# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 23:04:48 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N-(1-benzylpiperidin-4-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC1CCN(CC1)Cc2ccccc2
#
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
 8RV  8RV  N-(1-benzylpiperidin-4-yl)acetamide  ligand  37  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8RV
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
 8RV  N1   N  NH1   0  -0.628  -3.1733   0.1937   0.2014
 8RV  C4   C  CH2   0  -0.465  -1.6951   2.0987  -0.1464
 8RV  C5   C  CH2   0  -0.290  -0.6257   1.7429   0.8770
 8RV  C6   C  CH2   0  -0.282  -0.1851  -0.3454  -0.2234
 8RV  C7   C  CH2   0  -0.432  -1.2211  -0.0531  -1.2959
 8RV  C8   C  CH2   0  -0.316   1.4560   0.6216   1.2431
 8RV  C10  C  CR16  0  -0.283   3.1638   0.5030  -0.6068
 8RV  C13  C  CR16  0  -0.242   4.5121  -1.5618   0.6609
 8RV  C1   C  CH3   0  -0.778  -4.8956  -1.2758   1.0376
 8RV  C2   C  C     0   0.524  -4.1445  -0.6732  -0.1246
 8RV  C3   C  CH1   0  -0.102  -2.3292   0.8620  -0.7750
 8RV  N2   N  NT    0  -0.413   0.3898   0.8824   0.2999
 8RV  C9   C  CR6   0   0.084   2.6749   0.0098   0.6018
 8RV  C11  C  CR16  0  -0.242   4.3125  -0.0284  -1.1745
 8RV  C12  C  CR16  0  -0.271   4.9932  -1.0625  -0.5410
 8RV  C14  C  CR16  0  -0.314   3.3577  -1.0297   1.2241
 8RV  O1   O  O     0  -0.513  -4.4157  -0.9631  -1.2839
 8RV  H1   H  HNH1  0   0.396  -3.0062   0.3726   1.1779
 8RV  H2   H  HCH2  0   0.248  -2.4578   2.7258   0.3213
 8RV  H3   H  HCH2  0   0.244  -1.2399   2.6906  -0.9436
 8RV  H4   H  HCH2  0   0.246  -0.1505   2.6632   1.2250
 8RV  H5   H  HCH2  0   0.187  -1.0859   1.2864   1.7734
 8RV  H6   H  HCH2  0   0.192  -0.6363  -0.9528   0.5817
 8RV  H7   H  HCH2  0   0.244   0.6123  -0.9527  -0.6554
 8RV  H8   H  HCH2  0   0.228  -0.7331   0.4396  -2.1414
 8RV  H9   H  HCH2  0   0.241  -1.6421  -0.9878  -1.6693
 8RV  H10  H  HCH2  0   0.250   1.7474   1.5765   1.6929
 8RV  H11  H  HCH2  0   0.210   1.1229  -0.0172   2.0790
 8RV  H13  H  HCR6  0   0.252   5.0313  -2.3696   1.1609
 8RV  H14  H  HCH3  0   0.247  -4.5750  -0.9028   2.0085
 8RV  H15  H  HCH3  0   0.264  -5.9609  -1.0758   0.9254
 8RV  H16  H  HCH3  0   0.264  -4.7665  -2.3583   1.0263
 8RV  H17  H  HCH1  0   0.256  -2.9621   1.1715  -1.6096
 8RV  H19  H  HCR6  0   0.252   4.6784   0.3644  -2.1148
 8RV  H20  H  HCR6  0   0.252   5.8895  -1.4771  -0.9844
 8RV  H21  H  HCR6  0   0.247   2.9851  -1.4304   2.1598
 8RV  H12  H  HCR6  0   0.243   2.6291   1.3004  -1.1082

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
 8RV  C10  C11  aromatic  1.387  0.020  1.387
 8RV  C10  C9   aromatic  1.394  0.020  1.394
 8RV  C11  C12  aromatic  1.391  0.020  1.391
 8RV  C8   C9   single    1.507  0.020  1.507
 8RV  C8   N2   single    1.447  0.020  1.447
 8RV  C9   C14  aromatic  1.391  0.020  1.391
 8RV  C12  C13  aromatic  1.388  0.020  1.388
 8RV  C5   N2   single    1.451  0.020  1.451
 8RV  C5   C4   single    1.522  0.020  1.522
 8RV  N2   C6   single    1.453  0.020  1.453
 8RV  C14  C13  aromatic  1.390  0.020  1.390
 8RV  C4   C3   single    1.525  0.020  1.525
 8RV  C3   N1   single    1.453  0.020  1.453
 8RV  C3   C7   single    1.529  0.020  1.529
 8RV  C6   C7   single    1.520  0.020  1.520
 8RV  N1   C2   single    1.342  0.020  1.342
 8RV  C2   O1   double    1.225  0.020  1.225
 8RV  C2   C1   single    1.509  0.020  1.509
 8RV  N1   H1   single    0.860  0.020  1.020
 8RV  C4   H2   single    0.970  0.020  1.090
 8RV  C4   H3   single    0.970  0.020  1.090
 8RV  C5   H4   single    0.970  0.020  1.090
 8RV  C5   H5   single    0.970  0.020  1.090
 8RV  C6   H6   single    0.970  0.020  1.090
 8RV  C6   H7   single    0.970  0.020  1.090
 8RV  C7   H8   single    0.970  0.020  1.090
 8RV  C7   H9   single    0.970  0.020  1.090
 8RV  C8   H10  single    0.970  0.020  1.090
 8RV  C8   H11  single    0.970  0.020  1.090
 8RV  C10  H12  single    0.930  0.020  1.080
 8RV  C13  H13  single    0.930  0.020  1.080
 8RV  C1   H14  single    0.970  0.020  1.090
 8RV  C1   H15  single    0.970  0.020  1.090
 8RV  C1   H16  single    0.970  0.020  1.090
 8RV  C3   H17  single    0.970  0.020  1.090
 8RV  C11  H19  single    0.930  0.020  1.080
 8RV  C12  H20  single    0.930  0.020  1.080
 8RV  C14  H21  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
 8RV  H1   N1   C3   118.26  3.000
 8RV  H1   N1   C2   118.07  3.000
 8RV  C3   N1   C2   123.65  3.000
 8RV  H3   C4   H2   107.00  3.000
 8RV  H3   C4   C3   108.17  3.000
 8RV  H2   C4   C3   110.58  3.000
 8RV  H3   C4   C5   108.94  3.000
 8RV  H2   C4   C5   109.68  3.000
 8RV  C3   C4   C5   112.31  3.000
 8RV  H5   C5   H4   105.69  3.000
 8RV  H5   C5   N2   111.64  3.000
 8RV  H4   C5   N2   108.78  3.000
 8RV  H5   C5   C4   110.42  3.000
 8RV  H4   C5   C4   108.83  3.000
 8RV  N2   C5   C4   111.28  3.000
 8RV  H7   C6   H6   106.32  3.000
 8RV  H7   C6   N2   108.88  3.000
 8RV  H6   C6   N2   111.32  3.000
 8RV  H7   C6   C7   109.01  3.000
 8RV  H6   C6   C7   109.97  3.000
 8RV  N2   C6   C7   111.18  3.000
 8RV  H9   C7   H8   107.07  3.000
 8RV  H9   C7   C3   110.48  3.000
 8RV  H8   C7   C3   108.50  3.000
 8RV  H9   C7   C6   109.87  3.000
 8RV  H8   C7   C6   109.15  3.000
 8RV  C3   C7   C6   111.65  3.000
 8RV  H11  C8   H10  105.90  3.000
 8RV  H11  C8   C9   109.36  3.000
 8RV  H10  C8   C9   108.27  3.000
 8RV  H11  C8   N2   112.06  3.000
 8RV  H10  C8   N2   107.85  3.000
 8RV  C9   C8   N2   113.06  3.000
 8RV  H12  C10  C11  120.09  3.000
 8RV  H12  C10  C9   119.26  3.000
 8RV  C11  C10  C9   120.65  3.000
 8RV  H13  C13  C14  119.78  3.000
 8RV  H13  C13  C12  120.15  3.000
 8RV  C14  C13  C12  120.07  3.000
 8RV  H16  C1   H15  107.28  3.000
 8RV  H16  C1   H14  108.34  3.000
 8RV  H15  C1   H14  108.48  3.000
 8RV  H16  C1   C2   109.24  3.000
 8RV  H15  C1   C2   109.51  3.000
 8RV  H14  C1   C2   113.79  3.000
 8RV  O1   C2   C1   121.60  3.000
 8RV  C1   C2   N1   115.53  3.000
 8RV  O1   C2   N1   122.87  3.000
 8RV  H17  C3   C7   109.23  3.000
 8RV  H17  C3   C4   109.03  3.000
 8RV  C7   C3   C4   108.93  3.000
 8RV  H17  C3   N1   107.89  3.000
 8RV  C7   C3   N1   112.00  3.000
 8RV  C4   C3   N1   109.72  3.000
 8RV  C8   N2   C6   111.95  3.000
 8RV  C6   N2   C5   111.56  3.000
 8RV  C8   N2   C5   111.31  3.000
 8RV  C14  C9   C10  118.70  3.000
 8RV  C14  C9   C8   120.67  3.000
 8RV  C10  C9   C8   120.60  3.000
 8RV  H19  C11  C12  120.00  3.000
 8RV  H19  C11  C10  119.75  3.000
 8RV  C12  C11  C10  120.25  3.000
 8RV  H20  C12  C11  120.23  3.000
 8RV  H20  C12  C13  120.27  3.000
 8RV  C11  C12  C13  119.50  3.000
 8RV  H21  C14  C9   119.59  3.000
 8RV  H21  C14  C13  119.58  3.000
 8RV  C9   C14  C13  120.83  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
 8RV  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 8RV  CONST_02  C13  C14  C9   C10     0.00   0.0  0
 8RV  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 8RV  CONST_04  C12  C13  C14  C9      0.00   0.0  0
 8RV  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 8RV  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 8RV  CONST_07  C11  C10  C9   C8    180.00   0.0  0
 8RV  CONST_08  C13  C14  C9   C8    180.00   0.0  0
 8RV  CONST_09  H20  C12  C11  C10   180.00   0.0  0
 8RV  CONST_10  H21  C14  C9   C10   180.00   0.0  0
 8RV  CONST_11  H19  C11  C12  C13   180.00   0.0  0
 8RV  CONST_12  H13  C13  C14  C9    180.00   0.0  0
 8RV  CONST_13  H12  C10  C11  C12   180.00   0.0  0
 8RV  CONST_14  C3   N1   C2   C1    180.00   0.0  0
 8RV  CONST_15  O1   C2   N1   C3      0.00   0.0  0
 8RV  CONST_16  H1   N1   C2   C1      0.00   0.0  0
 8RV  Var_01    C6   N2   C5   C4    -58.26  30.0  1
 8RV  Var_02    C7   C6   N2   C5     59.25  30.0  1
 8RV  Var_03    N2   C5   C4   C3     55.23  30.0  1
 8RV  Var_04    N2   C6   C7   C3    -56.76  30.0  1
 8RV  Var_05    C9   C8   N2   C5   -166.59  30.0  1
 8RV  Var_06    N2   C8   C9   C10    43.98  30.0  2
 8RV  Var_07    H14  C1   C2   N1      1.97  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
 8RV  chir_01  C3  C4  N1  C7  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
 8RV  plan-1  C8   0.020
 8RV  plan-1  C10  0.020
 8RV  plan-1  C13  0.020
 8RV  plan-1  C9   0.020
 8RV  plan-1  C11  0.020
 8RV  plan-1  C12  0.020
 8RV  plan-1  C14  0.020
 8RV  plan-1  H13  0.020
 8RV  plan-1  H19  0.020
 8RV  plan-1  H20  0.020
 8RV  plan-1  H21  0.020
 8RV  plan-1  H12  0.020
 8RV  plan-2  N1   0.020
 8RV  plan-2  C1   0.020
 8RV  plan-2  C2   0.020
 8RV  plan-2  C3   0.020
 8RV  plan-2  O1   0.020
 8RV  plan-2  H1   0.020

