# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:01:57 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: N~6~-acetyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCC[C@H](N)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
 ALY  ALY  'N~6~-acetyl-L-lysine     '  L-peptide  28  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_ALY
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
 ALY  OH    O  O      0  -0.504  10.2159  20.1340   -7.1404
 ALY  CH    C  C      0   0.514  11.0456  21.0344   -7.1189
 ALY  CH3   C  CH3    0  -0.774  11.0082  22.1206   -6.0707
 ALY  NZ    N  NH1    0  -0.623  12.0460  21.1301   -8.0098
 ALY  CE    C  CH2    0  -0.281  12.2329  20.2152   -9.1158
 ALY  CD    C  CH2    0  -0.432  11.3575  20.5364  -10.3235
 ALY  CG    C  CH2    0  -0.440  11.5728  19.5896  -11.5017
 ALY  CB    C  CH2    0  -0.433  12.9539  19.7046  -12.1378
 ALY  CA    C  CH1    0  -0.151  13.1412  18.8543  -13.3962
 ALY  N     N  NH2    0  -0.808  14.5408  18.9422  -13.8060
 ALY  C     C  C      0   0.384  12.2059  19.3568  -14.5244
 ALY  O     O  O      0  -0.605  12.5293  20.4170  -15.0948
 ALY  OXT   O  OC    -1  -0.614  11.1873  18.6701  -14.7509
 ALY  HH31  H  HCH3   0   0.245  11.8569  22.8005   -6.1170
 ALY  HH32  H  HCH3   0   0.262  10.0944  22.7041   -6.1875
 ALY  HH33  H  HCH3   0   0.260  10.9789  21.6688   -5.0797
 ALY  HZ    H  HNH1   0   0.397  12.6632  21.9229   -7.9526
 ALY  HE3   H  HCH2   0   0.245  13.2885  20.2559   -9.3840
 ALY  HE2   H  HCH2   0   0.233  12.0355  19.1969   -8.7743
 ALY  HD3   H  HCH2   0   0.229  10.3100  20.4964  -10.0154
 ALY  HD2   H  HCH2   0   0.215  11.5495  21.5653  -10.6438
 ALY  HG3   H  HCH2   0   0.208  11.4023  18.5569  -11.1777
 ALY  HG2   H  HCH2   0   0.229  10.8047  19.7973  -12.2500
 ALY  HB3   H  HCH2   0   0.204  13.1586  20.7502  -12.3903
 ALY  HB2   H  HCH2   0   0.213  13.7179  19.4127  -11.4082
 ALY  HCA   H  HCH1   0   0.166  12.8451  17.8229  -13.1494
 ALY  H     H  HNH2   0   0.332  14.6879  18.3841  -14.6383
 ALY  H2    H  HNH2   0   0.329  15.1163  18.5119  -13.0913

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
 ALY  OH   CH    double  1.225  0.020  1.225
 ALY  CH   CH3   single  1.510  0.020  1.510
 ALY  CH   NZ    single  1.343  0.020  1.343
 ALY  CH3  HH31  single  0.970  0.020  1.090
 ALY  CH3  HH32  single  0.970  0.020  1.090
 ALY  CH3  HH33  single  0.970  0.020  1.090
 ALY  NZ   CE    single  1.447  0.020  1.447
 ALY  NZ   HZ    single  0.860  0.020  1.020
 ALY  CE   CD    single  1.526  0.020  1.526
 ALY  CE   HE3   single  0.970  0.020  1.090
 ALY  CE   HE2   single  0.970  0.020  1.090
 ALY  CD   CG    single  1.527  0.020  1.527
 ALY  CD   HD3   single  0.970  0.020  1.090
 ALY  CD   HD2   single  0.970  0.020  1.090
 ALY  CG   CB    single  1.525  0.020  1.525
 ALY  CG   HG3   single  0.970  0.020  1.090
 ALY  CG   HG2   single  0.970  0.020  1.090
 ALY  CB   CA    single  1.530  0.020  1.530
 ALY  CB   HB3   single  0.970  0.020  1.090
 ALY  CB   HB2   single  0.970  0.020  1.090
 ALY  CA   N     single  1.458  0.019  1.458
 ALY  CA   C     single  1.525  0.021  1.525
 ALY  CA   HCA   single  0.970  0.020  1.090
 ALY  N    H     single  0.860  0.020  0.860
 ALY  N    H2    single  0.890  0.020  1.040
 ALY  C    O     deloc   1.231  0.020  1.231
 ALY  C    OXT   deloc   1.249  0.020  1.249

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
 ALY  NZ    CH   CH3   115.32  3.000
 ALY  NZ    CH   OH    123.06  3.000
 ALY  CH3   CH   OH    121.62  3.000
 ALY  HH33  CH3  HH32  107.26  3.000
 ALY  HH33  CH3  HH31  108.59  3.000
 ALY  HH32  CH3  HH31  108.34  3.000
 ALY  HH33  CH3  CH    109.50  3.000
 ALY  HH32  CH3  CH    109.35  3.000
 ALY  HH31  CH3  CH    113.61  3.000
 ALY  HZ    NZ   CE    117.53  3.000
 ALY  HZ    NZ   CH    118.38  3.000
 ALY  CE    NZ   CH    123.92  3.000
 ALY  HE2   CE   HE3   106.67  3.000
 ALY  HE2   CE   CD    109.88  3.000
 ALY  HE3   CE   CD    110.67  3.000
 ALY  HE2   CE   NZ    109.09  3.000
 ALY  HE3   CE   NZ    106.83  3.000
 ALY  CD    CE   NZ    113.43  3.000
 ALY  HD2   CD   HD3   106.56  3.000
 ALY  HD2   CD   CG    109.41  3.000
 ALY  HD3   CD   CG    109.27  3.000
 ALY  HD2   CD   CE    109.20  3.000
 ALY  HD3   CD   CE    108.61  3.000
 ALY  CG    CD   CE    113.54  3.000
 ALY  HG2   CG   HG3   105.80  3.000
 ALY  HG2   CG   CB    109.68  3.000
 ALY  HG3   CG   CB    109.60  3.000
 ALY  HG2   CG   CD    108.16  3.000
 ALY  HG3   CG   CD    109.53  3.000
 ALY  CB    CG   CD    113.76  3.000
 ALY  HB2   CB   HB3   106.12  3.000
 ALY  HB2   CB   CA    108.31  3.000
 ALY  HB3   CB   CA    108.54  3.000
 ALY  HB2   CB   CG    109.49  3.000
 ALY  HB3   CB   CG    109.73  3.000
 ALY  CA    CB   CG    114.33  3.000
 ALY  HCA   CA   C     107.74  3.000
 ALY  HCA   CA   N     112.14  3.000
 ALY  C     CA   N     111.00  2.800
 ALY  HCA   CA   CB    107.65  3.000
 ALY  C     CA   CB    110.10  1.900
 ALY  N     CA   CB    110.50  1.700
 ALY  H2    N    H     105.26  3.000
 ALY  H2    N    CA    108.70  3.000
 ALY  H     N    CA    114.00  3.000
 ALY  OXT   C    O     126.59  3.000
 ALY  OXT   C    CA    116.49  3.000
 ALY  O     C    CA    120.80  1.700

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
 ALY  CONST_01  CE    NZ   CH  OH      0.00   0.0  0
 ALY  CONST_02  CE    NZ   CH  CH3   180.00   0.0  0
 ALY  CONST_03  HZ    NZ   CH  OH    180.00   0.0  0
 ALY  Var_01    CD    CE   NZ  CH     81.76  30.0  3
 ALY  Var_02    CG    CD   CE  NZ    178.85  30.0  3
 ALY  Var_03    CB    CG   CD  CE    -66.51  30.0  3
 ALY  Var_04    CA    CB   CG  CD   -174.76  30.0  3
 ALY  Var_05    HH31  CH3  CH  OH    174.67  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
 ALY  chir_01  CA  CB  N  C  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
 ALY  plan-1  OH   0.020
 ALY  plan-1  CH   0.020
 ALY  plan-1  CH3  0.020
 ALY  plan-1  NZ   0.020
 ALY  plan-1  CE   0.020
 ALY  plan-1  HZ   0.020
 ALY  plan-2  CA   0.020
 ALY  plan-2  C    0.020
 ALY  plan-2  O    0.020
 ALY  plan-2  OXT  0.020

