# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:39:15 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  18  9  .  2022-03-29  2022-03-29
;
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  -0.811  -1.0667  -1.9760   0.3848
 XPC  CB   C  CR15   0  -0.076  -0.9331  -0.6885  -0.2694
 XPC  CG   C  CH2    0  -0.301  -2.1939   0.1673  -0.1848
 XPC  ND   N  NR15   0  -0.602  -1.7632   1.5343  -0.4519
 XPC  CE   C  CH2    0  -0.275  -0.3937   1.6442   0.0805
 XPC  CA   C  CR15   0  -0.419   0.0831   0.2196   0.4249
 XPC  C    C  C      0   0.423   1.5558  -0.0857   0.1185
 XPC  O    O  O      0  -0.610   1.8555  -1.2902  -0.0409
 XPC  HN   H  HNH2   0   0.333  -1.6589  -2.5809  -0.1714
 XPC  HB   H  HCR5   0   0.183  -0.6567  -0.7771  -1.3339
 XPC  HG   H  HCH2   0   0.228  -2.9828  -0.1330  -0.8779
 XPC  HGA  H  HCH2   0   0.198  -2.6020   0.0898   0.8302
 XPC  HND  H  HNR5   0   0.341  -1.7266   1.6613  -1.4542
 XPC  HE   H  HCH2   0   0.217   0.2574   2.1180  -0.6544
 XPC  HEA  H  HCH2   0   0.204  -0.3790   2.2833   0.9674
 XPC  HA   H  HCR5   0   0.232  -0.0504   0.0546   1.5040
 XPC  HNA  H  HNH2   0   0.339  -0.1492  -2.4054   0.3881
 XPC  OXT  O  OC    -1  -0.606   2.3487   0.8757   0.0845

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  1.450  0.020  1.450
 XPC  CB   CG   single  1.526  0.020  1.526
 XPC  CG   HGA  single  0.970  0.020  1.090
 XPC  ND   CG   single  1.458  0.020  1.458
 XPC  ND   HND  single  0.890  0.020  1.040
 XPC  CE   ND   single  1.473  0.020  1.473
 XPC  CE   HE   single  0.970  0.020  1.090
 XPC  CE   CA   single  1.541  0.020  1.541
 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  deloc   1.247  0.020  1.247
 XPC  O    C    deloc   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

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  106.15  3.000
 XPC  HNA  N   CB  107.11  3.000
 XPC  HN   N   CB  109.65  3.000
 XPC  HB   CB  CA  108.62  3.000
 XPC  HB   CB  CG  107.78  3.000
 XPC  CA   CB  CG  101.00  3.000
 XPC  HB   CB  N   112.77  3.000
 XPC  CA   CB  N   110.40  1.500
 XPC  CG   CB  N   113.37  3.000
 XPC  HGA  CG  HG  107.40  3.000
 XPC  HG   CG  ND  110.79  3.000
 XPC  HGA  CG  ND  110.22  3.000
 XPC  HG   CG  CB  114.04  3.000
 XPC  ND   CG  CB  105.76  3.000
 XPC  HGA  CG  CB  108.61  3.000
 XPC  HND  ND  CE  108.37  3.000
 XPC  CE   ND  CG  106.16  3.000
 XPC  HND  ND  CG  108.07  3.000
 XPC  HEA  CE  HE  106.54  3.000
 XPC  HEA  CE  CA  110.78  3.000
 XPC  HE   CE  CA  111.57  3.000
 XPC  HEA  CE  ND  110.44  3.000
 XPC  CA   CE  ND  107.42  3.000
 XPC  HE   CE  ND  110.12  3.000
 XPC  HA   CA  C   110.00  3.000
 XPC  C    CA  CE  115.85  3.000
 XPC  HA   CA  CE  108.69  3.000
 XPC  C    CA  CB  110.50  1.500
 XPC  HA   CA  CB  109.00  3.000
 XPC  CE   CA  CB  103.99  3.000
 XPC  OXT  C   O   125.90  3.000
 XPC  O    C   CA  120.80  1.700
 XPC  OXT  C   CA  117.54  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  Var_01  CE  ND  CG  CB  -32.27  30.0  1
 XPC  Var_02  CA  CE  ND  CG   11.02  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

