# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 00:52:41 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: 1-iodo-3-methylbenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(I)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
 XQJ  XQJ  "1-iodo-3-methylbenzene"
  ligand  15  8  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XQJ
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
 XQJ  C01  C  CH3   0  -0.718  32.6706  -8.5104  0.9438
 XQJ  C02  C  CR6   0   0.103  33.0322  -8.2350  2.3740
 XQJ  C03  C  CR16  0  -0.293  32.6673  -9.1155  3.3896
 XQJ  C04  C  CR16  0  -0.231  33.0313  -8.8722  4.7054
 XQJ  C05  C  CR16  0  -0.246  33.7662  -7.7421  5.0399
 XQJ  C06  C  CR6   0  -0.201  34.1220  -6.8652  4.0267
 XQJ  C08  C  CR16  0  -0.268  33.7658  -7.0971  2.7067
 XQJ  I07  I  I     0   0.041  35.2241  -5.1337  4.5034
 XQJ  H1   H  HCH3  0   0.252  33.4377  -9.1204  0.4623
 XQJ  H2   H  HCH3  0   0.247  31.7298  -9.0545  0.8697
 XQJ  H3   H  HCH3  0   0.247  32.5797  -7.5897  0.3691
 XQJ  H4   H  HCR6  0   0.255  32.0894  -9.9994  3.1480
 XQJ  H5   H  HCR6  0   0.264  32.7406  -9.5649  5.4846
 XQJ  H6   H  HCR6  0   0.276  34.0445  -7.5590  6.0688
 XQJ  H7   H  HCR6  0   0.270  34.0484  -6.4015  1.9265

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
 XQJ  C01  C02  single    1.501  0.020  1.501
 XQJ  C02  C08  aromatic  1.394  0.020  1.394
 XQJ  C02  C03  aromatic  1.393  0.020  1.393
 XQJ  C08  C06  aromatic  1.387  0.020  1.387
 XQJ  C03  C04  aromatic  1.387  0.020  1.387
 XQJ  C06  I07  single    2.107  0.020  2.107
 XQJ  C06  C05  aromatic  1.386  0.020  1.386
 XQJ  C04  C05  aromatic  1.389  0.020  1.389
 XQJ  C01  H1   single    0.970  0.020  1.090
 XQJ  C01  H2   single    0.970  0.020  1.090
 XQJ  C01  H3   single    0.970  0.020  1.090
 XQJ  C03  H4   single    0.930  0.020  1.080
 XQJ  C04  H5   single    0.930  0.020  1.080
 XQJ  C05  H6   single    0.930  0.020  1.080
 XQJ  C08  H7   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
 XQJ  H3   C01  H2   108.31  3.000
 XQJ  H3   C01  H1   107.35  3.000
 XQJ  H2   C01  H1   107.32  3.000
 XQJ  H3   C01  C02  111.58  3.000
 XQJ  H2   C01  C02  111.38  3.000
 XQJ  H1   C01  C02  110.71  3.000
 XQJ  C08  C02  C03  118.68  3.000
 XQJ  C03  C02  C01  121.05  3.000
 XQJ  C08  C02  C01  120.26  3.000
 XQJ  H4   C03  C04  119.66  3.000
 XQJ  H4   C03  C02  119.53  3.000
 XQJ  C04  C03  C02  120.81  3.000
 XQJ  H5   C04  C05  119.31  3.000
 XQJ  H5   C04  C03  120.02  3.000
 XQJ  C05  C04  C03  120.67  3.000
 XQJ  H6   C05  C06  121.47  3.000
 XQJ  H6   C05  C04  120.20  3.000
 XQJ  C06  C05  C04  118.32  3.000
 XQJ  I07  C06  C08  119.15  3.000
 XQJ  I07  C06  C05  119.25  3.000
 XQJ  C08  C06  C05  121.60  3.000
 XQJ  H7   C08  C06  120.76  3.000
 XQJ  H7   C08  C02  119.32  3.000
 XQJ  C06  C08  C02  119.92  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
 XQJ  CONST_01  C05  C06  C08  C02     0.00   0.0  0
 XQJ  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 XQJ  CONST_03  C06  C08  C02  C03     0.00   0.0  0
 XQJ  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 XQJ  CONST_05  C08  C02  C03  C04     0.00   0.0  0
 XQJ  CONST_06  C08  C06  C05  C04     0.00   0.0  0
 XQJ  CONST_07  C06  C08  C02  C01   180.00   0.0  0
 XQJ  CONST_08  C04  C03  C02  C01   180.00   0.0  0
 XQJ  CONST_09  I07  C06  C08  C02   180.00   0.0  0
 XQJ  CONST_10  I07  C06  C05  C04   180.00   0.0  0
 XQJ  CONST_11  H5   C04  C03  C02   180.00   0.0  0
 XQJ  CONST_12  H7   C08  C02  C03   180.00   0.0  0
 XQJ  CONST_13  H6   C05  C04  C03   180.00   0.0  0
 XQJ  CONST_14  H7   C08  C06  C05   180.00   0.0  0
 XQJ  CONST_15  H4   C03  C04  C05   180.00   0.0  0
 XQJ  CONST_16  H5   C04  C05  C06   180.00   0.0  0
 XQJ  CONST_17  H4   C03  C02  C08   180.00   0.0  0
 XQJ  CONST_18  H6   C05  C06  C08   180.00   0.0  0
 XQJ  Var_01    H1   C01  C02  C03   -87.86  30.0  2
 XQJ  Var_02    H2   C01  C02  C03    31.47  30.0  2
 XQJ  Var_03    H3   C01  C02  C03   152.64  30.0  2
 XQJ  Var_04    H1   C01  C02  C08    90.94  30.0  2
 XQJ  Var_05    H2   C01  C02  C08  -149.73  30.0  2
 XQJ  Var_06    H3   C01  C02  C08   -28.56  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
 XQJ  plan-1  C01  0.020
 XQJ  plan-1  C02  0.020
 XQJ  plan-1  C03  0.020
 XQJ  plan-1  C04  0.020
 XQJ  plan-1  C05  0.020
 XQJ  plan-1  C06  0.020
 XQJ  plan-1  C08  0.020
 XQJ  plan-1  I07  0.020
 XQJ  plan-1  H4   0.020
 XQJ  plan-1  H5   0.020
 XQJ  plan-1  H6   0.020
 XQJ  plan-1  H7   0.020

