1.4901  -0.2294
 KVQ  O3'  O  OH1   0  -0.677   3.6084   2.7721   0.2267
 KVQ  C2'  C  CH1   0   0.024   1.7342   1.4194  -0.5280
 KVQ  O2'  O  OH1   0  -0.669   1.3712   2.2406  -1.6087
 KVQ  H1   H  HCR6  0   0.262  -2.1454   0.5096   2.0853
 KVQ  H2   H  HCR6  0   0.263  -4.0581   0.7483   3.6155
 KVQ  H3   H  HCR6  0   0.266  -6.7312  -0.2922   0.4362
 KVQ  H4   H  HCR6  0   0.257  -4.8408  -0.5379  -1.0885
 KVQ  H5   H  HCR6  0   0.264  -6.3627   0.3524   2.7987
 KVQ  H6   H  HCR5  0   0.309  -0.1611  -0.7400  -3.2649
 KVQ  H7   H  HCH1  0   0.237   1.9134  -0.2869  -1.8219
 KVQ  H8   H  HCH1  0   0.219   3.6812  -1.2003  -0.5008
 KVQ  H9   H  HCH2  0   0.213   4.4401  -1.9231   1.7548
 KVQ  H10  H  HCH2  0   0.196   2.8116  -1.6703   2.3851
 KVQ  H11  H  HOH1  0   0.457   3.2195  -3.8699   1.6646
 KVQ  H12  H  HCH1  0   0.210   3.0767   0.7419   1.7768
 KVQ  H13  H  HOH1  0   0.452   5.2884   1.3248   1.2529
 KVQ  H14  H  HCH1  0   0.221   3.7755   1.2288  -1.1476
 KVQ  H15  H  HOH1  0   0.462   3.9086   3.2954  -0.5213
 KVQ  H16  H  HCH1  0   0.219   1.1761   1.6894   0.3803
 KVQ  H17  H  HOH1  0   0.455   1.3953   3.1567  -1.3164

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
 KVQ  O3'  C3'  single    1.413  0.020  1.413
 KVQ  O4'  C4'  single    1.406  0.020  1.406
 KVQ  C3'  C4'  single    1.524  0.020  1.524
 KVQ  C3'  C2'  single    1.525  0.020  1.525
 KVQ  C4'  C5'  single    1.529  0.020  1.529
 KVQ  O2'  C2'  single    1.405  0.020  1.405
 KVQ  C2'  C1'  single    1.530  0.020  1.530
 KVQ  O6'  C6'  single    1.407  0.020  1.407
 KVQ  C5'  C6'  single    1.514  0.020  1.514
 KVQ  C5'  O5'  single    1.413  0.020  1.413
 KVQ  C1'  O5'  single    1.409  0.020  1.409
 KVQ  C1'  C1   single    1.493  0.020  1.493
 KVQ  C2   C1   aromatic  1.358  0.020  1.358
 KVQ  C2   S3   aromatic  1.710  0.020  1.710
 KVQ  C1   N5   aromatic  1.362  0.020  1.362
 KVQ  S3   C4   aromatic  1.735  0.020  1.735
 KVQ  N5   C4   aromatic  1.296  0.020  1.296
 KVQ  C4   C6   single    1.463  0.020  1.463
 KVQ  C6   C7   aromatic  1.395  0.020  1.395
 KVQ  C6   C11  aromatic  1.397  0.020  1.397
 KVQ  C7   C8   aromatic  1.386  0.020  1.386
 KVQ  C11  C10  aromatic  1.385  0.020  1.385
 KVQ  C8   C9   aromatic  1.388  0.020  1.388
 KVQ  C10  C9   aromatic  1.390  0.020  1.390
 KVQ  C11  H1   single    0.930  0.020  1.080
 KVQ  C10  H2   single    0.930  0.020  1.080
 KVQ  C8   H3   single    0.930  0.020  1.080
 KVQ  C7   H4   single    0.930  0.020  1.080
 KVQ  C9   H5   single    0.930  0.020  1.080
 KVQ  C2   H6   single    0.930  0.020  1.080
 KVQ  C1'  H7   single    0.970  0.020  1.090
 KVQ  C5'  H8   single    0.970  0.020  1.090
 KVQ  C6'  H9   single    0.970  0.020  1.090
 KVQ  C6'  H10  single    0.970  0.020  1.090
 KVQ  O6'  H11  single    0.850  0.020  0.980
 KVQ  C4'  H12  single    0.970  0.020  1.090
 KVQ  O4'  H13  single    0.850  0.020  0.980
 KVQ  C3'  H14  single    0.970  0.020  1.090
 KVQ  O3'  H15  single    0.850  0.020  0.980
 KVQ  C2'  H16  single    0.970  0.020  1.090
 KVQ  O2'  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
 KVQ  H1   C11  C6   119.57  3.000
 KVQ  H1   C11  C10  120.08  3.000
 KVQ  C6   C11  C10  120.35  3.000
 KVQ  H2   C10  C9   120.12  3.000
 KVQ  H2   C10  C11  119.57  3.000
 KVQ  C9   C10  C11  120.31  3.000
 KVQ  H3   C8   C9   120.23  3.000
 KVQ  H3   C8   C7   119.57  3.000
 KVQ  C9   C8   C7   120.21  3.000
 KVQ  H4   C7   C6   120.80  3.000
 KVQ  H4   C7   C8   118.74  3.000
 KVQ  C6   C7   C8   120.46  3.000
 KVQ  S3   C4   N5   113.52  3.000
 KVQ  N5   C4   C6   124.03  3.000
 KVQ  S3   C4   C6   122.45  3.000
 KVQ  H5   C9   C8   120.15  3.000
 KVQ  H5   C9   C10  120.20  3.000
 KVQ  C8   C9   C10  119.65  3.000
 KVQ  C4   C6   C7   121.68  3.000
 KVQ  C7   C6   C11  119.02  3.000
 KVQ  C4   C6   C11  119.29  3.000
 KVQ  C1   N5   C4   112.01  3.000
 KVQ  C2   S3   C4    89.44  3.000
 KVQ  H6   C2   C1   128.45  3.000
 KVQ  H6   C2   S3   121.61  3.000
 KVQ  C1   C2   S3   109.94  3.000
 KVQ  C1'  C1   C2   125.15  3.000
 KVQ  C2   C1   N5   115.09  3.000
 KVQ  C1'  C1   N5   119.75  3.000
 KVQ  H7   C1'  C2'  108.43  3.000
 KVQ  H7   C1'  O5'  110.44  3.000
 KVQ  C2'  C1'  O5'  109.80  3.000
 KVQ  H7   C1'  C1   108.36  3.000
 KVQ  O5'  C1'  C1   107.83  3.000
 KVQ  C2'  C1'  C1   111.97  3.000
 KVQ  C5'  O5'  C1'  113.88  3.000
 KVQ  H8   C5'  C4'  108.50  3.000
 KVQ  H8   C5'  C6'  109.15  3.000
 KVQ  C4'  C5'  C6'  111.81  3.000
 KVQ  H8   C5'  O5'  109.94  3.000
 KVQ  C6'  C5'  O5'  107.70  3.000
 KVQ  C4'  C5'  O5'  109.73  3.000
 KVQ  H10  C6'  H9   107.06  3.000
 KVQ  H10  C6'  O6'  111.93  3.000
 KVQ  H9   C6'  O6'  111.74  3.000
 KVQ  H10  C6'  C5'  108.73  3.000
 KVQ  H9   C6'  C5'  108.35  3.000
 KVQ  O6'  C6'  C5'  108.93  3.000
 KVQ  H11  O6'  C6'  107.97  3.000
 KVQ  H12  C4'  C3'  108.56  3.000
 KVQ  H12  C4'  O4'  110.95  3.000
 KVQ  C3'  C4'  O4'  111.41  3.000
 KVQ  H12  C4'  C5'  108.18  3.000
 KVQ  C3'  C4'  C5'  109.26  3.000
 KVQ  O4'  C4'  C5'  108.42  3.000
 KVQ  H13  O4'  C4'  107.76  3.000
 KVQ  H14  C3'  C2'  108.22  3.000
 KVQ  H14  C3'  O3'  110.56  3.000
 KVQ  C2'  C3'  O3'  111.63  3.000
 KVQ  H14  C3'  C4'  107.95  3.000
 KVQ  C2'  C3'  C4'  110.33  3.000
 KVQ  O3'  C3'  C4'  108.09  3.000
 KVQ  H15  O3'  C3'  109.08  3.000
 KVQ  H16  C2'  O2'  111.15  3.000
 KVQ  H16  C2'  C3'  108.91  3.000
 KVQ  O2'  C2'  C3'  112.12  3.000
 KVQ  H16  C2'  C1'  108.19  3.000
 KVQ  O2'  C2'  C1'  107.72  3.000
 KVQ  C3'  C2'  C1'  108.65  3.000
 KVQ  H17  O2'  C2'  108.44  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
 KVQ  CONST_01  S3   C4   C6   C11  180.00  0.0  0
 KVQ  CONST_02  N5   C4   C6   C11    0.00  0.0  0
 KVQ  CONST_03  C8   C7   C6   C11    0.00  0.0  0
 KVQ  CONST_04  C8   C9   C10  C11    0.00  0.0  0
 KVQ  CONST_05  C4   C6   C11  C10  180.00  0.0  0
 KVQ  CONST_06  C7   C6   C11  C10    0.00  0.0  0
 KVQ  CONST_07  C7   C8   C9   C10    0.00  0.0  0
 KVQ  CONST_08  C4   C6   C7   C8   180.00  0.0  0
 KVQ  CONST_09  S3   C4   C6   C7     0.00  0.0  0
 KVQ  CONST_10  N5   C4   C6   C7   180.00  0.0  0
 KVQ  CONST_11  C1   C2   S3   C4     0.00  0.0  0
 KVQ  CONST_12  C2   C1   N5   C4     0.00  0.0  0
 KVQ  CONST_13  C6   C7   C8   C9     0.00  0.0  0
 KVQ  CONST_14  C6   C11  C10  C9     0.00  0.0  0
 KVQ  CONST_15  C2   S3   C4   C6   180.00  0.0  0
 KVQ  CONST_16  C1   N5   C4   C6   180.00  0.0  0
 KVQ  CONST_17  S3   C2   C1   N5     0.00  0.0  0
 KVQ  CONST_18  C2   S3   C4   N5     0.00  0.0  0
 KVQ  CONST_19  C1   N5   C4   S3     0.00  0.0  0
 KVQ  CONST_20  C1'  C1   N5   C4   180.00  0.0  0
 KVQ  CONST_21  C1'  C1   C2   S3   180.00  0.0  0
 KVQ  CONST_22  H4   C7   C6   C11  180.00  0.0  0
 KVQ  CONST_23  H5   C9   C10  C11  180.00  0.0  0
 KVQ  CONST_24  H3   C8   C9   C10  180.00  0.0  0
 KVQ  CONST_25  H2   C10  C9   C8   180.00  0.0  0
 KVQ  CONST_26  H1   C11  C6   C7   180.00  0.0  0
 KVQ  CONST_27  H6   C2   S3   C4   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
 KVQ  chir_01  C1'  C2'  O5'  C1   negativ
 KVQ  chir_02  C5'  O5'  C6'  C4'  positiv
 KVQ  chir_03  C4'  O4'  C5'  C3'  positiv
 KVQ  chir_04  C3'  O3'  C4'  C2'  negativ
 KVQ  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
 KVQ  plan-1  C4   0.020
 KVQ  plan-1  C6   0.020
 KVQ  plan-1  N5   0.020
 KVQ  plan-1  S3   0.020
 KVQ  plan-1  C2   0.020
 KVQ  plan-1  C1   0.020
 KVQ  plan-1  C1'  0.020
 KVQ  plan-1  H6   0.020
 KVQ  plan-2  C11  0.020
 KVQ  plan-2  C10  0.020
 KVQ  plan-2  C8   0.020
 KVQ  plan-2  C7   0.020
 KVQ  plan-2  C4   0.020
 KVQ  plan-2  C9   0.020
 KVQ  plan-2  C6   0.020
 KVQ  plan-2  H1   0.020
 KVQ  plan-2  H2   0.020
 KVQ  plan-2  H3   0.020
 KVQ  plan-2  H4   0.020
 KVQ  plan-2  H5   0.020

