# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 09:44:22 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 3-[(4S)-2,5-dioxoimidazolidin-4-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@H]1NC(=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
 DI6  DI6  '3-[(4S)-2,5-dioxoimidazolidin-4-yl]propanoic acid'  ligand  19  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DI6
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
 DI6  N1   N  NR15   0  -0.699   2.7738  -0.2777  -0.3085
 DI6  C2   C  CR5    0   0.560   1.7880  -1.1301   0.0811
 DI6  O2   O  O      0  -0.437   1.7904  -2.3345  -0.0151
 DI6  C3   C  CR15   0  -0.201   0.6753  -0.2641   0.6476
 DI6  N4   N  NR15   0  -0.658   1.2153   1.0610   0.4514
 DI6  C5   C  CR5    0   0.670   2.4545   1.0598  -0.0746
 DI6  O5   O  O      0  -0.483   3.1771   2.0026  -0.3151
 DI6  C6   C  CH2    0  -0.406  -0.6588  -0.5109  -0.0490
 DI6  C7   C  CH2    0  -0.598  -1.7717   0.3548   0.5170
 DI6  C8   C  C      0   0.420  -3.1769   0.0623  -0.0449
 DI6  O9   O  O      0  -0.605  -3.3204  -0.9574  -0.7463
 DI6  O10  O  OC    -1  -0.627  -4.0664   0.8783   0.2717
 DI6  HN1  H  HNR5   0   0.426   3.6402  -0.5644  -0.7413
 DI6  H3   H  HCR5   0   0.299   0.5748  -0.4881   1.7166
 DI6  HN4  H  HNR5   0   0.415   0.8008   1.8978   0.8266
 DI6  H61  H  HCH2   0   0.231  -0.5414  -0.3344  -1.1216
 DI6  H62  H  HCH2   0   0.237  -0.9096  -1.5652   0.0754
 DI6  H71  H  HCH2   0   0.233  -1.8124   0.2291   1.6062
 DI6  H72  H  HCH2   0   0.224  -1.5572   1.4157   0.3554

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
 DI6  N1  C2   single  1.360  0.020  1.360
 DI6  N1  C5   single  1.395  0.020  1.395
 DI6  N1  HN1  single  0.860  0.020  1.020
 DI6  C2  O2   double  1.208  0.020  1.208
 DI6  C2  C3   single  1.520  0.020  1.520
 DI6  C3  N4   single  1.444  0.020  1.444
 DI6  C3  C6   single  1.525  0.020  1.525
 DI6  C3  H3   single  0.970  0.020  1.090
 DI6  N4  C5   single  1.346  0.020  1.346
 DI6  N4  HN4  single  0.860  0.020  1.020
 DI6  C5  O5   double  1.212  0.020  1.212
 DI6  C6  C7   single  1.519  0.020  1.519
 DI6  C6  H61  single  0.970  0.020  1.090
 DI6  C6  H62  single  0.970  0.020  1.090
 DI6  C7  C8   single  1.541  0.020  1.541
 DI6  C7  H71  single  0.970  0.020  1.090
 DI6  C7  H72  single  0.970  0.020  1.090
 DI6  C8  O9   deloc   1.246  0.020  1.246
 DI6  C8  O10  deloc   1.248  0.020  1.248

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
 DI6  HN1  N1  C5   122.71  3.000
 DI6  HN1  N1  C2   124.51  3.000
 DI6  C5   N1  C2   112.77  3.000
 DI6  C3   C2  O2   126.82  3.000
 DI6  C3   C2  N1   106.28  3.000
 DI6  O2   C2  N1   126.90  3.000
 DI6  H3   C3  C6   109.39  3.000
 DI6  H3   C3  N4   110.73  3.000
 DI6  C6   C3  N4   114.43  3.000
 DI6  H3   C3  C2   108.30  3.000
 DI6  C6   C3  C2   112.21  3.000
 DI6  N4   C3  C2   101.45  3.000
 DI6  HN4  N4  C5   121.71  3.000
 DI6  HN4  N4  C3   123.93  3.000
 DI6  C5   N4  C3   113.35  3.000
 DI6  O5   C5  N4   128.73  3.000
 DI6  O5   C5  N1   125.19  3.000
 DI6  N4   C5  N1   106.09  3.000
 DI6  H62  C6  H61  107.01  3.000
 DI6  H62  C6  C7   109.86  3.000
 DI6  H61  C6  C7   110.62  3.000
 DI6  H62  C6  C3   107.79  3.000
 DI6  H61  C6  C3   109.15  3.000
 DI6  C7   C6  C3   112.23  3.000
 DI6  H72  C7  H71  105.36  3.000
 DI6  H72  C7  C8   107.99  3.000
 DI6  H71  C7  C8   107.84  3.000
 DI6  H72  C7  C6   110.72  3.000
 DI6  H71  C7  C6   109.38  3.000
 DI6  C8   C7  C6   115.08  3.000
 DI6  O10  C8  O9   126.57  3.000
 DI6  O10  C8  C7   115.67  3.000
 DI6  O9   C8  C7   117.75  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
 DI6  CONST_01  C3   N4  C5  N1     0.00   0.0  0
 DI6  CONST_02  N4   C5  N1  C2     0.00   0.0  0
 DI6  CONST_03  C5   N1  C2  C3     0.00   0.0  0
 DI6  CONST_04  O5   C5  N1  C2   180.00   0.0  0
 DI6  CONST_05  C5   N1  C2  O2   180.00   0.0  0
 DI6  CONST_06  O5   C5  N4  C3   180.00   0.0  0
 DI6  CONST_07  HN4  N4  C5  N1   180.00   0.0  0
 DI6  CONST_08  HN1  N1  C2  C3   180.00   0.0  0
 DI6  Var_01    C8   C7  C6  C3  -174.34  30.0  3
 DI6  Var_02    O9   C8  C7  C6    10.18  30.0  3

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
 DI6  chir_01  C3  C2  N4  C6  negativ

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
 DI6  plan-1  N1   0.020
 DI6  plan-1  C2   0.020
 DI6  plan-1  O2   0.020
 DI6  plan-1  C3   0.020
 DI6  plan-1  N4   0.020
 DI6  plan-1  C5   0.020
 DI6  plan-1  O5   0.020
 DI6  plan-1  HN1  0.020
 DI6  plan-1  HN4  0.020
 DI6  plan-2  C7   0.020
 DI6  plan-2  C8   0.020
 DI6  plan-2  O9   0.020
 DI6  plan-2  O10  0.020

