# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:35:21 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-(5-iodo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN1C=C(I)C(=O)NC1=O)C(O)=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
 IWD  IWD  3-(5-iodo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine  ligand  22  15  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IWD
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
 IWD  N1   N  N      0  -0.512  -0.7179  -0.5115   1.2541
 IWD  C2   C  C      0   0.738  -2.0235  -0.0672   1.2119
 IWD  O2   O  OC     0  -0.469  -2.7234   0.0197   2.1970
 IWD  N3   N  NC1    0  -0.731  -2.4735   0.2693  -0.0394
 IWD  C4   C  C      0   0.603  -1.7828   0.2475  -1.2378
 IWD  O4   O  OC     0  -0.442  -2.3125   0.5917  -2.2740
 IWD  C5   C  C      0  -0.480  -0.4217  -0.2187  -1.0888
 IWD  I5   I  I      0   0.107   0.7653  -0.3222  -2.7913
 IWD  C6   C  C1     0   0.102   0.0402  -0.5689   0.1284
 IWD  C7   C  CH2    0  -0.329  -0.1207  -0.8234   2.5532
 IWD  C8   C  CH1    0  -0.228   0.4360   0.4238   3.2609
 IWD  N8   N  NH2    0  -0.785   1.3774   1.1937   2.4807
 IWD  C9   C  C      0   0.412   1.0430  -0.0516   4.6056
 IWD  O91  O  O      0  -0.591   2.2590   0.1281   4.7847
 IWD  O92  O  OC    -1  -0.614   0.2389  -0.6038   5.3830
 IWD  H3   H  HNC1   0   0.432  -3.4333   0.5914  -0.0799
 IWD  H6   H  H      0   0.332   1.0490  -0.9297   0.2739
 IWD  H71  H  HCH2   0   0.268   0.6783  -1.5433   2.3677
 IWD  H72  H  HCH2   0   0.274  -0.8676  -1.3155   3.1692
 IWD  H8   H  HCH1   0   0.239  -0.4136   1.0743   3.4941
 IWD  H81  H  HNH2   0   0.335   2.2110   0.6552   2.2848
 IWD  H82  H  HNH2   0   0.341   0.9811   1.4836   1.5962

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
 IWD  N1  C2   aromatic  1.380  0.020  1.380
 IWD  N1  C6   aromatic  1.358  0.020  1.358
 IWD  N1  C7   single    1.463  0.020  1.463
 IWD  C2  O2   double    1.212  0.020  1.212
 IWD  C2  N3   aromatic  1.372  0.020  1.372
 IWD  N3  C4   aromatic  1.383  0.020  1.383
 IWD  N3  H3   single    0.860  0.020  1.020
 IWD  C4  O4   double    1.214  0.020  1.214
 IWD  C4  C5   aromatic  1.446  0.020  1.446
 IWD  C5  I5   single    2.078  0.020  2.078
 IWD  C5  C6   aromatic  1.348  0.020  1.348
 IWD  C6  H6   single    0.930  0.020  1.080
 IWD  C7  C8   single    1.538  0.020  1.538
 IWD  C7  H71  single    0.970  0.020  1.090
 IWD  C7  H72  single    0.970  0.020  1.090
 IWD  C8  N8   single    1.445  0.020  1.445
 IWD  C8  C9   single    1.550  0.020  1.550
 IWD  C8  H8   single    0.970  0.020  1.090
 IWD  N8  H81  single    0.890  0.020  1.040
 IWD  N8  H82  single    0.890  0.020  1.040
 IWD  C9  O91  deloc     1.242  0.020  1.242
 IWD  C9  O92  deloc     1.247  0.020  1.247

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
 IWD  C7   N1  C6   119.93  3.000
 IWD  C7   N1  C2   118.81  3.000
 IWD  C6   N1  C2   121.09  3.000
 IWD  N3   C2  O2   122.32  3.000
 IWD  N3   C2  N1   114.66  3.000
 IWD  O2   C2  N1   123.02  3.000
 IWD  H3   N3  C4   116.32  3.000
 IWD  H3   N3  C2   115.17  3.000
 IWD  C4   N3  C2   128.51  3.000
 IWD  C5   C4  O4   126.16  3.000
 IWD  C5   C4  N3   112.69  3.000
 IWD  O4   C4  N3   121.15  3.000
 IWD  C6   C5  I5   122.08  3.000
 IWD  C6   C5  C4   119.94  3.000
 IWD  I5   C5  C4   117.99  3.000
 IWD  H6   C6  C5   121.86  3.000
 IWD  H6   C6  N1   115.05  3.000
 IWD  C5   C6  N1   123.09  3.000
 IWD  H72  C7  H71  107.52  3.000
 IWD  H72  C7  C8   110.81  3.000
 IWD  H71  C7  C8   110.37  3.000
 IWD  H72  C7  N1   108.63  3.000
 IWD  H71  C7  N1   106.77  3.000
 IWD  C8   C7  N1   112.54  3.000
 IWD  H8   C8  C9   107.53  3.000
 IWD  H8   C8  N8   107.69  3.000
 IWD  C9   C8  N8   112.13  3.000
 IWD  H8   C8  C7   107.39  3.000
 IWD  C9   C8  C7   106.99  3.000
 IWD  N8   C8  C7   114.80  3.000
 IWD  H82  N8  H81  107.82  3.000
 IWD  H82  N8  C8   111.69  3.000
 IWD  H81  N8  C8   110.97  3.000
 IWD  O92  C9  O91  127.24  3.000
 IWD  O92  C9  C8   115.09  3.000
 IWD  O91  C9  C8   117.65  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
 IWD  CONST_01  C4  N3  C2  N1    0.00   0.0  0
 IWD  CONST_02  C4  C5  C6  N1    0.00   0.0  0
 IWD  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 IWD  CONST_04  C5  C4  N3  C2    0.00   0.0  0
 IWD  CONST_05  C6  N1  C2  N3    0.00   0.0  0
 IWD  CONST_06  C6  C5  C4  N3    0.00   0.0  0
 IWD  CONST_07  I5  C5  C6  N1  180.00   0.0  0
 IWD  CONST_08  O4  C4  N3  C2  180.00   0.0  0
 IWD  CONST_09  C6  N1  C2  O2  180.00   0.0  0
 IWD  CONST_10  C4  N3  C2  O2  180.00   0.0  0
 IWD  CONST_11  C7  N1  C2  N3  180.00   0.0  0
 IWD  CONST_12  I5  C5  C4  N3  180.00   0.0  0
 IWD  CONST_13  C6  C5  C4  O4  180.00   0.0  0
 IWD  CONST_14  C7  N1  C6  C5  180.00   0.0  0
 IWD  CONST_15  H3  N3  C2  N1  180.00   0.0  0
 IWD  CONST_16  H6  C6  N1  C2  180.00   0.0  0
 IWD  CONST_17  C7  N1  C2  O2    0.00   0.0  0
 IWD  Var_01    C8  C7  N1  C2  -83.67  30.0  2

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
 IWD  chir_01  C8  C7  N8  C9  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
 IWD  plan-1  N1   0.020
 IWD  plan-1  C2   0.020
 IWD  plan-1  O2   0.020
 IWD  plan-1  N3   0.020
 IWD  plan-1  C4   0.020
 IWD  plan-1  O4   0.020
 IWD  plan-1  C5   0.020
 IWD  plan-1  I5   0.020
 IWD  plan-1  C6   0.020
 IWD  plan-1  C7   0.020
 IWD  plan-1  H3   0.020
 IWD  plan-1  H6   0.020
 IWD  plan-2  C8   0.020
 IWD  plan-2  C9   0.020
 IWD  plan-2  O91  0.020
 IWD  plan-2  O92  0.020

