# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:45:55 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-acetyl-N-(6-methoxypyridin-3-yl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)C2CCN(CC2)C(C)=O)cn1
#
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
 UPD  UPD  1-acetyl-N-(6-methoxypyridin-3-yl)piperidine-4-carboxamide  ligand  39  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UPD
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
 UPD  N1   N  NH1   0  -0.741  6.8532  -1.0460  26.2381
 UPD  C5   C  CH3   0  -0.808  6.6210  -2.4124  19.2507
 UPD  C6   C  CH2   0  -0.317  7.7482  -2.0156  21.8796
 UPD  C7   C  CH2   0  -0.412  6.9950  -1.3775  23.0397
 UPD  C8   C  CR6   0   0.242  6.3847  -0.2211  27.2697
 UPD  C10  C  CR16  0  -0.388  4.8763   0.3777  29.0296
 UPD  C13  C  CR16  0  -0.120  7.1133   0.9084  27.6031
 UPD  O1   O  O     0  -0.509  5.9896  -4.5683  20.0406
 UPD  N    N  NT    0  -0.436  7.1310  -3.2684  21.4884
 UPD  C3   C  CH2   0  -0.316  7.0599  -4.2378  22.5678
 UPD  C2   C  CH2   0  -0.416  6.2821  -3.6752  23.7514
 UPD  C1   C  CH1   0  -0.426  6.8941  -2.3576  24.2165
 UPD  C    C  C     0   0.566  6.0953  -1.7176  25.3344
 UPD  O    O  O     0  -0.467  4.8800  -1.7729  25.3928
 UPD  N2   N  N     0  -0.455  6.7790   1.7386  28.5865
 UPD  C11  C  CR6   0   0.525  5.6885   1.4897  29.2768
 UPD  O2   O  O2    0  -0.475  5.3202   2.3142  30.2616
 UPD  C12  C  CH3   0  -0.416  6.1234   3.4581  30.5087
 UPD  C9   C  CR16  0  -0.173  5.2345  -0.4873  28.0207
 UPD  H1   H  HNH1  0   0.412  7.8459  -1.0080  26.0622
 UPD  H2   H  HCH3  0   0.268  6.1464  -2.7632  18.3381
 UPD  H3   H  HCH3  0   0.264  6.1027  -1.5101  19.5783
 UPD  H4   H  HCH3  0   0.266  7.6486  -2.1320  19.0183
 UPD  H5   H  HCH2  0   0.246  8.7829  -2.2116  22.1803
 UPD  H6   H  HCH2  0   0.280  7.7907  -1.3269  21.0416
 UPD  H7   H  HCH2  0   0.254  7.5155  -0.4660  23.3408
 UPD  H8   H  HCH2  0   0.242  5.9930  -1.0890  22.7098
 UPD  H9   H  HCR6  0   0.277  3.9912   0.1979  29.6245
 UPD  H10  H  HCR6  0   0.273  8.0179   1.1529  27.0547
 UPD  H11  H  HCH2  0   0.268  6.5954  -5.1502  22.2055
 UPD  H12  H  HCH2  0   0.239  8.0793  -4.4902  22.8788
 UPD  H13  H  HCH2  0   0.237  5.2407  -3.5240  23.4589
 UPD  H14  H  HCH2  0   0.251  6.2901  -4.4063  24.5625
 UPD  H15  H  HCH1  0   0.263  7.9117  -2.5570  24.5752
 UPD  H16  H  HCH3  0   0.246  5.6542   3.9778  31.3401
 UPD  H17  H  HCH3  0   0.228  7.1440   3.1881  30.7834
 UPD  H18  H  HCH3  0   0.228  6.1595   4.1224  29.6442
 UPD  H19  H  HCR6  0   0.285  4.6308  -1.3616  27.8318
 UPD  C4   C  C     0   0.517  6.5506  -3.5078  20.2911

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
 UPD  C5   C4   single    1.512  0.020  1.512
 UPD  O1   C4   double    1.226  0.020  1.226
 UPD  C4   N    single    1.352  0.020  1.352
 UPD  N    C6   single    1.450  0.020  1.450
 UPD  N    C3   single    1.453  0.020  1.453
 UPD  C6   C7   single    1.523  0.020  1.523
 UPD  C3   C2   single    1.524  0.020  1.524
 UPD  C7   C1   single    1.535  0.020  1.535
 UPD  C2   C1   single    1.525  0.020  1.525
 UPD  C1   C    single    1.516  0.020  1.516
 UPD  O    C    double    1.218  0.020  1.218
 UPD  C    N1   single    1.357  0.020  1.357
 UPD  N1   C8   single    1.401  0.020  1.401
 UPD  C8   C13  aromatic  1.385  0.020  1.385
 UPD  C8   C9   aromatic  1.399  0.020  1.399
 UPD  C13  N2   aromatic  1.330  0.020  1.330
 UPD  C9   C10  aromatic  1.376  0.020  1.376
 UPD  N2   C11  aromatic  1.314  0.020  1.314
 UPD  C10  C11  aromatic  1.399  0.020  1.399
 UPD  C11  O2   single    1.336  0.020  1.336
 UPD  O2   C12  single    1.419  0.020  1.419
 UPD  N1   H1   single    0.860  0.020  1.020
 UPD  C5   H2   single    0.970  0.020  1.090
 UPD  C5   H3   single    0.970  0.020  1.090
 UPD  C5   H4   single    0.970  0.020  1.090
 UPD  C6   H5   single    0.970  0.020  1.090
 UPD  C6   H6   single    0.970  0.020  1.090
 UPD  C7   H7   single    0.970  0.020  1.090
 UPD  C7   H8   single    0.970  0.020  1.090
 UPD  C10  H9   single    0.930  0.020  1.080
 UPD  C13  H10  single    0.930  0.020  1.080
 UPD  C3   H11  single    0.970  0.020  1.090
 UPD  C3   H12  single    0.970  0.020  1.090
 UPD  C2   H13  single    0.970  0.020  1.090
 UPD  C2   H14  single    0.970  0.020  1.090
 UPD  C1   H15  single    0.970  0.020  1.090
 UPD  C12  H16  single    0.970  0.020  1.090
 UPD  C12  H17  single    0.970  0.020  1.090
 UPD  C12  H18  single    0.970  0.020  1.090
 UPD  C9   H19  single    0.930  0.020  1.080

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
 UPD  H1   N1   C    116.87  3.000
 UPD  H1   N1   C8   115.79  3.000
 UPD  C    N1   C8   126.49  3.000
 UPD  H4   C5   H3   107.40  3.000
 UPD  H4   C5   H2   108.40  3.000
 UPD  H3   C5   H2   108.17  3.000
 UPD  H4   C5   C4   112.13  3.000
 UPD  H3   C5   C4   111.74  3.000
 UPD  H2   C5   C4   108.88  3.000
 UPD  H6   C6   H5   106.77  3.000
 UPD  H6   C6   N    110.89  3.000
 UPD  H5   C6   N    108.75  3.000
 UPD  H6   C6   C7   109.97  3.000
 UPD  H5   C6   C7   109.45  3.000
 UPD  N    C6   C7   110.91  3.000
 UPD  H8   C7   H7   107.44  3.000
 UPD  H8   C7   C1   109.84  3.000
 UPD  H7   C7   C1   110.67  3.000
 UPD  H8   C7   C6   109.50  3.000
 UPD  H7   C7   C6   108.91  3.000
 UPD  C1   C7   C6   110.42  3.000
 UPD  C9   C8   C13  117.29  3.000
 UPD  C9   C8   N1   123.91  3.000
 UPD  C13  C8   N1   118.78  3.000
 UPD  H9   C10  C9   120.77  3.000
 UPD  H9   C10  C11  120.67  3.000
 UPD  C9   C10  C11  118.55  3.000
 UPD  H10  C13  N2   116.26  3.000
 UPD  H10  C13  C8   120.02  3.000
 UPD  N2   C13  C8   123.71  3.000
 UPD  C3   N    C6   113.39  3.000
 UPD  C3   N    C4   121.26  3.000
 UPD  C6   N    C4   125.06  3.000
 UPD  H12  C3   H11  107.41  3.000
 UPD  H12  C3   C2   109.85  3.000
 UPD  H11  C3   C2   110.54  3.000
 UPD  H12  C3   N    108.62  3.000
 UPD  H11  C3   N    109.50  3.000
 UPD  C2   C3   N    110.83  3.000
 UPD  H14  C2   H13  107.37  3.000
 UPD  H14  C2   C1   110.42  3.000
 UPD  H13  C2   C1   110.16  3.000
 UPD  H14  C2   C3   109.02  3.000
 UPD  H13  C2   C3   109.26  3.000
 UPD  C1   C2   C3   110.54  3.000
 UPD  H15  C1   C    108.93  3.000
 UPD  H15  C1   C2   108.35  3.000
 UPD  C    C1   C2   112.22  3.000
 UPD  H15  C1   C7   107.81  3.000
 UPD  C    C1   C7   109.30  3.000
 UPD  C2   C1   C7   110.13  3.000
 UPD  O    C    C1   122.83  3.000
 UPD  O    C    N1   123.21  3.000
 UPD  C1   C    N1   113.94  3.000
 UPD  C11  N2   C13  118.61  3.000
 UPD  O2   C11  N2   119.93  3.000
 UPD  O2   C11  C10  117.43  3.000
 UPD  N2   C11  C10  122.64  3.000
 UPD  C12  O2   C11  118.01  3.000
 UPD  H18  C12  H17  108.62  3.000
 UPD  H18  C12  H16  109.22  3.000
 UPD  H17  C12  H16  109.25  3.000
 UPD  H18  C12  O2   111.81  3.000
 UPD  H17  C12  O2   111.95  3.000
 UPD  H16  C12  O2   105.92  3.000
 UPD  H19  C9   C10  119.46  3.000
 UPD  H19  C9   C8   121.34  3.000
 UPD  C10  C9   C8   119.19  3.000
 UPD  N    C4   O1   122.06  3.000
 UPD  N    C4   C5   117.45  3.000
 UPD  O1   C4   C5   120.49  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
 UPD  CONST_01  C11  N2   C13  C8      0.00   0.0  0
 UPD  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 UPD  CONST_03  C13  C8   C9   C10     0.00   0.0  0
 UPD  CONST_04  C13  N2   C11  C10     0.00   0.0  0
 UPD  CONST_05  C9   C8   C13  N2      0.00   0.0  0
 UPD  CONST_06  C9   C10  C11  N2      0.00   0.0  0
 UPD  CONST_07  N2   C13  C8   N1    180.00   0.0  0
 UPD  CONST_08  C10  C9   C8   N1    180.00   0.0  0
 UPD  CONST_09  O2   C11  N2   C13   180.00   0.0  0
 UPD  CONST_10  C9   C10  C11  O2    180.00   0.0  0
 UPD  CONST_11  H9   C10  C9   C8    180.00   0.0  0
 UPD  CONST_12  H19  C9   C8   C13   180.00   0.0  0
 UPD  CONST_13  H10  C13  N2   C11   180.00   0.0  0
 UPD  CONST_14  C6   N    C4   C5      0.00   0.0  0
 UPD  CONST_15  C3   N    C4   C5    180.00   0.0  0
 UPD  CONST_16  O1   C4   N    C6    180.00   0.0  0
 UPD  CONST_17  C1   C    N1   C8    180.00   0.0  0
 UPD  CONST_18  C3   N    C4   O1      0.00   0.0  0
 UPD  CONST_22  O    C    N1   C8      0.00   0.0  0
 UPD  Var_01    C2   C3   N    C6     58.17  30.0  1
 UPD  Var_02    C3   N    C6   C7    -58.17  30.0  1
 UPD  Var_03    C1   C7   C6   N      55.38  30.0  1
 UPD  Var_04    C1   C2   C3   N     -55.61  30.0  1
 UPD  Var_05    H2   C5   C4   N     177.98  30.0  3
 UPD  Var_06    H16  C12  O2   C11  -179.69  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
 UPD  chir_01  C1  C7  C2  C  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
 UPD  plan-1  N1   0.020
 UPD  plan-1  C8   0.020
 UPD  plan-1  C10  0.020
 UPD  plan-1  C13  0.020
 UPD  plan-1  N2   0.020
 UPD  plan-1  C11  0.020
 UPD  plan-1  O2   0.020
 UPD  plan-1  C9   0.020
 UPD  plan-1  H9   0.020
 UPD  plan-1  H10  0.020
 UPD  plan-1  H19  0.020
 UPD  plan-2  N1   0.020
 UPD  plan-2  C8   0.020
 UPD  plan-2  C1   0.020
 UPD  plan-2  C    0.020
 UPD  plan-2  O    0.020
 UPD  plan-2  H1   0.020
 UPD  plan-3  C5   0.020
 UPD  plan-3  C6   0.020
 UPD  plan-3  O1   0.020
 UPD  plan-3  N    0.020
 UPD  plan-3  C3   0.020
 UPD  plan-3  C4   0.020

