# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 00:14:00 2021
#   Inital geometry file: a 155 line input string
#   Ligand name: ~{N}-[2-[(2~{S},4~{R})-2-[[(1~{S})-1-(2-chloranyl-4-methoxy-phenyl)ethyl]carbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-2-oxidanylidene-ethyl]-6-fluoranyl-quinoline-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)CN2C(=O)CNC(=O)c3ccc4cc(F)ccc4n3)c(Cl)c1
#
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
 O08  O08  ~{N}-[2-[(2~{S},4~{R})-2-[[(1~{S})-1-(2-chloranyl-4-methoxy-phenyl)ethyl]carbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-2-oxidanylidene-ethyl]-6-fluoranyl-quinoline-2-carboxamide  ligand  63  37  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O08
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
 O08  C1   C   CR6   0   0.370  21.6351   8.9999  47.2319
 O08  C2   C   CR16  0  -0.320  22.0162   7.8615  47.9442
 O08  C3   C   CR16  0  -0.303  21.8616   6.6117  47.3808
 O08  C4   C   CR6   0   0.189  21.3336   6.4274  46.1028
 O08  C5   C   CH1   0  -0.123  21.1438   5.0387  45.5251
 O08  C6   C   CH3   0  -0.672  19.7477   4.5100  45.8359
 O08  C8   C   CR15  0  -0.170  24.3206   3.1923  46.4278
 O08  C10  C   CR15  0  -0.001  26.3807   3.1879  47.6632
 O08  C11  C   CH2   0  -0.291  26.7187   2.9717  46.1984
 O08  C16  C   CR16  0  -0.293  27.0527  -0.2444  39.1549
 O08  C24  C   CR6   0  -0.106  20.9530   7.5767  45.4272
 O08  C25  C   CR16  0  -0.326  21.0945   8.8532  45.9597
 O08  O    O   O2    0  -0.468  21.8221  10.1832  47.8397
 O08  C    C   CH3   0  -0.441  21.4996  11.3661  47.1336
 O08  N    N   NH1   0  -0.648  22.1288   4.1074  46.0319
 O08  C7   C   C     0   0.565  23.4204   4.1584  45.6721
 O08  O1   O   O     0  -0.478  23.8622   4.9600  44.8677
 O08  N1   N   NR5   0  -0.481  25.4138   2.7186  45.6012
 O08  O2   O   OH1   0  -0.667  26.2515   1.9191  48.2624
 O08  C9   C   CH2   0  -0.518  25.0441   3.9159  47.5720
 O08  O3   O   O     0  -0.493  24.0356   1.8941  44.0349
 O08  C13  C   CH2   0  -0.377  26.3920   1.6420  43.6648
 O08  N2   N   NH1   0  -0.659  25.9797   1.1425  42.3861
 O08  C14  C   C     0   0.549  26.8480   0.7071  41.4731
 O08  O4   O   O     0  -0.483  28.0609   0.6852  41.6333
 O08  C15  C   CR6   0   0.098  26.2218   0.2334  40.1897
 O08  N3   N   N     0  -0.464  24.9202   0.2960  40.0967
 O08  C23  C   CR66  0   0.213  24.3236  -0.1102  38.9582
 O08  C18  C   CR66  0   0.100  25.0675  -0.6049  37.8573
 O08  C17  C   CR16  0  -0.181  26.4710  -0.6616  37.9924
 O08  C22  C   CR16  0  -0.274  22.9143  -0.0354  38.8622
 O08  C21  C   CR16  0  -0.408  22.2766  -0.4325  37.7216
 O08  C20  C   CR6   0   0.548  23.0390  -0.9188  36.6455
 O08  F    F   F     0  -0.308  22.3820  -1.2989  35.5423
 O08  C19  C   CR16  0  -0.485  24.3966  -1.0143  36.6851
 O08  H6   H   HCR6  0   0.268  22.4369   7.9657  48.9362
 O08  H7   H   HCR6  0   0.254  22.1687   5.7452  47.9531
 O08  H    H   HCH1  0   0.258  21.2625   5.0900  44.4408
 O08  H10  H   HCH3  0   0.247  18.9917   5.1811  45.4319
 O08  H8   H   HCH3  0   0.249  19.5969   3.5255  45.3913
 O08  H9   H   HCH3  0   0.236  19.5886   4.4345  46.9129
 O08  H1   H   HCR5  0   0.284  23.7412   2.3467  46.8106
 O08  H2   H   HCR5  0   0.250  27.1428   3.7963  48.1618
 O08  H15  H   HCH2  0   0.273  27.4030   2.1348  46.0579
 O08  H16  H   HCH2  0   0.262  27.1807   3.8683  45.7769
 O08  H25  H   HCR6  0   0.297  20.7805   9.7060  45.3739
 O08  H4   H   HCH3  0   0.264  21.7561  12.1954  47.7878
 O08  H3   H   HCH3  0   0.232  22.0744  11.4554  46.2081
 O08  H5   H   HCH3  0   0.232  20.4343  11.4224  46.8952
 O08  H11  H   HNH1  0   0.406  21.8294   3.3986  46.6830
 O08  H14  H   HOH1  0   0.455  25.9333   2.0404  49.1625
 O08  H13  H   HCH2  0   0.262  25.2257   4.9603  47.3076
 O08  H12  H   HCH2  0   0.278  24.4749   3.9003  48.5016
 O08  H18  H   HCH2  0   0.285  26.9154   0.8695  44.2398
 O08  H17  H   HCH2  0   0.282  27.0955   2.4725  43.5508
 O08  H19  H   HNH1  0   0.404  24.9920   1.1099  42.1726
 O08  H21  H   HCR6  0   0.279  27.0735  -1.0339  37.1734
 O08  H24  H   HCR6  0   0.281  22.3546   0.3431  39.7069
 O08  H23  H   HCR6  0   0.292  21.1994  -0.3784  37.6354
 O08  H22  H   HCR6  0   0.288  24.9542  -1.3946  35.8387
 O08  CL   CL  CL    0  -0.127  20.2527   7.4632  43.8381
 O08  C12  C   C     0   0.542  25.1719   2.0962  44.4437
 O08  H20  H   HCR6  0   0.277  28.1245  -0.2744  39.2863

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
 O08  F    C20  single    1.339  0.020  1.339
 O08  C20  C19  aromatic  1.361  0.020  1.361
 O08  C20  C21  aromatic  1.406  0.020  1.406
 O08  C19  C18  aromatic  1.411  0.020  1.411
 O08  C21  C22  aromatic  1.366  0.020  1.366
 O08  C18  C17  aromatic  1.411  0.020  1.411
 O08  C18  C23  aromatic  1.418  0.020  1.418
 O08  C17  C16  aromatic  1.365  0.020  1.365
 O08  C22  C23  aromatic  1.415  0.020  1.415
 O08  C23  N3   aromatic  1.348  0.020  1.348
 O08  C16  C15  aromatic  1.411  0.020  1.411
 O08  N3   C15  aromatic  1.306  0.020  1.306
 O08  C15  C14  single    1.505  0.020  1.505
 O08  C14  O4   double    1.224  0.020  1.224
 O08  C14  N2   single    1.333  0.020  1.333
 O08  N2   C13  single    1.433  0.020  1.433
 O08  C13  C12  single    1.517  0.020  1.517
 O08  O3   C12  double    1.224  0.020  1.224
 O08  CL   C24  single    1.740  0.020  1.740
 O08  C12  N1   single    1.336  0.020  1.336
 O08  O1   C7   double    1.219  0.020  1.219
 O08  C5   C6   single    1.525  0.020  1.525
 O08  C5   N    single    1.447  0.020  1.447
 O08  C5   C4   single    1.516  0.020  1.516
 O08  N1   C11  single    1.457  0.020  1.457
 O08  N1   C8   single    1.450  0.020  1.450
 O08  C7   N    single    1.342  0.020  1.342
 O08  C7   C8   single    1.521  0.020  1.521
 O08  C24  C4   aromatic  1.386  0.020  1.386
 O08  C24  C25  aromatic  1.390  0.020  1.390
 O08  C11  C10  single    1.519  0.020  1.519
 O08  C4   C3   aromatic  1.395  0.020  1.395
 O08  C8   C9   single    1.535  0.020  1.535
 O08  C25  C1   aromatic  1.390  0.020  1.390
 O08  C9   C10  single    1.525  0.020  1.525
 O08  C10  O2   single    1.409  0.020  1.409
 O08  C3   C2   aromatic  1.380  0.020  1.380
 O08  C1   C2   aromatic  1.396  0.020  1.396
 O08  C1   O    single    1.343  0.020  1.343
 O08  C    O    single    1.415  0.020  1.415
 O08  C2   H6   single    0.930  0.020  1.080
 O08  C3   H7   single    0.930  0.020  1.080
 O08  C5   H    single    0.970  0.020  1.090
 O08  C6   H10  single    0.970  0.020  1.090
 O08  C6   H8   single    0.970  0.020  1.090
 O08  C6   H9   single    0.970  0.020  1.090
 O08  C8   H1   single    0.970  0.020  1.090
 O08  C10  H2   single    0.970  0.020  1.090
 O08  C11  H15  single    0.970  0.020  1.090
 O08  C11  H16  single    0.970  0.020  1.090
 O08  C16  H20  single    0.930  0.020  1.080
 O08  C25  H25  single    0.930  0.020  1.080
 O08  C    H4   single    0.970  0.020  1.090
 O08  C    H3   single    0.970  0.020  1.090
 O08  C    H5   single    0.970  0.020  1.090
 O08  N    H11  single    0.860  0.020  1.020
 O08  O2   H14  single    0.850  0.020  0.980
 O08  C9   H13  single    0.970  0.020  1.090
 O08  C9   H12  single    0.970  0.020  1.090
 O08  C13  H18  single    0.970  0.020  1.090
 O08  C13  H17  single    0.970  0.020  1.090
 O08  N2   H19  single    0.860  0.020  1.020
 O08  C17  H21  single    0.930  0.020  1.080
 O08  C22  H24  single    0.930  0.020  1.080
 O08  C21  H23  single    0.930  0.020  1.080
 O08  C19  H22  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
 O08  O    C1   C25  124.14  3.000
 O08  O    C1   C2   116.71  3.000
 O08  C25  C1   C2   119.15  3.000
 O08  H6   C2   C3   120.33  3.000
 O08  H6   C2   C1   119.68  3.000
 O08  C3   C2   C1   119.99  3.000
 O08  H7   C3   C4   119.06  3.000
 O08  H7   C3   C2   118.51  3.000
 O08  C4   C3   C2   122.43  3.000
 O08  C24  C4   C5   122.64  3.000
 O08  C24  C4   C3   116.15  3.000
 O08  C5   C4   C3   121.17  3.000
 O08  H    C5   N    107.69  3.000
 O08  H    C5   C6   108.56  3.000
 O08  N    C5   C6   109.19  3.000
 O08  H    C5   C4   108.77  3.000
 O08  N    C5   C4   111.76  3.000
 O08  C6   C5   C4   110.77  3.000
 O08  H9   C6   H8   108.64  3.000
 O08  H9   C6   H10  107.91  3.000
 O08  H8   C6   H10  108.01  3.000
 O08  H9   C6   C5   111.01  3.000
 O08  H8   C6   C5   110.88  3.000
 O08  H10  C6   C5   110.27  3.000
 O08  H1   C8   C9   110.68  3.000
 O08  H1   C8   N1   110.26  3.000
 O08  C9   C8   N1   102.92  3.000
 O08  H1   C8   C7   110.56  3.000
 O08  C9   C8   C7   110.47  3.000
 O08  N1   C8   C7   111.73  3.000
 O08  H2   C10  C9   111.83  3.000
 O08  H2   C10  O2   111.74  3.000
 O08  C9   C10  O2   112.03  3.000
 O08  H2   C10  C11  111.30  3.000
 O08  O2   C10  C11  107.60  3.000
 O08  C9   C10  C11  101.85  3.000
 O08  H16  C11  H15  108.34  3.000
 O08  H16  C11  N1   111.28  3.000
 O08  H15  C11  N1   112.08  3.000
 O08  H16  C11  C10  110.44  3.000
 O08  H15  C11  C10  111.92  3.000
 O08  N1   C11  C10  102.75  3.000
 O08  H20  C16  C17  121.19  3.000
 O08  H20  C16  C15  120.31  3.000
 O08  C17  C16  C15  118.50  3.000
 O08  C25  C24  CL   116.78  3.000
 O08  C25  C24  C4   123.13  3.000
 O08  CL   C24  C4   120.09  3.000
 O08  H25  C25  C24  119.15  3.000
 O08  H25  C25  C1   121.71  3.000
 O08  C24  C25  C1   119.14  3.000
 O08  C    O    C1   118.61  3.000
 O08  H5   C    H3   108.88  3.000
 O08  H5   C    H4   108.78  3.000
 O08  H3   C    H4   108.86  3.000
 O08  H5   C    O    111.96  3.000
 O08  H3   C    O    111.78  3.000
 O08  H4   C    O    106.48  3.000
 O08  H11  N    C7   119.07  3.000
 O08  H11  N    C5   118.46  3.000
 O08  C7   N    C5   122.47  3.000
 O08  O1   C7   N    123.44  3.000
 O08  N    C7   C8   114.35  3.000
 O08  O1   C7   C8   122.08  3.000
 O08  C12  N1   C11  126.73  3.000
 O08  C11  N1   C8   112.63  3.000
 O08  C12  N1   C8   120.63  3.000
 O08  H14  O2   C10  108.34  3.000
 O08  H12  C9   H13  107.87  3.000
 O08  H12  C9   C10  113.57  3.000
 O08  H13  C9   C10  108.98  3.000
 O08  H12  C9   C8   112.50  3.000
 O08  H13  C9   C8   110.40  3.000
 O08  C10  C9   C8   103.46  3.000
 O08  H17  C13  H18  106.41  3.000
 O08  H17  C13  N2   110.88  3.000
 O08  H18  C13  N2   111.09  3.000
 O08  H17  C13  C12  110.08  3.000
 O08  H18  C13  C12  109.01  3.000
 O08  N2   C13  C12  109.33  3.000
 O08  H19  N2   C14  118.76  3.000
 O08  H19  N2   C13  118.73  3.000
 O08  C14  N2   C13  122.51  3.000
 O08  C15  C14  O4   121.24  3.000
 O08  O4   C14  N2   124.18  3.000
 O08  C15  C14  N2   114.58  3.000
 O08  N3   C15  C14  117.41  3.000
 O08  C14  C15  C16  119.16  3.000
 O08  N3   C15  C16  123.43  3.000
 O08  C23  N3   C15  119.12  3.000
 O08  C22  C23  C18  119.24  3.000
 O08  C22  C23  N3   118.84  3.000
 O08  C18  C23  N3   121.92  3.000
 O08  C19  C18  C17  122.73  3.000
 O08  C17  C18  C23  117.48  3.000
 O08  C19  C18  C23  119.79  3.000
 O08  H21  C17  C18  119.66  3.000
 O08  H21  C17  C16  120.80  3.000
 O08  C18  C17  C16  119.54  3.000
 O08  H24  C22  C21  120.82  3.000
 O08  H24  C22  C23  118.75  3.000
 O08  C21  C22  C23  120.43  3.000
 O08  H23  C21  C20  119.75  3.000
 O08  H23  C21  C22  121.12  3.000
 O08  C20  C21  C22  119.13  3.000
 O08  C19  C20  F    119.56  3.000
 O08  C19  C20  C21  122.87  3.000
 O08  F    C20  C21  117.57  3.000
 O08  H22  C19  C20  121.03  3.000
 O08  H22  C19  C18  120.42  3.000
 O08  C20  C19  C18  118.55  3.000
 O08  C13  C12  O3   121.71  3.000
 O08  O3   C12  N1   122.28  3.000
 O08  C13  C12  N1   116.01  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
 O08  CONST_01  C4   C24  C25  C1      0.00   0.0  0
 O08  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 O08  CONST_03  C24  C4   C3   C2      0.00   0.0  0
 O08  CONST_04  C24  C25  C1   C2      0.00   0.0  0
 O08  CONST_05  C25  C24  C4   C3      0.00   0.0  0
 O08  CONST_06  C25  C1   C2   C3      0.00   0.0  0
 O08  CONST_07  C19  C18  C17  C16   180.00   0.0  0
 O08  CONST_08  C23  C18  C17  C16     0.00   0.0  0
 O08  CONST_09  C23  N3   C15  C16     0.00   0.0  0
 O08  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 O08  CONST_11  C18  C23  N3   C15     0.00   0.0  0
 O08  CONST_12  C22  C23  N3   C15   180.00   0.0  0
 O08  CONST_13  C19  C18  C23  N3    180.00   0.0  0
 O08  CONST_14  C17  C18  C23  N3      0.00   0.0  0
 O08  CONST_15  C21  C22  C23  N3    180.00   0.0  0
 O08  CONST_16  C17  C16  C15  N3      0.00   0.0  0
 O08  CONST_17  C20  C19  C18  C23     0.00   0.0  0
 O08  CONST_18  C20  C21  C22  C23     0.00   0.0  0
 O08  CONST_19  C21  C20  C19  C18     0.00   0.0  0
 O08  CONST_20  C21  C22  C23  C18     0.00   0.0  0
 O08  CONST_21  C20  C19  C18  C17   180.00   0.0  0
 O08  CONST_22  C22  C23  C18  C17   180.00   0.0  0
 O08  CONST_23  C19  C20  C21  C22     0.00   0.0  0
 O08  CONST_24  C19  C18  C23  C22     0.00   0.0  0
 O08  CONST_25  CL   C24  C25  C1    180.00   0.0  0
 O08  CONST_26  C5   C4   C3   C2    180.00   0.0  0
 O08  CONST_27  CL   C24  C4   C3    180.00   0.0  0
 O08  CONST_28  O    C1   C2   C3    180.00   0.0  0
 O08  CONST_29  C25  C24  C4   C5    180.00   0.0  0
 O08  CONST_30  O    C1   C25  C24   180.00   0.0  0
 O08  CONST_31  C17  C16  C15  C14   180.00   0.0  0
 O08  CONST_32  C23  N3   C15  C14   180.00   0.0  0
 O08  CONST_33  F    C20  C19  C18   180.00   0.0  0
 O08  CONST_34  F    C20  C21  C22   180.00   0.0  0
 O08  CONST_35  H7   C3   C2   C1    180.00   0.0  0
 O08  CONST_36  H25  C25  C1   C2    180.00   0.0  0
 O08  CONST_37  H6   C2   C3   C4    180.00   0.0  0
 O08  CONST_38  H21  C17  C16  C15   180.00   0.0  0
 O08  CONST_39  H24  C22  C23  N3      0.00   0.0  0
 O08  CONST_40  H20  C16  C15  N3    180.00   0.0  0
 O08  CONST_41  H22  C19  C18  C23   180.00   0.0  0
 O08  CONST_42  H23  C21  C22  C23   180.00   0.0  0
 O08  CONST_43  C13  C12  N1   C8    180.00   0.0  0
 O08  CONST_44  O3   C12  N1   C8      0.00   0.0  0
 O08  CONST_45  C13  C12  N1   C11     0.00   0.0  0
 O08  CONST_46  O3   C12  N1   C11   180.00   0.0  0
 O08  CONST_47  C8   C7   N    C5    180.00   0.0  0
 O08  CONST_48  C15  C14  N2   C13   180.00   0.0  0
 O08  CONST_49  H11  N    C7   C8      0.00   0.0  0
 O08  CONST_50  H19  N2   C14  C15     0.00   0.0  0
 O08  CONST_51  O1   C7   N    C5      0.00   0.0  0
 O08  CONST_52  O4   C14  N2   C13     0.00   0.0  0
 O08  Var_01    C10  C11  N1   C8     19.43  30.0  1
 O08  Var_02    O4   C14  C15  C16     0.02  30.0  2
 O08  Var_03    N2   C13  C12  N1   -173.12  30.0  1
 O08  Var_04    H4   C    O    C1   -178.11  30.0  3
 O08  Var_05    C14  N2   C13  C12   178.15  30.0  1

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
 O08  chir_01  C5   C6  N    C4  positiv
 O08  chir_02  C8   N1  C7   C9  positiv
 O08  chir_03  C10  O2  C11  C9  negativ

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
 O08  plan-1  C1   0.020
 O08  plan-1  C2   0.020
 O08  plan-1  C3   0.020
 O08  plan-1  C4   0.020
 O08  plan-1  C5   0.020
 O08  plan-1  C24  0.020
 O08  plan-1  C25  0.020
 O08  plan-1  O    0.020
 O08  plan-1  H6   0.020
 O08  plan-1  H7   0.020
 O08  plan-1  H25  0.020
 O08  plan-1  CL   0.020
 O08  plan-2  C16  0.020
 O08  plan-2  C14  0.020
 O08  plan-2  C15  0.020
 O08  plan-2  N3   0.020
 O08  plan-2  C23  0.020
 O08  plan-2  C18  0.020
 O08  plan-2  C17  0.020
 O08  plan-2  C22  0.020
 O08  plan-2  C21  0.020
 O08  plan-2  C20  0.020
 O08  plan-2  F    0.020
 O08  plan-2  C19  0.020
 O08  plan-2  H21  0.020
 O08  plan-2  H24  0.020
 O08  plan-2  H23  0.020
 O08  plan-2  H22  0.020
 O08  plan-2  H20  0.020
 O08  plan-3  C13  0.020
 O08  plan-3  N2   0.020
 O08  plan-3  C14  0.020
 O08  plan-3  O4   0.020
 O08  plan-3  C15  0.020
 O08  plan-3  H19  0.020
 O08  plan-4  C8   0.020
 O08  plan-4  C11  0.020
 O08  plan-4  N1   0.020
 O08  plan-4  O3   0.020
 O08  plan-4  C13  0.020
 O08  plan-4  C12  0.020
 O08  plan-5  C5   0.020
 O08  plan-5  C8   0.020
 O08  plan-5  N    0.020
 O08  plan-5  C7   0.020
 O08  plan-5  O1   0.020
 O08  plan-5  H11  0.020

