# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:02:39 2022
#   Inital geometry file: a 37 line input string
#   Ligand name: 1-fluoranyl-4-iodanyl-benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(I)cc1
#
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
 Y8D  Y8D  1-fluoranyl-4-iodanyl-benzene  ligand  12  8  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y8D
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
 Y8D  C02  C  CR6   0   0.531  -38.0198  27.4626  -10.8078
 Y8D  C03  C  CR16  0  -0.398  -37.2231  26.4880  -10.2397
 Y8D  C04  C  CR16  0  -0.206  -37.0335  25.2943  -10.9215
 Y8D  C05  C  CR6   0  -0.232  -37.6446  25.1041  -12.1529
 Y8D  C07  C  CR16  0  -0.206  -38.4330  26.0971  -12.7181
 Y8D  C08  C  CR16  0  -0.399  -38.6243  27.2922  -12.0380
 Y8D  F01  F  F     0  -0.309  -38.2157  28.6058  -10.1388
 Y8D  I06  I  I     0   0.060  -37.3719  23.2882  -13.1742
 Y8D  H1   H  HCR6  0   0.290  -36.7555  26.6516   -9.2776
 Y8D  H2   H  HCR6  0   0.289  -36.4137  24.5274  -10.4781
 Y8D  H3   H  HCR6  0   0.289  -38.9064  25.9568  -13.6802
 Y8D  H4   H  HCR6  0   0.290  -39.2372  28.0744  -12.4667

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
 Y8D  I06  C05  single    2.101  0.020  2.101
 Y8D  C07  C05  aromatic  1.388  0.020  1.388
 Y8D  C07  C08  aromatic  1.388  0.020  1.388
 Y8D  C05  C04  aromatic  1.388  0.020  1.388
 Y8D  C08  C02  aromatic  1.381  0.020  1.381
 Y8D  C04  C03  aromatic  1.388  0.020  1.388
 Y8D  C02  C03  aromatic  1.381  0.020  1.381
 Y8D  C02  F01  single    1.339  0.020  1.339
 Y8D  C03  H1   single    0.930  0.020  1.080
 Y8D  C04  H2   single    0.930  0.020  1.080
 Y8D  C07  H3   single    0.930  0.020  1.080
 Y8D  C08  H4   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
 Y8D  F01  C02  C08  119.09  3.000
 Y8D  F01  C02  C03  118.78  3.000
 Y8D  C08  C02  C03  122.13  3.000
 Y8D  H1   C03  C04  120.52  3.000
 Y8D  H1   C03  C02  120.55  3.000
 Y8D  C04  C03  C02  118.93  3.000
 Y8D  H2   C04  C05  121.27  3.000
 Y8D  H2   C04  C03  119.14  3.000
 Y8D  C05  C04  C03  119.59  3.000
 Y8D  I06  C05  C07  119.60  3.000
 Y8D  C07  C05  C04  120.88  3.000
 Y8D  I06  C05  C04  119.51  3.000
 Y8D  H3   C07  C08  119.16  3.000
 Y8D  H3   C07  C05  121.20  3.000
 Y8D  C08  C07  C05  119.64  3.000
 Y8D  H4   C08  C07  120.41  3.000
 Y8D  H4   C08  C02  120.77  3.000
 Y8D  C07  C08  C02  118.83  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
 Y8D  CONST_01  C05  C07  C08  C02    0.00  0.0  0
 Y8D  CONST_02  C05  C04  C03  C02    0.00  0.0  0
 Y8D  CONST_03  C07  C05  C04  C03    0.00  0.0  0
 Y8D  CONST_04  C07  C08  C02  C03    0.00  0.0  0
 Y8D  CONST_05  C08  C07  C05  C04    0.00  0.0  0
 Y8D  CONST_06  C08  C02  C03  C04    0.00  0.0  0
 Y8D  CONST_07  I06  C05  C04  C03  180.00  0.0  0
 Y8D  CONST_08  F01  C02  C03  C04  180.00  0.0  0
 Y8D  CONST_09  F01  C02  C08  C07  180.00  0.0  0
 Y8D  CONST_10  I06  C05  C07  C08  180.00  0.0  0
 Y8D  CONST_11  H3   C07  C08  C02  180.00  0.0  0
 Y8D  CONST_12  H2   C04  C03  C02  180.00  0.0  0
 Y8D  CONST_13  H4   C08  C02  C03  180.00  0.0  0
 Y8D  CONST_14  H1   C03  C04  C05  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
 Y8D  plan-1  C02  0.020
 Y8D  plan-1  C03  0.020
 Y8D  plan-1  C04  0.020
 Y8D  plan-1  C05  0.020
 Y8D  plan-1  C07  0.020
 Y8D  plan-1  C08  0.020
 Y8D  plan-1  F01  0.020
 Y8D  plan-1  I06  0.020
 Y8D  plan-1  H1   0.020
 Y8D  plan-1  H2   0.020
 Y8D  plan-1  H3   0.020
 Y8D  plan-1  H4   0.020

