# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:18:49 2021
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-[(dimethylamino)methyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1ccc(cc1)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
 WHY  WHY  4-[(dimethylamino)methyl]benzonitrile  ligand  24  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WHY
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
 WHY  N1   N  NS    0  -0.256  15.7318  4.9344  -18.8271
 WHY  C4   C  CR16  0  -0.299  18.4440  7.4238  -21.9214
 WHY  C5   C  CR16  0  -0.224  17.4003  6.9043  -21.1746
 WHY  C6   C  CR6   0  -0.012  17.6628  5.9179  -20.2258
 WHY  C7   C  CSP   0   0.054  16.5945  5.3732  -19.4531
 WHY  C8   C  CR16  0  -0.226  18.9671  5.4597  -20.0299
 WHY  N    N  NT    0  -0.405  21.8476  6.6033  -22.9555
 WHY  C    C  CH3   0  -0.519  23.0770  7.2260  -23.3975
 WHY  C1   C  CH3   0  -0.520  21.3004  5.7382  -23.9801
 WHY  C3   C  CR6   0   0.098  19.7498  6.9807  -21.7329
 WHY  C9   C  CR16  0  -0.269  19.9975  5.9921  -20.7812
 WHY  H8   H  HCR6  0   0.266  18.2391  8.1844  -22.6647
 WHY  H9   H  HCR6  0   0.279  16.3893  7.2562  -21.3294
 WHY  H10  H  HCR6  0   0.278  19.1665  4.6932  -19.2929
 WHY  H1   H  HCH3  0   0.234  23.5173  7.8066  -22.5856
 WHY  H2   H  HCH3  0   0.235  23.7960  6.4587  -23.6869
 WHY  H    H  HCH3  0   0.194  22.9414  7.8992  -24.2575
 WHY  H4   H  HCH3  0   0.236  20.3975  5.2422  -23.6223
 WHY  H3   H  HCH3  0   0.196  21.0425  6.2772  -24.9049
 WHY  H5   H  HCH3  0   0.236  22.0216  4.9612  -24.2355
 WHY  H7   H  HCH2  0   0.262  21.3993  8.3000  -21.8607
 WHY  H6   H  HCH2  0   0.218  20.4758  8.1803  -23.3509
 WHY  H11  H  HCR6  0   0.261  21.0079  5.6336  -20.6353
 WHY  C2   C  CH2   0  -0.320  20.8845  7.5884  -22.5147

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
 WHY  C   N    single    1.447  0.020  1.447
 WHY  C1  N    single    1.448  0.020  1.448
 WHY  N   C2   single    1.446  0.020  1.446
 WHY  C2  C3   single    1.506  0.020  1.506
 WHY  C3  C4   aromatic  1.392  0.020  1.392
 WHY  C4  C5   aromatic  1.385  0.020  1.385
 WHY  C5  C6   aromatic  1.394  0.020  1.394
 WHY  C6  C7   single    1.427  0.020  1.427
 WHY  C7  N1   triple    1.153  0.020  1.153
 WHY  C8  C6   aromatic  1.396  0.020  1.396
 WHY  C9  C8   aromatic  1.382  0.020  1.382
 WHY  C3  C9   aromatic  1.394  0.020  1.394
 WHY  C4  H8   single    0.930  0.020  1.080
 WHY  C5  H9   single    0.930  0.020  1.080
 WHY  C8  H10  single    0.930  0.020  1.080
 WHY  C   H1   single    0.970  0.020  1.090
 WHY  C   H2   single    0.970  0.020  1.090
 WHY  C   H    single    0.970  0.020  1.090
 WHY  C1  H4   single    0.970  0.020  1.090
 WHY  C1  H3   single    0.970  0.020  1.090
 WHY  C1  H5   single    0.970  0.020  1.090
 WHY  C2  H7   single    0.970  0.020  1.090
 WHY  C2  H6   single    0.970  0.020  1.090
 WHY  C9  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
 WHY  H8   C4  C3  119.61  3.000
 WHY  H8   C4  C5  119.41  3.000
 WHY  C3   C4  C5  120.98  3.000
 WHY  H9   C5  C6  120.25  3.000
 WHY  H9   C5  C4  120.36  3.000
 WHY  C6   C5  C4  119.39  3.000
 WHY  C8   C6  C7  119.88  3.000
 WHY  C8   C6  C5  120.25  3.000
 WHY  C7   C6  C5  119.87  3.000
 WHY  C6   C7  N1  180.00  3.000
 WHY  H10  C8  C9  120.39  3.000
 WHY  H10  C8  C6  120.02  3.000
 WHY  C9   C8  C6  119.59  3.000
 WHY  C2   N   C1  111.77  3.000
 WHY  C2   N   C   111.45  3.000
 WHY  C1   N   C   111.22  3.000
 WHY  H    C   H2  107.71  3.000
 WHY  H    C   H1  107.80  3.000
 WHY  H2   C   H1  107.81  3.000
 WHY  H    C   N   113.40  3.000
 WHY  H2   C   N   109.78  3.000
 WHY  H1   C   N   110.16  3.000
 WHY  H5   C1  H3  107.88  3.000
 WHY  H5   C1  H4  107.48  3.000
 WHY  H3   C1  H4  107.71  3.000
 WHY  H5   C1  N   109.96  3.000
 WHY  H3   C1  N   112.98  3.000
 WHY  H4   C1  N   110.63  3.000
 WHY  C9   C3  C2  120.43  3.000
 WHY  C9   C3  C4  119.00  3.000
 WHY  C2   C3  C4  120.54  3.000
 WHY  H11  C9  C3  119.53  3.000
 WHY  H11  C9  C8  119.69  3.000
 WHY  C3   C9  C8  120.78  3.000
 WHY  H6   C2  H7  106.16  3.000
 WHY  H6   C2  C3  109.32  3.000
 WHY  H7   C2  C3  107.84  3.000
 WHY  H6   C2  N   112.40  3.000
 WHY  H7   C2  N   108.16  3.000
 WHY  C3   C2  N   112.65  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
 WHY  CONST_01  C8   C9  C3  C4     0.00   0.0  0
 WHY  CONST_02  C8   C6  C5  C4     0.00   0.0  0
 WHY  CONST_03  C9   C3  C4  C5     0.00   0.0  0
 WHY  CONST_04  C9   C8  C6  C5     0.00   0.0  0
 WHY  CONST_05  C3   C4  C5  C6     0.00   0.0  0
 WHY  CONST_06  C3   C9  C8  C6     0.00   0.0  0
 WHY  CONST_07  C7   C6  C5  C4   180.00   0.0  0
 WHY  CONST_08  C2   C3  C4  C5   180.00   0.0  0
 WHY  CONST_09  C9   C8  C6  C7   180.00   0.0  0
 WHY  CONST_10  C2   C3  C9  C8   180.00   0.0  0
 WHY  CONST_11  H11  C9  C3  C4   180.00   0.0  0
 WHY  CONST_12  H10  C8  C6  C5   180.00   0.0  0
 WHY  CONST_13  H8   C4  C5  C6   180.00   0.0  0
 WHY  CONST_14  H9   C5  C6  C8   180.00   0.0  0
 WHY  Var_01    N    C2  C3  C4  -139.52  30.0  2
 WHY  Var_02    C3   C2  N   C   -165.44  30.0  3
 WHY  Var_03    H4   C1  N   C    177.64  30.0  3
 WHY  Var_04    H1   C   N   C1  -175.29  30.0  3

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
 WHY  plan-1  N1   0.020
 WHY  plan-1  C4   0.020
 WHY  plan-1  C5   0.020
 WHY  plan-1  C6   0.020
 WHY  plan-1  C7   0.020
 WHY  plan-1  C8   0.020
 WHY  plan-1  C3   0.020
 WHY  plan-1  C9   0.020
 WHY  plan-1  H8   0.020
 WHY  plan-1  H9   0.020
 WHY  plan-1  H10  0.020
 WHY  plan-1  H11  0.020
 WHY  plan-1  C2   0.020

