# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:48:12 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(N)=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
 NLW  NLW  'L-leucinamide            '  L-peptide  23  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NLW
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
 NLW  CD2  C  CH3   0  -0.651   2.9979  -0.1239   1.1341
 NLW  CG   C  CH1   0  -0.222   1.9832   0.1990   0.0411
 NLW  CD1  C  CH3   0  -0.663   2.3309  -0.5335  -1.2499
 NLW  CB   C  CH2   0  -0.407   0.5754  -0.1402   0.5307
 NLW  CA   C  CH1   0  -0.223  -0.5554   0.2215  -0.4415
 NLW  N    N  NH2   0  -0.776  -0.5135   1.6286  -0.7702
 NLW  C    C  C     0   0.498  -1.8767  -0.2133   0.1985
 NLW  O    O  O     0  -0.493  -2.5256   0.5427   0.9090
 NLW  NH2  N  NH2   0  -0.797  -2.2408  -1.4802  -0.0456
 NLW  H1   H  HCH3  0   0.223   2.7704   0.4111   2.0583
 NLW  H2   H  HCH3  0   0.211   3.0026  -1.1924   1.3632
 NLW  H3   H  HCH3  0   0.225   4.0085   0.1536   0.8300
 NLW  H4   H  HCH1  0   0.219   2.0261   1.2741  -0.1544
 NLW  H5   H  HCH3  0   0.211   2.2574  -1.6165  -1.1184
 NLW  H6   H  HCH3  0   0.228   1.6698  -0.2533  -2.0711
 NLW  H7   H  HCH3  0   0.227   3.3515  -0.3089  -1.5654
 NLW  H8   H  HCH2  0   0.224   0.5241  -1.2115   0.7535
 NLW  H9   H  HCH2  0   0.228   0.3901   0.3763   1.4799
 NLW  H10  H  HCH1  0   0.249  -0.4174  -0.3435  -1.3691
 NLW  H11  H  HNH2  0   0.350  -1.2297   1.8475  -1.4514
 NLW  H12  H  HNH2  0   0.339  -0.7374   2.1721   0.0551
 NLW  H14  H  HNH2  0   0.404  -1.7028  -2.0794  -0.6471
 NLW  H15  H  HNH2  0   0.399  -3.0560  -1.8775   0.3928

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
 NLW  CD1  CG   single  1.525  0.020  1.525
 NLW  CG   CD2  single  1.526  0.020  1.526
 NLW  CG   CB   single  1.529  0.020  1.529
 NLW  CB   CA   single  1.530  0.020  1.530
 NLW  N    CA   single  1.458  0.019  1.458
 NLW  CA   C    single  1.525  0.021  1.525
 NLW  C    NH2  single  1.341  0.020  1.341
 NLW  C    O    double  1.231  0.020  1.231
 NLW  CD2  H1   single  0.970  0.020  1.090
 NLW  CD2  H2   single  0.970  0.020  1.090
 NLW  CD2  H3   single  0.970  0.020  1.090
 NLW  CG   H4   single  0.970  0.020  1.090
 NLW  CD1  H5   single  0.970  0.020  1.090
 NLW  CD1  H6   single  0.970  0.020  1.090
 NLW  CD1  H7   single  0.970  0.020  1.090
 NLW  CB   H8   single  0.970  0.020  1.090
 NLW  CB   H9   single  0.970  0.020  1.090
 NLW  CA   H10  single  0.970  0.020  1.090
 NLW  N    H11  single  0.890  0.020  1.040
 NLW  N    H12  single  0.890  0.020  1.040
 NLW  NH2  H14  single  0.860  0.020  1.020
 NLW  NH2  H15  single  0.860  0.020  1.020

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
 NLW  H3   CD2  H2   107.65  3.000
 NLW  H3   CD2  H1   107.71  3.000
 NLW  H2   CD2  H1   107.61  3.000
 NLW  H3   CD2  CG   111.25  3.000
 NLW  H2   CD2  CG   111.10  3.000
 NLW  H1   CD2  CG   111.35  3.000
 NLW  H4   CG   CB   108.15  3.000
 NLW  H4   CG   CD1  108.19  3.000
 NLW  CB   CG   CD1  112.00  3.000
 NLW  H4   CG   CD2  108.06  3.000
 NLW  CB   CG   CD2  109.64  3.000
 NLW  CD1  CG   CD2  110.68  3.000
 NLW  H7   CD1  H6   107.23  3.000
 NLW  H7   CD1  H5   107.54  3.000
 NLW  H6   CD1  H5   107.71  3.000
 NLW  H7   CD1  CG   111.04  3.000
 NLW  H6   CD1  CG   112.07  3.000
 NLW  H5   CD1  CG   111.02  3.000
 NLW  H9   CB   H8   106.06  3.000
 NLW  H9   CB   CA   108.24  3.000
 NLW  H8   CB   CA   108.96  3.000
 NLW  H9   CB   CG   109.17  3.000
 NLW  H8   CB   CG   108.98  3.000
 NLW  CA   CB   CG   115.05  3.000
 NLW  H10  CA   C    108.44  3.000
 NLW  H10  CA   N    107.81  3.000
 NLW  C    CA   N    111.00  2.800
 NLW  H10  CA   CB   108.80  3.000
 NLW  C    CA   CB   110.10  1.900
 NLW  N    CA   CB   110.50  1.700
 NLW  H12  N    H11  106.01  3.000
 NLW  H12  N    CA   109.29  3.000
 NLW  H11  N    CA   110.06  3.000
 NLW  NH2  C    O    123.06  3.000
 NLW  O    C    CA   120.80  1.700
 NLW  NH2  C    CA   115.25  3.000
 NLW  H15  NH2  H14  117.29  3.000
 NLW  H15  NH2  C    120.88  3.000
 NLW  H14  NH2  C    121.80  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
 NLW  CONST_01  H14  NH2  C   CA     0.00   0.0  0
 NLW  CONST_02  H15  NH2  C   CA   180.00   0.0  0
 NLW  Var_01    CA   CB   CG  CD2  176.25  30.0  3
 NLW  Var_02    H5   CD1  CG  CD2   64.37  30.0  3
 NLW  Var_03    H1   CD2  CG  CD1  178.86  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
 NLW  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
 NLW  plan-1  CA   0.020
 NLW  plan-1  C    0.020
 NLW  plan-1  O    0.020
 NLW  plan-1  NH2  0.020
 NLW  plan-1  H14  0.020
 NLW  plan-1  H15  0.020

