# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 10:57:42 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 4-azanyl-6-[[(1~{S})-1-(3-methyl-5-oxidanylidene-6-phenyl-[1,3]thiazolo[3,2-a]pyridin-7-yl)ethyl]amino]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ncnc(N)c1C#N)C2=C(C(=O)N3C(=CSC3=C2)C)c4ccccc4
#
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
 8TK  8TK  4-azanyl-6-[[(1~{S})-1-(3-methyl-5-oxidanylidene-6-phenyl-[1,3]thiazolo[3,2-a]pyridin-7-yl)ethyl]amino]pyrimidine-5-carbonitrile  ligand  47  29  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8TK
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
 8TK  C1   C  CH3   0  -0.696   5.2525  -0.1115  -1.7393
 8TK  C2   C  CR5   0   0.474   4.6358  -0.8511  -0.6017
 8TK  C3   C  CR15  0  -0.596   5.2315  -1.8756   0.0237
 8TK  N6   N  N     0  -0.640   3.3666  -0.5780  -0.0494
 8TK  C7   C  CR6   0   0.557   2.4959   0.4477  -0.4822
 8TK  C9   C  CR6   0  -0.266   1.2525   0.5301   0.2239
 8TK  C10  C  CR6   0   0.268   0.9324  -0.3296   1.2552
 8TK  C11  C  CR16  0  -0.485   1.8414  -1.3206   1.6491
 8TK  C12  C  CH1   0  -0.189  -0.4296  -0.2284   1.9257
 8TK  C14  C  CH3   0  -0.671  -0.5704  -1.0077   3.2245
 8TK  C16  C  CR6   0   0.617  -2.4860   0.0947   0.5951
 8TK  C20  C  CR16  0   0.090  -3.7589   1.9424   0.8495
 8TK  C27  C  CR16  0  -0.237  -1.3387   2.4264  -1.7608
 8TK  C30  C  CR16  0  -0.277   0.2293   2.7920   0.4931
 8TK  S4   S  S2    0   0.271   4.2843  -2.5513   1.3026
 8TK  C5   C  CR56  0   0.224   3.0309  -1.4109   0.9827
 8TK  O8   O  O     0  -0.477   2.8268   1.1902  -1.3974
 8TK  N15  N  NH1   0  -0.655  -1.4337  -0.6443   0.9607
 8TK  C17  C  CR6   0  -0.240  -3.3172  -0.2973  -0.4799
 8TK  C18  C  CR6   0   0.532  -4.3881   0.5564  -0.8188
 8TK  N19  N  N     0  -0.477  -4.5972   1.6901  -0.1367
 8TK  N21  N  N     0  -0.473  -2.7397   1.2191   1.2680
 8TK  N22  N  NH2   0  -0.822  -5.2186   0.2860  -1.8246
 8TK  C23  C  CSP   0   0.006  -3.0465  -1.4584  -1.2270
 8TK  N24  N  NS    0  -0.258  -2.8175  -2.4110  -1.8416
 8TK  C25  C  CR6   0   0.065   0.3333   1.6041  -0.2247
 8TK  C26  C  CR16  0  -0.286  -0.4509   1.4378  -1.3637
 8TK  C28  C  CR16  0  -0.261  -1.4432   3.6041  -1.0319
 8TK  C29  C  CR16  0  -0.237  -0.6520   3.7873   0.0927
 8TK  H1   H  HCH3  0   0.261   5.4148   0.9388  -1.5079
 8TK  H2   H  HCH3  0   0.251   6.2192  -0.5664  -1.9479
 8TK  H3   H  HCH3  0   0.261   4.6495  -0.1677  -2.6426
 8TK  H4   H  HCR5  0   0.322   6.2033  -2.2808  -0.2082
 8TK  H6   H  HCR6  0   0.286   1.6376  -2.0104   2.4537
 8TK  H7   H  HCH1  0   0.297  -0.6250   0.8218   2.1402
 8TK  H8   H  HCH3  0   0.233  -0.4876  -2.0843   3.0717
 8TK  H9   H  HCH3  0   0.242   0.1829  -0.7019   3.9506
 8TK  H10  H  HCH3  0   0.256  -1.5511  -0.8065   3.6532
 8TK  H11  H  HCR6  0   0.258  -3.9380   2.8634   1.3953
 8TK  H12  H  HCR6  0   0.250  -1.9554   2.2746  -2.6375
 8TK  H13  H  HCR6  0   0.246   0.8404   2.9359   1.3762
 8TK  H14  H  HNH1  0   0.404  -1.2584  -1.5097   0.4730
 8TK  H15  H  HNH2  0   0.414  -5.1708  -0.5654  -2.3572
 8TK  H16  H  HNH2  0   0.409  -5.9763   0.9176  -2.0203
 8TK  H17  H  HCR6  0   0.248  -0.3782   0.5217  -1.9379
 8TK  H18  H  HCR6  0   0.251  -2.1392   4.3737  -1.3399
 8TK  H19  H  HCR6  0   0.250  -0.7231   4.7037   0.6648

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
 8TK  C1   C2   single    1.490  0.020  1.490
 8TK  C3   C2   double    1.340  0.020  1.340
 8TK  C3   S4   single    1.729  0.020  1.729
 8TK  C2   N6   single    1.411  0.020  1.411
 8TK  S4   C5   single    1.724  0.020  1.724
 8TK  N6   C5   single    1.368  0.020  1.368
 8TK  N6   C7   single    1.413  0.020  1.413
 8TK  C5   C11  double    1.366  0.020  1.366
 8TK  O8   C7   double    1.224  0.020  1.224
 8TK  C7   C9   single    1.432  0.020  1.432
 8TK  C11  C10  single    1.401  0.020  1.401
 8TK  C9   C10  double    1.380  0.020  1.380
 8TK  C9   C25  single    1.483  0.020  1.483
 8TK  C10  C12  single    1.521  0.020  1.521
 8TK  C30  C25  aromatic  1.392  0.020  1.392
 8TK  C30  C29  aromatic  1.388  0.020  1.388
 8TK  C25  C26  aromatic  1.393  0.020  1.393
 8TK  C14  C12  single    1.521  0.020  1.521
 8TK  C29  C28  aromatic  1.387  0.020  1.387
 8TK  C12  N15  single    1.453  0.020  1.453
 8TK  C26  C27  aromatic  1.387  0.020  1.387
 8TK  N15  C16  single    1.337  0.020  1.337
 8TK  C28  C27  aromatic  1.389  0.020  1.389
 8TK  C16  N21  aromatic  1.335  0.020  1.335
 8TK  C16  C17  aromatic  1.414  0.020  1.414
 8TK  N24  C23  triple    1.157  0.020  1.157
 8TK  C23  C17  single    1.407  0.020  1.407
 8TK  N21  C20  aromatic  1.318  0.020  1.318
 8TK  C17  C18  aromatic  1.411  0.020  1.411
 8TK  C20  N19  aromatic  1.319  0.020  1.319
 8TK  C18  N19  aromatic  1.339  0.020  1.339
 8TK  C18  N22  single    1.332  0.020  1.332
 8TK  C1   H1   single    0.970  0.020  1.090
 8TK  C1   H2   single    0.970  0.020  1.090
 8TK  C1   H3   single    0.970  0.020  1.090
 8TK  C3   H4   single    0.930  0.020  1.080
 8TK  C11  H6   single    0.930  0.020  1.080
 8TK  C12  H7   single    0.970  0.020  1.090
 8TK  C14  H8   single    0.970  0.020  1.090
 8TK  C14  H9   single    0.970  0.020  1.090
 8TK  C14  H10  single    0.970  0.020  1.090
 8TK  C20  H11  single    0.930  0.020  1.080
 8TK  C27  H12  single    0.930  0.020  1.080
 8TK  C30  H13  single    0.930  0.020  1.080
 8TK  N15  H14  single    0.860  0.020  1.020
 8TK  N22  H15  single    0.860  0.020  1.020
 8TK  N22  H16  single    0.860  0.020  1.020
 8TK  C26  H17  single    0.930  0.020  1.080
 8TK  C28  H18  single    0.930  0.020  1.080
 8TK  C29  H19  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
 8TK  H3   C1   H2   108.16  3.000
 8TK  H3   C1   H1   108.01  3.000
 8TK  H2   C1   H1   108.17  3.000
 8TK  H3   C1   C2   112.26  3.000
 8TK  H2   C1   C2   107.84  3.000
 8TK  H1   C1   C2   112.25  3.000
 8TK  N6   C2   C3   111.42  3.000
 8TK  N6   C2   C1   125.10  3.000
 8TK  C3   C2   C1   123.48  3.000
 8TK  H4   C3   S4   120.40  3.000
 8TK  H4   C3   C2   125.99  3.000
 8TK  S4   C3   C2   113.60  3.000
 8TK  C5   N6   C7   121.45  3.000
 8TK  C7   N6   C2   125.08  3.000
 8TK  C5   N6   C2   113.47  3.000
 8TK  O8   C7   C9   124.64  3.000
 8TK  C9   C7   N6   115.19  3.000
 8TK  O8   C7   N6   120.17  3.000
 8TK  C25  C9   C10  122.23  3.000
 8TK  C25  C9   C7   115.50  3.000
 8TK  C10  C9   C7   122.26  3.000
 8TK  C12  C10  C11  120.26  3.000
 8TK  C12  C10  C9   119.69  3.000
 8TK  C11  C10  C9   120.01  3.000
 8TK  H6   C11  C5   119.06  3.000
 8TK  H6   C11  C10  122.62  3.000
 8TK  C5   C11  C10  118.32  3.000
 8TK  H7   C12  N15  106.42  3.000
 8TK  H7   C12  C14  108.00  3.000
 8TK  N15  C12  C14  110.87  3.000
 8TK  H7   C12  C10  108.15  3.000
 8TK  N15  C12  C10  107.87  3.000
 8TK  C14  C12  C10  115.15  3.000
 8TK  H10  C14  H9   107.95  3.000
 8TK  H10  C14  H8   107.81  3.000
 8TK  H9   C14  H8   108.53  3.000
 8TK  H10  C14  C12  108.96  3.000
 8TK  H9   C14  C12  111.16  3.000
 8TK  H8   C14  C12  112.28  3.000
 8TK  N21  C16  C17  120.33  3.000
 8TK  C17  C16  N15  121.15  3.000
 8TK  N21  C16  N15  118.52  3.000
 8TK  H11  C20  N21  115.69  3.000
 8TK  H11  C20  N19  115.69  3.000
 8TK  N21  C20  N19  128.61  3.000
 8TK  H12  C27  C28  120.07  3.000
 8TK  H12  C27  C26  119.78  3.000
 8TK  C28  C27  C26  120.15  3.000
 8TK  H13  C30  C29  119.86  3.000
 8TK  H13  C30  C25  119.44  3.000
 8TK  C29  C30  C25  120.70  3.000
 8TK  C5   S4   C3    90.15  3.000
 8TK  S4   C5   C11  125.87  3.000
 8TK  C11  C5   N6   122.77  3.000
 8TK  S4   C5   N6   111.36  3.000
 8TK  H14  N15  C16  118.61  3.000
 8TK  H14  N15  C12  116.52  3.000
 8TK  C16  N15  C12  124.55  3.000
 8TK  C23  C17  C18  121.19  3.000
 8TK  C18  C17  C16  117.45  3.000
 8TK  C23  C17  C16  121.28  3.000
 8TK  N22  C18  N19  117.32  3.000
 8TK  N22  C18  C17  122.12  3.000
 8TK  N19  C18  C17  120.55  3.000
 8TK  C18  N19  C20  116.33  3.000
 8TK  C20  N21  C16  116.69  3.000
 8TK  H16  N22  H15  117.68  3.000
 8TK  H16  N22  C18  119.28  3.000
 8TK  H15  N22  C18  122.84  3.000
 8TK  N24  C23  C17  180.00  3.000
 8TK  C26  C25  C30  118.79  3.000
 8TK  C26  C25  C9   120.65  3.000
 8TK  C30  C25  C9   120.56  3.000
 8TK  H17  C26  C25  119.77  3.000
 8TK  H17  C26  C27  119.60  3.000
 8TK  C25  C26  C27  120.63  3.000
 8TK  H18  C28  C29  120.24  3.000
 8TK  H18  C28  C27  120.13  3.000
 8TK  C29  C28  C27  119.64  3.000
 8TK  H19  C29  C28  120.18  3.000
 8TK  H19  C29  C30  119.74  3.000
 8TK  C28  C29  C30  120.08  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
 8TK  CONST_01  N19  C20  N21  C16     0.00   0.0  0
 8TK  CONST_02  N19  C18  C17  C16     0.00   0.0  0
 8TK  CONST_03  C17  C16  N21  C20     0.00   0.0  0
 8TK  CONST_04  C17  C18  N19  C20     0.00   0.0  0
 8TK  CONST_05  C30  C25  C26  C27     0.00   0.0  0
 8TK  CONST_06  C30  C29  C28  C27     0.00   0.0  0
 8TK  CONST_07  N21  C16  C17  C18     0.00   0.0  0
 8TK  CONST_08  N21  C20  N19  C18     0.00   0.0  0
 8TK  CONST_09  C28  C29  C30  C25     0.00   0.0  0
 8TK  CONST_10  C28  C27  C26  C25     0.00   0.0  0
 8TK  CONST_11  C29  C30  C25  C26     0.00   0.0  0
 8TK  CONST_12  C29  C28  C27  C26     0.00   0.0  0
 8TK  CONST_13  C29  C30  C25  C9    180.00   0.0  0
 8TK  CONST_14  C27  C26  C25  C9    180.00   0.0  0
 8TK  CONST_15  C9   C7   N6   C2    180.00   0.0  0
 8TK  CONST_16  C5   N6   C7   C9      0.00   0.0  0
 8TK  CONST_17  N22  C18  C17  C16   180.00   0.0  0
 8TK  CONST_18  N15  C16  N21  C20   180.00   0.0  0
 8TK  CONST_19  N22  C18  N19  C20   180.00   0.0  0
 8TK  CONST_20  C18  C17  C16  N15   180.00   0.0  0
 8TK  CONST_21  C23  C17  C18  N19   180.00   0.0  0
 8TK  CONST_22  C23  C17  C16  N21   180.00   0.0  0
 8TK  CONST_23  O8   C7   N6   C2      0.00   0.0  0
 8TK  CONST_24  O8   C7   N6   C5    180.00   0.0  0
 8TK  CONST_25  H13  C30  C25  C9      0.00   0.0  0
 8TK  CONST_26  H17  C26  C25  C9      0.00   0.0  0
 8TK  CONST_27  H11  C20  N21  C16   180.00   0.0  0
 8TK  CONST_28  H19  C29  C28  C27   180.00   0.0  0
 8TK  CONST_29  H18  C28  C29  C30   180.00   0.0  0
 8TK  CONST_30  H12  C27  C26  C25   180.00   0.0  0
 8TK  CONST_31  N21  C16  N15  C12     0.00   0.0  0
 8TK  CONST_32  C17  C16  N15  C12   180.00   0.0  0
 8TK  CONST_33  H14  N15  C16  C17     0.00   0.0  0
 8TK  CONST_34  H15  N22  C18  C17     0.00   0.0  0
 8TK  CONST_35  H16  N22  C18  C17   180.00   0.0  0
 8TK  Var_01    C30  C25  C9   C7   -101.08  30.0  2
 8TK  Var_02    H1   C1   C2   C3   -118.12  30.0  3

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
 8TK  chir_01  C12  C10  C14  N15  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
 8TK  plan-1  C16  0.020
 8TK  plan-1  C20  0.020
 8TK  plan-1  N15  0.020
 8TK  plan-1  C17  0.020
 8TK  plan-1  C18  0.020
 8TK  plan-1  N19  0.020
 8TK  plan-1  N21  0.020
 8TK  plan-1  N22  0.020
 8TK  plan-1  C23  0.020
 8TK  plan-1  N24  0.020
 8TK  plan-1  H11  0.020
 8TK  plan-2  C9   0.020
 8TK  plan-2  C27  0.020
 8TK  plan-2  C30  0.020
 8TK  plan-2  C25  0.020
 8TK  plan-2  C26  0.020
 8TK  plan-2  C28  0.020
 8TK  plan-2  C29  0.020
 8TK  plan-2  H12  0.020
 8TK  plan-2  H13  0.020
 8TK  plan-2  H17  0.020
 8TK  plan-2  H18  0.020
 8TK  plan-2  H19  0.020
 8TK  plan-3  C1   0.020
 8TK  plan-3  C2   0.020
 8TK  plan-3  C3   0.020
 8TK  plan-3  N6   0.020
 8TK  plan-3  C7   0.020
 8TK  plan-3  C9   0.020
 8TK  plan-3  C10  0.020
 8TK  plan-3  C11  0.020
 8TK  plan-3  C12  0.020
 8TK  plan-3  S4   0.020
 8TK  plan-3  C5   0.020
 8TK  plan-3  O8   0.020
 8TK  plan-3  C25  0.020
 8TK  plan-3  H4   0.020
 8TK  plan-3  H6   0.020
 8TK  plan-4  C12  0.020
 8TK  plan-4  C16  0.020
 8TK  plan-4  N15  0.020
 8TK  plan-4  H14  0.020
 8TK  plan-5  C18  0.020
 8TK  plan-5  N22  0.020
 8TK  plan-5  H15  0.020
 8TK  plan-5  H16  0.020

