# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:18:57 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,3S)-1-aminocyclopentane-1,3-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CC[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
 C5A  C5A  '(1S,3S)-1-aminocyclopentane-1,3-dicarboxylic acid'  ligand  21  12  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C5A
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
 C5A  N     N  NH2    0  -0.820  5.6075  -1.1645   0.0259
 C5A  CA    C  CT     0  -0.007  4.2902  -0.9512   0.6261
 C5A  C     C  C      0   0.425  3.9440  -2.2667   1.3785
 C5A  O     O  O      0  -0.588  3.7126  -2.2221   2.6002
 C5A  OXT   O  OC    -1  -0.628  3.9375  -3.2977   0.6695
 C5A  CB1   C  CH2    0  -0.442  3.1663  -0.6097  -0.3829
 C5A  CB2   C  CH2    0  -0.410  4.2966   0.2758   1.5350
 C5A  CG2   C  CH2    0  -0.434  2.8265   0.6347   1.7025
 C5A  CD    C  CH1    0  -0.368  2.1938   0.3522   0.3255
 C5A  CE    C  C      0   0.409  0.7218  -0.0897   0.3937
 C5A  OZ1   O  O      0  -0.613  0.3109  -0.8963  -0.4663
 C5A  OZ2   O  OC    -1  -0.625  0.0278   0.4337   1.2923
 C5A  HN1   H  HNH2   0   0.321  5.7905  -0.4157  -0.6338
 C5A  HN2   H  HNH2   0   0.326  5.5712  -2.0132  -0.5265
 C5A  HB11  H  HCH2   0   0.218  2.6656  -1.5010  -0.7584
 C5A  HB12  H  HCH2   0   0.199  3.6204  -0.1223  -1.2526
 C5A  HB21  H  HCH2   0   0.190  4.8227   1.0907   1.0211
 C5A  HB22  H  HCH2   0   0.212  4.8104   0.0985   2.4810
 C5A  HG21  H  HCH2   0   0.215  2.3839  -0.0077   2.4635
 C5A  HG22  H  HCH2   0   0.200  2.6747   1.6661   2.0265
 C5A  HD    H  HCH1   0   0.221  2.1806   1.2948  -0.2373

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
 C5A  N    CA    single  1.463  0.020  1.463
 C5A  CA   C     single  1.554  0.020  1.554
 C5A  CA   CB1   single  1.548  0.020  1.548
 C5A  CA   CB2   single  1.527  0.020  1.527
 C5A  C    O     deloc   1.244  0.020  1.244
 C5A  C    OXT   deloc   1.251  0.020  1.251
 C5A  CB1  CD    single  1.540  0.020  1.540
 C5A  CB2  CG2   single  1.523  0.020  1.523
 C5A  CG2  CD    single  1.542  0.020  1.542
 C5A  CD   CE    single  1.538  0.020  1.538
 C5A  CE   OZ1   deloc   1.249  0.020  1.249
 C5A  CE   OZ2   deloc   1.250  0.020  1.250
 C5A  N    HN1   single  0.890  0.020  1.040
 C5A  N    HN2   single  0.890  0.020  1.040
 C5A  CB1  HB11  single  0.970  0.020  1.090
 C5A  CB1  HB12  single  0.970  0.020  1.090
 C5A  CB2  HB21  single  0.970  0.020  1.090
 C5A  CB2  HB22  single  0.970  0.020  1.090
 C5A  CG2  HG21  single  0.970  0.020  1.090
 C5A  CG2  HG22  single  0.970  0.020  1.090
 C5A  CD   HD    single  0.970  0.020  1.090

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
 C5A  HN2   N    HN1   105.67  3.000
 C5A  HN2   N    CA    108.27  3.000
 C5A  HN1   N    CA    108.76  3.000
 C5A  CB2   CA   CB1   102.33  3.000
 C5A  CB2   CA   C     113.13  3.000
 C5A  CB1   CA   C     109.90  3.000
 C5A  CB2   CA   N     110.94  3.000
 C5A  CB1   CA   N     114.73  3.000
 C5A  C     CA   N     106.01  3.000
 C5A  OXT   C    O     125.79  3.000
 C5A  OXT   C    CA    115.10  3.000
 C5A  O     C    CA    119.11  3.000
 C5A  HB12  CB1  HB11  106.31  3.000
 C5A  HB12  CB1  CD    110.42  3.000
 C5A  HB11  CB1  CD    112.30  3.000
 C5A  HB12  CB1  CA    108.33  3.000
 C5A  HB11  CB1  CA    112.20  3.000
 C5A  CD    CB1  CA    107.24  3.000
 C5A  HB22  CB2  HB21  107.51  3.000
 C5A  HB22  CB2  CG2   113.43  3.000
 C5A  HB21  CB2  CG2   109.84  3.000
 C5A  HB22  CB2  CA    112.80  3.000
 C5A  HB21  CB2  CA    108.66  3.000
 C5A  CG2   CB2  CA    104.53  3.000
 C5A  HG22  CG2  HG21  107.05  3.000
 C5A  HG22  CG2  CD    112.41  3.000
 C5A  HG21  CG2  CD    110.43  3.000
 C5A  HG22  CG2  CB2   112.93  3.000
 C5A  HG21  CG2  CB2   109.27  3.000
 C5A  CD    CG2  CB2   104.76  3.000
 C5A  HD    CD   CE    104.94  3.000
 C5A  HD    CD   CG2   107.79  3.000
 C5A  CE    CD   CG2   113.94  3.000
 C5A  HD    CD   CB1   107.94  3.000
 C5A  CE    CD   CB1   116.43  3.000
 C5A  CG2   CD   CB1   105.43  3.000
 C5A  OZ2   CE   OZ1   125.65  3.000
 C5A  OZ2   CE   CD    116.28  3.000
 C5A  OZ1   CE   CD    118.03  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
 C5A  Var_01  CD  CG2  CB2  CA  -37.30  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
 C5A  chir_01  CA  C   CB1  CB2  negativ
 C5A  chir_02  CD  CE  CG2  CB1  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
 C5A  plan-1  CA   0.020
 C5A  plan-1  C    0.020
 C5A  plan-1  O    0.020
 C5A  plan-1  OXT  0.020
 C5A  plan-2  CD   0.020
 C5A  plan-2  CE   0.020
 C5A  plan-2  OZ1  0.020
 C5A  plan-2  OZ2  0.020

