# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 13:28:04 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: N-carboxy-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(O)=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
 NXA  NXA  'N-carboxy-L-alanine      '  ligand  16  9  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NXA
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
 NXA  N     N  NH1   0  -0.639  -0.3486  -0.2401   0.6229
 NXA  CA    C  CH1   0  -0.197   0.4802   0.0679  -0.5130
 NXA  C     C  C     0   0.550  -0.3919   0.1136  -1.7522
 NXA  OXT   O  OH1   0  -0.587   0.2825   0.5651  -2.7966
 NXA  CB    C  CH3   0  -0.652   1.6269  -0.9322  -0.6892
 NXA  OD1   O  OH1   0  -0.620  -0.8996  -0.3024   2.7652
 NXA  OD2   O  O     0  -0.517   0.9136   0.8767   2.1471
 NXA  C1    C  C     0   0.684  -0.0312   0.1665   1.8640
 NXA  O     O  O     0  -0.433  -1.5445  -0.2331  -1.7922
 NXA  H     H  HNH1  0   0.405  -1.1162  -0.8816   0.4947
 NXA  HA    H  HCH1  0   0.297   0.9038   1.0657  -0.3739
 NXA  HB    H  HOH1  0   0.488  -0.2768   0.5561  -3.5882
 NXA  HBC1  H  HCH3  0   0.239   1.2444  -1.9386  -0.8607
 NXA  HBC2  H  HCH3  0   0.246   2.2742  -0.6587  -1.5204
 NXA  HBC3  H  HCH3  0   0.252   2.2325  -0.9453   0.2154
 NXA  HD1   H  HOH1  0   0.484  -0.6445   0.0114   3.6426

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
 NXA  N    CA    single  1.439  0.020  1.439
 NXA  N    C1    single  1.344  0.020  1.344
 NXA  N    H     single  0.860  0.020  1.020
 NXA  CA   C     single  1.516  0.020  1.516
 NXA  CA   CB    single  1.532  0.020  1.532
 NXA  CA   HA    single  0.970  0.020  1.090
 NXA  C    OXT   single  1.323  0.020  1.323
 NXA  C    O     double  1.204  0.020  1.204
 NXA  OXT  HB    single  0.850  0.020  0.980
 NXA  CB   HBC1  single  0.970  0.020  1.090
 NXA  CB   HBC2  single  0.970  0.020  1.090
 NXA  CB   HBC3  single  0.970  0.020  1.090
 NXA  OD1  C1    single  1.337  0.020  1.337
 NXA  OD1  HD1   single  0.850  0.020  0.980
 NXA  OD2  C1    double  1.215  0.020  1.215

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
 NXA  H     N    C1    119.32  3.000
 NXA  H     N    CA    118.29  3.000
 NXA  C1    N    CA    121.87  3.000
 NXA  HA    CA   CB    108.70  3.000
 NXA  HA    CA   C     107.43  3.000
 NXA  CB    CA   C     110.87  3.000
 NXA  HA    CA   N     108.55  3.000
 NXA  CB    CA   N     112.47  3.000
 NXA  C     CA   N     108.68  3.000
 NXA  O     C    OXT   124.06  3.000
 NXA  O     C    CA    124.68  3.000
 NXA  OXT   C    CA    111.25  3.000
 NXA  HB    OXT  C     110.33  3.000
 NXA  HBC3  CB   HBC2  107.86  3.000
 NXA  HBC3  CB   HBC1  108.35  3.000
 NXA  HBC2  CB   HBC1  108.69  3.000
 NXA  HBC3  CB   CA    109.19  3.000
 NXA  HBC2  CB   CA    111.65  3.000
 NXA  HBC1  CB   CA    110.99  3.000
 NXA  HD1   OD1  C1    109.08  3.000
 NXA  OD2   C1   OD1   123.58  3.000
 NXA  OD2   C1   N     125.13  3.000
 NXA  OD1   C1   N     111.29  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
 NXA  CONST_01  HD1  OD1  C1  N    180.00   0.0  0
 NXA  CONST_02  HB   OXT  C   CA   180.00   0.0  0
 NXA  Var_01    OD1  C1   N   CA  -176.24  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
 NXA  chir_01  CA  N  C  CB  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
 NXA  plan-1  CA   0.020
 NXA  plan-1  C    0.020
 NXA  plan-1  OXT  0.020
 NXA  plan-1  O    0.020
 NXA  plan-1  HB   0.020
 NXA  plan-2  N    0.020
 NXA  plan-2  OD1  0.020
 NXA  plan-2  OD2  0.020
 NXA  plan-2  C1   0.020
 NXA  plan-2  HD1  0.020

