# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:19:14 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,3R)-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
 C5B  C5B  '(1S,3R)-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_C5B
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
 C5B  N     N  NH2    0  -0.817  -3.1218   4.0561  -2.4209
 C5B  CA    C  CT     0  -0.013  -2.5775   2.7205  -2.6389
 C5B  C     C  C      0   0.426  -3.6726   1.8761  -3.3400
 C5B  O     O  O      0  -0.625  -4.8029   1.9093  -2.8047
 C5B  OXT   O  OC    -1  -0.593  -3.3640   1.2213  -4.3531
 C5B  CB1   C  CH2    0  -0.440  -2.1250   1.9830  -1.3648
 C5B  CB2   C  CH2    0  -0.413  -1.2673   2.7797  -3.4253
 C5B  CG2   C  CH2    0  -0.420  -0.5329   1.4657  -3.1251
 C5B  CD    C  CH1    0  -0.360  -1.1880   0.8723  -1.8611
 C5B  CE    C  C      0   0.402  -0.2468   0.4079  -0.7384
 C5B  OZ1   O  O      0  -0.607   0.9396   0.7962  -0.7495
 C5B  OZ2   O  OC    -1  -0.634  -0.7702  -0.3111   0.1414
 C5B  HN1   H  HNH2   0   0.322  -2.5138   4.5638  -1.7873
 C5B  HN2   H  HNH2   0   0.326  -4.0128   3.9671  -1.9479
 C5B  HB11  H  HCH2   0   0.217  -2.9588   1.6142  -0.7643
 C5B  HB12  H  HCH2   0   0.203  -1.5647   2.6942  -0.7424
 C5B  HB21  H  HCH2   0   0.197  -0.6831   3.6249  -3.0440
 C5B  HB22  H  HCH2   0   0.210  -1.4221   2.9549  -4.4904
 C5B  HG21  H  HCH2   0   0.205  -0.6226   0.7722  -3.9609
 C5B  HG22  H  HCH2   0   0.205   0.5311   1.6334  -2.9595
 C5B  HD    H  HCH1   0   0.210  -1.8032   0.0134  -2.1457

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
 C5B  N    CA    single  1.459  0.020  1.459
 C5B  N    HN1   single  0.890  0.020  1.040
 C5B  N    HN2   single  0.890  0.020  1.040
 C5B  CA   C     single  1.550  0.020  1.550
 C5B  CA   CB1   single  1.540  0.020  1.540
 C5B  CA   CB2   single  1.529  0.020  1.529
 C5B  C    O     deloc   1.251  0.020  1.251
 C5B  C    OXT   deloc   1.245  0.020  1.245
 C5B  CB1  CD    single  1.536  0.020  1.536
 C5B  CB1  HB11  single  0.970  0.020  1.090
 C5B  CB1  HB12  single  0.970  0.020  1.090
 C5B  CB2  CG2   single  1.535  0.020  1.535
 C5B  CB2  HB21  single  0.970  0.020  1.090
 C5B  CB2  HB22  single  0.970  0.020  1.090
 C5B  CG2  CD    single  1.542  0.020  1.542
 C5B  CG2  HG21  single  0.970  0.020  1.090
 C5B  CG2  HG22  single  0.970  0.020  1.090
 C5B  CD   CE    single  1.537  0.020  1.537
 C5B  CD   HD    single  0.970  0.020  1.090
 C5B  CE   OZ1   deloc   1.248  0.020  1.248
 C5B  CE   OZ2   deloc   1.251  0.020  1.251

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
 C5B  HN2   N    HN1   106.23  3.000
 C5B  HN2   N    CA    108.52  3.000
 C5B  HN1   N    CA    109.15  3.000
 C5B  CB2   CA   CB1   101.08  3.000
 C5B  CB2   CA   C     113.19  3.000
 C5B  CB1   CA   C     108.71  3.000
 C5B  CB2   CA   N     111.16  3.000
 C5B  CB1   CA   N     115.11  3.000
 C5B  C     CA   N     107.62  3.000
 C5B  OXT   C    O     125.87  3.000
 C5B  OXT   C    CA    118.64  3.000
 C5B  O     C    CA    115.48  3.000
 C5B  HB12  CB1  HB11  107.25  3.000
 C5B  HB12  CB1  CD    109.88  3.000
 C5B  HB11  CB1  CD    113.54  3.000
 C5B  HB12  CB1  CA    107.97  3.000
 C5B  HB11  CB1  CA    113.11  3.000
 C5B  CD    CB1  CA    104.96  3.000
 C5B  HB22  CB2  HB21  106.96  3.000
 C5B  HB22  CB2  CG2   113.36  3.000
 C5B  HB21  CB2  CG2   109.70  3.000
 C5B  HB22  CB2  CA    112.76  3.000
 C5B  HB21  CB2  CA    107.91  3.000
 C5B  CG2   CB2  CA    106.03  3.000
 C5B  HG22  CG2  HG21  107.15  3.000
 C5B  HG22  CG2  CD    110.45  3.000
 C5B  HG21  CG2  CD    110.41  3.000
 C5B  HG22  CG2  CB2   111.41  3.000
 C5B  HG21  CG2  CB2   110.82  3.000
 C5B  CD    CG2  CB2   106.64  3.000
 C5B  HD    CD   CE    107.29  3.000
 C5B  HD    CD   CG2   109.13  3.000
 C5B  CE    CD   CG2   117.05  3.000
 C5B  HD    CD   CB1   107.99  3.000
 C5B  CE    CD   CB1   110.86  3.000
 C5B  CG2   CD   CB1   104.23  3.000
 C5B  OZ2   CE   OZ1   125.63  3.000
 C5B  OZ2   CE   CD    115.54  3.000
 C5B  OZ1   CE   CD    118.79  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
 C5B  Var_01  CD  CG2  CB2  CA  -17.27  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
 C5B  chir_01  CA  C   CB1  CB2  negativ
 C5B  chir_02  CD  CE  CG2  CB1  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
 C5B  plan-1  CA   0.020
 C5B  plan-1  C    0.020
 C5B  plan-1  O    0.020
 C5B  plan-1  OXT  0.020
 C5B  plan-2  CD   0.020
 C5B  plan-2  CE   0.020
 C5B  plan-2  OZ1  0.020
 C5B  plan-2  OZ2  0.020

