# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:11:02 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: [(4R)-2,5-dioxoimidazolidin-4-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[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
 5HY  5HY  '[(4R)-2,5-dioxoimidazolidin-4-yl]acetic acid'  ligand  16  11  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5HY
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
 5HY  C     C  CR5    0   0.553   1.2636  -1.1915  -0.1029
 5HY  N     N  NR15   0  -0.646   0.5580   0.9772  -0.3326
 5HY  O     O  O      0  -0.442   1.3460  -2.3980  -0.0876
 5HY  CA    C  CR15   0  -0.198   0.0493  -0.3630  -0.4821
 5HY  CB    C  CH2    0  -0.589  -1.1485  -0.6661   0.4062
 5HY  CG    C  C      0   0.435  -2.3929   0.1851   0.0839
 5HY  OAB   O  O      0  -0.490   2.5110   1.9935   0.3583
 5HY  NAF   N  NR15   0  -0.699   2.2393  -0.3041   0.2308
 5HY  CAI   C  CR5    0   0.665   1.8244   1.0247   0.1084
 5HY  OD1   O  OC    -1  -0.611  -3.4192  -0.0937   0.7288
 5HY  OD2   O  O      0  -0.603  -2.2687   1.0786  -0.7788
 5HY  HN    H  HNR5   0   0.408  -0.0256   1.7858  -0.4707
 5HY  HA    H  HCR5   0   0.293  -0.2003  -0.5714  -1.5275
 5HY  HB    H  HCH2   0   0.252  -1.4012  -1.7256   0.3124
 5HY  HBA   H  HCH2   0   0.248  -0.8762  -0.5090   1.4553
 5HY  HNAF  H  HNR5   0   0.423   3.1655  -0.5609   0.5406

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
 5HY  O    C     double  1.209  0.020  1.209
 5HY  C    CA    single  1.518  0.020  1.518
 5HY  C    NAF   single  1.360  0.020  1.360
 5HY  CA   N     single  1.441  0.020  1.441
 5HY  N    CAI   single  1.342  0.020  1.342
 5HY  N    HN    single  0.860  0.020  1.020
 5HY  CA   CB    single  1.522  0.020  1.522
 5HY  CA   HA    single  0.970  0.020  1.090
 5HY  CB   CG    single  1.542  0.020  1.542
 5HY  CB   HB    single  0.970  0.020  1.090
 5HY  CB   HBA   single  0.970  0.020  1.090
 5HY  CG   OD2   deloc   1.248  0.020  1.248
 5HY  CG   OD1   deloc   1.244  0.020  1.244
 5HY  CAI  OAB   double  1.213  0.020  1.213
 5HY  NAF  CAI   single  1.397  0.020  1.397
 5HY  NAF  HNAF  single  0.860  0.020  1.020

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
 5HY  NAF   C    CA   106.20  3.000
 5HY  NAF   C    O    126.78  3.000
 5HY  CA    C    O    127.02  3.000
 5HY  HN    N    CAI  124.31  3.000
 5HY  HN    N    CA   121.87  3.000
 5HY  CAI   N    CA   113.59  3.000
 5HY  HA    CA   CB   109.88  3.000
 5HY  HA    CA   N    110.88  3.000
 5HY  CB    CA   N    113.74  3.000
 5HY  HA    CA   C    108.48  3.000
 5HY  CB    CA   C    112.03  3.000
 5HY  N     CA   C    101.49  3.000
 5HY  HBA   CB   HB   106.18  3.000
 5HY  HBA   CB   CG   108.77  3.000
 5HY  HB    CB   CG   109.31  3.000
 5HY  HBA   CB   CA   109.56  3.000
 5HY  HB    CB   CA   108.96  3.000
 5HY  CG    CB   CA   113.79  3.000
 5HY  OD2   CG   OD1  126.94  3.000
 5HY  OD1   CG   CB   115.71  3.000
 5HY  OD2   CG   CB   117.35  3.000
 5HY  HNAF  NAF  CAI  122.75  3.000
 5HY  HNAF  NAF  C    124.56  3.000
 5HY  CAI   NAF  C    112.69  3.000
 5HY  NAF   CAI  OAB  124.97  3.000
 5HY  NAF   CAI  N    105.98  3.000
 5HY  OAB   CAI  N    129.05  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
 5HY  CONST_01  N     CAI  NAF  C      0.00   0.0  0
 5HY  CONST_02  CAI   NAF  C    CA     0.00   0.0  0
 5HY  CONST_03  NAF   CAI  N    CA     0.00   0.0  0
 5HY  CONST_04  OAB   CAI  NAF  C    180.00   0.0  0
 5HY  CONST_05  CAI   NAF  C    O    180.00   0.0  0
 5HY  CONST_06  OAB   CAI  N    CA   180.00   0.0  0
 5HY  CONST_07  HNAF  NAF  CAI  N    180.00   0.0  0
 5HY  CONST_08  HN    N    CAI  NAF  180.00   0.0  0
 5HY  Var_01    OD2   CG   CB   CA    -5.04  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
 5HY  chir_01  CA  C  N  CB  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
 5HY  plan-1  C     0.020
 5HY  plan-1  N     0.020
 5HY  plan-1  O     0.020
 5HY  plan-1  CA    0.020
 5HY  plan-1  OAB   0.020
 5HY  plan-1  NAF   0.020
 5HY  plan-1  CAI   0.020
 5HY  plan-1  HN    0.020
 5HY  plan-1  HNAF  0.020
 5HY  plan-2  CB    0.020
 5HY  plan-2  CG    0.020
 5HY  plan-2  OD1   0.020
 5HY  plan-2  OD2   0.020

