# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 16:05:58 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  17  11  .  2022-07-24  2023-02-02
;
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   0.386   2.7858  -0.2185  -0.0325
 AVN  O1    O   OC    -1  -0.601   2.6751  -1.4588  -0.0017
 AVN  O2    O   O      0  -0.603   3.7935   0.4327  -0.3675
 AVN  C2    C   CH1    0  -0.250   1.5348   0.5928   0.4055
 AVN  N1    N   NH2    0  -0.782   1.6580   2.0364   0.2814
 AVN  C3    C   CR15   0   0.054   0.2868   0.1661  -0.3648
 AVN  O3    O   O      0  -0.399  -0.1133  -1.1864  -0.0260
 AVN  N2    N   N      0  -0.083  -1.4762  -1.2568   0.0723
 AVN  C4    C   CR5    0   0.153  -1.9532  -0.0878   0.0298
 AVN  C5    C   CH2    0  -0.526  -0.9533   1.0068  -0.0635
 AVN  CL1   CL  CL     0  -0.078  -3.6351   0.1777   0.1634
 AVN  H2    H   HCH1   0   0.236   1.3445   0.3711   1.4632
 AVN  HN11  H   HNH2   0   0.346   2.3870   2.3477   0.9105
 AVN  HN12  H   HNH2   0   0.331   2.0194   2.2495  -0.6415
 AVN  H3    H   HCR5   0   0.240   0.4873   0.1854  -1.4436
 AVN  H51   H   HCH2   0   0.287  -0.8928   1.5491   0.8840
 AVN  H52   H   HCH2   0   0.289  -1.1828   1.7287  -0.8443

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    deloc   1.246  0.020  1.246
 AVN  C1  O2    deloc   1.246  0.020  1.246
 AVN  C1  C2    single  1.554  0.020  1.554
 AVN  C2  H2    single  0.970  0.020  1.090
 AVN  C2  N1    single  1.454  0.020  1.454
 AVN  C2  C3    single  1.527  0.020  1.527
 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  1.451  0.020  1.451
 AVN  C3  C5    single  1.528  0.020  1.528
 AVN  O3  N2    single  1.368  0.020  1.368
 AVN  N2  C4    double  1.263  0.020  1.263
 AVN  C4  CL1   single  1.708  0.020  1.708
 AVN  C4  C5    single  1.485  0.020  1.485
 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    117.01  3.000
 AVN  C2    C1  O1    116.19  3.000
 AVN  O2    C1  O1    126.80  3.000
 AVN  H2    C2  C3    106.74  3.000
 AVN  C3    C2  N1    107.67  3.000
 AVN  H2    C2  N1    107.31  3.000
 AVN  C3    C2  C1    111.70  3.000
 AVN  N1    C2  C1    115.21  3.000
 AVN  H2    C2  C1    107.81  3.000
 AVN  HN12  N1  HN11  104.15  3.000
 AVN  HN12  N1  C2    108.45  3.000
 AVN  HN11  N1  C2    108.26  3.000
 AVN  H3    C3  C5    109.42  3.000
 AVN  C5    C3  O3    104.07  3.000
 AVN  H3    C3  O3    107.24  3.000
 AVN  C5    C3  C2    114.20  3.000
 AVN  O3    C3  C2    111.60  3.000
 AVN  H3    C3  C2    109.97  3.000
 AVN  N2    O3  C3    109.85  3.000
 AVN  C4    N2  O3    109.03  3.000
 AVN  CL1   C4  C5    123.59  3.000
 AVN  C5    C4  N2    115.46  3.000
 AVN  CL1   C4  N2    120.87  3.000
 AVN  H52   C5  H51   107.73  3.000
 AVN  H52   C5  C4    113.09  3.000
 AVN  H51   C5  C4    110.39  3.000
 AVN  H52   C5  C3    113.25  3.000
 AVN  H51   C5  C3    113.50  3.000
 AVN  C4    C5  C3     98.81  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  Var_01  C5  C4  N2  O3  -1.96  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

