# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:24:40 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-(5-benzyl-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCC(=O)Nc2sc(Cc3ccccc3)cn2)n1
#
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
 3TK  3TK  N-(5-benzyl-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide  ligand  43  25  .  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_3TK
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
 3TK  C     C  C     0   0.567   0.8588  -0.8978  -0.7697
 3TK  N     N  NH1   0  -0.710  -0.2364  -0.0798  -0.7373
 3TK  O     O  O     0  -0.421   0.8322  -2.0696  -1.0653
 3TK  S     S  S2    0   0.213  -2.8084   0.6975  -0.7071
 3TK  C1    C  CR5   0   0.299  -1.5316  -0.4306  -1.0541
 3TK  N1    N  N     0  -0.393  -1.9131  -1.5347  -1.5946
 3TK  S1    S  S2    0   0.074   3.4729  -1.3821  -0.3973
 3TK  C2    C  CR15  0  -0.047  -3.2713  -1.5387  -1.7672
 3TK  N2    N  N     0  -0.440   5.9641  -1.0559   0.1781
 3TK  C3    C  CR5   0  -0.172  -3.9432  -0.4332  -1.3672
 3TK  N3    N  N     0  -0.428   4.6536   0.9137   0.2922
 3TK  C4    C  CH2   0  -0.592  -5.4050  -0.1382  -1.4270
 3TK  C5    C  CR6   0   0.124  -5.9914   0.1458  -0.0660
 3TK  C6    C  CR16  0  -0.284  -6.1251  -0.8805   0.8666
 3TK  C7    C  CR16  0  -0.241  -6.6456  -0.6268   2.1266
 3TK  C8    C  CR16  0  -0.268  -7.0350   0.6623   2.4737
 3TK  C9    C  CR16  0  -0.239  -6.9016   1.6909   1.5522
 3TK  C10   C  CR16  0  -0.317  -6.3831   1.4319   0.2884
 3TK  C11   C  CH2   0  -0.706   2.1325  -0.1729  -0.3963
 3TK  C12   C  CR6   0   0.220   4.8319  -0.3743   0.0776
 3TK  C13   C  CR6   0   0.285   7.0435  -0.3681   0.5386
 3TK  C14   C  CH3   0  -0.721   8.3310  -1.1167   0.6432
 3TK  C15   C  CR16  0  -0.400   6.9645   0.9974   0.7931
 3TK  C16   C  CR6   0   0.301   5.7314   1.6148   0.6546
 3TK  C17   C  CH3   0  -0.720   5.5417   3.0756   0.8960
 3TK  HN    H  HNH1  0   0.437  -0.0849   0.8723  -0.4372
 3TK  H2    H  HCR5  0   0.273  -3.7463  -2.4033  -2.2102
 3TK  H4    H  HCH2  0   0.282  -5.5902   0.7072  -2.0941
 3TK  H4A   H  HCH2  0   0.282  -5.8972  -1.0039  -1.8764
 3TK  H6    H  HCR6  0   0.250  -5.8202  -1.8864   0.6012
 3TK  H7    H  HCR6  0   0.256  -6.7495  -1.4351   2.8390
 3TK  H8    H  HCR6  0   0.256  -7.4423   0.8622   3.4564
 3TK  H9    H  HCR6  0   0.256  -7.2019   2.6971   1.8145
 3TK  H10   H  HCR6  0   0.252  -6.2863   2.2391  -0.4282
 3TK  H11   H  HCH2  0   0.325   2.3309   0.6235  -1.1161
 3TK  H11A  H  HCH2  0   0.322   2.0362   0.2914   0.5867
 3TK  H14   H  HCH3  0   0.265   8.6875  -1.3886  -0.3519
 3TK  H14A  H  HCH3  0   0.252   9.1032  -0.5233   1.1278
 3TK  H14B  H  HCH3  0   0.260   8.1938  -2.0419   1.2022
 3TK  H15   H  HCR6  0   0.273   7.8397   1.5582   1.0901
 3TK  H17   H  HCH3  0   0.263   5.1938   3.5668  -0.0138
 3TK  H17A  H  HCH3  0   0.262   4.7828   3.2395   1.6617
 3TK  H17B  H  HCH3  0   0.252   6.4655   3.5543   1.2134

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
 3TK  N    C     single    1.367  0.020  1.367
 3TK  C    O     double    1.209  0.020  1.209
 3TK  C    C11   single    1.512  0.020  1.512
 3TK  C1   N     single    1.379  0.020  1.379
 3TK  N    HN    single    0.860  0.020  1.020
 3TK  C3   S     aromatic  1.733  0.020  1.733
 3TK  C1   S     aromatic  1.739  0.020  1.739
 3TK  N1   C1    aromatic  1.287  0.020  1.287
 3TK  C2   N1    aromatic  1.369  0.020  1.369
 3TK  C12  S1    single    1.757  0.020  1.757
 3TK  C11  S1    single    1.805  0.020  1.805
 3TK  C2   C3    aromatic  1.354  0.020  1.354
 3TK  C2   H2    single    0.930  0.020  1.080
 3TK  C13  N2    aromatic  1.330  0.020  1.330
 3TK  N2   C12   aromatic  1.325  0.020  1.325
 3TK  C4   C3    single    1.492  0.020  1.492
 3TK  C16  N3    aromatic  1.336  0.020  1.336
 3TK  C12  N3    aromatic  1.318  0.020  1.318
 3TK  C5   C4    single    1.509  0.020  1.509
 3TK  C4   H4    single    0.970  0.020  1.090
 3TK  C4   H4A   single    0.970  0.020  1.090
 3TK  C6   C5    aromatic  1.393  0.020  1.393
 3TK  C5   C10   aromatic  1.390  0.020  1.390
 3TK  C7   C6    aromatic  1.387  0.020  1.387
 3TK  C6   H6    single    0.930  0.020  1.080
 3TK  C7   C8    aromatic  1.391  0.020  1.391
 3TK  C7   H7    single    0.930  0.020  1.080
 3TK  C8   C9    aromatic  1.387  0.020  1.387
 3TK  C8   H8    single    0.930  0.020  1.080
 3TK  C9   C10   aromatic  1.390  0.020  1.390
 3TK  C9   H9    single    0.930  0.020  1.080
 3TK  C10  H10   single    0.930  0.020  1.080
 3TK  C11  H11   single    0.970  0.020  1.090
 3TK  C11  H11A  single    0.970  0.020  1.090
 3TK  C14  C13   single    1.493  0.020  1.493
 3TK  C13  C15   aromatic  1.391  0.020  1.391
 3TK  C14  H14   single    0.970  0.020  1.090
 3TK  C14  H14A  single    0.970  0.020  1.090
 3TK  C14  H14B  single    0.970  0.020  1.090
 3TK  C15  C16   aromatic  1.386  0.020  1.386
 3TK  C15  H15   single    0.930  0.020  1.080
 3TK  C16  C17   single    1.493  0.020  1.493
 3TK  C17  H17   single    0.970  0.020  1.090
 3TK  C17  H17A  single    0.970  0.020  1.090
 3TK  C17  H17B  single    0.970  0.020  1.090

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
 3TK  C11   C    O     122.93  3.000
 3TK  C11   C    N     112.45  3.000
 3TK  O     C    N     124.62  3.000
 3TK  HN    N    C1    116.69  3.000
 3TK  HN    N    C     116.81  3.000
 3TK  C1    N    C     126.50  3.000
 3TK  C3    S    C1     88.94  3.000
 3TK  N1    C1   S     115.00  3.000
 3TK  N1    C1   N     126.38  3.000
 3TK  S     C1   N     118.61  3.000
 3TK  C2    N1   C1    110.46  3.000
 3TK  C12   S1   C11   100.95  3.000
 3TK  H2    C2   C3    123.77  3.000
 3TK  H2    C2   N1    119.32  3.000
 3TK  C3    C2   N1    116.91  3.000
 3TK  C13   N2   C12   116.62  3.000
 3TK  C4    C3   C2    129.46  3.000
 3TK  C4    C3   S     121.86  3.000
 3TK  C2    C3   S     108.69  3.000
 3TK  C16   N3   C12   116.61  3.000
 3TK  H4A   C4   H4    106.59  3.000
 3TK  H4A   C4   C5    110.19  3.000
 3TK  H4    C4   C5    109.82  3.000
 3TK  H4A   C4   C3    107.53  3.000
 3TK  H4    C4   C3    110.08  3.000
 3TK  C5    C4   C3    112.44  3.000
 3TK  C10   C5   C6    118.93  3.000
 3TK  C10   C5   C4    120.90  3.000
 3TK  C6    C5   C4    120.16  3.000
 3TK  H6    C6   C7    119.86  3.000
 3TK  H6    C6   C5    119.51  3.000
 3TK  C7    C6   C5    120.63  3.000
 3TK  H7    C7   C8    120.07  3.000
 3TK  H7    C7   C6    119.83  3.000
 3TK  C8    C7   C6    120.10  3.000
 3TK  H8    C8   C9    120.16  3.000
 3TK  H8    C8   C7    120.21  3.000
 3TK  C9    C8   C7    119.63  3.000
 3TK  H9    C9   C10   119.80  3.000
 3TK  H9    C9   C8    120.10  3.000
 3TK  C10   C9   C8    120.10  3.000
 3TK  H10   C10  C9    119.71  3.000
 3TK  H10   C10  C5    119.68  3.000
 3TK  C9    C10  C5    120.61  3.000
 3TK  H11A  C11  H11   107.44  3.000
 3TK  H11A  C11  S1    110.55  3.000
 3TK  H11   C11  S1    110.69  3.000
 3TK  H11A  C11  C     110.61  3.000
 3TK  H11   C11  C     109.87  3.000
 3TK  S1    C11  C     107.70  3.000
 3TK  N3    C12  N2    127.29  3.000
 3TK  N3    C12  S1    119.99  3.000
 3TK  N2    C12  S1    112.72  3.000
 3TK  C15   C13  C14   121.89  3.000
 3TK  C15   C13  N2    120.74  3.000
 3TK  C14   C13  N2    117.37  3.000
 3TK  H14B  C14  H14A  108.91  3.000
 3TK  H14B  C14  H14   107.30  3.000
 3TK  H14A  C14  H14   108.07  3.000
 3TK  H14B  C14  C13   110.67  3.000
 3TK  H14A  C14  C13   111.71  3.000
 3TK  H14   C14  C13   110.04  3.000
 3TK  H15   C15  C16   121.11  3.000
 3TK  H15   C15  C13   120.90  3.000
 3TK  C16   C15  C13   118.00  3.000
 3TK  C17   C16  C15   122.20  3.000
 3TK  C17   C16  N3    117.06  3.000
 3TK  C15   C16  N3    120.74  3.000
 3TK  H17B  C17  H17A  108.65  3.000
 3TK  H17B  C17  H17   108.43  3.000
 3TK  H17A  C17  H17   107.22  3.000
 3TK  H17B  C17  C16   111.71  3.000
 3TK  H17A  C17  C16   110.43  3.000
 3TK  H17   C17  C16   110.27  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
 3TK  CONST_01  N1   C2   C3   S      0.00   0.0  0
 3TK  CONST_02  C2   N1   C1   S      0.00   0.0  0
 3TK  CONST_03  C2   C3   S    C1     0.00   0.0  0
 3TK  CONST_04  C3   C2   N1   C1     0.00   0.0  0
 3TK  CONST_05  C3   S    C1   N1     0.00   0.0  0
 3TK  CONST_06  C16  C15  C13  N2     0.00   0.0  0
 3TK  CONST_07  C16  N3   C12  N2     0.00   0.0  0
 3TK  CONST_08  C13  C15  C16  N3     0.00   0.0  0
 3TK  CONST_09  C13  N2   C12  N3     0.00   0.0  0
 3TK  CONST_10  C8   C7   C6   C5     0.00   0.0  0
 3TK  CONST_11  C8   C9   C10  C5     0.00   0.0  0
 3TK  CONST_12  C9   C10  C5   C6     0.00   0.0  0
 3TK  CONST_13  C9   C8   C7   C6     0.00   0.0  0
 3TK  CONST_14  C10  C5   C6   C7     0.00   0.0  0
 3TK  CONST_15  C10  C9   C8   C7     0.00   0.0  0
 3TK  CONST_16  C15  C13  N2   C12    0.00   0.0  0
 3TK  CONST_17  C15  C16  N3   C12    0.00   0.0  0
 3TK  CONST_18  C3   S    C1   N    180.00   0.0  0
 3TK  CONST_19  C2   N1   C1   N    180.00   0.0  0
 3TK  CONST_20  C4   C3   S    C1   180.00   0.0  0
 3TK  CONST_21  C4   C3   C2   N1   180.00   0.0  0
 3TK  CONST_22  C13  N2   C12  S1   180.00   0.0  0
 3TK  CONST_23  C16  N3   C12  S1   180.00   0.0  0
 3TK  CONST_24  C7   C6   C5   C4   180.00   0.0  0
 3TK  CONST_25  C9   C10  C5   C4   180.00   0.0  0
 3TK  CONST_26  C14  C13  N2   C12  180.00   0.0  0
 3TK  CONST_27  C17  C16  N3   C12  180.00   0.0  0
 3TK  CONST_28  C17  C16  C15  C13  180.00   0.0  0
 3TK  CONST_29  C16  C15  C13  C14  180.00   0.0  0
 3TK  CONST_30  H2   C2   C3   S    180.00   0.0  0
 3TK  CONST_31  H15  C15  C13  N2   180.00   0.0  0
 3TK  CONST_32  H7   C7   C6   C5   180.00   0.0  0
 3TK  CONST_33  H9   C9   C10  C5   180.00   0.0  0
 3TK  CONST_34  H10  C10  C5   C6   180.00   0.0  0
 3TK  CONST_35  H8   C8   C7   C6   180.00   0.0  0
 3TK  CONST_36  H6   C6   C7   C8   180.00   0.0  0
 3TK  CONST_37  S    C1   N    C    180.00   0.0  0
 3TK  CONST_38  N1   C1   N    C      0.00   0.0  0
 3TK  CONST_39  HN   N    C1   S      0.00   0.0  0
 3TK  CONST_40  C1   N    C    O      0.00   0.0  0
 3TK  CONST_41  C11  C    N    C1   180.00   0.0  0
 3TK  Var_01    C5   C4   C3   S    -58.23  30.0  2
 3TK  Var_02    C6   C5   C4   C3   -70.24  30.0  2
 3TK  Var_03    H14  C14  C13  N2    71.23  30.0  2
 3TK  Var_04    H17  C17  C16  N3   -61.01  30.0  2
 3TK  Var_05    H11  C11  S1   C12   60.82  30.0  1
 3TK  Var_06    S1   C11  C    N    177.13  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
 3TK  plan-1  N    0.020
 3TK  plan-1  S    0.020
 3TK  plan-1  C1   0.020
 3TK  plan-1  N1   0.020
 3TK  plan-1  C2   0.020
 3TK  plan-1  C3   0.020
 3TK  plan-1  C4   0.020
 3TK  plan-1  H2   0.020
 3TK  plan-2  C4   0.020
 3TK  plan-2  C5   0.020
 3TK  plan-2  C6   0.020
 3TK  plan-2  C7   0.020
 3TK  plan-2  C8   0.020
 3TK  plan-2  C9   0.020
 3TK  plan-2  C10  0.020
 3TK  plan-2  H6   0.020
 3TK  plan-2  H7   0.020
 3TK  plan-2  H8   0.020
 3TK  plan-2  H9   0.020
 3TK  plan-2  H10  0.020
 3TK  plan-3  S1   0.020
 3TK  plan-3  N2   0.020
 3TK  plan-3  N3   0.020
 3TK  plan-3  C12  0.020
 3TK  plan-3  C13  0.020
 3TK  plan-3  C14  0.020
 3TK  plan-3  C15  0.020
 3TK  plan-3  C16  0.020
 3TK  plan-3  C17  0.020
 3TK  plan-3  H15  0.020
 3TK  plan-4  C    0.020
 3TK  plan-4  N    0.020
 3TK  plan-4  O    0.020
 3TK  plan-4  C1   0.020
 3TK  plan-4  C11  0.020
 3TK  plan-4  HN   0.020

