# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:39:03 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: N-methyl-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@@H](N)CC(C)C
#
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
 LNM  LNM  'N-methyl-L-leucinamide   '  L-peptide  26  10  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LNM
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
 LNM  N13   N  NH2   0  -0.776   0.2168  -1.9178   0.6172
 LNM  C14   C  CH1   0  -0.228  -0.0828  -0.5131   0.4334
 LNM  C15   C  C     0   0.531  -1.4871  -0.2662  -0.1214
 LNM  N16   N  NH1   0  -0.620  -2.1156   0.8178   0.3498
 LNM  C17   C  CH3   0  -0.512  -3.4142   1.2363  -0.1225
 LNM  C22   C  CH2   0  -0.403   0.9223   0.1338  -0.5260
 LNM  O23   O  O     0  -0.505  -1.9831  -1.0014  -0.9669
 LNM  C27   C  CH1   0  -0.225   2.3852   0.0395  -0.0919
 LNM  C28   C  CH3   0  -0.651   3.2838   0.5990  -1.1912
 LNM  C29   C  CH3   0  -0.664   2.6368   0.7688   1.2236
 LNM  HN13  H  HNH2  0   0.350  -0.4043  -2.3142   1.3117
 LNM  H14   H  HCH1  0   0.247  -0.0018  -0.0271   1.4107
 LNM  H17   H  HCH3  0   0.236  -3.3985   1.4830  -1.1848
 LNM  H17A  H  HCH3  0   0.237  -4.1672   0.4641   0.0373
 LNM  H22   H  HCH2  0   0.227   0.8078  -0.3321  -1.5110
 LNM  H22A  H  HCH2  0   0.223   0.6587   1.1898  -0.6570
 LNM  H27   H  HCH1  0   0.219   2.6293  -1.0172   0.0494
 LNM  H28   H  HCH3  0   0.211   3.0728   1.6571  -1.3676
 LNM  H28A  H  HCH3  0   0.224   4.3384   0.5130  -0.9235
 LNM  H28B  H  HCH3  0   0.223   3.1383   0.0704  -2.1354
 LNM  H29   H  HCH3  0   0.228   2.0781   0.3334   2.0528
 LNM  H29A  H  HCH3  0   0.227   3.6935   0.7336   1.4945
 LNM  H29B  H  HCH3  0   0.212   2.3508   1.8209   1.1447
 LNM  H25   H  HNH1  0   0.402  -1.6634   1.3769   1.0535
 LNM  H26   H  HCH3  0   0.249  -3.7124   2.1229   0.4295
 LNM  H2    H  HNH2  0   0.339   0.0251  -2.4170  -0.2436

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
 LNM  N13  HN13  single  0.890  0.020  1.040
 LNM  C14  N13   single  1.448  0.020  1.448
 LNM  C14  C15   single  1.530  0.020  1.530
 LNM  C14  H14   single  0.970  0.020  1.090
 LNM  C15  O23   double  1.225  0.020  1.225
 LNM  C15  N16   single  1.339  0.020  1.339
 LNM  N16  C17   single  1.444  0.020  1.444
 LNM  C17  H17   single  0.970  0.020  1.090
 LNM  C17  H17A  single  0.970  0.020  1.090
 LNM  C22  C14   single  1.533  0.020  1.533
 LNM  C22  H22   single  0.970  0.020  1.090
 LNM  C22  H22A  single  0.970  0.020  1.090
 LNM  C27  C22   single  1.529  0.020  1.529
 LNM  C27  C29   single  1.525  0.020  1.525
 LNM  C27  H27   single  0.970  0.020  1.090
 LNM  C28  C27   single  1.526  0.020  1.526
 LNM  C28  H28   single  0.970  0.020  1.090
 LNM  C28  H28A  single  0.970  0.020  1.090
 LNM  C28  H28B  single  0.970  0.020  1.090
 LNM  C29  H29   single  0.970  0.020  1.090
 LNM  C29  H29A  single  0.970  0.020  1.090
 LNM  C29  H29B  single  0.970  0.020  1.090
 LNM  N16  H25   single  0.860  0.020  1.020
 LNM  C17  H26   single  0.970  0.020  1.090
 LNM  N13  H2    single  0.890  0.020  1.040

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
 LNM  H2    N13  HN13  105.89  3.000
 LNM  H2    N13  C14   109.33  3.000
 LNM  HN13  N13  C14   109.87  3.000
 LNM  H14   C14  C22   108.84  3.000
 LNM  C22   C14  C15   107.87  3.000
 LNM  H14   C14  C15   108.67  3.000
 LNM  C22   C14  N13   110.68  3.000
 LNM  H14   C14  N13   107.58  3.000
 LNM  C15   C14  N13   113.11  3.000
 LNM  O23   C15  N16   122.60  3.000
 LNM  N16   C15  C14   115.72  3.000
 LNM  O23   C15  C14   121.66  3.000
 LNM  H25   N16  C17   118.16  3.000
 LNM  H25   N16  C15   119.02  3.000
 LNM  C17   N16  C15   122.81  3.000
 LNM  H26   C17  H17A  108.30  3.000
 LNM  H26   C17  H17   108.33  3.000
 LNM  H17A  C17  H17   108.23  3.000
 LNM  H26   C17  N16   108.50  3.000
 LNM  H17A  C17  N16   111.59  3.000
 LNM  H17   C17  N16   111.79  3.000
 LNM  H22A  C22  H22   106.08  3.000
 LNM  H22A  C22  C27   108.87  3.000
 LNM  H22   C22  C27   109.21  3.000
 LNM  C27   C22  C14   115.07  3.000
 LNM  H22A  C22  C14   108.89  3.000
 LNM  H22   C22  C14   108.34  3.000
 LNM  H27   C27  C29   108.29  3.000
 LNM  H27   C27  C28   108.42  3.000
 LNM  C29   C27  C28   110.42  3.000
 LNM  C28   C27  C22   109.65  3.000
 LNM  H27   C27  C22   108.05  3.000
 LNM  C29   C27  C22   111.92  3.000
 LNM  H28B  C28  H28A  107.62  3.000
 LNM  H28B  C28  H28   107.65  3.000
 LNM  H28A  C28  H28   107.60  3.000
 LNM  H28B  C28  C27   111.53  3.000
 LNM  H28A  C28  C27   111.31  3.000
 LNM  H28   C28  C27   110.95  3.000
 LNM  H29B  C29  H29A  107.60  3.000
 LNM  H29B  C29  H29   107.76  3.000
 LNM  H29A  C29  H29   107.12  3.000
 LNM  H29B  C29  C27   110.79  3.000
 LNM  H29A  C29  C27   111.00  3.000
 LNM  H29   C29  C27   112.36  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
 LNM  CONST_01  C17  N16  C15  C14  180.00   0.0  0
 LNM  CONST_02  O23  C15  N16  C17    0.00   0.0  0
 LNM  CONST_03  H25  N16  C15  C14    0.00   0.0  0
 LNM  Var_01    C29  C27  C22  C14  -62.50  30.0  1
 LNM  Var_02    H17  C17  N16  C15  -61.90  30.0  3
 LNM  Var_03    H29  C29  C27  C22   62.84  30.0  3
 LNM  Var_04    H28  C28  C27  C22   62.19  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
 LNM  chir_01  C14  N13  C15  C22  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
 LNM  plan-1  C14  0.020
 LNM  plan-1  C15  0.020
 LNM  plan-1  N16  0.020
 LNM  plan-1  C17  0.020
 LNM  plan-1  O23  0.020
 LNM  plan-1  H25  0.020

