# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 17:26:46 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  21  12  .  2022-03-22  2022-11-17
;
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  -0.621  -0.5458  -0.6798  -0.4140
 KKD  CA    C  CH1   0  -0.200  -0.0386   0.5127   0.1988
 KKD  C     C  C     0   0.557  -0.9614   1.6953  -0.0728
 KKD  O     O  O     0  -0.423  -1.9109   1.6625  -0.8083
 KKD  CB    C  CH2   0  -0.611   1.3772   0.7989  -0.2907
 KKD  CG    C  C     0   0.566   2.3539  -0.2521   0.1744
 KKD  OD1   O  O     0  -0.433   2.1956  -0.9564   1.1380
 KKD  OD2   O  OH1   0  -0.589   3.4382  -0.2794  -0.5878
 KKD  CT1   C  C     0   0.532  -1.5306  -1.4111   0.1466
 KKD  CT2   C  CH3   0  -0.781  -2.0294  -2.5643  -0.6835
 KKD  OT    O  O     0  -0.497  -1.9879  -1.1544   1.2499
 KKD  H     H  HNH1  0   0.406  -0.2906  -0.8666  -1.3710
 KKD  HA    H  HCH1  0   0.305  -0.0125   0.3667   1.2815
 KKD  OXT   O  OH1   0  -0.590  -0.5845   2.7644   0.6127
 KKD  HB3   H  HCH2  0   0.296   1.4074   0.8900  -1.3788
 KKD  HB2   H  HCH2  0   0.322   1.7297   1.7554   0.1041
 KKD  H2    H  HOH1  0   0.483   4.0758  -0.9197  -0.2371
 KKD  HT23  H  HCH3  0   0.252  -1.4042  -2.7801  -1.5479
 KKD  HT22  H  HCH3  0   0.267  -2.0953  -3.4590  -0.0667
 KKD  HT21  H  HCH3  0   0.271  -3.0353  -2.3379  -1.0398
 KKD  HXT   H  HOH1  0   0.488  -1.1701   3.5129   0.4209

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     double  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  1.508  0.020  1.508
 KKD  CA   N     single  1.458  0.019  1.458
 KKD  CG   OD1   double  1.204  0.020  1.204
 KKD  CG   OD2   single  1.326  0.020  1.326
 KKD  OT   CT1   double  1.222  0.020  1.222
 KKD  N    CT1   single  1.349  0.020  1.349
 KKD  CT1  CT2   single  1.506  0.020  1.506
 KKD  N    H     single  0.860  0.020  0.860
 KKD  CA   HA    single  0.970  0.020  0.970
 KKD  C    OXT   single  1.325  0.020  1.325
 KKD  CB   HB3   single  0.970  0.020  1.090
 KKD  CB   HB2   single  0.970  0.020  1.090
 KKD  OD2  H2    single  0.850  0.020  0.980
 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
 KKD  OXT  HXT   single  0.850  0.020  0.980

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   118.62  3.000
 KKD  H     N    CA    114.00  3.000
 KKD  CT1   N    CA    122.13  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     124.31  3.000
 KKD  OXT   C    CA    111.20  3.000
 KKD  O     C    CA    120.80  1.700
 KKD  HB2   CB   HB3   106.13  3.000
 KKD  HB2   CB   CG    106.83  3.000
 KKD  HB3   CB   CG    110.33  3.000
 KKD  HB2   CB   CA    110.34  3.000
 KKD  HB3   CB   CA    111.16  3.000
 KKD  CG    CB   CA    111.80  3.000
 KKD  OD2   CG   OD1   123.75  3.000
 KKD  OD2   CG   CB    111.51  3.000
 KKD  OD1   CG   CB    124.70  3.000
 KKD  H2    OD2  CG    110.10  3.000
 KKD  OT    CT1  CT2   122.33  3.000
 KKD  CT2   CT1  N     115.34  3.000
 KKD  OT    CT1  N     122.33  3.000
 KKD  HT21  CT2  HT22  107.44  3.000
 KKD  HT21  CT2  HT23  108.15  3.000
 KKD  HT22  CT2  HT23  108.77  3.000
 KKD  HT21  CT2  CT1   109.06  3.000
 KKD  HT22  CT2  CT1   109.70  3.000
 KKD  HT23  CT2  CT1   113.54  3.000
 KKD  HXT   OXT  C     110.41  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  CONST_04  HXT   OXT  C    CA   180.00   0.0  0
 KKD  CONST_05  H2    OD2  CG   CB   180.00   0.0  0
 KKD  Var_01    OD1   CG   CB   CA   -23.48  30.0  3
 KKD  Var_02    HT23  CT2  CT1  N     11.15  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-2  HXT  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
 KKD  plan-3  H2   0.020

