# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:59:09 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3R)-1-acetylpiperidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC[C@H](C1)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
 K1V  K1V  (3R)-1-acetylpiperidine-3-carboxamide  ligand  26  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_K1V
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
 K1V  N1   N  NH2   0  -0.801   3.0611   1.2611   0.7973
 K1V  C4   C  CH2   0  -0.430   1.0986  -1.4078   0.3282
 K1V  C5   C  CH1   0  -0.391   1.0281   0.1171   0.1734
 K1V  C6   C  CH2   0  -0.285  -0.0065   0.4879  -0.8927
 K1V  C7   C  C     0   0.540   2.3920   0.6647  -0.1985
 K1V  N    N  NT    0  -0.442  -1.2963  -0.0830  -0.5548
 K1V  C    C  CH3   0  -0.805  -3.5911   0.0203   0.2925
 K1V  O    O  O     0  -0.508  -2.2287   1.9275  -0.1290
 K1V  C1   C  C     0   0.514  -2.3156   0.7051  -0.1427
 K1V  C2   C  CH2   0  -0.320  -1.2792  -1.5328  -0.4668
 K1V  C3   C  CH2   0  -0.433  -0.2855  -1.9879   0.5943
 K1V  O1   O  O     0  -0.496   2.8474   0.5438  -1.3286
 K1V  H1   H  HNH2  0   0.408   2.6704   1.3534   1.7186
 K1V  H2   H  HNH2  0   0.400   3.9901   1.6215   0.6486
 K1V  H3   H  HCH2  0   0.232   1.5058  -1.8441  -0.5895
 K1V  H4   H  HCH2  0   0.251   1.7823  -1.6733   1.1373
 K1V  H5   H  HCH1  0   0.261   0.7054   0.5513   1.1263
 K1V  H6   H  HCH2  0   0.271  -0.1032   1.5664  -0.9858
 K1V  H7   H  HCH2  0   0.245   0.3075   0.0970  -1.8642
 K1V  H8   H  HCH3  0   0.268  -4.3218   0.7779   0.5636
 K1V  H9   H  HCH3  0   0.266  -4.0134  -0.5972  -0.5009
 K1V  H10  H  HCH3  0   0.263  -3.4288  -0.6242   1.1574
 K1V  H11  H  HCH2  0   0.275  -2.2721  -1.9172  -0.2518
 K1V  H12  H  HCH2  0   0.245  -0.9898  -1.9362  -1.4428
 K1V  H13  H  HCH2  0   0.246  -0.2416  -3.0786   0.6035
 K1V  H14  H  HCH2  0   0.229  -0.6421  -1.6710   1.5792

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
 K1V  C   C1   single  1.512  0.020  1.512
 K1V  O   C1   double  1.226  0.020  1.226
 K1V  C1  N    single  1.353  0.020  1.353
 K1V  N   C2   single  1.453  0.020  1.453
 K1V  N   C6   single  1.450  0.020  1.450
 K1V  C2  C3   single  1.523  0.020  1.523
 K1V  C3  C4   single  1.524  0.020  1.524
 K1V  C6  C5   single  1.531  0.020  1.531
 K1V  C5  C4   single  1.534  0.020  1.534
 K1V  C5  C7   single  1.516  0.020  1.516
 K1V  O1  C7   double  1.224  0.020  1.224
 K1V  C7  N1   single  1.340  0.020  1.340
 K1V  N1  H1   single  0.860  0.020  1.020
 K1V  N1  H2   single  0.860  0.020  1.020
 K1V  C4  H3   single  0.970  0.020  1.090
 K1V  C4  H4   single  0.970  0.020  1.090
 K1V  C5  H5   single  0.970  0.020  1.090
 K1V  C6  H6   single  0.970  0.020  1.090
 K1V  C6  H7   single  0.970  0.020  1.090
 K1V  C   H8   single  0.970  0.020  1.090
 K1V  C   H9   single  0.970  0.020  1.090
 K1V  C   H10  single  0.970  0.020  1.090
 K1V  C2  H11  single  0.970  0.020  1.090
 K1V  C2  H12  single  0.970  0.020  1.090
 K1V  C3  H13  single  0.970  0.020  1.090
 K1V  C3  H14  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
 K1V  H2   N1  H1   117.45  3.000
 K1V  H2   N1  C7   120.67  3.000
 K1V  H1   N1  C7   121.88  3.000
 K1V  H4   C4  H3   106.94  3.000
 K1V  H4   C4  C3   110.28  3.000
 K1V  H3   C4  C3   109.43  3.000
 K1V  H4   C4  C5   110.18  3.000
 K1V  H3   C4  C5   109.18  3.000
 K1V  C3   C4  C5   110.74  3.000
 K1V  H5   C5  C7   109.58  3.000
 K1V  H5   C5  C6   108.09  3.000
 K1V  C7   C5  C6   110.46  3.000
 K1V  H5   C5  C4   108.64  3.000
 K1V  C7   C5  C4   110.02  3.000
 K1V  C6   C5  C4   109.99  3.000
 K1V  H7   C6  H6   107.71  3.000
 K1V  H7   C6  N    108.77  3.000
 K1V  H6   C6  N    109.36  3.000
 K1V  H7   C6  C5   109.76  3.000
 K1V  H6   C6  C5   111.10  3.000
 K1V  N    C6  C5   110.08  3.000
 K1V  O1   C7  C5   121.70  3.000
 K1V  O1   C7  N1   122.97  3.000
 K1V  C5   C7  N1   115.32  3.000
 K1V  C2   N   C1   124.88  3.000
 K1V  C2   N   C6   113.36  3.000
 K1V  C1   N   C6   120.78  3.000
 K1V  H10  C   H9   107.45  3.000
 K1V  H10  C   H8   108.31  3.000
 K1V  H9   C   H8   108.41  3.000
 K1V  H10  C   C1   111.74  3.000
 K1V  H9   C   C1   111.95  3.000
 K1V  H8   C   C1   108.86  3.000
 K1V  O    C1  C    120.56  3.000
 K1V  O    C1  N    122.08  3.000
 K1V  C    C1  N    117.36  3.000
 K1V  H12  C2  H11  106.72  3.000
 K1V  H12  C2  C3   109.78  3.000
 K1V  H11  C2  C3   110.65  3.000
 K1V  H12  C2  N    108.47  3.000
 K1V  H11  C2  N    110.76  3.000
 K1V  C3   C2  N    110.37  3.000
 K1V  H14  C3  H13  107.15  3.000
 K1V  H14  C3  C2   109.13  3.000
 K1V  H13  C3  C2   109.30  3.000
 K1V  H14  C3  C4   110.05  3.000
 K1V  H13  C3  C4   110.20  3.000
 K1V  C2   C3  C4   110.92  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
 K1V  CONST_01  C   C1  N   C6   180.00   0.0  0
 K1V  CONST_02  O   C1  N   C6     0.00   0.0  0
 K1V  CONST_03  C2  N   C1  C      0.00   0.0  0
 K1V  CONST_04  C2  N   C1  O    180.00   0.0  0
 K1V  CONST_05  H1  N1  C7  C5     0.00   0.0  0
 K1V  CONST_06  H2  N1  C7  C5   180.00   0.0  0
 K1V  Var_01    N   C2  C3  C4   -54.86  30.0  1
 K1V  Var_02    C2  N   C6  C5   -60.24  30.0  1
 K1V  Var_03    C2  C3  C4  C5    53.18  30.0  1
 K1V  Var_04    C3  C2  N   C6    59.39  30.0  1
 K1V  Var_05    H8  C   C1  N   -178.24  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
 K1V  chir_01  C5  C6  C4  C7  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
 K1V  plan-1  N1  0.020
 K1V  plan-1  C5  0.020
 K1V  plan-1  C7  0.020
 K1V  plan-1  O1  0.020
 K1V  plan-1  H1  0.020
 K1V  plan-1  H2  0.020
 K1V  plan-2  C6  0.020
 K1V  plan-2  N   0.020
 K1V  plan-2  C   0.020
 K1V  plan-2  O   0.020
 K1V  plan-2  C1  0.020
 K1V  plan-2  C2  0.020

