# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 20:23:14 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-[[6-~{tert}-butyl-2-[methyl-[(3~{S})-1-methylpyrrolidin-3-yl]amino]-7~{H}-thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC[C@@H](C1)N(C)c2nc3CC(=[SH]c3c(n2)N(C)CCC#N)C(C)(C)C
#
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
 HWN  HWN  3-[[6-~{tert}-butyl-2-[methyl-[(3~{S})-1-methylpyrrolidin-3-yl]amino]-7~{H}-thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile  ligand  59  27  .  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_HWN
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
 HWN  C11  C  CH3   0  -0.643   7.1963  54.8112  62.5493
 HWN  C6   C  CR56  0   0.355   5.8250  50.6834  61.6656
 HWN  C8   C  CR5   0  -0.280   7.4102  52.4724  61.8014
 HWN  C3   C  CSP   0   0.120   6.1282  46.0348  56.9203
 HWN  N2   N  N     0  -0.544   5.4618  48.4325  60.2676
 HWN  C10  C  CT    0  -0.124   8.1592  53.6230  62.4402
 HWN  C4   C  CR6   0   0.597   6.6790  48.9691  60.2352
 HWN  C1   C  CH2   0  -0.317   7.2403  47.0581  58.8729
 HWN  C7   C  CH2   0  -0.515   6.1605  51.9213  62.4405
 HWN  N3   N  N     0  -0.514   4.6282  50.1335  61.7026
 HWN  C9   C  CR56  0  -0.351   6.8937  50.1671  60.9424
 HWN  N1   N  NS    0  -0.273   5.8325  45.0296  56.4448
 HWN  C2   C  CH2   0  -0.551   6.5048  47.2912  57.5442
 HWN  C5   C  CR6   0   0.632   4.4958  49.0049  60.9831
 HWN  N    N  NT    0  -0.491   7.6069  48.3036  59.5102
 HWN  C    C  CH3   0  -0.549   8.8863  48.8923  59.1685
 HWN  S    S  S3    0   0.220   8.3354  51.1600  61.2182
 HWN  C13  C  CH3   0  -0.632   8.6716  53.2769  63.8489
 HWN  C12  C  CH3   0  -0.646   9.3477  54.0456  61.5730
 HWN  C14  C  CH3   0  -0.537   2.1506  49.1154  61.5581
 HWN  C15  C  CH1   0  -0.109   3.0936  47.1618  60.2573
 HWN  C19  C  CH2   0  -0.266   2.6406  47.3702  58.8115
 HWN  N5   N  NT    0  -0.414   1.1988  47.4146  58.9196
 HWN  C18  C  CH3   0  -0.516   0.4998  47.4233  57.6611
 HWN  C17  C  CH2   0  -0.277   0.8504  46.3057  59.7902
 HWN  C16  C  CH2   0  -0.504   1.9738  46.2731  60.8388
 HWN  H1   H  HCH3  0   0.224   6.3350  54.5764  63.1777
 HWN  H2   H  HCH3  0   0.219   7.6975  55.6742  62.9928
 HWN  H3   H  HCH3  0   0.219   6.8227  55.1039  61.5664
 HWN  H4   H  HCH2  0   0.281   8.1509  46.4875  58.6958
 HWN  H5   H  HCH2  0   0.282   6.6126  46.4719  59.5401
 HWN  H6   H  HCH2  0   0.256   5.3328  52.6334  62.3930
 HWN  H7   H  HCH2  0   0.232   6.2515  51.6316  63.5038
 HWN  H8   H  HCH2  0   0.314   7.1309  47.8490  56.8450
 HWN  H9   H  HCH2  0   0.317   5.5979  47.8727  57.7162
 HWN  H10  H  HCH3  0   0.255   8.7781  49.8583  58.6750
 HWN  H11  H  HCH3  0   0.249   9.5323  49.0066  60.0408
 HWN  H12  H  HCH3  0   0.275   9.4007  48.2288  58.4786
 HWN  H13  H  HCH3  0   0.219   7.8569  52.9574  64.5026
 HWN  H14  H  HCH3  0   0.211   9.4032  52.4658  63.8152
 HWN  H15  H  HCH3  0   0.216   9.1545  54.1343  64.3248
 HWN  H16  H  HCH3  0   0.224   9.8341  54.9320  61.9867
 HWN  H17  H  HCH3  0   0.218  10.1113  53.2652  61.5093
 HWN  H18  H  HCH3  0   0.222   9.0256  54.2786  60.5566
 HWN  H19  H  HCH3  0   0.247   2.1972  50.1782  61.3316
 HWN  H20  H  HCH3  0   0.256   1.2324  48.7279  61.1296
 HWN  H21  H  HCH3  0   0.232   2.1041  49.0066  62.6438
 HWN  H22  H  HCH1  0   0.271   4.0442  46.6363  60.2799
 HWN  H23  H  HCH2  0   0.191   2.9871  46.5191  58.1958
 HWN  H24  H  HCH2  0   0.240   3.0433  48.2832  58.3670
 HWN  H26  H  HCH3  0   0.232  -0.5768  47.4811  57.8298
 HWN  H27  H  HCH3  0   0.232   0.7897  48.2964  57.0749
 HWN  H28  H  HCH3  0   0.190   0.6943  46.5276  57.0495
 HWN  H29  H  HCH2  0   0.234  -0.1407  46.4520  60.2255
 HWN  H30  H  HCH2  0   0.203   0.8252  45.3523  59.2376
 HWN  H31  H  HCH2  0   0.261   2.3442  45.2579  60.9751
 HWN  H32  H  HCH2  0   0.259   1.6414  46.6143  61.8183
 HWN  H33  H  HSH1  0   0.135   8.8666  50.2886  62.1866
 HWN  N4   N  NT    0  -0.487   3.2819  48.4147  60.9798

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
 HWN  C18  N5   single    1.440  0.020  1.440
 HWN  N1   C3   triple    1.151  0.020  1.151
 HWN  C    N    single    1.449  0.020  1.449
 HWN  C19  N5   single    1.446  0.020  1.446
 HWN  C19  C15  single    1.529  0.020  1.529
 HWN  C3   C2   single    1.452  0.020  1.452
 HWN  N5   C17  single    1.452  0.020  1.452
 HWN  N    C1   single    1.446  0.020  1.446
 HWN  N    C4   single    1.353  0.020  1.353
 HWN  C1   C2   single    1.537  0.020  1.537
 HWN  C15  C16  single    1.543  0.020  1.543
 HWN  C15  N4   single    1.458  0.020  1.458
 HWN  C4   N2   aromatic  1.331  0.020  1.331
 HWN  C4   C9   aromatic  1.408  0.020  1.408
 HWN  C16  C17  single    1.537  0.020  1.537
 HWN  N2   C5   aromatic  1.331  0.020  1.331
 HWN  C9   S    single    1.772  0.020  1.772
 HWN  C9   C6   aromatic  1.390  0.020  1.390
 HWN  C5   N4   single    1.350  0.020  1.350
 HWN  C5   N3   aromatic  1.345  0.020  1.345
 HWN  S    C8   double    1.708  0.020  1.708
 HWN  N4   C14  single    1.451  0.020  1.451
 HWN  C6   N3   aromatic  1.318  0.020  1.318
 HWN  C6   C7   single    1.498  0.020  1.498
 HWN  C12  C10  single    1.531  0.020  1.531
 HWN  C8   C7   single    1.508  0.020  1.508
 HWN  C8   C10  single    1.514  0.020  1.514
 HWN  C11  C10  single    1.533  0.020  1.533
 HWN  C10  C13  single    1.538  0.020  1.538
 HWN  C11  H1   single    0.970  0.020  1.090
 HWN  C11  H2   single    0.970  0.020  1.090
 HWN  C11  H3   single    0.970  0.020  1.090
 HWN  C1   H4   single    0.970  0.020  1.090
 HWN  C1   H5   single    0.970  0.020  1.090
 HWN  C7   H6   single    0.970  0.020  1.090
 HWN  C7   H7   single    0.970  0.020  1.090
 HWN  C2   H8   single    0.970  0.020  1.090
 HWN  C2   H9   single    0.970  0.020  1.090
 HWN  C    H10  single    0.970  0.020  1.090
 HWN  C    H11  single    0.970  0.020  1.090
 HWN  C    H12  single    0.970  0.020  1.090
 HWN  C13  H13  single    0.970  0.020  1.090
 HWN  C13  H14  single    0.970  0.020  1.090
 HWN  C13  H15  single    0.970  0.020  1.090
 HWN  C12  H16  single    0.970  0.020  1.090
 HWN  C12  H17  single    0.970  0.020  1.090
 HWN  C12  H18  single    0.970  0.020  1.090
 HWN  C14  H19  single    0.970  0.020  1.090
 HWN  C14  H20  single    0.970  0.020  1.090
 HWN  C14  H21  single    0.970  0.020  1.090
 HWN  C15  H22  single    0.970  0.020  1.090
 HWN  C19  H23  single    0.970  0.020  1.090
 HWN  C19  H24  single    0.970  0.020  1.090
 HWN  C18  H26  single    0.970  0.020  1.090
 HWN  C18  H27  single    0.970  0.020  1.090
 HWN  C18  H28  single    0.970  0.020  1.090
 HWN  C17  H29  single    0.970  0.020  1.090
 HWN  C17  H30  single    0.970  0.020  1.090
 HWN  C16  H31  single    0.970  0.020  1.090
 HWN  C16  H32  single    0.970  0.020  1.090
 HWN  S    H33  single    1.200  0.020  1.300

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
 HWN  H3   C11  H2   108.11  3.000
 HWN  H3   C11  H1   107.82  3.000
 HWN  H2   C11  H1   107.35  3.000
 HWN  H3   C11  C10  111.02  3.000
 HWN  H2   C11  C10  110.67  3.000
 HWN  H1   C11  C10  111.70  3.000
 HWN  C9   C6   N3   123.92  3.000
 HWN  N3   C6   C7   122.25  3.000
 HWN  C9   C6   C7   113.82  3.000
 HWN  S    C8   C7   108.22  3.000
 HWN  C7   C8   C10  120.59  3.000
 HWN  S    C8   C10  117.38  3.000
 HWN  C2   C3   N1   180.00  3.000
 HWN  C5   N2   C4   120.22  3.000
 HWN  C12  C10  C13  108.80  3.000
 HWN  C13  C10  C8   112.34  3.000
 HWN  C12  C10  C8   110.79  3.000
 HWN  C13  C10  C11  108.56  3.000
 HWN  C8   C10  C11  107.95  3.000
 HWN  C12  C10  C11  108.30  3.000
 HWN  N    C4   C9   125.69  3.000
 HWN  C9   C4   N2   118.07  3.000
 HWN  N    C4   N2   116.24  3.000
 HWN  H5   C1   H4   107.45  3.000
 HWN  H5   C1   N    109.89  3.000
 HWN  H4   C1   N    108.12  3.000
 HWN  H5   C1   C2   109.63  3.000
 HWN  H4   C1   C2   109.82  3.000
 HWN  N    C1   C2   111.82  3.000
 HWN  H7   C7   H6   105.95  3.000
 HWN  H7   C7   C8   115.79  3.000
 HWN  H6   C7   C8   111.78  3.000
 HWN  H7   C7   C6   107.41  3.000
 HWN  H6   C7   C6   110.26  3.000
 HWN  C8   C7   C6   105.56  3.000
 HWN  C5   N3   C6   115.13  3.000
 HWN  S    C9   C4   132.77  3.000
 HWN  S    C9   C6   109.66  3.000
 HWN  C4   C9   C6   117.41  3.000
 HWN  H9   C2   H8   107.79  3.000
 HWN  H9   C2   C1   110.02  3.000
 HWN  H8   C2   C1   110.90  3.000
 HWN  H9   C2   C3   108.26  3.000
 HWN  H8   C2   C3   108.39  3.000
 HWN  C1   C2   C3   111.37  3.000
 HWN  N3   C5   N4   117.18  3.000
 HWN  N3   C5   N2   125.23  3.000
 HWN  N4   C5   N2   117.59  3.000
 HWN  C    N    C1   118.01  3.000
 HWN  C1   N    C4   119.08  3.000
 HWN  C    N    C4   122.15  3.000
 HWN  H12  C    H11  106.93  3.000
 HWN  H12  C    H10  107.50  3.000
 HWN  H11  C    H10  109.13  3.000
 HWN  H12  C    N    108.64  3.000
 HWN  H11  C    N    112.12  3.000
 HWN  H10  C    N    112.28  3.000
 HWN  H33  S    C9    93.86  3.000
 HWN  H33  S    C8   116.44  3.000
 HWN  C9   S    C8    92.46  3.000
 HWN  H15  C13  H14  107.45  3.000
 HWN  H15  C13  H13  107.36  3.000
 HWN  H14  C13  H13  107.49  3.000
 HWN  H15  C13  C10  111.68  3.000
 HWN  H14  C13  C10  111.21  3.000
 HWN  H13  C13  C10  111.44  3.000
 HWN  H18  C12  H17  107.71  3.000
 HWN  H18  C12  H16  108.11  3.000
 HWN  H17  C12  H16  106.86  3.000
 HWN  H18  C12  C10  110.94  3.000
 HWN  H17  C12  C10  112.22  3.000
 HWN  H16  C12  C10  110.81  3.000
 HWN  H21  C14  H20  108.73  3.000
 HWN  H21  C14  H19  107.83  3.000
 HWN  H20  C14  H19  107.64  3.000
 HWN  H21  C14  N4   112.41  3.000
 HWN  H20  C14  N4   109.27  3.000
 HWN  H19  C14  N4   110.83  3.000
 HWN  H22  C15  C16  110.39  3.000
 HWN  H22  C15  C19  110.17  3.000
 HWN  C16  C15  C19  102.69  3.000
 HWN  H22  C15  N4   106.99  3.000
 HWN  C16  C15  N4   113.68  3.000
 HWN  C19  C15  N4   112.93  3.000
 HWN  H24  C19  H23  107.53  3.000
 HWN  H24  C19  N5   111.85  3.000
 HWN  H23  C19  N5   112.17  3.000
 HWN  H24  C19  C15  112.91  3.000
 HWN  H23  C19  C15  109.18  3.000
 HWN  N5   C19  C15  103.23  3.000
 HWN  C17  N5   C18  114.34  3.000
 HWN  C17  N5   C19  105.10  3.000
 HWN  C18  N5   C19  114.76  3.000
 HWN  H28  C18  H27  107.78  3.000
 HWN  H28  C18  H26  107.64  3.000
 HWN  H27  C18  H26  107.62  3.000
 HWN  H28  C18  N5   113.24  3.000
 HWN  H27  C18  N5   110.22  3.000
 HWN  H26  C18  N5   110.14  3.000
 HWN  H30  C17  H29  107.15  3.000
 HWN  H30  C17  C16  109.90  3.000
 HWN  H29  C17  C16  113.21  3.000
 HWN  H30  C17  N5   111.43  3.000
 HWN  H29  C17  N5   110.75  3.000
 HWN  C16  C17  N5   104.47  3.000
 HWN  H32  C16  H31  106.45  3.000
 HWN  H32  C16  C17  112.57  3.000
 HWN  H31  C16  C17  110.71  3.000
 HWN  H32  C16  C15  112.32  3.000
 HWN  H31  C16  C15  109.70  3.000
 HWN  C17  C16  C15  105.13  3.000
 HWN  C15  N4   C14  120.77  3.000
 HWN  C14  N4   C5   119.28  3.000
 HWN  C15  N4   C5   119.53  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
 HWN  CONST_01  N2   C4   C9   C6      0.00   0.0  0
 HWN  CONST_02  N2   C5   N3   C6      0.00   0.0  0
 HWN  CONST_03  N3   C5   N2   C4      0.00   0.0  0
 HWN  CONST_04  N3   C6   C9   C4      0.00   0.0  0
 HWN  CONST_05  C5   N2   C4   C9      0.00   0.0  0
 HWN  CONST_06  C5   N3   C6   C9      0.00   0.0  0
 HWN  CONST_07  N    C4   C9   C6    180.00   0.0  0
 HWN  CONST_08  N4   C5   N3   C6    180.00   0.0  0
 HWN  CONST_09  N4   C5   N2   C4    180.00   0.0  0
 HWN  CONST_10  N    C4   N2   C5    180.00   0.0  0
 HWN  CONST_11  S    C9   C4   N       0.00   0.0  0
 HWN  CONST_12  C15  N4   C5   N2      0.00   0.0  0
 HWN  CONST_13  C15  N4   C5   N3    180.00   0.0  0
 HWN  CONST_14  C    N    C4   N2    180.00   0.0  0
 HWN  CONST_15  C1   N    C4   N2      0.00   0.0  0
 HWN  CONST_16  C14  N4   C5   N2    180.00   0.0  0
 HWN  CONST_17  C9   C4   N    C1    180.00   0.0  0
 HWN  CONST_18  C14  N4   C5   N3      0.00   0.0  0
 HWN  CONST_19  C    N    C4   C9      0.00   0.0  0
 HWN  Var_01    C17  N5   C19  C15   -45.45  30.0  1
 HWN  Var_02    N5   C17  C16  C15   -14.52  30.0  1
 HWN  Var_03    C16  C17  N5   C19    37.34  30.0  1
 HWN  Var_04    S    C8   C10  C11   165.54  30.0  2
 HWN  Var_05    H26  C18  N5   C19  -178.67  30.0  3
 HWN  Var_06    C2   C1   N    C4     81.48  30.0  3
 HWN  Var_07    H16  C12  C10  C8    174.88  30.0  3
 HWN  Var_08    H1   C11  C10  C8     61.28  30.0  3
 HWN  Var_09    H13  C13  C10  C8    -56.31  30.0  3
 HWN  Var_10    H10  C    N    C4    -53.75  30.0  3
 HWN  Var_11    H19  C14  N4   C5     38.36  30.0  3
 HWN  Var_12    N    C1   C2   C3   -179.36  30.0  1
 HWN  Var_13    H8   C2   C3   N1    140.27  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
 HWN  chir_01  C15  C19  C16  N4  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
 HWN  plan-1  C4   0.020
 HWN  plan-1  C1   0.020
 HWN  plan-1  N    0.020
 HWN  plan-1  C    0.020
 HWN  plan-2  C5   0.020
 HWN  plan-2  C14  0.020
 HWN  plan-2  C15  0.020
 HWN  plan-2  N4   0.020
 HWN  plan-3  C6   0.020
 HWN  plan-3  C8   0.020
 HWN  plan-3  N2   0.020
 HWN  plan-3  C10  0.020
 HWN  plan-3  C4   0.020
 HWN  plan-3  C7   0.020
 HWN  plan-3  N3   0.020
 HWN  plan-3  C9   0.020
 HWN  plan-3  C5   0.020
 HWN  plan-3  N    0.020
 HWN  plan-3  S    0.020
 HWN  plan-3  H6   0.020
 HWN  plan-3  H7   0.020
 HWN  plan-3  H33  0.020
 HWN  plan-3  N4   0.020

