# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 23:22:45 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: (5S)-5-iododihydropyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: I[C@H]1CNC(=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
 IDH  IDH  (5S)-5-iododihydropyrimidine-2,4(1H,3H)-dione  ligand  14  9  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IDH
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
 IDH  N1    N  NH1   0  -0.641  -1.3367   0.0854   2.4305
 IDH  C2    C  C     0   0.678  -0.1981  -0.0414   3.1308
 IDH  O2    O  O     0  -0.484  -0.1168  -0.0462   4.3430
 IDH  N3    N  NH1   0  -0.702   0.9509  -0.1616   2.3439
 IDH  C4    C  C     0   0.607   1.0784   0.1072   1.0084
 IDH  O4    O  O     0  -0.414   2.1453   0.0562   0.4463
 IDH  C5    C  CH1   0  -0.612  -0.2268   0.5070   0.3535
 IDH  C6    C  CH2   0  -0.258  -1.4011  -0.1903   1.0137
 IDH  I5    I  I     0   0.053  -0.1767   0.0947  -1.7555
 IDH  H1    H  HNH1  0   0.423  -2.1956   0.1437   2.9546
 IDH  H3    H  HNH1  0   0.426   1.8082  -0.3367   2.8533
 IDH  H5    H  HCH1  0   0.361  -0.3343   1.5917   0.4480
 IDH  H6C1  H  HCH2  0   0.296  -2.3399   0.2001   0.6308
 IDH  H6C2  H  HCH2  0   0.267  -1.3736  -1.2659   0.8147

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
 IDH  N1  C2    single  1.343  0.020  1.343
 IDH  N1  C6    single  1.445  0.020  1.445
 IDH  N1  H1    single  0.860  0.020  1.020
 IDH  C2  O2    double  1.215  0.020  1.215
 IDH  C2  N3    single  1.398  0.020  1.398
 IDH  N3  C4    single  1.368  0.020  1.368
 IDH  N3  H3    single  0.860  0.020  1.020
 IDH  C4  O4    double  1.207  0.020  1.207
 IDH  C4  C5    single  1.514  0.020  1.514
 IDH  C5  C6    single  1.517  0.020  1.517
 IDH  C5  I5    single  2.150  0.020  2.150
 IDH  C5  H5    single  0.970  0.020  1.090
 IDH  C6  H6C1  single  0.970  0.020  1.090
 IDH  C6  H6C2  single  0.970  0.020  1.090

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
 IDH  H1    N1  C6    118.88  3.000
 IDH  H1    N1  C2    117.18  3.000
 IDH  C6    N1  C2    122.09  3.000
 IDH  N3    C2  O2    120.42  3.000
 IDH  N3    C2  N1    114.30  3.000
 IDH  O2    C2  N1    125.28  3.000
 IDH  H3    N3  C4    116.50  3.000
 IDH  H3    N3  C2    115.32  3.000
 IDH  C4    N3  C2    127.53  3.000
 IDH  C5    C4  O4    124.87  3.000
 IDH  C5    C4  N3    113.19  3.000
 IDH  O4    C4  N3    121.92  3.000
 IDH  H5    C5  I5    106.09  3.000
 IDH  H5    C5  C6    110.01  3.000
 IDH  I5    C5  C6    110.91  3.000
 IDH  H5    C5  C4    108.01  3.000
 IDH  I5    C5  C4    110.71  3.000
 IDH  C6    C5  C4    110.96  3.000
 IDH  H6C2  C6  H6C1  108.11  3.000
 IDH  H6C2  C6  C5    110.69  3.000
 IDH  H6C1  C6  C5    110.51  3.000
 IDH  H6C2  C6  N1    111.40  3.000
 IDH  H6C1  C6  N1    108.39  3.000
 IDH  C5    C6  N1    107.73  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
 IDH  CONST_01  C4    N3  C2  N1     0.00   0.0  0
 IDH  CONST_02  C5    C4  N3  C2     0.00   0.0  0
 IDH  CONST_03  C6    N1  C2  N3     0.00   0.0  0
 IDH  CONST_04  O4    C4  N3  C2   180.00   0.0  0
 IDH  CONST_05  C6    N1  C2  O2   180.00   0.0  0
 IDH  CONST_07  H3    N3  C2  N1   180.00   0.0  0
 IDH  CONST_08  H1    N1  C2  N3   180.00   0.0  0
 IDH  Var_01    H6C1  C6  N1  C2  -166.85  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 IDH  chir_01  C5  C4  C6  I5  positiv

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
 IDH  plan-1  N1  0.020
 IDH  plan-1  C2  0.020
 IDH  plan-1  O2  0.020
 IDH  plan-1  N3  0.020
 IDH  plan-1  C4  0.020
 IDH  plan-1  O4  0.020
 IDH  plan-1  C5  0.020
 IDH  plan-1  C6  0.020
 IDH  plan-1  H1  0.020
 IDH  plan-1  H3  0.020

