# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:57:32 2021
#   Inital geometry file: a 134 line input string
#   Ligand name: 3-[[6-~{tert}-butyl-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)c1nc2cc(sc2c(n1)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
 HWW  HWW  3-[[6-~{tert}-butyl-2-[3-(dimethylamino)propyl-methyl-amino]thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile  ligand  59  27  .  2022-07-25  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HWW
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
 HWW  C4   C  CH2   0  -0.292   4.2943  46.4757  61.5248
 HWW  C3   C  CH2   0  -0.454   3.5984  46.4190  60.1684
 HWW  N2   N  N     0  -0.540   6.1388  48.2940  60.7784
 HWW  C1   C  CH3   0  -0.529   3.6178  45.7213  57.2563
 HWW  N4   N  NS    0  -0.273   7.5255  44.0125  58.1228
 HWW  C11  C  CSP   0   0.122   7.8002  44.9718  58.6963
 HWW  C10  C  CH2   0  -0.548   8.1248  46.1997  59.4015
 HWW  C9   C  CH2   0  -0.318   7.5416  47.4265  58.6835
 HWW  C8   C  CH3   0  -0.557   9.1246  49.3060  58.9796
 HWW  C7   C  CR6   0   0.580   7.1081  49.1007  60.3741
 HWW  C12  C  CR56  0  -0.375   7.2495  50.3597  61.0042
 HWW  C15  C  CR56  0   0.344   6.3238  50.6669  62.0067
 HWW  C14  C  CR15  0  -0.298   6.5352  51.9739  62.5524
 HWW  C13  C  CR5   0  -0.053   7.5693  52.6365  61.9781
 HWW  C16  C  CT    0  -0.176   8.1025  54.0129  62.2897
 HWW  C19  C  CH3   0  -0.656   7.2698  54.6602  63.3961
 HWW  C18  C  CH3   0  -0.631   9.5601  53.9007  62.7578
 HWW  C17  C  CH3   0  -0.632   8.0330  54.8940  61.0357
 HWW  S    S  S2    0   0.181   8.3347  51.6921  60.7384
 HWW  N5   N  N     0  -0.535   5.3466  49.8419  62.3984
 HWW  C6   C  CR6   0   0.609   5.3048  48.6807  61.7540
 HWW  N1   N  NT    0  -0.492   4.3408  47.7994  62.1113
 HWW  C5   C  CH3   0  -0.514   3.3399  48.1908  63.0779
 HWW  C2   C  CH2   0  -0.265   3.7533  45.0334  59.5596
 HWW  N    N  NT    0  -0.404   3.0807  44.8568  58.2861
 HWW  C    C  CH3   0  -0.519   3.1559  43.4707  57.8731
 HWW  H1   H  HCH2  0   0.245   3.7889  45.8164  62.2327
 HWW  H2   H  HCH2  0   0.242   5.3118  46.0954  61.4201
 HWW  H3   H  HCH2  0   0.234   4.0473  47.1782  59.5249
 HWW  H4   H  HCH2  0   0.224   2.5380  46.6648  60.2750
 HWW  H5   H  HCH3  0   0.235   3.4206  46.7699  57.4768
 HWW  H6   H  HCH3  0   0.187   4.7064  45.6043  57.1204
 HWW  H7   H  HCH3  0   0.235   3.1403  45.4965  56.3018
 HWW  H8   H  HCH2  0   0.312   9.2116  46.2736  59.4759
 HWW  H9   H  HCH2  0   0.315   7.7264  46.1331  60.4151
 HWW  H10  H  HCH2  0   0.281   7.9303  47.4778  57.6668
 HWW  H11  H  HCH2  0   0.277   6.4599  47.3306  58.6150
 HWW  H12  H  HCH3  0   0.255   9.7625  49.4987  59.8423
 HWW  H13  H  HCH3  0   0.277   9.6787  48.6429  58.3199
 HWW  H14  H  HCH3  0   0.254   8.9590  50.2382  58.4360
 HWW  H15  H  HCR5  0   0.259   5.9203  52.3777  63.3439
 HWW  H16  H  HCH3  0   0.235   7.2987  54.0800  64.3196
 HWW  H17  H  HCH3  0   0.243   7.6652  55.6527  63.6155
 HWW  H18  H  HCH3  0   0.235   6.2263  54.7767  63.0989
 HWW  H19  H  HCH3  0   0.236   9.6475  53.2383  63.6199
 HWW  H20  H  HCH3  0   0.230  10.2119  53.5159  61.9715
 HWW  H21  H  HCH3  0   0.236   9.9364  54.8838  63.0455
 HWW  H22  H  HCH3  0   0.236   8.4038  55.8950  61.2636
 HWW  H23  H  HCH3  0   0.231   8.6397  54.4963  60.2201
 HWW  H24  H  HCH3  0   0.236   7.0074  54.9880  60.6756
 HWW  H25  H  HCH3  0   0.234   2.8564  49.1278  62.8014
 HWW  H26  H  HCH3  0   0.242   2.5746  47.4198  63.1229
 HWW  H27  H  HCH3  0   0.230   3.7563  48.3149  64.0801
 HWW  H28  H  HCH2  0   0.227   3.3440  44.2959  60.2575
 HWW  H29  H  HCH2  0   0.185   4.8317  44.8031  59.4706
 HWW  H31  H  HCH3  0   0.230   2.7023  42.8281  58.6293
 HWW  H32  H  HCH3  0   0.231   2.6095  43.3251  56.9401
 HWW  H33  H  HCH3  0   0.189   4.1897  43.1222  57.7155
 HWW  N3   N  NT    0  -0.491   7.8850  48.6574  59.3568

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
 HWW  C1   N    single    1.448  0.020  1.448
 HWW  C    N    single    1.448  0.020  1.448
 HWW  N4   C11  triple    1.151  0.020  1.151
 HWW  C9   C10  single    1.536  0.020  1.536
 HWW  C9   N3   single    1.444  0.020  1.444
 HWW  N    C2   single    1.451  0.020  1.451
 HWW  C11  C10  single    1.453  0.020  1.453
 HWW  C8   N3   single    1.449  0.020  1.449
 HWW  N3   C7   single    1.355  0.020  1.355
 HWW  C2   C3   single    1.521  0.020  1.521
 HWW  C3   C4   single    1.526  0.020  1.526
 HWW  C7   N2   aromatic  1.324  0.020  1.324
 HWW  C7   C12  aromatic  1.415  0.020  1.415
 HWW  N2   C6   aromatic  1.341  0.020  1.341
 HWW  S    C12  aromatic  1.739  0.020  1.739
 HWW  S    C13  aromatic  1.736  0.020  1.736
 HWW  C12  C15  aromatic  1.399  0.020  1.399
 HWW  C4   N1   single    1.449  0.020  1.449
 HWW  C17  C16  single    1.534  0.020  1.534
 HWW  C6   N1   single    1.354  0.020  1.354
 HWW  C6   N5   aromatic  1.329  0.020  1.329
 HWW  N1   C5   single    1.445  0.020  1.445
 HWW  C15  N5   aromatic  1.338  0.020  1.338
 HWW  C15  C14  aromatic  1.432  0.020  1.432
 HWW  C13  C16  single    1.509  0.020  1.509
 HWW  C13  C14  aromatic  1.356  0.020  1.356
 HWW  C16  C19  single    1.529  0.020  1.529
 HWW  C16  C18  single    1.535  0.020  1.535
 HWW  C4   H1   single    0.970  0.020  1.090
 HWW  C4   H2   single    0.970  0.020  1.090
 HWW  C3   H3   single    0.970  0.020  1.090
 HWW  C3   H4   single    0.970  0.020  1.090
 HWW  C1   H5   single    0.970  0.020  1.090
 HWW  C1   H6   single    0.970  0.020  1.090
 HWW  C1   H7   single    0.970  0.020  1.090
 HWW  C10  H8   single    0.970  0.020  1.090
 HWW  C10  H9   single    0.970  0.020  1.090
 HWW  C9   H10  single    0.970  0.020  1.090
 HWW  C9   H11  single    0.970  0.020  1.090
 HWW  C8   H12  single    0.970  0.020  1.090
 HWW  C8   H13  single    0.970  0.020  1.090
 HWW  C8   H14  single    0.970  0.020  1.090
 HWW  C14  H15  single    0.930  0.020  1.080
 HWW  C19  H16  single    0.970  0.020  1.090
 HWW  C19  H17  single    0.970  0.020  1.090
 HWW  C19  H18  single    0.970  0.020  1.090
 HWW  C18  H19  single    0.970  0.020  1.090
 HWW  C18  H20  single    0.970  0.020  1.090
 HWW  C18  H21  single    0.970  0.020  1.090
 HWW  C17  H22  single    0.970  0.020  1.090
 HWW  C17  H23  single    0.970  0.020  1.090
 HWW  C17  H24  single    0.970  0.020  1.090
 HWW  C5   H25  single    0.970  0.020  1.090
 HWW  C5   H26  single    0.970  0.020  1.090
 HWW  C5   H27  single    0.970  0.020  1.090
 HWW  C2   H28  single    0.970  0.020  1.090
 HWW  C2   H29  single    0.970  0.020  1.090
 HWW  C    H31  single    0.970  0.020  1.090
 HWW  C    H32  single    0.970  0.020  1.090
 HWW  C    H33  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
 HWW  H2   C4   H1   106.47  3.000
 HWW  H2   C4   N1   109.11  3.000
 HWW  H1   C4   N1   107.71  3.000
 HWW  H2   C4   C3   109.09  3.000
 HWW  H1   C4   C3   110.06  3.000
 HWW  N1   C4   C3   114.11  3.000
 HWW  H4   C3   H3   107.44  3.000
 HWW  H4   C3   C2   110.02  3.000
 HWW  H3   C3   C2   110.83  3.000
 HWW  H4   C3   C4   110.32  3.000
 HWW  H3   C3   C4   108.10  3.000
 HWW  C2   C3   C4   110.07  3.000
 HWW  C6   N2   C7   120.12  3.000
 HWW  H7   C1   H6   107.60  3.000
 HWW  H7   C1   H5   107.23  3.000
 HWW  H6   C1   H5   107.79  3.000
 HWW  H7   C1   N    109.69  3.000
 HWW  H6   C1   N    112.97  3.000
 HWW  H5   C1   N    111.32  3.000
 HWW  C10  C11  N4   180.00  3.000
 HWW  H9   C10  H8   107.72  3.000
 HWW  H9   C10  C9   110.13  3.000
 HWW  H8   C10  C9   110.83  3.000
 HWW  H9   C10  C11  108.53  3.000
 HWW  H8   C10  C11  108.22  3.000
 HWW  C9   C10  C11  111.30  3.000
 HWW  H11  C9   H10  107.46  3.000
 HWW  H11  C9   N3   109.92  3.000
 HWW  H10  C9   N3   108.06  3.000
 HWW  H11  C9   C10  109.66  3.000
 HWW  H10  C9   C10  109.77  3.000
 HWW  N3   C9   C10  111.86  3.000
 HWW  H14  C8   H13  107.22  3.000
 HWW  H14  C8   H12  109.38  3.000
 HWW  H13  C8   H12  106.84  3.000
 HWW  H14  C8   N3   112.46  3.000
 HWW  H13  C8   N3   108.72  3.000
 HWW  H12  C8   N3   111.94  3.000
 HWW  C12  C7   N3   124.63  3.000
 HWW  C12  C7   N2   118.64  3.000
 HWW  N3   C7   N2   116.73  3.000
 HWW  S    C12  C15  110.75  3.000
 HWW  C15  C12  C7   116.64  3.000
 HWW  S    C12  C7   132.54  3.000
 HWW  N5   C15  C14  124.00  3.000
 HWW  C14  C15  C12  112.08  3.000
 HWW  N5   C15  C12  123.92  3.000
 HWW  H15  C14  C13  124.17  3.000
 HWW  H15  C14  C15  122.43  3.000
 HWW  C13  C14  C15  113.40  3.000
 HWW  S    C13  C16  119.20  3.000
 HWW  C16  C13  C14  128.90  3.000
 HWW  S    C13  C14  111.89  3.000
 HWW  C17  C16  C18  109.53  3.000
 HWW  C18  C16  C19  109.12  3.000
 HWW  C17  C16  C19  108.89  3.000
 HWW  C18  C16  C13  109.39  3.000
 HWW  C19  C16  C13  110.08  3.000
 HWW  C17  C16  C13  109.83  3.000
 HWW  H18  C19  H17  107.72  3.000
 HWW  H18  C19  H16  108.22  3.000
 HWW  H17  C19  H16  107.70  3.000
 HWW  H18  C19  C16  111.66  3.000
 HWW  H17  C19  C16  109.48  3.000
 HWW  H16  C19  C16  111.91  3.000
 HWW  H21  C18  H20  107.56  3.000
 HWW  H21  C18  H19  108.12  3.000
 HWW  H20  C18  H19  107.91  3.000
 HWW  H21  C18  C16  110.00  3.000
 HWW  H20  C18  C16  111.91  3.000
 HWW  H19  C18  C16  111.19  3.000
 HWW  H24  C17  H23  107.90  3.000
 HWW  H24  C17  H22  108.01  3.000
 HWW  H23  C17  H22  107.54  3.000
 HWW  H24  C17  C16  111.21  3.000
 HWW  H23  C17  C16  112.10  3.000
 HWW  H22  C17  C16  109.91  3.000
 HWW  C13  S    C12   91.86  3.000
 HWW  C6   N5   C15  114.84  3.000
 HWW  N1   C6   N5   117.60  3.000
 HWW  N5   C6   N2   125.84  3.000
 HWW  N1   C6   N2   116.56  3.000
 HWW  C5   N1   C6   119.55  3.000
 HWW  C5   N1   C4   119.74  3.000
 HWW  C6   N1   C4   120.71  3.000
 HWW  H27  C5   H26  108.11  3.000
 HWW  H27  C5   H25  107.71  3.000
 HWW  H26  C5   H25  107.92  3.000
 HWW  H27  C5   N1   112.36  3.000
 HWW  H26  C5   N1   108.85  3.000
 HWW  H25  C5   N1   111.74  3.000
 HWW  H29  C2   H28  105.99  3.000
 HWW  H29  C2   N    110.85  3.000
 HWW  H28  C2   N    107.71  3.000
 HWW  H29  C2   C3   108.73  3.000
 HWW  H28  C2   C3   108.69  3.000
 HWW  N    C2   C3   114.51  3.000
 HWW  C    N    C2   110.04  3.000
 HWW  C2   N    C1   112.31  3.000
 HWW  C    N    C1   110.45  3.000
 HWW  H33  C    H32  107.77  3.000
 HWW  H33  C    H31  107.62  3.000
 HWW  H32  C    H31  107.81  3.000
 HWW  H33  C    N    113.08  3.000
 HWW  H32  C    N    110.22  3.000
 HWW  H31  C    N    110.15  3.000
 HWW  C7   N3   C8   122.66  3.000
 HWW  C7   N3   C9   119.51  3.000
 HWW  C8   N3   C9   117.61  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
 HWW  CONST_01  S    C12  C7   N2    180.00   0.0  0
 HWW  CONST_02  C15  C12  C7   N2      0.00   0.0  0
 HWW  CONST_03  C15  N5   C6   N2      0.00   0.0  0
 HWW  CONST_04  N5   C6   N2   C7      0.00   0.0  0
 HWW  CONST_05  C13  S    C12  C7    180.00   0.0  0
 HWW  CONST_06  N5   C15  C12  C7      0.00   0.0  0
 HWW  CONST_07  C14  C15  C12  C7    180.00   0.0  0
 HWW  CONST_08  C6   N2   C7   C12     0.00   0.0  0
 HWW  CONST_09  C14  C13  S    C12     0.00   0.0  0
 HWW  CONST_10  C6   N5   C15  C12     0.00   0.0  0
 HWW  CONST_11  C13  C14  C15  C12     0.00   0.0  0
 HWW  CONST_12  C13  S    C12  C15     0.00   0.0  0
 HWW  CONST_13  S    C13  C14  C15     0.00   0.0  0
 HWW  CONST_14  S    C12  C15  C14     0.00   0.0  0
 HWW  CONST_15  C6   N5   C15  C14   180.00   0.0  0
 HWW  CONST_16  N5   C15  C14  C13   180.00   0.0  0
 HWW  CONST_17  N5   C15  C12  S     180.00   0.0  0
 HWW  CONST_18  C6   N2   C7   N3    180.00   0.0  0
 HWW  CONST_19  S    C12  C7   N3      0.00   0.0  0
 HWW  CONST_20  C15  C12  C7   N3    180.00   0.0  0
 HWW  CONST_21  N1   C6   N2   C7    180.00   0.0  0
 HWW  CONST_22  C16  C13  S    C12   180.00   0.0  0
 HWW  CONST_23  N1   C6   N5   C15   180.00   0.0  0
 HWW  CONST_24  C16  C13  C14  C15   180.00   0.0  0
 HWW  CONST_25  H15  C14  C15  C12   180.00   0.0  0
 HWW  CONST_26  N2   C6   N1   C4      0.00   0.0  0
 HWW  CONST_27  N5   C6   N1   C4    180.00   0.0  0
 HWW  CONST_28  C9   N3   C7   N2      0.00   0.0  0
 HWW  CONST_29  C8   N3   C7   N2    180.00   0.0  0
 HWW  CONST_30  C5   N1   C6   N2    180.00   0.0  0
 HWW  CONST_31  C12  C7   N3   C9    180.00   0.0  0
 HWW  CONST_32  C12  C7   N3   C8      0.00   0.0  0
 HWW  CONST_33  C5   N1   C6   N5      0.00   0.0  0
 HWW  Var_01    C17  C16  C13  C14  -121.21  30.0  2
 HWW  Var_02    C6   N1   C4   C3    -83.10  30.0  3
 HWW  Var_03    C7   N3   C9   C10   -86.07  30.0  3
 HWW  Var_04    H12  C8   N3   C7     48.43  30.0  3
 HWW  Var_05    H22  C17  C16  C13   179.11  30.0  3
 HWW  Var_06    H16  C19  C16  C13    60.51  30.0  3
 HWW  Var_07    H19  C18  C16  C13   -56.73  30.0  3
 HWW  Var_08    H25  C5   N1   C6     52.39  30.0  3
 HWW  Var_09    N    C2   C3   C4    177.74  30.0  1
 HWW  Var_10    C1   N    C2   C3     63.25  30.0  2
 HWW  Var_11    C9   C10  C11  N4    -12.15  30.0  3
 HWW  Var_12    N3   C9   C10  C11  -178.59  30.0  1
 HWW  Var_13    C2   C3   C4   N1    172.95  30.0  2
 HWW  Var_14    H31  C    N    C1   -177.03  30.0  3
 HWW  Var_15    H5   C1   N    C2    -66.12  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
 HWW  plan-1  N2   0.020
 HWW  plan-1  C7   0.020
 HWW  plan-1  C12  0.020
 HWW  plan-1  C15  0.020
 HWW  plan-1  C14  0.020
 HWW  plan-1  C13  0.020
 HWW  plan-1  C16  0.020
 HWW  plan-1  S    0.020
 HWW  plan-1  N5   0.020
 HWW  plan-1  C6   0.020
 HWW  plan-1  N1   0.020
 HWW  plan-1  H15  0.020
 HWW  plan-1  N3   0.020
 HWW  plan-2  C4   0.020
 HWW  plan-2  C6   0.020
 HWW  plan-2  N1   0.020
 HWW  plan-2  C5   0.020
 HWW  plan-3  C9   0.020
 HWW  plan-3  C8   0.020
 HWW  plan-3  C7   0.020
 HWW  plan-3  N3   0.020

