# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 07:34:43 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 5-methyl-2-(5-methylpyridin-2-yl)pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(nc1)c2ccc(C)cn2
#
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
 EI3  EI3  5-methyl-2-(5-methylpyridin-2-yl)pyridine  ligand  26  14  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EI3
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
 EI3  C1    C  CH3   0  -0.726   4.9988  -0.0187  -0.0696
 EI3  C2    C  CR6   0   0.021   3.5032   0.0405  -0.0576
 EI3  C3    C  CR16  0  -0.183   2.8122   1.2477   0.0014
 EI3  C4    C  CR16  0  -0.291   1.4300   1.2535   0.0171
 EI3  C5    C  CR6   0   0.190   0.7515   0.0362  -0.0271
 EI3  N6    N  N     0  -0.430   1.4026  -1.1216  -0.0839
 EI3  C7    C  CR16  0  -0.115   2.7267  -1.1136  -0.0989
 EI3  C14   C  CR6   0   0.190  -0.7286  -0.0209  -0.0148
 EI3  N15   N  N     0  -0.430  -1.3797   1.1368   0.0422
 EI3  C16   C  CR16  0  -0.115  -2.7038   1.1289   0.0571
 EI3  C17   C  CR6   0   0.021  -3.4804  -0.0251   0.0151
 EI3  C18   C  CR16  0  -0.183  -2.7893  -1.2324  -0.0439
 EI3  C19   C  CR16  0  -0.291  -1.4071  -1.2382  -0.0594
 EI3  C20   C  CH3   0  -0.726  -4.9760   0.0342   0.0269
 EI3  H1    H  HCH3  0   0.253   5.4124   0.2938   0.8908
 EI3  H1A   H  HCH3  0   0.248   5.3562  -1.0274  -0.2723
 EI3  H1B   H  HCH3  0   0.251   5.4136   0.6437  -0.8297
 EI3  H3    H  HCR6  0   0.264   3.3567   2.1842   0.0338
 EI3  H4    H  HCR6  0   0.266   0.8783   2.1814   0.0626
 EI3  H7    H  HCR6  0   0.253   3.2101  -2.0850  -0.1496
 EI3  H16   H  HCR6  0   0.253  -3.1875   2.1001   0.1082
 EI3  H18   H  HCR6  0   0.264  -3.3334  -2.1690  -0.0768
 EI3  H19   H  HCR6  0   0.266  -0.8557  -2.1664  -0.1043
 EI3  H20   H  HCH3  0   0.253  -5.3897  -0.2781  -0.9335
 EI3  H20A  H  HCH3  0   0.251  -5.3913  -0.6280   0.7870
 EI3  H20B  H  HCH3  0   0.248  -5.3330   1.0430   0.2294

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
 EI3  C1   C2    single    1.497  0.020  1.497
 EI3  C2   C3    aromatic  1.392  0.020  1.392
 EI3  C2   C7    aromatic  1.392  0.020  1.392
 EI3  C3   C4    aromatic  1.382  0.020  1.382
 EI3  C4   C5    aromatic  1.394  0.020  1.394
 EI3  C5   N6    aromatic  1.329  0.020  1.329
 EI3  C5   C14   single    1.481  0.020  1.481
 EI3  N6   C7    aromatic  1.324  0.020  1.324
 EI3  C14  N15   aromatic  1.329  0.020  1.329
 EI3  C14  C19   aromatic  1.394  0.020  1.394
 EI3  N15  C16   aromatic  1.324  0.020  1.324
 EI3  C16  C17   aromatic  1.392  0.020  1.392
 EI3  C17  C18   aromatic  1.392  0.020  1.392
 EI3  C17  C20   single    1.497  0.020  1.497
 EI3  C18  C19   aromatic  1.382  0.020  1.382
 EI3  C1   H1    single    0.970  0.020  1.090
 EI3  C1   H1A   single    0.970  0.020  1.090
 EI3  C1   H1B   single    0.970  0.020  1.090
 EI3  C3   H3    single    0.930  0.020  1.080
 EI3  C4   H4    single    0.930  0.020  1.080
 EI3  C7   H7    single    0.930  0.020  1.080
 EI3  C16  H16   single    0.930  0.020  1.080
 EI3  C18  H18   single    0.930  0.020  1.080
 EI3  C19  H19   single    0.930  0.020  1.080
 EI3  C20  H20   single    0.970  0.020  1.090
 EI3  C20  H20A  single    0.970  0.020  1.090
 EI3  C20  H20B  single    0.970  0.020  1.090

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
 EI3  H1B   C1   H1A   107.94  3.000
 EI3  H1B   C1   H1    107.18  3.000
 EI3  H1A   C1   H1    107.73  3.000
 EI3  H1B   C1   C2    111.21  3.000
 EI3  H1A   C1   C2    111.47  3.000
 EI3  H1    C1   C2    111.12  3.000
 EI3  C7    C2   C3    116.32  3.000
 EI3  C7    C2   C1    121.63  3.000
 EI3  C3    C2   C1    122.04  3.000
 EI3  H3    C3   C4    119.90  3.000
 EI3  H3    C3   C2    120.08  3.000
 EI3  C4    C3   C2    120.02  3.000
 EI3  H4    C4   C5    120.18  3.000
 EI3  H4    C4   C3    120.97  3.000
 EI3  C5    C4   C3    118.86  3.000
 EI3  C14   C5   N6    117.14  3.000
 EI3  C14   C5   C4    121.31  3.000
 EI3  N6    C5   C4    121.56  3.000
 EI3  C7    N6   C5    119.01  3.000
 EI3  H7    C7   N6    116.11  3.000
 EI3  H7    C7   C2    119.65  3.000
 EI3  N6    C7   C2    124.24  3.000
 EI3  C19   C14  N15   121.56  3.000
 EI3  C19   C14  C5    121.31  3.000
 EI3  N15   C14  C5    117.14  3.000
 EI3  C16   N15  C14   119.01  3.000
 EI3  H16   C16  C17   119.63  3.000
 EI3  H16   C16  N15   116.14  3.000
 EI3  C17   C16  N15   124.23  3.000
 EI3  C20   C17  C18   122.05  3.000
 EI3  C20   C17  C16   121.63  3.000
 EI3  C18   C17  C16   116.32  3.000
 EI3  H18   C18  C19   119.87  3.000
 EI3  H18   C18  C17   120.10  3.000
 EI3  C19   C18  C17   120.03  3.000
 EI3  H19   C19  C18   120.95  3.000
 EI3  H19   C19  C14   120.19  3.000
 EI3  C18   C19  C14   118.85  3.000
 EI3  H20B  C20  H20A  107.95  3.000
 EI3  H20B  C20  H20   107.72  3.000
 EI3  H20A  C20  H20   107.17  3.000
 EI3  H20B  C20  C17   111.45  3.000
 EI3  H20A  C20  C17   111.22  3.000
 EI3  H20   C20  C17   111.13  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
 EI3  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 EI3  CONST_02  C5   N6   C7   C2     0.00   0.0  0
 EI3  CONST_03  N6   C7   C2   C3     0.00   0.0  0
 EI3  CONST_04  N6   C5   C4   C3     0.00   0.0  0
 EI3  CONST_05  C14  C5   C4   C3   180.00   0.0  0
 EI3  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 EI3  CONST_07  C7   N6   C5   C4     0.00   0.0  0
 EI3  CONST_08  N15  C14  C5   C4     0.00   0.0  0
 EI3  CONST_09  C19  C14  C5   C4   180.00   0.0  0
 EI3  CONST_10  C16  N15  C14  C5   180.00   0.0  0
 EI3  CONST_11  C18  C19  C14  C5   180.00   0.0  0
 EI3  CONST_12  N15  C14  C5   N6   180.00   0.0  0
 EI3  CONST_13  C19  C14  C5   N6     0.00   0.0  0
 EI3  CONST_14  C14  C5   N6   C7   180.00   0.0  0
 EI3  CONST_15  C17  C16  N15  C14    0.00   0.0  0
 EI3  CONST_16  C17  C18  C19  C14    0.00   0.0  0
 EI3  CONST_17  C18  C19  C14  N15    0.00   0.0  0
 EI3  CONST_18  C18  C17  C16  N15    0.00   0.0  0
 EI3  CONST_19  C19  C14  N15  C16    0.00   0.0  0
 EI3  CONST_20  C19  C18  C17  C16    0.00   0.0  0
 EI3  CONST_21  C4   C3   C2   C1   180.00   0.0  0
 EI3  CONST_22  N6   C7   C2   C1   180.00   0.0  0
 EI3  CONST_23  C20  C17  C16  N15  180.00   0.0  0
 EI3  CONST_24  C20  C17  C18  C19  180.00   0.0  0
 EI3  CONST_25  H4   C4   C3   C2   180.00   0.0  0
 EI3  CONST_26  H7   C7   C2   C3   180.00   0.0  0
 EI3  CONST_27  H3   C3   C4   C5   180.00   0.0  0
 EI3  CONST_28  H19  C19  C14  C5     0.00   0.0  0
 EI3  CONST_29  H16  C16  N15  C14  180.00   0.0  0
 EI3  CONST_30  H18  C18  C19  C14  180.00   0.0  0
 EI3  Var_01    H1   C1   C2   C3    68.59  30.0  2
 EI3  Var_02    H20  C20  C17  C16  111.13  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
 EI3  plan-1  C1   0.020
 EI3  plan-1  C2   0.020
 EI3  plan-1  C3   0.020
 EI3  plan-1  C4   0.020
 EI3  plan-1  C5   0.020
 EI3  plan-1  N6   0.020
 EI3  plan-1  C7   0.020
 EI3  plan-1  C14  0.020
 EI3  plan-1  H3   0.020
 EI3  plan-1  H4   0.020
 EI3  plan-1  H7   0.020
 EI3  plan-2  C5   0.020
 EI3  plan-2  C14  0.020
 EI3  plan-2  N15  0.020
 EI3  plan-2  C16  0.020
 EI3  plan-2  C17  0.020
 EI3  plan-2  C18  0.020
 EI3  plan-2  C19  0.020
 EI3  plan-2  C20  0.020
 EI3  plan-2  H16  0.020
 EI3  plan-2  H18  0.020
 EI3  plan-2  H19  0.020

