# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:50:09 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: {2-amino-6-[(2,6-difluorophenyl)carbonyl]imidazo[1,2-a]pyridin-3-yl}(phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2ccc(cn2c1C(=O)c3ccccc3)C(=O)c4c(F)cccc4F
#
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
 PM1  PM1  {2-amino-6-[(2,6-difluorophenyl)carbonyl]imidazo[1,2-a]pyridin-3-yl}(phenyl)methanone  ligand  41  28  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PM1
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
 PM1  C1    C  CR6   0  -0.180   0.2323   0.1409  -1.5977
 PM1  C2    C  CR16  0   0.076  -0.1910   0.3148  -0.3003
 PM1  N3    N  N     0  -0.580   0.4896  -0.2569   0.7063
 PM1  C4    C  CR56  0   0.578   1.6289  -1.0094   0.4896
 PM1  C5    C  CR16  0  -0.397   2.0863  -1.1909  -0.8233
 PM1  C6    C  CR16  0  -0.143   1.3907  -0.6267  -1.8532
 PM1  C10   C  CR5   0   0.109   0.2509  -0.2714   2.0880
 PM1  C11   C  CR5   0   0.356   1.3262  -1.0307   2.6031
 PM1  N12   N  N     0  -0.503   2.1355  -1.4670   1.6194
 PM1  C13   C  C     0   0.338  -0.8012   0.4694   2.7072
 PM1  C14   C  CR6   0  -0.088  -1.1034   0.1946   4.1429
 PM1  C15   C  CR16  0  -0.270  -1.2060   1.2599   5.0354
 PM1  C16   C  CR16  0  -0.245  -1.5511   1.0277   6.3579
 PM1  C17   C  CR16  0  -0.251  -1.8261  -0.2644   6.7896
 PM1  C18   C  CR16  0  -0.236  -1.7499  -1.3256   5.8975
 PM1  C19   C  CR16  0  -0.273  -1.3826  -1.0990   4.5784
 PM1  C23   C  C     0   0.391  -0.5379   0.7985  -2.6661
 PM1  C24   C  CR6   0  -0.477  -0.2504   0.3954  -4.0801
 PM1  C25   C  CR6   0   0.571   0.2197   1.3108  -5.0103
 PM1  C26   C  CR16  0  -0.421   0.4349   0.9845  -6.3335
 PM1  C27   C  CR16  0  -0.221   0.1511  -0.3095  -6.7472
 PM1  C28   C  CR16  0  -0.417  -0.3307  -1.2592  -5.8574
 PM1  C29   C  CR6   0   0.588  -0.5159  -0.8842  -4.5431
 PM1  O33   O  O     0  -0.365  -1.3768   1.6417  -2.4401
 PM1  O34   O  O     0  -0.441  -1.4669   1.3116   2.1099
 PM1  N35   N  NH2   0  -0.834   1.6087  -1.3412   3.8734
 PM1  F36   F  F     0  -0.293   0.4980   2.5477  -4.5893
 PM1  F39   F  F     0  -0.294  -0.9835  -1.7780  -3.6642
 PM1  H2    H  HCR6  0   0.331  -1.0633   0.8916  -0.0411
 PM1  H5    H  HCR6  0   0.292   2.9811  -1.7732  -0.9874
 PM1  H6    H  HCR6  0   0.277   1.7514  -0.7516  -2.8652
 PM1  H15   H  HCR6  0   0.265  -1.0003   2.2682   4.6997
 PM1  H16   H  HCR6  0   0.264  -1.6113   1.8556   7.0518
 PM1  H17   H  HCR6  0   0.265  -2.1024  -0.4438   7.8204
 PM1  H18   H  HCR6  0   0.265  -1.9759  -2.3307   6.2276
 PM1  H19   H  HCR6  0   0.270  -1.3284  -1.9284   3.8843
 PM1  H26   H  HCR6  0   0.293   0.8158   1.7244  -7.0242
 PM1  H27   H  HCR6  0   0.289   0.3077  -0.5816  -7.7817
 PM1  H28   H  HCR6  0   0.294  -0.5608  -2.2661  -6.1772
 PM1  H351  H  HNH2  0   0.405   2.5158  -1.7314   4.0660
 PM1  H352  H  HNH2  0   0.413   1.1459  -0.8833   4.6377

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
 PM1  C1   C2    aromatic  1.376  0.020  1.376
 PM1  C1   C6    aromatic  1.413  0.020  1.413
 PM1  C1   C23   single    1.472  0.020  1.472
 PM1  C2   N3    aromatic  1.343  0.020  1.343
 PM1  C2   H2    single    0.930  0.020  1.080
 PM1  N3   C4    aromatic  1.383  0.020  1.383
 PM1  N3   C10   aromatic  1.402  0.020  1.402
 PM1  C4   C5    aromatic  1.402  0.020  1.402
 PM1  C4   N12   aromatic  1.320  0.020  1.320
 PM1  C5   C6    aromatic  1.365  0.020  1.365
 PM1  C5   H5    single    0.930  0.020  1.080
 PM1  C6   H6    single    0.930  0.020  1.080
 PM1  C10  C11   aromatic  1.414  0.020  1.414
 PM1  C10  C13   single    1.428  0.020  1.428
 PM1  C11  N12   aromatic  1.346  0.020  1.346
 PM1  C11  N35   single    1.338  0.020  1.338
 PM1  C13  C14   single    1.493  0.020  1.493
 PM1  C13  O34   double    1.228  0.020  1.228
 PM1  C14  C15   aromatic  1.394  0.020  1.394
 PM1  C14  C19   aromatic  1.393  0.020  1.393
 PM1  C15  C16   aromatic  1.386  0.020  1.386
 PM1  C15  H15   single    0.930  0.020  1.080
 PM1  C16  C17   aromatic  1.390  0.020  1.390
 PM1  C16  H16   single    0.930  0.020  1.080
 PM1  C17  C18   aromatic  1.388  0.020  1.388
 PM1  C17  H17   single    0.930  0.020  1.080
 PM1  C18  C19   aromatic  1.388  0.020  1.388
 PM1  C18  H18   single    0.930  0.020  1.080
 PM1  C19  H19   single    0.930  0.020  1.080
 PM1  C23  C24   single    1.498  0.020  1.498
 PM1  C23  O33   double    1.211  0.020  1.211
 PM1  C24  C25   aromatic  1.387  0.020  1.387
 PM1  C24  C29   aromatic  1.387  0.020  1.387
 PM1  C25  C26   aromatic  1.380  0.020  1.380
 PM1  C25  F36   single    1.336  0.020  1.336
 PM1  C26  C27   aromatic  1.388  0.020  1.388
 PM1  C26  H26   single    0.930  0.020  1.080
 PM1  C27  C28   aromatic  1.388  0.020  1.388
 PM1  C27  H27   single    0.930  0.020  1.080
 PM1  C28  C29   aromatic  1.379  0.020  1.379
 PM1  C28  H28   single    0.930  0.020  1.080
 PM1  C29  F39   single    1.338  0.020  1.338
 PM1  N35  H351  single    0.890  0.020  1.040
 PM1  N35  H352  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
 PM1  C23   C1   C6    122.71  3.000
 PM1  C23   C1   C2    117.84  3.000
 PM1  C6    C1   C2    119.44  3.000
 PM1  H2    C2   N3    117.25  3.000
 PM1  H2    C2   C1    122.94  3.000
 PM1  N3    C2   C1    119.81  3.000
 PM1  C10   N3   C4    106.81  3.000
 PM1  C10   N3   C2    131.05  3.000
 PM1  C4    N3   C2    122.14  3.000
 PM1  N12   C4   C5    129.16  3.000
 PM1  N12   C4   N3    111.76  3.000
 PM1  C5    C4   N3    119.08  3.000
 PM1  H5    C5   C6    122.03  3.000
 PM1  H5    C5   C4    118.84  3.000
 PM1  C6    C5   C4    119.13  3.000
 PM1  H6    C6   C5    119.23  3.000
 PM1  H6    C6   C1    120.36  3.000
 PM1  C5    C6   C1    120.39  3.000
 PM1  C13   C10  C11   132.93  3.000
 PM1  C13   C10  N3    123.18  3.000
 PM1  C11   C10  N3    103.60  3.000
 PM1  N35   C11  N12   119.45  3.000
 PM1  N35   C11  C10   129.15  3.000
 PM1  N12   C11  C10   111.41  3.000
 PM1  C11   N12  C4    106.40  3.000
 PM1  O34   C13  C14   118.96  3.000
 PM1  O34   C13  C10   122.96  3.000
 PM1  C14   C13  C10   118.08  3.000
 PM1  C19   C14  C15   119.66  3.000
 PM1  C19   C14  C13   120.82  3.000
 PM1  C15   C14  C13   119.35  3.000
 PM1  H15   C15  C16   119.94  3.000
 PM1  H15   C15  C14   119.96  3.000
 PM1  C16   C15  C14   120.08  3.000
 PM1  H16   C16  C17   120.08  3.000
 PM1  H16   C16  C15   119.84  3.000
 PM1  C17   C16  C15   120.08  3.000
 PM1  H17   C17  C18   119.96  3.000
 PM1  H17   C17  C16   120.03  3.000
 PM1  C18   C17  C16   120.01  3.000
 PM1  H18   C18  C19   119.80  3.000
 PM1  H18   C18  C17   120.17  3.000
 PM1  C19   C18  C17   120.02  3.000
 PM1  H19   C19  C18   119.83  3.000
 PM1  H19   C19  C14   120.04  3.000
 PM1  C18   C19  C14   120.12  3.000
 PM1  O33   C23  C24   119.77  3.000
 PM1  O33   C23  C1    122.55  3.000
 PM1  C24   C23  C1    117.67  3.000
 PM1  C29   C24  C25   116.75  3.000
 PM1  C29   C24  C23   121.78  3.000
 PM1  C25   C24  C23   121.36  3.000
 PM1  F36   C25  C26   119.26  3.000
 PM1  F36   C25  C24   118.05  3.000
 PM1  C26   C25  C24   122.67  3.000
 PM1  H26   C26  C27   121.30  3.000
 PM1  H26   C26  C25   120.37  3.000
 PM1  C27   C26  C25   118.33  3.000
 PM1  H27   C27  C28   119.44  3.000
 PM1  H27   C27  C26   119.37  3.000
 PM1  C28   C27  C26   121.19  3.000
 PM1  H28   C28  C29   120.42  3.000
 PM1  H28   C28  C27   121.44  3.000
 PM1  C29   C28  C27   118.14  3.000
 PM1  F39   C29  C28   119.43  3.000
 PM1  F39   C29  C24   117.65  3.000
 PM1  C28   C29  C24   122.92  3.000
 PM1  H352  N35  H351  116.54  3.000
 PM1  H352  N35  C11   121.31  3.000
 PM1  H351  N35  C11   117.53  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
 PM1  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 PM1  CONST_02  C10   N3   C2   C1    180.00   0.0  0
 PM1  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 PM1  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 PM1  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 PM1  CONST_06  N12   C4   N3   C2    180.00   0.0  0
 PM1  CONST_07  C11   C10  N3   C2    180.00   0.0  0
 PM1  CONST_08  C6    C1   C2   N3      0.00   0.0  0
 PM1  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 PM1  CONST_10  C11   N12  C4   N3      0.00   0.0  0
 PM1  CONST_11  N12   C11  C10  N3      0.00   0.0  0
 PM1  CONST_12  C11   C10  N3   C4      0.00   0.0  0
 PM1  CONST_13  C10   C11  N12  C4      0.00   0.0  0
 PM1  CONST_14  C10   N3   C4   C5    180.00   0.0  0
 PM1  CONST_15  C11   N12  C4   C5    180.00   0.0  0
 PM1  CONST_16  N12   C4   C5   C6    180.00   0.0  0
 PM1  CONST_17  N12   C4   N3   C10     0.00   0.0  0
 PM1  CONST_18  C17   C16  C15  C14     0.00   0.0  0
 PM1  CONST_19  C17   C18  C19  C14     0.00   0.0  0
 PM1  CONST_20  C18   C19  C14  C15     0.00   0.0  0
 PM1  CONST_21  C18   C17  C16  C15     0.00   0.0  0
 PM1  CONST_22  C19   C14  C15  C16     0.00   0.0  0
 PM1  CONST_23  C19   C18  C17  C16     0.00   0.0  0
 PM1  CONST_24  C27   C26  C25  C24     0.00   0.0  0
 PM1  CONST_25  C27   C28  C29  C24     0.00   0.0  0
 PM1  CONST_26  C28   C29  C24  C25     0.00   0.0  0
 PM1  CONST_27  C28   C27  C26  C25     0.00   0.0  0
 PM1  CONST_28  C29   C24  C25  C26     0.00   0.0  0
 PM1  CONST_29  C29   C28  C27  C26     0.00   0.0  0
 PM1  CONST_30  C13   C10  N3   C2      0.00   0.0  0
 PM1  CONST_31  C23   C1   C2   N3    180.00   0.0  0
 PM1  CONST_32  N35   C11  C10  N3    180.00   0.0  0
 PM1  CONST_33  C13   C10  N3   C4    180.00   0.0  0
 PM1  CONST_34  N35   C11  N12  C4    180.00   0.0  0
 PM1  CONST_35  C23   C1   C6   C5    180.00   0.0  0
 PM1  CONST_36  C13   C10  C11  N12   180.00   0.0  0
 PM1  CONST_37  C16   C15  C14  C13   180.00   0.0  0
 PM1  CONST_38  C18   C19  C14  C13   180.00   0.0  0
 PM1  CONST_39  C26   C25  C24  C23   180.00   0.0  0
 PM1  CONST_40  C28   C29  C24  C23   180.00   0.0  0
 PM1  CONST_41  F39   C29  C24  C25   180.00   0.0  0
 PM1  CONST_42  F36   C25  C26  C27   180.00   0.0  0
 PM1  CONST_43  F39   C29  C28  C27   180.00   0.0  0
 PM1  CONST_44  F36   C25  C24  C29   180.00   0.0  0
 PM1  CONST_45  H5    C5   C6   C1    180.00   0.0  0
 PM1  CONST_46  H6    C6   C1   C2    180.00   0.0  0
 PM1  CONST_47  H2    C2   N3   C4    180.00   0.0  0
 PM1  CONST_48  H16   C16  C15  C14   180.00   0.0  0
 PM1  CONST_49  H18   C18  C19  C14   180.00   0.0  0
 PM1  CONST_50  H19   C19  C14  C15   180.00   0.0  0
 PM1  CONST_51  H17   C17  C16  C15   180.00   0.0  0
 PM1  CONST_52  H15   C15  C16  C17   180.00   0.0  0
 PM1  CONST_53  H26   C26  C25  C24   180.00   0.0  0
 PM1  CONST_54  H28   C28  C29  C24   180.00   0.0  0
 PM1  CONST_55  H27   C27  C26  C25   180.00   0.0  0
 PM1  CONST_56  H351  N35  C11  C10   180.00   0.0  0
 PM1  CONST_57  H352  N35  C11  C10     0.00   0.0  0
 PM1  Var_01    C25   C24  C23  C1   -118.64  30.0  2
 PM1  Var_02    C24   C23  C1   C2   -168.09  30.0  2
 PM1  Var_03    C14   C13  C10  N3    169.68  30.0  2
 PM1  Var_04    C15   C14  C13  C10   130.34  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
 PM1  plan-1  C13   0.020
 PM1  plan-1  C14   0.020
 PM1  plan-1  C15   0.020
 PM1  plan-1  C16   0.020
 PM1  plan-1  C17   0.020
 PM1  plan-1  C18   0.020
 PM1  plan-1  C19   0.020
 PM1  plan-1  H15   0.020
 PM1  plan-1  H16   0.020
 PM1  plan-1  H17   0.020
 PM1  plan-1  H18   0.020
 PM1  plan-1  H19   0.020
 PM1  plan-2  C23   0.020
 PM1  plan-2  C24   0.020
 PM1  plan-2  C25   0.020
 PM1  plan-2  C26   0.020
 PM1  plan-2  C27   0.020
 PM1  plan-2  C28   0.020
 PM1  plan-2  C29   0.020
 PM1  plan-2  F36   0.020
 PM1  plan-2  F39   0.020
 PM1  plan-2  H26   0.020
 PM1  plan-2  H27   0.020
 PM1  plan-2  H28   0.020
 PM1  plan-3  C1    0.020
 PM1  plan-3  C2    0.020
 PM1  plan-3  N3    0.020
 PM1  plan-3  C4    0.020
 PM1  plan-3  C5    0.020
 PM1  plan-3  C6    0.020
 PM1  plan-3  C10   0.020
 PM1  plan-3  C11   0.020
 PM1  plan-3  N12   0.020
 PM1  plan-3  C13   0.020
 PM1  plan-3  C23   0.020
 PM1  plan-3  N35   0.020
 PM1  plan-3  H2    0.020
 PM1  plan-3  H5    0.020
 PM1  plan-3  H6    0.020
 PM1  plan-4  C11   0.020
 PM1  plan-4  N35   0.020
 PM1  plan-4  H351  0.020
 PM1  plan-4  H352  0.020
 PM1  plan-5  C10   0.020
 PM1  plan-5  C13   0.020
 PM1  plan-5  C14   0.020
 PM1  plan-5  O34   0.020
 PM1  plan-6  C1    0.020
 PM1  plan-6  C23   0.020
 PM1  plan-6  C24   0.020
 PM1  plan-6  O33   0.020

