# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 16:41:31 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  31  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 OK
;

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  -0.325  -1.8939  -1.2025   0.6958
 AVO  CAE  C  CH2    0  -0.473  -3.1740  -1.6151  -0.0260
 AVO  CAF  C  CH2    0  -0.477  -3.6867  -0.3386  -0.7229
 AVO  CAH  C  CH2    0  -0.321  -2.7334   0.7609  -0.2845
 AVO  N    N  NT1    1  -0.539  -1.4526   0.0382  -0.0054
 AVO  CA   C  CH1    0  -0.214  -0.4305   0.9017   0.6563
 AVO  C    C  C      0   0.450   0.2726   1.7509  -0.4392
 AVO  OXT  O  OC    -1  -0.574   1.0890   2.5797  -0.0090
 AVO  O    O  O      0  -0.560  -0.0019   1.4638  -1.6148
 AVO  CB   C  CH2    0  -0.564   0.6142   0.1204   1.4586
 AVO  CG   C  CR5    0   0.299   1.5988  -0.6416   0.6438
 AVO  CD2  C  CR15   0  -0.110   1.7407  -1.9743   0.4241
 AVO  NE2  N  NR15   1  -0.541   2.8353  -2.1318  -0.3820
 AVO  CE1  C  CR15   0   0.252   3.3612  -0.9527  -0.6554
 AVO  ND1  N  NR15   0  -0.581   2.6285  -0.0406  -0.0433
 AVO  HE4  H  HCH2   0   0.300  -2.0813  -0.9364   1.7350
 AVO  HAG  H  HCH2   0   0.299  -1.1107  -1.9535   0.6554
 AVO  HAE  H  HCH2   0   0.269  -2.9710  -2.3987  -0.7538
 AVO  HE2  H  HCH2   0   0.273  -3.8898  -2.0135   0.6897
 AVO  HE3  H  HCH2   0   0.267  -3.6624  -0.4537  -1.8057
 AVO  HAF  H  HCH2   0   0.275  -4.7079  -0.0915  -0.4414
 AVO  HAH  H  HCH2   0   0.305  -2.5614   1.5344  -1.0265
 AVO  HE5  H  HCH2   0   0.293  -3.0450   1.2216   0.6525
 AVO  H    H  HNT1   0   0.444  -1.0485  -0.1952  -0.9213
 AVO  HA   H  HCH1   0   0.318  -0.9678   1.5430   1.3573
 AVO  HB2  H  HCH2   0   0.322   1.1457   0.8567   2.0628
 AVO  HB1  H  HCH2   0   0.305   0.1418  -0.5565   2.1693
 AVO  HD2  H  HCR5   0   0.334   1.1681  -2.8113   0.7834
 AVO  H2   H  HNR5   0   0.463   3.2001  -3.0142  -0.7126
 AVO  HE1  H  HCR5   0   0.361   4.2298  -0.7678  -1.2629
 AVO  HD1  H  HNR5   0   0.452   2.7971   0.9585  -0.0820

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    deloc     1.241  0.020  1.241
 AVO  C    OXT  deloc     1.240  0.020  1.240
 AVO  C    CA   single    1.554  0.020  1.554
 AVO  NE2  CD2  aromatic  1.369  0.020  1.369
 AVO  NE2  CE1  aromatic  1.320  0.020  1.320
 AVO  CD2  CG   aromatic  1.358  0.020  1.358
 AVO  CAH  CAF  single    1.520  0.020  1.520
 AVO  CAH  N    single    1.497  0.020  1.497
 AVO  CE1  ND1  aromatic  1.320  0.020  1.320
 AVO  CA   N    single    1.493  0.020  1.493
 AVO  CA   CB   single    1.532  0.020  1.532
 AVO  CG   ND1  aromatic  1.376  0.020  1.376
 AVO  CG   CB   single    1.488  0.020  1.488
 AVO  CAF  CAE  single    1.542  0.020  1.542
 AVO  N    CAG  single    1.492  0.020  1.492
 AVO  CAG  CAE  single    1.526  0.020  1.526
 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  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  109.18  3.000
 AVO  HAG  CAG  N    110.14  3.000
 AVO  HE4  CAG  N    107.23  3.000
 AVO  HAG  CAG  CAE  113.60  3.000
 AVO  HE4  CAG  CAE  111.90  3.000
 AVO  N    CAG  CAE  104.52  3.000
 AVO  HE2  CAE  HAE  107.39  3.000
 AVO  HE2  CAE  CAF  112.44  3.000
 AVO  HAE  CAE  CAF  110.84  3.000
 AVO  HE2  CAE  CAG  109.87  3.000
 AVO  HAE  CAE  CAG  110.76  3.000
 AVO  CAF  CAE  CAG  105.59  3.000
 AVO  HAF  CAF  HE3  107.60  3.000
 AVO  HAF  CAF  CAH  110.48  3.000
 AVO  HE3  CAF  CAH  110.44  3.000
 AVO  HAF  CAF  CAE  112.54  3.000
 AVO  HE3  CAF  CAE  110.76  3.000
 AVO  CAH  CAF  CAE  105.06  3.000
 AVO  HE5  CAH  HAH  109.37  3.000
 AVO  HE5  CAH  N    106.77  3.000
 AVO  HAH  CAH  N    109.63  3.000
 AVO  HE5  CAH  CAF  112.00  3.000
 AVO  HAH  CAH  CAF  114.69  3.000
 AVO  N    CAH  CAF  103.96  3.000
 AVO  H    N    CA   104.90  3.000
 AVO  H    N    CAH  106.25  3.000
 AVO  CA   N    CAH  112.91  3.000
 AVO  H    N    CAG  110.26  3.000
 AVO  CA   N    CAG  118.38  3.000
 AVO  CAH  N    CAG  103.65  3.000
 AVO  HA   CA   CB   107.40  3.000
 AVO  HA   CA   C    110.75  3.000
 AVO  CB   CA   C    109.84  3.000
 AVO  HA   CA   N    106.71  3.000
 AVO  CB   CA   N    113.84  3.000
 AVO  C    CA   N    108.27  3.000
 AVO  O    C    OXT  128.96  3.000
 AVO  OXT  C    CA   114.74  3.000
 AVO  O    C    CA   116.18  3.000
 AVO  HB1  CB   HB2  105.63  3.000
 AVO  HB1  CB   CG   109.03  3.000
 AVO  HB2  CB   CG   109.07  3.000
 AVO  HB1  CB   CA   111.28  3.000
 AVO  HB2  CB   CA   106.15  3.000
 AVO  CG   CB   CA   115.20  3.000
 AVO  ND1  CG   CD2  105.64  3.000
 AVO  ND1  CG   CB   123.02  3.000
 AVO  CD2  CG   CB   131.32  3.000
 AVO  HD2  CD2  NE2  122.20  3.000
 AVO  HD2  CD2  CG   130.83  3.000
 AVO  NE2  CD2  CG   106.96  3.000
 AVO  H2   NE2  CE1  124.66  3.000
 AVO  H2   NE2  CD2  125.59  3.000
 AVO  CE1  NE2  CD2  109.75  3.000
 AVO  HE1  CE1  ND1  126.22  3.000
 AVO  HE1  CE1  NE2  126.31  3.000
 AVO  ND1  CE1  NE2  107.46  3.000
 AVO  HD1  ND1  CE1  124.80  3.000
 AVO  HD1  ND1  CG   125.02  3.000
 AVO  CE1  ND1  CG   110.18  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  Var_01    CAH  CAF  CAE  CAG    -3.98  30.0  1
 AVO  Var_02    N    CAH  CAF  CAE    27.51  30.0  1
 AVO  Var_03    N    CAG  CAE  CAF   -21.12  30.0  1
 AVO  Var_04    CD2  CG   CB   CA   -107.64  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

