# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 27 21:54:54 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5-({(1R,1aS,6bR)-1-[5-(trifluoromethyl)-1H-benzimidazol-2-yl]-1a,6b-dihydro-1H-cyclopropa[b][1]benzofuran-5-yl}oxy)-3,4-dihydro-1,8-naphthyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc2[nH]c(nc2c1)[C@@H]3[C@H]4Oc5ccc(Oc6ccnc7NC(=O)CCc67)cc5[C@@H]34
#
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
 3K3  3K3  5-({(1R,1aS,6bR)-1-[5-(trifluoromethyl)-1H-benzimidazol-2-yl]-1a,6b-dihydro-1H-cyclopropa[b][1]benzofuran-5-yl}oxy)-3,4-dihydro-1,8-naphthyridin-2(1H)-one  ligand  52  35  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3K3
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
 3K3  F2   F  F     0  -0.304  -7.9817   1.7834   2.1572
 3K3  C19  C  CT    0   1.046  -8.2175   1.3699   0.9079
 3K3  F    F  F     0  -0.316  -9.3441   0.6406   0.9457
 3K3  F1   F  F     0  -0.317  -8.5070   2.4652   0.1857
 3K3  C18  C  CR6   0  -0.211  -7.0756   0.6040   0.3249
 3K3  C17  C  CR16  0  -0.291  -7.2522   0.0309  -0.9468
 3K3  C16  C  CR16  0  -0.294  -6.2404  -0.6804  -1.5604
 3K3  C20  C  CR16  0  -0.380  -5.8815   0.4814   1.0153
 3K3  C21  C  CR56  0   0.168  -4.8549  -0.2358   0.4086
 3K3  C15  C  CR56  0   0.346  -5.0459  -0.8025  -0.8622
 3K3  N    N  NR15  0  -0.719  -3.8606  -1.4187  -1.1461
 3K3  N1   N  N     0  -0.488  -3.5889  -0.5105   0.8622
 3K3  C14  C  CR5   0   0.552  -3.0330  -1.2149  -0.0875
 3K3  C13  C  CH1   0  -0.433  -1.6783  -1.7622  -0.0488
 3K3  C9   C  CR15  0   0.030  -1.2141  -2.3335   1.2631
 3K3  O2   O  O     0  -0.463  -0.2144  -3.3179   1.2117
 3K3  C10  C  CR15  0  -0.321  -0.6506  -1.0282   0.8054
 3K3  C11  C  CR56  0   0.079   0.7469  -1.3740   0.4829
 3K3  C8   C  CR56  0   0.360   0.9087  -2.7366   0.7212
 3K3  C7   C  CR16  0  -0.346   2.1007  -3.3903   0.4804
 3K3  C6   C  CR16  0  -0.300   3.1675  -2.6256   0.0189
 3K3  C12  C  CR16  0  -0.373   1.8085  -0.6139   0.0324
 3K3  C5   C  CR6   0   0.294   3.0167  -1.2627  -0.1923
 3K3  O1   O  O2    0  -0.504   4.0838  -0.5379  -0.6807
 3K3  C4   C  CR6   0   0.422   4.9741  -0.0152   0.1868
 3K3  C22  C  CR16  0  -0.422   4.8634  -0.1282   1.5724
 3K3  C23  C  CR16  0  -0.067   5.8642   0.4331   2.3413
 3K3  N2   N  N     0  -0.449   6.9109   1.0818   1.8461
 3K3  C24  C  CR6   0   0.484   6.9830   1.1850   0.5282
 3K3  N3   N  NH1   0  -0.704   8.0971   1.8507   0.0348
 3K3  C    C  C     0   0.521   8.2378   2.3238  -1.2355
 3K3  O    O  O     0  -0.459   9.2399   2.9188  -1.5820
 3K3  C3   C  CR6   0  -0.117   6.0552   0.6591  -0.3676
 3K3  C2   C  CH2   0  -0.481   6.3073   0.8007  -1.8378
 3K3  C1   C  CH2   0  -0.596   7.0459   2.1011  -2.1291
 3K3  H1   H  HCR6  0   0.273  -8.1961   0.1390  -1.4652
 3K3  H2   H  HCR6  0   0.277  -6.3828  -1.1194  -2.5383
 3K3  H3   H  HCR6  0   0.269  -5.7292   0.9171   1.9934
 3K3  H4   H  HNR5  0   0.426  -3.6371  -1.9377  -1.9813
 3K3  H6   H  HCH1  0   0.306  -1.3285  -2.2265  -0.9648
 3K3  H7   H  HCR5  0   0.294  -1.9118  -2.4528   2.0822
 3K3  H8   H  HCR5  0   0.293  -0.9215  -0.0760   1.2430
 3K3  H9   H  HCR6  0   0.280   2.2139  -4.4517   0.6550
 3K3  H10  H  HCR6  0   0.282   4.1219  -3.0976  -0.1765
 3K3  H11  H  HCR6  0   0.279   1.7063   0.4484  -0.1498
 3K3  H12  H  HCR6  0   0.288   4.0381  -0.6372   2.0485
 3K3  H13  H  HCR6  0   0.270   5.8150   0.3531   3.4210
 3K3  H14  H  HNH1  0   0.405   8.8149   2.0846   0.7081
 3K3  H15  H  HCH2  0   0.269   6.8977  -0.0509  -2.1909
 3K3  H16  H  HCH2  0   0.273   5.3773   0.7856  -2.4040
 3K3  H17  H  HCH2  0   0.288   6.3711   2.9499  -1.9729
 3K3  H18  H  HCH2  0   0.282   7.3741   2.1418  -3.1663

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
 3K3  F    C19  single    1.343  0.020  1.343
 3K3  C17  C16  aromatic  1.381  0.020  1.381
 3K3  C17  C18  aromatic  1.406  0.020  1.406
 3K3  C16  C15  aromatic  1.389  0.020  1.389
 3K3  C19  C18  single    1.494  0.020  1.494
 3K3  C19  F1   single    1.343  0.020  1.343
 3K3  C19  F2   single    1.337  0.020  1.337
 3K3  C18  C20  aromatic  1.385  0.020  1.385
 3K3  C15  N    aromatic  1.366  0.020  1.366
 3K3  C15  C21  aromatic  1.404  0.020  1.404
 3K3  N    C14  aromatic  1.359  0.020  1.359
 3K3  C20  C21  aromatic  1.391  0.020  1.391
 3K3  C21  N1   aromatic  1.373  0.020  1.373
 3K3  C9   O2   single    1.404  0.020  1.404
 3K3  C9   C13  single    1.504  0.020  1.504
 3K3  C9   C10  single    1.494  0.020  1.494
 3K3  O2   C8   single    1.356  0.020  1.356
 3K3  C14  N1   aromatic  1.307  0.020  1.307
 3K3  C14  C13  single    1.462  0.020  1.462
 3K3  C13  C10  single    1.525  0.020  1.525
 3K3  C10  C11  single    1.475  0.020  1.475
 3K3  C8   C7   aromatic  1.381  0.020  1.381
 3K3  C8   C11  aromatic  1.393  0.020  1.393
 3K3  C7   C6   aromatic  1.391  0.020  1.391
 3K3  C11  C12  aromatic  1.381  0.020  1.381
 3K3  C6   C5   aromatic  1.387  0.020  1.387
 3K3  C12  C5   aromatic  1.390  0.020  1.390
 3K3  C5   O1   single    1.379  0.020  1.379
 3K3  O1   C4   single    1.348  0.020  1.348
 3K3  C22  C4   aromatic  1.395  0.020  1.395
 3K3  C22  C23  aromatic  1.381  0.020  1.381
 3K3  C4   C3   aromatic  1.390  0.020  1.390
 3K3  C23  N2   aromatic  1.327  0.020  1.327
 3K3  C3   C2   single    1.498  0.020  1.498
 3K3  C3   C24  aromatic  1.393  0.020  1.393
 3K3  N2   C24  aromatic  1.324  0.020  1.324
 3K3  C2   C1   single    1.524  0.020  1.524
 3K3  C24  N3   single    1.388  0.020  1.388
 3K3  C1   C    single    1.506  0.020  1.506
 3K3  N3   C    single    1.363  0.020  1.363
 3K3  C    O    double    1.216  0.020  1.216
 3K3  C17  H1   single    0.930  0.020  1.080
 3K3  C16  H2   single    0.930  0.020  1.080
 3K3  C20  H3   single    0.930  0.020  1.080
 3K3  N    H4   single    0.860  0.020  1.020
 3K3  C13  H6   single    0.970  0.020  1.090
 3K3  C9   H7   single    0.970  0.020  1.090
 3K3  C10  H8   single    0.970  0.020  1.090
 3K3  C7   H9   single    0.930  0.020  1.080
 3K3  C6   H10  single    0.930  0.020  1.080
 3K3  C12  H11  single    0.930  0.020  1.080
 3K3  C22  H12  single    0.930  0.020  1.080
 3K3  C23  H13  single    0.930  0.020  1.080
 3K3  N3   H14  single    0.860  0.020  1.020
 3K3  C2   H15  single    0.970  0.020  1.090
 3K3  C2   H16  single    0.970  0.020  1.090
 3K3  C1   H17  single    0.970  0.020  1.090
 3K3  C1   H18  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
 3K3  C18  C19  F1   111.90  3.000
 3K3  F1   C19  F    106.09  3.000
 3K3  C18  C19  F    111.96  3.000
 3K3  F1   C19  F2   106.75  3.000
 3K3  C18  C19  F2   112.86  3.000
 3K3  F    C19  F2   106.85  3.000
 3K3  C20  C18  C17  121.55  3.000
 3K3  C20  C18  C19  120.67  3.000
 3K3  C17  C18  C19  117.78  3.000
 3K3  H1   C17  C16  118.54  3.000
 3K3  H1   C17  C18  120.14  3.000
 3K3  C16  C17  C18  121.33  3.000
 3K3  H2   C16  C15  122.15  3.000
 3K3  H2   C16  C17  120.97  3.000
 3K3  C15  C16  C17  116.88  3.000
 3K3  H3   C20  C21  119.88  3.000
 3K3  H3   C20  C18  122.45  3.000
 3K3  C21  C20  C18  117.67  3.000
 3K3  N1   C21  C15  110.10  3.000
 3K3  N1   C21  C20  129.76  3.000
 3K3  C15  C21  C20  120.15  3.000
 3K3  N    C15  C21  104.61  3.000
 3K3  C21  C15  C16  122.43  3.000
 3K3  N    C15  C16  132.96  3.000
 3K3  H4   N    C14  125.97  3.000
 3K3  H4   N    C15  126.64  3.000
 3K3  C14  N    C15  107.39  3.000
 3K3  C14  N1   C21  105.08  3.000
 3K3  C13  C14  N1   125.24  3.000
 3K3  C13  C14  N    121.93  3.000
 3K3  N1   C14  N    112.82  3.000
 3K3  H6   C13  C10  117.50  3.000
 3K3  H6   C13  C9   118.32  3.000
 3K3  C10  C13  C9    59.09  3.000
 3K3  H6   C13  C14  115.89  3.000
 3K3  C10  C13  C14  117.34  3.000
 3K3  C9   C13  C14  116.83  3.000
 3K3  H7   C9   C10  124.84  3.000
 3K3  H7   C9   O2   114.16  3.000
 3K3  C10  C9   O2   109.45  3.000
 3K3  H7   C9   C13  120.19  3.000
 3K3  C10  C9   C13   61.14  3.000
 3K3  O2   C9   C13  117.01  3.000
 3K3  C8   O2   C9   107.59  3.000
 3K3  H8   C10  C11  122.12  3.000
 3K3  H8   C10  C9   123.40  3.000
 3K3  C11  C10  C9   102.68  3.000
 3K3  H8   C10  C13  118.77  3.000
 3K3  C11  C10  C13  113.78  3.000
 3K3  C9   C10  C13   59.78  3.000
 3K3  C12  C11  C8   120.33  3.000
 3K3  C12  C11  C10  132.09  3.000
 3K3  C8   C11  C10  107.58  3.000
 3K3  C7   C8   C11  122.26  3.000
 3K3  C11  C8   O2   112.64  3.000
 3K3  C7   C8   O2   125.10  3.000
 3K3  H9   C7   C6   120.84  3.000
 3K3  H9   C7   C8   121.79  3.000
 3K3  C6   C7   C8   117.36  3.000
 3K3  H10  C6   C5   119.78  3.000
 3K3  H10  C6   C7   119.75  3.000
 3K3  C5   C6   C7   120.47  3.000
 3K3  H11  C12  C5   120.86  3.000
 3K3  H11  C12  C11  121.49  3.000
 3K3  C5   C12  C11  117.65  3.000
 3K3  O1   C5   C12  118.99  3.000
 3K3  O1   C5   C6   119.07  3.000
 3K3  C12  C5   C6   121.91  3.000
 3K3  C4   O1   C5   119.12  3.000
 3K3  C3   C4   C22  119.83  3.000
 3K3  C3   C4   O1   116.43  3.000
 3K3  C22  C4   O1   123.74  3.000
 3K3  H12  C22  C23  119.98  3.000
 3K3  H12  C22  C4   122.46  3.000
 3K3  C23  C22  C4   117.56  3.000
 3K3  H13  C23  N2   116.33  3.000
 3K3  H13  C23  C22  119.45  3.000
 3K3  N2   C23  C22  124.22  3.000
 3K3  C24  N2   C23  116.90  3.000
 3K3  C3   C24  N3   119.14  3.000
 3K3  N3   C24  N2   115.77  3.000
 3K3  C3   C24  N2   125.07  3.000
 3K3  H14  N3   C    117.83  3.000
 3K3  H14  N3   C24  116.34  3.000
 3K3  C    N3   C24  125.49  3.000
 3K3  C1   C    O    123.75  3.000
 3K3  O    C    N3   121.38  3.000
 3K3  C1   C    N3   114.83  3.000
 3K3  C2   C3   C24  118.90  3.000
 3K3  C24  C3   C4   116.42  3.000
 3K3  C2   C3   C4   124.62  3.000
 3K3  H16  C2   H15  106.39  3.000
 3K3  H16  C2   C1   109.06  3.000
 3K3  H15  C2   C1   109.93  3.000
 3K3  H16  C2   C3   111.42  3.000
 3K3  H15  C2   C3   109.49  3.000
 3K3  C1   C2   C3   110.47  3.000
 3K3  H18  C1   H17  107.01  3.000
 3K3  H18  C1   C2   111.11  3.000
 3K3  H17  C1   C2   109.60  3.000
 3K3  H18  C1   C    108.73  3.000
 3K3  H17  C1   C    106.76  3.000
 3K3  C2   C1   C    113.35  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
 3K3  CONST_01  C15  C16  C17  C18     0.00   0.0  0
 3K3  CONST_02  C15  C21  C20  C18     0.00   0.0  0
 3K3  CONST_03  N1   C21  C20  C18   180.00   0.0  0
 3K3  CONST_04  N    C15  C16  C17   180.00   0.0  0
 3K3  CONST_05  C21  C15  C16  C17     0.00   0.0  0
 3K3  CONST_06  C21  C20  C18  C17     0.00   0.0  0
 3K3  CONST_07  C20  C18  C17  C16     0.00   0.0  0
 3K3  CONST_08  C14  N    C15  C16   180.00   0.0  0
 3K3  CONST_09  C20  C21  C15  C16     0.00   0.0  0
 3K3  CONST_10  N1   C21  C15  C16   180.00   0.0  0
 3K3  CONST_11  N    C15  C21  C20   180.00   0.0  0
 3K3  CONST_12  C14  N1   C21  C20   180.00   0.0  0
 3K3  CONST_13  C14  N    C15  C21     0.00   0.0  0
 3K3  CONST_14  N    C14  N1   C21     0.00   0.0  0
 3K3  CONST_15  N1   C14  N    C15     0.00   0.0  0
 3K3  CONST_16  C14  N1   C21  C15     0.00   0.0  0
 3K3  CONST_17  N1   C21  C15  N       0.00   0.0  0
 3K3  CONST_18  C6   C7   C8   C11     0.00   0.0  0
 3K3  CONST_19  C6   C5   C12  C11     0.00   0.0  0
 3K3  CONST_20  C5   C6   C7   C8      0.00   0.0  0
 3K3  CONST_21  C5   C12  C11  C8      0.00   0.0  0
 3K3  CONST_22  C12  C11  C8   C7      0.00   0.0  0
 3K3  CONST_23  C12  C5   C6   C7      0.00   0.0  0
 3K3  CONST_24  N2   C23  C22  C4      0.00   0.0  0
 3K3  CONST_25  N2   C24  C3   C4      0.00   0.0  0
 3K3  CONST_26  C24  C3   C4   C22     0.00   0.0  0
 3K3  CONST_27  C24  N2   C23  C22     0.00   0.0  0
 3K3  CONST_28  C3   C4   C22  C23     0.00   0.0  0
 3K3  CONST_29  C3   C24  N2   C23     0.00   0.0  0
 3K3  CONST_30  C13  C14  N1   C21   180.00   0.0  0
 3K3  CONST_31  C13  C14  N    C15   180.00   0.0  0
 3K3  CONST_32  C1   C    N3   C24     0.00   0.0  0
 3K3  CONST_33  C16  C17  C18  C19   180.00   0.0  0
 3K3  CONST_34  C21  C20  C18  C19   180.00   0.0  0
 3K3  CONST_35  O1   C5   C12  C11   180.00   0.0  0
 3K3  CONST_36  O1   C5   C6   C7    180.00   0.0  0
 3K3  CONST_37  C23  C22  C4   O1    180.00   0.0  0
 3K3  CONST_38  C2   C3   C4   O1      0.00   0.0  0
 3K3  CONST_39  C24  C3   C4   O1    180.00   0.0  0
 3K3  CONST_40  O    C    N3   C24   180.00   0.0  0
 3K3  CONST_41  H2   C16  C17  C18   180.00   0.0  0
 3K3  CONST_42  H3   C20  C18  C17   180.00   0.0  0
 3K3  CONST_43  H4   N    C15  C16     0.00   0.0  0
 3K3  CONST_44  H1   C17  C18  C20   180.00   0.0  0
 3K3  CONST_45  H9   C7   C8   O2      0.00   0.0  0
 3K3  CONST_46  H11  C12  C11  C10     0.00   0.0  0
 3K3  CONST_47  H10  C6   C7   C8    180.00   0.0  0
 3K3  CONST_48  H13  C23  C22  C4    180.00   0.0  0
 3K3  CONST_49  H12  C22  C23  N2    180.00   0.0  0
 3K3  CONST_50  H14  N3   C    C1    180.00   0.0  0
 3K3  Var_01    C9   C13  C14  N    -138.99  30.0  2
 3K3  Var_02    O2   C9   C13  C14   154.34  30.0  1
 3K3  Var_03    C8   C11  C10  C13   -61.32  30.0  1
 3K3  Var_04    C7   C8   O2   C9   -177.82  30.0  1
 3K3  Var_05    C1   C2   C3   C4    150.18  30.0  1
 3K3  Var_06    C    N3   C24  N2   -164.96  30.0  1
 3K3  Var_07    C2   C1   C    N3    -33.97  30.0  1
 3K3  Var_08    C3   C2   C1   C      48.17  30.0  1
 3K3  Var_09    C22  C4   O1   C5     -1.98  30.0  2
 3K3  Var_10    C17  C18  C19  F2    175.17  30.0  2

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
 3K3  chir_01  C13  C9  C14  C10  both
 3K3  chir_02  C9   O2  C10  C13  both
 3K3  chir_03  C10  C9  C13  C11  both

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
 3K3  plan-1  C19  0.020
 3K3  plan-1  C18  0.020
 3K3  plan-1  C17  0.020
 3K3  plan-1  C16  0.020
 3K3  plan-1  C20  0.020
 3K3  plan-1  C21  0.020
 3K3  plan-1  C15  0.020
 3K3  plan-1  N    0.020
 3K3  plan-1  N1   0.020
 3K3  plan-1  C14  0.020
 3K3  plan-1  C13  0.020
 3K3  plan-1  H1   0.020
 3K3  plan-1  H2   0.020
 3K3  plan-1  H3   0.020
 3K3  plan-1  H4   0.020
 3K3  plan-2  O1   0.020
 3K3  plan-2  C4   0.020
 3K3  plan-2  C22  0.020
 3K3  plan-2  C23  0.020
 3K3  plan-2  N2   0.020
 3K3  plan-2  C24  0.020
 3K3  plan-2  N3   0.020
 3K3  plan-2  C3   0.020
 3K3  plan-2  C2   0.020
 3K3  plan-2  H12  0.020
 3K3  plan-2  H13  0.020
 3K3  plan-3  O2   0.020
 3K3  plan-3  C10  0.020
 3K3  plan-3  C11  0.020
 3K3  plan-3  C8   0.020
 3K3  plan-3  C7   0.020
 3K3  plan-3  C6   0.020
 3K3  plan-3  C12  0.020
 3K3  plan-3  C5   0.020
 3K3  plan-3  O1   0.020
 3K3  plan-3  H9   0.020
 3K3  plan-3  H10  0.020
 3K3  plan-3  H11  0.020
 3K3  plan-4  C24  0.020
 3K3  plan-4  N3   0.020
 3K3  plan-4  C    0.020
 3K3  plan-4  O    0.020
 3K3  plan-4  C1   0.020
 3K3  plan-4  H14  0.020

