# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:38:16 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: 8-(2,6-dimethylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1,5-c]pyrimidin-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(c(C)n1)c2cnc(NCc3c(F)ccc4OCCc34)n5cnc(c25)[S](C)(=O)=O
#
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
 Q3A  Q3A  8-(2,6-dimethylpyridin-3-yl)-N-[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]-1-(methylsulfonyl)imidazo[1,5-c]pyrimidin-5-amine  ligand  55  33  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Q3A
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
 Q3A  C16  C  CR6   0   0.506  13.4227  26.3650  20.4496
 Q3A  C12  C  CH2   0  -0.182  10.0815  24.9926  23.3247
 Q3A  C11  C  CH2   0  -0.539  11.2895  24.2169  22.7774
 Q3A  C10  C  CR56  0  -0.041  11.9566  25.2603  21.9316
 Q3A  C15  C  CR16  0  -0.415  12.8291  27.5824  20.7061
 Q3A  C14  C  CR16  0  -0.354  11.7644  27.6559  21.6023
 Q3A  C13  C  CR56  0   0.410  11.3488  26.4818  22.1996
 Q3A  C6   C  CR16  0  -0.043  15.0611  23.5825  24.6286
 Q3A  C9   C  CR6   0  -0.128  13.0202  25.1752  21.0513
 Q3A  C1   C  CR6   0   0.240  17.3842  23.2329  29.0913
 Q3A  C2   C  CR16  0  -0.348  17.3633  22.0940  28.2998
 Q3A  C7   C  CR6   0   0.801  15.4909  23.7985  22.3989
 Q3A  C3   C  CR16  0  -0.174  17.0244  22.2225  26.9613
 Q3A  C4   C  CR6   0  -0.074  16.7354  23.4736  26.4445
 Q3A  C5   C  CR6   0  -0.120  16.3661  23.6308  25.0232
 Q3A  O2   O  OS    0  -0.671  21.1545  24.5092  24.3334
 Q3A  O1   O  OS    0  -0.653  19.4977  24.6232  26.2140
 Q3A  C20  C  CH3   0  -0.785  20.3311  22.2612  25.4062
 Q3A  C18  C  CR5   0  -0.288  18.6943  23.9000  23.8257
 Q3A  C17  C  CR56  0   0.543  17.3203  23.7928  23.9855
 Q3A  C21  C  CR6   0   0.238  16.7732  24.5695  27.3161
 Q3A  C22  C  CH3   0  -0.747  16.4648  25.9504  26.8254
 Q3A  N4   N  N     0  -0.451  17.0835  24.4353  28.5972
 Q3A  C    C  CH3   0  -0.718  17.7343  23.1728  30.5466
 Q3A  N3   N  N     0  -0.381  19.0263  23.9896  22.5107
 Q3A  C19  C  CR15  0   0.085  17.9212  23.9601  21.8413
 Q3A  N2   N  N     0  -0.611  16.8420  23.8457  22.6827
 Q3A  N    N  N     0  -0.474  14.6224  23.6770  23.3548
 Q3A  N1   N  NH1   0  -0.682  15.1142  23.8698  21.1206
 Q3A  C8   C  CH2   0  -0.390  13.7160  23.8758  20.7400
 Q3A  F    F  F     0  -0.319  14.4428  26.3152  19.5675
 Q3A  O    O  O     0  -0.495  10.3440  26.3892  23.0956
 Q3A  H12  H  HCH2  0   0.245   9.9225  24.8451  24.3916
 Q3A  H11  H  HCH2  0   0.237   9.1649  24.7212  22.7961
 Q3A  H10  H  HCH2  0   0.268  10.9741  23.3367  22.2164
 Q3A  H9   H  HCH2  0   0.281  11.9653  23.8774  23.5648
 Q3A  H14  H  HCR6  0   0.278  13.1850  28.4731  20.2051
 Q3A  H13  H  HCR6  0   0.272  11.2864  28.6029  21.8139
 Q3A  H5   H  HCR6  0   0.273  14.2859  23.4592  25.3761
 Q3A  H3   H  HCR6  0   0.262  17.6022  21.1261  28.7197
 Q3A  H4   H  HCR6  0   0.269  16.9836  21.3498  26.3200
 Q3A  H18  H  HCH3  0   0.308  21.1454  22.2545  26.1306
 Q3A  H17  H  HCH3  0   0.287  19.4473  21.7994  25.8387
 Q3A  H16  H  HCH3  0   0.294  20.6302  21.7353  24.5024
 Q3A  H21  H  HCH3  0   0.250  16.6034  26.6746  27.6253
 Q3A  H20  H  HCH3  0   0.248  17.1152  26.2261  25.9943
 Q3A  H19  H  HCH3  0   0.248  15.4371  26.0297  26.4674
 Q3A  H1   H  HCH3  0   0.250  18.5650  23.8425  30.7728
 Q3A  H2   H  HCH3  0   0.251  16.8895  23.4909  31.1599
 Q3A  H    H  HCH3  0   0.242  18.0145  22.1665  30.8523
 Q3A  H15  H  HCR5  0   0.313  17.8412  24.0154  20.7682
 Q3A  H6   H  HNH1  0   0.423  15.7925  23.9867  20.3887
 Q3A  H7   H  HCH2  0   0.282  13.2043  23.0526  21.2363
 Q3A  H8   H  HCH2  0   0.296  13.6855  23.6714  19.6705
 Q3A  S    S  S     0   1.183  19.9843  23.9588  25.0099

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
 Q3A  F    C16  single    1.350  0.020  1.350
 Q3A  C15  C16  aromatic  1.379  0.020  1.379
 Q3A  C15  C14  aromatic  1.394  0.020  1.394
 Q3A  C16  C9   aromatic  1.393  0.020  1.393
 Q3A  C8   C9   single    1.506  0.020  1.506
 Q3A  C8   N1   single    1.449  0.020  1.449
 Q3A  C9   C10  aromatic  1.383  0.020  1.383
 Q3A  C14  C13  aromatic  1.381  0.020  1.381
 Q3A  N1   C7   single    1.335  0.020  1.335
 Q3A  C13  C10  aromatic  1.390  0.020  1.390
 Q3A  C13  O    single    1.349  0.020  1.349
 Q3A  C10  C11  single    1.500  0.020  1.500
 Q3A  C19  N3   aromatic  1.292  0.020  1.292
 Q3A  C19  N2   aromatic  1.373  0.020  1.373
 Q3A  C7   N2   aromatic  1.381  0.020  1.381
 Q3A  C7   N    aromatic  1.297  0.020  1.297
 Q3A  N3   C18  aromatic  1.359  0.020  1.359
 Q3A  N2   C17  aromatic  1.389  0.020  1.389
 Q3A  O    C12  single    1.439  0.020  1.439
 Q3A  C11  C12  single    1.536  0.020  1.536
 Q3A  N    C6   aromatic  1.351  0.020  1.351
 Q3A  C18  C17  aromatic  1.387  0.020  1.387
 Q3A  C18  S    single    1.752  0.020  1.752
 Q3A  C17  C5   aromatic  1.419  0.020  1.419
 Q3A  O2   S    double    1.459  0.020  1.459
 Q3A  C6   C5   aromatic  1.364  0.020  1.364
 Q3A  C5   C4   single    1.477  0.020  1.477
 Q3A  S    C20  single    1.777  0.020  1.777
 Q3A  S    O1   double    1.459  0.020  1.459
 Q3A  C4   C3   aromatic  1.384  0.020  1.384
 Q3A  C4   C21  aromatic  1.401  0.020  1.401
 Q3A  C3   C2   aromatic  1.387  0.020  1.387
 Q3A  C22  C21  single    1.498  0.020  1.498
 Q3A  C21  N4   aromatic  1.325  0.020  1.325
 Q3A  C2   C1   aromatic  1.387  0.020  1.387
 Q3A  N4   C1   aromatic  1.334  0.020  1.334
 Q3A  C1   C    single    1.498  0.020  1.498
 Q3A  C12  H12  single    0.970  0.020  1.090
 Q3A  C12  H11  single    0.970  0.020  1.090
 Q3A  C11  H10  single    0.970  0.020  1.090
 Q3A  C11  H9   single    0.970  0.020  1.090
 Q3A  C15  H14  single    0.930  0.020  1.080
 Q3A  C14  H13  single    0.930  0.020  1.080
 Q3A  C6   H5   single    0.930  0.020  1.080
 Q3A  C2   H3   single    0.930  0.020  1.080
 Q3A  C3   H4   single    0.930  0.020  1.080
 Q3A  C20  H18  single    0.970  0.020  1.090
 Q3A  C20  H17  single    0.970  0.020  1.090
 Q3A  C20  H16  single    0.970  0.020  1.090
 Q3A  C22  H21  single    0.970  0.020  1.090
 Q3A  C22  H20  single    0.970  0.020  1.090
 Q3A  C22  H19  single    0.970  0.020  1.090
 Q3A  C    H1   single    0.970  0.020  1.090
 Q3A  C    H2   single    0.970  0.020  1.090
 Q3A  C    H    single    0.970  0.020  1.090
 Q3A  C19  H15  single    0.930  0.020  1.080
 Q3A  N1   H6   single    0.860  0.020  1.020
 Q3A  C8   H7   single    0.970  0.020  1.090
 Q3A  C8   H8   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
 Q3A  F    C16  C9   117.99  3.000
 Q3A  C9   C16  C15  123.34  3.000
 Q3A  F    C16  C15  118.67  3.000
 Q3A  H11  C12  H12  108.54  3.000
 Q3A  H11  C12  O    108.49  3.000
 Q3A  H12  C12  O    108.30  3.000
 Q3A  H11  C12  C11  111.22  3.000
 Q3A  H12  C12  C11  113.30  3.000
 Q3A  O    C12  C11  106.84  3.000
 Q3A  H9   C11  H10  107.40  3.000
 Q3A  H9   C11  C10  110.35  3.000
 Q3A  H10  C11  C10  113.59  3.000
 Q3A  H9   C11  C12  112.76  3.000
 Q3A  H10  C11  C12  111.31  3.000
 Q3A  C10  C11  C12  101.50  3.000
 Q3A  C9   C10  C13  120.85  3.000
 Q3A  C13  C10  C11  107.94  3.000
 Q3A  C9   C10  C11  131.16  3.000
 Q3A  H14  C15  C14  120.37  3.000
 Q3A  H14  C15  C16  119.94  3.000
 Q3A  C14  C15  C16  119.68  3.000
 Q3A  H13  C14  C13  121.78  3.000
 Q3A  H13  C14  C15  120.63  3.000
 Q3A  C13  C14  C15  117.59  3.000
 Q3A  O    C13  C14  124.72  3.000
 Q3A  O    C13  C10  113.15  3.000
 Q3A  C14  C13  C10  122.13  3.000
 Q3A  H5   C6   N    115.22  3.000
 Q3A  H5   C6   C5   119.25  3.000
 Q3A  N    C6   C5   125.53  3.000
 Q3A  C8   C9   C10  122.66  3.000
 Q3A  C10  C9   C16  116.40  3.000
 Q3A  C8   C9   C16  120.94  3.000
 Q3A  C    C1   N4   116.65  3.000
 Q3A  C    C1   C2   121.66  3.000
 Q3A  N4   C1   C2   121.68  3.000
 Q3A  H3   C2   C3   120.77  3.000
 Q3A  H3   C2   C1   120.65  3.000
 Q3A  C3   C2   C1   118.58  3.000
 Q3A  N1   C7   N    121.45  3.000
 Q3A  N    C7   N2   120.44  3.000
 Q3A  N1   C7   N2   118.10  3.000
 Q3A  H4   C3   C4   119.94  3.000
 Q3A  H4   C3   C2   120.38  3.000
 Q3A  C4   C3   C2   119.68  3.000
 Q3A  C21  C4   C5   121.49  3.000
 Q3A  C21  C4   C3   117.98  3.000
 Q3A  C5   C4   C3   120.51  3.000
 Q3A  C17  C5   C4   123.21  3.000
 Q3A  C4   C5   C6   120.92  3.000
 Q3A  C17  C5   C6   115.83  3.000
 Q3A  H16  C20  H17  110.42  3.000
 Q3A  H16  C20  H18  110.11  3.000
 Q3A  H17  C20  H18  109.90  3.000
 Q3A  H16  C20  S    109.28  3.000
 Q3A  H17  C20  S    109.63  3.000
 Q3A  H18  C20  S    107.45  3.000
 Q3A  N3   C18  C17  111.00  3.000
 Q3A  C17  C18  S    130.84  3.000
 Q3A  N3   C18  S    118.15  3.000
 Q3A  N2   C17  C18  103.31  3.000
 Q3A  C18  C17  C5   139.37  3.000
 Q3A  N2   C17  C5   117.31  3.000
 Q3A  N4   C21  C22  117.28  3.000
 Q3A  N4   C21  C4   121.92  3.000
 Q3A  C22  C21  C4   120.80  3.000
 Q3A  H19  C22  H20  107.05  3.000
 Q3A  H19  C22  H21  108.24  3.000
 Q3A  H20  C22  H21  108.42  3.000
 Q3A  H19  C22  C21  111.62  3.000
 Q3A  H20  C22  C21  111.09  3.000
 Q3A  H21  C22  C21  110.28  3.000
 Q3A  C21  N4   C1   120.14  3.000
 Q3A  H    C    H2   108.12  3.000
 Q3A  H    C    H1   108.26  3.000
 Q3A  H2   C    H1   107.10  3.000
 Q3A  H    C    C1   111.72  3.000
 Q3A  H2   C    C1   110.69  3.000
 Q3A  H1   C    C1   110.78  3.000
 Q3A  C19  N3   C18  106.90  3.000
 Q3A  H15  C19  N2   123.79  3.000
 Q3A  H15  C19  N3   125.32  3.000
 Q3A  N2   C19  N3   110.89  3.000
 Q3A  C19  N2   C17  107.90  3.000
 Q3A  C17  N2   C7   121.89  3.000
 Q3A  C19  N2   C7   130.21  3.000
 Q3A  C7   N    C6   118.95  3.000
 Q3A  H6   N1   C8   117.37  3.000
 Q3A  H6   N1   C7   120.88  3.000
 Q3A  C8   N1   C7   121.61  3.000
 Q3A  H8   C8   H7   107.01  3.000
 Q3A  H8   C8   N1   106.50  3.000
 Q3A  H7   C8   N1   109.30  3.000
 Q3A  H8   C8   C9   110.60  3.000
 Q3A  H7   C8   C9   109.93  3.000
 Q3A  N1   C8   C9   113.26  3.000
 Q3A  C13  O    C12  107.94  3.000
 Q3A  C18  S    C20  105.21  3.000
 Q3A  C20  S    O1   108.43  3.000
 Q3A  C18  S    O1   109.12  3.000
 Q3A  O1   S    O2   118.57  3.000
 Q3A  C20  S    O2   107.88  3.000
 Q3A  C18  S    O2   106.84  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
 Q3A  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 Q3A  CONST_02  C13  C10  C9   C16     0.00   0.0  0
 Q3A  CONST_03  C15  C16  C9   C10     0.00   0.0  0
 Q3A  CONST_04  C15  C14  C13  C10     0.00   0.0  0
 Q3A  CONST_05  C9   C16  C15  C14     0.00   0.0  0
 Q3A  CONST_06  C9   C10  C13  C14     0.00   0.0  0
 Q3A  CONST_07  N2   C7   N    C6      0.00   0.0  0
 Q3A  CONST_08  N2   C17  C5   C6      0.00   0.0  0
 Q3A  CONST_09  C18  C17  C5   C6    180.00   0.0  0
 Q3A  CONST_12  C4   C3   C2   C1      0.00   0.0  0
 Q3A  CONST_13  C4   C21  N4   C1      0.00   0.0  0
 Q3A  CONST_14  C5   C4   C3   C2    180.00   0.0  0
 Q3A  CONST_15  C21  C4   C3   C2      0.00   0.0  0
 Q3A  CONST_16  C21  N4   C1   C2      0.00   0.0  0
 Q3A  CONST_17  N3   C19  N2   C7    180.00   0.0  0
 Q3A  CONST_18  C18  C17  N2   C7    180.00   0.0  0
 Q3A  CONST_19  C5   C17  N2   C7      0.00   0.0  0
 Q3A  CONST_20  C5   C6   N    C7      0.00   0.0  0
 Q3A  CONST_22  N4   C21  C4   C3      0.00   0.0  0
 Q3A  CONST_23  N4   C1   C2   C3      0.00   0.0  0
 Q3A  CONST_24  N2   C17  C5   C4    180.00   0.0  0
 Q3A  CONST_25  C18  C17  C5   C4      0.00   0.0  0
 Q3A  CONST_26  N    C6   C5   C4    180.00   0.0  0
 Q3A  CONST_27  C19  N2   C17  C5    180.00   0.0  0
 Q3A  CONST_28  N3   C18  C17  C5    180.00   0.0  0
 Q3A  CONST_29  N4   C21  C4   C5    180.00   0.0  0
 Q3A  CONST_30  N2   C19  N3   C18     0.00   0.0  0
 Q3A  CONST_31  C19  N2   C17  C18     0.00   0.0  0
 Q3A  CONST_32  N3   C19  N2   C17     0.00   0.0  0
 Q3A  CONST_33  N    C7   N2   C17     0.00   0.0  0
 Q3A  CONST_34  C19  N3   C18  C17     0.00   0.0  0
 Q3A  CONST_35  N    C6   C5   C17     0.00   0.0  0
 Q3A  CONST_37  N2   C17  C18  N3      0.00   0.0  0
 Q3A  CONST_38  N    C7   N2   C19   180.00   0.0  0
 Q3A  CONST_39  C8   C9   C10  C11     0.00   0.0  0
 Q3A  CONST_40  F    C16  C9   C10   180.00   0.0  0
 Q3A  CONST_41  C8   C9   C16  C15   180.00   0.0  0
 Q3A  CONST_42  F    C16  C15  C14   180.00   0.0  0
 Q3A  CONST_43  C8   C9   C10  C13   180.00   0.0  0
 Q3A  CONST_44  N1   C7   N    C6    180.00   0.0  0
 Q3A  CONST_45  C22  C21  N4   C1    180.00   0.0  0
 Q3A  CONST_46  C22  C21  C4   C3    180.00   0.0  0
 Q3A  CONST_47  C    C1   C2   C3    180.00   0.0  0
 Q3A  CONST_48  S    C18  C17  C5      0.00   0.0  0
 Q3A  CONST_49  C22  C21  C4   C5      0.00   0.0  0
 Q3A  CONST_50  C19  N3   C18  S     180.00   0.0  0
 Q3A  CONST_51  N2   C17  C18  S     180.00   0.0  0
 Q3A  CONST_52  N1   C7   N2   C17   180.00   0.0  0
 Q3A  CONST_53  C    C1   N4   C21   180.00   0.0  0
 Q3A  CONST_54  N1   C7   N2   C19     0.00   0.0  0
 Q3A  CONST_55  H13  C14  C15  C16   180.00   0.0  0
 Q3A  CONST_56  H14  C15  C14  C13   180.00   0.0  0
 Q3A  CONST_57  H4   C3   C2   C1    180.00   0.0  0
 Q3A  CONST_58  H15  C19  N2   C7      0.00   0.0  0
 Q3A  CONST_59  H5   C6   N    C7    180.00   0.0  0
 Q3A  CONST_60  H3   C2   C3   C4    180.00   0.0  0
 Q3A  CONST_61  C8   N1   C7   N2    180.00   0.0  0
 Q3A  CONST_62  C8   N1   C7   N       0.00   0.0  0
 Q3A  CONST_63  H6   N1   C7   N2      0.00   0.0  0
 Q3A  Var_01    C14  C13  O    C12   171.27  30.0  1
 Q3A  Var_02    C9   C10  C11  C12  -172.28  30.0  1
 Q3A  Var_03    O    C12  C11  C10   -15.51  30.0  1
 Q3A  Var_04    N1   C8   C9   C16    62.41  30.0  2
 Q3A  Var_05    C7   N1   C8   C9     73.02  30.0  3
 Q3A  Var_06    N3   C18  S    O2     17.26  30.0  2
 Q3A  Var_07    H1   C    C1   C2    124.24  30.0  2
 Q3A  Var_08    H21  C22  C21  C4   -176.55  30.0  2
 Q3A  Var_09    H18  C20  S    C18   178.98  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
 Q3A  plan-1  C1   0.020
 Q3A  plan-1  C2   0.020
 Q3A  plan-1  C3   0.020
 Q3A  plan-1  C4   0.020
 Q3A  plan-1  C5   0.020
 Q3A  plan-1  C21  0.020
 Q3A  plan-1  C22  0.020
 Q3A  plan-1  N4   0.020
 Q3A  plan-1  C    0.020
 Q3A  plan-1  H3   0.020
 Q3A  plan-1  H4   0.020
 Q3A  plan-2  C16  0.020
 Q3A  plan-2  C11  0.020
 Q3A  plan-2  C10  0.020
 Q3A  plan-2  C15  0.020
 Q3A  plan-2  C14  0.020
 Q3A  plan-2  C13  0.020
 Q3A  plan-2  C9   0.020
 Q3A  plan-2  C8   0.020
 Q3A  plan-2  F    0.020
 Q3A  plan-2  O    0.020
 Q3A  plan-2  H14  0.020
 Q3A  plan-2  H13  0.020
 Q3A  plan-3  C6   0.020
 Q3A  plan-3  C7   0.020
 Q3A  plan-3  C4   0.020
 Q3A  plan-3  C5   0.020
 Q3A  plan-3  C18  0.020
 Q3A  plan-3  C17  0.020
 Q3A  plan-3  N3   0.020
 Q3A  plan-3  C19  0.020
 Q3A  plan-3  N2   0.020
 Q3A  plan-3  N    0.020
 Q3A  plan-3  N1   0.020
 Q3A  plan-3  H5   0.020
 Q3A  plan-3  H15  0.020
 Q3A  plan-3  S    0.020
 Q3A  plan-4  C7   0.020
 Q3A  plan-4  N1   0.020
 Q3A  plan-4  C8   0.020
 Q3A  plan-4  H6   0.020

