# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 18:26:07 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (2S)-amino[(5S)-3-chloro-4,5-dihydroisoxazol-5-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H]1CC(=NO1)Cl)C(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
 AVN  AVN  '(2S)-amino[(5S)-3-chloro-4,5-dihydroisoxazol-5-yl]ethanoic acid'  L-peptide  18  11  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_AVN
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
 AVN  C1    C   C     0   0.540   2.5513  -0.3728  -0.0419
 AVN  O1    O   OH1   0  -0.580   2.7466  -1.3798   0.7932
 AVN  O2    O   O     0  -0.445   3.2118  -0.1847  -1.0341
 AVN  C2    C   CH1   0  -0.231   1.4107   0.5447   0.3788
 AVN  N1    N   NH2   0  -0.776   1.7971   1.9336   0.4681
 AVN  C3    C   CR15  0   0.022   0.2842   0.4224  -0.6501
 AVN  O3    O   O     0  -0.406  -0.0328  -0.9740  -0.8339
 AVN  N2    N   N     0  -0.076  -1.1862  -1.2782  -0.1536
 AVN  C4    C   CR5   0   0.175  -1.7296  -0.2003   0.2208
 AVN  C5    C   CH2   0  -0.544  -1.0149   1.0485  -0.1600
 AVN  CL1   CL  CL    0  -0.060  -3.2065  -0.2122   1.0684
 AVN  HO1   H   HOH1  0   0.482   3.4798  -1.9338   0.4833
 AVN  H2    H   HCH1  0   0.281   1.0338   0.2292   1.3554
 AVN  HN11  H   HNH2  0   0.369   2.4187   2.0800   1.2523
 AVN  HN12  H   HNH2  0   0.354   2.2984   2.2195  -0.3643
 AVN  H3    H   HCR5  0   0.282   0.6107   0.8146  -1.6150
 AVN  H51   H   HCH2  0   0.303  -0.8697   1.7313   0.6769
 AVN  H52   H   HCH2  0   0.309  -1.5662   1.5817  -0.9376

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
 AVN  C1  O1    single  1.323  0.020  1.323
 AVN  C1  O2    double  1.207  0.020  1.207
 AVN  C1  C2    single  1.523  0.020  1.523
 AVN  O1  HO1   single  0.850  0.020  0.980
 AVN  C2  H2    single  0.970  0.020  1.090
 AVN  C2  N1    single  1.444  0.020  1.444
 AVN  C2  C3    single  1.531  0.020  1.531
 AVN  N1  HN11  single  0.890  0.020  1.040
 AVN  N1  HN12  single  0.890  0.020  1.040
 AVN  C3  H3    single  0.970  0.020  1.090
 AVN  C3  O3    single  1.444  0.020  1.444
 AVN  C3  C5    single  1.523  0.020  1.523
 AVN  O3  N2    single  1.373  0.020  1.373
 AVN  N2  C4    double  1.264  0.020  1.264
 AVN  C4  CL1   single  1.703  0.020  1.703
 AVN  C4  C5    single  1.488  0.020  1.488
 AVN  C5  H51   single  0.970  0.020  1.090
 AVN  C5  H52   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
 AVN  C2    C1  O2    122.90  3.000
 AVN  C2    C1  O1    113.25  3.000
 AVN  O2    C1  O1    123.85  3.000
 AVN  HO1   O1  C1    110.16  3.000
 AVN  H2    C2  C3    108.89  3.000
 AVN  C3    C2  N1    108.37  3.000
 AVN  H2    C2  N1    108.33  3.000
 AVN  C3    C2  C1    108.50  3.000
 AVN  N1    C2  C1    113.32  3.000
 AVN  H2    C2  C1    109.33  3.000
 AVN  HN12  N1  HN11  106.99  3.000
 AVN  HN12  N1  C2    110.68  3.000
 AVN  HN11  N1  C2    110.58  3.000
 AVN  H3    C3  C5    113.07  3.000
 AVN  C5    C3  O3    104.55  3.000
 AVN  H3    C3  O3    107.50  3.000
 AVN  C5    C3  C2    112.24  3.000
 AVN  O3    C3  C2    108.93  3.000
 AVN  H3    C3  C2    110.20  3.000
 AVN  N2    O3  C3    109.62  3.000
 AVN  C4    N2  O3    108.60  3.000
 AVN  CL1   C4  C5    123.34  3.000
 AVN  C5    C4  N2    115.68  3.000
 AVN  CL1   C4  N2    120.96  3.000
 AVN  H52   C5  H51   107.95  3.000
 AVN  H52   C5  C4    110.45  3.000
 AVN  H51   C5  C4    113.15  3.000
 AVN  H52   C5  C3    113.71  3.000
 AVN  H51   C5  C3    113.02  3.000
 AVN  C4    C5  C3     98.45  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
 AVN  CONST_01  HO1  O1  C1  O2  0.00   0.0  0
 AVN  Var_01    C5   C4  N2  O3  0.22  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
 AVN  chir_01  C2  C1  N1  C3  negativ
 AVN  chir_02  C3  O3  C5  C2  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
 AVN  plan-1  C1   0.020
 AVN  plan-1  O1   0.020
 AVN  plan-1  O2   0.020
 AVN  plan-1  C2   0.020
 AVN  plan-1  HO1  0.020

