# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:29:35 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: N-(1-acetylpiperidin-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC(CC1)NC(=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
 T7D  T7D  N-(1-acetylpiperidin-4-yl)benzamide  ligand  36  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T7D
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
 T7D  N1   N  NH1   0  -0.661   0.6406   0.0316   0.2925
 T7D  C4   C  CH1   0  -0.057  -0.7076  -0.4223   0.5671
 T7D  C5   C  CH2   0  -0.430  -1.3901  -0.9924  -0.6771
 T7D  C6   C  CH2   0  -0.324  -2.8395  -1.3574  -0.3747
 T7D  C7   C  C     0   0.533   1.7168  -0.7705   0.3131
 T7D  C8   C  CR6   0  -0.032   3.0251  -0.1188  -0.0104
 T7D  C10  C  CR16  0  -0.242   5.4212  -0.1019   0.2673
 T7D  C13  C  CR16  0  -0.297   3.1264   0.9956  -0.8413
 T7D  N    N  NT    0  -0.433  -3.5518  -0.2110   0.1626
 T7D  C    C  CH3   0  -0.806  -5.0543   1.7154   0.0094
 T7D  O    O  O     0  -0.507  -4.8253   0.0535  -1.6817
 T7D  C1   C  C     0   0.516  -4.4665   0.4537  -0.5808
 T7D  C11  C  CR16  0  -0.252   5.5143   1.0160  -0.5524
 T7D  C12  C  CR16  0  -0.241   4.3656   1.5583  -1.1119
 T7D  C2   C  CH2   0  -0.329  -2.9637   0.2947   1.3885
 T7D  C3   C  CH2   0  -0.452  -1.5214   0.7266   1.1541
 T7D  C9   C  CR16  0  -0.272   4.1849  -0.6720   0.5285
 T7D  O1   O  O     0  -0.492   1.6578  -1.9594   0.5997
 T7D  H11  H  HNH1  0   0.406   0.7662   1.0140   0.1084
 T7D  H6   H  HCH1  0   0.246  -0.6464  -1.2149   1.3196
 T7D  H8   H  HCH2  0   0.231  -1.3566  -0.2559  -1.4855
 T7D  H7   H  HCH2  0   0.248  -0.8546  -1.8801  -1.0197
 T7D  H10  H  HCH2  0   0.268  -3.3451  -1.7165  -1.2662
 T7D  H9   H  HCH2  0   0.244  -2.8739  -2.1622   0.3673
 T7D  H13  H  HCR6  0   0.263   6.3139  -0.5307   0.7033
 T7D  H16  H  HCR6  0   0.260   2.2489   1.4233  -1.3102
 T7D  H    H  HCH3  0   0.263  -4.2903   2.4769   0.1722
 T7D  H17  H  HCH3  0   0.269  -5.7951   2.1157  -0.6776
 T7D  H1   H  HCH3  0   0.267  -5.5389   1.5302   0.9684
 T7D  H14  H  HCR6  0   0.264   6.4797   1.4602  -0.7571
 T7D  H15  H  HCR6  0   0.264   4.4317   2.4186  -1.7646
 T7D  H3   H  HCH2  0   0.280  -3.5474   1.1196   1.7854
 T7D  H2   H  HCH2  0   0.252  -2.9949  -0.5004   2.1401
 T7D  H5   H  HCH2  0   0.257  -1.0803   1.0536   2.0980
 T7D  H4   H  HCH2  0   0.237  -1.5108   1.5834   0.4712
 T7D  H12  H  HCR6  0   0.259   4.1180  -1.5442   1.1652

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
 T7D  C1   C    single    1.512  0.020  1.512
 T7D  C1   O    double    1.225  0.020  1.225
 T7D  N    C1   single    1.353  0.020  1.353
 T7D  C2   N    single    1.451  0.020  1.451
 T7D  C3   C2   single    1.524  0.020  1.524
 T7D  C4   C3   single    1.525  0.020  1.525
 T7D  C4   C5   single    1.529  0.020  1.529
 T7D  C5   C6   single    1.525  0.020  1.525
 T7D  C6   N    single    1.453  0.020  1.453
 T7D  N1   C4   single    1.449  0.020  1.449
 T7D  C7   N1   single    1.342  0.020  1.342
 T7D  O1   C7   double    1.224  0.020  1.224
 T7D  C7   C8   single    1.497  0.020  1.497
 T7D  C8   C9   aromatic  1.393  0.020  1.393
 T7D  C10  C9   aromatic  1.386  0.020  1.386
 T7D  C11  C10  aromatic  1.389  0.020  1.389
 T7D  C12  C11  aromatic  1.388  0.020  1.388
 T7D  C13  C12  aromatic  1.388  0.020  1.388
 T7D  C8   C13  aromatic  1.394  0.020  1.394
 T7D  N1   H11  single    0.860  0.020  1.020
 T7D  C4   H6   single    0.970  0.020  1.090
 T7D  C5   H8   single    0.970  0.020  1.090
 T7D  C5   H7   single    0.970  0.020  1.090
 T7D  C6   H10  single    0.970  0.020  1.090
 T7D  C6   H9   single    0.970  0.020  1.090
 T7D  C10  H13  single    0.930  0.020  1.080
 T7D  C13  H16  single    0.930  0.020  1.080
 T7D  C    H    single    0.970  0.020  1.090
 T7D  C    H17  single    0.970  0.020  1.090
 T7D  C    H1   single    0.970  0.020  1.090
 T7D  C11  H14  single    0.930  0.020  1.080
 T7D  C12  H15  single    0.930  0.020  1.080
 T7D  C2   H3   single    0.970  0.020  1.090
 T7D  C2   H2   single    0.970  0.020  1.090
 T7D  C3   H5   single    0.970  0.020  1.090
 T7D  C3   H4   single    0.970  0.020  1.090
 T7D  C9   H12  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
 T7D  H11  N1   C7   119.05  3.000
 T7D  H11  N1   C4   117.15  3.000
 T7D  C7   N1   C4   123.77  3.000
 T7D  H6   C4   C3   108.10  3.000
 T7D  H6   C4   C5   108.32  3.000
 T7D  C3   C4   C5   110.84  3.000
 T7D  H6   C4   N1   107.77  3.000
 T7D  C5   C4   N1   112.20  3.000
 T7D  C3   C4   N1   109.47  3.000
 T7D  H7   C5   H8   107.48  3.000
 T7D  H7   C5   C6   109.50  3.000
 T7D  H8   C5   C6   109.68  3.000
 T7D  H7   C5   C4   109.85  3.000
 T7D  H8   C5   C4   109.67  3.000
 T7D  C6   C5   C4   110.61  3.000
 T7D  H9   C6   H10  107.38  3.000
 T7D  H9   C6   N    108.29  3.000
 T7D  H10  C6   N    109.65  3.000
 T7D  H9   C6   C5   109.89  3.000
 T7D  H10  C6   C5   111.03  3.000
 T7D  N    C6   C5   110.52  3.000
 T7D  O1   C7   C8   121.02  3.000
 T7D  C8   C7   N1   115.93  3.000
 T7D  O1   C7   N1   123.04  3.000
 T7D  C9   C8   C13  119.17  3.000
 T7D  C13  C8   C7   122.71  3.000
 T7D  C9   C8   C7   118.11  3.000
 T7D  H13  C10  C9   119.79  3.000
 T7D  H13  C10  C11  120.08  3.000
 T7D  C9   C10  C11  120.12  3.000
 T7D  H16  C13  C12  118.62  3.000
 T7D  H16  C13  C8   121.00  3.000
 T7D  C12  C13  C8   120.36  3.000
 T7D  C2   N    C1   124.54  3.000
 T7D  C2   N    C6   112.89  3.000
 T7D  C1   N    C6   121.06  3.000
 T7D  H1   C    H17  108.40  3.000
 T7D  H1   C    H    107.37  3.000
 T7D  H17  C    H    108.34  3.000
 T7D  H1   C    C1   111.99  3.000
 T7D  H17  C    C1   109.01  3.000
 T7D  H    C    C1   111.62  3.000
 T7D  O    C1   C    120.63  3.000
 T7D  O    C1   N    122.09  3.000
 T7D  C    C1   N    117.28  3.000
 T7D  H14  C11  C12  120.11  3.000
 T7D  H14  C11  C10  120.11  3.000
 T7D  C12  C11  C10  119.78  3.000
 T7D  H15  C12  C11  120.22  3.000
 T7D  H15  C12  C13  119.65  3.000
 T7D  C11  C12  C13  120.13  3.000
 T7D  H2   C2   H3   106.60  3.000
 T7D  H2   C2   C3   109.78  3.000
 T7D  H3   C2   C3   110.47  3.000
 T7D  H2   C2   N    108.39  3.000
 T7D  H3   C2   N    110.85  3.000
 T7D  C3   C2   N    110.64  3.000
 T7D  H4   C3   H5   107.50  3.000
 T7D  H4   C3   C2   109.07  3.000
 T7D  H5   C3   C2   109.53  3.000
 T7D  H4   C3   C4   110.12  3.000
 T7D  H5   C3   C4   110.04  3.000
 T7D  C2   C3   C4   110.53  3.000
 T7D  H12  C9   C10  119.84  3.000
 T7D  H12  C9   C8   119.74  3.000
 T7D  C10  C9   C8   120.41  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
 T7D  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 T7D  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 T7D  CONST_03  C13  C8   C9   C10    0.00   0.0  0
 T7D  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 T7D  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 T7D  CONST_06  C9   C8   C13  C12    0.00   0.0  0
 T7D  CONST_07  C10  C9   C8   C7   180.00   0.0  0
 T7D  CONST_08  C12  C13  C8   C7   180.00   0.0  0
 T7D  CONST_09  H13  C10  C9   C8   180.00   0.0  0
 T7D  CONST_10  H15  C12  C13  C8   180.00   0.0  0
 T7D  CONST_11  H14  C11  C12  C13  180.00   0.0  0
 T7D  CONST_12  H12  C9   C8   C13  180.00   0.0  0
 T7D  CONST_13  H16  C13  C12  C11  180.00   0.0  0
 T7D  CONST_14  C8   C7   N1   C4   180.00   0.0  0
 T7D  CONST_15  C    C1   N    C6   180.00   0.0  0
 T7D  CONST_16  O    C1   N    C6     0.00   0.0  0
 T7D  CONST_17  C2   N    C1   C      0.00   0.0  0
 T7D  CONST_18  C2   N    C1   O    180.00   0.0  0
 T7D  CONST_19  O1   C7   N1   C4     0.00   0.0  0
 T7D  CONST_20  H11  N1   C7   C8     0.00   0.0  0
 T7D  Var_01    N    C2   C3   C4   -55.60  30.0  1
 T7D  Var_02    N    C6   C5   C4    55.25  30.0  1
 T7D  Var_03    C2   N    C6   C5   -59.54  30.0  1
 T7D  Var_04    C3   C2   N    C6    59.74  30.0  1
 T7D  Var_05    C9   C8   C7   N1   152.63  30.0  2
 T7D  Var_06    H    C    C1   N     62.52  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
 T7D  chir_01  C4  C3  C5  N1  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
 T7D  plan-1  C7   0.020
 T7D  plan-1  C8   0.020
 T7D  plan-1  C10  0.020
 T7D  plan-1  C13  0.020
 T7D  plan-1  C11  0.020
 T7D  plan-1  C12  0.020
 T7D  plan-1  C9   0.020
 T7D  plan-1  H13  0.020
 T7D  plan-1  H16  0.020
 T7D  plan-1  H14  0.020
 T7D  plan-1  H15  0.020
 T7D  plan-1  H12  0.020
 T7D  plan-2  N1   0.020
 T7D  plan-2  C4   0.020
 T7D  plan-2  C7   0.020
 T7D  plan-2  C8   0.020
 T7D  plan-2  O1   0.020
 T7D  plan-2  H11  0.020
 T7D  plan-3  C6   0.020
 T7D  plan-3  N    0.020
 T7D  plan-3  C    0.020
 T7D  plan-3  O    0.020
 T7D  plan-3  C1   0.020
 T7D  plan-3  C2   0.020

