# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 21:36:13 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: 2,3,5-tris(iodanyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(I)cc(I)c1I
#
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
 GE9  GE9  "2,3,5-tris(iodanyl)benzamide"
  ligand  16  12  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GE9
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
 GE9  C01  C  CR6   0  -0.242  125.9465  128.6559  187.2373
 GE9  C02  C  CR6   0  -0.188  124.9981  127.7316  187.6704
 GE9  C03  C  CR6   0   0.027  127.2653  128.5326  187.6740
 GE9  C04  C  CR16  0  -0.218  127.6245  127.5056  188.5372
 GE9  C05  C  CR6   0  -0.207  126.6719  126.5879  188.9475
 GE9  C06  C  CR16  0  -0.195  125.3595  126.6906  188.5205
 GE9  C07  C  C     0   0.438  128.3714  129.4339  187.1839
 GE9  I01  I  I     0   0.125  122.9802  127.8117  187.1021
 GE9  I02  I  I     0   0.102  127.2182  125.0294  190.2388
 GE9  I03  I  I     0   0.133  125.4299  130.2680  185.9995
 GE9  N01  N  NH2   0  -0.774  128.9072  130.2073  188.1321
 GE9  O01  O  O     0  -0.442  128.7390  129.3952  186.0245
 GE9  H1   H  HCR6  0   0.302  128.6503  127.4291  188.8730
 GE9  H2   H  HCR6  0   0.308  124.6177  125.9742  188.8443
 GE9  H3   H  HNH2  0   0.412  129.6764  130.8219  187.9145
 GE9  H4   H  HNH2  0   0.420  128.5384  130.2363  189.0677

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
 GE9  I03  C01  single    2.097  0.020  2.097
 GE9  O01  C07  double    1.217  0.020  1.217
 GE9  I01  C02  single    2.098  0.020  2.098
 GE9  C01  C02  aromatic  1.393  0.020  1.393
 GE9  C01  C03  aromatic  1.395  0.020  1.395
 GE9  C07  C03  single    1.509  0.020  1.509
 GE9  C07  N01  single    1.336  0.020  1.336
 GE9  C02  C06  aromatic  1.392  0.020  1.392
 GE9  C03  C04  aromatic  1.389  0.020  1.389
 GE9  C06  C05  aromatic  1.384  0.020  1.384
 GE9  C04  C05  aromatic  1.385  0.020  1.385
 GE9  C05  I02  single    2.096  0.020  2.096
 GE9  C04  H1   single    0.930  0.020  1.080
 GE9  C06  H2   single    0.930  0.020  1.080
 GE9  N01  H3   single    0.860  0.020  1.020
 GE9  N01  H4   single    0.860  0.020  1.020

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
 GE9  I03  C01  C03  119.06  3.000
 GE9  C03  C01  C02  119.19  3.000
 GE9  I03  C01  C02  121.71  3.000
 GE9  I01  C02  C06  116.35  3.000
 GE9  C06  C02  C01  120.61  3.000
 GE9  I01  C02  C01  123.04  3.000
 GE9  C07  C03  C04  117.01  3.000
 GE9  C04  C03  C01  120.30  3.000
 GE9  C07  C03  C01  122.60  3.000
 GE9  H1   C04  C05  120.88  3.000
 GE9  H1   C04  C03  119.36  3.000
 GE9  C05  C04  C03  119.75  3.000
 GE9  I02  C05  C06  119.50  3.000
 GE9  I02  C05  C04  119.73  3.000
 GE9  C06  C05  C04  120.77  3.000
 GE9  H2   C06  C05  120.61  3.000
 GE9  H2   C06  C02  120.03  3.000
 GE9  C05  C06  C02  119.36  3.000
 GE9  O01  C07  N01  125.00  3.000
 GE9  N01  C07  C03  114.17  3.000
 GE9  O01  C07  C03  120.80  3.000
 GE9  H4   N01  H3   117.56  3.000
 GE9  H4   N01  C07  121.99  3.000
 GE9  H3   N01  C07  120.38  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
 GE9  CONST_01  C05  C06  C02  C01    0.00   0.0  0
 GE9  CONST_02  C05  C04  C03  C01    0.00   0.0  0
 GE9  CONST_03  C04  C03  C01  C02    0.00   0.0  0
 GE9  CONST_04  C04  C05  C06  C02    0.00   0.0  0
 GE9  CONST_05  C06  C02  C01  C03    0.00   0.0  0
 GE9  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 GE9  CONST_07  C07  C03  C01  C02  180.00   0.0  0
 GE9  CONST_08  I02  C05  C06  C02  180.00   0.0  0
 GE9  CONST_09  I01  C02  C01  C03  180.00   0.0  0
 GE9  CONST_10  I02  C05  C04  C03  180.00   0.0  0
 GE9  CONST_11  I03  C01  C03  C04  180.00   0.0  0
 GE9  CONST_12  I01  C02  C06  C05  180.00   0.0  0
 GE9  CONST_13  C07  C03  C04  C05  180.00   0.0  0
 GE9  CONST_14  I03  C01  C02  C06  180.00   0.0  0
 GE9  CONST_15  H2   C06  C02  C01  180.00   0.0  0
 GE9  CONST_16  H1   C04  C03  C01  180.00   0.0  0
 GE9  CONST_17  H2   C06  C05  C04  180.00   0.0  0
 GE9  CONST_18  H1   C04  C05  C06  180.00   0.0  0
 GE9  CONST_19  H3   N01  C07  C03  180.00   0.0  0
 GE9  CONST_20  H4   N01  C07  C03    0.00   0.0  0
 GE9  CONST_21  H3   N01  C07  O01    0.00   0.0  0
 GE9  CONST_22  H4   N01  C07  O01  180.00   0.0  0
 GE9  Var_01    O01  C07  C03  C01  -66.76  30.0  2
 GE9  Var_02    N01  C07  C03  C01  115.41  30.0  2
 GE9  Var_03    O01  C07  C03  C04  109.70  30.0  2
 GE9  Var_04    N01  C07  C03  C04  -68.13  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
 GE9  plan-1  C01  0.020
 GE9  plan-1  C02  0.020
 GE9  plan-1  C03  0.020
 GE9  plan-1  C04  0.020
 GE9  plan-1  C05  0.020
 GE9  plan-1  C06  0.020
 GE9  plan-1  C07  0.020
 GE9  plan-1  I01  0.020
 GE9  plan-1  I02  0.020
 GE9  plan-1  I03  0.020
 GE9  plan-1  H1   0.020
 GE9  plan-1  H2   0.020
 GE9  plan-2  C03  0.020
 GE9  plan-2  C07  0.020
 GE9  plan-2  N01  0.020
 GE9  plan-2  O01  0.020
 GE9  plan-2  H3   0.020
 GE9  plan-2  H4   0.020

