# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:53:39 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: 3-[(2-methyl-1H-imidazol-1-yl)methyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nccn1Cc2cccc(c2)C#N
#
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
 RXS  RXS  3-[(2-methyl-1H-imidazol-1-yl)methyl]benzonitrile  ligand  26  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RXS
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
 RXS  N1   N  NR5   0  -0.435  14.9385  -18.6157  -15.0713
 RXS  C4   C  CH2   0  -0.362  15.0634  -17.9480  -13.7988
 RXS  C5   C  CR6   0   0.099  13.7480  -17.7939  -13.0740
 RXS  C6   C  CR16  0  -0.261  12.7159  -18.7153  -13.2239
 RXS  C7   C  CR16  0  -0.228  11.5269  -18.5729  -12.5216
 RXS  C8   C  CR16  0  -0.252  11.3487  -17.5101  -11.6529
 RXS  C10  C  CSP   0   0.058  12.2143  -15.4787  -10.6152
 RXS  N    N  N     0  -0.462  14.4002  -18.9703  -17.1726
 RXS  C    C  CH3   0  -0.752  13.9471  -16.6787  -16.2985
 RXS  C1   C  CR5   0   0.429  14.4155  -18.0855  -16.2061
 RXS  C11  C  CR16  0  -0.294  13.5731  -16.7226  -12.2102
 RXS  C2   C  CR15  0  -0.221  14.9263  -20.1165  -16.6434
 RXS  C3   C  CR15  0  -0.118  15.2648  -19.9196  -15.3389
 RXS  C9   C  CR6   0   0.024  12.3808  -16.5859  -11.5014
 RXS  N2   N  NS    0  -0.250  12.0790  -14.5853   -9.9003
 RXS  H1   H  HCH2  0   0.303  15.7547  -18.5278  -13.1858
 RXS  H2   H  HCH2  0   0.288  15.5243  -16.9700  -13.9455
 RXS  H3   H  HCR6  0   0.272  12.8306  -19.5545  -13.8988
 RXS  H4   H  HCR6  0   0.277  10.7342  -19.2963  -12.6541
 RXS  H5   H  HCR6  0   0.284  10.4246  -17.3937  -11.1036
 RXS  H6   H  HCH3  0   0.268  13.5657  -16.4909  -17.2992
 RXS  H7   H  HCH3  0   0.254  13.1488  -16.4660  -15.5855
 RXS  H8   H  HCH3  0   0.259  14.7544  -15.9690  -16.1077
 RXS  H9   H  HCR6  0   0.281  14.3587  -15.9881  -12.0831
 RXS  H10  H  HCR5  0   0.247  15.0356  -21.0170  -17.2279
 RXS  H11  H  HCR5  0   0.290  15.7012  -20.5647  -14.5942

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
 RXS  N    C2   aromatic  1.368  0.020  1.368
 RXS  N    C1   aromatic  1.310  0.020  1.310
 RXS  C2   C3   aromatic  1.362  0.020  1.362
 RXS  C    C1   single    1.486  0.020  1.486
 RXS  C1   N1   aromatic  1.357  0.020  1.357
 RXS  C3   N1   aromatic  1.371  0.020  1.371
 RXS  N1   C4   single    1.442  0.020  1.442
 RXS  C4   C5   single    1.510  0.020  1.510
 RXS  C6   C5   aromatic  1.392  0.020  1.392
 RXS  C6   C7   aromatic  1.388  0.020  1.388
 RXS  C5   C11  aromatic  1.387  0.020  1.387
 RXS  C7   C8   aromatic  1.384  0.020  1.384
 RXS  C11  C9   aromatic  1.394  0.020  1.394
 RXS  C8   C9   aromatic  1.394  0.020  1.394
 RXS  C9   C10  single    1.428  0.020  1.428
 RXS  C10  N2   triple    1.152  0.020  1.152
 RXS  C4   H1   single    0.970  0.020  1.090
 RXS  C4   H2   single    0.970  0.020  1.090
 RXS  C6   H3   single    0.930  0.020  1.080
 RXS  C7   H4   single    0.930  0.020  1.080
 RXS  C8   H5   single    0.930  0.020  1.080
 RXS  C    H6   single    0.970  0.020  1.090
 RXS  C    H7   single    0.970  0.020  1.090
 RXS  C    H8   single    0.970  0.020  1.090
 RXS  C11  H9   single    0.930  0.020  1.080
 RXS  C2   H10  single    0.930  0.020  1.080
 RXS  C3   H11  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
 RXS  C3   N1   C1   107.47  3.000
 RXS  C3   N1   C4   126.30  3.000
 RXS  C1   N1   C4   126.16  3.000
 RXS  H2   C4   H1   106.52  3.000
 RXS  H2   C4   C5   109.94  3.000
 RXS  H1   C4   C5   109.67  3.000
 RXS  H2   C4   N1   109.44  3.000
 RXS  H1   C4   N1   107.73  3.000
 RXS  C5   C4   N1   113.29  3.000
 RXS  C11  C5   C6   119.00  3.000
 RXS  C11  C5   C4   119.18  3.000
 RXS  C6   C5   C4   121.79  3.000
 RXS  H3   C6   C7   119.04  3.000
 RXS  H3   C6   C5   120.11  3.000
 RXS  C7   C6   C5   120.85  3.000
 RXS  H4   C7   C8   119.75  3.000
 RXS  H4   C7   C6   119.82  3.000
 RXS  C8   C7   C6   120.43  3.000
 RXS  H5   C8   C9   120.42  3.000
 RXS  H5   C8   C7   120.76  3.000
 RXS  C9   C8   C7   118.82  3.000
 RXS  N2   C10  C9   180.00  3.000
 RXS  C2   N    C1   106.02  3.000
 RXS  H8   C    H7   107.46  3.000
 RXS  H8   C    H6   107.93  3.000
 RXS  H7   C    H6   108.13  3.000
 RXS  H8   C    C1   111.81  3.000
 RXS  H7   C    C1   112.00  3.000
 RXS  H6   C    C1   109.36  3.000
 RXS  C    C1   N    126.14  3.000
 RXS  C    C1   N1   122.91  3.000
 RXS  N    C1   N1   110.94  3.000
 RXS  H9   C11  C9   119.63  3.000
 RXS  H9   C11  C5   120.36  3.000
 RXS  C9   C11  C5   120.02  3.000
 RXS  H10  C2   C3   127.89  3.000
 RXS  H10  C2   N    121.92  3.000
 RXS  C3   C2   N    110.18  3.000
 RXS  H11  C3   C2   132.53  3.000
 RXS  H11  C3   N1   122.08  3.000
 RXS  C2   C3   N1   105.39  3.000
 RXS  C11  C9   C10  119.43  3.000
 RXS  C10  C9   C8   119.69  3.000
 RXS  C11  C9   C8   120.88  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
 RXS  CONST_01  C2   N    C1   N1     0.00   0.0  0
 RXS  CONST_02  N    C2   C3   N1     0.00   0.0  0
 RXS  CONST_03  C8   C7   C6   C5     0.00   0.0  0
 RXS  CONST_04  C8   C9   C11  C5     0.00   0.0  0
 RXS  CONST_05  C9   C11  C5   C6     0.00   0.0  0
 RXS  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 RXS  CONST_07  C11  C5   C6   C7     0.00   0.0  0
 RXS  CONST_08  C11  C9   C8   C7     0.00   0.0  0
 RXS  CONST_09  C3   N1   C1   N      0.00   0.0  0
 RXS  CONST_10  C3   C2   N    C1     0.00   0.0  0
 RXS  CONST_11  C2   C3   N1   C1     0.00   0.0  0
 RXS  CONST_12  N    C1   N1   C4   180.00   0.0  0
 RXS  CONST_13  C2   C3   N1   C4   180.00   0.0  0
 RXS  CONST_14  C7   C6   C5   C4   180.00   0.0  0
 RXS  CONST_15  C9   C11  C5   C4   180.00   0.0  0
 RXS  CONST_16  C10  C9   C11  C5   180.00   0.0  0
 RXS  CONST_17  C10  C9   C8   C7   180.00   0.0  0
 RXS  CONST_18  C2   N    C1   C    180.00   0.0  0
 RXS  CONST_19  C3   N1   C1   C    180.00   0.0  0
 RXS  CONST_20  H10  C2   C3   N1   180.00   0.0  0
 RXS  CONST_21  H4   C7   C6   C5   180.00   0.0  0
 RXS  CONST_22  H9   C11  C5   C6   180.00   0.0  0
 RXS  CONST_23  H5   C8   C7   C6   180.00   0.0  0
 RXS  CONST_24  H3   C6   C7   C8   180.00   0.0  0
 RXS  CONST_25  H11  C3   C2   N    180.00   0.0  0
 RXS  Var_01    C6   C5   C4   N1    30.31  30.0  2
 RXS  Var_02    C1   N1   C4   C5    73.76  30.0  2
 RXS  Var_03    H6   C    C1   N1  -179.61  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
 RXS  plan-1  N1   0.020
 RXS  plan-1  C4   0.020
 RXS  plan-1  N    0.020
 RXS  plan-1  C    0.020
 RXS  plan-1  C1   0.020
 RXS  plan-1  C2   0.020
 RXS  plan-1  C3   0.020
 RXS  plan-1  H10  0.020
 RXS  plan-1  H11  0.020
 RXS  plan-2  C4   0.020
 RXS  plan-2  C5   0.020
 RXS  plan-2  C6   0.020
 RXS  plan-2  C7   0.020
 RXS  plan-2  C8   0.020
 RXS  plan-2  C10  0.020
 RXS  plan-2  C11  0.020
 RXS  plan-2  C9   0.020
 RXS  plan-2  N2   0.020
 RXS  plan-2  H3   0.020
 RXS  plan-2  H4   0.020
 RXS  plan-2  H5   0.020
 RXS  plan-2  H9   0.020

