# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:19:52 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  20  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  -0.698   2.7493  -0.3129  -0.3078
 DI6  C2    C  CR5   0   0.564   1.7521  -1.1468   0.0898
 DI6  O2    O  O     0  -0.431   1.7377  -2.3518   0.0177
 DI6  C3    C  CR15  0  -0.207   0.6449  -0.2551   0.6307
 DI6  N4    N  NR15  0  -0.660   1.1877   1.0612   0.3915
 DI6  C5    C  CR5   0   0.673   2.4434   1.0315  -0.1037
 DI6  O5    O  O     0  -0.476   3.1822   1.9604  -0.3408
 DI6  C6    C  CH2   0  -0.421  -0.6830  -0.5246  -0.0664
 DI6  C7    C  CH2   0  -0.594  -1.7869   0.3668   0.4759
 DI6  C8    C  C     0   0.557  -3.1378   0.0477  -0.1042
 DI6  O9    O  O     0  -0.441  -3.3693  -0.8563  -0.8671
 DI6  O10   O  OH1   0  -0.595  -4.0689   0.8884   0.3324
 DI6  HN1   H  HNR5  0   0.429   3.6177  -0.6183  -0.7238
 DI6  H3    H  HCR5  0   0.311   0.5421  -0.4469   1.7054
 DI6  HN4   H  HNR5  0   0.418   0.8186   1.8984   0.8121
 DI6  H61   H  HCH2  0   0.256  -0.5655  -0.3760  -1.1420
 DI6  H62   H  HCH2  0   0.260  -0.9372  -1.5736   0.0931
 DI6  H71   H  HCH2  0   0.291  -1.8580   0.2736   1.5649
 DI6  H72   H  HCH2  0   0.284  -1.5785   1.4227   0.2815
 DI6  HO10  H  HOH1  0   0.481  -4.9303   0.6541  -0.0441

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  1.359  0.020  1.359
 DI6  N1   C5    single  1.394  0.020  1.394
 DI6  N1   HN1   single  0.860  0.020  1.020
 DI6  C2   O2    double  1.207  0.020  1.207
 DI6  C2   C3    single  1.521  0.020  1.521
 DI6  C3   N4    single  1.444  0.020  1.444
 DI6  C3   C6    single  1.524  0.020  1.524
 DI6  C3   H3    single  0.970  0.020  1.090
 DI6  N4   C5    single  1.350  0.020  1.350
 DI6  N4   HN4   single  0.860  0.020  1.020
 DI6  C5   O5    double  1.210  0.020  1.210
 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  1.504  0.020  1.504
 DI6  C7   H71   single  0.970  0.020  1.090
 DI6  C7   H72   single  0.970  0.020  1.090
 DI6  C8   O9    double  1.205  0.020  1.205
 DI6  C8   O10   single  1.328  0.020  1.328
 DI6  O10  HO10  single  0.850  0.020  0.980

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   122.72  3.000
 DI6  HN1   N1   C2   124.44  3.000
 DI6  C5    N1   C2   112.83  3.000
 DI6  C3    C2   O2   126.71  3.000
 DI6  C3    C2   N1   106.16  3.000
 DI6  O2    C2   N1   127.13  3.000
 DI6  H3    C3   C6   109.62  3.000
 DI6  H3    C3   N4   110.92  3.000
 DI6  C6    C3   N4   114.40  3.000
 DI6  H3    C3   C2   108.31  3.000
 DI6  C6    C3   C2   111.59  3.000
 DI6  N4    C3   C2   101.65  3.000
 DI6  HN4   N4   C5   120.82  3.000
 DI6  HN4   N4   C3   123.44  3.000
 DI6  C5    N4   C3   112.97  3.000
 DI6  O5    C5   N4   128.51  3.000
 DI6  O5    C5   N1   125.29  3.000
 DI6  N4    C5   N1   106.20  3.000
 DI6  H62   C6   H61  107.44  3.000
 DI6  H62   C6   C7   110.04  3.000
 DI6  H61   C6   C7   110.48  3.000
 DI6  H62   C6   C3   107.84  3.000
 DI6  H61   C6   C3   109.43  3.000
 DI6  C7    C6   C3   111.48  3.000
 DI6  H72   C7   H71  105.74  3.000
 DI6  H72   C7   C8   107.90  3.000
 DI6  H71   C7   C8   107.89  3.000
 DI6  H72   C7   C6   111.38  3.000
 DI6  H71   C7   C6   110.62  3.000
 DI6  C8    C7   C6   112.98  3.000
 DI6  O10   C8   O9   123.24  3.000
 DI6  O10   C8   C7   111.62  3.000
 DI6  O9    C8   C7   125.15  3.000
 DI6  HO10  O10  C8   110.02  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  CONST_09  HO10  O10  C8  C7   180.00   0.0  0
 DI6  Var_01    C8    C7   C6  C3  -175.04  30.0  3
 DI6  Var_02    O9    C8   C7  C6     3.69  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
 DI6  plan-2  HO10  0.020

