# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:56:38 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (2~{S})-3-(1~{H}-imidazol-3-ium-5-yl)-2-pyrrolidin-1-ium-1-yl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1[nH]c[nH+]c1)[NH+]2CCCC2
#
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
 AVO  AVO  '(2~{S})-3-(1~{H}-imidazol-3-ium-5-yl)-2-pyrrolidin-1-ium-1-yl-propanoic acid'  ligand  32  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AVO
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
 AVO  CAG  C  CH2   0  -0.339  -1.9943  -1.1268   0.8981
 AVO  CAE  C  CH2   0  -0.473  -3.1713  -1.6298   0.0802
 AVO  CAF  C  CH2   0  -0.477  -3.5984  -0.4413  -0.8015
 AVO  CAH  C  CH2   0  -0.325  -2.5860   0.6633  -0.5247
 AVO  N    N  N     1  -0.548  -1.3881  -0.0520   0.0436
 AVO  CA   C  CH1   0  -0.211  -0.4400   0.8439   0.7560
 AVO  C    C  C     0   0.553   0.2002   1.7802  -0.2575
 AVO  OXT  O  OH1   0  -0.564   0.7498   2.8106   0.3424
 AVO  O    O  O     0  -0.404   0.2453   1.5416  -1.4347
 AVO  CB   C  CH2   0  -0.582   0.6586   0.0730   1.5099
 AVO  CG   C  CR5   0   0.288   1.6014  -0.6578   0.6207
 AVO  CD2  C  CR15  0  -0.099   1.5578  -1.9158   0.1106
 AVO  NE2  N  NR15  1  -0.536   2.6645  -2.0643  -0.6779
 AVO  CE1  C  CR15  0   0.262   3.3770  -0.9547  -0.6630
 AVO  ND1  N  NR15  0  -0.583   2.7490  -0.0908   0.1148
 AVO  HE4  H  HCH2  0   0.316  -2.3061  -0.6499   1.8266
 AVO  HAG  H  HCH2  0   0.308  -1.2572  -1.8920   1.1216
 AVO  HAE  H  HCH2  0   0.275  -2.8686  -2.4769  -0.5336
 AVO  HE2  H  HCH2  0   0.285  -3.9651  -1.9699   0.7410
 AVO  HE3  H  HCH2  0   0.276  -3.5875  -0.7173  -1.8538
 AVO  HAF  H  HCH2  0   0.282  -4.5992  -0.0894  -0.5624
 AVO  HAH  H  HCH2  0   0.319  -2.2928   1.2260  -1.4045
 AVO  HE5  H  HCH2  0   0.309  -2.9310   1.3495   0.2474
 AVO  H    H  H     0   0.461  -0.8959  -0.4961  -0.7390
 AVO  HA   H  HCH1  0   0.372  -1.0228   1.4086   1.4860
 AVO  H1   H  HOH1  0   0.505   1.2119   3.3817  -0.2930
 AVO  HB2  H  HCH2  0   0.350   1.2011   0.7944   2.1221
 AVO  HB1  H  HCH2  0   0.339   0.2025  -0.6196   2.2160
 AVO  HD2  H  HCR5  0   0.342   0.8510  -2.7142   0.2553
 AVO  H2   H  HNR5  0   0.470   2.9108  -2.8977  -1.1952
 AVO  HE1  H  HCR5  0   0.369   4.3045  -0.7843  -1.1812
 AVO  HD1  H  HNR5  0   0.462   3.1058   0.8313   0.3298

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
 AVO  O    C    double    1.202  0.020  1.202
 AVO  C    OXT  single    1.313  0.020  1.313
 AVO  C    CA   single    1.521  0.020  1.521
 AVO  NE2  CD2  aromatic  1.367  0.020  1.367
 AVO  NE2  CE1  aromatic  1.319  0.020  1.319
 AVO  CD2  CG   aromatic  1.358  0.020  1.358
 AVO  CAH  CAF  single    1.524  0.020  1.524
 AVO  CAH  N    single    1.507  0.020  1.507
 AVO  CE1  ND1  aromatic  1.321  0.020  1.321
 AVO  CA   N    single    1.486  0.020  1.486
 AVO  CA   CB   single    1.539  0.020  1.539
 AVO  CG   ND1  aromatic  1.376  0.020  1.376
 AVO  CG   CB   single    1.488  0.020  1.488
 AVO  CAF  CAE  single    1.540  0.020  1.540
 AVO  N    CAG  single    1.501  0.020  1.501
 AVO  CAG  CAE  single    1.519  0.020  1.519
 AVO  CAG  HE4  single    0.970  0.020  1.090
 AVO  CAG  HAG  single    0.970  0.020  1.090
 AVO  CAE  HAE  single    0.970  0.020  1.090
 AVO  CAE  HE2  single    0.970  0.020  1.090
 AVO  CAF  HE3  single    0.970  0.020  1.090
 AVO  CAF  HAF  single    0.970  0.020  1.090
 AVO  CAH  HAH  single    0.970  0.020  1.090
 AVO  CAH  HE5  single    0.970  0.020  1.090
 AVO  N    H    single    0.860  0.020  1.020
 AVO  CA   HA   single    0.970  0.020  1.090
 AVO  OXT  H1   single    0.850  0.020  0.980
 AVO  CB   HB2  single    0.970  0.020  1.090
 AVO  CB   HB1  single    0.970  0.020  1.090
 AVO  CD2  HD2  single    0.930  0.020  1.080
 AVO  NE2  H2   single    0.860  0.020  1.020
 AVO  CE1  HE1  single    0.930  0.020  1.080
 AVO  ND1  HD1  single    0.860  0.020  1.020

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
 AVO  HAG  CAG  HE4  109.11  3.000
 AVO  HAG  CAG  N    110.35  3.000
 AVO  HE4  CAG  N    106.70  3.000
 AVO  HAG  CAG  CAE  113.80  3.000
 AVO  HE4  CAG  CAE  112.46  3.000
 AVO  N    CAG  CAE  104.09  3.000
 AVO  HE2  CAE  HAE  107.58  3.000
 AVO  HE2  CAE  CAF  112.76  3.000
 AVO  HAE  CAE  CAF  110.77  3.000
 AVO  HE2  CAE  CAG  110.00  3.000
 AVO  HAE  CAE  CAG  110.23  3.000
 AVO  CAF  CAE  CAG  105.52  3.000
 AVO  HAF  CAF  HE3  107.69  3.000
 AVO  HAF  CAF  CAH  109.69  3.000
 AVO  HE3  CAF  CAH  110.67  3.000
 AVO  HAF  CAF  CAE  112.28  3.000
 AVO  HE3  CAF  CAE  110.81  3.000
 AVO  CAH  CAF  CAE  105.73  3.000
 AVO  HE5  CAH  HAH  109.50  3.000
 AVO  HE5  CAH  N    106.48  3.000
 AVO  HAH  CAH  N    109.71  3.000
 AVO  HE5  CAH  CAF  112.03  3.000
 AVO  HAH  CAH  CAF  114.10  3.000
 AVO  N    CAH  CAF  104.63  3.000
 AVO  H    N    CA   108.70  3.000
 AVO  H    N    CAH  107.42  3.000
 AVO  CA   N    CAH  113.69  3.000
 AVO  H    N    CAG  108.55  3.000
 AVO  CA   N    CAG  114.61  3.000
 AVO  CAH  N    CAG  103.51  3.000
 AVO  HA   CA   CB   108.21  3.000
 AVO  HA   CA   C    110.60  3.000
 AVO  CB   CA   C    109.53  3.000
 AVO  HA   CA   N    106.97  3.000
 AVO  CB   CA   N    112.84  3.000
 AVO  C    CA   N    108.67  3.000
 AVO  O    C    OXT  125.99  3.000
 AVO  OXT  C    CA   110.78  3.000
 AVO  O    C    CA   123.10  3.000
 AVO  H1   OXT  C    111.20  3.000
 AVO  HB1  CB   HB2  105.37  3.000
 AVO  HB1  CB   CG   109.90  3.000
 AVO  HB2  CB   CG   110.19  3.000
 AVO  HB1  CB   CA   109.70  3.000
 AVO  HB2  CB   CA   107.38  3.000
 AVO  CG   CB   CA   113.92  3.000
 AVO  ND1  CG   CD2  105.68  3.000
 AVO  ND1  CG   CB   123.07  3.000
 AVO  CD2  CG   CB   131.23  3.000
 AVO  HD2  CD2  NE2  121.93  3.000
 AVO  HD2  CD2  CG   131.13  3.000
 AVO  NE2  CD2  CG   106.93  3.000
 AVO  H2   NE2  CE1  124.59  3.000
 AVO  H2   NE2  CD2  125.57  3.000
 AVO  CE1  NE2  CD2  109.85  3.000
 AVO  HE1  CE1  ND1  126.13  3.000
 AVO  HE1  CE1  NE2  126.41  3.000
 AVO  ND1  CE1  NE2  107.46  3.000
 AVO  HD1  ND1  CE1  123.60  3.000
 AVO  HD1  ND1  CG   126.25  3.000
 AVO  CE1  ND1  CG   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
 AVO  CONST_01  CE1  NE2  CD2  CG     0.00   0.0  0
 AVO  CONST_02  NE2  CE1  ND1  CG     0.00   0.0  0
 AVO  CONST_03  ND1  CE1  NE2  CD2    0.00   0.0  0
 AVO  CONST_04  CE1  ND1  CG   CD2    0.00   0.0  0
 AVO  CONST_05  ND1  CG   CD2  NE2    0.00   0.0  0
 AVO  CONST_06  NE2  CD2  CG   CB   180.00   0.0  0
 AVO  CONST_07  CE1  ND1  CG   CB   180.00   0.0  0
 AVO  CONST_08  H2   NE2  CD2  CG   180.00   0.0  0
 AVO  CONST_09  HE1  CE1  ND1  CG   180.00   0.0  0
 AVO  CONST_10  HD1  ND1  CG   CD2  180.00   0.0  0
 AVO  CONST_11  HD2  CD2  NE2  CE1  180.00   0.0  0
 AVO  CONST_12  H1   OXT  C    CA   180.00   0.0  0
 AVO  Var_01    CAH  CAF  CAE  CAG    3.92  30.0  1
 AVO  Var_02    N    CAH  CAF  CAE   20.68  30.0  1
 AVO  Var_03    N    CAG  CAE  CAF  -27.14  30.0  1
 AVO  Var_04    CD2  CG   CB   CA   -89.14  30.0  2

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
 AVO  chir_01  N   CAH  CA  CAG  negativ
 AVO  chir_02  CA  N    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
 AVO  plan-1  CB   0.020
 AVO  plan-1  CG   0.020
 AVO  plan-1  CD2  0.020
 AVO  plan-1  NE2  0.020
 AVO  plan-1  CE1  0.020
 AVO  plan-1  ND1  0.020
 AVO  plan-1  HD2  0.020
 AVO  plan-1  H2   0.020
 AVO  plan-1  HE1  0.020
 AVO  plan-1  HD1  0.020
 AVO  plan-2  CA   0.020
 AVO  plan-2  C    0.020
 AVO  plan-2  OXT  0.020
 AVO  plan-2  O    0.020
 AVO  plan-2  H1   0.020

