# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:27:58 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 2-(imidazo[1,2-a]pyridin-2-yl)-N-phenylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1cn2ccccc2n1)Nc3ccccc3
#
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
 F5N  F5N  2-(imidazo[1,2-a]pyridin-2-yl)-N-phenylacetamide  ligand  32  19  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F5N
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
 F5N  O1    O  O     0  -0.446  -0.7309  -0.4014  -1.1707
 F5N  C2    C  C     0   0.574  -0.9553   0.5674  -0.4712
 F5N  C3    C  CH2   0  -0.696   0.1126   1.6061  -0.1683
 F5N  C4    C  CR5   0   0.190   1.4700   1.0024  -0.1052
 F5N  C5    C  CR15  0  -0.116   2.4874   1.1548  -1.0093
 F5N  N6    N  N     0  -0.506   3.5238   0.4065  -0.5172
 F5N  C7    C  CR16  0   0.071   4.7799   0.1988  -1.0053
 F5N  C8    C  CR16  0  -0.377   5.6345  -0.5972  -0.3157
 F5N  C9    C  CR16  0  -0.132   5.2217  -1.2048   0.8986
 F5N  C10   C  CR16  0  -0.382   3.9654  -0.9930   1.3846
 F5N  C11   C  CR56  0   0.527   3.0798  -0.1642   0.6645
 F5N  N12   N  N     0  -0.487   1.8358   0.1943   0.9210
 F5N  N13   N  NH1   0  -0.745  -2.1599   0.8503   0.0837
 F5N  C14   C  CR6   0   0.390  -3.3712   0.1574  -0.0155
 F5N  C15   C  CR16  0  -0.293  -3.5809  -0.9519  -0.8367
 F5N  C16   C  CR16  0  -0.212  -4.8292  -1.5611  -0.8606
 F5N  C17   C  CR16  0  -0.240  -5.8778  -1.0903  -0.0849
 F5N  C18   C  CR16  0  -0.213  -5.6667   0.0143   0.7306
 F5N  C19   C  CR16  0  -0.324  -4.4286   0.6319   0.7660
 F5N  H3    H  HCH2  0   0.291   0.0724   2.3564  -0.9630
 F5N  H3A   H  HCH2  0   0.259  -0.1081   2.1297   0.7648
 F5N  H5    H  HCR5  0   0.266   2.5605   1.7121  -1.9277
 F5N  H7    H  HCR6  0   0.276   5.0285   0.6891  -1.9345
 F5N  H8    H  HCR6  0   0.257   6.6294  -0.7600  -0.7029
 F5N  H9    H  HCR6  0   0.253   5.9117  -1.8401   1.4362
 F5N  H10   H  HCR6  0   0.257   3.6247  -1.4419   2.3071
 F5N  HN13  H  HNH1  0   0.378  -2.1931   1.6744   0.6649
 F5N  H15   H  HCR6  0   0.269  -2.7899  -1.3435  -1.4539
 F5N  H16   H  HCR6  0   0.230  -4.9744  -2.4208  -1.5021
 F5N  H17   H  HCR6  0   0.227  -6.8444  -1.5750  -0.1150
 F5N  H18   H  HCR6  0   0.229  -6.4681   0.4002   1.3471
 F5N  H19   H  HCR6  0   0.222  -4.2781   1.4920   1.4084

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
 F5N  C2   O1    double    1.216  0.020  1.216
 F5N  N13  C2    single    1.356  0.020  1.356
 F5N  C3   C2    single    1.520  0.020  1.520
 F5N  C3   C4    single    1.487  0.020  1.487
 F5N  C3   H3    single    0.970  0.020  1.090
 F5N  C3   H3A   single    0.970  0.020  1.090
 F5N  C5   C4    aromatic  1.370  0.020  1.370
 F5N  C4   N12   aromatic  1.357  0.020  1.357
 F5N  C5   N6    aromatic  1.370  0.020  1.370
 F5N  C5   H5    single    0.930  0.020  1.080
 F5N  C7   N6    aromatic  1.363  0.020  1.363
 F5N  N6   C11   aromatic  1.385  0.020  1.385
 F5N  C7   C8    aromatic  1.356  0.020  1.356
 F5N  C7   H7    single    0.930  0.020  1.080
 F5N  C8   C9    aromatic  1.419  0.020  1.419
 F5N  C8   H8    single    0.930  0.020  1.080
 F5N  C9   C10   aromatic  1.364  0.020  1.364
 F5N  C9   H9    single    0.930  0.020  1.080
 F5N  C11  C10   aromatic  1.411  0.020  1.411
 F5N  C10  H10   single    0.930  0.020  1.080
 F5N  N12  C11   aromatic  1.320  0.020  1.320
 F5N  N13  C14   single    1.399  0.020  1.399
 F5N  N13  HN13  single    0.860  0.020  1.020
 F5N  C19  C14   aromatic  1.398  0.020  1.398
 F5N  C14  C15   aromatic  1.396  0.020  1.396
 F5N  C15  C16   aromatic  1.389  0.020  1.389
 F5N  C15  H15   single    0.930  0.020  1.080
 F5N  C17  C16   aromatic  1.387  0.020  1.387
 F5N  C16  H16   single    0.930  0.020  1.080
 F5N  C18  C17   aromatic  1.389  0.020  1.389
 F5N  C17  H17   single    0.930  0.020  1.080
 F5N  C19  C18   aromatic  1.384  0.020  1.384
 F5N  C18  H18   single    0.930  0.020  1.080
 F5N  C19  H19   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
 F5N  N13   C2   C3   113.57  3.000
 F5N  C3    C2   O1   121.97  3.000
 F5N  N13   C2   O1   124.44  3.000
 F5N  H3A   C3   H3   106.52  3.000
 F5N  H3A   C3   C4   110.05  3.000
 F5N  H3    C3   C4   110.05  3.000
 F5N  H3A   C3   C2   110.84  3.000
 F5N  H3    C3   C2   107.35  3.000
 F5N  C4    C3   C2   111.86  3.000
 F5N  N12   C4   C5   111.43  3.000
 F5N  N12   C4   C3   121.34  3.000
 F5N  C5    C4   C3   127.23  3.000
 F5N  H5    C5   N6   122.53  3.000
 F5N  H5    C5   C4   132.15  3.000
 F5N  N6    C5   C4   105.32  3.000
 F5N  C11   N6   C7   122.54  3.000
 F5N  C11   N6   C5   106.79  3.000
 F5N  C7    N6   C5   130.67  3.000
 F5N  H7    C7   C8   123.99  3.000
 F5N  H7    C7   N6   116.81  3.000
 F5N  C8    C7   N6   119.20  3.000
 F5N  H8    C8   C9   120.68  3.000
 F5N  H8    C8   C7   119.12  3.000
 F5N  C9    C8   C7   120.20  3.000
 F5N  H9    C9   C10  120.14  3.000
 F5N  H9    C9   C8   119.43  3.000
 F5N  C10   C9   C8   120.43  3.000
 F5N  H10   C10  C11  118.79  3.000
 F5N  H10   C10  C9   122.01  3.000
 F5N  C11   C10  C9   119.19  3.000
 F5N  N12   C11  C10  130.71  3.000
 F5N  N12   C11  N6   110.86  3.000
 F5N  C10   C11  N6   118.44  3.000
 F5N  C11   N12  C4   105.60  3.000
 F5N  HN13  N13  C14  114.64  3.000
 F5N  HN13  N13  C2   115.81  3.000
 F5N  C14   N13  C2   129.55  3.000
 F5N  C19   C14  C15  119.01  3.000
 F5N  C15   C14  N13  124.43  3.000
 F5N  C19   C14  N13  116.57  3.000
 F5N  H15   C15  C16  119.38  3.000
 F5N  H15   C15  C14  121.04  3.000
 F5N  C16   C15  C14  119.57  3.000
 F5N  H16   C16  C17  119.98  3.000
 F5N  H16   C16  C15  118.62  3.000
 F5N  C17   C16  C15  121.40  3.000
 F5N  H17   C17  C18  120.56  3.000
 F5N  H17   C17  C16  120.53  3.000
 F5N  C18   C17  C16  118.91  3.000
 F5N  H18   C18  C19  119.26  3.000
 F5N  H18   C18  C17  120.36  3.000
 F5N  C19   C18  C17  120.38  3.000
 F5N  H19   C19  C18  119.56  3.000
 F5N  H19   C19  C14  119.71  3.000
 F5N  C18   C19  C14  120.73  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
 F5N  CONST_01  C7    N6   C5   C4   180.00   0.0  0
 F5N  CONST_02  C11   N6   C5   C4     0.00   0.0  0
 F5N  CONST_03  N6    C11  N12  C4     0.00   0.0  0
 F5N  CONST_04  C10   C11  N12  C4   180.00   0.0  0
 F5N  CONST_05  C11   N12  C4   C5     0.00   0.0  0
 F5N  CONST_06  C8    C7   N6   C5   180.00   0.0  0
 F5N  CONST_07  C10   C11  N6   C5   180.00   0.0  0
 F5N  CONST_08  N12   C11  N6   C5     0.00   0.0  0
 F5N  CONST_09  N12   C4   C5   N6     0.00   0.0  0
 F5N  CONST_10  C9    C8   C7   N6     0.00   0.0  0
 F5N  CONST_11  C9    C10  C11  N6     0.00   0.0  0
 F5N  CONST_12  C10   C11  N6   C7     0.00   0.0  0
 F5N  CONST_13  N12   C11  N6   C7   180.00   0.0  0
 F5N  CONST_14  C10   C9   C8   C7     0.00   0.0  0
 F5N  CONST_15  C11   N6   C7   C8     0.00   0.0  0
 F5N  CONST_16  C11   C10  C9   C8     0.00   0.0  0
 F5N  CONST_17  N12   C11  C10  C9   180.00   0.0  0
 F5N  CONST_18  C17   C18  C19  C14    0.00   0.0  0
 F5N  CONST_19  C17   C16  C15  C14    0.00   0.0  0
 F5N  CONST_20  C18   C19  C14  C15    0.00   0.0  0
 F5N  CONST_21  C18   C17  C16  C15    0.00   0.0  0
 F5N  CONST_22  C19   C14  C15  C16    0.00   0.0  0
 F5N  CONST_23  C19   C18  C17  C16    0.00   0.0  0
 F5N  CONST_24  N6    C5   C4   C3   180.00   0.0  0
 F5N  CONST_25  C11   N12  C4   C3   180.00   0.0  0
 F5N  CONST_26  C18   C19  C14  N13  180.00   0.0  0
 F5N  CONST_27  C16   C15  C14  N13  180.00   0.0  0
 F5N  CONST_28  H7    C7   N6   C5     0.00   0.0  0
 F5N  CONST_29  H8    C8   C7   N6   180.00   0.0  0
 F5N  CONST_30  H10   C10  C11  N6   180.00   0.0  0
 F5N  CONST_31  H5    C5   N6   C7     0.00   0.0  0
 F5N  CONST_32  H9    C9   C8   C7   180.00   0.0  0
 F5N  CONST_33  H18   C18  C19  C14  180.00   0.0  0
 F5N  CONST_34  H16   C16  C15  C14  180.00   0.0  0
 F5N  CONST_35  H19   C19  C14  C15  180.00   0.0  0
 F5N  CONST_36  H17   C17  C16  C15  180.00   0.0  0
 F5N  CONST_37  H15   C15  C16  C17  180.00   0.0  0
 F5N  CONST_38  C19   C14  N13  C2   180.00   0.0  0
 F5N  CONST_39  C15   C14  N13  C2     0.00   0.0  0
 F5N  CONST_40  HN13  N13  C14  C15  180.00   0.0  0
 F5N  CONST_41  C14   N13  C2   O1     0.00   0.0  0
 F5N  CONST_42  C14   N13  C2   C3   180.00   0.0  0
 F5N  Var_01    C5    C4   C3   C2   109.04  30.0  2
 F5N  Var_02    C4    C3   C2   O1   -32.41  30.0  1

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
 F5N  plan-1  N13   0.020
 F5N  plan-1  C14   0.020
 F5N  plan-1  C15   0.020
 F5N  plan-1  C16   0.020
 F5N  plan-1  C17   0.020
 F5N  plan-1  C18   0.020
 F5N  plan-1  C19   0.020
 F5N  plan-1  H15   0.020
 F5N  plan-1  H16   0.020
 F5N  plan-1  H17   0.020
 F5N  plan-1  H18   0.020
 F5N  plan-1  H19   0.020
 F5N  plan-2  C3    0.020
 F5N  plan-2  C4    0.020
 F5N  plan-2  C5    0.020
 F5N  plan-2  N6    0.020
 F5N  plan-2  C7    0.020
 F5N  plan-2  C8    0.020
 F5N  plan-2  C9    0.020
 F5N  plan-2  C10   0.020
 F5N  plan-2  C11   0.020
 F5N  plan-2  N12   0.020
 F5N  plan-2  H5    0.020
 F5N  plan-2  H7    0.020
 F5N  plan-2  H8    0.020
 F5N  plan-2  H9    0.020
 F5N  plan-2  H10   0.020
 F5N  plan-3  O1    0.020
 F5N  plan-3  C2    0.020
 F5N  plan-3  C3    0.020
 F5N  plan-3  N13   0.020
 F5N  plan-3  C14   0.020
 F5N  plan-3  HN13  0.020

