# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 19:11:08 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-naphthalen-2-yl-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)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
 KVH  KVH  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-naphthalen-2-yl-1,3-thiazol-4-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_KVH
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
 KVH  C8   C  CR66  0   0.150  -4.7729  -0.0189   0.1315
 KVH  C7   C  CR16  0  -0.402  -3.5765  -0.7659   0.0908
 KVH  C9   C  CR66  0   0.105  -4.7057   1.3976   0.1172
 KVH  C10  C  CR16  0  -0.295  -3.4332   2.0154   0.0621
 KVH  C11  C  CR16  0  -0.288  -2.2908   1.2718   0.0218
 KVH  C12  C  CR16  0  -0.311  -6.0397  -0.6473   0.1844
 KVH  C13  C  CR16  0  -0.255  -7.1850   0.1001   0.2213
 KVH  C1   C  CR5   0   0.383   1.0677  -1.2808  -0.1111
 KVH  C14  C  CR16  0  -0.255  -7.1171   1.5094   0.2077
 KVH  C15  C  CR16  0  -0.306  -5.9047   2.1435   0.1572
 KVH  C6   C  CR6   0   0.096  -2.3515  -0.1460   0.0358
 KVH  C4   C  CR5   0   0.011  -1.1022  -0.9032  -0.0126
 KVH  C2   C  CR15  0  -0.575   0.6527  -2.5736  -0.0778
 KVH  N5   N  N     0  -0.405   0.0703  -0.3539  -0.0736
 KVH  S3   S  S2    0   0.242  -1.0552  -2.6378  -0.0001
 KVH  C1'  C  CH1   0  -0.041   2.4884  -0.8295  -0.1998
 KVH  O5'  O  O2    0  -0.495   2.7598  -0.0395   0.9349
 KVH  C5'  C  CH1   0  -0.014   4.1049   0.3842   1.0286
 KVH  C6'  C  CH2   0  -0.157   4.2626   1.1304   2.3357
 KVH  O6'  O  OH1   0  -0.671   4.0159   0.2426   3.3999
 KVH  C4'  C  CH1   0   0.037   4.4534   1.2579  -0.1774
 KVH  O4'  O  OH1   0  -0.673   5.8042   1.6340  -0.0818
 KVH  C3'  C  CH1   0  -0.032   4.1836   0.4748  -1.4572
 KVH  O3'  O  OH1   0  -0.678   4.4434   1.3151  -2.5640
 KVH  C2'  C  CH1   0   0.028   2.7425  -0.0194  -1.4717
 KVH  O2'  O  OH1   0  -0.670   2.4757  -0.8555  -2.5682
 KVH  H1   H  HCR6  0   0.254  -3.6565  -1.8477   0.1023
 KVH  H2   H  HCR6  0   0.260  -3.3739   3.0969   0.0516
 KVH  H3   H  HCR6  0   0.262  -1.3262   1.7583  -0.0223
 KVH  H4   H  HCR6  0   0.259  -6.0904  -1.7294   0.1942
 KVH  H5   H  HCR6  0   0.262  -8.1501  -0.3880   0.2612
 KVH  H6   H  HCR6  0   0.262  -8.0303   2.0892   0.2374
 KVH  H7   H  HCR6  0   0.259  -5.8512   3.2253   0.1476
 KVH  H8   H  HCR5  0   0.310   1.2535  -3.4695  -0.0960
 KVH  H9   H  HCH1  0   0.237   3.1417  -1.7167  -0.2161
 KVH  H10  H  HCH1  0   0.219   4.7748  -0.4919   1.0286
 KVH  H11  H  HCH2  0   0.212   5.2758   1.5429   2.3786
 KVH  H12  H  HCH2  0   0.196   3.5670   1.9811   2.3437
 KVH  H13  H  HOH1  0   0.457   4.1484   0.7230   4.2219
 KVH  H14  H  HCH1  0   0.210   3.7940   2.1414  -0.1640
 KVH  H15  H  HOH1  0   0.452   6.0205   2.1489  -0.8665
 KVH  H16  H  HCH1  0   0.225   4.8502  -0.3997  -1.4692
 KVH  H17  H  HOH1  0   0.463   4.9347   0.8209  -3.2251
 KVH  H18  H  HCH1  0   0.218   2.0705   0.8516  -1.4608
 KVH  H19  H  HOH1  0   0.454   2.5203  -0.3263  -3.3707

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
 KVH  O3'  C3'  single    1.414  0.020  1.414
 KVH  O4'  C4'  single    1.405  0.020  1.405
 KVH  C3'  C4'  single    1.525  0.020  1.525
 KVH  C3'  C2'  single    1.524  0.020  1.524
 KVH  C4'  C5'  single    1.529  0.020  1.529
 KVH  O2'  C2'  single    1.404  0.020  1.404
 KVH  C2'  C1'  single    1.529  0.020  1.529
 KVH  O6'  C6'  single    1.408  0.020  1.408
 KVH  C5'  C6'  single    1.513  0.020  1.513
 KVH  C5'  O5'  single    1.413  0.020  1.413
 KVH  C1'  O5'  single    1.409  0.020  1.409
 KVH  C1'  C1   single    1.493  0.020  1.493
 KVH  C2   C1   aromatic  1.358  0.020  1.358
 KVH  C2   S3   aromatic  1.711  0.020  1.711
 KVH  C1   N5   aromatic  1.362  0.020  1.362
 KVH  S3   C4   aromatic  1.735  0.020  1.735
 KVH  N5   C4   aromatic  1.296  0.020  1.296
 KVH  C4   C6   single    1.462  0.020  1.462
 KVH  C6   C7   aromatic  1.374  0.020  1.374
 KVH  C6   C11  aromatic  1.419  0.020  1.419
 KVH  C7   C8   aromatic  1.411  0.020  1.411
 KVH  C11  C10  aromatic  1.364  0.020  1.364
 KVH  C8   C12  aromatic  1.415  0.020  1.415
 KVH  C8   C9   aromatic  1.418  0.020  1.418
 KVH  C12  C13  aromatic  1.368  0.020  1.368
 KVH  C10  C9   aromatic  1.416  0.020  1.416
 KVH  C9   C15  aromatic  1.413  0.020  1.413
 KVH  C13  C14  aromatic  1.411  0.020  1.411
 KVH  C15  C14  aromatic  1.369  0.020  1.369
 KVH  C7   H1   single    0.930  0.020  1.080
 KVH  C10  H2   single    0.930  0.020  1.080
 KVH  C11  H3   single    0.930  0.020  1.080
 KVH  C12  H4   single    0.930  0.020  1.080
 KVH  C13  H5   single    0.930  0.020  1.080
 KVH  C14  H6   single    0.930  0.020  1.080
 KVH  C15  H7   single    0.930  0.020  1.080
 KVH  C2   H8   single    0.930  0.020  1.080
 KVH  C1'  H9   single    0.970  0.020  1.090
 KVH  C5'  H10  single    0.970  0.020  1.090
 KVH  C6'  H11  single    0.970  0.020  1.090
 KVH  C6'  H12  single    0.970  0.020  1.090
 KVH  O6'  H13  single    0.850  0.020  0.980
 KVH  C4'  H14  single    0.970  0.020  1.090
 KVH  O4'  H15  single    0.850  0.020  0.980
 KVH  C3'  H16  single    0.970  0.020  1.090
 KVH  O3'  H17  single    0.850  0.020  0.980
 KVH  C2'  H18  single    0.970  0.020  1.090
 KVH  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
 KVH  C12  C8   C9   119.10  3.000
 KVH  C9   C8   C7   119.23  3.000
 KVH  C12  C8   C7   121.67  3.000
 KVH  H1   C7   C6   121.08  3.000
 KVH  H1   C7   C8   117.71  3.000
 KVH  C6   C7   C8   121.21  3.000
 KVH  C15  C9   C10  122.25  3.000
 KVH  C15  C9   C8   119.14  3.000
 KVH  C10  C9   C8   118.61  3.000
 KVH  H2   C10  C11  119.89  3.000
 KVH  H2   C10  C9   119.03  3.000
 KVH  C11  C10  C9   121.08  3.000
 KVH  H3   C11  C6   119.22  3.000
 KVH  H3   C11  C10  120.21  3.000
 KVH  C6   C11  C10  120.57  3.000
 KVH  H4   C12  C13  120.41  3.000
 KVH  H4   C12  C8   119.07  3.000
 KVH  C13  C12  C8   120.52  3.000
 KVH  H5   C13  C14  119.59  3.000
 KVH  H5   C13  C12  120.07  3.000
 KVH  C14  C13  C12  120.34  3.000
 KVH  C1'  C1   N5   119.51  3.000
 KVH  N5   C1   C2   115.05  3.000
 KVH  C1'  C1   C2   125.44  3.000
 KVH  H6   C14  C15  120.01  3.000
 KVH  H6   C14  C13  119.62  3.000
 KVH  C15  C14  C13  120.37  3.000
 KVH  H7   C15  C14  120.45  3.000
 KVH  H7   C15  C9   119.02  3.000
 KVH  C14  C15  C9   120.53  3.000
 KVH  C4   C6   C11  118.73  3.000
 KVH  C11  C6   C7   119.30  3.000
 KVH  C4   C6   C7   121.97  3.000
 KVH  S3   C4   N5   113.55  3.000
 KVH  N5   C4   C6   123.72  3.000
 KVH  S3   C4   C6   122.74  3.000
 KVH  H8   C2   S3   121.71  3.000
 KVH  H8   C2   C1   128.31  3.000
 KVH  S3   C2   C1   109.99  3.000
 KVH  C4   N5   C1   112.04  3.000
 KVH  C2   S3   C4    89.38  3.000
 KVH  H9   C1'  C2'  108.41  3.000
 KVH  H9   C1'  O5'  110.43  3.000
 KVH  C2'  C1'  O5'  109.93  3.000
 KVH  H9   C1'  C1   108.76  3.000
 KVH  O5'  C1'  C1   107.75  3.000
 KVH  C2'  C1'  C1   111.57  3.000
 KVH  C5'  O5'  C1'  113.88  3.000
 KVH  H10  C5'  C4'  108.38  3.000
 KVH  H10  C5'  C6'  109.17  3.000
 KVH  C4'  C5'  C6'  112.07  3.000
 KVH  H10  C5'  O5'  109.87  3.000
 KVH  C6'  C5'  O5'  107.71  3.000
 KVH  C4'  C5'  O5'  109.62  3.000
 KVH  H12  C6'  H11  107.09  3.000
 KVH  H12  C6'  O6'  111.83  3.000
 KVH  H11  C6'  O6'  111.73  3.000
 KVH  H12  C6'  C5'  108.79  3.000
 KVH  H11  C6'  C5'  108.42  3.000
 KVH  O6'  C6'  C5'  108.89  3.000
 KVH  H13  O6'  C6'  107.89  3.000
 KVH  H14  C4'  C3'  108.42  3.000
 KVH  H14  C4'  O4'  111.08  3.000
 KVH  C3'  C4'  O4'  111.39  3.000
 KVH  H14  C4'  C5'  108.17  3.000
 KVH  C3'  C4'  C5'  109.16  3.000
 KVH  O4'  C4'  C5'  108.56  3.000
 KVH  H15  O4'  C4'  107.67  3.000
 KVH  H16  C3'  C2'  108.38  3.000
 KVH  H16  C3'  O3'  110.65  3.000
 KVH  C2'  C3'  O3'  111.05  3.000
 KVH  H16  C3'  C4'  108.08  3.000
 KVH  C2'  C3'  C4'  110.00  3.000
 KVH  O3'  C3'  C4'  108.63  3.000
 KVH  H17  O3'  C3'  109.08  3.000
 KVH  H18  C2'  O2'  111.29  3.000
 KVH  H18  C2'  C3'  108.71  3.000
 KVH  O2'  C2'  C3'  112.35  3.000
 KVH  H18  C2'  C1'  108.04  3.000
 KVH  O2'  C2'  C1'  107.60  3.000
 KVH  C3'  C2'  C1'  108.73  3.000
 KVH  H19  O2'  C2'  108.35  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
 KVH  CONST_01  C4   C6   C7   C8   180.00  0.0  0
 KVH  CONST_02  C11  C6   C7   C8     0.00  0.0  0
 KVH  CONST_03  C14  C13  C12  C8     0.00  0.0  0
 KVH  CONST_04  C11  C10  C9   C8     0.00  0.0  0
 KVH  CONST_05  C14  C15  C9   C8     0.00  0.0  0
 KVH  CONST_06  S3   C4   C6   C7     0.00  0.0  0
 KVH  CONST_07  N5   C4   C6   C7   180.00  0.0  0
 KVH  CONST_08  C10  C11  C6   C7     0.00  0.0  0
 KVH  CONST_09  C13  C12  C8   C7   180.00  0.0  0
 KVH  CONST_10  C10  C9   C8   C7     0.00  0.0  0
 KVH  CONST_11  C15  C9   C8   C7   180.00  0.0  0
 KVH  CONST_12  C6   C7   C8   C9     0.00  0.0  0
 KVH  CONST_13  C13  C12  C8   C9     0.00  0.0  0
 KVH  CONST_14  C6   C11  C10  C9     0.00  0.0  0
 KVH  CONST_15  C13  C14  C15  C9     0.00  0.0  0
 KVH  CONST_16  C4   C6   C11  C10  180.00  0.0  0
 KVH  CONST_17  C12  C8   C9   C10  180.00  0.0  0
 KVH  CONST_18  C14  C15  C9   C10  180.00  0.0  0
 KVH  CONST_19  S3   C4   C6   C11  180.00  0.0  0
 KVH  CONST_20  N5   C4   C6   C11    0.00  0.0  0
 KVH  CONST_21  C15  C9   C10  C11  180.00  0.0  0
 KVH  CONST_22  C6   C7   C8   C12  180.00  0.0  0
 KVH  CONST_23  C15  C9   C8   C12    0.00  0.0  0
 KVH  CONST_24  C15  C14  C13  C12    0.00  0.0  0
 KVH  CONST_25  C4   S3   C2   C1     0.00  0.0  0
 KVH  CONST_26  S3   C4   N5   C1     0.00  0.0  0
 KVH  CONST_27  C6   C4   N5   C1   180.00  0.0  0
 KVH  CONST_28  C2   S3   C4   C6   180.00  0.0  0
 KVH  CONST_29  C2   C1   N5   C4     0.00  0.0  0
 KVH  CONST_30  N5   C4   S3   C2     0.00  0.0  0
 KVH  CONST_31  S3   C2   C1   N5     0.00  0.0  0
 KVH  CONST_32  C1'  C1   N5   C4   180.00  0.0  0
 KVH  CONST_33  C1'  C1   C2   S3   180.00  0.0  0
 KVH  CONST_34  H5   C13  C12  C8   180.00  0.0  0
 KVH  CONST_35  H2   C10  C9   C8   180.00  0.0  0
 KVH  CONST_36  H7   C15  C9   C8   180.00  0.0  0
 KVH  CONST_37  H3   C11  C6   C7   180.00  0.0  0
 KVH  CONST_38  H4   C12  C8   C7     0.00  0.0  0
 KVH  CONST_39  H1   C7   C8   C9   180.00  0.0  0
 KVH  CONST_40  H6   C14  C15  C9   180.00  0.0  0
 KVH  CONST_41  H8   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
 KVH  chir_01  C1'  C2'  O5'  C1   negativ
 KVH  chir_02  C5'  O5'  C6'  C4'  positiv
 KVH  chir_03  C4'  O4'  C5'  C3'  positiv
 KVH  chir_04  C3'  O3'  C4'  C2'  negativ
 KVH  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
 KVH  plan-1  C1   0.020
 KVH  plan-1  C6   0.020
 KVH  plan-1  C4   0.020
 KVH  plan-1  C2   0.020
 KVH  plan-1  N5   0.020
 KVH  plan-1  S3   0.020
 KVH  plan-1  C1'  0.020
 KVH  plan-1  H8   0.020
 KVH  plan-2  C8   0.020
 KVH  plan-2  C7   0.020
 KVH  plan-2  C9   0.020
 KVH  plan-2  C10  0.020
 KVH  plan-2  C11  0.020
 KVH  plan-2  C12  0.020
 KVH  plan-2  C13  0.020
 KVH  plan-2  C14  0.020
 KVH  plan-2  C15  0.020
 KVH  plan-2  C6   0.020
 KVH  plan-2  C4   0.020
 KVH  plan-2  H1   0.020
 KVH  plan-2  H2   0.020
 KVH  plan-2  H3   0.020
 KVH  plan-2  H4   0.020
 KVH  plan-2  H5   0.020
 KVH  plan-2  H6   0.020
 KVH  plan-2  H7   0.020

