# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 09:15:14 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: (3S,4R)-4-aminopyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CNC[C@@H]1C(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
 XPC  XPC  '(3S,4R)-4-aminopyrrolidine-3-carboxylic acid'  peptide  19  9  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XPC
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
 XPC  N    N  NH2   0  -0.802  -1.0756  -1.9459   0.6014
 XPC  CB   C  CH1   0  -0.098  -0.8638  -0.7737  -0.2318
 XPC  CG   C  CH2   0  -0.266  -2.1356   0.0904  -0.3549
 XPC  ND   N  NH1   0  -0.612  -1.7541   1.4228   0.1073
 XPC  CE   C  CH2   0  -0.263  -0.3230   1.5556  -0.0875
 XPC  CA   C  CH1   0  -0.402   0.1617   0.1854   0.3790
 XPC  C    C  C     0   0.561   1.5884  -0.1448   0.0488
 XPC  O    O  O     0  -0.442   1.9731  -1.2097  -0.3694
 XPC  HN   H  HNH2  0   0.347  -1.7752  -2.5388   0.1707
 XPC  HB   H  HCH1  0   0.223  -0.5259  -1.0336  -1.2436
 XPC  HG   H  HCH2  0   0.212  -2.4876   0.0843  -1.3924
 XPC  HGA  H  HCH2  0   0.216  -2.9406  -0.3174   0.2629
 XPC  HND  H  HNH1  0   0.352  -2.2695   2.1496  -0.3694
 XPC  HE   H  HCH2  0   0.206  -0.0306   1.7243  -1.1351
 XPC  HEA  H  HCH2  0   0.241   0.0829   2.3755   0.5061
 XPC  HA   H  HCH1  0   0.294   0.0669   0.1410   1.4718
 XPC  HNA  H  HNH2  0   0.343  -0.2281  -2.5011   0.6092
 XPC  OXT  O  OH1   0  -0.593   2.4067   0.8706   0.3000
 XPC  HXT  H  HOH1  0   0.481   3.3215   0.6170   0.1045

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
 XPC  N    HN   single  0.890  0.020  1.040
 XPC  N    HNA  single  0.890  0.020  1.040
 XPC  CB   N    single  1.454  0.020  1.454
 XPC  CB   CG   single  1.542  0.020  1.542
 XPC  CG   HGA  single  0.970  0.020  1.090
 XPC  ND   CG   single  1.461  0.020  1.461
 XPC  ND   HND  single  0.890  0.020  1.040
 XPC  CE   ND   single  1.450  0.020  1.450
 XPC  CE   HE   single  0.970  0.020  1.090
 XPC  CE   CA   single  1.526  0.020  1.526
 XPC  CA   CB   single  1.521  0.033  1.521
 XPC  CA   HA   single  0.970  0.020  0.970
 XPC  C    CA   single  1.525  0.021  1.525
 XPC  C    OXT  single  1.328  0.020  1.328
 XPC  O    C    double  1.231  0.020  1.231
 XPC  HB   CB   single  0.970  0.020  1.090
 XPC  HG   CG   single  0.970  0.020  1.090
 XPC  HEA  CE   single  0.970  0.020  1.090
 XPC  OXT  HXT  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
 XPC  HNA  N    HN  105.08  3.000
 XPC  HNA  N    CB  108.93  3.000
 XPC  HN   N    CB  109.20  3.000
 XPC  HB   CB   CA  108.04  3.000
 XPC  HB   CB   CG  108.23  3.000
 XPC  CA   CB   CG  103.48  3.000
 XPC  HB   CB   N   112.47  3.000
 XPC  CA   CB   N   110.40  1.500
 XPC  CG   CB   N   112.17  3.000
 XPC  HGA  CG   HG  107.24  3.000
 XPC  HG   CG   ND  112.86  3.000
 XPC  HGA  CG   ND  110.71  3.000
 XPC  HG   CG   CB  109.72  3.000
 XPC  ND   CG   CB  105.69  3.000
 XPC  HGA  CG   CB  110.66  3.000
 XPC  HND  ND   CE  111.97  3.000
 XPC  CE   ND   CG  107.37  3.000
 XPC  HND  ND   CG  111.94  3.000
 XPC  HEA  CE   HE  107.70  3.000
 XPC  HEA  CE   CA  112.97  3.000
 XPC  HE   CE   CA  110.13  3.000
 XPC  HEA  CE   ND  111.28  3.000
 XPC  CA   CE   ND  100.96  3.000
 XPC  HE   CE   ND  113.83  3.000
 XPC  HA   CA   C   110.00  3.000
 XPC  C    CA   CE  115.60  3.000
 XPC  HA   CA   CE  108.25  3.000
 XPC  C    CA   CB  110.50  1.500
 XPC  HA   CA   CB  109.00  3.000
 XPC  CE   CA   CB  103.16  3.000
 XPC  OXT  C    O   122.94  3.000
 XPC  O    C    CA  120.80  1.700
 XPC  OXT  C    CA  120.80  1.700
 XPC  HXT  OXT  C   110.08  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
 XPC  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 XPC  Var_01    CE   ND   CG  CB   25.07  30.0  1
 XPC  Var_02    CA   CE   ND  CG  -42.05  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
 XPC  chir_01  CB  N   CG  CA  negativ
 XPC  chir_02  CA  CE  CB  C   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
 XPC  plan-1  CA   0.020
 XPC  plan-1  C    0.020
 XPC  plan-1  O    0.020
 XPC  plan-1  OXT  0.020
 XPC  plan-1  HXT  0.020

