# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 09:47:49 2020
#   Inital geometry file: a 37 line input string
#   Ligand name: 1,2,3,4,5-pentachlorobenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)c(Cl)c(Cl)c1Cl
#
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
 5CL  5CL  1,2,3,4,5-pentachlorobenzene  ligand  12  11  .  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_5CL
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
 5CL  C1   C   CR6   0  -0.011   1.2265   1.1237  0.0438
 5CL  C2   C   CR16  0  -0.173   0.0277   1.8129  0.0396
 5CL  C3   C   CR6   0  -0.011  -1.1661   1.1150  0.0349
 5CL  C4   C   CR6   0   0.042  -1.1736  -0.2761  0.0341
 5CL  C5   C   CR6   0   0.040   0.0377  -0.9638  0.0381
 5CL  C6   C   CR6   0   0.042   1.2441  -0.2674  0.0435
 5CL  CL1  CL  CL    0  -0.044  -2.6508  -1.1336  0.0278
 5CL  CL2  CL  CL    0  -0.039   0.0440  -2.6725  0.0368
 5CL  CL3  CL  CL    0  -0.044   2.7273  -1.1141  0.0488
 5CL  CL4  CL  CL    0  -0.063  -2.6410   1.9891  0.0299
 5CL  CL5  CL  CL    0  -0.063   2.6951   2.0083  0.0502
 5CL  H2   H   HCR6  0   0.322   0.0239   2.8933  0.0396

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
 5CL  C1  C2   aromatic  1.383  0.020  1.383
 5CL  C1  C6   aromatic  1.391  0.020  1.391
 5CL  C1  CL5  single    1.714  0.020  1.714
 5CL  C2  C3   aromatic  1.383  0.020  1.383
 5CL  C2  H2   single    0.930  0.020  1.080
 5CL  C3  C4   aromatic  1.391  0.020  1.391
 5CL  C3  CL4  single    1.714  0.020  1.714
 5CL  C4  C5   aromatic  1.393  0.020  1.393
 5CL  C4  CL1  single    1.708  0.020  1.708
 5CL  C5  C6   aromatic  1.393  0.020  1.393
 5CL  C5  CL2  single    1.709  0.020  1.709
 5CL  C6  CL3  single    1.708  0.020  1.708

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
 5CL  CL5  C1  C6  120.34  3.000
 5CL  CL5  C1  C2  119.04  3.000
 5CL  C6   C1  C2  120.62  3.000
 5CL  H2   C2  C3  120.11  3.000
 5CL  H2   C2  C1  120.09  3.000
 5CL  C3   C2  C1  119.79  3.000
 5CL  CL4  C3  C4  120.34  3.000
 5CL  CL4  C3  C2  119.04  3.000
 5CL  C4   C3  C2  120.62  3.000
 5CL  CL1  C4  C5  120.28  3.000
 5CL  CL1  C4  C3  120.45  3.000
 5CL  C5   C4  C3  119.27  3.000
 5CL  CL2  C5  C6  119.79  3.000
 5CL  CL2  C5  C4  119.80  3.000
 5CL  C6   C5  C4  120.42  3.000
 5CL  CL3  C6  C5  120.28  3.000
 5CL  CL3  C6  C1  120.44  3.000
 5CL  C5   C6  C1  119.28  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
 5CL  CONST_01  C4   C3  C2  C1    0.00  0.0  0
 5CL  CONST_02  C4   C5  C6  C1    0.00  0.0  0
 5CL  CONST_03  C5   C6  C1  C2    0.00  0.0  0
 5CL  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 5CL  CONST_05  C6   C1  C2  C3    0.00  0.0  0
 5CL  CONST_06  C6   C5  C4  C3    0.00  0.0  0
 5CL  CONST_07  CL4  C3  C2  C1  180.00  0.0  0
 5CL  CONST_08  CL2  C5  C6  C1  180.00  0.0  0
 5CL  CONST_09  CL3  C6  C1  C2  180.00  0.0  0
 5CL  CONST_10  CL1  C4  C3  C2  180.00  0.0  0
 5CL  CONST_11  CL5  C1  C2  C3  180.00  0.0  0
 5CL  CONST_12  CL2  C5  C4  C3  180.00  0.0  0
 5CL  CONST_13  CL3  C6  C5  C4  180.00  0.0  0
 5CL  CONST_14  CL4  C3  C4  C5  180.00  0.0  0
 5CL  CONST_15  CL5  C1  C6  C5  180.00  0.0  0
 5CL  CONST_16  CL1  C4  C5  C6  180.00  0.0  0
 5CL  CONST_17  H2   C2  C3  C4  180.00  0.0  0

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
 5CL  plan-1  C1   0.020
 5CL  plan-1  C2   0.020
 5CL  plan-1  C3   0.020
 5CL  plan-1  C4   0.020
 5CL  plan-1  C5   0.020
 5CL  plan-1  C6   0.020
 5CL  plan-1  CL1  0.020
 5CL  plan-1  CL2  0.020
 5CL  plan-1  CL3  0.020
 5CL  plan-1  CL4  0.020
 5CL  plan-1  CL5  0.020
 5CL  plan-1  H2   0.020

