# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:55:40 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: ~{N}-[[2,6-bis(chloranyl)phenyl]methyl]-2-oxidanyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(=O)NCc1c(Cl)cccc1Cl
#
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
 5QA  5QA  ~{N}-[[2,6-bis(chloranyl)phenyl]methyl]-2-oxidanyl-ethanamide  ligand  23  14  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5QA
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
 5QA  C4   C   CR16  0  -0.285  -3.4325  -0.2343   0.9074
 5QA  C5   C   CR16  0  -0.186  -3.0926   1.0549   0.5367
 5QA  C6   C   CR6   0  -0.123  -1.8613   1.2866  -0.0583
 5QA  C7   C   C     0   0.507   2.5711  -0.2678  -0.0813
 5QA  C8   C   CH2   0  -0.265   3.4585  -0.2294   1.1514
 5QA  O1   O   O     0  -0.483   2.8468  -0.9259  -1.0674
 5QA  O    O   OH1   0  -0.658   4.6966  -0.7916   0.8322
 5QA  N    N   NH1   0  -0.624   1.4507   0.4687   0.0437
 5QA  C1   C   CR6   0   0.249  -0.9450   0.2650  -0.3077
 5QA  CL   CL  CL    0  -0.113  -1.4779   2.9255  -0.4817
 5QA  C3   C   CR16  0  -0.189  -2.5496  -1.2796   0.6905
 5QA  C2   C   CR6   0  -0.115  -1.3274  -1.0157   0.0965
 5QA  CL1  CL  CL    0  -0.106  -0.2434  -2.3432  -0.1507
 5QA  H1   H   HCR6  0   0.281  -4.3900  -0.4266   1.3716
 5QA  H2   H   HCR6  0   0.287  -3.7757   1.8744   0.7109
 5QA  H3   H   HCH2  0   0.229   3.5428   0.8083   1.5008
 5QA  H4   H   HCH2  0   0.241   2.9376  -0.7821   1.9453
 5QA  H5   H   HOH1  0   0.461   5.2041  -0.8632   1.6457
 5QA  H6   H   HNH1  0   0.403   1.3330   1.0354   0.8693
 5QA  H7   H   HCH2  0   0.270   0.4015   1.4628  -1.4711
 5QA  H8   H   HCH2  0   0.279   0.6012  -0.2589  -1.6888
 5QA  H9   H   HCR6  0   0.288  -2.8092  -2.2884   0.9797
 5QA  C    C   CH2   0  -0.349   0.3977   0.5088  -0.9447

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
 5QA  O1   C7  double    1.217  0.020  1.217
 5QA  C    N   single    1.445  0.020  1.445
 5QA  C    C1  single    1.506  0.020  1.506
 5QA  C7   N   single    1.347  0.020  1.347
 5QA  C7   C8  single    1.519  0.020  1.519
 5QA  CL   C6  single    1.736  0.020  1.736
 5QA  C1   C6  aromatic  1.395  0.020  1.395
 5QA  C1   C2  aromatic  1.396  0.020  1.396
 5QA  C8   O   single    1.397  0.020  1.397
 5QA  CL1  C2  single    1.732  0.020  1.732
 5QA  C6   C5  aromatic  1.387  0.020  1.387
 5QA  C2   C3  aromatic  1.384  0.020  1.384
 5QA  C5   C4  aromatic  1.384  0.020  1.384
 5QA  C3   C4  aromatic  1.385  0.020  1.385
 5QA  C4   H1  single    0.930  0.020  1.080
 5QA  C5   H2  single    0.930  0.020  1.080
 5QA  C8   H3  single    0.970  0.020  1.090
 5QA  C8   H4  single    0.970  0.020  1.090
 5QA  O    H5  single    0.850  0.020  0.980
 5QA  N    H6  single    0.860  0.020  1.020
 5QA  C    H7  single    0.970  0.020  1.090
 5QA  C    H8  single    0.970  0.020  1.090
 5QA  C3   H9  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
 5QA  H1   C4  C3  119.82  3.000
 5QA  H1   C4  C5  119.88  3.000
 5QA  C3   C4  C5  120.30  3.000
 5QA  H2   C5  C6  120.23  3.000
 5QA  H2   C5  C4  120.52  3.000
 5QA  C6   C5  C4  119.25  3.000
 5QA  CL   C6  C1  120.19  3.000
 5QA  C1   C6  C5  122.52  3.000
 5QA  CL   C6  C5  117.29  3.000
 5QA  N    C7  O1  124.01  3.000
 5QA  N    C7  C8  113.38  3.000
 5QA  O1   C7  C8  122.59  3.000
 5QA  H4   C8  H3  106.37  3.000
 5QA  H4   C8  O   112.51  3.000
 5QA  H3   C8  O   112.65  3.000
 5QA  H4   C8  C7  107.25  3.000
 5QA  H3   C8  C7  109.08  3.000
 5QA  O    C8  C7  108.79  3.000
 5QA  H5   O   C8  107.73  3.000
 5QA  H6   N   C   117.35  3.000
 5QA  H6   N   C7  118.72  3.000
 5QA  C    N   C7  123.92  3.000
 5QA  C2   C1  C   121.00  3.000
 5QA  C2   C1  C6  116.11  3.000
 5QA  C    C1  C6  122.87  3.000
 5QA  H9   C3  C2  120.31  3.000
 5QA  H9   C3  C4  120.61  3.000
 5QA  C2   C3  C4  119.08  3.000
 5QA  CL1  C2  C3  117.89  3.000
 5QA  C3   C2  C1  122.74  3.000
 5QA  CL1  C2  C1  119.36  3.000
 5QA  H8   C   H7  106.66  3.000
 5QA  H8   C   C1  109.98  3.000
 5QA  H7   C   C1  110.44  3.000
 5QA  H8   C   N   108.17  3.000
 5QA  H7   C   N   110.63  3.000
 5QA  C1   C   N   110.85  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
 5QA  CONST_01  C1   C6  C5  C4    0.00   0.0  0
 5QA  CONST_02  C1   C2  C3  C4    0.00   0.0  0
 5QA  CONST_03  C2   C1  C6  C5    0.00   0.0  0
 5QA  CONST_04  C2   C3  C4  C5    0.00   0.0  0
 5QA  CONST_05  C3   C2  C1  C6    0.00   0.0  0
 5QA  CONST_06  C3   C4  C5  C6    0.00   0.0  0
 5QA  CONST_07  CL   C6  C5  C4  180.00   0.0  0
 5QA  CONST_08  CL1  C2  C3  C4  180.00   0.0  0
 5QA  CONST_09  C    C1  C6  C5  180.00   0.0  0
 5QA  CONST_10  CL1  C2  C1  C6  180.00   0.0  0
 5QA  CONST_11  C3   C2  C1  C   180.00   0.0  0
 5QA  CONST_12  C2   C1  C6  CL  180.00   0.0  0
 5QA  CONST_13  H9   C3  C4  C5  180.00   0.0  0
 5QA  CONST_14  H1   C4  C5  C6  180.00   0.0  0
 5QA  CONST_15  H2   C5  C6  C1  180.00   0.0  0
 5QA  CONST_16  C    N   C7  C8  180.00   0.0  0
 5QA  CONST_17  C    N   C7  O1    0.00   0.0  0
 5QA  CONST_18  H6   N   C7  C8    0.00   0.0  0
 5QA  Var_01    N    C   C1  C6  103.53  30.0  2
 5QA  Var_02    C1   C   N   C7  129.56  30.0  2
 5QA  Var_03    O    C8  C7  O1   13.02  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
 5QA  plan-1  C4   0.020
 5QA  plan-1  C5   0.020
 5QA  plan-1  C6   0.020
 5QA  plan-1  C1   0.020
 5QA  plan-1  CL   0.020
 5QA  plan-1  C3   0.020
 5QA  plan-1  C2   0.020
 5QA  plan-1  CL1  0.020
 5QA  plan-1  H1   0.020
 5QA  plan-1  H2   0.020
 5QA  plan-1  H9   0.020
 5QA  plan-1  C    0.020
 5QA  plan-2  C7   0.020
 5QA  plan-2  C8   0.020
 5QA  plan-2  O1   0.020
 5QA  plan-2  N    0.020
 5QA  plan-2  H6   0.020
 5QA  plan-2  C    0.020

