# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:50:36 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-(4-aminopiperidin-1-yl)-N-(5-cyclopropyl-1H-pyrazol-3-yl)thieno[3,2-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCN(CC1)c2nc(Nc3cc([nH]n3)C4CC4)c5sccc5n2
#
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
 4T3  4T3  2-(4-aminopiperidin-1-yl)-N-(5-cyclopropyl-1H-pyrazol-3-yl)thieno[3,2-d]pyrimidin-4-amine  ligand  46  25  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4T3
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
 4T3  C4   C  CR56  0  -0.400   2.2548  -1.2408   0.3725
 4T3  C5   C  CR56  0   0.314   3.1365  -0.2023   0.0843
 4T3  C7   C  CR6   0   0.621   1.4393   1.0850  -0.6510
 4T3  C13  C  CR5   0   0.496  -3.5271  -1.4294  -0.0571
 4T3  C17  C  CH1   0  -0.372  -4.8279  -0.8200  -0.3611
 4T3  C21  C  CH2   0  -0.331   1.8362   3.4329  -1.1671
 4T3  C22  C  CH2   0  -0.432   1.5437   4.2404   0.0938
 4T3  C24  C  CH2   0  -0.447  -0.8041   3.3471   0.0136
 4T3  C1   C  CR15  0  -0.204   4.4889  -0.5578   0.4040
 4T3  C2   C  CR15  0  -0.444   4.5806  -1.8102   0.9079
 4T3  S3   S  S2    0   0.209   3.0642  -2.6213   1.0279
 4T3  N6   N  N     0  -0.531   2.7414   0.9696  -0.4226
 4T3  N8   N  N     0  -0.531   0.5087   0.1443  -0.3986
 4T3  C9   C  CR6   0   0.584   0.8889  -1.0098   0.1119
 4T3  N10  N  NH1   0  -0.763  -0.0243  -1.9683   0.3894
 4T3  C11  C  CR5   0   0.459  -1.4040  -1.9177   0.2633
 4T3  C12  C  CR15  0  -0.554  -2.2624  -0.8840  -0.1585
 4T3  N14  N  NR15  0  -0.523  -3.3568  -2.6832   0.3919
 4T3  N16  N  N     0  -0.329  -2.0752  -3.0038   0.5952
 4T3  C18  C  CH2   0  -0.475  -5.9497  -1.6257  -0.9610
 4T3  C19  C  CH2   0  -0.476  -6.0543  -1.1487   0.4483
 4T3  N20  N  NT    0  -0.482   1.0007   2.2446  -1.2184
 4T3  C23  C  CH1   0  -0.083   0.0629   4.5971   0.1984
 4T3  C25  C  CH2   0  -0.341  -0.4110   2.5808  -1.2457
 4T3  N26  N  NH2   0  -0.791  -0.1853   5.3220   1.4360
 4T3  H1   H  HCH1  0   0.277  -4.7415   0.2047  -0.7004
 4T3  H2   H  HCH2  0   0.238   1.6148   4.0335  -2.0541
 4T3  H3   H  HCH2  0   0.265   2.8835   3.1515  -1.2188
 4T3  H4   H  HCH2  0   0.218   1.8497   3.6577   0.9705
 4T3  H5   H  HCH2  0   0.235   2.1456   5.1524   0.0949
 4T3  H6   H  HCH2  0   0.218  -0.6910   2.6899   0.8832
 4T3  H7   H  HCH2  0   0.232  -1.8593   3.6306  -0.0377
 4T3  H8   H  HCR5  0   0.273   5.3338   0.0984   0.2544
 4T3  H9   H  HCR5  0   0.308   5.4757  -2.3240   1.2242
 4T3  H10  H  HNH1  0   0.409   0.3151  -2.8397   0.7686
 4T3  H11  H  HCR5  0   0.285  -2.0061   0.1054  -0.4843
 4T3  H12  H  HNR5  0   0.418  -4.0657  -3.3698   0.5933
 4T3  H13  H  HCH2  0   0.266  -6.5563  -1.1428  -1.7158
 4T3  H14  H  HCH2  0   0.257  -5.7802  -2.6812  -1.1362
 4T3  H15  H  HCH2  0   0.257  -5.9588  -1.8760   1.2450
 4T3  H16  H  HCH2  0   0.266  -6.7339  -0.3361   0.6689
 4T3  H17  H  HCH1  0   0.215  -0.1668   5.2855  -0.6248
 4T3  H18  H  HCH2  0   0.270  -1.0063   1.6821  -1.3687
 4T3  H19  H  HCH2  0   0.241  -0.5820   3.2033  -2.1292
 4T3  H20  H  HNH2  0   0.342  -1.1596   5.5975   1.4749
 4T3  H21  H  HNH2  0   0.333  -0.0495   4.6942   2.2212

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
 4T3  S3   C2   aromatic  1.724  0.020  1.724
 4T3  S3   C4   aromatic  1.729  0.020  1.729
 4T3  C2   C1   aromatic  1.353  0.020  1.353
 4T3  N16  N14  aromatic  1.337  0.020  1.337
 4T3  N16  C11  aromatic  1.319  0.020  1.319
 4T3  N10  C11  single    1.386  0.020  1.386
 4T3  N10  C9   single    1.353  0.020  1.353
 4T3  C4   C9   aromatic  1.410  0.020  1.410
 4T3  C4   C5   aromatic  1.392  0.020  1.392
 4T3  C1   C5   aromatic  1.434  0.020  1.434
 4T3  N14  C13  aromatic  1.343  0.020  1.343
 4T3  C11  C12  aromatic  1.408  0.020  1.408
 4T3  C9   N8   aromatic  1.318  0.020  1.318
 4T3  C5   N6   aromatic  1.337  0.020  1.337
 4T3  C13  C12  aromatic  1.381  0.020  1.381
 4T3  C13  C17  single    1.468  0.020  1.468
 4T3  N8   C7   aromatic  1.347  0.020  1.347
 4T3  N6   C7   aromatic  1.327  0.020  1.327
 4T3  C7   N20  single    1.363  0.020  1.363
 4T3  C17  C19  single    1.506  0.020  1.506
 4T3  C17  C18  single    1.506  0.020  1.506
 4T3  N20  C21  single    1.453  0.020  1.453
 4T3  N20  C25  single    1.451  0.020  1.451
 4T3  C19  C18  single    1.492  0.020  1.492
 4T3  C21  C22  single    1.526  0.020  1.526
 4T3  C25  C24  single    1.526  0.020  1.526
 4T3  C22  C23  single    1.527  0.020  1.527
 4T3  C24  C23  single    1.532  0.020  1.532
 4T3  C23  N26  single    1.456  0.020  1.456
 4T3  C17  H1   single    0.970  0.020  1.090
 4T3  C21  H2   single    0.970  0.020  1.090
 4T3  C21  H3   single    0.970  0.020  1.090
 4T3  C22  H4   single    0.970  0.020  1.090
 4T3  C22  H5   single    0.970  0.020  1.090
 4T3  C24  H6   single    0.970  0.020  1.090
 4T3  C24  H7   single    0.970  0.020  1.090
 4T3  C1   H8   single    0.930  0.020  1.080
 4T3  C2   H9   single    0.930  0.020  1.080
 4T3  N10  H10  single    0.860  0.020  1.020
 4T3  C12  H11  single    0.930  0.020  1.080
 4T3  N14  H12  single    0.860  0.020  1.020
 4T3  C18  H13  single    0.970  0.020  1.090
 4T3  C18  H14  single    0.970  0.020  1.090
 4T3  C19  H15  single    0.970  0.020  1.090
 4T3  C19  H16  single    0.970  0.020  1.090
 4T3  C23  H17  single    0.970  0.020  1.090
 4T3  C25  H18  single    0.970  0.020  1.090
 4T3  C25  H19  single    0.970  0.020  1.090
 4T3  N26  H20  single    0.890  0.020  1.040
 4T3  N26  H21  single    0.890  0.020  1.040

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
 4T3  C9   C4   S3   130.87  3.000
 4T3  C9   C4   C5   116.95  3.000
 4T3  S3   C4   C5   112.17  3.000
 4T3  N6   C5   C1   125.49  3.000
 4T3  N6   C5   C4   123.04  3.000
 4T3  C1   C5   C4   111.47  3.000
 4T3  N20  C7   N8   116.73  3.000
 4T3  N20  C7   N6   117.46  3.000
 4T3  N8   C7   N6   125.80  3.000
 4T3  N14  C13  C12  106.09  3.000
 4T3  C12  C13  C17  129.21  3.000
 4T3  N14  C13  C17  124.70  3.000
 4T3  H1   C17  C19  116.10  3.000
 4T3  H1   C17  C18  116.16  3.000
 4T3  C19  C17  C18   59.37  3.000
 4T3  H1   C17  C13  112.77  3.000
 4T3  C18  C17  C13  121.36  3.000
 4T3  C19  C17  C13  121.31  3.000
 4T3  H3   C21  H2   107.39  3.000
 4T3  H3   C21  N20  109.93  3.000
 4T3  H2   C21  N20  107.70  3.000
 4T3  H3   C21  C22  111.19  3.000
 4T3  H2   C21  C22  109.92  3.000
 4T3  N20  C21  C22  110.59  3.000
 4T3  H5   C22  H4   106.81  3.000
 4T3  H5   C22  C23  109.83  3.000
 4T3  H4   C22  C23  109.89  3.000
 4T3  H5   C22  C21  109.69  3.000
 4T3  H4   C22  C21  109.03  3.000
 4T3  C23  C22  C21  111.48  3.000
 4T3  H7   C24  H6   106.99  3.000
 4T3  H7   C24  C25  109.88  3.000
 4T3  H6   C24  C25  109.10  3.000
 4T3  H7   C24  C23  109.88  3.000
 4T3  H6   C24  C23  109.58  3.000
 4T3  C25  C24  C23  111.32  3.000
 4T3  H8   C1   C2   124.11  3.000
 4T3  H8   C1   C5   123.78  3.000
 4T3  C2   C1   C5   112.11  3.000
 4T3  H9   C2   S3   119.01  3.000
 4T3  H9   C2   C1   127.30  3.000
 4T3  S3   C2   C1   113.69  3.000
 4T3  C2   S3   C4    90.56  3.000
 4T3  C7   N6   C5   115.57  3.000
 4T3  C9   N8   C7   119.00  3.000
 4T3  N10  C9   N8   120.35  3.000
 4T3  N8   C9   C4   119.64  3.000
 4T3  N10  C9   C4   120.01  3.000
 4T3  H10  N10  C11  113.61  3.000
 4T3  H10  N10  C9   117.51  3.000
 4T3  C11  N10  C9   128.85  3.000
 4T3  N16  C11  C12  111.69  3.000
 4T3  C12  C11  N10  131.35  3.000
 4T3  N16  C11  N10  116.96  3.000
 4T3  H11  C12  C11  128.49  3.000
 4T3  H11  C12  C13  127.25  3.000
 4T3  C11  C12  C13  104.26  3.000
 4T3  H12  N14  N16  118.75  3.000
 4T3  H12  N14  C13  127.89  3.000
 4T3  N16  N14  C13  113.36  3.000
 4T3  N14  N16  C11  104.60  3.000
 4T3  H14  C18  H13  114.19  3.000
 4T3  H14  C18  C19  118.38  3.000
 4T3  H13  C18  C19  118.50  3.000
 4T3  H14  C18  C17  117.98  3.000
 4T3  H13  C18  C17  117.18  3.000
 4T3  C19  C18  C17   60.31  3.000
 4T3  H16  C19  H15  114.19  3.000
 4T3  H16  C19  C18  118.48  3.000
 4T3  H15  C19  C18  118.30  3.000
 4T3  H16  C19  C17  117.21  3.000
 4T3  H15  C19  C17  118.05  3.000
 4T3  C18  C19  C17   60.32  3.000
 4T3  C25  N20  C21  111.74  3.000
 4T3  C25  N20  C7   121.18  3.000
 4T3  C21  N20  C7   119.72  3.000
 4T3  H17  C23  N26  106.84  3.000
 4T3  H17  C23  C24  107.63  3.000
 4T3  N26  C23  C24  114.35  3.000
 4T3  H17  C23  C22  107.35  3.000
 4T3  N26  C23  C22  109.87  3.000
 4T3  C24  C23  C22  110.48  3.000
 4T3  H19  C25  H18  107.10  3.000
 4T3  H19  C25  N20  107.40  3.000
 4T3  H18  C25  N20  110.12  3.000
 4T3  H19  C25  C24  109.91  3.000
 4T3  H18  C25  C24  111.60  3.000
 4T3  N20  C25  C24  110.57  3.000
 4T3  H21  N26  H20  105.50  3.000
 4T3  H21  N26  C23  109.09  3.000
 4T3  H20  N26  C23  109.39  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
 4T3  CONST_01  C1   C2   S3   C4      0.00   0.0  0
 4T3  CONST_02  C7   N8   C9   C4      0.00   0.0  0
 4T3  CONST_03  C2   C1   C5   C4      0.00   0.0  0
 4T3  CONST_04  C7   N6   C5   C4      0.00   0.0  0
 4T3  CONST_05  C2   S3   C4   C5      0.00   0.0  0
 4T3  CONST_06  N8   C9   C4   C5      0.00   0.0  0
 4T3  CONST_07  S3   C2   C1   C5      0.00   0.0  0
 4T3  CONST_08  N8   C7   N6   C5      0.00   0.0  0
 4T3  CONST_09  C1   C5   N6   C7    180.00   0.0  0
 4T3  CONST_10  C11  N16  N14  C13     0.00   0.0  0
 4T3  CONST_11  N16  C11  C12  C13     0.00   0.0  0
 4T3  CONST_12  S3   C4   C5   C1      0.00   0.0  0
 4T3  CONST_13  C9   C4   C5   C1    180.00   0.0  0
 4T3  CONST_14  C9   C4   S3   C2    180.00   0.0  0
 4T3  CONST_15  N6   C5   C1   C2    180.00   0.0  0
 4T3  CONST_16  N8   C9   C4   S3    180.00   0.0  0
 4T3  CONST_17  N6   C5   C4   S3    180.00   0.0  0
 4T3  CONST_18  C9   C4   C5   N6      0.00   0.0  0
 4T3  CONST_19  C9   N8   C7   N6      0.00   0.0  0
 4T3  CONST_20  N14  C13  C12  C11     0.00   0.0  0
 4T3  CONST_21  N14  N16  C11  C12     0.00   0.0  0
 4T3  CONST_22  N16  N14  C13  C12     0.00   0.0  0
 4T3  CONST_23  N20  C7   N6   C5    180.00   0.0  0
 4T3  CONST_24  N16  N14  C13  C17   180.00   0.0  0
 4T3  CONST_25  C11  C12  C13  C17   180.00   0.0  0
 4T3  CONST_26  N20  C7   N8   C9    180.00   0.0  0
 4T3  CONST_27  N10  C9   C4   C5    180.00   0.0  0
 4T3  CONST_28  N10  C9   N8   C7    180.00   0.0  0
 4T3  CONST_29  N10  C11  C12  C13   180.00   0.0  0
 4T3  CONST_30  N10  C9   C4   S3      0.00   0.0  0
 4T3  CONST_31  N14  N16  C11  N10   180.00   0.0  0
 4T3  CONST_32  H9   C2   S3   C4    180.00   0.0  0
 4T3  CONST_33  H8   C1   C5   C4    180.00   0.0  0
 4T3  CONST_34  H12  N14  C13  C17     0.00   0.0  0
 4T3  CONST_35  H11  C12  C13  C17     0.00   0.0  0
 4T3  Var_01    C22  C21  N20  C7    -89.55  30.0  1
 4T3  Var_02    C24  C25  N20  C7     88.90  30.0  1
 4T3  Var_03    C18  C19  C17  C13  -110.36  30.0  1
 4T3  Var_04    N8   C7   N20  C21   162.17  30.0  1
 4T3  Var_05    C19  C17  C13  C12  -145.12  30.0  2
 4T3  Var_06    C23  C22  C21  N20   -55.54  30.0  1
 4T3  Var_07    C23  C24  C25  N20    55.71  30.0  1
 4T3  Var_08    C11  N10  C9   C4    176.92  30.0  2
 4T3  Var_09    N16  C11  N10  C9    179.50  30.0  2

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
 4T3  chir_02  C23  C22  C24  N26  negativ
 4T3  chir_03  C17  C13  C19  C18  both

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
 4T3  plan-1  C13  0.020
 4T3  plan-1  C17  0.020
 4T3  plan-1  N10  0.020
 4T3  plan-1  C11  0.020
 4T3  plan-1  C12  0.020
 4T3  plan-1  N14  0.020
 4T3  plan-1  N16  0.020
 4T3  plan-1  H11  0.020
 4T3  plan-1  H12  0.020
 4T3  plan-2  C4   0.020
 4T3  plan-2  C5   0.020
 4T3  plan-2  C7   0.020
 4T3  plan-2  C1   0.020
 4T3  plan-2  C2   0.020
 4T3  plan-2  S3   0.020
 4T3  plan-2  N6   0.020
 4T3  plan-2  N8   0.020
 4T3  plan-2  C9   0.020
 4T3  plan-2  N10  0.020
 4T3  plan-2  N20  0.020
 4T3  plan-2  H8   0.020
 4T3  plan-2  H9   0.020

