# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 21:00:56 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: N-acetyl-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)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
 LAY  LAY  'N-acetyl-L-leucine       '  L-peptide  27  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_LAY
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
 LAY  CN    C  C     0   0.523   1.9035   1.1124   0.1642
 LAY  O     O  O     0  -0.498   2.4264   0.4934   1.0798
 LAY  CH3   C  CH3   0  -0.781   2.5569   2.2885  -0.5128
 LAY  N     N  NH1   0  -0.628   0.6934   0.7695  -0.3198
 LAY  CA    C  CH1   0  -0.177  -0.0075  -0.3859   0.1655
 LAY  C     C  C     0   0.548   0.7536  -1.6565  -0.1801
 LAY  ON    O  O     0  -0.436   1.5131  -1.7688  -1.1062
 LAY  CB    C  CH2   0  -0.457  -1.4113  -0.4615  -0.4445
 LAY  CG    C  CH1   0  -0.237  -2.2960   0.7564  -0.1631
 LAY  CD1   C  CH3   0  -0.652  -3.6538   0.5527  -0.8273
 LAY  CD2   C  CH3   0  -0.663  -2.4589   1.0174   1.3300
 LAY  OXT   O  OH1   0  -0.592   0.4350  -2.6476   0.6418
 LAY  HH31  H  HCH3  0   0.263   3.3178   2.7195   0.1330
 LAY  HH32  H  HCH3  0   0.272   3.0411   1.9566  -1.4332
 LAY  HH33  H  HCH3  0   0.257   1.8364   3.0607  -0.7795
 LAY  H     H  HNH1  0   0.406   0.3373   1.2458  -1.1332
 LAY  HA    H  HCH1  0   0.282  -0.0963  -0.3316   1.2536
 LAY  HB1C  H  HCH2  0   0.250  -1.3232  -0.6056  -1.5264
 LAY  HB2C  H  HCH2  0   0.253  -1.9069  -1.3532  -0.0515
 LAY  HXT   H  HOH1  0   0.483   0.8836  -3.4629   0.3716
 LAY  HG    H  HCH1  0   0.224  -1.8357   1.6414  -0.6158
 LAY  HD11  H  HCH3  0   0.228  -3.5515   0.3716  -1.8986
 LAY  HD12  H  HCH3  0   0.217  -4.1770  -0.3033  -0.3942
 LAY  HD13  H  HCH3  0   0.231  -4.2894   1.4295  -0.6976
 LAY  HD21  H  HCH3  0   0.231  -1.5175   1.2886   1.8097
 LAY  HD22  H  HCH3  0   0.234  -3.1561   1.8385   1.5036
 LAY  HD23  H  HCH3  0   0.219  -2.8535   0.1356   1.8409

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
 LAY  CN   O     double  1.223  0.020  1.223
 LAY  CN   CH3   single  1.506  0.020  1.506
 LAY  CN   N     single  1.348  0.020  1.348
 LAY  N    CA    single  1.458  0.019  1.458
 LAY  CA   C     single  1.525  0.021  1.525
 LAY  CA   CB    single  1.530  0.020  1.530
 LAY  C    ON    double  1.203  0.020  1.203
 LAY  C    OXT   single  1.326  0.020  1.326
 LAY  CB   CG    single  1.531  0.020  1.531
 LAY  CG   CD1   single  1.525  0.020  1.525
 LAY  CG   CD2   single  1.524  0.020  1.524
 LAY  CH3  HH31  single  0.970  0.020  1.090
 LAY  CH3  HH32  single  0.970  0.020  1.090
 LAY  CH3  HH33  single  0.970  0.020  1.090
 LAY  N    H     single  0.860  0.020  0.860
 LAY  CA   HA    single  0.970  0.020  0.970
 LAY  CB   HB1C  single  0.970  0.020  1.090
 LAY  CB   HB2C  single  0.970  0.020  1.090
 LAY  OXT  HXT   single  0.850  0.020  0.980
 LAY  CG   HG    single  0.970  0.020  1.090
 LAY  CD1  HD11  single  0.970  0.020  1.090
 LAY  CD1  HD12  single  0.970  0.020  1.090
 LAY  CD1  HD13  single  0.970  0.020  1.090
 LAY  CD2  HD21  single  0.970  0.020  1.090
 LAY  CD2  HD22  single  0.970  0.020  1.090
 LAY  CD2  HD23  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
 LAY  N     CN   CH3   115.26  3.000
 LAY  N     CN   O     121.61  3.000
 LAY  CH3   CN   O     123.12  3.000
 LAY  HH33  CH3  HH32  107.61  3.000
 LAY  HH33  CH3  HH31  109.11  3.000
 LAY  HH32  CH3  HH31  108.12  3.000
 LAY  HH33  CH3  CN    112.13  3.000
 LAY  HH32  CH3  CN    109.51  3.000
 LAY  HH31  CH3  CN    110.26  3.000
 LAY  H     N    CA    114.00  3.000
 LAY  H     N    CN    119.15  3.000
 LAY  CA    N    CN    121.44  3.000
 LAY  HA    CA   CB    109.00  3.000
 LAY  HA    CA   C     109.00  3.000
 LAY  CB    CA   C     110.10  1.900
 LAY  HA    CA   N     110.00  3.000
 LAY  CB    CA   N     110.50  1.700
 LAY  C     CA   N     111.00  2.800
 LAY  OXT   C    ON    123.98  3.000
 LAY  OXT   C    CA    111.30  3.000
 LAY  ON    C    CA    124.67  3.000
 LAY  HB2C  CB   HB1C  106.52  3.000
 LAY  HB2C  CB   CG    108.70  3.000
 LAY  HB1C  CB   CG    109.44  3.000
 LAY  HB2C  CB   CA    108.21  3.000
 LAY  HB1C  CB   CA    109.03  3.000
 LAY  CG    CB   CA    114.63  3.000
 LAY  HG    CG   CD2   108.14  3.000
 LAY  HG    CG   CD1   107.58  3.000
 LAY  CD2   CG   CD1   110.75  3.000
 LAY  HG    CG   CB    108.89  3.000
 LAY  CD2   CG   CB    112.21  3.000
 LAY  CD1   CG   CB    109.15  3.000
 LAY  HD13  CD1  HD12  107.67  3.000
 LAY  HD13  CD1  HD11  107.75  3.000
 LAY  HD12  CD1  HD11  107.69  3.000
 LAY  HD13  CD1  CG    111.08  3.000
 LAY  HD12  CD1  CG    110.99  3.000
 LAY  HD11  CD1  CG    111.48  3.000
 LAY  HD23  CD2  HD22  107.58  3.000
 LAY  HD23  CD2  HD21  107.86  3.000
 LAY  HD22  CD2  HD21  107.13  3.000
 LAY  HD23  CD2  CG    111.00  3.000
 LAY  HD22  CD2  CG    110.67  3.000
 LAY  HD21  CD2  CG    112.40  3.000
 LAY  HXT   OXT  C     110.16  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
 LAY  CONST_01  CA    N    CN  O      0.00   0.0  0
 LAY  CONST_02  CA    N    CN  CH3  180.00   0.0  0
 LAY  CONST_03  H     N    CN  O    180.00   0.0  0
 LAY  CONST_04  HXT   OXT  C   CA   180.00   0.0  0
 LAY  Var_01    CD1   CG   CB  CA   179.82  30.0  3
 LAY  Var_02    HH31  CH3  CN  O    -21.18  30.0  3
 LAY  Var_03    HD11  CD1  CG  CB   -56.38  30.0  3
 LAY  Var_04    HD21  CD2  CG  CB    64.83  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
 LAY  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
 LAY  plan-1  CN   0.020
 LAY  plan-1  O    0.020
 LAY  plan-1  CH3  0.020
 LAY  plan-1  N    0.020
 LAY  plan-1  CA   0.020
 LAY  plan-1  H    0.020
 LAY  plan-2  CA   0.020
 LAY  plan-2  C    0.020
 LAY  plan-2  ON   0.020
 LAY  plan-2  OXT  0.020
 LAY  plan-2  HXT  0.020

