# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 17:59:42 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (3S,4S)-3-amino-4-methyl-3,4-dihydro-2H-pyran-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C=COC(=O)[C@H]1N
#
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
 0AB  0AB  (3S,4S)-3-amino-4-methyl-3,4-dihydro-2H-pyran-2-one  L-peptide  18  9  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0AB
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
 0AB  N     N  NH2   0  -0.780  -6.2472  16.4488  22.6202
 0AB  CA    C  CH1   0  -0.247  -5.2020  17.0434  21.8292
 0AB  C     C  C     0   0.527  -4.5377  18.2518  22.4785
 0AB  O     O  O     0  -0.399  -4.6806  18.5856  23.6205
 0AB  CB    C  CH1   0  -0.282  -5.6615  17.3738  20.4034
 0AB  CG1   C  CH3   0  -0.659  -6.9065  18.2596  20.3472
 0AB  CG2   C  C1    0  -0.302  -4.5126  18.0182  19.6904
 0AB  O1    O  O2    0  -0.435  -3.6850  18.9590  21.7109
 0AB  C1    C  C1    0   0.028  -3.6172  18.7294  20.3548
 0AB  HN1   H  HNH2  0   0.359  -5.8700  16.0877  23.4864
 0AB  HA2   H  HNH2  0   0.352  -6.9387  17.1403  22.8818
 0AB  HB    H  HCH1  0   0.300  -4.3973  16.3031  21.7253
 0AB  HA    H  HCH1  0   0.269  -5.8969  16.4226  19.9207
 0AB  HG11  H  HCH3  0   0.227  -6.7496  19.2143  20.8541
 0AB  HG12  H  HCH3  0   0.247  -7.1659  18.4787  19.3115
 0AB  HG13  H  HCH3  0   0.238  -7.7671  17.7682  20.8017
 0AB  HG2   H  H     0   0.272  -4.4117  17.9276  18.6174
 0AB  H1    H  H     0   0.284  -2.7679  19.2296  19.9115

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
 0AB  N    CA    single  1.458  0.019  1.458
 0AB  N    HN1   single  0.890  0.020  1.040
 0AB  N    HA2   single  0.890  0.020  1.040
 0AB  CA   C     single  1.525  0.021  1.525
 0AB  CA   CB    single  1.540  0.027  1.540
 0AB  CA   HB    single  0.970  0.020  1.090
 0AB  C    O     double  1.231  0.020  1.231
 0AB  C    O1    single  1.348  0.020  1.348
 0AB  CB   CG1   single  1.529  0.020  1.529
 0AB  CB   CG2   single  1.498  0.020  1.498
 0AB  CB   HA    single  0.970  0.020  1.090
 0AB  CG1  HG11  single  0.970  0.020  1.090
 0AB  CG1  HG12  single  0.970  0.020  1.090
 0AB  CG1  HG13  single  0.970  0.020  1.090
 0AB  CG2  C1    double  1.322  0.020  1.322
 0AB  CG2  HG2   single  0.930  0.020  1.080
 0AB  O1   C1    single  1.377  0.020  1.377
 0AB  C1   H1    single  0.930  0.020  1.080

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
 0AB  HA2   N    HN1   106.10  3.000
 0AB  HA2   N    CA    110.85  3.000
 0AB  HN1   N    CA    110.32  3.000
 0AB  HB    CA   CB    106.06  3.000
 0AB  HB    CA   C     104.80  3.000
 0AB  CB    CA   C     111.40  1.900
 0AB  HB    CA   N     107.79  3.000
 0AB  CB    CA   N     111.50  1.700
 0AB  C     CA   N     111.00  2.800
 0AB  O1    C    O     118.16  3.000
 0AB  O1    C    CA    116.69  3.000
 0AB  O     C    CA    120.80  1.700
 0AB  HA    CB   CG2   109.25  3.000
 0AB  HA    CB   CG1   108.23  3.000
 0AB  CG2   CB   CG1   110.97  3.000
 0AB  HA    CB   CA    109.00  3.000
 0AB  CG2   CB   CA    107.78  3.000
 0AB  CG1   CB   CA    113.75  3.000
 0AB  HG13  CG1  HG12  107.38  3.000
 0AB  HG13  CG1  HG11  108.29  3.000
 0AB  HG12  CG1  HG11  107.43  3.000
 0AB  HG13  CG1  CB    111.49  3.000
 0AB  HG12  CG1  CB    110.19  3.000
 0AB  HG11  CG1  CB    111.86  3.000
 0AB  HG2   CG2  C1    118.70  3.000
 0AB  HG2   CG2  CB    120.52  3.000
 0AB  C1    CG2  CB    120.77  3.000
 0AB  C1    O1   C     120.30  3.000
 0AB  H1    C1   O1    111.43  3.000
 0AB  H1    C1   CG2   125.10  3.000
 0AB  O1    C1   CG2   123.44  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
 0AB  Var_01  CG2  C1  O1   C   12.84  30.0  1
 0AB  Var_02  O1   C1  CG2  CB  -1.75  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
 0AB  chir_01  CA  N    C    CB  positiv
 0AB  chir_02  CB  CG2  CG1  CA  positiv

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
 0AB  plan-1  CA  0.020
 0AB  plan-1  C   0.020
 0AB  plan-1  O   0.020
 0AB  plan-1  O1  0.020

