# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:31:33 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-[[4-(2-azanylpyridin-4-yl)oxy-3-fluoro-phenyl]amino]-N-(2,4-difluorophenyl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(Oc2ccc(Nc3ncccc3C(=O)Nc4ccc(F)cc4F)cc2F)ccn1
#
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
 L8V  L8V  2-[[4-(2-azanylpyridin-4-yl)oxy-3-fluoro-phenyl]amino]-N-(2,4-difluorophenyl)pyridine-3-carboxamide  ligand  49  33  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L8V
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
 L8V  N1    N  N     0  -0.470  -7.5309   2.1674  -1.3742
 L8V  C2    C  CR6   0   0.459  -6.2395   1.9584  -1.6224
 L8V  C3    C  CR16  0  -0.483  -5.3760   1.3413  -0.6995
 L8V  C4    C  CR6   0   0.463  -5.9044   0.9360   0.5080
 L8V  O5    O  O2    0  -0.497  -5.1824   0.3344   1.4836
 L8V  C6    C  CR6   0   0.120  -3.8690   0.0266   1.2447
 L8V  C7    C  CR16  0  -0.287  -2.8460   0.8389   1.7070
 L8V  C8    C  CR16  0  -0.387  -1.5269   0.4860   1.5019
 L8V  C9    C  CR6   0   0.406  -1.1901  -0.6916   0.8188
 L8V  C10   C  CR16  0  -0.507  -2.2203  -1.5114   0.3497
 L8V  C11   C  CR6   0   0.554  -3.5282  -1.1328   0.5714
 L8V  F12   F  F     0  -0.304  -4.5114  -1.9160   0.1118
 L8V  N13   N  NH1   0  -0.800   0.1631  -0.9308   0.6481
 L8V  C14   C  CR6   0   0.549   0.8271  -1.9986   0.1249
 L8V  C15   C  CR6   0  -0.232   2.2393  -1.9379  -0.0510
 L8V  C16   C  CR16  0  -0.167   2.8677  -3.0838  -0.5185
 L8V  C17   C  CR16  0  -0.362   2.1348  -4.2141  -0.8407
 L8V  C18   C  CR16  0  -0.021   0.7636  -4.1426  -0.6851
 L8V  N19   N  N     0  -0.475   0.1323  -3.0774  -0.2154
 L8V  C20   C  C     0   0.574   3.0126  -0.7125   0.2699
 L8V  O21   O  O     0  -0.482   2.6074   0.1342   1.0580
 L8V  N22   N  NH1   0  -0.747   4.2002  -0.5770  -0.3681
 L8V  C23   C  CR6   0   0.160   5.0486   0.5246  -0.1626
 L8V  C24   C  CR16  0  -0.253   5.5817   0.8266   1.0851
 L8V  C25   C  CR16  0  -0.426   6.4164   1.9184   1.2613
 L8V  C26   C  CR6   0   0.544   6.7245   2.6990   0.1634
 L8V  C27   C  CR16  0  -0.565   6.2285   2.4306  -1.0974
 L8V  C28   C  CR6   0   0.530   5.3856   1.3460  -1.2302
 L8V  F29   F  F     0  -0.307   7.5347   3.7522   0.3183
 L8V  C30   C  CR16  0  -0.060  -8.0037   1.7687  -0.1963
 L8V  C31   C  CR16  0  -0.433  -7.2572   1.1518   0.7835
 L8V  F32   F  F     0  -0.297   4.8792   1.0680  -2.4353
 L8V  N33   N  NH2   0  -0.834  -5.7553   2.4092  -2.8128
 L8V  H3    H  HCR6  0   0.284  -4.3319   1.2053  -0.9488
 L8V  H7    H  HCR6  0   0.286  -3.0863   1.7511   2.2375
 L8V  H8    H  HCR6  0   0.275  -0.7439   1.1363   1.8722
 L8V  H10   H  HCR6  0   0.311  -2.0113  -2.4300  -0.1739
 L8V  HN13  H  HNH1  0   0.432   0.7802  -0.2078   1.0023
 L8V  H16   H  HCR6  0   0.280   3.9449  -3.1147  -0.6218
 L8V  H17   H  HCR6  0   0.276   2.6112  -5.1130  -1.2023
 L8V  H18   H  HCR6  0   0.273   0.1370  -4.9893  -0.9422
 L8V  HN22  H  HNH1  0   0.422   4.4093  -1.1831  -1.1459
 L8V  H24   H  HCR6  0   0.290   5.3504   0.1930   1.9303
 L8V  H25   H  HCR6  0   0.291   6.8279   2.1483   2.2345
 L8V  H27   H  HCR6  0   0.310   6.4775   3.0500  -1.9491
 L8V  H30   H  HCR6  0   0.260  -9.0584   1.9521  -0.0223
 L8V  H31   H  HCR6  0   0.271  -7.7001   0.8432   1.7199
 L8V  HN33  H  HNH2  0   0.384  -6.4371   2.6005  -3.5284
 L8V  HN3A  H  HNH2  0   0.392  -4.8972   2.0090  -3.1530

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
 L8V  N1   C2    aromatic  1.332  0.020  1.332
 L8V  N1   C30   aromatic  1.330  0.020  1.330
 L8V  C2   C3    aromatic  1.406  0.020  1.406
 L8V  C2   N33   single    1.362  0.020  1.362
 L8V  C3   C4    aromatic  1.379  0.020  1.379
 L8V  C4   O5    single    1.355  0.020  1.355
 L8V  C4   C31   aromatic  1.397  0.020  1.397
 L8V  O5   C6    single    1.370  0.020  1.370
 L8V  C6   C7    aromatic  1.386  0.020  1.386
 L8V  C6   C11   aromatic  1.383  0.020  1.383
 L8V  C7   C8    aromatic  1.381  0.020  1.381
 L8V  C8   C9    aromatic  1.402  0.020  1.402
 L8V  C9   C10   aromatic  1.398  0.020  1.398
 L8V  C9   N13   single    1.385  0.020  1.385
 L8V  C10  C11   aromatic  1.380  0.020  1.380
 L8V  C11  F12   single    1.338  0.020  1.338
 L8V  N13  C14   single    1.362  0.020  1.362
 L8V  C14  C15   aromatic  1.424  0.020  1.424
 L8V  C14  N19   aromatic  1.328  0.020  1.328
 L8V  C15  C16   aromatic  1.388  0.020  1.388
 L8V  C15  C20   single    1.484  0.020  1.484
 L8V  C16  C17   aromatic  1.385  0.020  1.385
 L8V  C17  C18   aromatic  1.382  0.020  1.382
 L8V  C18  N19   aromatic  1.324  0.020  1.324
 L8V  C20  O21   double    1.226  0.020  1.226
 L8V  C20  N22   single    1.355  0.020  1.355
 L8V  N22  C23   single    1.405  0.020  1.405
 L8V  C23  C24   aromatic  1.390  0.020  1.390
 L8V  C23  C28   aromatic  1.389  0.020  1.389
 L8V  C24  C25   aromatic  1.386  0.020  1.386
 L8V  C25  C26   aromatic  1.382  0.020  1.382
 L8V  C26  C27   aromatic  1.381  0.020  1.381
 L8V  C26  F29   single    1.338  0.020  1.338
 L8V  C27  C28   aromatic  1.380  0.020  1.380
 L8V  C28  F32   single    1.336  0.020  1.336
 L8V  C30  C31   aromatic  1.378  0.020  1.378
 L8V  C3   H3    single    0.930  0.020  1.080
 L8V  C7   H7    single    0.930  0.020  1.080
 L8V  C8   H8    single    0.930  0.020  1.080
 L8V  C10  H10   single    0.930  0.020  1.080
 L8V  N13  HN13  single    0.860  0.020  1.020
 L8V  C16  H16   single    0.930  0.020  1.080
 L8V  C17  H17   single    0.930  0.020  1.080
 L8V  C18  H18   single    0.930  0.020  1.080
 L8V  N22  HN22  single    0.860  0.020  1.020
 L8V  C24  H24   single    0.930  0.020  1.080
 L8V  C25  H25   single    0.930  0.020  1.080
 L8V  C27  H27   single    0.930  0.020  1.080
 L8V  C30  H30   single    0.930  0.020  1.080
 L8V  C31  H31   single    0.930  0.020  1.080
 L8V  N33  HN33  single    0.890  0.020  1.040
 L8V  N33  HN3A  single    0.890  0.020  1.040

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
 L8V  C30   N1   C2    117.56  3.000
 L8V  N33   C2   C3    120.04  3.000
 L8V  N33   C2   N1    117.11  3.000
 L8V  C3    C2   N1    122.82  3.000
 L8V  H3    C3   C4    122.31  3.000
 L8V  H3    C3   C2    119.76  3.000
 L8V  C4    C3   C2    117.93  3.000
 L8V  C31   C4   O5    116.27  3.000
 L8V  C31   C4   C3    119.88  3.000
 L8V  O5    C4   C3    123.85  3.000
 L8V  C6    O5   C4    119.02  3.000
 L8V  C11   C6   C7    118.15  3.000
 L8V  C11   C6   O5    120.62  3.000
 L8V  C7    C6   O5    121.19  3.000
 L8V  H7    C7   C8    120.02  3.000
 L8V  H7    C7   C6    119.59  3.000
 L8V  C8    C7   C6    120.39  3.000
 L8V  H8    C8   C9    119.81  3.000
 L8V  H8    C8   C7    119.11  3.000
 L8V  C9    C8   C7    121.09  3.000
 L8V  N13   C9   C10   125.28  3.000
 L8V  N13   C9   C8    116.09  3.000
 L8V  C10   C9   C8    118.62  3.000
 L8V  H10   C10  C11   119.72  3.000
 L8V  H10   C10  C9    121.34  3.000
 L8V  C11   C10  C9    118.94  3.000
 L8V  F12   C11  C10   118.73  3.000
 L8V  F12   C11  C6    118.47  3.000
 L8V  C10   C11  C6    122.80  3.000
 L8V  HN13  N13  C14   113.35  3.000
 L8V  HN13  N13  C9    115.36  3.000
 L8V  C14   N13  C9    131.24  3.000
 L8V  N19   C14  C15   121.46  3.000
 L8V  N19   C14  N13   118.72  3.000
 L8V  C15   C14  N13   119.83  3.000
 L8V  C20   C15  C16   121.23  3.000
 L8V  C20   C15  C14   121.68  3.000
 L8V  C16   C15  C14   117.09  3.000
 L8V  H16   C16  C17   118.75  3.000
 L8V  H16   C16  C15   120.41  3.000
 L8V  C17   C16  C15   120.83  3.000
 L8V  H17   C17  C18   121.23  3.000
 L8V  H17   C17  C16   121.59  3.000
 L8V  C18   C17  C16   117.17  3.000
 L8V  H18   C18  N19   115.90  3.000
 L8V  H18   C18  C17   120.43  3.000
 L8V  N19   C18  C17   123.68  3.000
 L8V  C18   N19  C14   119.68  3.000
 L8V  N22   C20  O21   121.57  3.000
 L8V  N22   C20  C15   115.95  3.000
 L8V  O21   C20  C15   122.49  3.000
 L8V  HN22  N22  C23   117.32  3.000
 L8V  HN22  N22  C20   119.01  3.000
 L8V  C23   N22  C20   122.59  3.000
 L8V  C28   C23  C24   117.94  3.000
 L8V  C28   C23  N22   119.85  3.000
 L8V  C24   C23  N22   122.21  3.000
 L8V  H24   C24  C25   119.41  3.000
 L8V  H24   C24  C23   119.49  3.000
 L8V  C25   C24  C23   121.09  3.000
 L8V  H25   C25  C26   120.67  3.000
 L8V  H25   C25  C24   120.74  3.000
 L8V  C26   C25  C24   118.58  3.000
 L8V  F29   C26  C27   118.43  3.000
 L8V  F29   C26  C25   119.19  3.000
 L8V  C27   C26  C25   122.37  3.000
 L8V  H27   C27  C28   120.98  3.000
 L8V  H27   C27  C26   121.64  3.000
 L8V  C28   C27  C26   117.38  3.000
 L8V  F32   C28  C27   118.79  3.000
 L8V  F32   C28  C23   118.57  3.000
 L8V  C27   C28  C23   122.63  3.000
 L8V  H30   C30  C31   119.25  3.000
 L8V  H30   C30  N1    115.91  3.000
 L8V  C31   C30  N1    124.85  3.000
 L8V  H31   C31  C30   121.47  3.000
 L8V  H31   C31  C4    121.56  3.000
 L8V  C30   C31  C4    116.97  3.000
 L8V  HN3A  N33  HN33  114.39  3.000
 L8V  HN3A  N33  C2    117.84  3.000
 L8V  HN33  N33  C2    116.32  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
 L8V  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 L8V  CONST_02  C4   C31  C30  N1     0.00   0.0  0
 L8V  CONST_03  C31  C30  N1   C2     0.00   0.0  0
 L8V  CONST_04  C31  C4   C3   C2     0.00   0.0  0
 L8V  CONST_05  C30  N1   C2   C3     0.00   0.0  0
 L8V  CONST_06  C30  C31  C4   C3     0.00   0.0  0
 L8V  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 L8V  CONST_08  C9   C10  C11  C6     0.00   0.0  0
 L8V  CONST_09  C10  C11  C6   C7     0.00   0.0  0
 L8V  CONST_10  C10  C9   C8   C7     0.00   0.0  0
 L8V  CONST_11  C11  C6   C7   C8     0.00   0.0  0
 L8V  CONST_12  C11  C10  C9   C8     0.00   0.0  0
 L8V  CONST_13  C17  C16  C15  C14    0.00   0.0  0
 L8V  CONST_14  C17  C18  N19  C14    0.00   0.0  0
 L8V  CONST_15  C18  N19  C14  C15    0.00   0.0  0
 L8V  CONST_16  C18  C17  C16  C15    0.00   0.0  0
 L8V  CONST_17  N19  C14  C15  C16    0.00   0.0  0
 L8V  CONST_18  N19  C18  C17  C16    0.00   0.0  0
 L8V  CONST_19  C26  C25  C24  C23    0.00   0.0  0
 L8V  CONST_20  C26  C27  C28  C23    0.00   0.0  0
 L8V  CONST_21  C27  C28  C23  C24    0.00   0.0  0
 L8V  CONST_22  C27  C26  C25  C24    0.00   0.0  0
 L8V  CONST_23  C28  C23  C24  C25    0.00   0.0  0
 L8V  CONST_24  C28  C27  C26  C25    0.00   0.0  0
 L8V  CONST_25  O5   C4   C3   C2   180.00   0.0  0
 L8V  CONST_26  N33  C2   C3   C4   180.00   0.0  0
 L8V  CONST_27  C30  C31  C4   O5   180.00   0.0  0
 L8V  CONST_28  C8   C7   C6   O5   180.00   0.0  0
 L8V  CONST_29  C10  C11  C6   O5   180.00   0.0  0
 L8V  CONST_30  F12  C11  C6   C7   180.00   0.0  0
 L8V  CONST_31  N13  C9   C8   C7   180.00   0.0  0
 L8V  CONST_32  F12  C11  C10  C9   180.00   0.0  0
 L8V  CONST_33  N13  C9   C10  C11  180.00   0.0  0
 L8V  CONST_34  C16  C15  C14  N13  180.00   0.0  0
 L8V  CONST_35  C18  N19  C14  N13  180.00   0.0  0
 L8V  CONST_36  C20  C15  C16  C17  180.00   0.0  0
 L8V  CONST_37  C20  C15  C14  N19  180.00   0.0  0
 L8V  CONST_38  C25  C24  C23  N22  180.00   0.0  0
 L8V  CONST_39  C27  C28  C23  N22  180.00   0.0  0
 L8V  CONST_40  F32  C28  C23  C24  180.00   0.0  0
 L8V  CONST_41  F29  C26  C25  C24  180.00   0.0  0
 L8V  CONST_42  F32  C28  C27  C26  180.00   0.0  0
 L8V  CONST_43  F29  C26  C27  C28  180.00   0.0  0
 L8V  CONST_44  N33  C2   N1   C30  180.00   0.0  0
 L8V  CONST_45  H3   C3   C2   N1   180.00   0.0  0
 L8V  CONST_46  H31  C31  C30  N1   180.00   0.0  0
 L8V  CONST_47  H30  C30  N1   C2   180.00   0.0  0
 L8V  CONST_48  H8   C8   C7   C6   180.00   0.0  0
 L8V  CONST_49  H10  C10  C11  C6   180.00   0.0  0
 L8V  CONST_50  H7   C7   C8   C9   180.00   0.0  0
 L8V  CONST_51  H16  C16  C15  C14  180.00   0.0  0
 L8V  CONST_52  H18  C18  N19  C14  180.00   0.0  0
 L8V  CONST_53  H17  C17  C16  C15  180.00   0.0  0
 L8V  CONST_54  H25  C25  C24  C23  180.00   0.0  0
 L8V  CONST_55  H27  C27  C28  C23  180.00   0.0  0
 L8V  CONST_56  H24  C24  C25  C26  180.00   0.0  0
 L8V  CONST_57  C23  N22  C20  C15  180.00   0.0  0
 L8V  CONST_63  C23  N22  C20  O21    0.00   0.0  0
 L8V  Var_01    C7   C6   O5   C4    99.40  30.0  2
 L8V  Var_02    C31  C4   O5   C6   176.33  30.0  2
 L8V  Var_03    C14  N13  C9   C8   174.89  30.0  2
 L8V  Var_04    C15  C14  N13  C9   174.05  30.0  2
 L8V  Var_05    O21  C20  C15  C14   23.20  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
 L8V  plan-1  N1    0.020
 L8V  plan-1  C2    0.020
 L8V  plan-1  C3    0.020
 L8V  plan-1  C4    0.020
 L8V  plan-1  O5    0.020
 L8V  plan-1  C30   0.020
 L8V  plan-1  C31   0.020
 L8V  plan-1  N33   0.020
 L8V  plan-1  H3    0.020
 L8V  plan-1  H30   0.020
 L8V  plan-1  H31   0.020
 L8V  plan-2  O5    0.020
 L8V  plan-2  C6    0.020
 L8V  plan-2  C7    0.020
 L8V  plan-2  C8    0.020
 L8V  plan-2  C9    0.020
 L8V  plan-2  C10   0.020
 L8V  plan-2  C11   0.020
 L8V  plan-2  F12   0.020
 L8V  plan-2  N13   0.020
 L8V  plan-2  H7    0.020
 L8V  plan-2  H8    0.020
 L8V  plan-2  H10   0.020
 L8V  plan-3  N13   0.020
 L8V  plan-3  C14   0.020
 L8V  plan-3  C15   0.020
 L8V  plan-3  C16   0.020
 L8V  plan-3  C17   0.020
 L8V  plan-3  C18   0.020
 L8V  plan-3  N19   0.020
 L8V  plan-3  C20   0.020
 L8V  plan-3  H16   0.020
 L8V  plan-3  H17   0.020
 L8V  plan-3  H18   0.020
 L8V  plan-4  N22   0.020
 L8V  plan-4  C23   0.020
 L8V  plan-4  C24   0.020
 L8V  plan-4  C25   0.020
 L8V  plan-4  C26   0.020
 L8V  plan-4  C27   0.020
 L8V  plan-4  C28   0.020
 L8V  plan-4  F29   0.020
 L8V  plan-4  F32   0.020
 L8V  plan-4  H24   0.020
 L8V  plan-4  H25   0.020
 L8V  plan-4  H27   0.020
 L8V  plan-5  C15   0.020
 L8V  plan-5  C20   0.020
 L8V  plan-5  O21   0.020
 L8V  plan-5  N22   0.020
 L8V  plan-5  C23   0.020
 L8V  plan-5  HN22  0.020
 L8V  plan-6  C2    0.020
 L8V  plan-6  N33   0.020
 L8V  plan-6  HN33  0.020
 L8V  plan-6  HN3A  0.020

