# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:03:40 2021
#   Inital geometry file: a 42 line input string
#   Ligand name: pyrazolidine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)N1CCCN1
#
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
 ZPO  ZPO  'pyrazolidine-1-carboxylic acid'  peptide  16  8  .  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_ZPO
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
 ZPO  N    N  NR15  0  -0.460  -4.7478  3.5472  -7.3716
 ZPO  CB   C  CH2   0  -0.384  -5.3174  3.7158  -5.0715
 ZPO  CG   C  CH2   0  -0.516  -6.5685  3.3686  -5.8665
 ZPO  O    O  O     0  -0.363  -3.1990  5.7617  -7.1654
 ZPO  CD   C  CH2   0  -0.305  -5.9733  2.7674  -7.1297
 ZPO  NA   N  NR5   0  -0.267  -4.4026  4.1310  -6.1263
 ZPO  H    H  HNR5  0   0.361  -4.0003  2.9115  -7.6239
 ZPO  HB3  H  HCH2  0   0.255  -4.9268  2.8427  -4.5414
 ZPO  HB2  H  HCH2  0   0.257  -5.4783  4.5102  -4.3495
 ZPO  HG2  H  HCH2  0   0.269  -7.1254  4.2792  -6.0935
 ZPO  HG3  H  HCH2  0   0.253  -7.2301  2.6790  -5.3460
 ZPO  HD2  H  HCH2  0   0.227  -6.6438  2.8398  -7.9860
 ZPO  HD3  H  HCH2  0   0.255  -5.7529  1.7084  -6.9698
 ZPO  OXT  O  OH1   0  -0.671  -3.5667  5.8202  -4.9504
 ZPO  HXT  H  HOH1  0   0.447  -3.0431  6.6285  -5.0232
 ZPO  C    C  C     0   0.641  -3.7009  5.2856  -6.1679

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
 ZPO  N    CD   single  1.473  0.014  1.473
 ZPO  N    NA   single  1.418  0.020  1.418
 ZPO  CD   CG   single  1.520  0.020  1.520
 ZPO  O    C    double  1.231  0.020  1.231
 ZPO  NA   C    single  1.352  0.020  1.352
 ZPO  NA   CB   single  1.457  0.020  1.457
 ZPO  CG   CB   single  1.522  0.020  1.522
 ZPO  N    H    single  0.860  0.020  1.020
 ZPO  CB   HB3  single  0.970  0.020  1.090
 ZPO  CB   HB2  single  0.970  0.020  1.090
 ZPO  CG   HG2  single  0.970  0.020  1.090
 ZPO  CG   HG3  single  0.970  0.020  1.090
 ZPO  CD   HD2  single  0.970  0.020  1.090
 ZPO  CD   HD3  single  0.970  0.020  1.090
 ZPO  C    OXT  single  1.336  0.020  1.336
 ZPO  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
 ZPO  H    N    NA   107.30  3.000
 ZPO  H    N    CD   108.82  3.000
 ZPO  NA   N    CD   106.04  3.000
 ZPO  HB2  CB   HB3  108.35  3.000
 ZPO  HB2  CB   NA   111.48  3.000
 ZPO  HB3  CB   NA   110.75  3.000
 ZPO  HB2  CB   CG   113.10  3.000
 ZPO  HB3  CB   CG   111.38  3.000
 ZPO  NA   CB   CG   101.71  3.000
 ZPO  HG3  CG   HG2  108.54  3.000
 ZPO  HG3  CG   CD   112.63  3.000
 ZPO  HG2  CG   CD   110.91  3.000
 ZPO  HG3  CG   CB   113.23  3.000
 ZPO  HG2  CG   CB   109.74  3.000
 ZPO  CD   CG   CB   101.67  3.000
 ZPO  HD3  CD   HD2  107.65  3.000
 ZPO  HD3  CD   CG   109.90  3.000
 ZPO  HD2  CD   CG   112.69  3.000
 ZPO  HD3  CD   N    111.66  3.000
 ZPO  HD2  CD   N    110.35  3.000
 ZPO  CG   CD   N    103.20  1.500
 ZPO  C    NA   CB   126.28  3.000
 ZPO  CB   NA   N    111.45  3.000
 ZPO  C    NA   N    116.81  3.000
 ZPO  HXT  OXT  C    108.69  3.000
 ZPO  OXT  C    NA   111.46  3.000
 ZPO  OXT  C    O    123.38  3.000
 ZPO  NA   C    O    125.09  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
 ZPO  CONST_01  HXT  OXT  C   NA  180.00   0.0  0
 ZPO  Var_01    CB   CG   CD  N   -35.64  30.0  1
 ZPO  Var_02    CD   N    NA  CB    2.56  30.0  1
 ZPO  Var_03    NA   N    CD  CG   21.17  30.0  1
 ZPO  Var_04    NA   CB   CG  CD   35.99  30.0  1
 ZPO  Var_05    O    C    NA  N   -10.16  30.0  2

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
 ZPO  plan-1  O    0.020
 ZPO  plan-1  NA   0.020
 ZPO  plan-1  OXT  0.020
 ZPO  plan-1  HXT  0.020
 ZPO  plan-1  C    0.020

