# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 16:02:06 2021
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-[[2-[3-(dimethylamino)propyl-methyl-amino]thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCN(C)c1nc2ccsc2c(n1)N(C)CCC#N
#
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
 HWT  HWT  3-[[2-[3-(dimethylamino)propyl-methyl-amino]thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile  ligand  47  23  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HWT
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
 HWT  C1   C  CH3   0  -0.505   1.3815  45.6224  57.8936
 HWT  C2   C  CH2   0  -0.239   3.3365  45.1432  59.2186
 HWT  C3   C  CH2   0  -0.450   3.4873  46.5158  59.8583
 HWT  C4   C  CH2   0  -0.279   4.3360  46.4419  61.1239
 HWT  C5   C  CH3   0  -0.499   3.4496  48.1163  62.7330
 HWT  C6   C  CR6   0   0.614   5.3349  48.6534  61.3234
 HWT  C7   C  CR6   0   0.582   7.0306  49.1171  59.8287
 HWT  N1   N  NT    0  -0.493   4.4816  47.7129  61.8040
 HWT  N2   N  N     0  -0.531   6.1767  48.2608  60.3557
 HWT  N3   N  NT    0  -0.485   7.8214  48.6211  58.8361
 HWT  N4   N  NS    0  -0.236  12.0862  50.7088  58.0270
 HWT  C8   C  CH3   0  -0.505   7.7224  47.2056  58.5321
 HWT  C11  C  CSP   0   0.115  11.2528  50.0975  58.5307
 HWT  C10  C  CH2   0  -0.541  10.1745  49.3338  59.1356
 HWT  C9   C  CH2   0  -0.335   8.9101  49.3564  58.2568
 HWT  C12  C  CR56  0  -0.352   7.0524  50.4458  60.3192
 HWT  C15  C  CR56  0   0.319   6.1455  50.7414  61.3469
 HWT  C14  C  CR15  0  -0.173   6.2572  52.1011  61.7872
 HWT  C13  C  CR15  0  -0.419   7.2042  52.7846  61.1121
 HWT  S    S  S2    0   0.176   8.0027  51.8461  59.9128
 HWT  N5   N  N     0  -0.497   5.2779  49.8661  61.8525
 HWT  N    N  NT    0  -0.387   2.7561  45.1792  57.8917
 HWT  C    C  CH3   0  -0.494   2.8868  43.9027  57.2301
 HWT  H1   H  HCH3  0   0.229   1.2969  46.6415  58.2701
 HWT  H2   H  HCH3  0   0.221   0.9946  45.6273  56.8737
 HWT  H3   H  HCH3  0   0.182   0.7162  44.9846  58.4985
 HWT  H4   H  HCH2  0   0.178   2.7655  44.4812  59.8960
 HWT  H5   H  HCH2  0   0.206   4.3318  44.6953  59.1281
 HWT  H6   H  HCH2  0   0.233   3.9643  47.1906  59.1438
 HWT  H7   H  HCH2  0   0.221   2.5116  46.9398  60.1091
 HWT  H8   H  HCH2  0   0.225   3.8876  45.7429  61.8334
 HWT  H9   H  HCH2  0   0.241   5.3242  46.0505  60.8828
 HWT  H10  H  HCH3  0   0.249   3.8690  48.6885  63.5571
 HWT  H11  H  HCH3  0   0.221   2.6727  48.7279  62.2656
 HWT  H12  H  HCH3  0   0.221   2.9791  47.2242  63.1408
 HWT  H13  H  HCH3  0   0.263   6.6996  46.9282  58.2855
 HWT  H14  H  HCH3  0   0.216   8.3524  46.9898  57.6716
 HWT  H15  H  HCH3  0   0.231   8.0457  46.5774  59.3644
 HWT  H16  H  HCH2  0   0.293  10.5135  48.3065  59.2852
 HWT  H17  H  HCH2  0   0.305   9.9660  49.7504  60.1229
 HWT  H18  H  HCH2  0   0.277   8.6175  50.3827  58.0369
 HWT  H19  H  HCH2  0   0.270   9.1417  48.9157  57.2875
 HWT  H20  H  HCR5  0   0.248   5.6441  52.5168  62.5725
 HWT  H21  H  HCR5  0   0.270   7.4865  53.8174  61.2443
 HWT  H23  H  HCH3  0   0.216   3.9380  43.6148  57.1759
 HWT  H24  H  HCH3  0   0.182   2.3430  43.0852  57.7308
 HWT  H25  H  HCH3  0   0.219   2.5111  43.9714  56.2081

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
 HWT  N4   C11  triple    1.150  0.020  1.150
 HWT  C11  C10  single    1.453  0.020  1.453
 HWT  C1   N    single    1.444  0.020  1.444
 HWT  C    N    single    1.444  0.020  1.444
 HWT  C10  C9   single    1.540  0.020  1.540
 HWT  N    C2   single    1.449  0.020  1.449
 HWT  C9   N3   single    1.436  0.020  1.436
 HWT  C8   N3   single    1.451  0.020  1.451
 HWT  N3   C7   single    1.363  0.020  1.363
 HWT  C2   C3   single    1.522  0.020  1.522
 HWT  C3   C4   single    1.526  0.020  1.526
 HWT  C7   N2   aromatic  1.319  0.020  1.319
 HWT  C7   C12  aromatic  1.417  0.020  1.417
 HWT  N2   C6   aromatic  1.341  0.020  1.341
 HWT  S    C12  aromatic  1.740  0.020  1.740
 HWT  S    C13  aromatic  1.719  0.020  1.719
 HWT  C12  C15  aromatic  1.402  0.020  1.402
 HWT  C4   N1   single    1.449  0.020  1.449
 HWT  C6   N1   single    1.358  0.020  1.358
 HWT  C6   N5   aromatic  1.324  0.020  1.324
 HWT  N1   C5   single    1.446  0.020  1.446
 HWT  C15  N5   aromatic  1.332  0.020  1.332
 HWT  C15  C14  aromatic  1.434  0.020  1.434
 HWT  C13  C14  aromatic  1.349  0.020  1.349
 HWT  C1   H1   single    0.970  0.020  1.090
 HWT  C1   H2   single    0.970  0.020  1.090
 HWT  C1   H3   single    0.970  0.020  1.090
 HWT  C2   H4   single    0.970  0.020  1.090
 HWT  C2   H5   single    0.970  0.020  1.090
 HWT  C3   H6   single    0.970  0.020  1.090
 HWT  C3   H7   single    0.970  0.020  1.090
 HWT  C4   H8   single    0.970  0.020  1.090
 HWT  C4   H9   single    0.970  0.020  1.090
 HWT  C5   H10  single    0.970  0.020  1.090
 HWT  C5   H11  single    0.970  0.020  1.090
 HWT  C5   H12  single    0.970  0.020  1.090
 HWT  C8   H13  single    0.970  0.020  1.090
 HWT  C8   H14  single    0.970  0.020  1.090
 HWT  C8   H15  single    0.970  0.020  1.090
 HWT  C10  H16  single    0.970  0.020  1.090
 HWT  C10  H17  single    0.970  0.020  1.090
 HWT  C9   H18  single    0.970  0.020  1.090
 HWT  C9   H19  single    0.970  0.020  1.090
 HWT  C14  H20  single    0.930  0.020  1.080
 HWT  C13  H21  single    0.930  0.020  1.080
 HWT  C    H23  single    0.970  0.020  1.090
 HWT  C    H24  single    0.970  0.020  1.090
 HWT  C    H25  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
 HWT  H3   C1   H2   107.54  3.000
 HWT  H3   C1   H1   107.74  3.000
 HWT  H2   C1   H1   106.94  3.000
 HWT  H3   C1   N    113.42  3.000
 HWT  H2   C1   N    109.74  3.000
 HWT  H1   C1   N    111.18  3.000
 HWT  H5   C2   H4   105.97  3.000
 HWT  H5   C2   N    107.38  3.000
 HWT  H4   C2   N    111.65  3.000
 HWT  H5   C2   C3   108.27  3.000
 HWT  H4   C2   C3   109.48  3.000
 HWT  N    C2   C3   113.72  3.000
 HWT  H7   C3   H6   107.47  3.000
 HWT  H7   C3   C4   108.96  3.000
 HWT  H6   C3   C4   109.24  3.000
 HWT  H7   C3   C2   110.98  3.000
 HWT  H6   C3   C2   108.99  3.000
 HWT  C4   C3   C2   111.11  3.000
 HWT  H9   C4   H8   106.63  3.000
 HWT  H9   C4   N1   109.13  3.000
 HWT  H8   C4   N1   107.32  3.000
 HWT  H9   C4   C3   109.77  3.000
 HWT  H8   C4   C3   109.96  3.000
 HWT  N1   C4   C3   113.76  3.000
 HWT  H12  C5   H11  108.15  3.000
 HWT  H12  C5   H10  108.31  3.000
 HWT  H11  C5   H10  107.68  3.000
 HWT  H12  C5   N1   108.71  3.000
 HWT  H11  C5   N1   112.86  3.000
 HWT  H10  C5   N1   111.00  3.000
 HWT  N5   C6   N2   125.68  3.000
 HWT  N5   C6   N1   117.76  3.000
 HWT  N2   C6   N1   116.55  3.000
 HWT  C12  C7   N3   125.79  3.000
 HWT  C12  C7   N2   118.72  3.000
 HWT  N3   C7   N2   115.49  3.000
 HWT  C6   N1   C5   118.86  3.000
 HWT  C5   N1   C4   118.33  3.000
 HWT  C6   N1   C4   120.31  3.000
 HWT  C7   N2   C6   120.30  3.000
 HWT  C9   N3   C8   117.83  3.000
 HWT  C8   N3   C7   117.91  3.000
 HWT  C9   N3   C7   123.20  3.000
 HWT  H15  C8   H14  108.50  3.000
 HWT  H15  C8   H13  107.73  3.000
 HWT  H14  C8   H13  108.33  3.000
 HWT  H15  C8   N3   112.42  3.000
 HWT  H14  C8   N3   108.64  3.000
 HWT  H13  C8   N3   111.12  3.000
 HWT  C10  C11  N4   180.00  3.000
 HWT  H17  C10  H16  107.12  3.000
 HWT  H17  C10  C9   110.71  3.000
 HWT  H16  C10  C9   110.29  3.000
 HWT  H17  C10  C11  108.52  3.000
 HWT  H16  C10  C11  108.73  3.000
 HWT  C9   C10  C11  111.34  3.000
 HWT  H19  C9   H18  104.98  3.000
 HWT  H19  C9   C10  109.09  3.000
 HWT  H18  C9   C10  110.46  3.000
 HWT  H19  C9   N3   108.24  3.000
 HWT  H18  C9   N3   111.11  3.000
 HWT  C10  C9   N3   112.63  3.000
 HWT  S    C12  C15  110.77  3.000
 HWT  C15  C12  C7   116.21  3.000
 HWT  S    C12  C7   133.02  3.000
 HWT  N5   C15  C14  123.87  3.000
 HWT  C14  C15  C12  112.01  3.000
 HWT  N5   C15  C12  124.12  3.000
 HWT  H20  C14  C13  124.58  3.000
 HWT  H20  C14  C15  122.99  3.000
 HWT  C13  C14  C15  112.43  3.000
 HWT  H21  C13  S    119.11  3.000
 HWT  H21  C13  C14  127.40  3.000
 HWT  S    C13  C14  113.49  3.000
 HWT  C13  S    C12   91.30  3.000
 HWT  C15  N5   C6   114.96  3.000
 HWT  C    N    C2   111.19  3.000
 HWT  C2   N    C1   112.81  3.000
 HWT  C    N    C1   110.99  3.000
 HWT  H25  C    H24  107.60  3.000
 HWT  H25  C    H23  107.57  3.000
 HWT  H24  C    H23  107.59  3.000
 HWT  H25  C    N    110.02  3.000
 HWT  H24  C    N    113.76  3.000
 HWT  H23  C    N    110.08  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
 HWT  CONST_01  C12  C7   N2   C6      0.00   0.0  0
 HWT  CONST_02  C12  C15  N5   C6      0.00   0.0  0
 HWT  CONST_03  C14  C15  N5   C6    180.00   0.0  0
 HWT  CONST_04  N5   C6   N2   C7      0.00   0.0  0
 HWT  CONST_05  C13  S    C12  C7    180.00   0.0  0
 HWT  CONST_06  N5   C15  C12  C7      0.00   0.0  0
 HWT  CONST_07  C14  C15  C12  C7    180.00   0.0  0
 HWT  CONST_08  S    C12  C7   N2    180.00   0.0  0
 HWT  CONST_09  C15  C12  C7   N2      0.00   0.0  0
 HWT  CONST_10  C15  N5   C6   N2      0.00   0.0  0
 HWT  CONST_11  C14  C13  S    C12     0.00   0.0  0
 HWT  CONST_12  C13  C14  C15  C12     0.00   0.0  0
 HWT  CONST_13  C13  S    C12  C15     0.00   0.0  0
 HWT  CONST_14  S    C13  C14  C15     0.00   0.0  0
 HWT  CONST_15  S    C12  C15  C14     0.00   0.0  0
 HWT  CONST_16  N5   C15  C14  C13   180.00   0.0  0
 HWT  CONST_17  N5   C15  C12  S     180.00   0.0  0
 HWT  CONST_18  N3   C7   N2   C6    180.00   0.0  0
 HWT  CONST_19  N1   C6   N2   C7    180.00   0.0  0
 HWT  CONST_20  C15  N5   C6   N1    180.00   0.0  0
 HWT  CONST_21  S    C12  C7   N3      0.00   0.0  0
 HWT  CONST_22  C15  C12  C7   N3    180.00   0.0  0
 HWT  CONST_23  H21  C13  S    C12   180.00   0.0  0
 HWT  CONST_24  H20  C14  C15  C12   180.00   0.0  0
 HWT  CONST_25  N2   C6   N1   C4      0.00   0.0  0
 HWT  CONST_26  N5   C6   N1   C4    180.00   0.0  0
 HWT  CONST_27  N2   C6   N1   C5    180.00   0.0  0
 HWT  CONST_28  N5   C6   N1   C5      0.00   0.0  0
 HWT  CONST_29  C9   N3   C7   N2    180.00   0.0  0
 HWT  CONST_30  C8   N3   C7   N2      0.00   0.0  0
 HWT  CONST_31  C12  C7   N3   C8    180.00   0.0  0
 HWT  CONST_32  C12  C7   N3   C9      0.00   0.0  0
 HWT  Var_01    C6   N1   C4   C3    -76.76  30.0  3
 HWT  Var_02    C10  C9   N3   C7     79.22  30.0  2
 HWT  Var_03    H10  C5   N1   C6    -51.27  30.0  3
 HWT  Var_04    H13  C8   N3   C7     56.39  30.0  3
 HWT  Var_05    C3   C2   N    C1    -66.31  30.0  3
 HWT  Var_06    N1   C4   C3   C2   -178.16  30.0  3
 HWT  Var_07    N    C2   C3   C4   -169.22  30.0  1
 HWT  Var_08    C11  C10  C9   N3   -179.38  30.0  2
 HWT  Var_09    C9   C10  C11  N4      0.18  30.0  3
 HWT  Var_10    H23  C    N    C1    176.10  30.0  3
 HWT  Var_11    H1   C1   N    C2     62.10  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
 HWT  plan-1  C6   0.020
 HWT  plan-1  C7   0.020
 HWT  plan-1  N1   0.020
 HWT  plan-1  N2   0.020
 HWT  plan-1  N3   0.020
 HWT  plan-1  C12  0.020
 HWT  plan-1  C15  0.020
 HWT  plan-1  C14  0.020
 HWT  plan-1  C13  0.020
 HWT  plan-1  S    0.020
 HWT  plan-1  N5   0.020
 HWT  plan-1  H20  0.020
 HWT  plan-1  H21  0.020
 HWT  plan-2  C4   0.020
 HWT  plan-2  C5   0.020
 HWT  plan-2  C6   0.020
 HWT  plan-2  N1   0.020
 HWT  plan-3  C7   0.020
 HWT  plan-3  N3   0.020
 HWT  plan-3  C8   0.020
 HWT  plan-3  C9   0.020

