# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:33:11 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2,6-dichlorophenoxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1c(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
 KNL  KNL  '(2,6-dichlorophenoxy)acetic acid'  ligand  19  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KNL
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
 KNL  CL1  CL  CL    0  -0.086  -0.4568  -2.6759   0.2112
 KNL  O1   O   OH1   0  -0.590   3.8611   0.0021  -1.0569
 KNL  O2   O   O2    0  -0.458   0.6946   0.0043   0.4914
 KNL  CL2  CL  CL    0  -0.086  -0.4584   2.6825   0.1996
 KNL  O3   O   O     0  -0.424   3.2650   0.0061   1.1012
 KNL  C1   C   C     0   0.506   2.9834   0.0041  -0.0658
 KNL  C2   C   CH2   0  -0.271   1.5776   0.0026  -0.6109
 KNL  C3   C   CR16  0  -0.276  -3.3465   0.0011  -0.3915
 KNL  C4   C   CR16  0  -0.217  -2.6739  -1.2031  -0.2510
 KNL  C5   C   CR6   0  -0.137  -1.3159  -1.1917   0.0220
 KNL  C6   C   CR6   0   0.485  -0.6168   0.0033   0.1715
 KNL  C7   C   CR6   0  -0.137  -1.3167   1.1969   0.0166
 KNL  C8   C   CR16  0  -0.217  -2.6747   1.2063  -0.2568
 KNL  H1   H   HOH1  0   0.490   4.7652   0.0028  -0.7070
 KNL  H2   H   HCH2  0   0.277   1.4378  -0.8815  -1.2429
 KNL  H3   H   HCH2  0   0.277   1.4367   0.8841  -1.2464
 KNL  H4   H   HCR6  0   0.282  -4.4071   0.0000  -0.6011
 KNL  H5   H   HCR6  0   0.290  -3.1981  -2.1426  -0.3580
 KNL  H6   H   HCR6  0   0.290  -3.1988   2.1452  -0.3686

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
 KNL  CL1  C5  single    1.725  0.020  1.725
 KNL  O1   C1  single    1.324  0.020  1.324
 KNL  O1   H1  single    0.850  0.020  0.980
 KNL  O2   C2  single    1.412  0.020  1.412
 KNL  O2   C6  single    1.350  0.020  1.350
 KNL  CL2  C7  single    1.725  0.020  1.725
 KNL  O3   C1  double    1.201  0.020  1.201
 KNL  C1   C2  single    1.508  0.020  1.508
 KNL  C2   H2  single    0.970  0.020  1.090
 KNL  C2   H3  single    0.970  0.020  1.090
 KNL  C3   C4  aromatic  1.386  0.020  1.386
 KNL  C3   C8  aromatic  1.386  0.020  1.386
 KNL  C3   H4  single    0.930  0.020  1.080
 KNL  C4   C5  aromatic  1.385  0.020  1.385
 KNL  C4   H5  single    0.930  0.020  1.080
 KNL  C5   C6  aromatic  1.393  0.020  1.393
 KNL  C6   C7  aromatic  1.392  0.020  1.392
 KNL  C7   C8  aromatic  1.385  0.020  1.385
 KNL  C8   H6  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
 KNL  H1  O1  C1   110.37  3.000
 KNL  C6  O2  C2   114.99  3.000
 KNL  C2  C1  O3   124.76  3.000
 KNL  C2  C1  O1   110.33  3.000
 KNL  O3  C1  O1   124.90  3.000
 KNL  H3  C2  H2   107.35  3.000
 KNL  H3  C2  C1   109.19  3.000
 KNL  H2  C2  C1   109.16  3.000
 KNL  H3  C2  O2   111.79  3.000
 KNL  H2  C2  O2   111.80  3.000
 KNL  C1  C2  O2   107.50  3.000
 KNL  H4  C3  C8   119.67  3.000
 KNL  H4  C3  C4   119.65  3.000
 KNL  C8  C3  C4   120.68  3.000
 KNL  H5  C4  C5   120.13  3.000
 KNL  H5  C4  C3   120.64  3.000
 KNL  C5  C4  C3   119.23  3.000
 KNL  C6  C5  C4   121.36  3.000
 KNL  C6  C5  CL1  118.45  3.000
 KNL  C4  C5  CL1  120.18  3.000
 KNL  C7  C6  C5   118.12  3.000
 KNL  C7  C6  O2   120.94  3.000
 KNL  C5  C6  O2   120.92  3.000
 KNL  C8  C7  C6   121.37  3.000
 KNL  C8  C7  CL2  120.18  3.000
 KNL  C6  C7  CL2  118.44  3.000
 KNL  H6  C8  C7   120.10  3.000
 KNL  H6  C8  C3   120.67  3.000
 KNL  C7  C8  C3   119.23  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
 KNL  CONST_01  C6  C5  C4  C3     0.00   0.0  0
 KNL  CONST_02  C6  C7  C8  C3     0.00   0.0  0
 KNL  CONST_03  C7  C8  C3  C4     0.00   0.0  0
 KNL  CONST_04  C7  C6  C5  C4     0.00   0.0  0
 KNL  CONST_05  C8  C3  C4  C5     0.00   0.0  0
 KNL  CONST_06  C8  C7  C6  C5     0.00   0.0  0
 KNL  CONST_07  C3  C4  C5  CL1  180.00   0.0  0
 KNL  CONST_08  C7  C6  C5  CL1  180.00   0.0  0
 KNL  CONST_09  C4  C5  C6  O2   180.00   0.0  0
 KNL  CONST_10  C8  C7  C6  O2   180.00   0.0  0
 KNL  CONST_11  C5  C6  C7  CL2  180.00   0.0  0
 KNL  CONST_12  C3  C8  C7  CL2  180.00   0.0  0
 KNL  CONST_13  H6  C8  C3  C4   180.00   0.0  0
 KNL  CONST_14  H4  C3  C4  C5   180.00   0.0  0
 KNL  CONST_15  H5  C4  C5  C6   180.00   0.0  0
 KNL  CONST_16  H1  O1  C1  O3     0.00   0.0  0
 KNL  Var_01    C5  C6  O2  C2    90.88  30.0  2
 KNL  Var_02    H2  C2  O2  C6   -60.21  30.0  3
 KNL  Var_03    O2  C2  C1  O1   179.98  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
 KNL  plan-1  CL1  0.020
 KNL  plan-1  O2   0.020
 KNL  plan-1  CL2  0.020
 KNL  plan-1  C3   0.020
 KNL  plan-1  C4   0.020
 KNL  plan-1  C5   0.020
 KNL  plan-1  C6   0.020
 KNL  plan-1  C7   0.020
 KNL  plan-1  C8   0.020
 KNL  plan-1  H4   0.020
 KNL  plan-1  H5   0.020
 KNL  plan-1  H6   0.020
 KNL  plan-2  O1   0.020
 KNL  plan-2  O3   0.020
 KNL  plan-2  C1   0.020
 KNL  plan-2  C2   0.020
 KNL  plan-2  H1   0.020

