# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:20:11 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N,N-dimethyl-5-({2-methyl-6-[(5-methylpyrazin-2-yl)carbamoyl]-1-benzofuran-4-yl}oxy)pyrimidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)c1ncc(Oc2cc(cc3oc(C)cc23)C(=O)Nc4cnc(C)cn4)cn1
#
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
 S41  S41  N,N-dimethyl-5-({2-methyl-6-[(5-methylpyrazin-2-yl)carbamoyl]-1-benzofuran-4-yl}oxy)pyrimidine-2-carboxamide  ligand  52  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S41
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
 S41  C1    C  CR56  0   0.384  -4.1354   0.9309  -0.0507
 S41  C2    C  CR56  0   0.013  -3.8432  -0.4262   0.0851
 S41  C3    C  CR6   0   0.304  -2.5158  -0.7997   0.2873
 S41  C4    C  CR16  0  -0.401  -1.5398   0.1774   0.3294
 S41  C5    C  CR6   0  -0.074  -1.8754   1.5332   0.1682
 S41  C6    C  CR16  0  -0.376  -3.1911   1.9379  -0.0076
 S41  O7    O  O     0  -0.450  -5.4610   1.0887  -0.2359
 S41  C8    C  CR5   0   0.373  -6.0275  -0.1509  -0.2182
 S41  C9    C  CR15  0  -0.406  -5.0939  -1.1111  -0.0261
 S41  C10   C  CH3   0  -0.753  -7.4919  -0.2165  -0.4046
 S41  C11   C  C     0   0.535  -0.8215   2.5881   0.2098
 S41  O12   O  O2    0  -0.492  -2.2773  -2.1308   0.4617
 S41  O13   O  O     0  -0.430  -1.0416   3.7031   0.6311
 S41  N14   N  NH1   0  -0.748   0.3870   2.1811  -0.2923
 S41  C15   C  CR6   0   0.184  -0.9945  -2.5765   0.3882
 S41  C16   C  CR16  0  -0.061  -0.3425  -3.0334   1.5212
 S41  N17   N  N     0  -0.378   0.8948  -3.5032   1.4568
 S41  C18   C  CR6   0   0.222   1.4827  -3.4822   0.2726
 S41  N19   N  N     0  -0.370   0.9406  -3.0736  -0.8650
 S41  C20   C  CR16  0  -0.060  -0.3060  -2.6309  -0.8137
 S41  C21   C  C     0   0.520   2.8642  -4.0831   0.2016
 S41  N22   N  NT    0  -0.436   3.8469  -3.3044  -0.2673
 S41  O23   O  O     0  -0.483   2.9982  -5.2469   0.5512
 S41  C24   C  CH3   0  -0.527   5.1675  -3.8491  -0.5064
 S41  C25   C  CH3   0  -0.514   3.7069  -1.8915  -0.5606
 S41  C26   C  CR6   0   0.470   1.5740   2.9008  -0.3283
 S41  N27   N  N     0  -0.368   1.7975   3.8626   0.5439
 S41  C28   C  CR16  0  -0.125   2.9617   4.4928   0.4626
 S41  C29   C  CR6   0   0.199   3.9320   4.1663  -0.4763
 S41  N30   N  N     0  -0.365   3.6983   3.1765  -1.3398
 S41  C31   C  CR16  0  -0.168   2.5421   2.5530  -1.2778
 S41  C32   C  CH3   0  -0.715   5.2372   4.8884  -0.5602
 S41  H4    H  HCR6  0   0.285  -0.5136  -0.0927   0.5415
 S41  H6    H  HCR6  0   0.280  -3.4563   2.9795  -0.1260
 S41  H9    H  HCR5  0   0.272  -5.2780  -2.1713   0.0264
 S41  H10   H  HCH3  0   0.265  -8.0168   0.3271   0.3826
 S41  H10A  H  HCH3  0   0.265  -7.7895   0.2163  -1.3610
 S41  H10B  H  HCH3  0   0.265  -7.8208  -1.2529  -0.3809
 S41  HN14  H  HNH1  0   0.418   0.3760   1.3464  -0.8587
 S41  H16   H  HCR6  0   0.304  -0.8335  -3.0255   2.4884
 S41  H20   H  HCR6  0   0.310  -0.7650  -2.3087  -1.7424
 S41  H24   H  HCH3  0   0.249   5.4669  -3.6532  -1.5371
 S41  H24A  H  HCH3  0   0.248   5.8975  -3.3817   0.1564
 S41  H24B  H  HCH3  0   0.262   5.1771  -4.9206  -0.3379
 S41  H25   H  HCH3  0   0.252   2.8611  -1.4503  -0.0413
 S41  H25A  H  HCH3  0   0.256   4.6022  -1.3737  -0.2173
 S41  H25B  H  HCH3  0   0.251   3.5960  -1.7132  -1.6312
 S41  H28   H  HCR6  0   0.269   3.1351   5.2862   1.1806
 S41  H31   H  HCR6  0   0.282   2.3625   1.7550  -1.9917
 S41  H32   H  HCH3  0   0.256   6.0730   4.1959  -0.4560
 S41  H32A  H  HCH3  0   0.257   5.3428   5.3829  -1.5268
 S41  H32B  H  HCH3  0   0.248   5.3236   5.6457   0.2170

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
 S41  C1   C2    aromatic  1.395  0.020  1.395
 S41  C1   C6    aromatic  1.381  0.020  1.381
 S41  C1   O7    aromatic  1.348  0.020  1.348
 S41  C2   C3    aromatic  1.394  0.020  1.394
 S41  C2   C9    aromatic  1.430  0.020  1.430
 S41  C3   C4    aromatic  1.382  0.020  1.382
 S41  C3   O12   single    1.363  0.020  1.363
 S41  C4   C5    aromatic  1.406  0.020  1.406
 S41  C5   C6    aromatic  1.388  0.020  1.388
 S41  C5   C11   single    1.492  0.020  1.492
 S41  O7   C8    aromatic  1.363  0.020  1.363
 S41  C8   C9    aromatic  1.353  0.020  1.353
 S41  C8   C10   single    1.478  0.020  1.478
 S41  C11  O13   double    1.212  0.020  1.212
 S41  C11  N14   single    1.370  0.020  1.370
 S41  O12  C15   single    1.360  0.020  1.360
 S41  N14  C26   single    1.389  0.020  1.389
 S41  C15  C16   aromatic  1.385  0.020  1.385
 S41  C15  C20   aromatic  1.386  0.020  1.386
 S41  C16  N17   aromatic  1.325  0.020  1.325
 S41  N17  C18   aromatic  1.322  0.020  1.322
 S41  C18  N19   aromatic  1.325  0.020  1.325
 S41  C18  C21   single    1.508  0.020  1.508
 S41  N19  C20   aromatic  1.324  0.020  1.324
 S41  C21  N22   single    1.339  0.020  1.339
 S41  C21  O23   double    1.223  0.020  1.223
 S41  N22  C24   single    1.448  0.020  1.448
 S41  N22  C25   single    1.450  0.020  1.450
 S41  C26  N27   aromatic  1.317  0.020  1.317
 S41  C26  C31   aromatic  1.400  0.020  1.400
 S41  N27  C28   aromatic  1.326  0.020  1.326
 S41  C28  C29   aromatic  1.389  0.020  1.389
 S41  C29  N30   aromatic  1.334  0.020  1.334
 S41  C29  C32   single    1.494  0.020  1.494
 S41  N30  C31   aromatic  1.315  0.020  1.315
 S41  C4   H4    single    0.930  0.020  1.080
 S41  C6   H6    single    0.930  0.020  1.080
 S41  C9   H9    single    0.930  0.020  1.080
 S41  C10  H10   single    0.970  0.020  1.090
 S41  C10  H10A  single    0.970  0.020  1.090
 S41  C10  H10B  single    0.970  0.020  1.090
 S41  N14  HN14  single    0.860  0.020  1.020
 S41  C16  H16   single    0.930  0.020  1.080
 S41  C20  H20   single    0.930  0.020  1.080
 S41  C24  H24   single    0.970  0.020  1.090
 S41  C24  H24A  single    0.970  0.020  1.090
 S41  C24  H24B  single    0.970  0.020  1.090
 S41  C25  H25   single    0.970  0.020  1.090
 S41  C25  H25A  single    0.970  0.020  1.090
 S41  C25  H25B  single    0.970  0.020  1.090
 S41  C28  H28   single    0.930  0.020  1.080
 S41  C31  H31   single    0.930  0.020  1.080
 S41  C32  H32   single    0.970  0.020  1.090
 S41  C32  H32A  single    0.970  0.020  1.090
 S41  C32  H32B  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
 S41  O7    C1   C6    126.26  3.000
 S41  O7    C1   C2    109.47  3.000
 S41  C6    C1   C2    124.27  3.000
 S41  C9    C2   C3    135.71  3.000
 S41  C9    C2   C1    105.97  3.000
 S41  C3    C2   C1    118.32  3.000
 S41  O12   C3   C4    124.26  3.000
 S41  O12   C3   C2    116.54  3.000
 S41  C4    C3   C2    119.18  3.000
 S41  H4    C4   C5    119.31  3.000
 S41  H4    C4   C3    119.95  3.000
 S41  C5    C4   C3    120.66  3.000
 S41  C11   C5   C6    117.85  3.000
 S41  C11   C5   C4    120.67  3.000
 S41  C6    C5   C4    121.47  3.000
 S41  H6    C6   C5    121.83  3.000
 S41  H6    C6   C1    122.08  3.000
 S41  C5    C6   C1    116.08  3.000
 S41  C8    O7   C1    107.49  3.000
 S41  C10   C8   C9    132.09  3.000
 S41  C10   C8   O7    116.78  3.000
 S41  C9    C8   O7    111.13  3.000
 S41  H9    C9   C8    125.97  3.000
 S41  H9    C9   C2    128.09  3.000
 S41  C8    C9   C2    105.94  3.000
 S41  H10B  C10  H10A  108.34  3.000
 S41  H10B  C10  H10   108.27  3.000
 S41  H10A  C10  H10   107.67  3.000
 S41  H10B  C10  C8    109.83  3.000
 S41  H10A  C10  C8    111.30  3.000
 S41  H10   C10  C8    111.32  3.000
 S41  N14   C11  O13   124.10  3.000
 S41  N14   C11  C5    113.76  3.000
 S41  O13   C11  C5    122.13  3.000
 S41  C15   O12  C3    118.55  3.000
 S41  HN14  N14  C26   115.06  3.000
 S41  HN14  N14  C11   116.22  3.000
 S41  C26   N14  C11   127.55  3.000
 S41  C20   C15  C16   117.55  3.000
 S41  C20   C15  O12   121.89  3.000
 S41  C16   C15  O12   120.53  3.000
 S41  H16   C16  N17   117.94  3.000
 S41  H16   C16  C15   120.93  3.000
 S41  N17   C16  C15   121.13  3.000
 S41  C18   N17  C16   116.94  3.000
 S41  C21   C18  N19   117.21  3.000
 S41  C21   C18  N17   116.30  3.000
 S41  N19   C18  N17   126.30  3.000
 S41  C20   N19  C18   117.07  3.000
 S41  H20   C20  N19   117.67  3.000
 S41  H20   C20  C15   121.36  3.000
 S41  N19   C20  C15   120.97  3.000
 S41  O23   C21  N22   124.99  3.000
 S41  O23   C21  C18   117.79  3.000
 S41  N22   C21  C18   117.20  3.000
 S41  C25   N22  C24   114.91  3.000
 S41  C25   N22  C21   124.53  3.000
 S41  C24   N22  C21   120.55  3.000
 S41  H24B  C24  H24A  108.84  3.000
 S41  H24B  C24  H24   108.77  3.000
 S41  H24A  C24  H24   108.26  3.000
 S41  H24B  C24  N22   110.73  3.000
 S41  H24A  C24  N22   110.40  3.000
 S41  H24   C24  N22   109.79  3.000
 S41  H25B  C25  H25A  108.36  3.000
 S41  H25B  C25  H25   108.89  3.000
 S41  H25A  C25  H25   107.23  3.000
 S41  H25B  C25  N22   111.57  3.000
 S41  H25A  C25  N22   108.66  3.000
 S41  H25   C25  N22   111.99  3.000
 S41  C31   C26  N27   120.88  3.000
 S41  C31   C26  N14   118.68  3.000
 S41  N27   C26  N14   120.41  3.000
 S41  C28   N27  C26   117.07  3.000
 S41  H28   C28  C29   120.53  3.000
 S41  H28   C28  N27   116.59  3.000
 S41  C29   C28  N27   122.88  3.000
 S41  C32   C29  N30   118.38  3.000
 S41  C32   C29  C28   122.32  3.000
 S41  N30   C29  C28   119.30  3.000
 S41  C31   N30  C29   118.38  3.000
 S41  H31   C31  N30   117.57  3.000
 S41  H31   C31  C26   120.95  3.000
 S41  N30   C31  C26   121.47  3.000
 S41  H32B  C32  H32A  108.03  3.000
 S41  H32B  C32  H32   108.23  3.000
 S41  H32A  C32  H32   107.36  3.000
 S41  H32B  C32  C29   111.44  3.000
 S41  H32A  C32  C29   110.70  3.000
 S41  H32   C32  C29   110.94  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
 S41  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 S41  CONST_02  C8    C9   C2   C1      0.00   0.0  0
 S41  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 S41  CONST_04  C9    C8   O7   C1      0.00   0.0  0
 S41  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 S41  CONST_06  C8    O7   C1   C2      0.00   0.0  0
 S41  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 S41  CONST_08  O7    C8   C9   C2      0.00   0.0  0
 S41  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 S41  CONST_10  O7    C1   C2   C3    180.00   0.0  0
 S41  CONST_11  C8    C9   C2   C3    180.00   0.0  0
 S41  CONST_12  C6    C5   C4   C3      0.00   0.0  0
 S41  CONST_13  C9    C2   C3   C4    180.00   0.0  0
 S41  CONST_14  O7    C1   C6   C5    180.00   0.0  0
 S41  CONST_15  C9    C2   C1   C6    180.00   0.0  0
 S41  CONST_16  C8    O7   C1   C6    180.00   0.0  0
 S41  CONST_17  C9    C2   C1   O7      0.00   0.0  0
 S41  CONST_18  C18   N17  C16  C15     0.00   0.0  0
 S41  CONST_19  C18   N19  C20  C15     0.00   0.0  0
 S41  CONST_20  N19   C20  C15  C16     0.00   0.0  0
 S41  CONST_21  N19   C18  N17  C16     0.00   0.0  0
 S41  CONST_22  C20   C15  C16  N17     0.00   0.0  0
 S41  CONST_23  C20   N19  C18  N17     0.00   0.0  0
 S41  CONST_24  C29   C28  N27  C26     0.00   0.0  0
 S41  CONST_25  C29   N30  C31  C26     0.00   0.0  0
 S41  CONST_26  N30   C31  C26  N27     0.00   0.0  0
 S41  CONST_27  N30   C29  C28  N27     0.00   0.0  0
 S41  CONST_28  C31   C26  N27  C28     0.00   0.0  0
 S41  CONST_29  C31   N30  C29  C28     0.00   0.0  0
 S41  CONST_30  O12   C3   C2   C1    180.00   0.0  0
 S41  CONST_31  C11   C5   C6   C1    180.00   0.0  0
 S41  CONST_32  C10   C8   O7   C1    180.00   0.0  0
 S41  CONST_33  C10   C8   C9   C2    180.00   0.0  0
 S41  CONST_34  C11   C5   C4   C3    180.00   0.0  0
 S41  CONST_35  O12   C3   C4   C5    180.00   0.0  0
 S41  CONST_36  O12   C3   C2   C9      0.00   0.0  0
 S41  CONST_37  N17   C16  C15  O12   180.00   0.0  0
 S41  CONST_38  N19   C20  C15  O12   180.00   0.0  0
 S41  CONST_39  C28   N27  C26  N14   180.00   0.0  0
 S41  CONST_40  N30   C31  C26  N14   180.00   0.0  0
 S41  CONST_41  C21   C18  N17  C16   180.00   0.0  0
 S41  CONST_42  C21   C18  N19  C20   180.00   0.0  0
 S41  CONST_43  C32   C29  C28  N27   180.00   0.0  0
 S41  CONST_44  C32   C29  N30  C31   180.00   0.0  0
 S41  CONST_45  H9    C9   C2   C1    180.00   0.0  0
 S41  CONST_46  H6    C6   C1   C2    180.00   0.0  0
 S41  CONST_47  H4    C4   C3   C2    180.00   0.0  0
 S41  CONST_48  H20   C20  C15  C16   180.00   0.0  0
 S41  CONST_49  H16   C16  N17  C18   180.00   0.0  0
 S41  CONST_50  H28   C28  N27  C26   180.00   0.0  0
 S41  CONST_51  H31   C31  C26  N27   180.00   0.0  0
 S41  CONST_52  C26   N14  C11  C5    180.00   0.0  0
 S41  CONST_55  HN14  N14  C26  N27   180.00   0.0  0
 S41  CONST_56  C26   N14  C11  O13     0.00   0.0  0
 S41  CONST_57  C24   N22  C21  C18   180.00   0.0  0
 S41  CONST_58  C25   N22  C21  C18     0.00   0.0  0
 S41  CONST_59  C24   N22  C21  O23     0.00   0.0  0
 S41  CONST_60  C25   N22  C21  O23   180.00   0.0  0
 S41  Var_01    C16   C15  O12  C3    110.61  30.0  2
 S41  Var_02    O13   C11  C5   C4   -148.24  30.0  2
 S41  Var_03    N22   C21  C18  N17  -124.08  30.0  2
 S41  Var_04    H10   C10  C8   O7    -60.65  30.0  2
 S41  Var_05    H32   C32  C29  C28   122.93  30.0  2
 S41  Var_06    H24   C24  N22  C21   125.00  30.0  3
 S41  Var_07    H25   C25  N22  C21    20.60  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
 S41  plan-1  O12   0.020
 S41  plan-1  C15   0.020
 S41  plan-1  C16   0.020
 S41  plan-1  N17   0.020
 S41  plan-1  C18   0.020
 S41  plan-1  N19   0.020
 S41  plan-1  C20   0.020
 S41  plan-1  C21   0.020
 S41  plan-1  H16   0.020
 S41  plan-1  H20   0.020
 S41  plan-2  N14   0.020
 S41  plan-2  C26   0.020
 S41  plan-2  N27   0.020
 S41  plan-2  C28   0.020
 S41  plan-2  C29   0.020
 S41  plan-2  N30   0.020
 S41  plan-2  C31   0.020
 S41  plan-2  C32   0.020
 S41  plan-2  H28   0.020
 S41  plan-2  H31   0.020
 S41  plan-3  C1    0.020
 S41  plan-3  C2    0.020
 S41  plan-3  C3    0.020
 S41  plan-3  C4    0.020
 S41  plan-3  C5    0.020
 S41  plan-3  C6    0.020
 S41  plan-3  O7    0.020
 S41  plan-3  C8    0.020
 S41  plan-3  C9    0.020
 S41  plan-3  C10   0.020
 S41  plan-3  C11   0.020
 S41  plan-3  O12   0.020
 S41  plan-3  H4    0.020
 S41  plan-3  H6    0.020
 S41  plan-3  H9    0.020
 S41  plan-4  C5    0.020
 S41  plan-4  C11   0.020
 S41  plan-4  O13   0.020
 S41  plan-4  N14   0.020
 S41  plan-4  C26   0.020
 S41  plan-4  HN14  0.020
 S41  plan-5  C18   0.020
 S41  plan-5  C21   0.020
 S41  plan-5  N22   0.020
 S41  plan-5  O23   0.020
 S41  plan-5  C24   0.020
 S41  plan-5  C25   0.020

