# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 16:10:37 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 2-[3,5,6-tris(chloranyl)pyridin-2-yl]oxyethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1nc(Cl)c(Cl)cc1Cl
#
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
 SBK  SBK  '2-[3,5,6-tris(chloranyl)pyridin-2-yl]oxyethanoic acid'  ligand  18  14  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SBK
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
 SBK  C01   C   CR16  0  -0.008  -1.5297  -1.4943   0.0011
 SBK  C02   C   CR6   0  -0.215  -0.1552  -1.4734  -0.0304
 SBK  C03   C   CR6   0   0.624   0.4882  -0.2265  -0.0395
 SBK  N04   N   N     0  -0.450  -0.1887   0.8972  -0.0233
 SBK  C05   C   CR6   0   0.193  -1.5033   0.8785   0.0065
 SBK  C06   C   CR6   0  -0.088  -2.2349  -0.2951   0.0208
 SBK  CL6   CL  CL    0  -0.078  -3.9487  -0.3033   0.0628
 SBK  CL5   CL  CL    0  -0.058  -2.2973   2.4033   0.0288
 SBK  O09   O   O2    0  -0.433   1.8114  -0.2123  -0.0640
 SBK  C10   C   CH2   0  -0.259   2.4537   1.0409  -0.0499
 SBK  C11   C   C     0   0.496   3.9388   0.7785   0.0197
 SBK  O12   O   OH1   0  -0.590   4.5997   1.9358  -0.0022
 SBK  O13   O   O     0  -0.369   4.4553  -0.2961   0.0917
 SBK  CL2   CL  CL    0  -0.056   0.7604  -2.9189  -0.0554
 SBK  H011  H   HCR6  0   0.295  -2.0611  -2.4354   0.0124
 SBK  H101  H   HCH2  0   0.268   2.2205   1.6253  -0.9449
 SBK  H102  H   HCH2  0   0.270   2.1525   1.6409   0.8142
 SBK  H1    H   HOH1  0   0.460   5.5460   1.7563   0.0752

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
 SBK  O13  C11   double    1.194  0.020  1.194
 SBK  C11  C10   single    1.510  0.020  1.510
 SBK  C11  O12   single    1.333  0.020  1.333
 SBK  C10  O09   single    1.408  0.020  1.408
 SBK  O09  C03   single    1.324  0.020  1.324
 SBK  N04  C03   aromatic  1.312  0.020  1.312
 SBK  N04  C05   aromatic  1.315  0.020  1.315
 SBK  C03  C02   aromatic  1.403  0.020  1.403
 SBK  CL5  C05   single    1.719  0.020  1.719
 SBK  C05  C06   aromatic  1.383  0.020  1.383
 SBK  CL2  C02   single    1.711  0.020  1.711
 SBK  C02  C01   aromatic  1.375  0.020  1.375
 SBK  C06  C01   aromatic  1.391  0.020  1.391
 SBK  C06  CL6   single    1.714  0.020  1.714
 SBK  C01  H011  single    0.930  0.020  1.080
 SBK  C10  H101  single    0.970  0.020  1.090
 SBK  C10  H102  single    0.970  0.020  1.090
 SBK  O12  H1    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
 SBK  H011  C01  C06   120.07  3.000
 SBK  H011  C01  C02   120.33  3.000
 SBK  C06   C01  C02   119.60  3.000
 SBK  CL2   C02  C03   120.35  3.000
 SBK  CL2   C02  C01   121.49  3.000
 SBK  C03   C02  C01   118.16  3.000
 SBK  O09   C03  N04   120.46  3.000
 SBK  N04   C03  C02   121.64  3.000
 SBK  O09   C03  C02   117.91  3.000
 SBK  C05   N04  C03   120.25  3.000
 SBK  CL5   C05  C06   120.54  3.000
 SBK  C06   C05  N04   122.76  3.000
 SBK  CL5   C05  N04   116.70  3.000
 SBK  CL6   C06  C05   122.22  3.000
 SBK  CL6   C06  C01   120.20  3.000
 SBK  C05   C06  C01   117.58  3.000
 SBK  C10   O09  C03   117.73  3.000
 SBK  H102  C10  H101  107.13  3.000
 SBK  H102  C10  C11   109.25  3.000
 SBK  H101  C10  C11   109.89  3.000
 SBK  H102  C10  O09   111.73  3.000
 SBK  H101  C10  O09   111.71  3.000
 SBK  C11   C10  O09   107.13  3.000
 SBK  O13   C11  O12   124.59  3.000
 SBK  O12   C11  C10   109.64  3.000
 SBK  O13   C11  C10   125.77  3.000
 SBK  H1    O12  C11   108.84  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
 SBK  CONST_01  N04   C03  C02  C01    0.00   0.0  0
 SBK  CONST_02  N04   C05  C06  C01    0.00   0.0  0
 SBK  CONST_03  C05   N04  C03  C02    0.00   0.0  0
 SBK  CONST_04  C05   C06  C01  C02    0.00   0.0  0
 SBK  CONST_05  C06   C05  N04  C03    0.00   0.0  0
 SBK  CONST_06  C06   C01  C02  C03    0.00   0.0  0
 SBK  CONST_07  O09   C03  C02  C01  180.00   0.0  0
 SBK  CONST_08  CL5   C05  C06  C01  180.00   0.0  0
 SBK  CONST_09  CL6   C06  C01  C02  180.00   0.0  0
 SBK  CONST_10  CL5   C05  N04  C03  180.00   0.0  0
 SBK  CONST_11  CL2   C02  C03  N04  180.00   0.0  0
 SBK  CONST_12  CL6   C06  C05  N04  180.00   0.0  0
 SBK  CONST_13  O09   C03  N04  C05  180.00   0.0  0
 SBK  CONST_14  CL2   C02  C01  C06  180.00   0.0  0
 SBK  CONST_15  H011  C01  C02  C03  180.00   0.0  0
 SBK  CONST_16  H1    O12  C11  C10  180.00   0.0  0
 SBK  Var_01    C11   C10  O09  C03  175.91  30.0  1
 SBK  Var_02    O13   C11  C10  O09   -2.15  30.0  2

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
 SBK  plan-1  C01   0.020
 SBK  plan-1  C02   0.020
 SBK  plan-1  C03   0.020
 SBK  plan-1  N04   0.020
 SBK  plan-1  C05   0.020
 SBK  plan-1  C06   0.020
 SBK  plan-1  CL6   0.020
 SBK  plan-1  CL5   0.020
 SBK  plan-1  O09   0.020
 SBK  plan-1  CL2   0.020
 SBK  plan-1  H011  0.020
 SBK  plan-2  C10   0.020
 SBK  plan-2  C11   0.020
 SBK  plan-2  O12   0.020
 SBK  plan-2  O13   0.020
 SBK  plan-2  H1    0.020

