# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 17:11:40 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (2S)-2-amino-4-[(2S)-2-methylpiperidin-1-yl]-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCCCN1C(=O)C[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
 M64  M64  '(2S)-2-amino-4-[(2S)-2-methylpiperidin-1-yl]-4-oxobutanoic acid'  L-peptide  32  15  .  2022-09-22  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_M64
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
 M64  C13  C  CH2    0  -0.443   3.4301  -1.1471   0.8411
 M64  C15  C  CH1    0  -0.087   2.6964   0.7675  -0.6285
 M64  C04  C  C      0   0.403  -3.4428  -0.5331   0.0312
 M64  C06  C  CH1    0  -0.196  -2.2485   0.4126   0.3086
 M64  C07  C  CH2    0  -0.607  -0.9893  -0.2593  -0.2531
 M64  C08  C  C      0   0.564   0.2363   0.6432  -0.2822
 M64  C11  C  CH2    0  -0.349   1.5678  -1.3457  -0.8252
 M64  C12  C  CH2    0  -0.427   2.1246  -1.8621   0.4964
 M64  C14  C  CH2    0  -0.416   3.3125   0.3725   0.7146
 M64  C16  C  CH3    0  -0.658   2.7485   2.2634  -0.8966
 M64  N10  N  NT     0  -0.453   1.3889   0.1014  -0.7531
 M64  N17  N  NH2    0  -0.800  -2.1750   0.7582   1.7161
 M64  O09  O  O      0  -0.498   0.1540   1.8125   0.0712
 M64  H1   H  HCH2   0   0.236   3.7540  -1.4171   1.8484
 M64  H2   H  HCH2   0   0.218   4.2135  -1.4979   0.1609
 M64  H3   H  HCH1   0   0.234   3.3026   0.3044  -1.4148
 M64  H9   H  HCH1   0   0.209  -2.4281   1.3295  -0.2623
 M64  H10  H  HCH2   0   0.254  -0.7792  -1.1516   0.3467
 M64  H11  H  HCH2   0   0.267  -1.1823  -0.6163  -1.2691
 M64  H12  H  HCH2   0   0.249   2.2744  -1.5550  -1.6328
 M64  H13  H  HCH2   0   0.271   0.6413  -1.8431  -1.0989
 M64  H14  H  HCH2   0   0.237   2.2877  -2.9403   0.4339
 M64  H15  H  HCH2   0   0.222   1.3816  -1.6994   1.2843
 M64  H16  H  HCH2   0   0.222   2.6980   0.7827   1.5229
 M64  H17  H  HCH2   0   0.232   4.3018   0.8270   0.8121
 M64  H18  H  HCH3   0   0.231   2.3813   2.8605  -0.0675
 M64  H19  H  HCH3   0   0.223   3.7927   2.5305  -1.0681
 M64  H20  H  HCH3   0   0.229   2.1915   2.5347  -1.7934
 M64  H30  H  HNH2   0   0.324  -2.2554  -0.0869   2.2667
 M64  H4   H  HNH2   0   0.333  -1.2788   1.1760   1.9261
 M64  O05  O  O      0  -0.602  -3.9522  -1.1213   1.0041
 M64  OXT  O  OC    -1  -0.620  -3.7757  -0.6489  -1.1659

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
 M64  C13  C12  single  1.528  0.020  1.528
 M64  C13  C14  single  1.529  0.020  1.529
 M64  C15  C16  single  1.521  0.020  1.521
 M64  C15  N10  single  1.473  0.020  1.473
 M64  C15  C14  single  1.530  0.020  1.530
 M64  C04  O05  deloc   1.246  0.020  1.246
 M64  C04  C06  single  1.548  0.020  1.548
 M64  C06  C07  single  1.534  0.020  1.534
 M64  C06  N17  single  1.451  0.020  1.451
 M64  C07  C08  single  1.522  0.020  1.522
 M64  C08  N10  single  1.358  0.020  1.358
 M64  C08  O09  double  1.224  0.020  1.224
 M64  C11  N10  single  1.460  0.020  1.460
 M64  C11  C12  single  1.524  0.020  1.524
 M64  C13  H1   single  0.970  0.020  1.090
 M64  C13  H2   single  0.970  0.020  1.090
 M64  C15  H3   single  0.970  0.020  1.090
 M64  C06  H9   single  0.970  0.020  1.090
 M64  C07  H10  single  0.970  0.020  1.090
 M64  C07  H11  single  0.970  0.020  1.090
 M64  C11  H12  single  0.970  0.020  1.090
 M64  C11  H13  single  0.970  0.020  1.090
 M64  C12  H14  single  0.970  0.020  1.090
 M64  C12  H15  single  0.970  0.020  1.090
 M64  C14  H16  single  0.970  0.020  1.090
 M64  C14  H17  single  0.970  0.020  1.090
 M64  C16  H18  single  0.970  0.020  1.090
 M64  C16  H19  single  0.970  0.020  1.090
 M64  C16  H20  single  0.970  0.020  1.090
 M64  N17  H30  single  0.890  0.020  1.040
 M64  C04  OXT  deloc   1.248  0.020  1.248
 M64  N17  H4   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
 M64  H2   C13  H1   106.35  3.000
 M64  H2   C13  C14  108.78  3.000
 M64  H1   C13  C14  110.16  3.000
 M64  H2   C13  C12  108.74  3.000
 M64  H1   C13  C12  110.24  3.000
 M64  C14  C13  C12  112.37  3.000
 M64  H3   C15  N10  103.85  3.000
 M64  H3   C15  C16  105.69  3.000
 M64  N10  C15  C16  117.41  3.000
 M64  H3   C15  C14  107.35  3.000
 M64  N10  C15  C14  108.37  3.000
 M64  C16  C15  C14  113.27  3.000
 M64  OXT  C04  O05  126.60  3.000
 M64  OXT  C04  C06  115.74  3.000
 M64  O05  C04  C06  117.64  3.000
 M64  H9   C06  N17  108.34  3.000
 M64  H9   C06  C07  108.09  3.000
 M64  N17  C06  C07  114.71  3.000
 M64  H9   C06  C04  106.95  3.000
 M64  N17  C06  C04  110.99  3.000
 M64  C07  C06  C04  107.46  3.000
 M64  H11  C07  H10  106.05  3.000
 M64  H11  C07  C08  108.53  3.000
 M64  H10  C07  C08  109.81  3.000
 M64  H11  C07  C06  109.77  3.000
 M64  H10  C07  C06  108.29  3.000
 M64  C08  C07  C06  114.09  3.000
 M64  O09  C08  N10  122.57  3.000
 M64  O09  C08  C07  120.43  3.000
 M64  N10  C08  C07  116.96  3.000
 M64  H13  C11  H12  106.10  3.000
 M64  H13  C11  N10  111.21  3.000
 M64  H12  C11  N10  107.78  3.000
 M64  H13  C11  C12  112.01  3.000
 M64  H12  C11  C12  109.85  3.000
 M64  N10  C11  C12  109.74  3.000
 M64  H15  C12  H14  106.80  3.000
 M64  H15  C12  C11  109.01  3.000
 M64  H14  C12  C11  109.84  3.000
 M64  H15  C12  C13  110.36  3.000
 M64  H14  C12  C13  110.32  3.000
 M64  C11  C12  C13  110.44  3.000
 M64  H17  C14  H16  106.63  3.000
 M64  H17  C14  C15  109.60  3.000
 M64  H16  C14  C15  108.99  3.000
 M64  H17  C14  C13  109.65  3.000
 M64  H16  C14  C13  110.75  3.000
 M64  C15  C14  C13  111.11  3.000
 M64  H20  C16  H19  107.38  3.000
 M64  H20  C16  H18  108.58  3.000
 M64  H19  C16  H18  108.00  3.000
 M64  H20  C16  C15  111.86  3.000
 M64  H19  C16  C15  107.53  3.000
 M64  H18  C16  C15  113.25  3.000
 M64  C11  N10  C08  121.11  3.000
 M64  C11  N10  C15  110.11  3.000
 M64  C08  N10  C15  122.94  3.000
 M64  H4   N17  H30  107.62  3.000
 M64  H4   N17  C06  110.17  3.000
 M64  H30  N17  C06  108.96  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
 M64  CONST_01  C07  C08  N10  C15  180.00   0.0  0
 M64  CONST_02  O09  C08  N10  C15    0.00   0.0  0
 M64  Var_01    N10  C11  C12  C13  -56.39  30.0  1
 M64  Var_02    C12  C11  N10  C15   65.92  30.0  1
 M64  Var_03    C12  C13  C14  C15  -49.65  30.0  1
 M64  Var_04    C14  C13  C12  C11   48.93  30.0  1
 M64  Var_05    N10  C08  C07  C06  179.18  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
 M64  chir_01  C15  C16  N10  C14  positiv
 M64  chir_02  C06  N17  C04  C07  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
 M64  plan-1  C15  0.020
 M64  plan-1  C07  0.020
 M64  plan-1  C08  0.020
 M64  plan-1  C11  0.020
 M64  plan-1  N10  0.020
 M64  plan-1  O09  0.020
 M64  plan-2  C04  0.020
 M64  plan-2  C06  0.020
 M64  plan-2  O05  0.020
 M64  plan-2  OXT  0.020

