# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:23:17 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: [3-amino-2-(2-methylphenyl)-1-oxidopyridin-4-yl](2,4-difluorophenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1c2c(N)c(cc[n+]2[O-])C(=O)c3ccc(F)cc3F
#
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
 I39  I39  '[3-amino-2-(2-methylphenyl)-1-oxidopyridin-4-yl](2,4-difluorophenyl)methanone'  ligand  39  25  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I39
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
 I39  O10   O  O      0  -0.377   2.2908  -2.7668  -0.1226
 I39  C9    C  C      0   0.409   1.7537  -1.6785  -0.1437
 I39  C4    C  CR6    0  -0.348   2.5558  -0.4393   0.0440
 I39  C3    C  CR6    0   0.588   3.6165  -0.3773   0.9430
 I39  F8    F  F      0  -0.285   3.8598  -1.4106   1.7467
 I39  C2    C  CR16   0  -0.561   4.4175   0.7392   1.0701
 I39  C5    C  CR16   0  -0.210   2.3263   0.6800  -0.7592
 I39  C6    C  CR16   0  -0.408   3.1195   1.8094  -0.6778
 I39  C1    C  CR6    0   0.560   4.1509   1.8142   0.2440
 I39  F7    F  F      0  -0.297   4.9200   2.8979   0.3491
 I39  C11   C  CR6    0  -0.040   0.3114  -1.5566  -0.4506
 I39  C16   C  CR16   0  -0.370  -0.2241  -2.4757  -1.3519
 I39  C15   C  CR16   0  -0.065  -1.5367  -2.4516  -1.7207
 I39  N14   N  NR6    1  -0.031  -2.3783  -1.5257  -1.1826
 I39  O23   O  O     -1  -0.533  -3.5894  -1.5105  -1.5368
 I39  C13   C  CR6    0   0.152  -1.9252  -0.6358  -0.2717
 I39  C12   C  CR6    0   0.267  -0.5735  -0.6223   0.1300
 I39  N24   N  NH2    0  -0.845  -0.2111   0.2493   1.0948
 I39  C17   C  CR6    0  -0.008  -2.9071   0.3186   0.2848
 I39  C22   C  CR6    0   0.113  -3.2907   1.4504  -0.4451
 I39  C25   C  CH3    0  -0.745  -2.7616   1.6965  -1.8257
 I39  C21   C  CR16   0  -0.303  -4.1931   2.3346   0.1388
 I39  C20   C  CR16   0  -0.240  -4.7028   2.1118   1.4111
 I39  C19   C  CR16   0  -0.264  -4.3115   0.9923   2.1299
 I39  C18   C  CR16   0  -0.259  -3.4110   0.1012   1.5643
 I39  H2    H  HCR6   0   0.314   5.2234   0.7675   1.7914
 I39  H5    H  HCR6   0   0.292   1.5186   0.6570  -1.4792
 I39  H6    H  HCR6   0   0.298   2.9411   2.6651  -1.3140
 I39  H16   H  HCR6   0   0.293   0.4156  -3.2191  -1.8065
 I39  H15   H  HCR6   0   0.307  -1.9785  -3.1272  -2.4359
 I39  HN24  H  HNH2   0   0.411   0.7515   0.3818   1.3440
 I39  HN2A  H  HNH2   0   0.409  -0.8370   0.9884   1.3641
 I39  H25   H  HCH3   0   0.252  -3.1853   0.9814  -2.5331
 I39  H25A  H  HCH3   0   0.254  -3.0141   2.6970  -2.1738
 I39  H25B  H  HCH3   0   0.241  -1.6762   1.5929  -1.8726
 I39  H21   H  HCR6   0   0.253  -4.5036   3.2143  -0.4123
 I39  H20   H  HCR6   0   0.259  -5.4023   2.8168   1.8413
 I39  H19   H  HCR6   0   0.259  -4.7003   0.8127   3.1234
 I39  H18   H  HCR6   0   0.259  -3.0947  -0.7740   2.1188

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
 I39  O10  C9    double    1.214  0.020  1.214
 I39  C9   C4    single    1.488  0.020  1.488
 I39  C9   C11   single    1.480  0.020  1.480
 I39  C4   C3    aromatic  1.392  0.020  1.392
 I39  C4   C5    aromatic  1.397  0.020  1.397
 I39  C3   F8    single    1.331  0.020  1.331
 I39  C3   C2    aromatic  1.380  0.020  1.380
 I39  C2   C1    aromatic  1.382  0.020  1.382
 I39  C5   C6    aromatic  1.382  0.020  1.382
 I39  C6   C1    aromatic  1.383  0.020  1.383
 I39  C1   F7    single    1.333  0.020  1.333
 I39  C11  C16   aromatic  1.394  0.020  1.394
 I39  C11  C12   aromatic  1.412  0.020  1.412
 I39  C16  C15   aromatic  1.364  0.020  1.364
 I39  C15  N14   aromatic  1.362  0.020  1.362
 I39  N14  O23   single    1.262  0.020  1.262
 I39  N14  C13   aromatic  1.352  0.020  1.352
 I39  C13  C12   aromatic  1.410  0.020  1.410
 I39  C13  C17   single    1.478  0.020  1.478
 I39  C12  N24   single    1.350  0.020  1.350
 I39  C17  C22   aromatic  1.400  0.020  1.400
 I39  C17  C18   aromatic  1.392  0.020  1.392
 I39  C22  C25   single    1.499  0.020  1.499
 I39  C22  C21   aromatic  1.392  0.020  1.392
 I39  C21  C20   aromatic  1.389  0.020  1.389
 I39  C20  C19   aromatic  1.387  0.020  1.387
 I39  C19  C18   aromatic  1.387  0.020  1.387
 I39  C2   H2    single    0.930  0.020  1.080
 I39  C5   H5    single    0.930  0.020  1.080
 I39  C6   H6    single    0.930  0.020  1.080
 I39  C16  H16   single    0.930  0.020  1.080
 I39  C15  H15   single    0.930  0.020  1.080
 I39  N24  HN24  single    0.890  0.020  1.040
 I39  N24  HN2A  single    0.890  0.020  1.040
 I39  C25  H25   single    0.970  0.020  1.090
 I39  C25  H25A  single    0.970  0.020  1.090
 I39  C25  H25B  single    0.970  0.020  1.090
 I39  C21  H21   single    0.930  0.020  1.080
 I39  C20  H20   single    0.930  0.020  1.080
 I39  C19  H19   single    0.930  0.020  1.080
 I39  C18  H18   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
 I39  C11   C9   C4    118.88  3.000
 I39  C11   C9   O10   120.58  3.000
 I39  C4    C9   O10   120.40  3.000
 I39  C5    C4   C3    117.45  3.000
 I39  C5    C4   C9    120.42  3.000
 I39  C3    C4   C9    121.96  3.000
 I39  C2    C3   F8    117.79  3.000
 I39  C2    C3   C4    122.54  3.000
 I39  F8    C3   C4    119.64  3.000
 I39  H2    C2   C1    121.46  3.000
 I39  H2    C2   C3    121.00  3.000
 I39  C1    C2   C3    117.54  3.000
 I39  H5    C5   C6    119.00  3.000
 I39  H5    C5   C4    119.22  3.000
 I39  C6    C5   C4    121.77  3.000
 I39  H6    C6   C1    120.83  3.000
 I39  H6    C6   C5    121.14  3.000
 I39  C1    C6   C5    118.03  3.000
 I39  F7    C1   C6    119.05  3.000
 I39  F7    C1   C2    118.29  3.000
 I39  C6    C1   C2    122.66  3.000
 I39  C12   C11  C16   117.48  3.000
 I39  C12   C11  C9    125.47  3.000
 I39  C16   C11  C9    117.01  3.000
 I39  H16   C16  C15   117.91  3.000
 I39  H16   C16  C11   119.86  3.000
 I39  C15   C16  C11   122.20  3.000
 I39  H15   C15  N14   115.77  3.000
 I39  H15   C15  C16   124.24  3.000
 I39  N14   C15  C16   119.99  3.000
 I39  C13   N14  O23   120.20  3.000
 I39  C13   N14  C15   120.45  3.000
 I39  O23   N14  C15   119.36  3.000
 I39  C17   C13  C12   121.56  3.000
 I39  C17   C13  N14   117.14  3.000
 I39  C12   C13  N14   121.30  3.000
 I39  N24   C12  C13   117.85  3.000
 I39  N24   C12  C11   123.58  3.000
 I39  C13   C12  C11   118.51  3.000
 I39  HN2A  N24  HN24  115.71  3.000
 I39  HN2A  N24  C12   119.94  3.000
 I39  HN24  N24  C12   121.37  3.000
 I39  C18   C17  C22   120.40  3.000
 I39  C18   C17  C13   119.05  3.000
 I39  C22   C17  C13   120.51  3.000
 I39  C21   C22  C25   120.73  3.000
 I39  C21   C22  C17   118.19  3.000
 I39  C25   C22  C17   121.07  3.000
 I39  H25B  C25  H25A  107.71  3.000
 I39  H25B  C25  H25   107.22  3.000
 I39  H25A  C25  H25   107.74  3.000
 I39  H25B  C25  C22   112.03  3.000
 I39  H25A  C25  C22   111.30  3.000
 I39  H25   C25  C22   110.63  3.000
 I39  H21   C21  C20   119.42  3.000
 I39  H21   C21  C22   119.22  3.000
 I39  C20   C21  C22   121.36  3.000
 I39  H20   C20  C19   120.14  3.000
 I39  H20   C20  C21   119.79  3.000
 I39  C19   C20  C21   120.06  3.000
 I39  H19   C19  C18   120.06  3.000
 I39  H19   C19  C20   120.58  3.000
 I39  C18   C19  C20   119.36  3.000
 I39  H18   C18  C19   119.99  3.000
 I39  H18   C18  C17   119.40  3.000
 I39  C19   C18  C17   120.61  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
 I39  CONST_01  C1    C2   C3   C4     0.00   0.0  0
 I39  CONST_02  C1    C6   C5   C4     0.00   0.0  0
 I39  CONST_03  C6    C5   C4   C3     0.00   0.0  0
 I39  CONST_04  C6    C1   C2   C3     0.00   0.0  0
 I39  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 I39  CONST_06  C5    C6   C1   C2     0.00   0.0  0
 I39  CONST_07  N14   C15  C16  C11    0.00   0.0  0
 I39  CONST_08  N14   C13  C12  C11    0.00   0.0  0
 I39  CONST_09  C17   C13  C12  C11  180.00   0.0  0
 I39  CONST_10  C13   C12  C11  C16    0.00   0.0  0
 I39  CONST_11  C13   N14  C15  C16    0.00   0.0  0
 I39  CONST_12  C12   C11  C16  C15    0.00   0.0  0
 I39  CONST_13  C12   C13  N14  C15    0.00   0.0  0
 I39  CONST_14  C17   C13  N14  C15  180.00   0.0  0
 I39  CONST_17  C21   C22  C17  C13  180.00   0.0  0
 I39  CONST_18  C19   C18  C17  C13  180.00   0.0  0
 I39  CONST_21  C20   C21  C22  C17    0.00   0.0  0
 I39  CONST_22  C20   C19  C18  C17    0.00   0.0  0
 I39  CONST_23  C19   C18  C17  C22    0.00   0.0  0
 I39  CONST_24  C19   C20  C21  C22    0.00   0.0  0
 I39  CONST_25  C18   C17  C22  C21    0.00   0.0  0
 I39  CONST_26  C18   C19  C20  C21    0.00   0.0  0
 I39  CONST_27  C2    C3   C4   C9   180.00   0.0  0
 I39  CONST_28  C6    C5   C4   C9   180.00   0.0  0
 I39  CONST_29  C15   C16  C11  C9   180.00   0.0  0
 I39  CONST_30  C13   C12  C11  C9   180.00   0.0  0
 I39  CONST_31  F7    C1   C2   C3   180.00   0.0  0
 I39  CONST_32  C5    C4   C3   F8   180.00   0.0  0
 I39  CONST_33  C1    C2   C3   F8   180.00   0.0  0
 I39  CONST_34  F7    C1   C6   C5   180.00   0.0  0
 I39  CONST_35  N24   C12  C11  C16  180.00   0.0  0
 I39  CONST_36  O23   N14  C15  C16  180.00   0.0  0
 I39  CONST_37  N24   C12  C13  N14  180.00   0.0  0
 I39  CONST_38  C12   C13  N14  O23  180.00   0.0  0
 I39  CONST_39  C17   C13  N14  O23    0.00   0.0  0
 I39  CONST_40  C25   C22  C17  C13    0.00   0.0  0
 I39  CONST_41  C17   C13  C12  N24    0.00   0.0  0
 I39  CONST_42  C18   C17  C22  C25  180.00   0.0  0
 I39  CONST_43  C20   C21  C22  C25  180.00   0.0  0
 I39  CONST_44  H2    C2   C3   C4   180.00   0.0  0
 I39  CONST_45  H6    C6   C5   C4   180.00   0.0  0
 I39  CONST_46  H5    C5   C4   C3   180.00   0.0  0
 I39  CONST_47  H15   C15  C16  C11  180.00   0.0  0
 I39  CONST_48  H16   C16  C15  N14  180.00   0.0  0
 I39  CONST_49  H18   C18  C17  C13    0.00   0.0  0
 I39  CONST_50  H21   C21  C22  C17  180.00   0.0  0
 I39  CONST_51  H19   C19  C18  C17  180.00   0.0  0
 I39  CONST_52  H20   C20  C21  C22  180.00   0.0  0
 I39  CONST_53  HN24  N24  C12  C11    0.00   0.0  0
 I39  CONST_54  HN2A  N24  C12  C11  180.00   0.0  0
 I39  Var_01    C16   C11  C9   C4   142.41  30.0  2
 I39  Var_02    C11   C9   C4   C3   146.23  30.0  3
 I39  Var_03    H25   C25  C22  C17   70.53  30.0  2

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
 I39  plan-1  C9    0.020
 I39  plan-1  C4    0.020
 I39  plan-1  C3    0.020
 I39  plan-1  F8    0.020
 I39  plan-1  C2    0.020
 I39  plan-1  C5    0.020
 I39  plan-1  C6    0.020
 I39  plan-1  C1    0.020
 I39  plan-1  F7    0.020
 I39  plan-1  H2    0.020
 I39  plan-1  H5    0.020
 I39  plan-1  H6    0.020
 I39  plan-2  C9    0.020
 I39  plan-2  C11   0.020
 I39  plan-2  C16   0.020
 I39  plan-2  C15   0.020
 I39  plan-2  N14   0.020
 I39  plan-2  O23   0.020
 I39  plan-2  C13   0.020
 I39  plan-2  C12   0.020
 I39  plan-2  N24   0.020
 I39  plan-2  C17   0.020
 I39  plan-2  H16   0.020
 I39  plan-2  H15   0.020
 I39  plan-3  C13   0.020
 I39  plan-3  C17   0.020
 I39  plan-3  C22   0.020
 I39  plan-3  C25   0.020
 I39  plan-3  C21   0.020
 I39  plan-3  C20   0.020
 I39  plan-3  C19   0.020
 I39  plan-3  C18   0.020
 I39  plan-3  H21   0.020
 I39  plan-3  H20   0.020
 I39  plan-3  H19   0.020
 I39  plan-3  H18   0.020
 I39  plan-4  C12   0.020
 I39  plan-4  N24   0.020
 I39  plan-4  HN24  0.020
 I39  plan-4  HN2A  0.020
 I39  plan-5  O10   0.020
 I39  plan-5  C9    0.020
 I39  plan-5  C4    0.020
 I39  plan-5  C11   0.020

