# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 14:00:32 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 6-[5-[(2-azanylpyrimidin-4-yl)amino]-2-hydroxy-phenyl]-N-methylidene-1-benzothiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(Nc2ccc(O)c(c2)c3ccc4cc(sc4c3)C(=O)N=C)n1
#
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
 MK3  MK3  6-[5-[(2-azanylpyrimidin-4-yl)amino]-2-hydroxy-phenyl]-N-methylidene-1-benzothiophene-2-carboxamide  ligand  43  28  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MK3
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
 MK3  C1    C  CR6   0   0.553   4.1582  -2.8680  -0.0936
 MK3  N1    N  N     0  -0.526   3.8587  -1.5692   0.0133
 MK3  O1    O  OH1   0  -0.625   0.1112   3.8032  -0.1632
 MK3  S1    S  S2    0   0.260  -4.1021   0.8305   0.6690
 MK3  C2    C  CR16  0  -0.025   6.3330  -2.5659   0.4012
 MK3  N2    N  N     0  -0.488   5.3576  -3.4191   0.0886
 MK3  O2    O  O     0  -0.396  -6.7999  -1.3920  -1.1178
 MK3  C3    C  CR16  0  -0.467   6.1553  -1.2127   0.5348
 MK3  N3    N  NH2   0  -0.821   3.1471  -3.6889  -0.4522
 MK3  C4    C  CR6   0   0.570   4.8435  -0.7402   0.3230
 MK3  N4    N  NH1   0  -0.782   4.6038   0.5891   0.4441
 MK3  C5    C  CR6   0   0.357   3.4363   1.3376   0.2807
 MK3  N5    N  N     0  -0.366  -6.8922  -0.0629   0.7438
 MK3  C6    C  CR16  0  -0.361   2.1809   0.8152  -0.0199
 MK3  C7    C  CR6   0  -0.013   1.0615   1.6379  -0.1542
 MK3  C8    C  CR6   0   0.302   1.1969   3.0195   0.0047
 MK3  C9    C  CR16  0  -0.365   2.4501   3.5449   0.3046
 MK3  C10   C  CR16  0  -0.352   3.5491   2.7204   0.4427
 MK3  C11   C  CR6   0   0.080  -0.2362   1.0148  -0.4932
 MK3  C12   C  CR16  0  -0.295  -0.2972   0.0962  -1.5625
 MK3  C13   C  CR16  0  -0.296  -1.4683  -0.5379  -1.9043
 MK3  C14   C  CR16  0  -0.310  -1.3819   1.2884   0.2385
 MK3  C15   C  CR56  0  -0.198  -2.5661   0.6446  -0.1059
 MK3  C16   C  CR56  0   0.207  -2.6332  -0.2686  -1.1743
 MK3  C17   C  CR15  0  -0.203  -3.9445  -0.7988  -1.3415
 MK3  C18   C  CR5   0  -0.314  -4.8245  -0.3082  -0.4301
 MK3  C19   C  C     0   0.468  -6.2387  -0.6761  -0.3182
 MK3  C20   C  C2    0  -0.238  -7.4151  -0.7416   1.6700
 MK3  HO1   H  HOH1  0   0.475   0.3484   4.7286  -0.0365
 MK3  H2    H  HCR6  0   0.264   7.3164  -2.9979   0.5541
 MK3  H3    H  HCR6  0   0.270   6.9733  -0.5532   0.7879
 MK3  HN3   H  HNH2  0   0.391   2.2041  -3.3489  -0.3764
 MK3  HN3A  H  HNH2  0   0.392   3.2779  -4.6793  -0.3398
 MK3  HN4   H  HNH1  0   0.414   5.4167   1.1377   0.6780
 MK3  H6    H  HCR6  0   0.291   2.0599  -0.2499  -0.1361
 MK3  H9    H  HCR6  0   0.275   2.5746   4.6150   0.4245
 MK3  H10   H  HCR6  0   0.274   4.5091   3.1625   0.6822
 MK3  H12   H  HCR6  0   0.261   0.6000  -0.1015  -2.1351
 MK3  H13   H  HCR6  0   0.264  -1.4944  -1.2352  -2.7316
 MK3  H14   H  HCR6  0   0.268  -1.3578   1.9725   1.0758
 MK3  H17   H  HCR5  0   0.282  -4.2104  -1.5173  -2.1045
 MK3  H20   H  H     0   0.256  -7.3494  -1.8275   1.7350
 MK3  H20A  H  H     0   0.265  -7.9555  -0.2288   2.4583

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
 MK3  N3   C1    single    1.351  0.020  1.351
 MK3  C1   N1    aromatic  1.337  0.020  1.337
 MK3  C1   N2    aromatic  1.332  0.020  1.332
 MK3  N1   C4    aromatic  1.324  0.020  1.324
 MK3  O1   C8    single    1.349  0.020  1.349
 MK3  O1   HO1   single    0.850  0.020  0.980
 MK3  C18  S1    aromatic  1.740  0.020  1.740
 MK3  C15  S1    aromatic  1.730  0.020  1.730
 MK3  N2   C2    aromatic  1.333  0.020  1.333
 MK3  C2   C3    aromatic  1.371  0.020  1.371
 MK3  C2   H2    single    0.930  0.020  1.080
 MK3  O2   C19   double    1.211  0.020  1.211
 MK3  C4   C3    aromatic  1.410  0.020  1.410
 MK3  C3   H3    single    0.930  0.020  1.080
 MK3  N3   HN3   single    0.890  0.020  1.040
 MK3  N3   HN3A  single    0.890  0.020  1.040
 MK3  C4   N4    single    1.356  0.020  1.356
 MK3  C5   N4    single    1.396  0.020  1.396
 MK3  N4   HN4   single    0.860  0.020  1.020
 MK3  C6   C5    aromatic  1.393  0.020  1.393
 MK3  C10  C5    aromatic  1.397  0.020  1.397
 MK3  C19  N5    single    1.390  0.020  1.390
 MK3  N5   C20   double    1.262  0.020  1.262
 MK3  C7   C6    aromatic  1.396  0.020  1.396
 MK3  C6   H6    single    0.930  0.020  1.080
 MK3  C11  C7    single    1.479  0.020  1.479
 MK3  C8   C7    aromatic  1.397  0.020  1.397
 MK3  C8   C9    aromatic  1.392  0.020  1.392
 MK3  C9   C10   aromatic  1.381  0.020  1.381
 MK3  C9   H9    single    0.930  0.020  1.080
 MK3  C10  H10   single    0.930  0.020  1.080
 MK3  C12  C11   aromatic  1.411  0.020  1.411
 MK3  C11  C14   aromatic  1.387  0.020  1.387
 MK3  C13  C12   aromatic  1.375  0.020  1.375
 MK3  C12  H12   single    0.930  0.020  1.080
 MK3  C13  C16   aromatic  1.401  0.020  1.401
 MK3  C13  H13   single    0.930  0.020  1.080
 MK3  C15  C14   aromatic  1.391  0.020  1.391
 MK3  C14  H14   single    0.930  0.020  1.080
 MK3  C16  C15   aromatic  1.407  0.020  1.407
 MK3  C17  C16   aromatic  1.424  0.020  1.424
 MK3  C17  C18   aromatic  1.359  0.020  1.359
 MK3  C17  H17   single    0.930  0.020  1.080
 MK3  C19  C18   single    1.466  0.020  1.466
 MK3  C20  H20   single    0.930  0.020  1.080
 MK3  C20  H20A  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
 MK3  N3    C1   N2   117.30  3.000
 MK3  N2    C1   N1   126.33  3.000
 MK3  N3    C1   N1   116.35  3.000
 MK3  C4    N1   C1   117.40  3.000
 MK3  HO1   O1   C8   110.08  3.000
 MK3  C18   S1   C15   90.88  3.000
 MK3  H2    C2   C3   119.78  3.000
 MK3  H2    C2   N2   116.20  3.000
 MK3  C3    C2   N2   124.03  3.000
 MK3  C2    N2   C1   115.22  3.000
 MK3  H3    C3   C4   122.32  3.000
 MK3  H3    C3   C2   121.80  3.000
 MK3  C4    C3   C2   115.88  3.000
 MK3  HN3A  N3   HN3  116.54  3.000
 MK3  HN3A  N3   C1   118.14  3.000
 MK3  HN3   N3   C1   118.46  3.000
 MK3  N4    C4   C3   118.65  3.000
 MK3  N4    C4   N1   120.21  3.000
 MK3  C3    C4   N1   121.15  3.000
 MK3  HN4   N4   C5   114.18  3.000
 MK3  HN4   N4   C4   114.30  3.000
 MK3  C5    N4   C4   131.51  3.000
 MK3  C10   C5   C6   117.99  3.000
 MK3  C10   C5   N4   116.71  3.000
 MK3  C6    C5   N4   125.30  3.000
 MK3  C20   N5   C19  121.23  3.000
 MK3  H6    C6   C7   118.82  3.000
 MK3  H6    C6   C5   119.67  3.000
 MK3  C7    C6   C5   121.51  3.000
 MK3  C11   C7   C8   121.85  3.000
 MK3  C8    C7   C6   119.62  3.000
 MK3  C11   C7   C6   118.52  3.000
 MK3  C9    C8   C7   119.01  3.000
 MK3  C9    C8   O1   122.15  3.000
 MK3  C7    C8   O1   118.83  3.000
 MK3  H9    C9   C10  119.14  3.000
 MK3  H9    C9   C8   120.00  3.000
 MK3  C10   C9   C8   120.86  3.000
 MK3  H10   C10  C9   118.92  3.000
 MK3  H10   C10  C5   120.07  3.000
 MK3  C9    C10  C5   121.01  3.000
 MK3  C14   C11  C12  119.51  3.000
 MK3  C14   C11  C7   121.39  3.000
 MK3  C12   C11  C7   119.07  3.000
 MK3  H12   C12  C13  119.35  3.000
 MK3  H12   C12  C11  118.94  3.000
 MK3  C13   C12  C11  121.70  3.000
 MK3  H13   C13  C16  120.14  3.000
 MK3  H13   C13  C12  120.51  3.000
 MK3  C16   C13  C12  119.34  3.000
 MK3  H14   C14  C15  120.22  3.000
 MK3  H14   C14  C11  120.99  3.000
 MK3  C15   C14  C11  118.77  3.000
 MK3  C16   C15  C14  121.93  3.000
 MK3  C16   C15  S1   111.55  3.000
 MK3  C14   C15  S1   126.52  3.000
 MK3  C17   C16  C15  112.01  3.000
 MK3  C17   C16  C13  129.26  3.000
 MK3  C15   C16  C13  118.74  3.000
 MK3  H17   C17  C18  123.65  3.000
 MK3  H17   C17  C16  123.82  3.000
 MK3  C18   C17  C16  112.53  3.000
 MK3  C19   C18  C17  125.84  3.000
 MK3  C19   C18  S1   121.12  3.000
 MK3  C17   C18  S1   113.03  3.000
 MK3  C18   C19  N5   113.66  3.000
 MK3  C18   C19  O2   123.04  3.000
 MK3  N5    C19  O2   123.20  3.000
 MK3  H20A  C20  H20  117.25  3.000
 MK3  H20A  C20  N5   119.05  3.000
 MK3  H20   C20  N5   123.69  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
 MK3  CONST_01  C3    C4   N1   C1     0.00   0.0  0
 MK3  CONST_02  C3    C2   N2   C1     0.00   0.0  0
 MK3  CONST_03  C2    N2   C1   N1     0.00   0.0  0
 MK3  CONST_04  C2    C3   C4   N1     0.00   0.0  0
 MK3  CONST_05  C16   C17  C18  S1     0.00   0.0  0
 MK3  CONST_06  C11   C14  C15  S1   180.00   0.0  0
 MK3  CONST_07  C13   C16  C15  S1   180.00   0.0  0
 MK3  CONST_08  C17   C16  C15  S1     0.00   0.0  0
 MK3  CONST_09  C4    N1   C1   N2     0.00   0.0  0
 MK3  CONST_10  C4    C3   C2   N2     0.00   0.0  0
 MK3  CONST_11  C11   C7   C6   C5   180.00   0.0  0
 MK3  CONST_12  C8    C7   C6   C5     0.00   0.0  0
 MK3  CONST_13  C8    C9   C10  C5     0.00   0.0  0
 MK3  CONST_14  C9    C10  C5   C6     0.00   0.0  0
 MK3  CONST_17  C9    C8   C7   C6     0.00   0.0  0
 MK3  CONST_18  C10   C5   C6   C7     0.00   0.0  0
 MK3  CONST_19  C13   C12  C11  C7   180.00   0.0  0
 MK3  CONST_20  C15   C14  C11  C7   180.00   0.0  0
 MK3  CONST_21  C10   C9   C8   C7     0.00   0.0  0
 MK3  CONST_24  C11   C7   C8   C9   180.00   0.0  0
 MK3  CONST_25  C16   C13  C12  C11    0.00   0.0  0
 MK3  CONST_26  C16   C15  C14  C11    0.00   0.0  0
 MK3  CONST_27  C15   C14  C11  C12    0.00   0.0  0
 MK3  CONST_28  C15   C16  C13  C12    0.00   0.0  0
 MK3  CONST_29  C17   C16  C13  C12  180.00   0.0  0
 MK3  CONST_30  C14   C11  C12  C13    0.00   0.0  0
 MK3  CONST_31  C14   C15  C16  C13    0.00   0.0  0
 MK3  CONST_32  C18   C17  C16  C13  180.00   0.0  0
 MK3  CONST_33  C18   S1   C15  C14  180.00   0.0  0
 MK3  CONST_34  C17   C16  C15  C14  180.00   0.0  0
 MK3  CONST_35  C17   C18  S1   C15    0.00   0.0  0
 MK3  CONST_36  C18   C17  C16  C15    0.00   0.0  0
 MK3  CONST_37  C18   S1   C15  C16    0.00   0.0  0
 MK3  CONST_38  N4    C4   N1   C1   180.00   0.0  0
 MK3  CONST_39  C6    C7   C8   O1   180.00   0.0  0
 MK3  CONST_40  C11   C7   C8   O1     0.00   0.0  0
 MK3  CONST_41  C10   C9   C8   O1   180.00   0.0  0
 MK3  CONST_42  N3    C1   N2   C2   180.00   0.0  0
 MK3  CONST_43  N4    C4   C3   C2   180.00   0.0  0
 MK3  CONST_44  C4    N1   C1   N3   180.00   0.0  0
 MK3  CONST_45  C7    C6   C5   N4   180.00   0.0  0
 MK3  CONST_46  C9    C10  C5   N4   180.00   0.0  0
 MK3  CONST_47  C19   C18  S1   C15  180.00   0.0  0
 MK3  CONST_48  C19   C18  C17  C16  180.00   0.0  0
 MK3  CONST_49  H2    C2   N2   C1   180.00   0.0  0
 MK3  CONST_50  H3    C3   C4   N1   180.00   0.0  0
 MK3  CONST_51  H17   C17  C18  S1   180.00   0.0  0
 MK3  CONST_52  H14   C14  C15  S1     0.00   0.0  0
 MK3  CONST_53  H9    C9   C10  C5   180.00   0.0  0
 MK3  CONST_54  H10   C10  C5   C6   180.00   0.0  0
 MK3  CONST_55  H12   C12  C11  C7     0.00   0.0  0
 MK3  CONST_56  H6    C6   C7   C8   180.00   0.0  0
 MK3  CONST_57  H13   C13  C12  C11  180.00   0.0  0
 MK3  CONST_59  HN3A  N3   C1   N1   180.00   0.0  0
 MK3  Var_01    C5    N4   C4   N1    -0.97  30.0  2
 MK3  Var_02    C6    C5   N4   C4     2.42  30.0  2
 MK3  Var_03    O2    C19  C18  S1   174.75  30.0  2
 MK3  Var_04    H20   C20  N5   C19    3.39   0.0  2

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
 MK3  plan-1  C1    0.020
 MK3  plan-1  N1    0.020
 MK3  plan-1  C2    0.020
 MK3  plan-1  N2    0.020
 MK3  plan-1  C3    0.020
 MK3  plan-1  N3    0.020
 MK3  plan-1  C4    0.020
 MK3  plan-1  N4    0.020
 MK3  plan-1  H2    0.020
 MK3  plan-1  H3    0.020
 MK3  plan-2  O1    0.020
 MK3  plan-2  N4    0.020
 MK3  plan-2  C5    0.020
 MK3  plan-2  C6    0.020
 MK3  plan-2  C7    0.020
 MK3  plan-2  C8    0.020
 MK3  plan-2  C9    0.020
 MK3  plan-2  C10   0.020
 MK3  plan-2  C11   0.020
 MK3  plan-2  H6    0.020
 MK3  plan-2  H9    0.020
 MK3  plan-2  H10   0.020
 MK3  plan-3  S1    0.020
 MK3  plan-3  C7    0.020
 MK3  plan-3  C11   0.020
 MK3  plan-3  C12   0.020
 MK3  plan-3  C13   0.020
 MK3  plan-3  C14   0.020
 MK3  plan-3  C15   0.020
 MK3  plan-3  C16   0.020
 MK3  plan-3  C17   0.020
 MK3  plan-3  C18   0.020
 MK3  plan-3  C19   0.020
 MK3  plan-3  H12   0.020
 MK3  plan-3  H13   0.020
 MK3  plan-3  H14   0.020
 MK3  plan-3  H17   0.020
 MK3  plan-4  O2    0.020
 MK3  plan-4  N5    0.020
 MK3  plan-4  C18   0.020
 MK3  plan-4  C19   0.020
 MK3  plan-4  C20   0.020
 MK3  plan-4  H20   0.020
 MK3  plan-4  H20A  0.020
 MK3  plan-5  C1    0.020
 MK3  plan-5  N3    0.020
 MK3  plan-5  HN3   0.020
 MK3  plan-5  HN3A  0.020

