# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 18:19:28 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 8-[3-chloranyl-5-[1-methyl-2,2-bis(oxidanylidene)-3~{H}-2,1-benzothiazol-5-yl]pyridin-4-yl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1c2ccc(cc2C[S]1(=O)=O)c3cncc(Cl)c3N4CCC5(CC4)CNC(=O)O5
#
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
 5Y6  5Y6  8-[3-chloranyl-5-[1-methyl-2,2-bis(oxidanylidene)-3~{H}-2,1-benzothiazol-5-yl]pyridin-4-yl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one  ligand  51  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5Y6
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
 5Y6  C2   C   CR5   0   0.663   3.2245  -3.7794  -0.1192
 5Y6  C4   C   CH2   0  -0.273   3.9305  -1.7335   0.7241
 5Y6  C5   C   CR5   0   0.204   2.6098  -1.5646  -0.0668
 5Y6  C6   C   CH2   0  -0.457   1.4870  -0.9883   0.7812
 5Y6  C7   C   CH2   0  -0.329   1.7136   0.4932   1.0436
 5Y6  C11  C   CR6   0   0.498   1.3654   2.4694  -0.3519
 5Y6  C12  C   CR6   0  -0.191   2.0977   3.6562  -0.4653
 5Y6  C16  C   CR16  0  -0.092  -0.5797   3.8841  -0.4963
 5Y6  C17  C   CR6   0  -0.072  -0.0360   2.6124  -0.3862
 5Y6  C18  C   CR6   0   0.028  -0.9328   1.4369  -0.3663
 5Y6  C19  C   CR16  0  -0.326  -1.8389   1.2465   0.6769
 5Y6  C21  C   CH2   0  -0.638  -3.6650  -0.2393   1.7196
 5Y6  C27  C   CR56  0   0.457  -2.6401  -0.7561  -0.3948
 5Y6  O1   O   O     0  -0.498   3.1401  -4.9587  -0.3727
 5Y6  N3   N   NR15  0  -0.657   4.2269  -3.1197   0.4815
 5Y6  N8   N   NT    0  -0.515   1.9272   1.2173  -0.1938
 5Y6  C9   C   CH2   0  -0.324   3.0222   0.7339  -1.0058
 5Y6  C10  C   CH2   0  -0.448   2.7961  -0.7398  -1.3350
 5Y6  CL   CL  CL    0  -0.101   3.8207   3.6657  -0.3347
 5Y6  C14  C   CR16  0  -0.049   1.4521   4.8761  -0.6069
 5Y6  N15  N   N     0  -0.406   0.1358   4.9959  -0.6121
 5Y6  C20  C   CR56  0  -0.015  -2.6761   0.1493   0.6669
 5Y6  S22  S   S     0   1.362  -4.7366  -1.3971   0.8535
 5Y6  O23  O   OS    0  -0.648  -5.0758  -2.5683   1.6406
 5Y6  O24  O   OS    0  -0.649  -5.8229  -0.6927   0.1910
 5Y6  N25  N   NR5   0  -0.703  -3.5364  -1.8139  -0.2528
 5Y6  C26  C   CH3   0  -0.550  -3.8903  -2.6786  -1.3624
 5Y6  C28  C   CR16  0  -0.311  -1.7685  -0.5664  -1.4560
 5Y6  C29  C   CR16  0  -0.270  -0.9127   0.5254  -1.4196
 5Y6  O30  O   O     0  -0.481   2.2544  -2.9088  -0.4416
 5Y6  H1   H   HCH2  0   0.260   4.7234  -1.0827   0.3517
 5Y6  H2   H   HCH2  0   0.259   3.7987  -1.5273   1.7898
 5Y6  H3   H   HCH2  0   0.259   0.5361  -1.1181   0.2610
 5Y6  H4   H   HCH2  0   0.254   1.4228  -1.5222   1.7324
 5Y6  H5   H   HCH2  0   0.273   0.8508   0.9044   1.5655
 5Y6  H6   H   HCH2  0   0.244   2.5734   0.6336   1.7153
 5Y6  H7   H   HCR6  0   0.267  -1.6586   3.9969  -0.5227
 5Y6  H8   H   HCR6  0   0.268  -1.8749   1.9468   1.5025
 5Y6  H9   H   HCH2  0   0.334  -3.2037  -0.7782   2.5494
 5Y6  H10  H   HCH2  0   0.333  -4.2695   0.5799   2.1066
 5Y6  H11  H   HNR5  0   0.414   5.0032  -3.6033   0.9010
 5Y6  H12  H   HCH2  0   0.268   3.0639   1.3004  -1.9355
 5Y6  H13  H   HCH2  0   0.227   3.9948   0.8599  -0.5136
 5Y6  H14  H   HCH2  0   0.254   3.6499  -1.1167  -1.9044
 5Y6  H15  H   HCH2  0   0.250   1.9074  -0.8379  -1.9632
 5Y6  H16  H   HCR6  0   0.283   2.0365   5.7857  -0.6938
 5Y6  H17  H   HCH3  0   0.275  -2.9916  -3.1743  -1.7236
 5Y6  H18  H   HCH3  0   0.273  -4.5712  -3.4535  -1.0167
 5Y6  H19  H   HCH3  0   0.256  -4.3541  -2.1328  -2.1856
 5Y6  H20  H   HCR6  0   0.282  -1.7388  -1.2508  -2.2931
 5Y6  H21  H   HCR6  0   0.260  -0.2221   0.6755  -2.2395

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
 5Y6  O1   C2   double    1.209  0.020  1.209
 5Y6  C2   O30  single    1.343  0.020  1.343
 5Y6  C2   N3   single    1.342  0.020  1.342
 5Y6  O30  C5   single    1.440  0.020  1.440
 5Y6  CL   C12  single    1.728  0.020  1.728
 5Y6  C6   C5   single    1.521  0.020  1.521
 5Y6  C6   C7   single    1.521  0.020  1.521
 5Y6  N3   C4   single    1.438  0.020  1.438
 5Y6  C5   C4   single    1.549  0.020  1.549
 5Y6  C5   C10  single    1.524  0.020  1.524
 5Y6  C7   N8   single    1.450  0.020  1.450
 5Y6  C12  C14  aromatic  1.387  0.020  1.387
 5Y6  C12  C11  aromatic  1.399  0.020  1.399
 5Y6  C10  C9   single    1.527  0.020  1.527
 5Y6  N8   C11  single    1.381  0.020  1.381
 5Y6  N8   C9   single    1.446  0.020  1.446
 5Y6  C14  N15  aromatic  1.322  0.020  1.322
 5Y6  C11  C17  aromatic  1.409  0.020  1.409
 5Y6  N15  C16  aromatic  1.327  0.020  1.327
 5Y6  C17  C16  aromatic  1.387  0.020  1.387
 5Y6  C17  C18  single    1.479  0.020  1.479
 5Y6  C19  C18  aromatic  1.395  0.020  1.395
 5Y6  C19  C20  aromatic  1.380  0.020  1.380
 5Y6  C18  C29  aromatic  1.393  0.020  1.393
 5Y6  C21  C20  single    1.496  0.020  1.496
 5Y6  C21  S22  single    1.800  0.020  1.800
 5Y6  C20  C27  aromatic  1.396  0.020  1.396
 5Y6  C29  C28  aromatic  1.388  0.020  1.388
 5Y6  O24  S22  double    1.454  0.020  1.454
 5Y6  S22  O23  double    1.451  0.020  1.451
 5Y6  S22  N25  single    1.685  0.020  1.685
 5Y6  C27  C28  aromatic  1.386  0.020  1.386
 5Y6  C27  N25  single    1.394  0.020  1.394
 5Y6  N25  C26  single    1.451  0.020  1.451
 5Y6  C4   H1   single    0.970  0.020  1.090
 5Y6  C4   H2   single    0.970  0.020  1.090
 5Y6  C6   H3   single    0.970  0.020  1.090
 5Y6  C6   H4   single    0.970  0.020  1.090
 5Y6  C7   H5   single    0.970  0.020  1.090
 5Y6  C7   H6   single    0.970  0.020  1.090
 5Y6  C16  H7   single    0.930  0.020  1.080
 5Y6  C19  H8   single    0.930  0.020  1.080
 5Y6  C21  H9   single    0.970  0.020  1.090
 5Y6  C21  H10  single    0.970  0.020  1.090
 5Y6  N3   H11  single    0.860  0.020  1.020
 5Y6  C9   H12  single    0.970  0.020  1.090
 5Y6  C9   H13  single    0.970  0.020  1.090
 5Y6  C10  H14  single    0.970  0.020  1.090
 5Y6  C10  H15  single    0.970  0.020  1.090
 5Y6  C14  H16  single    0.930  0.020  1.080
 5Y6  C26  H17  single    0.970  0.020  1.090
 5Y6  C26  H18  single    0.970  0.020  1.090
 5Y6  C26  H19  single    0.970  0.020  1.090
 5Y6  C28  H20  single    0.930  0.020  1.080
 5Y6  C29  H21  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
 5Y6  O30  C2   N3   109.17  3.000
 5Y6  N3   C2   O1   128.71  3.000
 5Y6  O30  C2   O1   122.11  3.000
 5Y6  H2   C4   H1   107.92  3.000
 5Y6  H2   C4   N3   111.78  3.000
 5Y6  H1   C4   N3   111.56  3.000
 5Y6  H2   C4   C5   111.99  3.000
 5Y6  H1   C4   C5   112.36  3.000
 5Y6  N3   C4   C5   101.23  3.000
 5Y6  O30  C5   C10  108.59  3.000
 5Y6  C10  C5   C6   110.43  3.000
 5Y6  O30  C5   C6   108.47  3.000
 5Y6  C10  C5   C4   112.32  3.000
 5Y6  C6   C5   C4   112.72  3.000
 5Y6  O30  C5   C4   103.98  3.000
 5Y6  H4   C6   H3   107.79  3.000
 5Y6  H4   C6   C7   109.53  3.000
 5Y6  H3   C6   C7   109.13  3.000
 5Y6  H4   C6   C5   110.10  3.000
 5Y6  H3   C6   C5   109.41  3.000
 5Y6  C7   C6   C5   110.81  3.000
 5Y6  H6   C7   H5   106.16  3.000
 5Y6  H6   C7   N8   110.02  3.000
 5Y6  H5   C7   N8   109.71  3.000
 5Y6  H6   C7   C6   110.25  3.000
 5Y6  H5   C7   C6   109.41  3.000
 5Y6  N8   C7   C6   111.17  3.000
 5Y6  N8   C11  C17  119.95  3.000
 5Y6  C17  C11  C12  115.63  3.000
 5Y6  N8   C11  C12  124.42  3.000
 5Y6  C14  C12  CL   117.83  3.000
 5Y6  C14  C12  C11  120.70  3.000
 5Y6  CL   C12  C11  121.36  3.000
 5Y6  H7   C16  N15  116.54  3.000
 5Y6  H7   C16  C17  119.13  3.000
 5Y6  N15  C16  C17  124.30  3.000
 5Y6  C18  C17  C16  119.47  3.000
 5Y6  C18  C17  C11  121.48  3.000
 5Y6  C16  C17  C11  118.99  3.000
 5Y6  C29  C18  C19  119.05  3.000
 5Y6  C29  C18  C17  120.08  3.000
 5Y6  C19  C18  C17  120.83  3.000
 5Y6  H8   C19  C20  119.95  3.000
 5Y6  H8   C19  C18  120.23  3.000
 5Y6  C20  C19  C18  119.81  3.000
 5Y6  H10  C21  H9   109.61  3.000
 5Y6  H10  C21  S22  108.93  3.000
 5Y6  H9   C21  S22  107.44  3.000
 5Y6  H10  C21  C20  114.94  3.000
 5Y6  H9   C21  C20  112.57  3.000
 5Y6  S22  C21  C20  102.83  3.000
 5Y6  C28  C27  N25  125.88  3.000
 5Y6  N25  C27  C20  113.47  3.000
 5Y6  C28  C27  C20  120.65  3.000
 5Y6  H11  N3   C4   123.50  3.000
 5Y6  H11  N3   C2   121.78  3.000
 5Y6  C4   N3   C2   113.29  3.000
 5Y6  C9   N8   C11  123.13  3.000
 5Y6  C9   N8   C7   115.08  3.000
 5Y6  C11  N8   C7   119.38  3.000
 5Y6  H13  C9   H12  106.81  3.000
 5Y6  H13  C9   C10  109.80  3.000
 5Y6  H12  C9   C10  108.88  3.000
 5Y6  H13  C9   N8   112.39  3.000
 5Y6  H12  C9   N8   109.53  3.000
 5Y6  C10  C9   N8   109.35  3.000
 5Y6  H15  C10  H14  107.75  3.000
 5Y6  H15  C10  C9   109.33  3.000
 5Y6  H14  C10  C9   109.23  3.000
 5Y6  H15  C10  C5   109.29  3.000
 5Y6  H14  C10  C5   110.01  3.000
 5Y6  C9   C10  C5   111.16  3.000
 5Y6  H16  C14  N15  117.41  3.000
 5Y6  H16  C14  C12  119.65  3.000
 5Y6  N15  C14  C12  122.92  3.000
 5Y6  C14  N15  C16  117.43  3.000
 5Y6  C27  C20  C21  112.58  3.000
 5Y6  C27  C20  C19  120.37  3.000
 5Y6  C21  C20  C19  127.05  3.000
 5Y6  N25  S22  O24  110.66  3.000
 5Y6  N25  S22  O23  108.84  3.000
 5Y6  O24  S22  O23  117.60  3.000
 5Y6  N25  S22  C21   92.92  3.000
 5Y6  O23  S22  C21  113.41  3.000
 5Y6  O24  S22  C21  110.63  3.000
 5Y6  C26  N25  S22  118.43  3.000
 5Y6  C26  N25  C27  122.10  3.000
 5Y6  S22  N25  C27  109.71  3.000
 5Y6  H19  C26  H18  109.27  3.000
 5Y6  H19  C26  H17  109.17  3.000
 5Y6  H18  C26  H17  107.34  3.000
 5Y6  H19  C26  N25  112.49  3.000
 5Y6  H18  C26  N25  109.52  3.000
 5Y6  H17  C26  N25  108.91  3.000
 5Y6  H20  C28  C29  120.08  3.000
 5Y6  H20  C28  C27  121.54  3.000
 5Y6  C29  C28  C27  118.38  3.000
 5Y6  H21  C29  C28  118.86  3.000
 5Y6  H21  C29  C18  119.42  3.000
 5Y6  C28  C29  C18  121.72  3.000
 5Y6  C5   O30  C2   111.37  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
 5Y6  CONST_01  N15  C14  C12  C11     0.00   0.0  0
 5Y6  CONST_02  N15  C16  C17  C11     0.00   0.0  0
 5Y6  CONST_05  C16  N15  C14  C12     0.00   0.0  0
 5Y6  CONST_06  C16  C17  C11  C12     0.00   0.0  0
 5Y6  CONST_07  C18  C17  C11  C12   180.00   0.0  0
 5Y6  CONST_10  C14  C12  C11  C17     0.00   0.0  0
 5Y6  CONST_11  C14  N15  C16  C17     0.00   0.0  0
 5Y6  CONST_12  C20  C19  C18  C17   180.00   0.0  0
 5Y6  CONST_13  C28  C29  C18  C17   180.00   0.0  0
 5Y6  CONST_14  N15  C16  C17  C18   180.00   0.0  0
 5Y6  CONST_15  C27  C20  C19  C18     0.00   0.0  0
 5Y6  CONST_16  C27  C28  C29  C18     0.00   0.0  0
 5Y6  CONST_17  C28  C29  C18  C19     0.00   0.0  0
 5Y6  CONST_18  C28  C27  C20  C19     0.00   0.0  0
 5Y6  CONST_19  C29  C18  C19  C20     0.00   0.0  0
 5Y6  CONST_20  C29  C28  C27  C20     0.00   0.0  0
 5Y6  CONST_21  N8   C11  C17  C16   180.00   0.0  0
 5Y6  CONST_22  N8   C11  C17  C18     0.00   0.0  0
 5Y6  CONST_23  C14  C12  C11  N8    180.00   0.0  0
 5Y6  CONST_24  CL   C12  C11  C17   180.00   0.0  0
 5Y6  CONST_25  CL   C12  C11  N8      0.00   0.0  0
 5Y6  CONST_26  N15  C14  C12  CL    180.00   0.0  0
 5Y6  CONST_27  H16  C14  C12  C11   180.00   0.0  0
 5Y6  CONST_28  H7   C16  C17  C11   180.00   0.0  0
 5Y6  CONST_29  H8   C19  C18  C17     0.00   0.0  0
 5Y6  CONST_30  H21  C29  C18  C17     0.00   0.0  0
 5Y6  CONST_31  H20  C28  C29  C18   180.00   0.0  0
 5Y6  Var_01    C6   C5   O30  C2   -126.86  30.0  3
 5Y6  Var_02    C5   C4   N3   C2     -9.33  30.0  1
 5Y6  Var_03    O30  C2   N3   C4      5.75  30.0  1
 5Y6  Var_04    C7   C6   C5   C4     73.41  30.0  1
 5Y6  Var_05    C9   C10  C5   C4    -71.88  30.0  1
 5Y6  Var_06    N3   C2   O30  C5      1.08  30.0  1
 5Y6  Var_07    N8   C7   C6   C5     53.06  30.0  1
 5Y6  Var_08    N8   C9   C10  C5    -55.49  30.0  1
 5Y6  Var_09    N3   C4   C5   C6    126.36  30.0  3
 5Y6  Var_10    C11  N8   C7   C6    140.28  30.0  1
 5Y6  Var_11    C12  C11  N8   C7    114.03  30.0  2
 5Y6  Var_12    C10  C9   N8   C7     57.40  30.0  1
 5Y6  Var_13    S22  C21  C20  C19   162.52  30.0  1
 5Y6  Var_14    C27  N25  S22  C21   -26.77  30.0  1
 5Y6  Var_15    N25  S22  C21  C20    25.31  30.0  1
 5Y6  Var_16    S22  N25  C27  C20    19.76  30.0  1
 5Y6  Var_17    H17  C26  N25  C27    60.76  30.0  3

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
 5Y6  plan-1  C2   0.020
 5Y6  plan-1  C4   0.020
 5Y6  plan-1  N3   0.020
 5Y6  plan-1  H11  0.020
 5Y6  plan-2  C17  0.020
 5Y6  plan-2  C18  0.020
 5Y6  plan-2  C19  0.020
 5Y6  plan-2  C21  0.020
 5Y6  plan-2  C27  0.020
 5Y6  plan-2  C20  0.020
 5Y6  plan-2  N25  0.020
 5Y6  plan-2  C28  0.020
 5Y6  plan-2  C29  0.020
 5Y6  plan-2  H8   0.020
 5Y6  plan-2  H20  0.020
 5Y6  plan-2  H21  0.020
 5Y6  plan-3  C11  0.020
 5Y6  plan-3  C12  0.020
 5Y6  plan-3  C16  0.020
 5Y6  plan-3  C17  0.020
 5Y6  plan-3  C18  0.020
 5Y6  plan-3  N8   0.020
 5Y6  plan-3  CL   0.020
 5Y6  plan-3  C14  0.020
 5Y6  plan-3  N15  0.020
 5Y6  plan-3  H7   0.020
 5Y6  plan-3  H16  0.020
 5Y6  plan-4  C27  0.020
 5Y6  plan-4  S22  0.020
 5Y6  plan-4  N25  0.020
 5Y6  plan-4  C26  0.020
 5Y6  plan-5  C2   0.020
 5Y6  plan-5  O1   0.020
 5Y6  plan-5  N3   0.020
 5Y6  plan-5  O30  0.020

