# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:42:25 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: ~{N}-[[2,6-bis(chloranyl)phenyl]methyl]-~{N}-methyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1c(Cl)cccc1Cl)C(C)=O
#
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
 5Q9  5Q9  ~{N}-[[2,6-bis(chloranyl)phenyl]methyl]-~{N}-methyl-ethanamide  ligand  25  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5Q9
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
 5Q9  C4   C   CR6   0   0.254  -0.6877   0.2236   0.3313
 5Q9  C5   C   CR6   0  -0.125  -2.0001  -0.2505   0.3535
 5Q9  C6   C   CR16  0  -0.189  -3.0555   0.4405  -0.2233
 5Q9  C7   C   CR16  0  -0.286  -2.8100   1.6470  -0.8544
 5Q9  C8   C   CR16  0  -0.190  -1.5228   2.1560  -0.9081
 5Q9  O    O   O     0  -0.498   3.1837  -0.1748   0.8987
 5Q9  C1   C   C     0   0.533   2.6851  -0.8968   0.0474
 5Q9  C    C   CH3   0  -0.804   3.5497  -1.5995  -0.9732
 5Q9  N    N   NT    0  -0.437   1.3449  -1.0999  -0.0348
 5Q9  C2   C   CH3   0  -0.528   0.7439  -2.1159  -0.8738
 5Q9  C3   C   CH2   0  -0.369   0.4667  -0.5144   0.9615
 5Q9  C9   C   CR6   0  -0.117  -0.4912   1.4433  -0.3205
 5Q9  CL   CL  CL    0  -0.105   1.1005   2.1198  -0.3975
 5Q9  CL1  CL  CL    0  -0.112  -2.3719  -1.7683   1.1102
 5Q9  H1   H   HCR6  0   0.286  -4.0576   0.0378  -0.1803
 5Q9  H2   H   HCR6  0   0.281  -3.6258   2.1939  -1.3069
 5Q9  H3   H   HCR6  0   0.286  -1.3234   3.0978  -1.3998
 5Q9  H4   H   HCH3  0   0.266   3.4754  -2.6839  -0.8846
 5Q9  H5   H   HCH3  0   0.265   3.2716  -1.3369  -1.9941
 5Q9  H6   H   HCH3  0   0.268   4.5861  -1.3141  -0.8140
 5Q9  H7   H   HCH3  0   0.242   0.5774  -3.0443  -0.3219
 5Q9  H8   H   HCH3  0   0.252  -0.2179  -1.7707  -1.2508
 5Q9  H9   H   HCH3  0   0.269   1.3583  -2.3355  -1.7401
 5Q9  H10  H   HCH2  0   0.291   1.0465   0.1706   1.5757
 5Q9  H11  H   HCH2  0   0.267   0.0926  -1.2953   1.6254

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
 5Q9  O    C1   double    1.223  0.020  1.223
 5Q9  C1   C    single    1.511  0.020  1.511
 5Q9  C1   N    single    1.358  0.020  1.358
 5Q9  C3   N    single    1.451  0.020  1.451
 5Q9  C3   C4   single    1.508  0.020  1.508
 5Q9  N    C2   single    1.448  0.020  1.448
 5Q9  CL1  C5   single    1.736  0.020  1.736
 5Q9  C4   C5   aromatic  1.396  0.020  1.396
 5Q9  C4   C9   aromatic  1.397  0.020  1.397
 5Q9  CL   C9   single    1.731  0.020  1.731
 5Q9  C5   C6   aromatic  1.387  0.020  1.387
 5Q9  C9   C8   aromatic  1.385  0.020  1.385
 5Q9  C6   C7   aromatic  1.384  0.020  1.384
 5Q9  C8   C7   aromatic  1.385  0.020  1.385
 5Q9  C6   H1   single    0.930  0.020  1.080
 5Q9  C7   H2   single    0.930  0.020  1.080
 5Q9  C8   H3   single    0.930  0.020  1.080
 5Q9  C    H4   single    0.970  0.020  1.090
 5Q9  C    H5   single    0.970  0.020  1.090
 5Q9  C    H6   single    0.970  0.020  1.090
 5Q9  C2   H7   single    0.970  0.020  1.090
 5Q9  C2   H8   single    0.970  0.020  1.090
 5Q9  C2   H9   single    0.970  0.020  1.090
 5Q9  C3   H10  single    0.970  0.020  1.090
 5Q9  C3   H11  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
 5Q9  C9   C4  C3   120.97  3.000
 5Q9  C9   C4  C5   115.87  3.000
 5Q9  C3   C4  C5   123.15  3.000
 5Q9  CL1  C5  C6   116.99  3.000
 5Q9  C6   C5  C4   122.66  3.000
 5Q9  CL1  C5  C4   120.35  3.000
 5Q9  H1   C6  C7   120.50  3.000
 5Q9  H1   C6  C5   120.22  3.000
 5Q9  C7   C6  C5   119.28  3.000
 5Q9  H2   C7  C8   119.93  3.000
 5Q9  H2   C7  C6   119.87  3.000
 5Q9  C8   C7  C6   120.20  3.000
 5Q9  H3   C8  C9   120.26  3.000
 5Q9  H3   C8  C7   120.61  3.000
 5Q9  C9   C8  C7   119.13  3.000
 5Q9  N    C1  C    117.02  3.000
 5Q9  N    C1  O    122.21  3.000
 5Q9  C    C1  O    120.77  3.000
 5Q9  H6   C   H5   108.49  3.000
 5Q9  H6   C   H4   108.31  3.000
 5Q9  H5   C   H4   107.35  3.000
 5Q9  H6   C   C1   108.95  3.000
 5Q9  H5   C   C1   111.99  3.000
 5Q9  H4   C   C1   111.63  3.000
 5Q9  C3   N   C2   115.44  3.000
 5Q9  C2   N   C1   123.34  3.000
 5Q9  C3   N   C1   119.68  3.000
 5Q9  H9   C2  H8   106.73  3.000
 5Q9  H9   C2  H7   108.53  3.000
 5Q9  H8   C2  H7   108.03  3.000
 5Q9  H9   C2  N    111.69  3.000
 5Q9  H8   C2  N    110.16  3.000
 5Q9  H7   C2  N    111.51  3.000
 5Q9  H11  C3  H10  106.86  3.000
 5Q9  H11  C3  N    109.66  3.000
 5Q9  H10  C3  N    108.61  3.000
 5Q9  H11  C3  C4   110.00  3.000
 5Q9  H10  C3  C4   109.62  3.000
 5Q9  N    C3  C4   111.94  3.000
 5Q9  CL   C9  C8   117.71  3.000
 5Q9  C8   C9  C4   122.86  3.000
 5Q9  CL   C9  C4   119.43  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
 5Q9  CONST_01  C7   C6  C5  C4    0.00   0.0  0
 5Q9  CONST_02  C7   C8  C9  C4    0.00   0.0  0
 5Q9  CONST_03  C8   C9  C4  C5    0.00   0.0  0
 5Q9  CONST_04  C8   C7  C6  C5    0.00   0.0  0
 5Q9  CONST_05  C9   C4  C5  C6    0.00   0.0  0
 5Q9  CONST_06  C9   C8  C7  C6    0.00   0.0  0
 5Q9  CONST_07  CL   C9  C4  C5  180.00   0.0  0
 5Q9  CONST_08  C3   C4  C5  C6  180.00   0.0  0
 5Q9  CONST_09  CL1  C5  C6  C7  180.00   0.0  0
 5Q9  CONST_10  CL   C9  C8  C7  180.00   0.0  0
 5Q9  CONST_11  C3   C4  C9  C8  180.00   0.0  0
 5Q9  CONST_12  CL1  C5  C4  C9  180.00   0.0  0
 5Q9  CONST_13  H1   C6  C5  C4  180.00   0.0  0
 5Q9  CONST_14  H3   C8  C9  C4  180.00   0.0  0
 5Q9  CONST_15  H2   C7  C6  C5  180.00   0.0  0
 5Q9  CONST_16  C3   N   C1  O     0.00   0.0  0
 5Q9  CONST_17  C2   N   C1  O   180.00   0.0  0
 5Q9  CONST_18  C3   N   C1  C   180.00   0.0  0
 5Q9  CONST_19  C2   N   C1  C     0.00   0.0  0
 5Q9  Var_01    N    C3  C4  C5  107.89  30.0  2
 5Q9  Var_02    C1   N   C3  C4  130.42  30.0  3
 5Q9  Var_03    H4   C   C1  O   117.59  30.0  3
 5Q9  Var_04    H7   C2  N   C1   93.35  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
 5Q9  plan-1  C4   0.020
 5Q9  plan-1  C5   0.020
 5Q9  plan-1  C6   0.020
 5Q9  plan-1  C7   0.020
 5Q9  plan-1  C8   0.020
 5Q9  plan-1  C3   0.020
 5Q9  plan-1  C9   0.020
 5Q9  plan-1  CL   0.020
 5Q9  plan-1  CL1  0.020
 5Q9  plan-1  H1   0.020
 5Q9  plan-1  H2   0.020
 5Q9  plan-1  H3   0.020
 5Q9  plan-2  O    0.020
 5Q9  plan-2  C1   0.020
 5Q9  plan-2  C    0.020
 5Q9  plan-2  N    0.020
 5Q9  plan-2  C2   0.020
 5Q9  plan-2  C3   0.020

