# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:14:02 2021
#   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  33  15  .  2022-09-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.438  67.9637  -24.7773  198.3797
 M64  C15  C  CH1   0  -0.097  68.0581  -27.0971  197.3975
 M64  C04  C  C     0   0.545  72.5559  -29.5998  196.5709
 M64  C06  C  CH1   0  -0.199  72.0229  -28.9598  197.8397
 M64  C07  C  CH2   0  -0.606  70.6589  -28.3246  197.5583
 M64  C08  C  C     0   0.583  69.9454  -27.8855  198.8271
 M64  C11  C  CH2   0  -0.333  67.9981  -26.8279  199.8324
 M64  C12  C  CH2   0  -0.432  68.0176  -25.2983  199.8235
 M64  C14  C  CH2   0  -0.465  67.2589  -25.7875  197.4845
 M64  C16  C  CH3   0  -0.651  67.1722  -28.2688  196.9942
 M64  N10  N  NT    0  -0.460  68.7239  -27.3387  198.6817
 M64  N17  N  NH2   0  -0.800  72.9621  -27.9541  198.2911
 M64  O09  O  O     0  -0.510  70.4650  -28.0454  199.9276
 M64  H1   H  HCH2  0   0.241  67.4572  -23.8119  198.3406
 M64  H2   H  HCH2  0   0.225  68.9756  -24.6084  198.0017
 M64  H3   H  HCH1  0   0.260  68.8261  -26.9519  196.6368
 M64  H9   H  HCH1  0   0.257  71.8767  -29.7824  198.5563
 M64  H10  H  HCH2  0   0.281  70.8104  -27.4678  196.8954
 M64  H11  H  HCH2  0   0.285  70.0149  -29.0215  197.0189
 M64  H12  H  HCH2  0   0.247  66.9698  -27.1925  199.7714
 M64  H13  H  HCH2  0   0.266  68.4201  -27.2326  200.7472
 M64  H14  H  HCH2  0   0.233  68.9134  -24.9286  200.3258
 M64  H15  H  HCH2  0   0.231  67.1605  -24.9354  200.3948
 M64  H16  H  HCH2  0   0.227  66.2528  -25.9831  197.8702
 M64  H17  H  HCH2  0   0.253  67.1274  -25.3979  196.4736
 M64  H18  H  HCH3  0   0.234  66.6869  -28.0636  196.0393
 M64  H19  H  HCH3  0   0.235  67.7420  -29.1923  196.8882
 M64  H20  H  HCH3  0   0.228  66.3896  -28.4369  197.7363
 M64  H30  H  HNH2  0   0.356  72.6543  -27.6232  199.1959
 M64  OXT  O  OH1   0  -0.595  71.7557  -30.5658  196.1330
 M64  HXT  H  HOH1  0   0.483  72.1202  -30.9554  195.3245
 M64  H4   H  HNH2  0   0.350  73.8708  -28.3725  198.4448
 M64  O05  O  O     0  -0.434  73.5863  -29.2989  196.0263

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  1.536  0.020  1.536
 M64  C13  C14  single  1.523  0.020  1.523
 M64  C15  C16  single  1.523  0.020  1.523
 M64  C15  N10  single  1.467  0.020  1.467
 M64  C15  C14  single  1.537  0.020  1.537
 M64  C04  O05  double  1.204  0.020  1.204
 M64  C04  C06  single  1.518  0.020  1.518
 M64  C06  C07  single  1.531  0.020  1.531
 M64  C06  N17  single  1.448  0.020  1.448
 M64  C07  C08  single  1.520  0.020  1.520
 M64  C08  N10  single  1.346  0.020  1.346
 M64  C08  O09  double  1.228  0.020  1.228
 M64  C11  N10  single  1.453  0.020  1.453
 M64  C11  C12  single  1.530  0.020  1.530
 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  single  1.329  0.020  1.329
 M64  OXT  HXT  single  0.850  0.020  0.980
 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   106.30  3.000
 M64  H2   C13  C14  109.12  3.000
 M64  H1   C13  C14  110.55  3.000
 M64  H2   C13  C12  110.18  3.000
 M64  H1   C13  C12  110.50  3.000
 M64  C14  C13  C12  110.11  3.000
 M64  H3   C15  N10  108.24  3.000
 M64  H3   C15  C16  109.10  3.000
 M64  N10  C15  C16  111.66  3.000
 M64  H3   C15  C14  106.99  3.000
 M64  N10  C15  C14  109.09  3.000
 M64  C16  C15  C14  111.60  3.000
 M64  OXT  C04  O05  123.24  3.000
 M64  OXT  C04  C06  111.76  3.000
 M64  O05  C04  C06  124.99  3.000
 M64  H9   C06  N17  113.72  3.000
 M64  H9   C06  C07  108.14  3.000
 M64  N17  C06  C07  110.31  3.000
 M64  H9   C06  C04  106.01  3.000
 M64  N17  C06  C04  109.01  3.000
 M64  C07  C06  C04  109.53  3.000
 M64  H11  C07  H10  106.40  3.000
 M64  H11  C07  C08  108.65  3.000
 M64  H10  C07  C08  110.16  3.000
 M64  H11  C07  C06  110.59  3.000
 M64  H10  C07  C06  108.24  3.000
 M64  C08  C07  C06  112.62  3.000
 M64  O09  C08  N10  122.26  3.000
 M64  O09  C08  C07  120.79  3.000
 M64  N10  C08  C07  116.94  3.000
 M64  H13  C11  H12  106.77  3.000
 M64  H13  C11  N10  110.00  3.000
 M64  H12  C11  N10  107.97  3.000
 M64  H13  C11  C12  111.88  3.000
 M64  H12  C11  C12  110.20  3.000
 M64  N10  C11  C12  109.91  3.000
 M64  H15  C12  H14  106.90  3.000
 M64  H15  C12  C11  108.62  3.000
 M64  H14  C12  C11  110.27  3.000
 M64  H15  C12  C13  110.57  3.000
 M64  H14  C12  C13  110.27  3.000
 M64  C11  C12  C13  110.14  3.000
 M64  H17  C14  H16  106.22  3.000
 M64  H17  C14  C15  108.33  3.000
 M64  H16  C14  C15  110.21  3.000
 M64  H17  C14  C13  111.32  3.000
 M64  H16  C14  C13  109.67  3.000
 M64  C15  C14  C13  110.97  3.000
 M64  H20  C16  H19  108.08  3.000
 M64  H20  C16  H18  107.77  3.000
 M64  H19  C16  H18  107.87  3.000
 M64  H20  C16  C15  110.82  3.000
 M64  H19  C16  C15  111.92  3.000
 M64  H18  C16  C15  110.23  3.000
 M64  C11  N10  C08  120.70  3.000
 M64  C11  N10  C15  114.12  3.000
 M64  C08  N10  C15  124.99  3.000
 M64  H4   N17  H30  105.82  3.000
 M64  H4   N17  C06  110.03  3.000
 M64  H30  N17  C06  107.98  3.000
 M64  HXT  OXT  C04  109.93  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     0.00   0.0  0
 M64  CONST_02  O09  C08  N10  C15   180.00   0.0  0
 M64  CONST_03  C11  N10  C08  C07   180.00   0.0  0
 M64  CONST_04  O09  C08  N10  C11     0.00   0.0  0
 M64  CONST_05  HXT  OXT  C04  C06   180.00   0.0  0
 M64  Var_01    N10  C11  C12  C13    34.82  30.0  1
 M64  Var_02    C12  C11  N10  C15   -69.31  30.0  1
 M64  Var_03    C12  C13  C14  C15   -64.51  30.0  1
 M64  Var_04    C14  C13  C12  C11    27.19  30.0  1
 M64  Var_05    N10  C08  C07  C06  -178.71  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  OXT  0.020
 M64  plan-2  HXT  0.020
 M64  plan-2  O05  0.020

