# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:24:58 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCC(=O)Nc2sc(Cc3cccc4ccccc34)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
 3TE  3TE  2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide  ligand  49  29  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3TE
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
 3TE  C1   C  CR5   0   0.305   0.6941  -1.2277   0.7238
 3TE  C2   C  CR15  0  -0.044   2.3101  -2.6442   1.1003
 3TE  C3   C  CR5   0  -0.159   3.0743  -1.5265   1.1318
 3TE  C4   C  CH2   0  -0.636   4.5497  -1.4191   1.3447
 3TE  C5   C  CR6   0   0.118   5.2615  -0.8092   0.1611
 3TE  C6   C  CR66  0   0.078   5.4433   0.5989   0.0470
 3TE  S    S  S2    0   0.202   2.0554  -0.1523   0.8497
 3TE  N1   N  N     0  -0.394   0.9711  -2.4757   0.8723
 3TE  C7   C  CR16  0  -0.336   5.0277   1.5137   1.0468
 3TE  C8   C  CR16  0  -0.249   5.2093   2.8618   0.8938
 3TE  N2   N  N     0  -0.440  -6.8638  -0.7072  -0.0439
 3TE  C9   C  CR16  0  -0.259   5.8208   3.3740  -0.2676
 3TE  C10  C  CR16  0  -0.311   6.2425   2.5195  -1.2483
 3TE  O    O  O     0  -0.420  -1.8367  -2.5733   0.4500
 3TE  C    C  C     0   0.566  -1.7269  -1.3736   0.3525
 3TE  C15  C  CH2   0  -0.706  -2.8982  -0.4626   0.0597
 3TE  S1   S  S2    0   0.075  -4.4038  -1.4545   0.1609
 3TE  C16  C  CR6   0   0.219  -5.6312  -0.2263  -0.1098
 3TE  N3   N  N     0  -0.429  -5.2722   1.0202  -0.3459
 3TE  C20  C  CR6   0   0.302  -6.2572   1.9017  -0.5330
 3TE  C21  C  CH3   0  -0.720  -5.8611   3.3124  -0.8179
 3TE  C19  C  CR16  0  -0.400  -7.5842   1.5041  -0.4766
 3TE  C17  C  CR6   0   0.285  -7.8537   0.1625  -0.2278
 3TE  C18  C  CH3   0  -0.720  -9.2491  -0.3627  -0.1485
 3TE  N    N  NH1   0  -0.710  -0.5509  -0.6875   0.4827
 3TE  C14  C  CR16  0  -0.316   5.7034  -1.6279  -0.8466
 3TE  C13  C  CR16  0  -0.244   6.3288  -1.1103  -1.9973
 3TE  C12  C  CR16  0  -0.332   6.5037   0.2378  -2.1339
 3TE  C11  C  CR66  0   0.117   6.0676   1.1213  -1.1198
 3TE  H1   H  HCR5  0   0.272   2.7005  -3.6425   1.2436
 3TE  H2   H  HCH2  0   0.286   4.7657  -0.8735   2.2656
 3TE  H3   H  HCH2  0   0.295   4.9225  -2.4319   1.5068
 3TE  H4   H  HCR6  0   0.251   4.5707   1.1535   1.9590
 3TE  H5   H  HCR6  0   0.261   4.8853   3.5393   1.6730
 3TE  H6   H  HCR6  0   0.259   5.9591   4.4416  -0.3774
 3TE  H7   H  HCR6  0   0.257   6.7180   2.9041  -2.1424
 3TE  H8   H  HCH2  0   0.319  -2.9361   0.3634   0.7711
 3TE  H9   H  HCH2  0   0.327  -2.7888  -0.0301  -0.9371
 3TE  H10  H  HCH3  0   0.265  -5.4100   3.3799  -1.8094
 3TE  H11  H  HCH3  0   0.252  -6.7151   3.9851  -0.7867
 3TE  H12  H  HCH3  0   0.260  -5.1155   3.6548  -0.1007
 3TE  H13  H  HCR6  0   0.273  -8.3853   2.2156  -0.6194
 3TE  H14  H  HCH3  0   0.263  -9.4347  -0.7939   0.8360
 3TE  H15  H  HCH3  0   0.251  -9.9843   0.4189  -0.3267
 3TE  H16  H  HCH3  0   0.262  -9.3999  -1.1561  -0.8813
 3TE  H17  H  HNH1  0   0.437  -0.5988   0.3170   0.3925
 3TE  H18  H  HCR6  0   0.253   5.5636  -2.6991  -0.7594
 3TE  H19  H  HCR6  0   0.258   6.6650  -1.7873  -2.7717
 3TE  H20  H  HCR6  0   0.256   6.9766   0.6462  -3.0188

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
 3TE  S1   C16  single    1.757  0.020  1.757
 3TE  S1   C15  single    1.806  0.020  1.806
 3TE  N2   C16  aromatic  1.325  0.020  1.325
 3TE  N2   C17  aromatic  1.330  0.020  1.330
 3TE  C18  C17  single    1.493  0.020  1.493
 3TE  C8   C9   aromatic  1.409  0.020  1.409
 3TE  C8   C7   aromatic  1.369  0.020  1.369
 3TE  C16  N3   aromatic  1.319  0.020  1.319
 3TE  C9   C10  aromatic  1.367  0.020  1.367
 3TE  C17  C19  aromatic  1.391  0.020  1.391
 3TE  C15  C    single    1.512  0.020  1.512
 3TE  O    C    double    1.209  0.020  1.209
 3TE  C    N    single    1.368  0.020  1.368
 3TE  C7   C6   aromatic  1.417  0.020  1.417
 3TE  N3   C20  aromatic  1.335  0.020  1.335
 3TE  C10  C11  aromatic  1.415  0.020  1.415
 3TE  C19  C20  aromatic  1.386  0.020  1.386
 3TE  N    C1   single    1.378  0.020  1.378
 3TE  C20  C21  single    1.493  0.020  1.493
 3TE  S    C1   aromatic  1.739  0.020  1.739
 3TE  S    C3   aromatic  1.734  0.020  1.734
 3TE  C1   N1   aromatic  1.287  0.020  1.287
 3TE  C6   C11  aromatic  1.423  0.020  1.423
 3TE  C6   C5   aromatic  1.424  0.020  1.424
 3TE  C11  C12  aromatic  1.414  0.020  1.414
 3TE  N1   C2   aromatic  1.369  0.020  1.369
 3TE  C3   C2   aromatic  1.354  0.020  1.354
 3TE  C3   C4   single    1.494  0.020  1.494
 3TE  C4   C5   single    1.510  0.020  1.510
 3TE  C5   C14  aromatic  1.372  0.020  1.372
 3TE  C12  C13  aromatic  1.366  0.020  1.366
 3TE  C14  C13  aromatic  1.408  0.020  1.408
 3TE  C2   H1   single    0.930  0.020  1.080
 3TE  C4   H2   single    0.970  0.020  1.090
 3TE  C4   H3   single    0.970  0.020  1.090
 3TE  C7   H4   single    0.930  0.020  1.080
 3TE  C8   H5   single    0.930  0.020  1.080
 3TE  C9   H6   single    0.930  0.020  1.080
 3TE  C10  H7   single    0.930  0.020  1.080
 3TE  C15  H8   single    0.970  0.020  1.090
 3TE  C15  H9   single    0.970  0.020  1.090
 3TE  C21  H10  single    0.970  0.020  1.090
 3TE  C21  H11  single    0.970  0.020  1.090
 3TE  C21  H12  single    0.970  0.020  1.090
 3TE  C19  H13  single    0.930  0.020  1.080
 3TE  C18  H14  single    0.970  0.020  1.090
 3TE  C18  H15  single    0.970  0.020  1.090
 3TE  C18  H16  single    0.970  0.020  1.090
 3TE  N    H17  single    0.860  0.020  1.020
 3TE  C14  H18  single    0.930  0.020  1.080
 3TE  C13  H19  single    0.930  0.020  1.080
 3TE  C12  H20  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
 3TE  N    C1   N1   126.48  3.000
 3TE  N1   C1   S    115.01  3.000
 3TE  N    C1   S    118.50  3.000
 3TE  H1   C2   N1   119.26  3.000
 3TE  H1   C2   C3   123.71  3.000
 3TE  N1   C2   C3   117.02  3.000
 3TE  S    C3   C4   123.12  3.000
 3TE  C4   C3   C2   128.29  3.000
 3TE  S    C3   C2   108.58  3.000
 3TE  H3   C4   H2   105.71  3.000
 3TE  H3   C4   C5   109.28  3.000
 3TE  H2   C4   C5   111.47  3.000
 3TE  H3   C4   C3   106.96  3.000
 3TE  H2   C4   C3   110.57  3.000
 3TE  C5   C4   C3   112.51  3.000
 3TE  C14  C5   C6   119.35  3.000
 3TE  C14  C5   C4   119.13  3.000
 3TE  C6   C5   C4   121.49  3.000
 3TE  C11  C6   C7   118.05  3.000
 3TE  C11  C6   C5   118.99  3.000
 3TE  C7   C6   C5   122.96  3.000
 3TE  C3   S    C1    88.95  3.000
 3TE  C2   N1   C1   110.43  3.000
 3TE  H4   C7   C8   118.56  3.000
 3TE  H4   C7   C6   120.24  3.000
 3TE  C8   C7   C6   121.19  3.000
 3TE  H5   C8   C9   119.73  3.000
 3TE  H5   C8   C7   119.76  3.000
 3TE  C9   C8   C7   120.51  3.000
 3TE  C17  N2   C16  116.62  3.000
 3TE  H6   C9   C10  120.29  3.000
 3TE  H6   C9   C8   119.85  3.000
 3TE  C10  C9   C8   119.86  3.000
 3TE  H7   C10  C11  118.69  3.000
 3TE  H7   C10  C9   120.36  3.000
 3TE  C11  C10  C9   120.95  3.000
 3TE  N    C    C15  112.47  3.000
 3TE  N    C    O    124.64  3.000
 3TE  C15  C    O    122.89  3.000
 3TE  H9   C15  H8   107.39  3.000
 3TE  H9   C15  S1   110.62  3.000
 3TE  H8   C15  S1   110.51  3.000
 3TE  H9   C15  C    109.74  3.000
 3TE  H8   C15  C    110.90  3.000
 3TE  S1   C15  C    107.70  3.000
 3TE  C16  S1   C15  100.94  3.000
 3TE  N3   C16  S1   119.88  3.000
 3TE  N3   C16  N2   127.26  3.000
 3TE  S1   C16  N2   112.86  3.000
 3TE  C20  N3   C16  116.64  3.000
 3TE  C19  C20  C21  122.19  3.000
 3TE  C21  C20  N3   117.06  3.000
 3TE  C19  C20  N3   120.74  3.000
 3TE  H12  C21  H11  108.91  3.000
 3TE  H12  C21  H10  107.19  3.000
 3TE  H11  C21  H10  108.20  3.000
 3TE  H12  C21  C20  110.67  3.000
 3TE  H11  C21  C20  111.76  3.000
 3TE  H10  C21  C20  109.97  3.000
 3TE  H13  C19  C17  121.00  3.000
 3TE  H13  C19  C20  121.01  3.000
 3TE  C17  C19  C20  117.99  3.000
 3TE  C18  C17  C19  122.00  3.000
 3TE  C19  C17  N2   120.74  3.000
 3TE  C18  C17  N2   117.27  3.000
 3TE  H16  C18  H15  108.62  3.000
 3TE  H16  C18  H14  107.19  3.000
 3TE  H15  C18  H14  108.48  3.000
 3TE  H16  C18  C17  110.45  3.000
 3TE  H15  C18  C17  111.73  3.000
 3TE  H14  C18  C17  110.24  3.000
 3TE  H17  N    C    116.73  3.000
 3TE  H17  N    C1   116.64  3.000
 3TE  C    N    C1   126.63  3.000
 3TE  H18  C14  C13  119.10  3.000
 3TE  H18  C14  C5   119.30  3.000
 3TE  C13  C14  C5   121.60  3.000
 3TE  H19  C13  C12  120.39  3.000
 3TE  H19  C13  C14  119.53  3.000
 3TE  C12  C13  C14  120.08  3.000
 3TE  H20  C12  C11  119.01  3.000
 3TE  H20  C12  C13  120.64  3.000
 3TE  C11  C12  C13  120.35  3.000
 3TE  C12  C11  C10  120.95  3.000
 3TE  C12  C11  C6   119.61  3.000
 3TE  C10  C11  C6   119.44  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
 3TE  CONST_01  C2   C3   S    C1     0.00   0.0  0
 3TE  CONST_02  C3   C2   N1   C1     0.00   0.0  0
 3TE  CONST_03  S    C1   N1   C2     0.00   0.0  0
 3TE  CONST_04  N1   C1   S    C3     0.00   0.0  0
 3TE  CONST_05  C8   C7   C6   C5   180.00   0.0  0
 3TE  CONST_06  C10  C11  C6   C5   180.00   0.0  0
 3TE  CONST_07  C12  C11  C6   C5     0.00   0.0  0
 3TE  CONST_08  C12  C13  C14  C5     0.00   0.0  0
 3TE  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 3TE  CONST_10  C9   C10  C11  C6     0.00   0.0  0
 3TE  CONST_11  C13  C12  C11  C6     0.00   0.0  0
 3TE  CONST_12  C13  C14  C5   C6     0.00   0.0  0
 3TE  CONST_13  N1   C2   C3   S      0.00   0.0  0
 3TE  CONST_14  C10  C9   C8   C7     0.00   0.0  0
 3TE  CONST_15  C10  C11  C6   C7     0.00   0.0  0
 3TE  CONST_16  C12  C11  C6   C7   180.00   0.0  0
 3TE  CONST_17  C14  C5   C6   C7   180.00   0.0  0
 3TE  CONST_18  C11  C10  C9   C8     0.00   0.0  0
 3TE  CONST_19  C11  C6   C7   C8     0.00   0.0  0
 3TE  CONST_20  C20  N3   C16  N2     0.00   0.0  0
 3TE  CONST_21  C20  C19  C17  N2     0.00   0.0  0
 3TE  CONST_22  C12  C11  C10  C9   180.00   0.0  0
 3TE  CONST_23  C13  C12  C11  C10  180.00   0.0  0
 3TE  CONST_24  C19  C17  N2   C16    0.00   0.0  0
 3TE  CONST_25  C19  C20  N3   C16    0.00   0.0  0
 3TE  CONST_26  C17  N2   C16  N3     0.00   0.0  0
 3TE  CONST_27  C17  C19  C20  N3     0.00   0.0  0
 3TE  CONST_28  C11  C6   C5   C14    0.00   0.0  0
 3TE  CONST_29  C11  C12  C13  C14    0.00   0.0  0
 3TE  CONST_30  C4   C3   S    C1   180.00   0.0  0
 3TE  CONST_31  N    C1   N1   C2   180.00   0.0  0
 3TE  CONST_32  N    C1   S    C3   180.00   0.0  0
 3TE  CONST_33  N1   C2   C3   C4   180.00   0.0  0
 3TE  CONST_34  C7   C6   C5   C4     0.00   0.0  0
 3TE  CONST_35  C11  C6   C5   C4   180.00   0.0  0
 3TE  CONST_36  C13  C14  C5   C4   180.00   0.0  0
 3TE  CONST_37  C17  N2   C16  S1   180.00   0.0  0
 3TE  CONST_38  C20  N3   C16  S1   180.00   0.0  0
 3TE  CONST_39  C18  C17  N2   C16  180.00   0.0  0
 3TE  CONST_40  C21  C20  N3   C16  180.00   0.0  0
 3TE  CONST_41  C18  C17  C19  C20  180.00   0.0  0
 3TE  CONST_42  C17  C19  C20  C21  180.00   0.0  0
 3TE  CONST_43  H1   C2   N1   C1   180.00   0.0  0
 3TE  CONST_44  H4   C7   C6   C5     0.00   0.0  0
 3TE  CONST_45  H19  C13  C14  C5   180.00   0.0  0
 3TE  CONST_46  H5   C8   C7   C6   180.00   0.0  0
 3TE  CONST_47  H7   C10  C11  C6   180.00   0.0  0
 3TE  CONST_48  H20  C12  C11  C6   180.00   0.0  0
 3TE  CONST_49  H18  C14  C5   C6   180.00   0.0  0
 3TE  CONST_50  H6   C9   C8   C7   180.00   0.0  0
 3TE  CONST_51  H13  C19  C17  N2   180.00   0.0  0
 3TE  CONST_52  C    N    C1   S    180.00   0.0  0
 3TE  CONST_53  C    N    C1   N1     0.00   0.0  0
 3TE  CONST_54  H17  N    C1   S      0.00   0.0  0
 3TE  CONST_55  C15  C    N    C1   180.00   0.0  0
 3TE  CONST_56  O    C    N    C1     0.00   0.0  0
 3TE  Var_01    C5   C4   C3   C2   118.32  30.0  2
 3TE  Var_02    C6   C5   C4   C3    88.96  30.0  2
 3TE  Var_03    N3   C16  S1   C15    1.82  30.0  2
 3TE  Var_04    H14  C18  C17  N2    60.16  30.0  2
 3TE  Var_05    H10  C21  C20  N3    69.56  30.0  2
 3TE  Var_06    H8   C15  S1   C16   55.59  30.0  3
 3TE  Var_07    S1   C15  C    O      8.76  30.0  2

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
 3TE  plan-1  C1   0.020
 3TE  plan-1  C2   0.020
 3TE  plan-1  C3   0.020
 3TE  plan-1  C4   0.020
 3TE  plan-1  S    0.020
 3TE  plan-1  N1   0.020
 3TE  plan-1  N    0.020
 3TE  plan-1  H1   0.020
 3TE  plan-2  N2   0.020
 3TE  plan-2  S1   0.020
 3TE  plan-2  C16  0.020
 3TE  plan-2  N3   0.020
 3TE  plan-2  C20  0.020
 3TE  plan-2  C21  0.020
 3TE  plan-2  C19  0.020
 3TE  plan-2  C17  0.020
 3TE  plan-2  C18  0.020
 3TE  plan-2  H13  0.020
 3TE  plan-3  C4   0.020
 3TE  plan-3  C5   0.020
 3TE  plan-3  C6   0.020
 3TE  plan-3  C7   0.020
 3TE  plan-3  C8   0.020
 3TE  plan-3  C9   0.020
 3TE  plan-3  C10  0.020
 3TE  plan-3  C14  0.020
 3TE  plan-3  C13  0.020
 3TE  plan-3  C12  0.020
 3TE  plan-3  C11  0.020
 3TE  plan-3  H4   0.020
 3TE  plan-3  H5   0.020
 3TE  plan-3  H6   0.020
 3TE  plan-3  H7   0.020
 3TE  plan-3  H18  0.020
 3TE  plan-3  H19  0.020
 3TE  plan-3  H20  0.020
 3TE  plan-4  C1   0.020
 3TE  plan-4  O    0.020
 3TE  plan-4  C    0.020
 3TE  plan-4  C15  0.020
 3TE  plan-4  N    0.020
 3TE  plan-4  H17  0.020

