# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:18:36 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-acetyl-N-methyl-N-phenylpiperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C(=O)C1CCN(CC1)C(C)=O)c2ccccc2
#
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
 UPJ  UPJ  1-acetyl-N-methyl-N-phenylpiperidine-4-carboxamide  ligand  39  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UPJ
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
 UPJ  N1   N  NT    0  -0.539   5.4989  -2.9086  26.4779
 UPJ  C5   C  CH3   0  -0.807   6.8104  -2.6633  19.5003
 UPJ  C6   C  CH2   0  -0.319   7.3447  -3.3212  22.2555
 UPJ  C7   C  CH2   0  -0.410   6.5322  -2.6986  23.3844
 UPJ  C8   C  CH3   0  -0.533   4.6979  -2.2086  27.4734
 UPJ  C10  C  CR16  0  -0.252   7.1573  -4.5277  27.2401
 UPJ  C13  C  CR16  0  -0.261   9.1264  -2.5706  27.1509
 UPJ  O1   O  O     0  -0.510   5.3741  -4.5631  19.5077
 UPJ  N    N  NT    0  -0.432   6.5043  -4.1541  21.4173
 UPJ  C3   C  CH2   0  -0.320   5.8636  -5.2340  22.1469
 UPJ  C2   C  CH2   0  -0.413   4.9940  -4.6823  23.2698
 UPJ  C1   C  CH1   0  -0.423   5.8189  -3.7893  24.1962
 UPJ  C    C  C     0   0.575   4.9502  -3.1457  25.2616
 UPJ  O    O  O     0  -0.491   3.7980  -2.8119  25.0241
 UPJ  C9   C  CR6   0   0.247   6.8390  -3.2405  26.8219
 UPJ  C14  C  CR16  0  -0.251   7.8241  -2.2604  26.7848
 UPJ  C12  C  CR16  0  -0.248   9.4480  -3.8599  27.5537
 UPJ  C11  C  CR16  0  -0.260   8.4619  -4.8371  27.5979
 UPJ  H1   H  HCH3  0   0.268   6.4780  -2.5911  18.4681
 UPJ  H2   H  HCH3  0   0.263   6.5328  -1.7412  20.0133
 UPJ  H3   H  HCH3  0   0.265   7.8987  -2.7260  19.5070
 UPJ  H4   H  HCH2  0   0.246   8.1428  -3.9433  22.6736
 UPJ  H5   H  HCH2  0   0.278   7.8281  -2.5459  21.6686
 UPJ  H6   H  HCH2  0   0.253   7.1982  -2.1146  24.0226
 UPJ  H7   H  HCH2  0   0.239   5.7980  -2.0087  22.9592
 UPJ  H8   H  HCH3  0   0.251   5.2854  -2.0986  28.3802
 UPJ  H9   H  HCH3  0   0.245   4.4076  -1.2164  27.1276
 UPJ  H10  H  HCH3  0   0.249   3.7944  -2.7673  27.7178
 UPJ  H11  H  HCR6  0   0.267   6.3839  -5.2847  27.2755
 UPJ  H12  H  HCR6  0   0.263   9.8899  -1.8049  27.1169
 UPJ  H13  H  HCH2  0   0.266   5.2727  -5.8339  21.4608
 UPJ  H14  H  HCH2  0   0.240   6.6427  -5.8809  22.5639
 UPJ  H15  H  HCH2  0   0.235   4.1623  -4.1184  22.8428
 UPJ  H16  H  HCH2  0   0.247   4.5681  -5.5175  23.8304
 UPJ  H17  H  HCH1  0   0.266   6.5905  -4.4080  24.6623
 UPJ  H18  H  HCR6  0   0.268   7.5692  -1.2558  26.4706
 UPJ  H19  H  HCR6  0   0.262  10.4643  -4.1032  27.8344
 UPJ  H20  H  HCR6  0   0.263   8.7080  -5.8420  27.9151
 UPJ  C4   C  C     0   0.515   6.1651  -3.8722  20.1397

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
 UPJ  C5   C4   single    1.512  0.020  1.512
 UPJ  O1   C4   double    1.226  0.020  1.226
 UPJ  C4   N    single    1.352  0.020  1.352
 UPJ  N    C6   single    1.450  0.020  1.450
 UPJ  N    C3   single    1.452  0.020  1.452
 UPJ  C6   C7   single    1.524  0.020  1.524
 UPJ  C3   C2   single    1.524  0.020  1.524
 UPJ  C7   C1   single    1.535  0.020  1.535
 UPJ  C2   C1   single    1.528  0.020  1.528
 UPJ  C1   C    single    1.518  0.020  1.518
 UPJ  O    C    double    1.223  0.020  1.223
 UPJ  C    N1   single    1.355  0.020  1.355
 UPJ  N1   C9   single    1.423  0.020  1.423
 UPJ  N1   C8   single    1.457  0.020  1.457
 UPJ  C14  C9   aromatic  1.390  0.020  1.390
 UPJ  C14  C13  aromatic  1.388  0.020  1.388
 UPJ  C9   C10  aromatic  1.390  0.020  1.390
 UPJ  C13  C12  aromatic  1.388  0.020  1.388
 UPJ  C10  C11  aromatic  1.388  0.020  1.388
 UPJ  C12  C11  aromatic  1.389  0.020  1.389
 UPJ  C5   H1   single    0.970  0.020  1.090
 UPJ  C5   H2   single    0.970  0.020  1.090
 UPJ  C5   H3   single    0.970  0.020  1.090
 UPJ  C6   H4   single    0.970  0.020  1.090
 UPJ  C6   H5   single    0.970  0.020  1.090
 UPJ  C7   H6   single    0.970  0.020  1.090
 UPJ  C7   H7   single    0.970  0.020  1.090
 UPJ  C8   H8   single    0.970  0.020  1.090
 UPJ  C8   H9   single    0.970  0.020  1.090
 UPJ  C8   H10  single    0.970  0.020  1.090
 UPJ  C10  H11  single    0.930  0.020  1.080
 UPJ  C13  H12  single    0.930  0.020  1.080
 UPJ  C3   H13  single    0.970  0.020  1.090
 UPJ  C3   H14  single    0.970  0.020  1.090
 UPJ  C2   H15  single    0.970  0.020  1.090
 UPJ  C2   H16  single    0.970  0.020  1.090
 UPJ  C1   H17  single    0.970  0.020  1.090
 UPJ  C14  H18  single    0.930  0.020  1.080
 UPJ  C12  H19  single    0.930  0.020  1.080
 UPJ  C11  H20  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
 UPJ  C9   N1   C    123.88  3.000
 UPJ  C9   N1   C8   117.69  3.000
 UPJ  C    N1   C8   118.34  3.000
 UPJ  H3   C5   H2   107.44  3.000
 UPJ  H3   C5   H1   108.36  3.000
 UPJ  H2   C5   H1   108.22  3.000
 UPJ  H3   C5   C4   112.17  3.000
 UPJ  H2   C5   C4   111.61  3.000
 UPJ  H1   C5   C4   108.91  3.000
 UPJ  H5   C6   H4   106.71  3.000
 UPJ  H5   C6   N    110.83  3.000
 UPJ  H4   C6   N    108.47  3.000
 UPJ  H5   C6   C7   110.25  3.000
 UPJ  H4   C6   C7   109.75  3.000
 UPJ  N    C6   C7   110.72  3.000
 UPJ  H7   C7   H6   107.42  3.000
 UPJ  H7   C7   C1   109.99  3.000
 UPJ  H6   C7   C1   110.75  3.000
 UPJ  H7   C7   C6   109.13  3.000
 UPJ  H6   C7   C6   109.04  3.000
 UPJ  C1   C7   C6   110.44  3.000
 UPJ  H10  C8   H9   108.47  3.000
 UPJ  H10  C8   H8   108.24  3.000
 UPJ  H9   C8   H8   108.46  3.000
 UPJ  H10  C8   N1   111.27  3.000
 UPJ  H9   C8   N1   111.53  3.000
 UPJ  H8   C8   N1   108.77  3.000
 UPJ  H11  C10  C11  120.47  3.000
 UPJ  H11  C10  C9   119.58  3.000
 UPJ  C11  C10  C9   119.95  3.000
 UPJ  H12  C13  C12  120.19  3.000
 UPJ  H12  C13  C14  119.72  3.000
 UPJ  C12  C13  C14  120.10  3.000
 UPJ  C3   N    C6   113.11  3.000
 UPJ  C3   N    C4   121.28  3.000
 UPJ  C6   N    C4   124.89  3.000
 UPJ  H14  C3   H13  107.54  3.000
 UPJ  H14  C3   C2   109.83  3.000
 UPJ  H13  C3   C2   110.79  3.000
 UPJ  H14  C3   N    108.46  3.000
 UPJ  H13  C3   N    109.47  3.000
 UPJ  C2   C3   N    110.66  3.000
 UPJ  H16  C2   H15  107.37  3.000
 UPJ  H16  C2   C1   110.25  3.000
 UPJ  H15  C2   C1   110.26  3.000
 UPJ  H16  C2   C3   108.90  3.000
 UPJ  H15  C2   C3   109.49  3.000
 UPJ  C1   C2   C3   110.50  3.000
 UPJ  H17  C1   C    110.15  3.000
 UPJ  H17  C1   C2   107.98  3.000
 UPJ  C    C1   C2   111.36  3.000
 UPJ  H17  C1   C7   107.43  3.000
 UPJ  C    C1   C7   109.62  3.000
 UPJ  C2   C1   C7   110.20  3.000
 UPJ  O    C    C1   121.24  3.000
 UPJ  O    C    N1   120.53  3.000
 UPJ  C1   C    N1   118.19  3.000
 UPJ  C14  C9   C10  119.91  3.000
 UPJ  C10  C9   N1   120.29  3.000
 UPJ  C14  C9   N1   119.77  3.000
 UPJ  H18  C14  C9   119.67  3.000
 UPJ  H18  C14  C13  120.31  3.000
 UPJ  C9   C14  C13  120.01  3.000
 UPJ  H19  C12  C11  120.02  3.000
 UPJ  H19  C12  C13  120.11  3.000
 UPJ  C11  C12  C13  119.87  3.000
 UPJ  H20  C11  C12  120.08  3.000
 UPJ  H20  C11  C10  119.76  3.000
 UPJ  C12  C11  C10  120.16  3.000
 UPJ  N    C4   O1   122.13  3.000
 UPJ  N    C4   C5   117.34  3.000
 UPJ  O1   C4   C5   120.53  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
 UPJ  CONST_01  C13  C14  C9   C10    0.00   0.0  0
 UPJ  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 UPJ  CONST_03  C12  C13  C14  C9     0.00   0.0  0
 UPJ  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 UPJ  CONST_05  C11  C10  C9   C14    0.00   0.0  0
 UPJ  CONST_06  C11  C12  C13  C14    0.00   0.0  0
 UPJ  CONST_07  C13  C14  C9   N1   180.00   0.0  0
 UPJ  CONST_08  C11  C10  C9   N1   180.00   0.0  0
 UPJ  CONST_09  H18  C14  C9   C10  180.00   0.0  0
 UPJ  CONST_10  H19  C12  C11  C10  180.00   0.0  0
 UPJ  CONST_11  H20  C11  C12  C13  180.00   0.0  0
 UPJ  CONST_12  H12  C13  C14  C9   180.00   0.0  0
 UPJ  CONST_13  H11  C10  C9   C14  180.00   0.0  0
 UPJ  CONST_14  C6   N    C4   C5     0.00   0.0  0
 UPJ  CONST_15  C3   N    C4   C5   180.00   0.0  0
 UPJ  CONST_16  O1   C4   N    C6   180.00   0.0  0
 UPJ  CONST_17  C3   N    C4   O1     0.00   0.0  0
 UPJ  CONST_18  C9   N1   C    C1     0.00   0.0  0
 UPJ  CONST_23  C1   C    N1   C8   180.00   0.0  0
 UPJ  CONST_24  C9   N1   C    O    180.00   0.0  0
 UPJ  CONST_25  O    C    N1   C8     0.00   0.0  0
 UPJ  Var_01    C2   C3   N    C6    59.12  30.0  1
 UPJ  Var_02    C3   N    C6   C7   -59.04  30.0  1
 UPJ  Var_03    C1   C7   C6   N     55.59  30.0  1
 UPJ  Var_04    C1   C2   C3   N    -55.88  30.0  1
 UPJ  Var_05    H1   C5   C4   N    177.47  30.0  3
 UPJ  Var_06    H8   C8   N1   C9    -2.94  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
 UPJ  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
 UPJ  plan-1  N1   0.020
 UPJ  plan-1  C10  0.020
 UPJ  plan-1  C13  0.020
 UPJ  plan-1  C9   0.020
 UPJ  plan-1  C14  0.020
 UPJ  plan-1  C12  0.020
 UPJ  plan-1  C11  0.020
 UPJ  plan-1  H11  0.020
 UPJ  plan-1  H12  0.020
 UPJ  plan-1  H18  0.020
 UPJ  plan-1  H19  0.020
 UPJ  plan-1  H20  0.020
 UPJ  plan-2  C5   0.020
 UPJ  plan-2  C6   0.020
 UPJ  plan-2  O1   0.020
 UPJ  plan-2  N    0.020
 UPJ  plan-2  C3   0.020
 UPJ  plan-2  C4   0.020
 UPJ  plan-3  N1   0.020
 UPJ  plan-3  C8   0.020
 UPJ  plan-3  C1   0.020
 UPJ  plan-3  C    0.020
 UPJ  plan-3  O    0.020
 UPJ  plan-3  C9   0.020

