# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 15:58:51 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2R)-2-amino-1-[(2S)-2-methylpiperidin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)C(=O)N1CCCC[C@@H]1C
#
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
 8CN  8CN  "(2R)-2-amino-1-[(2S)-2-methylpiperidin-1-yl]propan-1-one"
  ligand  30  12  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8CN
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
 8CN  C10  C  CH2   0  -0.424   0.6810  3.8310   -6.5092
 8CN  C01  C  CH3   0  -0.647   1.5724  4.6066  -12.4324
 8CN  C02  C  CH1   0  -0.246   0.8895  3.8970  -11.2769
 8CN  N03  N  NH2   0  -0.798   1.4444  2.5501  -11.1431
 8CN  C04  C  C     0   0.590   1.1411  4.6272   -9.9527
 8CN  O05  O  O     0  -0.499   2.0495  5.4432   -9.8633
 8CN  N06  N  NT    0  -0.461   0.3648  4.3001   -8.8932
 8CN  C07  C  CH2   0  -0.328  -0.8211  3.4551   -8.9445
 8CN  C08  C  CH2   0  -0.430  -0.7673  2.3535   -7.8965
 8CN  C09  C  CH2   0  -0.450  -0.5527  2.9380   -6.5079
 8CN  C11  C  CH1   0  -0.115   0.6314  4.9133   -7.5885
 8CN  C12  C  CH3   0  -0.660  -0.3667  6.0249   -7.2760
 8CN  H1   H  HCH2  0   0.228   1.5669  3.2114   -6.6799
 8CN  H2   H  HCH2  0   0.234   0.8155  4.3101   -5.5367
 8CN  H4   H  HCH3  0   0.225   2.6526  4.6420  -12.3005
 8CN  H5   H  HCH3  0   0.228   1.3601  4.0749  -13.3613
 8CN  H6   H  HCH1  0   0.228  -0.1869  3.8995  -11.4963
 8CN  H7   H  HNH2  0   0.356   0.9279  2.0084  -10.4613
 8CN  H8   H  HNH2  0   0.352   1.3284  2.0606  -12.0226
 8CN  H10  H  HCH2  0   0.247  -1.7097  4.0729   -8.7774
 8CN  H11  H  HCH2  0   0.268  -0.9388  3.0213   -9.9326
 8CN  H12  H  HCH2  0   0.238  -1.6960  1.7808   -7.9419
 8CN  H13  H  HCH2  0   0.224   0.0466  1.6618   -8.1368
 8CN  H14  H  HCH2  0   0.221  -1.4374  3.5067   -6.2057
 8CN  H15  H  HCH2  0   0.238  -0.4351  2.1402   -5.7719
 8CN  H16  H  HCH1  0   0.259   1.6188  5.3657   -7.6493
 8CN  H17  H  HCH3  0   0.232  -0.1033  6.4991   -6.3299
 8CN  H18  H  HCH3  0   0.235  -0.3478  6.7915   -8.0510
 8CN  H19  H  HCH3  0   0.226  -1.3914  5.6637   -7.1856
 8CN  H3   H  HCH3  0   0.229   1.2040  5.6253  -12.5471

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
 8CN  C01  C02  single  1.518  0.020  1.518
 8CN  N03  C02  single  1.463  0.020  1.463
 8CN  C02  C04  single  1.533  0.020  1.533
 8CN  O05  C04  double  1.224  0.020  1.224
 8CN  C04  N06  single  1.354  0.020  1.354
 8CN  C07  N06  single  1.457  0.020  1.457
 8CN  C07  C08  single  1.521  0.020  1.521
 8CN  N06  C11  single  1.466  0.020  1.466
 8CN  C08  C09  single  1.522  0.020  1.522
 8CN  C11  C12  single  1.526  0.020  1.526
 8CN  C11  C10  single  1.529  0.020  1.529
 8CN  C09  C10  single  1.523  0.020  1.523
 8CN  C10  H1   single  0.970  0.020  1.090
 8CN  C10  H2   single  0.970  0.020  1.090
 8CN  C01  H3   single  0.970  0.020  1.090
 8CN  C01  H4   single  0.970  0.020  1.090
 8CN  C01  H5   single  0.970  0.020  1.090
 8CN  C02  H6   single  0.970  0.020  1.090
 8CN  N03  H7   single  0.890  0.020  1.040
 8CN  N03  H8   single  0.890  0.020  1.040
 8CN  C07  H10  single  0.970  0.020  1.090
 8CN  C07  H11  single  0.970  0.020  1.090
 8CN  C08  H12  single  0.970  0.020  1.090
 8CN  C08  H13  single  0.970  0.020  1.090
 8CN  C09  H14  single  0.970  0.020  1.090
 8CN  C09  H15  single  0.970  0.020  1.090
 8CN  C11  H16  single  0.970  0.020  1.090
 8CN  C12  H17  single  0.970  0.020  1.090
 8CN  C12  H18  single  0.970  0.020  1.090
 8CN  C12  H19  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
 8CN  H2   C10  H1   106.71  3.000
 8CN  H2   C10  C11  108.77  3.000
 8CN  H1   C10  C11  108.47  3.000
 8CN  H2   C10  C09  110.87  3.000
 8CN  H1   C10  C09  108.90  3.000
 8CN  C11  C10  C09  112.91  3.000
 8CN  H5   C01  H4   108.18  3.000
 8CN  H5   C01  H3   107.47  3.000
 8CN  H4   C01  H3   108.54  3.000
 8CN  H5   C01  C02  109.43  3.000
 8CN  H4   C01  C02  111.67  3.000
 8CN  H3   C01  C02  111.41  3.000
 8CN  H6   C02  C04  109.41  3.000
 8CN  H6   C02  N03  113.08  3.000
 8CN  C04  C02  N03  107.30  3.000
 8CN  H6   C02  C01  106.72  3.000
 8CN  C04  C02  C01  111.16  3.000
 8CN  N03  C02  C01  109.23  3.000
 8CN  H8   N03  H7   105.53  3.000
 8CN  H8   N03  C02  108.79  3.000
 8CN  H7   N03  C02  111.14  3.000
 8CN  N06  C04  O05  121.96  3.000
 8CN  N06  C04  C02  117.83  3.000
 8CN  O05  C04  C02  120.15  3.000
 8CN  C11  N06  C07  114.95  3.000
 8CN  C11  N06  C04  119.42  3.000
 8CN  C07  N06  C04  125.40  3.000
 8CN  H11  C07  H10  106.05  3.000
 8CN  H11  C07  C08  109.96  3.000
 8CN  H10  C07  C08  109.40  3.000
 8CN  H11  C07  N06  110.61  3.000
 8CN  H10  C07  N06  109.14  3.000
 8CN  C08  C07  N06  111.52  3.000
 8CN  H13  C08  H12  106.97  3.000
 8CN  H13  C08  C09  109.76  3.000
 8CN  H12  C08  C09  111.05  3.000
 8CN  H13  C08  C07  109.43  3.000
 8CN  H12  C08  C07  108.73  3.000
 8CN  C09  C08  C07  110.82  3.000
 8CN  H15  C09  H14  106.30  3.000
 8CN  H15  C09  C08  110.47  3.000
 8CN  H14  C09  C08  109.74  3.000
 8CN  H15  C09  C10  109.98  3.000
 8CN  H14  C09  C10  110.51  3.000
 8CN  C08  C09  C10  109.80  3.000
 8CN  H16  C11  C12  107.59  3.000
 8CN  H16  C11  N06  106.81  3.000
 8CN  C12  C11  N06  111.59  3.000
 8CN  H16  C11  C10  107.72  3.000
 8CN  C12  C11  C10  113.09  3.000
 8CN  N06  C11  C10  109.75  3.000
 8CN  H19  C12  H18  107.95  3.000
 8CN  H19  C12  H17  107.41  3.000
 8CN  H18  C12  H17  107.86  3.000
 8CN  H19  C12  C11  112.98  3.000
 8CN  H18  C12  C11  110.80  3.000
 8CN  H17  C12  C11  109.65  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
 8CN  CONST_01  C07  N06  C04  C02     0.00   0.0  0
 8CN  CONST_02  C11  N06  C04  C02   180.00   0.0  0
 8CN  CONST_03  C07  N06  C04  O05   180.00   0.0  0
 8CN  CONST_04  C11  N06  C04  O05     0.00   0.0  0
 8CN  Var_01    C07  C08  C09  C10   -54.01  30.0  1
 8CN  Var_02    C09  C08  C07  N06    54.90  30.0  1
 8CN  Var_03    C11  N06  C07  C08   -56.03  30.0  1
 8CN  Var_04    C11  C10  C09  C08    54.08  30.0  1
 8CN  Var_05    C08  C07  N06  C04   129.41  30.0  1
 8CN  Var_06    H12  C08  C09  C10  -174.97  30.0  1
 8CN  Var_07    H13  C08  C09  C10    66.96  30.0  1
 8CN  Var_08    H12  C08  C07  N06   177.22  30.0  1
 8CN  Var_09    H13  C08  C07  N06   -66.27  30.0  1
 8CN  Var_10    H14  C09  C08  C07    67.64  30.0  1
 8CN  Var_11    H15  C09  C08  C07  -175.47  30.0  1
 8CN  Var_12    H1   C10  C09  C08   -66.47  30.0  1
 8CN  Var_13    H2   C10  C09  C08   176.42  30.0  1
 8CN  Var_14    H10  C07  C08  C09   -65.93  30.0  1
 8CN  Var_15    H11  C07  C08  C09   177.98  30.0  1
 8CN  Var_16    H10  C07  N06  C11    64.95  30.0  1
 8CN  Var_17    H11  C07  N06  C11  -178.74  30.0  1
 8CN  Var_18    H14  C09  C10  C11   -67.11  30.0  1
 8CN  Var_19    H15  C09  C10  C11   175.83  30.0  1
 8CN  Var_20    H10  C07  N06  C04  -109.61  30.0  1
 8CN  Var_21    H11  C07  N06  C04     6.70  30.0  1

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
 8CN  chir_01  C02  C01  N03  C04  negativ
 8CN  chir_02  C11  N06  C12  C10  negativ

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
 8CN  plan-1  C02  0.020
 8CN  plan-1  C04  0.020
 8CN  plan-1  O05  0.020
 8CN  plan-1  N06  0.020
 8CN  plan-1  C07  0.020
 8CN  plan-1  C11  0.020

