# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 06:49:45 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-{5-[(2E,4S)-2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl]thiophen-3-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N)N[C@@](C)(CC1=O)c2scc(c2)c3cccc(c3)C#N
#
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
 13W  13W  3-{5-[(2E,4S)-2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl]thiophen-3-yl}benzonitrile  ligand  39  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_13W
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
 13W  C1   C  CR16  0  -0.225   3.8690  -1.9696  -0.9168
 13W  C2   C  CR16  0  -0.255   4.8531  -1.4744  -0.0790
 13W  C3   C  CR6   0   0.032   4.5984  -0.3029   0.6332
 13W  C4   C  CR16  0  -0.318   3.3817   0.3622   0.5105
 13W  C5   C  CR6   0   0.123   2.3955  -0.1316  -0.3397
 13W  C6   C  CR16  0  -0.303   2.6574  -1.3071  -1.0472
 13W  C7   C  CR5   0   0.207   1.1135   0.5692  -0.4907
 13W  C8   C  CR15  0  -0.281  -0.1102  -0.0729  -0.8572
 13W  C9   C  CR5   0  -0.109  -1.1683   0.7776  -0.9310
 13W  S1   S  S2    0   0.248  -0.6782   2.3900  -0.5601
 13W  C10  C  CR15  0  -0.571   0.9407   1.9111  -0.3016
 13W  C11  C  CT    0  -0.013  -2.6038   0.4564  -1.3047
 13W  C12  C  CH2   0  -0.558  -3.5740   1.0210  -0.2748
 13W  C13  C  C     0   0.563  -3.4086   0.3528   1.0615
 13W  N1   N  NT    0  -0.537  -3.0180  -0.9654   1.0345
 13W  C14  C  C     0   0.623  -2.8356  -1.6987  -0.1496
 13W  N2   N  NH1   0  -0.641  -2.8299  -0.9674  -1.3010
 13W  N3   N  N     0  -0.691  -2.6872  -2.9617  -0.2073
 13W  C15  C  CH3   0  -0.638  -2.9166   0.9989  -2.6960
 13W  C16  C  CH3   0  -0.573  -2.8403  -1.6782   2.2896
 13W  O1   O  O     0  -0.450  -3.6256   0.9362   2.1038
 13W  C17  C  CSP   0   0.054   5.5946   0.2199   1.5129
 13W  N4   N  NS    0  -0.249   6.3995   0.6411   2.2214
 13W  H1   H  HCR6  0   0.277   4.0475  -2.8766  -1.4775
 13W  H2   H  HCR6  0   0.284   5.8007  -1.9846   0.0251
 13W  H3   H  HCR6  0   0.278   3.2054   1.2584   1.0908
 13W  H4   H  HCR6  0   0.270   1.9133  -1.7083  -1.7229
 13W  H5   H  HCR5  0   0.267  -0.1953  -1.1361  -1.0339
 13W  H6   H  HCR5  0   0.298   1.6844   2.6489  -0.0394
 13W  H7   H  HCH2  0   0.285  -3.4629   2.0969  -0.1423
 13W  H8   H  HCH2  0   0.306  -4.5983   0.8445  -0.6183
 13W  H9   H  H     0   0.353  -2.7973  -3.4192   0.6864
 13W  H11  H  HCH3  0   0.252  -2.2523   0.5547  -3.4384
 13W  H12  H  HCH3  0   0.252  -3.9473   0.7741  -2.9709
 13W  H13  H  HCH3  0   0.245  -2.7810   2.0794  -2.7288
 13W  H14  H  HCH3  0   0.259  -3.6537  -2.3824   2.4667
 13W  H15  H  HCH3  0   0.260  -1.8953  -2.2183   2.2805
 13W  H16  H  HCH3  0   0.279  -2.8199  -0.9669   3.1060
 13W  H17  H  HNH1  0   0.397  -2.5594  -1.4919  -2.1194

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
 13W  C1   C6   aromatic  1.387  0.020  1.387
 13W  C1   C2   aromatic  1.384  0.020  1.384
 13W  C6   C5   aromatic  1.397  0.020  1.397
 13W  C10  S1   aromatic  1.708  0.020  1.708
 13W  C10  C7   aromatic  1.366  0.020  1.366
 13W  S1   C9   aromatic  1.726  0.020  1.726
 13W  C2   C3   aromatic  1.394  0.020  1.394
 13W  C5   C7   single    1.469  0.020  1.469
 13W  C5   C4   aromatic  1.393  0.020  1.393
 13W  C7   C8   aromatic  1.430  0.020  1.430
 13W  C9   C8   aromatic  1.360  0.020  1.360
 13W  C9   C11  single    1.518  0.020  1.518
 13W  C15  C11  single    1.526  0.020  1.526
 13W  C3   C4   aromatic  1.392  0.020  1.392
 13W  C3   C17  single    1.428  0.020  1.428
 13W  C11  C12  single    1.523  0.020  1.523
 13W  C11  N2   single    1.442  0.020  1.442
 13W  C17  N4   triple    1.152  0.020  1.152
 13W  C12  C13  single    1.503  0.020  1.503
 13W  N2   C14  single    1.364  0.020  1.364
 13W  C13  O1   double    1.214  0.020  1.214
 13W  C13  N1   single    1.375  0.020  1.375
 13W  C14  N1   single    1.405  0.020  1.405
 13W  C14  N3   double    1.273  0.020  1.273
 13W  N1   C16  single    1.454  0.020  1.454
 13W  C1   H1   single    0.930  0.020  1.080
 13W  C2   H2   single    0.930  0.020  1.080
 13W  C4   H3   single    0.930  0.020  1.080
 13W  C6   H4   single    0.930  0.020  1.080
 13W  C8   H5   single    0.930  0.020  1.080
 13W  C10  H6   single    0.930  0.020  1.080
 13W  C12  H7   single    0.970  0.020  1.090
 13W  C12  H8   single    0.970  0.020  1.090
 13W  N3   H9   single    0.890  0.020  1.040
 13W  C15  H11  single    0.970  0.020  1.090
 13W  C15  H12  single    0.970  0.020  1.090
 13W  C15  H13  single    0.970  0.020  1.090
 13W  C16  H14  single    0.970  0.020  1.090
 13W  C16  H15  single    0.970  0.020  1.090
 13W  C16  H16  single    0.970  0.020  1.090
 13W  N2   H17  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
 13W  H1   C1   C6   119.75  3.000
 13W  H1   C1   C2   119.78  3.000
 13W  C6   C1   C2   120.47  3.000
 13W  H2   C2   C3   120.49  3.000
 13W  H2   C2   C1   120.84  3.000
 13W  C3   C2   C1   118.67  3.000
 13W  C17  C3   C4   119.28  3.000
 13W  C17  C3   C2   119.65  3.000
 13W  C4   C3   C2   121.07  3.000
 13W  H3   C4   C5   120.38  3.000
 13W  H3   C4   C3   119.40  3.000
 13W  C5   C4   C3   120.22  3.000
 13W  C7   C5   C6   120.87  3.000
 13W  C7   C5   C4   120.77  3.000
 13W  C6   C5   C4   118.35  3.000
 13W  H4   C6   C5   119.95  3.000
 13W  H4   C6   C1   118.83  3.000
 13W  C5   C6   C1   121.21  3.000
 13W  C10  C7   C8   111.62  3.000
 13W  C8   C7   C5   124.00  3.000
 13W  C10  C7   C5   124.39  3.000
 13W  H5   C8   C9   123.03  3.000
 13W  H5   C8   C7   123.43  3.000
 13W  C9   C8   C7   113.52  3.000
 13W  C11  C9   S1   121.29  3.000
 13W  C11  C9   C8   128.11  3.000
 13W  S1   C9   C8   110.60  3.000
 13W  C10  S1   C9    92.28  3.000
 13W  H6   C10  S1   119.87  3.000
 13W  H6   C10  C7   128.14  3.000
 13W  S1   C10  C7   111.98  3.000
 13W  C15  C11  N2   108.74  3.000
 13W  N2   C11  C12  105.33  3.000
 13W  C15  C11  C12  110.74  3.000
 13W  N2   C11  C9   110.90  3.000
 13W  C12  C11  C9   110.95  3.000
 13W  C15  C11  C9   110.07  3.000
 13W  H8   C12  H7   107.02  3.000
 13W  H8   C12  C13  108.08  3.000
 13W  H7   C12  C13  108.64  3.000
 13W  H8   C12  C11  108.91  3.000
 13W  H7   C12  C11  112.53  3.000
 13W  C13  C12  C11  111.48  3.000
 13W  O1   C13  N1   121.89  3.000
 13W  N1   C13  C12  116.10  3.000
 13W  O1   C13  C12  122.00  3.000
 13W  C16  N1   C14  117.11  3.000
 13W  C16  N1   C13  119.19  3.000
 13W  C14  N1   C13  123.63  3.000
 13W  N3   C14  N2   119.55  3.000
 13W  N3   C14  N1   124.84  3.000
 13W  N2   C14  N1   115.61  3.000
 13W  H17  N2   C14  114.02  3.000
 13W  H17  N2   C11  117.99  3.000
 13W  C14  N2   C11  122.16  3.000
 13W  H9   N3   C14  113.36  3.000
 13W  H13  C15  H12  108.34  3.000
 13W  H13  C15  H11  107.91  3.000
 13W  H12  C15  H11  108.67  3.000
 13W  H13  C15  C11  110.77  3.000
 13W  H12  C15  C11  110.51  3.000
 13W  H11  C15  C11  110.55  3.000
 13W  H16  C16  H15  108.42  3.000
 13W  H16  C16  H14  108.41  3.000
 13W  H15  C16  H14  109.18  3.000
 13W  H16  C16  N1   109.33  3.000
 13W  H15  C16  N1   110.00  3.000
 13W  H14  C16  N1   111.44  3.000
 13W  N4   C17  C3   180.00  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
 13W  CONST_01  C7   C5   C6   C1    180.00   0.0  0
 13W  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 13W  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 13W  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 13W  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 13W  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 13W  CONST_07  C6   C5   C4   C3      0.00   0.0  0
 13W  CONST_08  C7   C5   C4   C3    180.00   0.0  0
 13W  CONST_11  S1   C10  C7   C5    180.00   0.0  0
 13W  CONST_12  C9   C8   C7   C5    180.00   0.0  0
 13W  CONST_15  C9   S1   C10  C7      0.00   0.0  0
 13W  CONST_16  S1   C9   C8   C7      0.00   0.0  0
 13W  CONST_17  S1   C10  C7   C8      0.00   0.0  0
 13W  CONST_18  C10  S1   C9   C8      0.00   0.0  0
 13W  CONST_19  C10  C7   C8   C9      0.00   0.0  0
 13W  CONST_20  C11  C9   C8   C7    180.00   0.0  0
 13W  CONST_21  C11  C9   S1   C10   180.00   0.0  0
 13W  CONST_23  C14  N1   C13  C12     0.00   0.0  0
 13W  CONST_24  N2   C14  N1   C13     0.00   0.0  0
 13W  CONST_25  C17  C3   C2   C1    180.00   0.0  0
 13W  CONST_26  C17  C3   C4   C5    180.00   0.0  0
 13W  CONST_28  C16  N1   C13  C12   180.00   0.0  0
 13W  CONST_29  N3   C14  N1   C13   180.00   0.0  0
 13W  CONST_30  O1   C13  N1   C14   180.00   0.0  0
 13W  CONST_31  C16  N1   C14  N2    180.00   0.0  0
 13W  CONST_32  H4   C6   C1   C2    180.00   0.0  0
 13W  CONST_33  H3   C4   C3   C2    180.00   0.0  0
 13W  CONST_34  H1   C1   C2   C3    180.00   0.0  0
 13W  CONST_35  H2   C2   C3   C4    180.00   0.0  0
 13W  CONST_36  H6   C10  C7   C5      0.00   0.0  0
 13W  CONST_37  H5   C8   C7   C5      0.00   0.0  0
 13W  CONST_38  H17  N2   C14  N1    180.00   0.0  0
 13W  CONST_39  C16  N1   C14  N3      0.00   0.0  0
 13W  CONST_40  O1   C13  N1   C16     0.00   0.0  0
 13W  CONST_41  H9   N3   C14  N1      0.00   0.0  0
 13W  Var_01    H7   C12  C13  N1   -156.32  30.0  1
 13W  Var_02    H14  C16  N1   C13   106.13  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
 13W  chir_01  C11  C9  C12  N2  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
 13W  plan-1  C5   0.020
 13W  plan-1  C7   0.020
 13W  plan-1  C8   0.020
 13W  plan-1  C9   0.020
 13W  plan-1  S1   0.020
 13W  plan-1  C10  0.020
 13W  plan-1  C11  0.020
 13W  plan-1  H5   0.020
 13W  plan-1  H6   0.020
 13W  plan-2  C1   0.020
 13W  plan-2  C2   0.020
 13W  plan-2  C3   0.020
 13W  plan-2  C4   0.020
 13W  plan-2  C5   0.020
 13W  plan-2  C6   0.020
 13W  plan-2  C7   0.020
 13W  plan-2  C17  0.020
 13W  plan-2  N4   0.020
 13W  plan-2  H1   0.020
 13W  plan-2  H2   0.020
 13W  plan-2  H3   0.020
 13W  plan-2  H4   0.020
 13W  plan-3  C11  0.020
 13W  plan-3  C12  0.020
 13W  plan-3  C13  0.020
 13W  plan-3  N1   0.020
 13W  plan-3  C14  0.020
 13W  plan-3  N2   0.020
 13W  plan-3  N3   0.020
 13W  plan-3  C16  0.020
 13W  plan-3  O1   0.020
 13W  plan-3  H9   0.020
 13W  plan-3  H17  0.020

