# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 05:00:35 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 2-(pyridin-2-yl)pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccc(nc1)c2ncccn2
#
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
 9BS  9BS  2-(pyridin-2-yl)pyrimidine  ligand  19  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9BS
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
 9BS  N3  N  N     0  -0.405   1.3958   1.1877  -0.0447
 9BS  C4  C  CR6   0   0.144  -0.7070   0.0216   0.0201
 9BS  N2  N  N     0  -0.465   1.3853  -1.1647   0.0799
 9BS  C7  C  CR16  0  -0.022   2.7102  -1.1627   0.0528
 9BS  C6  C  CR6   0   0.357   0.7807   0.0143   0.0842
 9BS  C9  C  CR16  0  -0.021   2.7193   1.1798  -0.0905
 9BS  C8  C  CR16  0  -0.348   3.4477   0.0046  -0.0463
 9BS  C1  C  CR16  0  -0.192  -2.8011   1.1859   0.0183
 9BS  C2  C  CR16  0  -0.342  -3.4402  -0.0485  -0.0058
 9BS  C3  C  CR16  0  -0.029  -2.6475  -1.1872  -0.0576
 9BS  N1  N  N     0  -0.395  -1.3161  -1.1577  -0.0454
 9BS  C5  C  CR16  0  -0.258  -1.4182   1.2226  -0.0040
 9BS  H1  H  HCR6  0   0.283   3.1977  -2.1316   0.0451
 9BS  H2  H  HCR6  0   0.296   3.2127   2.1443  -0.1442
 9BS  H3  H  HCR6  0   0.282   4.5266   0.0008  -0.0941
 9BS  H4  H  HCR6  0   0.290  -3.3774   2.1020   0.0433
 9BS  H5  H  HCR6  0   0.268  -4.5164  -0.1327  -0.0105
 9BS  H6  H  HCR6  0   0.282  -3.1071  -2.1686  -0.1017
 9BS  H7  H  HCR6  0   0.276  -0.8867   2.1627   0.0091

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
 9BS  C7  N2  aromatic  1.325  0.020  1.325
 9BS  C7  C8  aromatic  1.384  0.020  1.384
 9BS  N2  C6  aromatic  1.325  0.020  1.325
 9BS  C5  C1  aromatic  1.384  0.020  1.384
 9BS  C5  C4  aromatic  1.396  0.020  1.396
 9BS  C8  C9  aromatic  1.383  0.020  1.383
 9BS  C1  C2  aromatic  1.390  0.020  1.390
 9BS  C6  C4  single    1.489  0.020  1.489
 9BS  C6  N3  aromatic  1.331  0.020  1.331
 9BS  C4  N1  aromatic  1.329  0.020  1.329
 9BS  C9  N3  aromatic  1.324  0.020  1.324
 9BS  C2  C3  aromatic  1.388  0.020  1.388
 9BS  N1  C3  aromatic  1.332  0.020  1.332
 9BS  C7  H1  single    0.930  0.020  1.080
 9BS  C9  H2  single    0.930  0.020  1.080
 9BS  C8  H3  single    0.930  0.020  1.080
 9BS  C1  H4  single    0.930  0.020  1.080
 9BS  C2  H5  single    0.930  0.020  1.080
 9BS  C3  H6  single    0.930  0.020  1.080
 9BS  C5  H7  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
 9BS  C9  N3  C6  117.38  3.000
 9BS  C5  C4  N1  121.95  3.000
 9BS  N1  C4  C6  117.11  3.000
 9BS  C5  C4  C6  120.92  3.000
 9BS  C6  N2  C7  117.06  3.000
 9BS  H1  C7  C8  120.88  3.000
 9BS  H1  C7  N2  116.62  3.000
 9BS  C8  C7  N2  122.37  3.000
 9BS  N2  C6  C4  117.40  3.000
 9BS  C4  C6  N3  116.95  3.000
 9BS  N2  C6  N3  124.97  3.000
 9BS  H2  C9  C8  121.16  3.000
 9BS  H2  C9  N3  116.81  3.000
 9BS  C8  C9  N3  122.02  3.000
 9BS  H3  C8  C9  121.85  3.000
 9BS  H3  C8  C7  122.17  3.000
 9BS  C9  C8  C7  115.98  3.000
 9BS  H4  C1  C5  120.66  3.000
 9BS  H4  C1  C2  120.47  3.000
 9BS  C5  C1  C2  118.86  3.000
 9BS  H5  C2  C3  120.33  3.000
 9BS  H5  C2  C1  121.84  3.000
 9BS  C3  C2  C1  117.81  3.000
 9BS  H6  C3  N1  116.36  3.000
 9BS  H6  C3  C2  120.11  3.000
 9BS  N1  C3  C2  123.52  3.000
 9BS  C3  N1  C4  118.57  3.000
 9BS  H7  C5  C1  120.98  3.000
 9BS  H7  C5  C4  119.86  3.000
 9BS  C1  C5  C4  119.09  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
 9BS  CONST_01  C7  N2  C6  N3    0.00  0.0  0
 9BS  CONST_02  C5  C4  C6  N3    0.00  0.0  0
 9BS  CONST_03  N1  C4  C6  N3  180.00  0.0  0
 9BS  CONST_04  C7  C8  C9  N3    0.00  0.0  0
 9BS  CONST_05  C2  C1  C5  C4    0.00  0.0  0
 9BS  CONST_06  C7  N2  C6  C4  180.00  0.0  0
 9BS  CONST_07  C9  N3  C6  C4  180.00  0.0  0
 9BS  CONST_08  C2  C3  N1  C4    0.00  0.0  0
 9BS  CONST_09  C9  C8  C7  N2    0.00  0.0  0
 9BS  CONST_10  C5  C4  C6  N2  180.00  0.0  0
 9BS  CONST_11  N1  C4  C6  N2    0.00  0.0  0
 9BS  CONST_12  C9  N3  C6  N2    0.00  0.0  0
 9BS  CONST_13  C8  C7  N2  C6    0.00  0.0  0
 9BS  CONST_14  C1  C5  C4  C6  180.00  0.0  0
 9BS  CONST_15  C3  N1  C4  C6  180.00  0.0  0
 9BS  CONST_16  C8  C9  N3  C6    0.00  0.0  0
 9BS  CONST_17  N1  C4  C5  C1    0.00  0.0  0
 9BS  CONST_18  N1  C3  C2  C1    0.00  0.0  0
 9BS  CONST_19  C5  C1  C2  C3    0.00  0.0  0
 9BS  CONST_20  C5  C4  N1  C3    0.00  0.0  0
 9BS  CONST_21  H3  C8  C9  N3  180.00  0.0  0
 9BS  CONST_22  H4  C1  C5  C4  180.00  0.0  0
 9BS  CONST_23  H6  C3  N1  C4  180.00  0.0  0
 9BS  CONST_24  H2  C9  C8  C7  180.00  0.0  0
 9BS  CONST_25  H1  C7  N2  C6  180.00  0.0  0
 9BS  CONST_26  H7  C5  C4  C6    0.00  0.0  0
 9BS  CONST_27  H5  C2  C3  N1  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
 9BS  plan-1  N3  0.020
 9BS  plan-1  C4  0.020
 9BS  plan-1  N2  0.020
 9BS  plan-1  C7  0.020
 9BS  plan-1  C6  0.020
 9BS  plan-1  C9  0.020
 9BS  plan-1  C8  0.020
 9BS  plan-1  H1  0.020
 9BS  plan-1  H2  0.020
 9BS  plan-1  H3  0.020
 9BS  plan-2  C4  0.020
 9BS  plan-2  C6  0.020
 9BS  plan-2  C1  0.020
 9BS  plan-2  C2  0.020
 9BS  plan-2  C3  0.020
 9BS  plan-2  N1  0.020
 9BS  plan-2  C5  0.020
 9BS  plan-2  H4  0.020
 9BS  plan-2  H5  0.020
 9BS  plan-2  H6  0.020
 9BS  plan-2  H7  0.020

