# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:16:10 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: N-acetyl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(C)=O)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
 AYA  AYA  'N-acetyl-L-alanine       '  L-peptide  17  9  .  2012-08-28  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AYA
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
 AYA  N    N  NH1    0  -0.611  44.4904  32.5270  107.2689
 AYA  CA   C  CH1    0  -0.187  43.3343  33.3621  107.5072
 AYA  CB   C  CH3    0  -0.684  43.8043  34.7788  107.8196
 AYA  C    C  C      0   0.406  42.3299  33.3838  106.3207
 AYA  O    O  O      0  -0.613  41.2030  33.8366  106.6040
 AYA  OXT  O  OC    -1  -0.597  42.7363  32.9944  105.2129
 AYA  CT   C  C      0   0.514  44.4177  31.1899  107.2118
 AYA  OT   O  O      0  -0.512  43.4040  30.5629  107.4981
 AYA  CM   C  CH3    0  -0.776  45.6843  30.4839  106.7870
 AYA  H    H  HNH1   0   0.387  45.3231  32.9715  106.9171
 AYA  HA   H  HCH1   0   0.225  42.8109  32.9745  108.3848
 AYA  HB1  H  HCH3   0   0.236  42.9541  35.4185  108.0482
 AYA  HB2  H  HCH3   0   0.231  44.4769  34.7941  108.6784
 AYA  HB3  H  HCH3   0   0.222  44.3329  35.2157  106.9690
 AYA  HM1  H  HCH3   0   0.256  45.9325  29.7101  107.5129
 AYA  HM2  H  HCH3   0   0.259  45.5155  29.9875  105.8307
 AYA  HM3  H  HCH3   0   0.243  46.5421  31.1454  106.6797

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
 AYA  N   CA   single  1.458  0.019  1.458
 AYA  N   CT   single  1.340  0.020  1.340
 AYA  N   H    single  0.860  0.020  0.860
 AYA  CA  CB   single  1.521  0.033  1.521
 AYA  CA  C    single  1.525  0.021  1.525
 AYA  CA  HA   single  0.970  0.020  0.970
 AYA  CB  HB1  single  0.970  0.020  1.090
 AYA  CB  HB2  single  0.970  0.020  1.090
 AYA  CB  HB3  single  0.970  0.020  1.090
 AYA  C   O    deloc   1.231  0.020  1.231
 AYA  C   OXT  deloc   1.243  0.020  1.243
 AYA  CT  OT   double  1.226  0.020  1.226
 AYA  CT  CM   single  1.511  0.020  1.511
 AYA  CM  HM1  single  0.970  0.020  1.090
 AYA  CM  HM2  single  0.970  0.020  1.090
 AYA  CM  HM3  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
 AYA  H    N   CT   118.05  3.000
 AYA  H    N   CA   114.00  3.000
 AYA  CT   N   CA   122.67  3.000
 AYA  HA   CA  C    109.00  3.000
 AYA  HA   CA  CB   109.00  3.000
 AYA  C    CA  CB   110.50  1.500
 AYA  HA   CA  N    110.00  3.000
 AYA  C    CA  N    111.00  2.800
 AYA  CB   CA  N    110.40  1.500
 AYA  HB3  CB  HB2  107.99  3.000
 AYA  HB3  CB  HB1  107.84  3.000
 AYA  HB2  CB  HB1  107.94  3.000
 AYA  HB3  CB  CA   111.17  3.000
 AYA  HB2  CB  CA   111.37  3.000
 AYA  HB1  CB  CA   110.39  3.000
 AYA  OXT  C   O    127.72  3.000
 AYA  OXT  C   CA   117.70  3.000
 AYA  O    C   CA   120.80  1.700
 AYA  CM   CT  OT   121.32  3.000
 AYA  CM   CT  N    115.64  3.000
 AYA  OT   CT  N    123.03  3.000
 AYA  HM3  CM  HM2  108.19  3.000
 AYA  HM3  CM  HM1  108.53  3.000
 AYA  HM2  CM  HM1  107.23  3.000
 AYA  HM3  CM  CT   113.85  3.000
 AYA  HM2  CM  CT   109.23  3.000
 AYA  HM1  CM  CT   109.60  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
 AYA  CONST_01  OT   CT  N   CA    0.00   0.0  0
 AYA  CONST_02  CM   CT  N   CA  180.00   0.0  0
 AYA  CONST_03  H    N   CT  OT  180.00   0.0  0
 AYA  Var_01    HM1  CM  CT  N   127.97  30.0  3

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
 AYA  chir_01  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
 AYA  plan-1  N    0.020
 AYA  plan-1  CA   0.020
 AYA  plan-1  CT   0.020
 AYA  plan-1  OT   0.020
 AYA  plan-1  CM   0.020
 AYA  plan-1  H    0.020
 AYA  plan-2  CA   0.020
 AYA  plan-2  C    0.020
 AYA  plan-2  O    0.020
 AYA  plan-2  OXT  0.020

