# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:50:18 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: ~{N}-(3,4-dichlorophenyl)-~{N}'-oxidanyl-propanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)CC(=O)Nc1ccc(Cl)c(Cl)c1
#
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
 EEK  EEK  ~{N}-(3,4-dichlorophenyl)-~{N}'-oxidanyl-propanediamide  ligand  24  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EEK
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
 EEK  C10  C   C     0   0.529  -4.3125  -0.2385   0.3846
 EEK  C15  C   CR16  0  -0.343   1.3403  -2.0240   0.1717
 EEK  C02  C   CR6   0  -0.028   3.2273  -0.5564  -0.0511
 EEK  C03  C   CR6   0   0.023   2.3558   0.4968  -0.2889
 EEK  C05  C   CR16  0  -0.279   0.9816   0.3062  -0.3011
 EEK  C06  C   CR6   0   0.385   0.4616  -0.9654  -0.0699
 EEK  C08  C   C     0   0.571  -1.9532  -0.4475  -0.3195
 EEK  C09  C   CH2   0  -0.733  -3.2986  -1.1421  -0.2840
 EEK  C16  C   CR16  0  -0.205   2.7047  -1.8205   0.1808
 EEK  N07  N   NH1   0  -0.749  -0.9012  -1.2607  -0.0551
 EEK  N11  N   NH1   0  -0.362  -5.3523   0.0749  -0.4027
 EEK  O12  O   OH1   0  -0.541  -6.2765   0.9793   0.0171
 EEK  O13  O   O     0  -0.467  -4.1905   0.1286   1.5379
 EEK  O14  O   O     0  -0.452  -1.8602   0.7332  -0.5929
 EEK  CL4  CL  CL    0  -0.093   2.9657   2.0829  -0.5738
 EEK  H1   H   HCR6  0   0.289   0.9551  -3.0188   0.3575
 EEK  H2   H   HCR6  0   0.310   0.3375   1.1497  -0.4852
 EEK  H3   H   HCH2  0   0.309  -3.2644  -2.0830   0.2678
 EEK  H4   H   HCH2  0   0.313  -3.5725  -1.3897  -1.3130
 EEK  H5   H   HCR6  0   0.294   3.3702  -2.6515   0.3692
 EEK  H6   H   HNH1  0   0.426  -1.1226  -2.2205   0.1632
 EEK  H7   H   HNH1  0   0.421  -5.3711  -0.1304  -1.3913
 EEK  H8   H   HOH1  0   0.480  -7.0049   0.4687   0.3946
 EEK  CL1  CL  CL    0  -0.099   4.9324  -0.3184  -0.0381

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
 EEK  O12  N11  single    1.360  0.020  1.360
 EEK  N11  C10  single    1.341  0.020  1.341
 EEK  C10  C09  single    1.514  0.020  1.514
 EEK  C10  O13  double    1.216  0.020  1.216
 EEK  C09  C08  single    1.515  0.020  1.515
 EEK  C08  O14  double    1.216  0.020  1.216
 EEK  C08  N07  single    1.356  0.020  1.356
 EEK  N07  C06  single    1.394  0.020  1.394
 EEK  C06  C15  aromatic  1.397  0.020  1.397
 EEK  C06  C05  aromatic  1.393  0.020  1.393
 EEK  C15  C16  aromatic  1.380  0.020  1.380
 EEK  C05  C03  aromatic  1.387  0.020  1.387
 EEK  C16  C02  aromatic  1.387  0.020  1.387
 EEK  C03  C02  aromatic  1.388  0.020  1.388
 EEK  C03  CL4  single    1.723  0.020  1.723
 EEK  C02  CL1  single    1.722  0.020  1.722
 EEK  C15  H1   single    0.930  0.020  1.080
 EEK  C05  H2   single    0.930  0.020  1.080
 EEK  C09  H3   single    0.970  0.020  1.090
 EEK  C09  H4   single    0.970  0.020  1.090
 EEK  C16  H5   single    0.930  0.020  1.080
 EEK  N07  H6   single    0.860  0.020  1.020
 EEK  N11  H7   single    0.860  0.020  1.020
 EEK  O12  H8   single    0.850  0.020  0.980

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
 EEK  O13  C10  N11  124.32  3.000
 EEK  O13  C10  C09  122.12  3.000
 EEK  N11  C10  C09  113.54  3.000
 EEK  H1   C15  C16  119.09  3.000
 EEK  H1   C15  C06  120.14  3.000
 EEK  C16  C15  C06  120.77  3.000
 EEK  CL1  C02  C16  119.85  3.000
 EEK  CL1  C02  C03  121.23  3.000
 EEK  C16  C02  C03  118.92  3.000
 EEK  CL4  C03  C05  118.39  3.000
 EEK  CL4  C03  C02  120.31  3.000
 EEK  C05  C03  C02  121.29  3.000
 EEK  H2   C05  C06  121.32  3.000
 EEK  H2   C05  C03  119.10  3.000
 EEK  C06  C05  C03  119.58  3.000
 EEK  N07  C06  C05  124.05  3.000
 EEK  C05  C06  C15  119.05  3.000
 EEK  N07  C06  C15  116.90  3.000
 EEK  O14  C08  N07  124.55  3.000
 EEK  N07  C08  C09  114.19  3.000
 EEK  O14  C08  C09  121.25  3.000
 EEK  H4   C09  H3   106.77  3.000
 EEK  H4   C09  C08  107.72  3.000
 EEK  H3   C09  C08  112.30  3.000
 EEK  H4   C09  C10  112.53  3.000
 EEK  H3   C09  C10  108.20  3.000
 EEK  C08  C09  C10  109.36  3.000
 EEK  H5   C16  C02  119.84  3.000
 EEK  H5   C16  C15  119.77  3.000
 EEK  C02  C16  C15  120.39  3.000
 EEK  H6   N07  C08  116.26  3.000
 EEK  H6   N07  C06  114.73  3.000
 EEK  C08  N07  C06  128.99  3.000
 EEK  H7   N11  O12  115.14  3.000
 EEK  H7   N11  C10  122.79  3.000
 EEK  O12  N11  C10  120.08  3.000
 EEK  H8   O12  N11  106.36  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
 EEK  CONST_01  C03  C05  C06  C15    0.00   0.0  0
 EEK  CONST_02  C03  C02  C16  C15    0.00   0.0  0
 EEK  CONST_03  C06  C15  C16  C02    0.00   0.0  0
 EEK  CONST_04  C06  C05  C03  C02    0.00   0.0  0
 EEK  CONST_05  C16  C15  C06  C05    0.00   0.0  0
 EEK  CONST_06  C16  C02  C03  C05    0.00   0.0  0
 EEK  CONST_07  CL1  C02  C16  C15  180.00   0.0  0
 EEK  CONST_08  N07  C06  C05  C03  180.00   0.0  0
 EEK  CONST_09  CL1  C02  C03  C05  180.00   0.0  0
 EEK  CONST_10  CL4  C03  C05  C06  180.00   0.0  0
 EEK  CONST_11  N07  C06  C15  C16  180.00   0.0  0
 EEK  CONST_12  CL4  C03  C02  C16  180.00   0.0  0
 EEK  CONST_13  H2   C05  C06  C15  180.00   0.0  0
 EEK  CONST_14  H1   C15  C16  C02  180.00   0.0  0
 EEK  CONST_15  H5   C16  C02  C03  180.00   0.0  0
 EEK  CONST_16  C08  N07  C06  C15  180.00   0.0  0
 EEK  CONST_17  C08  N07  C06  C05    0.00   0.0  0
 EEK  CONST_18  H6   N07  C06  C15    0.00   0.0  0
 EEK  CONST_19  C09  C08  N07  C06  180.00   0.0  0
 EEK  CONST_20  O14  C08  N07  C06    0.00   0.0  0
 EEK  CONST_21  O12  N11  C10  C09  180.00   0.0  0
 EEK  CONST_22  O13  C10  N11  O12    0.00   0.0  0
 EEK  CONST_23  H7   N11  C10  C09    0.00   0.0  0
 EEK  Var_01    O14  C08  C09  C10  -41.81  30.0  3
 EEK  Var_02    N11  C10  C09  C08  120.22  30.0  1

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
 EEK  plan-1  C15  0.020
 EEK  plan-1  C02  0.020
 EEK  plan-1  C03  0.020
 EEK  plan-1  C05  0.020
 EEK  plan-1  C06  0.020
 EEK  plan-1  C16  0.020
 EEK  plan-1  N07  0.020
 EEK  plan-1  CL4  0.020
 EEK  plan-1  H1   0.020
 EEK  plan-1  H2   0.020
 EEK  plan-1  H5   0.020
 EEK  plan-1  CL1  0.020
 EEK  plan-2  C10  0.020
 EEK  plan-2  C09  0.020
 EEK  plan-2  N11  0.020
 EEK  plan-2  O12  0.020
 EEK  plan-2  O13  0.020
 EEK  plan-2  H7   0.020
 EEK  plan-3  C06  0.020
 EEK  plan-3  C08  0.020
 EEK  plan-3  C09  0.020
 EEK  plan-3  N07  0.020
 EEK  plan-3  O14  0.020
 EEK  plan-3  H6   0.020

