# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 09:01:42 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 2-methyl-6-oxo-1,6-dihydro-3,4'-bipyridine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(C=C(C#N)C(=O)N1)c2ccncc2
#
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
 MIL  MIL  2-methyl-6-oxo-1,6-dihydro-3,4'-bipyridine-5-carbonitrile  ligand  25  16  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MIL
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
 MIL  C1    C  CR6   0  -0.070   0.1572  -0.0248  -0.1838
 MIL  C2    C  CR6   0   0.410   1.4567  -0.1045   0.2736
 MIL  C4    C  CR6   0   0.557   0.7468  -0.0364   2.6154
 MIL  C5    C  CR6   0  -0.242  -0.6053   0.0264   2.1198
 MIL  C6    C  CR16  0  -0.099  -0.8692   0.0270   0.7749
 MIL  C2A   C  CH3   0  -0.754   2.6640  -0.2056  -0.5942
 MIL  C5A   C  CSP   0   0.067  -1.6457   0.0924   3.0809
 MIL  C1'   C  CR6   0   0.117  -0.1884  -0.0105  -1.6175
 MIL  C2'   C  CR16  0  -0.367  -1.1424  -0.8908  -2.1221
 MIL  C3'   C  CR16  0  -0.056  -1.4669  -0.8348  -3.4682
 MIL  C5'   C  CR16  0  -0.055  -0.0100   0.8631  -3.8397
 MIL  C6'   C  CR16  0  -0.364   0.3833   0.8914  -2.5106
 MIL  O4    O  OC    0  -0.460   1.0772  -0.0374   3.7897
 MIL  N3    N  NR16  0  -0.701   1.6867  -0.1064   1.6026
 MIL  N5A   N  NS    0  -0.254  -2.4911   0.1478   3.8630
 MIL  N4'   N  N     0  -0.406  -0.9158   0.0205  -4.3215
 MIL  H6    H  HCR6  0   0.302  -1.8980   0.0828   0.4402
 MIL  H2A1  H  HCH3  0   0.284   3.4360  -0.8056  -0.1146
 MIL  H2A2  H  HCH3  0   0.280   2.4274  -0.6552  -1.5545
 MIL  H2A3  H  HCH3  0   0.290   3.0824   0.7852  -0.7786
 MIL  H2'   H  HCR6  0   0.275  -1.6189  -1.6240  -1.4845
 MIL  H3'   H  HCR6  0   0.268  -2.2043  -1.5185  -3.8737
 MIL  H5'   H  HCR6  0   0.269   0.4256   1.5638  -4.5432
 MIL  H6'   H  HCR6  0   0.273   1.1091   1.6245  -2.1841
 MIL  HN3   H  HNR6  0   0.435   2.6489  -0.1786   1.9133

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
 MIL  C1   C2    aromatic  1.380  0.020  1.380
 MIL  C1   C6    aromatic  1.405  0.020  1.405
 MIL  C1   C1'   single    1.475  0.020  1.475
 MIL  C2   C2A   single    1.490  0.020  1.490
 MIL  C2   N3    aromatic  1.349  0.020  1.349
 MIL  C4   C5    aromatic  1.441  0.020  1.441
 MIL  C4   O4    double    1.220  0.020  1.220
 MIL  C4   N3    aromatic  1.383  0.020  1.383
 MIL  C5   C6    aromatic  1.371  0.020  1.371
 MIL  C5   C5A   single    1.418  0.020  1.418
 MIL  C6   H6    single    0.930  0.020  1.080
 MIL  C2A  H2A1  single    0.970  0.020  1.090
 MIL  C2A  H2A2  single    0.970  0.020  1.090
 MIL  C2A  H2A3  single    0.970  0.020  1.090
 MIL  C5A  N5A   triple    1.153  0.020  1.153
 MIL  C1'  C2'   aromatic  1.393  0.020  1.393
 MIL  C1'  C6'   aromatic  1.392  0.020  1.392
 MIL  C2'  C3'   aromatic  1.386  0.020  1.386
 MIL  C2'  H2'   single    0.930  0.020  1.080
 MIL  C3'  N4'   aromatic  1.328  0.020  1.328
 MIL  C3'  H3'   single    0.930  0.020  1.080
 MIL  C5'  C6'   aromatic  1.386  0.020  1.386
 MIL  C5'  N4'   aromatic  1.328  0.020  1.328
 MIL  C5'  H5'   single    0.930  0.020  1.080
 MIL  C6'  H6'   single    0.930  0.020  1.080
 MIL  N3   HN3   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
 MIL  C1'   C1   C6    119.44  3.000
 MIL  C1'   C1   C2    122.92  3.000
 MIL  C6    C1   C2    117.63  3.000
 MIL  N3    C2   C2A   115.82  3.000
 MIL  N3    C2   C1    119.16  3.000
 MIL  C2A   C2   C1    125.01  3.000
 MIL  N3    C4   O4    121.37  3.000
 MIL  N3    C4   C5    112.82  3.000
 MIL  O4    C4   C5    125.81  3.000
 MIL  C5A   C5   C6    121.59  3.000
 MIL  C5A   C5   C4    117.21  3.000
 MIL  C6    C5   C4    121.20  3.000
 MIL  H6    C6   C5    119.08  3.000
 MIL  H6    C6   C1    119.00  3.000
 MIL  C5    C6   C1    121.92  3.000
 MIL  H2A3  C2A  H2A2  108.05  3.000
 MIL  H2A3  C2A  H2A1  107.62  3.000
 MIL  H2A2  C2A  H2A1  108.40  3.000
 MIL  H2A3  C2A  C2    110.33  3.000
 MIL  H2A2  C2A  C2    111.50  3.000
 MIL  H2A1  C2A  C2    110.81  3.000
 MIL  N5A   C5A  C5    180.00  3.000
 MIL  C6'   C1'  C2'   117.28  3.000
 MIL  C6'   C1'  C1    122.25  3.000
 MIL  C2'   C1'  C1    120.44  3.000
 MIL  H2'   C2'  C3'   119.78  3.000
 MIL  H2'   C2'  C1'   121.09  3.000
 MIL  C3'   C2'  C1'   119.13  3.000
 MIL  H3'   C3'  N4'   116.62  3.000
 MIL  H3'   C3'  C2'   119.80  3.000
 MIL  N4'   C3'  C2'   123.58  3.000
 MIL  H5'   C5'  N4'   116.67  3.000
 MIL  H5'   C5'  C6'   119.66  3.000
 MIL  N4'   C5'  C6'   123.67  3.000
 MIL  H6'   C6'  C5'   119.56  3.000
 MIL  H6'   C6'  C1'   121.39  3.000
 MIL  C5'   C6'  C1'   119.03  3.000
 MIL  HN3   N3   C4    115.10  3.000
 MIL  HN3   N3   C2    117.64  3.000
 MIL  C4    N3   C2    127.25  3.000
 MIL  C5'   N4'  C3'   117.30  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
 MIL  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 MIL  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 MIL  CONST_03  C3'   C2'  C1'  C1    180.00   0.0  0
 MIL  CONST_04  C5'   C6'  C1'  C1    180.00   0.0  0
 MIL  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 MIL  CONST_08  C5    C4   N3   C2      0.00   0.0  0
 MIL  CONST_09  C1'   C1   C6   C5    180.00   0.0  0
 MIL  CONST_10  N3    C2   C1   C6      0.00   0.0  0
 MIL  CONST_13  N3    C4   C5   C6      0.00   0.0  0
 MIL  CONST_14  N3    C2   C1   C1'   180.00   0.0  0
 MIL  CONST_15  N4'   C3'  C2'  C1'     0.00   0.0  0
 MIL  CONST_16  N4'   C5'  C6'  C1'     0.00   0.0  0
 MIL  CONST_17  C5'   C6'  C1'  C2'     0.00   0.0  0
 MIL  CONST_18  C5'   N4'  C3'  C2'     0.00   0.0  0
 MIL  CONST_19  C6'   C1'  C2'  C3'     0.00   0.0  0
 MIL  CONST_20  C6'   C5'  N4'  C3'     0.00   0.0  0
 MIL  CONST_21  C5A   C5   C6   C1    180.00   0.0  0
 MIL  CONST_22  O4    C4   N3   C2    180.00   0.0  0
 MIL  CONST_23  C2A   C2   N3   C4    180.00   0.0  0
 MIL  CONST_24  C2A   C2   C1   C6    180.00   0.0  0
 MIL  CONST_25  O4    C4   C5   C6    180.00   0.0  0
 MIL  CONST_26  C1'   C1   C2   C2A     0.00   0.0  0
 MIL  CONST_27  N3    C4   C5   C5A   180.00   0.0  0
 MIL  CONST_28  HN3   N3   C2   C1    180.00   0.0  0
 MIL  CONST_29  H2'   C2'  C1'  C1      0.00   0.0  0
 MIL  CONST_30  H6'   C6'  C1'  C1      0.00   0.0  0
 MIL  CONST_31  H6    C6   C1   C2    180.00   0.0  0
 MIL  CONST_32  H3'   C3'  C2'  C1'   180.00   0.0  0
 MIL  CONST_33  H5'   C5'  C6'  C1'   180.00   0.0  0
 MIL  Var_01    H2A1  C2A  C2   C1   -146.93  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
 MIL  plan-1  C1   0.020
 MIL  plan-1  C2   0.020
 MIL  plan-1  C4   0.020
 MIL  plan-1  C5   0.020
 MIL  plan-1  C6   0.020
 MIL  plan-1  C2A  0.020
 MIL  plan-1  C5A  0.020
 MIL  plan-1  C1'  0.020
 MIL  plan-1  O4   0.020
 MIL  plan-1  N3   0.020
 MIL  plan-1  N5A  0.020
 MIL  plan-1  H6   0.020
 MIL  plan-1  HN3  0.020
 MIL  plan-2  C1   0.020
 MIL  plan-2  C1'  0.020
 MIL  plan-2  C2'  0.020
 MIL  plan-2  C3'  0.020
 MIL  plan-2  C5'  0.020
 MIL  plan-2  C6'  0.020
 MIL  plan-2  N4'  0.020
 MIL  plan-2  H2'  0.020
 MIL  plan-2  H3'  0.020
 MIL  plan-2  H5'  0.020
 MIL  plan-2  H6'  0.020

