# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:17:54 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 4-(1H-imidazol-5-yl)pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1cncc1c2ccncc2
#
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
 4F9  4F9  4-(1H-imidazol-5-yl)pyridine  ligand  18  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4F9
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
 4F9  C7  C  CR16  0  -0.405   1.2123   1.1930   0.0042
 4F9  C4  C  CR16  0  -0.381   1.1422  -1.1834   0.0076
 4F9  C6  C  CR16  0  -0.058   2.5912   1.0967   0.0054
 4F9  C5  C  CR16  0  -0.059   2.5275  -1.1662   0.0087
 4F9  C2  C  CR15  0  -0.240  -1.8612   1.1698   0.0081
 4F9  C   C  CR15  0   0.094  -3.1003  -0.5544   0.0006
 4F9  C3  C  CR6   0   0.172   0.4451   0.0253   0.0053
 4F9  C1  C  CR5   0   0.321  -1.0040   0.0936   0.0046
 4F9  N2  N  N     0  -0.412   3.2548  -0.0561   0.0077
 4F9  N   N  NR15  0  -0.635  -1.8330  -0.9979   0.0001
 4F9  N1  N  N     0  -0.431  -3.1548   0.7561   0.0055
 4F9  H1  H  HCR6  0   0.262   0.7518   2.1717   0.0022
 4F9  H2  H  HCR6  0   0.259   0.6362  -2.1396   0.0090
 4F9  H3  H  HCR6  0   0.267   3.1907   2.0003   0.0045
 4F9  H4  H  HCR6  0   0.267   3.0723  -2.1040   0.0106
 4F9  H6  H  HCR5  0   0.287  -3.9446  -1.2261  -0.0034
 4F9  H7  H  HNR5  0   0.427  -1.5636  -1.9693  -0.0038
 4F9  H5  H  HCR5  0   0.265  -1.6044   2.2181   0.0117

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
 4F9  N1  C2  aromatic  1.358  0.020  1.358
 4F9  N1  C   aromatic  1.312  0.020  1.312
 4F9  C2  C1  aromatic  1.376  0.020  1.376
 4F9  C   N   aromatic  1.343  0.020  1.343
 4F9  C1  N   aromatic  1.371  0.020  1.371
 4F9  C1  C3  single    1.451  0.020  1.451
 4F9  C7  C3  aromatic  1.397  0.020  1.397
 4F9  C7  C6  aromatic  1.382  0.020  1.382
 4F9  C3  C4  aromatic  1.395  0.020  1.395
 4F9  C6  N2  aromatic  1.330  0.020  1.330
 4F9  C4  C5  aromatic  1.385  0.020  1.385
 4F9  N2  C5  aromatic  1.327  0.020  1.327
 4F9  C7  H1  single    0.930  0.020  1.080
 4F9  C4  H2  single    0.930  0.020  1.080
 4F9  C6  H3  single    0.930  0.020  1.080
 4F9  C5  H4  single    0.930  0.020  1.080
 4F9  C2  H5  single    0.930  0.020  1.080
 4F9  C   H6  single    0.930  0.020  1.080
 4F9  N   H7  single    0.860  0.020  1.020

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
 4F9  H1  C7  C3  121.50  3.000
 4F9  H1  C7  C6  119.20  3.000
 4F9  C3  C7  C6  119.31  3.000
 4F9  H2  C4  C3  122.14  3.000
 4F9  H2  C4  C5  118.60  3.000
 4F9  C3  C4  C5  119.26  3.000
 4F9  H3  C6  N2  116.52  3.000
 4F9  H3  C6  C7  119.57  3.000
 4F9  N2  C6  C7  123.92  3.000
 4F9  H4  C5  N2  116.62  3.000
 4F9  H4  C5  C4  119.44  3.000
 4F9  N2  C5  C4  123.94  3.000
 4F9  H5  C2  N1  121.50  3.000
 4F9  H5  C2  C1  127.70  3.000
 4F9  N1  C2  C1  110.80  3.000
 4F9  H6  C   N1  126.12  3.000
 4F9  H6  C   N   122.20  3.000
 4F9  N1  C   N   111.67  3.000
 4F9  C1  C3  C4  122.68  3.000
 4F9  C4  C3  C7  116.72  3.000
 4F9  C1  C3  C7  120.60  3.000
 4F9  N   C1  C3  124.51  3.000
 4F9  C3  C1  C2  131.24  3.000
 4F9  N   C1  C2  104.25  3.000
 4F9  C5  N2  C6  116.85  3.000
 4F9  H7  N   C1  127.29  3.000
 4F9  H7  N   C   124.79  3.000
 4F9  C1  N   C   107.92  3.000
 4F9  C   N1  C2  105.36  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
 4F9  CONST_01  C2  C1  C3  C7    0.00  0.0  0
 4F9  CONST_02  N   C1  C3  C7  180.00  0.0  0
 4F9  CONST_03  C5  C4  C3  C7    0.00  0.0  0
 4F9  CONST_04  C5  N2  C6  C7    0.00  0.0  0
 4F9  CONST_05  C2  C1  C3  C4  180.00  0.0  0
 4F9  CONST_06  N   C1  C3  C4    0.00  0.0  0
 4F9  CONST_07  C6  C7  C3  C4    0.00  0.0  0
 4F9  CONST_08  C6  N2  C5  C4    0.00  0.0  0
 4F9  CONST_09  C1  C3  C7  C6  180.00  0.0  0
 4F9  CONST_10  C1  C3  C4  C5  180.00  0.0  0
 4F9  CONST_11  N   C   N1  C2    0.00  0.0  0
 4F9  CONST_12  C   N   C1  C2    0.00  0.0  0
 4F9  CONST_13  C1  C2  N1  C     0.00  0.0  0
 4F9  CONST_14  C3  C1  N   C   180.00  0.0  0
 4F9  CONST_15  N1  C2  C1  C3  180.00  0.0  0
 4F9  CONST_16  N2  C6  C7  C3    0.00  0.0  0
 4F9  CONST_17  N2  C5  C4  C3    0.00  0.0  0
 4F9  CONST_18  N1  C   N   C1    0.00  0.0  0
 4F9  CONST_19  N1  C2  C1  N     0.00  0.0  0
 4F9  CONST_20  H2  C4  C3  C7  180.00  0.0  0
 4F9  CONST_21  H1  C7  C3  C4  180.00  0.0  0
 4F9  CONST_22  H4  C5  N2  C6  180.00  0.0  0
 4F9  CONST_23  H3  C6  N2  C5  180.00  0.0  0
 4F9  CONST_24  H6  C   N1  C2  180.00  0.0  0
 4F9  CONST_25  H7  N   C1  C2  180.00  0.0  0
 4F9  CONST_26  H5  C2  N1  C   180.00  0.0  0

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
 4F9  plan-1  C2  0.020
 4F9  plan-1  C   0.020
 4F9  plan-1  C3  0.020
 4F9  plan-1  C1  0.020
 4F9  plan-1  N   0.020
 4F9  plan-1  N1  0.020
 4F9  plan-1  H6  0.020
 4F9  plan-1  H7  0.020
 4F9  plan-1  H5  0.020
 4F9  plan-2  C7  0.020
 4F9  plan-2  C4  0.020
 4F9  plan-2  C6  0.020
 4F9  plan-2  C5  0.020
 4F9  plan-2  C3  0.020
 4F9  plan-2  C1  0.020
 4F9  plan-2  N2  0.020
 4F9  plan-2  H1  0.020
 4F9  plan-2  H2  0.020
 4F9  plan-2  H3  0.020
 4F9  plan-2  H4  0.020

