# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:33:53 2021
#   Inital geometry file: a 106 line input string
#   Ligand name: 3-[methyl-[2-[methyl(piperidin-4-yl)amino]thieno[3,2-d]pyrimidin-4-yl]amino]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCC#N)c1nc(nc2ccsc12)N(C)C3CCNCC3
#
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
 HWQ  HWQ  3-[methyl-[2-[methyl(piperidin-4-yl)amino]thieno[3,2-d]pyrimidin-4-yl]amino]propanenitrile  ligand  45  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_HWQ
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
 HWQ  C1   C  CH2   0  -0.312  7.7753  48.1134  58.4366
 HWQ  C2   C  CH2   0  -0.550  8.0962  46.7830  59.1376
 HWQ  C3   C  CSP   0   0.123  7.8986  45.6559  58.2433
 HWQ  C4   C  CR6   0   0.598  6.9462  49.4955  60.2274
 HWQ  C5   C  CR6   0   0.618  4.9217  48.8089  61.1130
 HWQ  C6   C  CR56  0   0.303  5.8286  50.6708  61.9885
 HWQ  C7   C  CR15  0  -0.212  5.9014  51.8197  62.8418
 HWQ  N1   N  NS    0  -0.276  7.7217  44.7774  57.5213
 HWQ  N2   N  N     0  -0.551  5.9306  48.6491  60.2448
 HWQ  N3   N  N     0  -0.537  4.8200  49.7916  62.0007
 HWQ  C9   C  CR56  0  -0.373  6.9339  50.5858  61.1328
 HWQ  C8   C  CR15  0  -0.441  7.0129  52.5565  62.6171
 HWQ  N    N  NT    0  -0.491  7.9257  49.2432  59.3275
 HWQ  C    C  CH3   0  -0.557  9.1880  49.9547  59.3307
 HWQ  S    S  S2    0   0.200  8.0243  51.9166  61.3856
 HWQ  N4   N  NT    0  -0.498  3.9284  47.8863  61.0894
 HWQ  C10  C  CH3   0  -0.525  2.8673  47.9822  62.0678
 HWQ  C11  C  CH1   0  -0.100  3.9322  46.7708  60.1546
 HWQ  C15  C  CH2   0  -0.440  4.1228  45.4236  60.8504
 HWQ  C14  C  CH2   0  -0.322  4.1272  44.2947  59.8186
 HWQ  N5   N  NH1   0  -0.573  2.9597  44.2768  58.9535
 HWQ  C13  C  CH2   0  -0.319  2.7548  45.5609  58.3046
 HWQ  C12  C  CH2   0  -0.434  2.6861  46.7442  59.2710
 HWQ  H1   H  HCH2  0   0.282  8.4475  48.2545  57.5922
 HWQ  H2   H  HCH2  0   0.276  6.7608  48.0829  58.0427
 HWQ  H3   H  HCH2  0   0.316  9.1277  46.7689  59.4939
 HWQ  H4   H  HCH2  0   0.314  7.4408  46.6512  59.9998
 HWQ  H5   H  HCR5  0   0.269  5.1459  52.0641  63.5744
 HWQ  H6   H  HCR5  0   0.305  7.3076  53.4664  63.1181
 HWQ  H7   H  HCH3  0   0.254  9.6643  49.9419  60.3117
 HWQ  H8   H  HCH3  0   0.279  9.8694  49.4636  58.6414
 HWQ  H9   H  HCH3  0   0.254  9.0807  50.9873  58.9936
 HWQ  H10  H  HCH3  0   0.237  3.2570  47.9996  63.0862
 HWQ  H11  H  HCH3  0   0.235  2.2562  48.8758  61.9299
 HWQ  H12  H  HCH3  0   0.243  2.2184  47.1159  61.9765
 HWQ  H13  H  HCH1  0   0.259  4.7907  46.9250  59.5013
 HWQ  H14  H  HCH2  0   0.220  3.3192  45.2498  61.5745
 HWQ  H15  H  HCH2  0   0.232  5.0623  45.4232  61.4111
 HWQ  H16  H  HCH2  0   0.239  4.2116  43.3280  60.3186
 HWQ  H17  H  HCH2  0   0.213  5.0148  44.3940  59.1826
 HWQ  H18  H  HNH1  0   0.339  2.1414  44.0544  59.5086
 HWQ  H20  H  HCH2  0   0.214  3.5803  45.7189  57.6013
 HWQ  H21  H  HCH2  0   0.239  1.8433  45.5132  57.7060
 HWQ  H22  H  HCH2  0   0.232  2.6067  47.6811  58.7130
 HWQ  H23  H  HCH2  0   0.219  1.7804  46.6547  59.8800

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
 HWQ  C13  N5   single    1.453  0.020  1.453
 HWQ  C13  C12  single    1.529  0.020  1.529
 HWQ  N1   C3   triple    1.151  0.020  1.151
 HWQ  C1   C2   single    1.538  0.020  1.538
 HWQ  C1   N    single    1.447  0.020  1.447
 HWQ  N5   C14  single    1.453  0.020  1.453
 HWQ  C3   C2   single    1.452  0.020  1.452
 HWQ  C    N    single    1.449  0.020  1.449
 HWQ  C12  C11  single    1.528  0.020  1.528
 HWQ  N    C4   single    1.354  0.020  1.354
 HWQ  C14  C15  single    1.529  0.020  1.529
 HWQ  C11  C15  single    1.528  0.020  1.528
 HWQ  C11  N4   single    1.455  0.020  1.455
 HWQ  N2   C4   aromatic  1.322  0.020  1.322
 HWQ  N2   C5   aromatic  1.341  0.020  1.341
 HWQ  C4   C9   aromatic  1.417  0.020  1.417
 HWQ  N4   C5   single    1.356  0.020  1.356
 HWQ  N4   C10  single    1.447  0.020  1.447
 HWQ  C5   N3   aromatic  1.328  0.020  1.328
 HWQ  C9   S    aromatic  1.739  0.020  1.739
 HWQ  C9   C6   aromatic  1.400  0.020  1.400
 HWQ  S    C8   aromatic  1.717  0.020  1.717
 HWQ  N3   C6   aromatic  1.338  0.020  1.338
 HWQ  C6   C7   aromatic  1.433  0.020  1.433
 HWQ  C8   C7   aromatic  1.352  0.020  1.352
 HWQ  C1   H1   single    0.970  0.020  1.090
 HWQ  C1   H2   single    0.970  0.020  1.090
 HWQ  C2   H3   single    0.970  0.020  1.090
 HWQ  C2   H4   single    0.970  0.020  1.090
 HWQ  C7   H5   single    0.930  0.020  1.080
 HWQ  C8   H6   single    0.930  0.020  1.080
 HWQ  C    H7   single    0.970  0.020  1.090
 HWQ  C    H8   single    0.970  0.020  1.090
 HWQ  C    H9   single    0.970  0.020  1.090
 HWQ  C10  H10  single    0.970  0.020  1.090
 HWQ  C10  H11  single    0.970  0.020  1.090
 HWQ  C10  H12  single    0.970  0.020  1.090
 HWQ  C11  H13  single    0.970  0.020  1.090
 HWQ  C15  H14  single    0.970  0.020  1.090
 HWQ  C15  H15  single    0.970  0.020  1.090
 HWQ  C14  H16  single    0.970  0.020  1.090
 HWQ  C14  H17  single    0.970  0.020  1.090
 HWQ  N5   H18  single    0.890  0.020  1.040
 HWQ  C13  H20  single    0.970  0.020  1.090
 HWQ  C13  H21  single    0.970  0.020  1.090
 HWQ  C12  H22  single    0.970  0.020  1.090
 HWQ  C12  H23  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
 HWQ  H2   C1   H1   107.36  3.000
 HWQ  H2   C1   N    109.97  3.000
 HWQ  H1   C1   N    108.19  3.000
 HWQ  H2   C1   C2   109.59  3.000
 HWQ  H1   C1   C2   109.69  3.000
 HWQ  N    C1   C2   111.92  3.000
 HWQ  H4   C2   H3   107.95  3.000
 HWQ  H4   C2   C3   108.13  3.000
 HWQ  H3   C2   C3   108.64  3.000
 HWQ  H4   C2   C1   109.84  3.000
 HWQ  H3   C2   C1   110.93  3.000
 HWQ  C3   C2   C1   111.24  3.000
 HWQ  N1   C3   C2   180.00  3.000
 HWQ  N    C4   C9   125.05  3.000
 HWQ  C9   C4   N2   118.52  3.000
 HWQ  N    C4   N2   116.43  3.000
 HWQ  N4   C5   N3   117.32  3.000
 HWQ  N3   C5   N2   125.36  3.000
 HWQ  N4   C5   N2   117.32  3.000
 HWQ  C9   C6   N3   124.10  3.000
 HWQ  N3   C6   C7   124.03  3.000
 HWQ  C9   C6   C7   111.87  3.000
 HWQ  H5   C7   C8   124.34  3.000
 HWQ  H5   C7   C6   123.35  3.000
 HWQ  C8   C7   C6   112.31  3.000
 HWQ  C5   N2   C4   120.68  3.000
 HWQ  C6   N3   C5   114.98  3.000
 HWQ  S    C9   C6   111.08  3.000
 HWQ  C6   C9   C4   116.35  3.000
 HWQ  S    C9   C4   132.55  3.000
 HWQ  H6   C8   S    119.08  3.000
 HWQ  H6   C8   C7   127.33  3.000
 HWQ  S    C8   C7   113.59  3.000
 HWQ  C    N    C4   122.49  3.000
 HWQ  C4   N    C1   118.67  3.000
 HWQ  C    N    C1   118.39  3.000
 HWQ  H9   C    H8   107.06  3.000
 HWQ  H9   C    H7   109.38  3.000
 HWQ  H8   C    H7   106.94  3.000
 HWQ  H9   C    N    112.22  3.000
 HWQ  H8   C    N    108.84  3.000
 HWQ  H7   C    N    112.13  3.000
 HWQ  C8   S    C9    91.15  3.000
 HWQ  C11  N4   C10  119.15  3.000
 HWQ  C10  N4   C5   118.72  3.000
 HWQ  C11  N4   C5   122.06  3.000
 HWQ  H12  C10  H11  107.93  3.000
 HWQ  H12  C10  H10  107.74  3.000
 HWQ  H11  C10  H10  107.76  3.000
 HWQ  H12  C10  N4   109.18  3.000
 HWQ  H11  C10  N4   112.31  3.000
 HWQ  H10  C10  N4   111.75  3.000
 HWQ  H13  C11  C12  107.36  3.000
 HWQ  H13  C11  C15  107.43  3.000
 HWQ  C12  C11  C15  110.47  3.000
 HWQ  H13  C11  N4   106.18  3.000
 HWQ  C15  C11  N4   112.55  3.000
 HWQ  C12  C11  N4   112.50  3.000
 HWQ  H15  C15  H14  106.93  3.000
 HWQ  H15  C15  C14  110.06  3.000
 HWQ  H14  C15  C14  109.33  3.000
 HWQ  H15  C15  C11  109.92  3.000
 HWQ  H14  C15  C11  110.44  3.000
 HWQ  C14  C15  C11  110.11  3.000
 HWQ  H17  C14  H16  106.46  3.000
 HWQ  H17  C14  N5   107.83  3.000
 HWQ  H16  C14  N5   108.90  3.000
 HWQ  H17  C14  C15  109.07  3.000
 HWQ  H16  C14  C15  110.17  3.000
 HWQ  N5   C14  C15  114.11  3.000
 HWQ  H18  N5   C13  108.94  3.000
 HWQ  H18  N5   C14  108.98  3.000
 HWQ  C13  N5   C14  111.60  3.000
 HWQ  H21  C13  H20  106.46  3.000
 HWQ  H21  C13  C12  110.05  3.000
 HWQ  H20  C13  C12  109.14  3.000
 HWQ  H21  C13  N5   108.90  3.000
 HWQ  H20  C13  N5   107.92  3.000
 HWQ  C12  C13  N5   114.07  3.000
 HWQ  H23  C12  H22  107.08  3.000
 HWQ  H23  C12  C13  108.99  3.000
 HWQ  H22  C12  C13  110.11  3.000
 HWQ  H23  C12  C11  110.76  3.000
 HWQ  H22  C12  C11  109.84  3.000
 HWQ  C13  C12  C11  110.02  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
 HWQ  CONST_01  N3   C5   N2   C4      0.00   0.0  0
 HWQ  CONST_02  C8   S    C9   C4    180.00   0.0  0
 HWQ  CONST_03  N3   C6   C9   C4      0.00   0.0  0
 HWQ  CONST_04  C7   C6   C9   C4    180.00   0.0  0
 HWQ  CONST_05  C9   C4   N2   C5      0.00   0.0  0
 HWQ  CONST_06  C9   C6   N3   C5      0.00   0.0  0
 HWQ  CONST_07  C7   C6   N3   C5    180.00   0.0  0
 HWQ  CONST_08  N2   C4   C9   C6      0.00   0.0  0
 HWQ  CONST_09  C8   S    C9   C6      0.00   0.0  0
 HWQ  CONST_10  N2   C5   N3   C6      0.00   0.0  0
 HWQ  CONST_11  S    C8   C7   C6      0.00   0.0  0
 HWQ  CONST_12  S    C9   C6   C7      0.00   0.0  0
 HWQ  CONST_13  C9   S    C8   C7      0.00   0.0  0
 HWQ  CONST_14  S    C9   C4   N2    180.00   0.0  0
 HWQ  CONST_15  S    C9   C6   N3    180.00   0.0  0
 HWQ  CONST_16  C8   C7   C6   N3    180.00   0.0  0
 HWQ  CONST_17  C8   C7   C6   C9      0.00   0.0  0
 HWQ  CONST_18  N4   C5   N2   C4    180.00   0.0  0
 HWQ  CONST_19  N    C4   N2   C5    180.00   0.0  0
 HWQ  CONST_20  N    C4   C9   C6    180.00   0.0  0
 HWQ  CONST_21  N4   C5   N3   C6    180.00   0.0  0
 HWQ  CONST_22  S    C9   C4   N       0.00   0.0  0
 HWQ  CONST_23  C11  N4   C5   N2      0.00   0.0  0
 HWQ  CONST_24  C11  N4   C5   N3    180.00   0.0  0
 HWQ  CONST_25  H6   C8   C7   C6    180.00   0.0  0
 HWQ  CONST_26  H5   C7   C6   N3      0.00   0.0  0
 HWQ  CONST_27  N2   C4   N    C1      0.00   0.0  0
 HWQ  CONST_28  C9   C4   N    C1    180.00   0.0  0
 HWQ  CONST_29  C    N    C4   N2    180.00   0.0  0
 HWQ  CONST_30  C10  N4   C5   N2    180.00   0.0  0
 HWQ  CONST_31  C10  N4   C5   N3      0.00   0.0  0
 HWQ  CONST_32  C    N    C4   C9      0.00   0.0  0
 HWQ  Var_01    N5   C13  C12  C11    54.56  30.0  1
 HWQ  Var_02    N5   C14  C15  C11   -54.24  30.0  1
 HWQ  Var_03    C13  N5   C14  C15    53.75  30.0  1
 HWQ  Var_04    C12  C13  N5   C14   -53.93  30.0  1
 HWQ  Var_05    C4   N    C1   C2    -77.96  30.0  3
 HWQ  Var_06    H7   C    N    C4     51.89  30.0  3
 HWQ  Var_07    H10  C10  N4   C5    -55.02  30.0  3
 HWQ  Var_08    N    C1   C2   C3    178.13  30.0  1
 HWQ  Var_09    H3   C2   C3   N1   -152.50  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
 HWQ  chir_01  C11  C12  C15  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
 HWQ  plan-1  C4   0.020
 HWQ  plan-1  C5   0.020
 HWQ  plan-1  C6   0.020
 HWQ  plan-1  C7   0.020
 HWQ  plan-1  N2   0.020
 HWQ  plan-1  N3   0.020
 HWQ  plan-1  C9   0.020
 HWQ  plan-1  C8   0.020
 HWQ  plan-1  N    0.020
 HWQ  plan-1  S    0.020
 HWQ  plan-1  N4   0.020
 HWQ  plan-1  H5   0.020
 HWQ  plan-1  H6   0.020
 HWQ  plan-2  C1   0.020
 HWQ  plan-2  C4   0.020
 HWQ  plan-2  N    0.020
 HWQ  plan-2  C    0.020
 HWQ  plan-3  C5   0.020
 HWQ  plan-3  N4   0.020
 HWQ  plan-3  C10  0.020
 HWQ  plan-3  C11  0.020

