# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:32:39 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 5-iodopyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: IC1=CNC(=O)NC1=O
#
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
 IUR  IUR  5-iodopyrimidine-2,4(1H,3H)-dione  ligand  12  9  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IUR
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
 IUR  N1  N  NR16  0  -0.666   1.3708  -0.0082   2.3531
 IUR  C2  C  CR6   0   0.696   0.2512  -0.0021   3.1453
 IUR  O2  O  O     0  -0.466   0.2950  -0.0109   4.3553
 IUR  N3  N  NR16  0  -0.717  -0.9228   0.0149   2.4352
 IUR  C4  C  CR6   0   0.613  -1.0905   0.0292   1.0597
 IUR  O4  O  O     0  -0.438  -2.1985   0.0450   0.5671
 IUR  C5  C  CR6   0  -0.465   0.1627   0.0222   0.3281
 IUR  C6  C  CR16  0   0.114   1.3301   0.0035   0.9985
 IUR  I5  I  I     0   0.112   0.0781   0.0409  -1.7470
 IUR  H1  H  HNR6  0   0.446   2.2671  -0.0224   2.8184
 IUR  H3  H  HNR6  0   0.434  -1.7697   0.0204   2.9910
 IUR  H6  H  HCR6  0   0.338   2.2932  -0.0030   0.5089

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
 IUR  N1  C2  single  1.372  0.020  1.372
 IUR  N1  C6  single  1.355  0.020  1.355
 IUR  N1  H1  single  0.860  0.020  1.020
 IUR  C2  O2  double  1.211  0.020  1.211
 IUR  C2  N3  single  1.372  0.020  1.372
 IUR  N3  C4  single  1.386  0.020  1.386
 IUR  N3  H3  single  0.860  0.020  1.020
 IUR  C4  O4  double  1.213  0.020  1.213
 IUR  C4  C5  single  1.451  0.020  1.451
 IUR  C5  C6  double  1.346  0.020  1.346
 IUR  C5  I5  single  2.077  0.020  2.077
 IUR  C6  H6  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
 IUR  H1  N1  C6  119.16  3.000
 IUR  H1  N1  C2  117.28  3.000
 IUR  C6  N1  C2  123.55  3.000
 IUR  N3  C2  O2  123.24  3.000
 IUR  N3  C2  N1  113.55  3.000
 IUR  O2  C2  N1  123.20  3.000
 IUR  H3  N3  C4  116.32  3.000
 IUR  H3  N3  C2  115.56  3.000
 IUR  C4  N3  C2  128.12  3.000
 IUR  C5  C4  O4  125.75  3.000
 IUR  C5  C4  N3  113.32  3.000
 IUR  O4  C4  N3  120.93  3.000
 IUR  I5  C5  C6  122.20  3.000
 IUR  I5  C5  C4  117.94  3.000
 IUR  C6  C5  C4  119.86  3.000
 IUR  H6  C6  C5  123.18  3.000
 IUR  H6  C6  N1  115.22  3.000
 IUR  C5  C6  N1  121.59  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
 IUR  CONST_01  C4  N3  C2  N1    0.00  0.0  0
 IUR  CONST_02  C5  C4  N3  C2    0.00  0.0  0
 IUR  CONST_03  C6  N1  C2  N3    0.00  0.0  0
 IUR  CONST_04  O4  C4  N3  C2  180.00  0.0  0
 IUR  CONST_05  C6  N1  C2  O2  180.00  0.0  0
 IUR  CONST_06  C4  N3  C2  O2  180.00  0.0  0
 IUR  CONST_07  H3  N3  C2  N1  180.00  0.0  0
 IUR  CONST_08  H1  N1  C2  N3  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
 IUR  plan-1  N1  0.020
 IUR  plan-1  C2  0.020
 IUR  plan-1  O2  0.020
 IUR  plan-1  N3  0.020
 IUR  plan-1  C4  0.020
 IUR  plan-1  O4  0.020
 IUR  plan-1  C5  0.020
 IUR  plan-1  C6  0.020
 IUR  plan-1  I5  0.020
 IUR  plan-1  H1  0.020
 IUR  plan-1  H3  0.020
 IUR  plan-1  H6  0.020

