# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:03:24 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2R,4R)-4-aminopyrrolidine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CN[C@H](C1)C(O)=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
 52A  52A  '(2R,4R)-4-aminopyrrolidine-2,4-dicarboxylic acid'  ligand  22  12  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_52A
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
 52A  N     N  NH2   0  -0.788  -0.6518  -4.4418   1.3721
 52A  CA    C  CT    0  -0.042  -1.6946  -3.4848   1.0816
 52A  C     C  C     0   0.555  -3.0767  -4.0814   0.8379
 52A  O     O  O     0  -0.437  -3.9235  -3.5770   0.1400
 52A  OXT   O  OH1   0  -0.591  -3.2797  -5.2003   1.5207
 52A  CB1   C  CH2   0  -0.470  -1.3102  -2.5601  -0.0778
 52A  CB2   C  CH2   0  -0.314  -1.8321  -2.4511   2.2286
 52A  CG1   C  CH1   0  -0.212  -1.9597  -1.1909   0.2698
 52A  NG2   N  NH1   0  -0.577  -2.4109  -1.2609   1.6479
 52A  CD    C  C     0   0.539  -0.9452  -0.0862   0.0737
 52A  OE1   O  O     0  -0.434  -0.4139   0.5441   0.9501
 52A  OE2   O  OH1   0  -0.598  -0.6803   0.0885  -1.2185
 52A  HN1   H  HNH2  0   0.354  -0.5453  -5.1033   0.6128
 52A  HN2   H  HNH2  0   0.354  -0.8764  -4.9854   2.1955
 52A  HOXT  H  HOH1  0   0.482  -4.1859  -5.5130   1.3799
 52A  HB11  H  HCH2  0   0.270  -1.6248  -2.9244  -1.0544
 52A  HB12  H  HCH2  0   0.266  -0.2204  -2.4968  -0.0868
 52A  HB21  H  HCH2  0   0.260  -2.4226  -2.8020   3.0766
 52A  HB22  H  HCH2  0   0.248  -0.8182  -2.2561   2.5926
 52A  HG1   H  HCH1  0   0.290  -2.8027  -0.9942  -0.3957
 52A  HNG2  H  HNH1  0   0.364  -3.4187  -1.3095   1.6757
 52A  HOE2  H  HOH1  0   0.481   0.0008   0.7684  -1.3304

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
 52A  N    CA    single  1.445  0.020  1.445
 52A  CA   C     single  1.525  0.020  1.525
 52A  CA   CB1   single  1.532  0.020  1.532
 52A  CA   CB2   single  1.550  0.020  1.550
 52A  C    O     double  1.208  0.020  1.208
 52A  C    OXT   single  1.326  0.020  1.326
 52A  CB1  CG1   single  1.555  0.020  1.555
 52A  CB2  NG2   single  1.445  0.020  1.445
 52A  CG1  NG2   single  1.452  0.020  1.452
 52A  CG1  CD    single  1.513  0.020  1.513
 52A  CD   OE1   double  1.203  0.020  1.203
 52A  CD   OE2   single  1.331  0.020  1.331
 52A  N    HN1   single  0.890  0.020  1.040
 52A  N    HN2   single  0.890  0.020  1.040
 52A  OXT  HOXT  single  0.850  0.020  0.980
 52A  CB1  HB11  single  0.970  0.020  1.090
 52A  CB1  HB12  single  0.970  0.020  1.090
 52A  CB2  HB21  single  0.970  0.020  1.090
 52A  CB2  HB22  single  0.970  0.020  1.090
 52A  CG1  HG1   single  0.970  0.020  1.090
 52A  NG2  HNG2  single  0.890  0.020  1.040
 52A  OE2  HOE2  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
 52A  HN2   N    HN1   106.41  3.000
 52A  HN2   N    CA    111.05  3.000
 52A  HN1   N    CA    110.97  3.000
 52A  CB2   CA   CB1   100.35  3.000
 52A  CB2   CA   C     107.38  3.000
 52A  CB1   CA   C     110.03  3.000
 52A  CB2   CA   N     110.91  3.000
 52A  CB1   CA   N     111.77  3.000
 52A  C     CA   N     115.29  3.000
 52A  OXT   C    O     122.85  3.000
 52A  OXT   C    CA    112.73  3.000
 52A  O     C    CA    124.37  3.000
 52A  HOXT  OXT  C     109.91  3.000
 52A  HB12  CB1  HB11  107.48  3.000
 52A  HB12  CB1  CG1   111.58  3.000
 52A  HB11  CB1  CG1   112.00  3.000
 52A  HB12  CB1  CA    106.96  3.000
 52A  HB11  CB1  CA    113.85  3.000
 52A  CG1   CB1  CA    104.92  3.000
 52A  HB22  CB2  HB21  107.46  3.000
 52A  HB22  CB2  NG2   110.97  3.000
 52A  HB21  CB2  NG2   111.12  3.000
 52A  HB22  CB2  CA    106.42  3.000
 52A  HB21  CB2  CA    114.11  3.000
 52A  NG2   CB2  CA    106.70  3.000
 52A  HG1   CG1  CD    107.89  3.000
 52A  HG1   CG1  NG2   110.32  3.000
 52A  CD    CG1  NG2   111.51  3.000
 52A  HG1   CG1  CB1   110.17  3.000
 52A  CD    CG1  CB1   109.51  3.000
 52A  NG2   CG1  CB1   107.43  3.000
 52A  HNG2  NG2  CG1   109.81  3.000
 52A  HNG2  NG2  CB2   110.43  3.000
 52A  CG1   NG2  CB2   107.26  3.000
 52A  OE2   CD   OE1   123.41  3.000
 52A  OE2   CD   CG1   110.81  3.000
 52A  OE1   CD   CG1   125.76  3.000
 52A  HOE2  OE2  CD    110.13  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
 52A  CONST_01  HOXT  OXT  C    CA   180.00   0.0  0
 52A  CONST_02  HOE2  OE2  CD   CG1  180.00   0.0  0
 52A  Var_01    CG1   NG2  CB2  CA   -31.13  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
 52A  chir_01  CA   C    CB1  CB2  negativ
 52A  chir_02  CG1  NG2  CB1  CD   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
 52A  plan-1  CA    0.020
 52A  plan-1  C     0.020
 52A  plan-1  O     0.020
 52A  plan-1  OXT   0.020
 52A  plan-1  HOXT  0.020
 52A  plan-2  CG1   0.020
 52A  plan-2  CD    0.020
 52A  plan-2  OE1   0.020
 52A  plan-2  OE2   0.020
 52A  plan-2  HOE2  0.020

