# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 13:44:10 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: N-acetyl-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](CC(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
 KKD  KKD  'N-acetyl-L-aspartic acid '  L-peptide  19  12  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KKD
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
 KKD  N     N  NH1    0  -0.609  -0.4932  -0.7535  -0.3622
 KKD  CA    C  CH1    0  -0.177  -0.0075   0.4735   0.2261
 KKD  C     C  C      0   0.408  -0.9706   1.6659   0.0057
 KKD  O     O  O      0  -0.602  -1.8772   1.5392  -0.8355
 KKD  CB    C  CH2    0  -0.598   1.3733   0.7854  -0.3395
 KKD  CG    C  C      0   0.407   2.4310  -0.2871  -0.0190
 KKD  OD1   O  O      0  -0.613   2.4515  -0.7198   1.1507
 KKD  OD2   O  OC    -1  -0.620   3.2025  -0.6164  -0.9432
 KKD  CT1   C  C      0   0.520  -1.5466  -1.4193   0.1221
 KKD  CT2   C  CH3    0  -0.781  -2.0346  -2.5737  -0.7204
 KKD  OT    O  O      0  -0.527  -2.0854  -1.1369   1.1882
 KKD  H     H  HNH1   0   0.383  -0.1806  -0.9812  -1.2921
 KKD  HA    H  HCH1   0   0.225   0.1024   0.3156   1.3006
 KKD  OXT   O  OC    -1  -0.624  -0.7214   2.6768   0.6952
 KKD  HB3   H  HCH2   0   0.207   1.3072   0.9486  -1.4201
 KKD  HB2   H  HCH2   0   0.240   1.7047   1.7331   0.0946
 KKD  HT23  H  HCH3   0   0.243  -1.3945  -2.7949  -1.5731
 KKD  HT22  H  HCH3   0   0.257  -2.1154  -3.4699  -0.1062
 KKD  HT21  H  HCH3   0   0.260  -3.0333  -2.3468  -1.0961

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
 KKD  C    O     deloc   1.231  0.020  1.231
 KKD  C    CA    single  1.525  0.021  1.525
 KKD  CB   CA    single  1.530  0.020  1.530
 KKD  CB   CG    single  1.540  0.020  1.540
 KKD  CA   N     single  1.458  0.019  1.458
 KKD  CG   OD1   deloc   1.247  0.020  1.247
 KKD  CG   OD2   deloc   1.248  0.020  1.248
 KKD  OT   CT1   double  1.227  0.020  1.227
 KKD  N    CT1   single  1.337  0.020  1.337
 KKD  CT1  CT2   single  1.510  0.020  1.510
 KKD  N    H     single  0.860  0.020  0.860
 KKD  CA   HA    single  0.970  0.020  0.970
 KKD  C    OXT   deloc   1.249  0.020  1.249
 KKD  CB   HB3   single  0.970  0.020  1.090
 KKD  CB   HB2   single  0.970  0.020  1.090
 KKD  CT2  HT23  single  0.970  0.020  1.090
 KKD  CT2  HT22  single  0.970  0.020  1.090
 KKD  CT2  HT21  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
 KKD  H     N    CT1   117.80  3.000
 KKD  H     N    CA    114.00  3.000
 KKD  CT1   N    CA    122.70  3.000
 KKD  HA    CA   CB    109.00  3.000
 KKD  HA    CA   C     109.00  3.000
 KKD  CB    CA   C     110.10  1.900
 KKD  HA    CA   N     110.00  3.000
 KKD  CB    CA   N     110.50  1.700
 KKD  C     CA   N     111.00  2.800
 KKD  OXT   C    O     126.99  3.000
 KKD  OXT   C    CA    114.87  3.000
 KKD  O     C    CA    120.80  1.700
 KKD  HB2   CB   HB3   106.31  3.000
 KKD  HB2   CB   CG    108.22  3.000
 KKD  HB3   CB   CG    110.53  3.000
 KKD  HB2   CB   CA    107.72  3.000
 KKD  HB3   CB   CA    109.99  3.000
 KKD  CG    CB   CA    113.73  3.000
 KKD  OD2   CG   OD1   126.35  3.000
 KKD  OD2   CG   CB    117.01  3.000
 KKD  OD1   CG   CB    116.62  3.000
 KKD  OT    CT1  CT2   121.24  3.000
 KKD  CT2   CT1  N     115.67  3.000
 KKD  OT    CT1  N     123.08  3.000
 KKD  HT21  CT2  HT22  107.30  3.000
 KKD  HT21  CT2  HT23  108.10  3.000
 KKD  HT22  CT2  HT23  108.54  3.000
 KKD  HT21  CT2  CT1   109.21  3.000
 KKD  HT22  CT2  CT1   109.77  3.000
 KKD  HT23  CT2  CT1   113.72  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
 KKD  CONST_01  OT    CT1  N    CA     0.00   0.0  0
 KKD  CONST_02  CT2   CT1  N    CA   180.00   0.0  0
 KKD  CONST_03  H     N    CT1  CT2    0.00   0.0  0
 KKD  Var_01    OD1   CG   CB   CA   -44.45  30.0  3
 KKD  Var_02    HT23  CT2  CT1  N      6.51  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
 KKD  chir_01  CA  C  CB  N  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
 KKD  plan-1  N    0.020
 KKD  plan-1  CA   0.020
 KKD  plan-1  CT1  0.020
 KKD  plan-1  CT2  0.020
 KKD  plan-1  OT   0.020
 KKD  plan-1  H    0.020
 KKD  plan-2  CA   0.020
 KKD  plan-2  C    0.020
 KKD  plan-2  O    0.020
 KKD  plan-2  OXT  0.020
 KKD  plan-3  CB   0.020
 KKD  plan-3  CG   0.020
 KKD  plan-3  OD1  0.020
 KKD  plan-3  OD2  0.020

