# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 05:13:14 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 3-ethyl-2-(propan-2-ylamino)-7-(pyridin-3-yl)thieno[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)c2scc(c3cccnc3)c2N=C1NC(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
 EPK  EPK  3-ethyl-2-(propan-2-ylamino)-7-(pyridin-3-yl)thieno[3,2-d]pyrimidin-4(3H)-one  ligand  40  22  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EPK
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
 EPK  C1   C  CR56  0  -0.426  -0.6854   1.8421  -0.0605
 EPK  C2   C  CR56  0   0.302   0.1628   0.7559  -0.0787
 EPK  C3   C  CR6   0   0.767  -1.5696  -0.6938  -0.2428
 EPK  N1   N  NR6   0  -0.586  -2.4865   0.3391  -0.2534
 EPK  N2   N  N     0  -0.529  -0.2767  -0.5122  -0.1678
 EPK  C4   C  CR6   0   0.591  -2.0964   1.6787  -0.1338
 EPK  C5   C  CR5   0   0.152   1.5433   1.1534   0.0049
 EPK  S1   S  S2    0   0.259   0.1496   3.3399   0.0612
 EPK  C6   C  CR15  0  -0.554   1.6505   2.5120   0.0805
 EPK  N3   N  NH1   0  -0.689  -2.0337  -1.9503  -0.3394
 EPK  O1   O  O     0  -0.477  -2.9162   2.5836  -0.1046
 EPK  C7   C  CR6   0  -0.001   2.6859   0.2349  -0.0040
 EPK  N4   N  N     0  -0.402   3.6539  -1.8464   0.7027
 EPK  C8   C  CH2   0  -0.375  -3.9253   0.0758  -0.3378
 EPK  C9   C  CR16  0  -0.098   2.6414  -0.9921   0.6631
 EPK  C10  C  CH1   0  -0.088  -1.1627  -3.1183  -0.2735
 EPK  C11  C  CR16  0  -0.072   4.7775  -1.5193   0.0741
 EPK  C12  C  CR16  0  -0.196   3.8724   0.5578  -0.6591
 EPK  C13  C  CH3   0  -0.658  -4.5481  -0.2136   1.0180
 EPK  C14  C  CH3   0  -0.655  -0.7838  -3.4550   1.1636
 EPK  C15  C  CH3   0  -0.672  -1.8621  -4.2805  -0.9606
 EPK  C16  C  CR16  0  -0.316   4.9357  -0.3282  -0.6174
 EPK  H1   H  HCR5  0   0.305   2.5632   3.0833   0.1695
 EPK  H2   H  HNH1  0   0.413  -3.0183  -2.1283  -0.2384
 EPK  H3   H  HCH2  0   0.289  -4.3888   0.9536  -0.7781
 EPK  H4   H  HCH2  0   0.266  -4.0952  -0.7340  -1.0465
 EPK  H5   H  HCR6  0   0.268   1.7426  -1.2877   1.1901
 EPK  H6   H  HCH1  0   0.252  -0.2565  -2.8720  -0.8272
 EPK  H7   H  HCR6  0   0.265   5.5886  -2.2369   0.1223
 EPK  H8   H  HCR6  0   0.268   3.9580   1.4872  -1.2083
 EPK  H9   H  HCH3  0   0.248  -5.6125  -0.4113   0.8961
 EPK  H10  H  HCH3  0   0.228  -4.1043  -1.0815   1.5074
 EPK  H11  H  HCH3  0   0.245  -4.4378   0.6406   1.6843
 EPK  H12  H  HCH3  0   0.230  -0.0816  -4.2893   1.1857
 EPK  H13  H  HCH3  0   0.243  -0.3098  -2.6052   1.6540
 EPK  H14  H  HCH3  0   0.221  -1.6642  -3.7409   1.7428
 EPK  H15  H  HCH3  0   0.242  -2.1172  -4.0375  -1.9922
 EPK  H16  H  HCH3  0   0.242  -1.2122  -5.1550  -0.9711
 EPK  H17  H  HCH3  0   0.227  -2.7794  -4.5566  -0.4356
 EPK  H18  H  HCR6  0   0.273   5.8673  -0.1056  -1.1193

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
 EPK  C11  C16  aromatic  1.386  0.020  1.386
 EPK  C11  N4   aromatic  1.328  0.020  1.328
 EPK  C16  C12  aromatic  1.385  0.020  1.385
 EPK  N4   C9   aromatic  1.325  0.020  1.325
 EPK  C15  C10  single    1.521  0.020  1.521
 EPK  C12  C7   aromatic  1.393  0.020  1.393
 EPK  C9   C7   aromatic  1.397  0.020  1.397
 EPK  C10  N3   single    1.458  0.020  1.458
 EPK  C10  C14  single    1.524  0.020  1.524
 EPK  C7   C5   single    1.466  0.020  1.466
 EPK  N3   C3   single    1.343  0.020  1.343
 EPK  N2   C3   double    1.308  0.020  1.308
 EPK  N2   C2   single    1.345  0.020  1.345
 EPK  C5   C2   aromatic  1.439  0.020  1.439
 EPK  C5   C6   aromatic  1.365  0.020  1.365
 EPK  C13  C8   single    1.520  0.020  1.520
 EPK  C3   N1   single    1.381  0.020  1.381
 EPK  C2   C1   aromatic  1.378  0.020  1.378
 EPK  C6   S1   aromatic  1.714  0.020  1.714
 EPK  N1   C8   single    1.465  0.020  1.465
 EPK  N1   C4   single    1.400  0.020  1.400
 EPK  C1   C4   single    1.422  0.020  1.422
 EPK  C1   S1   aromatic  1.719  0.020  1.719
 EPK  C4   O1   double    1.221  0.020  1.221
 EPK  C6   H1   single    0.930  0.020  1.080
 EPK  N3   H2   single    0.860  0.020  1.020
 EPK  C8   H3   single    0.970  0.020  1.090
 EPK  C8   H4   single    0.970  0.020  1.090
 EPK  C9   H5   single    0.930  0.020  1.080
 EPK  C10  H6   single    0.970  0.020  1.090
 EPK  C11  H7   single    0.930  0.020  1.080
 EPK  C12  H8   single    0.930  0.020  1.080
 EPK  C13  H9   single    0.970  0.020  1.090
 EPK  C13  H10  single    0.970  0.020  1.090
 EPK  C13  H11  single    0.970  0.020  1.090
 EPK  C14  H12  single    0.970  0.020  1.090
 EPK  C14  H13  single    0.970  0.020  1.090
 EPK  C14  H14  single    0.970  0.020  1.090
 EPK  C15  H15  single    0.970  0.020  1.090
 EPK  C15  H16  single    0.970  0.020  1.090
 EPK  C15  H17  single    0.970  0.020  1.090
 EPK  C16  H18  single    0.930  0.020  1.080

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
 EPK  S1   C1   C4   125.84  3.000
 EPK  S1   C1   C2   112.87  3.000
 EPK  C4   C1   C2   121.29  3.000
 EPK  C5   C2   N2   125.30  3.000
 EPK  C5   C2   C1   111.83  3.000
 EPK  N2   C2   C1   122.87  3.000
 EPK  N3   C3   N2   118.40  3.000
 EPK  N2   C3   N1   123.57  3.000
 EPK  N3   C3   N1   118.02  3.000
 EPK  C8   N1   C4   116.77  3.000
 EPK  C4   N1   C3   121.99  3.000
 EPK  C8   N1   C3   121.19  3.000
 EPK  C3   N2   C2   117.24  3.000
 EPK  O1   C4   N1   121.59  3.000
 EPK  O1   C4   C1   125.42  3.000
 EPK  N1   C4   C1   112.99  3.000
 EPK  C7   C5   C6   124.25  3.000
 EPK  C6   C5   C2   110.70  3.000
 EPK  C7   C5   C2   125.04  3.000
 EPK  C6   S1   C1    90.30  3.000
 EPK  H1   C6   S1   119.03  3.000
 EPK  H1   C6   C5   126.67  3.000
 EPK  S1   C6   C5   114.29  3.000
 EPK  H2   N3   C10  116.00  3.000
 EPK  H2   N3   C3   119.78  3.000
 EPK  C10  N3   C3   122.66  3.000
 EPK  C12  C7   C9   117.07  3.000
 EPK  C9   C7   C5   121.50  3.000
 EPK  C12  C7   C5   121.42  3.000
 EPK  C11  N4   C9   118.25  3.000
 EPK  H4   C8   H3   105.69  3.000
 EPK  H4   C8   C13  112.01  3.000
 EPK  H3   C8   C13  109.92  3.000
 EPK  H4   C8   N1   108.92  3.000
 EPK  H3   C8   N1   107.29  3.000
 EPK  C13  C8   N1   112.66  3.000
 EPK  H5   C9   N4   116.33  3.000
 EPK  H5   C9   C7   119.89  3.000
 EPK  N4   C9   C7   123.78  3.000
 EPK  H6   C10  C15  109.00  3.000
 EPK  H6   C10  C14  108.80  3.000
 EPK  C15  C10  C14  111.81  3.000
 EPK  H6   C10  N3   107.01  3.000
 EPK  C14  C10  N3   111.59  3.000
 EPK  C15  C10  N3   108.48  3.000
 EPK  H7   C11  C16  120.37  3.000
 EPK  H7   C11  N4   116.67  3.000
 EPK  C16  C11  N4   122.96  3.000
 EPK  H8   C12  C16  120.25  3.000
 EPK  H8   C12  C7   120.31  3.000
 EPK  C16  C12  C7   119.44  3.000
 EPK  H11  C13  H10  107.96  3.000
 EPK  H11  C13  H9   108.04  3.000
 EPK  H10  C13  H9   107.66  3.000
 EPK  H11  C13  C8   110.79  3.000
 EPK  H10  C13  C8   112.65  3.000
 EPK  H9   C13  C8   109.58  3.000
 EPK  H14  C14  H13  108.44  3.000
 EPK  H14  C14  H12  107.94  3.000
 EPK  H13  C14  H12  107.90  3.000
 EPK  H14  C14  C10  110.95  3.000
 EPK  H13  C14  C10  111.12  3.000
 EPK  H12  C14  C10  110.37  3.000
 EPK  H17  C15  H16  107.62  3.000
 EPK  H17  C15  H15  108.34  3.000
 EPK  H16  C15  H15  108.02  3.000
 EPK  H17  C15  C10  111.24  3.000
 EPK  H16  C15  C10  110.08  3.000
 EPK  H15  C15  C10  111.40  3.000
 EPK  H18  C16  C12  121.05  3.000
 EPK  H18  C16  C11  120.44  3.000
 EPK  C12  C16  C11  118.50  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
 EPK  CONST_01  C7   C5   C2   C1   180.00   0.0  0
 EPK  CONST_02  C6   C5   C2   C1     0.00   0.0  0
 EPK  CONST_03  C5   C6   S1   C1     0.00   0.0  0
 EPK  CONST_06  S1   C6   C5   C2     0.00   0.0  0
 EPK  CONST_07  C6   S1   C1   C2     0.00   0.0  0
 EPK  CONST_08  C16  C12  C7   C5   180.00   0.0  0
 EPK  CONST_09  N4   C9   C7   C5   180.00   0.0  0
 EPK  CONST_10  S1   C1   C2   C5     0.00   0.0  0
 EPK  CONST_11  C7   C5   C6   S1   180.00   0.0  0
 EPK  CONST_14  C11  C16  C12  C7     0.00   0.0  0
 EPK  CONST_15  C11  N4   C9   C7     0.00   0.0  0
 EPK  CONST_16  C12  C16  C11  N4     0.00   0.0  0
 EPK  CONST_17  C12  C7   C9   N4     0.00   0.0  0
 EPK  CONST_18  C16  C11  N4   C9     0.00   0.0  0
 EPK  CONST_19  C16  C12  C7   C9     0.00   0.0  0
 EPK  CONST_20  C7   C5   C2   N2     0.00   0.0  0
 EPK  CONST_21  C3   N1   C4   C1     0.00   0.0  0
 EPK  CONST_22  N1   C3   N2   C2     0.00   0.0  0
 EPK  CONST_23  C4   N1   C3   N2     0.00   0.0  0
 EPK  CONST_24  C8   N1   C4   C1   180.00   0.0  0
 EPK  CONST_25  N3   C3   N2   C2   180.00   0.0  0
 EPK  CONST_26  O1   C4   N1   C3   180.00   0.0  0
 EPK  CONST_27  C8   N1   C3   N2   180.00   0.0  0
 EPK  CONST_28  N3   C3   N1   C4   180.00   0.0  0
 EPK  CONST_29  H1   C6   S1   C1   180.00   0.0  0
 EPK  CONST_30  H8   C12  C7   C5     0.00   0.0  0
 EPK  CONST_31  H5   C9   C7   C5     0.00   0.0  0
 EPK  CONST_32  H18  C16  C12  C7   180.00   0.0  0
 EPK  CONST_33  H7   C11  N4   C9   180.00   0.0  0
 EPK  CONST_34  C10  N3   C3   N1   180.00   0.0  0
 EPK  CONST_35  C10  N3   C3   N2     0.00   0.0  0
 EPK  CONST_36  C8   N1   C3   N3     0.00   0.0  0
 EPK  CONST_37  C8   N1   C4   O1     0.00   0.0  0
 EPK  CONST_38  H2   N3   C3   N1     0.00   0.0  0
 EPK  Var_01    C13  C8   N1   C3    84.42  30.0  3
 EPK  Var_02    C15  C10  N3   C3  -157.10  30.0  2
 EPK  Var_03    H9   C13  C8   N1  -179.44  30.0  3
 EPK  Var_04    H15  C15  C10  N3    57.33  30.0  3
 EPK  Var_05    H12  C14  C10  N3  -176.30  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
 EPK  plan-1  C5   0.020
 EPK  plan-1  C7   0.020
 EPK  plan-1  N4   0.020
 EPK  plan-1  C9   0.020
 EPK  plan-1  C11  0.020
 EPK  plan-1  C12  0.020
 EPK  plan-1  C16  0.020
 EPK  plan-1  H5   0.020
 EPK  plan-1  H7   0.020
 EPK  plan-1  H8   0.020
 EPK  plan-1  H18  0.020
 EPK  plan-2  C1   0.020
 EPK  plan-2  C2   0.020
 EPK  plan-2  C3   0.020
 EPK  plan-2  N1   0.020
 EPK  plan-2  N2   0.020
 EPK  plan-2  C4   0.020
 EPK  plan-2  C5   0.020
 EPK  plan-2  S1   0.020
 EPK  plan-2  C6   0.020
 EPK  plan-2  N3   0.020
 EPK  plan-2  O1   0.020
 EPK  plan-2  C7   0.020
 EPK  plan-2  C8   0.020
 EPK  plan-2  C10  0.020
 EPK  plan-2  H1   0.020
 EPK  plan-2  H2   0.020

