# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 23:45:32 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: ~{N}-[6-[6-methoxy-5-(methylsulfonylamino)pyridin-3-yl]-2-benzofuran-4-yl]-2-morpholin-4-yl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cc1N[S](C)(=O)=O)c2cc(NC(=O)CN3CCOCC3)c4cocc4c2
#
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
 6PF  6PF  ~{N}-[6-[6-methoxy-5-(methylsulfonylamino)pyridin-3-yl]-2-benzofuran-4-yl]-2-morpholin-4-yl-ethanamide  ligand  56  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6PF
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
 6PF  N1   N  NC1   0  -0.814   5.1608   0.5351  -0.5180
 6PF  N3   N  NT    0  -0.417  -5.7729   0.8129  -0.1596
 6PF  C4   C  CR16  0  -0.188   2.9794  -0.3040   0.1296
 6PF  C5   C  CR6   0   0.130   3.9236   0.6988   0.1429
 6PF  C6   C  CH3   0  -0.791   4.9639   2.4952  -2.4539
 6PF  C7   C  CR6   0   0.085   0.7251  -1.1842   0.7911
 6PF  C8   C  CR16  0  -0.416   1.0877  -2.4912   0.9228
 6PF  C10  C  CR15  0  -0.040   0.0597  -4.8336   1.0755
 6PF  C13  C  CR6   0   0.350  -1.6690  -1.7081   0.6787
 6PF  C15  C  CH2   0  -0.414  -5.1634  -0.3340   0.4529
 6PF  C17  C  CH2   0  -0.191  -7.7949   2.1160  -0.5120
 6PF  C20  C  CR16  0  -0.405  -0.6558  -0.7945   0.6654
 6PF  O4   O  O     0  -0.445  -3.0687   0.8482   0.5708
 6PF  C14  C  C     0   0.526  -3.6478  -0.2165   0.5114
 6PF  C19  C  CH2   0  -0.310  -5.5430   0.8574  -1.5940
 6PF  C18  C  CH2   0  -0.188  -6.1843   2.0986  -2.1828
 6PF  O5   O  O2    0  -0.484  -7.5654   2.1532  -1.9032
 6PF  C16  C  CH2   0  -0.305  -7.1979   0.8728   0.1180
 6PF  N2   N  NH1   0  -0.751  -3.0240  -1.4260   0.5348
 6PF  C12  C  CR56  0  -0.058  -1.3188  -3.0893   0.8307
 6PF  C11  C  CR15  0  -0.040  -2.0422  -4.2471   0.9019
 6PF  O3   O  O     0  -0.370  -1.2044  -5.2820   1.0475
 6PF  C9   C  CR56  0   0.035   0.0615  -3.4727   0.9440
 6PF  C3   C  CR6   0  -0.027   1.7506  -0.1251   0.7714
 6PF  C2   C  CR16  0  -0.096   1.5580   1.0899   1.4124
 6PF  N    N  N     0  -0.452   2.4654   2.0614   1.4499
 6PF  S    S  S     0   1.318   5.2368   0.7629  -2.1667
 6PF  O1   O  OS    0  -0.663   6.5992   0.4315  -2.5457
 6PF  O2   O  OS    0  -0.656   4.1254   0.0292  -2.7471
 6PF  C1   C  CR6   0   0.530   3.6100   1.8854   0.8327
 6PF  O    O  O2    0  -0.469   4.5369   2.8380   0.8435
 6PF  C    C  CH3   0  -0.417   4.2533   4.0491   1.5341
 6PF  H1   H  HNC1  0   0.420   5.9671   0.9267  -0.0412
 6PF  H3   H  HCR6  0   0.277   3.1998  -1.2280  -0.3889
 6PF  H4   H  HCH3  0   0.296   5.7458   3.0691  -1.9635
 6PF  H5   H  HCH3  0   0.308   4.9966   2.6588  -3.5298
 6PF  H6   H  HCH3  0   0.291   3.9854   2.7739  -2.0700
 6PF  H7   H  HCR6  0   0.257   2.1240  -2.7825   1.0376
 6PF  H8   H  HCR5  0   0.296   0.8412  -5.5660   1.1926
 6PF  H9   H  HCH2  0   0.293  -5.5061  -0.4075   1.4912
 6PF  H10  H  HCH2  0   0.233  -5.4571  -1.2812  -0.0309
 6PF  H11  H  HCH2  0   0.202  -7.3700   3.0075  -0.0287
 6PF  H12  H  HCH2  0   0.239  -8.8746   2.1313  -0.3568
 6PF  H13  H  HCR6  0   0.277  -0.8742   0.2508   0.5220
 6PF  H14  H  HCH2  0   0.248  -4.4716   0.8935  -1.8010
 6PF  H15  H  HCH2  0   0.203  -5.9425  -0.0417  -2.0946
 6PF  H16  H  HCH2  0   0.202  -5.6770   2.9903  -1.7872
 6PF  H17  H  HCH2  0   0.239  -6.0686   2.0991  -3.2675
 6PF  H18  H  HCH2  0   0.202  -7.7276  -0.0200  -0.2566
 6PF  H19  H  HCH2  0   0.247  -7.3547   0.9129   1.1986
 6PF  H20  H  HNH1  0   0.419  -3.6301  -2.2270   0.4508
 6PF  H21  H  HCR5  0   0.296  -3.0949  -4.4778   0.8710
 6PF  H22  H  HCR6  0   0.266   0.6328   1.2901   1.9416
 6PF  H23  H  HCH3  0   0.235   3.3819   4.5543   1.1171
 6PF  H24  H  HCH3  0   0.235   4.0852   3.8751   2.5971
 6PF  H25  H  HCH3  0   0.252   5.1313   4.6755   1.4043

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
 6PF  O1   S    double    1.452  0.020  1.452
 6PF  O2   S    double    1.453  0.020  1.453
 6PF  S    N1   single    1.666  0.020  1.666
 6PF  S    C6   single    1.777  0.020  1.777
 6PF  C18  O5   single    1.410  0.020  1.410
 6PF  C18  C19  single    1.516  0.020  1.516
 6PF  N1   C5   single    1.412  0.020  1.412
 6PF  O5   C17  single    1.411  0.020  1.411
 6PF  C19  N3   single    1.453  0.020  1.453
 6PF  C5   C4   aromatic  1.377  0.020  1.377
 6PF  C5   C1   aromatic  1.408  0.020  1.408
 6PF  O    C    single    1.423  0.020  1.423
 6PF  O    C1   single    1.329  0.020  1.329
 6PF  C4   C3   aromatic  1.398  0.020  1.398
 6PF  C17  C16  single    1.516  0.020  1.516
 6PF  N3   C16  single    1.453  0.020  1.453
 6PF  N3   C15  single    1.436  0.020  1.436
 6PF  C1   N    aromatic  1.312  0.020  1.312
 6PF  O4   C14  double    1.213  0.020  1.213
 6PF  C15  C14  single    1.521  0.020  1.521
 6PF  C14  N2   single    1.361  0.020  1.361
 6PF  C3   C7   single    1.474  0.020  1.474
 6PF  C3   C2   aromatic  1.387  0.020  1.387
 6PF  N    C2   aromatic  1.330  0.020  1.330
 6PF  C20  C7   aromatic  1.440  0.020  1.440
 6PF  C20  C13  aromatic  1.364  0.020  1.364
 6PF  N2   C13  single    1.391  0.020  1.391
 6PF  C7   C8   aromatic  1.363  0.020  1.363
 6PF  C13  C12  aromatic  1.433  0.020  1.433
 6PF  C8   C9   aromatic  1.420  0.020  1.420
 6PF  C12  C9   aromatic  1.437  0.020  1.437
 6PF  C12  C11  aromatic  1.367  0.020  1.367
 6PF  C9   C10  aromatic  1.367  0.020  1.367
 6PF  C11  O3   aromatic  1.339  0.020  1.339
 6PF  C10  O3   aromatic  1.342  0.020  1.342
 6PF  N1   H1   single    0.890  0.020  1.040
 6PF  C4   H3   single    0.930  0.020  1.080
 6PF  C6   H4   single    0.970  0.020  1.090
 6PF  C6   H5   single    0.970  0.020  1.090
 6PF  C6   H6   single    0.970  0.020  1.090
 6PF  C8   H7   single    0.930  0.020  1.080
 6PF  C10  H8   single    0.930  0.020  1.080
 6PF  C15  H9   single    0.970  0.020  1.090
 6PF  C15  H10  single    0.970  0.020  1.090
 6PF  C17  H11  single    0.970  0.020  1.090
 6PF  C17  H12  single    0.970  0.020  1.090
 6PF  C20  H13  single    0.930  0.020  1.080
 6PF  C19  H14  single    0.970  0.020  1.090
 6PF  C19  H15  single    0.970  0.020  1.090
 6PF  C18  H16  single    0.970  0.020  1.090
 6PF  C18  H17  single    0.970  0.020  1.090
 6PF  C16  H18  single    0.970  0.020  1.090
 6PF  C16  H19  single    0.970  0.020  1.090
 6PF  N2   H20  single    0.860  0.020  1.020
 6PF  C11  H21  single    0.930  0.020  1.080
 6PF  C2   H22  single    0.930  0.020  1.080
 6PF  C    H23  single    0.970  0.020  1.090
 6PF  C    H24  single    0.970  0.020  1.090
 6PF  C    H25  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
 6PF  H1   N1   S    112.07  3.000
 6PF  H1   N1   C5   115.55  3.000
 6PF  S    N1   C5   119.16  3.000
 6PF  C16  N3   C19  110.03  3.000
 6PF  C16  N3   C15  111.58  3.000
 6PF  C19  N3   C15  112.23  3.000
 6PF  H3   C4   C3   120.54  3.000
 6PF  H3   C4   C5   119.12  3.000
 6PF  C3   C4   C5   120.33  3.000
 6PF  C1   C5   C4   117.75  3.000
 6PF  C1   C5   N1   121.48  3.000
 6PF  C4   C5   N1   120.77  3.000
 6PF  H6   C6   H5   109.72  3.000
 6PF  H6   C6   H4   110.66  3.000
 6PF  H5   C6   H4   110.17  3.000
 6PF  H6   C6   S    109.33  3.000
 6PF  H5   C6   S    107.56  3.000
 6PF  H4   C6   S    109.35  3.000
 6PF  C3   C7   C20  118.12  3.000
 6PF  C20  C7   C8   121.54  3.000
 6PF  C3   C7   C8   120.35  3.000
 6PF  H7   C8   C9   120.28  3.000
 6PF  H7   C8   C7   121.53  3.000
 6PF  C9   C8   C7   118.17  3.000
 6PF  H8   C10  C9   133.32  3.000
 6PF  H8   C10  O3   117.29  3.000
 6PF  C9   C10  O3   109.38  3.000
 6PF  C12  C13  N2   116.38  3.000
 6PF  C12  C13  C20  117.71  3.000
 6PF  N2   C13  C20  125.90  3.000
 6PF  H10  C15  H9   105.94  3.000
 6PF  H10  C15  C14  110.39  3.000
 6PF  H9   C15  C14  106.28  3.000
 6PF  H10  C15  N3   112.68  3.000
 6PF  H9   C15  N3   108.96  3.000
 6PF  C14  C15  N3   112.19  3.000
 6PF  H12  C17  H11  107.97  3.000
 6PF  H12  C17  C16  110.01  3.000
 6PF  H11  C17  C16  109.27  3.000
 6PF  H12  C17  O5   107.52  3.000
 6PF  H11  C17  O5   110.44  3.000
 6PF  C16  C17  O5   111.55  3.000
 6PF  H13  C20  C13  120.03  3.000
 6PF  H13  C20  C7   117.93  3.000
 6PF  C13  C20  C7   122.00  3.000
 6PF  N2   C14  O4   124.06  3.000
 6PF  N2   C14  C15  112.87  3.000
 6PF  O4   C14  C15  123.04  3.000
 6PF  H15  C19  H14  107.22  3.000
 6PF  H15  C19  C18  109.73  3.000
 6PF  H14  C19  C18  108.33  3.000
 6PF  H15  C19  N3   111.43  3.000
 6PF  H14  C19  N3   110.08  3.000
 6PF  C18  C19  N3   109.96  3.000
 6PF  H17  C18  H16  107.96  3.000
 6PF  H17  C18  O5   107.52  3.000
 6PF  H16  C18  O5   110.44  3.000
 6PF  H17  C18  C19  109.97  3.000
 6PF  H16  C18  C19  109.21  3.000
 6PF  O5   C18  C19  111.65  3.000
 6PF  C18  O5   C17  110.73  3.000
 6PF  H19  C16  H18  107.24  3.000
 6PF  H19  C16  C17  108.92  3.000
 6PF  H18  C16  C17  109.46  3.000
 6PF  H19  C16  N3   109.35  3.000
 6PF  H18  C16  N3   111.87  3.000
 6PF  C17  C16  N3   109.91  3.000
 6PF  H20  N2   C14  115.41  3.000
 6PF  H20  N2   C13  115.66  3.000
 6PF  C14  N2   C13  128.92  3.000
 6PF  C9   C12  C11  106.15  3.000
 6PF  C11  C12  C13  133.83  3.000
 6PF  C9   C12  C13  120.02  3.000
 6PF  H21  C11  O3   116.65  3.000
 6PF  H21  C11  C12  134.14  3.000
 6PF  O3   C11  C12  109.21  3.000
 6PF  C11  O3   C10  109.48  3.000
 6PF  C12  C9   C10  105.78  3.000
 6PF  C10  C9   C8   133.65  3.000
 6PF  C12  C9   C8   120.56  3.000
 6PF  C2   C3   C7   121.77  3.000
 6PF  C2   C3   C4   116.50  3.000
 6PF  C7   C3   C4   121.71  3.000
 6PF  H22  C2   N    115.68  3.000
 6PF  H22  C2   C3   120.37  3.000
 6PF  N    C2   C3   123.93  3.000
 6PF  C1   N    C2   118.94  3.000
 6PF  O2   S    O1   119.87  3.000
 6PF  O2   S    C6   108.07  3.000
 6PF  O1   S    C6   108.93  3.000
 6PF  C6   S    N1   106.63  3.000
 6PF  O2   S    N1   106.94  3.000
 6PF  O1   S    N1   105.65  3.000
 6PF  O    C1   N    120.55  3.000
 6PF  N    C1   C5   122.53  3.000
 6PF  O    C1   C5   116.91  3.000
 6PF  C    O    C1   118.36  3.000
 6PF  H25  C    H24  109.47  3.000
 6PF  H25  C    H23  109.46  3.000
 6PF  H24  C    H23  108.88  3.000
 6PF  H25  C    O    105.77  3.000
 6PF  H24  C    O    111.60  3.000
 6PF  H23  C    O    111.60  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
 6PF  CONST_01  N    C1   C5   C4      0.00   0.0  0
 6PF  CONST_04  N    C2   C3   C4      0.00   0.0  0
 6PF  CONST_05  C7   C3   C4   C5    180.00   0.0  0
 6PF  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 6PF  CONST_07  C2   N    C1   C5      0.00   0.0  0
 6PF  CONST_08  N    C2   C3   C7    180.00   0.0  0
 6PF  CONST_09  C12  C13  C20  C7      0.00   0.0  0
 6PF  CONST_10  C12  C9   C8   C7      0.00   0.0  0
 6PF  CONST_11  C10  C9   C8   C7    180.00   0.0  0
 6PF  CONST_13  C13  C20  C7   C8      0.00   0.0  0
 6PF  CONST_14  C13  C12  C9   C8      0.00   0.0  0
 6PF  CONST_15  C11  C12  C9   C8    180.00   0.0  0
 6PF  CONST_16  O3   C10  C9   C8    180.00   0.0  0
 6PF  CONST_17  C13  C12  C9   C10   180.00   0.0  0
 6PF  CONST_18  C11  C12  C9   C10     0.00   0.0  0
 6PF  CONST_19  C12  C11  O3   C10     0.00   0.0  0
 6PF  CONST_20  C3   C7   C20  C13   180.00   0.0  0
 6PF  CONST_21  O3   C11  C12  C13   180.00   0.0  0
 6PF  CONST_23  C9   C8   C7   C20     0.00   0.0  0
 6PF  CONST_24  C9   C12  C13  C20     0.00   0.0  0
 6PF  CONST_25  C11  C12  C13  C20   180.00   0.0  0
 6PF  CONST_26  O3   C10  C9   C12     0.00   0.0  0
 6PF  CONST_27  C9   C10  O3   C11     0.00   0.0  0
 6PF  CONST_28  C9   C12  C11  O3      0.00   0.0  0
 6PF  CONST_29  C3   C7   C8   C9    180.00   0.0  0
 6PF  CONST_30  C1   C5   C4   C3      0.00   0.0  0
 6PF  CONST_31  C1   N    C2   C3      0.00   0.0  0
 6PF  CONST_32  C3   C4   C5   N1    180.00   0.0  0
 6PF  CONST_33  N    C1   C5   N1    180.00   0.0  0
 6PF  CONST_34  O    C1   C5   C4    180.00   0.0  0
 6PF  CONST_35  N2   C13  C20  C7    180.00   0.0  0
 6PF  CONST_36  C9   C12  C13  N2    180.00   0.0  0
 6PF  CONST_37  C11  C12  C13  N2      0.00   0.0  0
 6PF  CONST_38  O    C1   N    C2    180.00   0.0  0
 6PF  CONST_39  H22  C2   C3   C4    180.00   0.0  0
 6PF  CONST_40  H3   C4   C3   C7      0.00   0.0  0
 6PF  CONST_41  H13  C20  C7   C8    180.00   0.0  0
 6PF  CONST_42  H8   C10  C9   C8      0.00   0.0  0
 6PF  CONST_43  H7   C8   C9   C10     0.00   0.0  0
 6PF  CONST_44  H21  C11  O3   C10   180.00   0.0  0
 6PF  CONST_46  C14  N2   C13  C20     0.00   0.0  0
 6PF  CONST_47  C12  C13  N2   C14   180.00   0.0  0
 6PF  CONST_50  H20  N2   C13  C20   180.00   0.0  0
 6PF  CONST_51  O4   C14  N2   C13     0.00   0.0  0
 6PF  CONST_52  C15  C14  N2   C13   180.00   0.0  0
 6PF  Var_01    O5   C18  C19  N3    -57.03  30.0  1
 6PF  Var_02    O5   C17  C16  N3     57.32  30.0  1
 6PF  Var_03    C19  C18  O5   C17    57.55  30.0  1
 6PF  Var_04    C19  N3   C16  C17   -56.35  30.0  1
 6PF  Var_05    C16  C17  O5   C18   -57.68  30.0  1
 6PF  Var_06    C16  N3   C19  C18    56.19  30.0  1
 6PF  Var_07    O4   C14  C15  N3     28.36  30.0  3
 6PF  Var_08    O1   S    N1   C5   -176.05  30.0  2
 6PF  Var_09    H23  C    O    C1    -60.46  30.0  3
 6PF  Var_10    H4   C6   S    N1     61.15  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
 6PF  plan-1  N1   0.020
 6PF  plan-1  C4   0.020
 6PF  plan-1  C5   0.020
 6PF  plan-1  C7   0.020
 6PF  plan-1  C3   0.020
 6PF  plan-1  C2   0.020
 6PF  plan-1  N    0.020
 6PF  plan-1  C1   0.020
 6PF  plan-1  O    0.020
 6PF  plan-1  H3   0.020
 6PF  plan-1  H22  0.020
 6PF  plan-2  C7   0.020
 6PF  plan-2  C8   0.020
 6PF  plan-2  C10  0.020
 6PF  plan-2  C13  0.020
 6PF  plan-2  C20  0.020
 6PF  plan-2  N2   0.020
 6PF  plan-2  C12  0.020
 6PF  plan-2  C11  0.020
 6PF  plan-2  O3   0.020
 6PF  plan-2  C9   0.020
 6PF  plan-2  C3   0.020
 6PF  plan-2  H7   0.020
 6PF  plan-2  H8   0.020
 6PF  plan-2  H13  0.020
 6PF  plan-2  H21  0.020
 6PF  plan-3  N1   0.020
 6PF  plan-3  C5   0.020
 6PF  plan-3  S    0.020
 6PF  plan-3  H1   0.020
 6PF  plan-4  C13  0.020
 6PF  plan-4  C15  0.020
 6PF  plan-4  O4   0.020
 6PF  plan-4  C14  0.020
 6PF  plan-4  N2   0.020
 6PF  plan-4  H20  0.020

