# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:48:26 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 4-benzyl-1-[(4-methylphenyl)carbonyl]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)C(=O)N2CCC(CC2)Cc3ccccc3
#
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
 4PI  4PI  4-benzyl-1-[(4-methylphenyl)carbonyl]piperidine  ligand  45  22  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4PI
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
 4PI  C1    C  CR6   0   0.097  -6.0684  -4.5481  -3.5823
 4PI  C2    C  CR16  0  -0.287  -6.4219  -3.6696  -2.5583
 4PI  C3    C  CR16  0  -0.260  -5.5558  -2.6726  -2.1398
 4PI  C7    C  CH2   0  -0.319  -1.1856  -0.6297  -1.6987
 4PI  C8    C  CH2   0  -0.421  -0.8543  -0.5674  -0.2141
 4PI  C9    C  CH1   0  -0.241  -0.3308  -1.9105   0.2888
 4PI  C10   C  CH2   0  -0.407  -1.3172  -3.0138  -0.0810
 4PI  C11   C  CH2   0  -0.317  -1.6449  -3.0103  -1.5699
 4PI  C21   C  CR6   0   0.141   0.6105  -3.1097   2.3144
 4PI  C22   C  CR16  0  -0.315  -0.1078  -4.0652   3.0287
 4PI  C24   C  CR16  0  -0.275   1.8465  -5.4589   3.2175
 4PI  C27   C  CH3   0  -0.723  -7.0232  -5.6066  -4.0494
 4PI  N12   N  NT    0  -0.443  -2.1251  -1.7017  -1.9887
 4PI  C23   C  CR16  0  -0.242   0.5020  -5.2310   3.4765
 4PI  C25   C  CR16  0  -0.240   2.5759  -4.5115   2.5089
 4PI  C26   C  CR16  0  -0.309   1.9614  -3.3499   2.0639
 4PI  O32   O  O     0  -0.493  -3.8617  -0.2793  -2.2927
 4PI  C4    C  CR6   0  -0.087  -4.2930  -2.5503  -2.7128
 4PI  C5    C  CR16  0  -0.244  -3.9331  -3.4196  -3.7378
 4PI  C6    C  CR16  0  -0.292  -4.8143  -4.4002  -4.1689
 4PI  H2    H  HCR6  0   0.251  -7.3927  -3.7620  -2.0858
 4PI  H3    H  HCR6  0   0.257  -5.8612  -1.9973  -1.3503
 4PI  H71   H  HCH2  0   0.263  -1.5920   0.3146  -2.0503
 4PI  H72   H  HCH2  0   0.242  -0.2721  -0.8259  -2.2695
 4PI  H81   H  HCH2  0   0.239  -0.1098   0.2155  -0.0479
 4PI  H82   H  HCH2  0   0.225  -1.7499  -0.2818   0.3482
 4PI  H9    H  HCH1  0   0.225   0.6149  -2.1189  -0.2289
 4PI  H101  H  HCH2  0   0.219  -2.2454  -2.8867   0.4877
 4PI  H102  H  HCH2  0   0.245  -0.9181  -3.9957   0.1838
 4PI  H111  H  HCH2  0   0.240  -0.7533  -3.2628  -2.1522
 4PI  H112  H  HCH2  0   0.273  -2.3903  -3.7717  -1.7805
 4PI  H22   H  HCR6  0   0.245  -1.1572  -3.8959   3.2405
 4PI  H24   H  HCR6  0   0.252   2.3238  -6.3648   3.5681
 4PI  H271  H  HCH3  0   0.245  -6.5200  -6.3595  -4.6544
 4PI  H272  H  HCH3  0   0.247  -7.5006  -6.1109  -3.2094
 4PI  H273  H  HCH3  0   0.251  -7.8193  -5.1732  -4.6581
 4PI  H23   H  HCR6  0   0.252  -0.0750  -5.9609   4.0302
 4PI  H25   H  HCR6  0   0.252   3.6263  -4.6767   2.3049
 4PI  H26   H  HCR6  0   0.245   2.5408  -2.6154   1.5158
 4PI  H5    H  HCR6  0   0.264  -2.9616  -3.3328  -4.2091
 4PI  H6    H  HCR6  0   0.252  -4.5175  -5.0630  -4.9730
 4PI  C31   C  C     0   0.513  -3.4082  -1.4182  -2.2967
 4PI  C37   C  CH2   0  -0.501  -0.0448  -1.8609   1.7938
 4PI  H371  H  HCH2  0   0.237  -0.9822  -1.6791   2.3285
 4PI  H372  H  HCH2  0   0.245   0.6017  -1.0015   1.9961

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
 4PI  C1   C27   single    1.500  0.020  1.500
 4PI  C1   C6    aromatic  1.392  0.020  1.392
 4PI  C1   C2    aromatic  1.395  0.020  1.395
 4PI  C2   C3    aromatic  1.385  0.020  1.385
 4PI  C2   H2    single    0.930  0.020  1.080
 4PI  C3   C4    aromatic  1.392  0.020  1.392
 4PI  C3   H3    single    0.930  0.020  1.080
 4PI  C7   N12   single    1.455  0.020  1.455
 4PI  C7   C8    single    1.522  0.020  1.522
 4PI  C7   H71   single    0.970  0.020  1.090
 4PI  C7   H72   single    0.970  0.020  1.090
 4PI  C8   C9    single    1.527  0.020  1.527
 4PI  C8   H81   single    0.970  0.020  1.090
 4PI  C8   H82   single    0.970  0.020  1.090
 4PI  C9   C10   single    1.525  0.020  1.525
 4PI  C9   C37   single    1.533  0.020  1.533
 4PI  C9   H9    single    0.970  0.020  1.090
 4PI  C10  C11   single    1.525  0.020  1.525
 4PI  C10  H101  single    0.970  0.020  1.090
 4PI  C10  H102  single    0.970  0.020  1.090
 4PI  C11  N12   single    1.455  0.020  1.455
 4PI  C11  H111  single    0.970  0.020  1.090
 4PI  C11  H112  single    0.970  0.020  1.090
 4PI  C21  C26   aromatic  1.395  0.020  1.395
 4PI  C21  C37   single    1.503  0.020  1.503
 4PI  C21  C22   aromatic  1.393  0.020  1.393
 4PI  C22  C23   aromatic  1.390  0.020  1.390
 4PI  C22  H22   single    0.930  0.020  1.080
 4PI  C24  C25   aromatic  1.390  0.020  1.390
 4PI  C24  C23   aromatic  1.388  0.020  1.388
 4PI  C24  H24   single    0.930  0.020  1.080
 4PI  C27  H271  single    0.970  0.020  1.090
 4PI  C27  H272  single    0.970  0.020  1.090
 4PI  C27  H273  single    0.970  0.020  1.090
 4PI  C31  O32   double    1.226  0.020  1.226
 4PI  C31  C4    single    1.496  0.020  1.496
 4PI  C31  N12   single    1.350  0.020  1.350
 4PI  C23  H23   single    0.930  0.020  1.080
 4PI  C25  C26   aromatic  1.387  0.020  1.387
 4PI  C25  H25   single    0.930  0.020  1.080
 4PI  C26  H26   single    0.930  0.020  1.080
 4PI  C37  H371  single    0.970  0.020  1.090
 4PI  C37  H372  single    0.970  0.020  1.090
 4PI  C4   C5    aromatic  1.391  0.020  1.391
 4PI  C5   C6    aromatic  1.387  0.020  1.387
 4PI  C5   H5    single    0.930  0.020  1.080
 4PI  C6   H6    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
 4PI  C6    C1   C27   121.13  3.000
 4PI  C6    C1   C2    118.08  3.000
 4PI  C27   C1   C2    120.78  3.000
 4PI  H2    C2   C3    119.32  3.000
 4PI  H2    C2   C1    119.57  3.000
 4PI  C3    C2   C1    121.11  3.000
 4PI  H3    C3   C4    120.08  3.000
 4PI  H3    C3   C2    119.52  3.000
 4PI  C4    C3   C2    120.40  3.000
 4PI  H72   C7   H71   107.40  3.000
 4PI  H72   C7   N12   107.63  3.000
 4PI  H71   C7   N12   109.54  3.000
 4PI  H72   C7   C8    109.52  3.000
 4PI  H71   C7   C8    111.19  3.000
 4PI  N12   C7   C8    111.42  3.000
 4PI  H82   C8   H81   106.98  3.000
 4PI  H82   C8   C9    109.92  3.000
 4PI  H81   C8   C9    110.27  3.000
 4PI  H82   C8   C7    109.47  3.000
 4PI  H81   C8   C7    109.01  3.000
 4PI  C9    C8   C7    111.09  3.000
 4PI  H9    C9   C37   107.97  3.000
 4PI  H9    C9   C10   107.78  3.000
 4PI  C37   C9   C10   112.46  3.000
 4PI  H9    C9   C8    107.87  3.000
 4PI  C37   C9   C8    111.04  3.000
 4PI  C10   C9   C8    109.55  3.000
 4PI  H102  C10  H101  106.73  3.000
 4PI  H102  C10  C11   108.50  3.000
 4PI  H101  C10  C11   108.93  3.000
 4PI  H102  C10  C9    110.80  3.000
 4PI  H101  C10  C9    109.75  3.000
 4PI  C11   C10  C9    111.97  3.000
 4PI  H112  C11  H111  107.11  3.000
 4PI  H112  C11  N12   110.37  3.000
 4PI  H111  C11  N12   108.85  3.000
 4PI  H112  C11  C10   109.59  3.000
 4PI  H111  C11  C10   110.12  3.000
 4PI  N12   C11  C10   110.73  3.000
 4PI  C37   C21  C26   120.20  3.000
 4PI  C37   C21  C22   121.52  3.000
 4PI  C26   C21  C22   118.26  3.000
 4PI  H22   C22  C23   119.53  3.000
 4PI  H22   C22  C21   119.50  3.000
 4PI  C23   C22  C21   120.97  3.000
 4PI  H24   C24  C25   120.28  3.000
 4PI  H24   C24  C23   120.27  3.000
 4PI  C25   C24  C23   119.45  3.000
 4PI  H273  C27  H272  107.10  3.000
 4PI  H273  C27  H271  107.56  3.000
 4PI  H272  C27  H271  108.10  3.000
 4PI  H273  C27  C1    110.95  3.000
 4PI  H272  C27  C1    111.42  3.000
 4PI  H271  C27  C1    111.51  3.000
 4PI  C31   N12  C11   124.62  3.000
 4PI  C31   N12  C7    120.31  3.000
 4PI  C11   N12  C7    113.09  3.000
 4PI  H23   C23  C24   120.07  3.000
 4PI  H23   C23  C22   119.77  3.000
 4PI  C24   C23  C22   120.17  3.000
 4PI  H25   C25  C26   119.80  3.000
 4PI  H25   C25  C24   120.09  3.000
 4PI  C26   C25  C24   120.11  3.000
 4PI  H26   C26  C25   119.51  3.000
 4PI  H26   C26  C21   119.45  3.000
 4PI  C25   C26  C21   121.04  3.000
 4PI  C5    C4   C31   121.65  3.000
 4PI  C5    C4   C3    118.88  3.000
 4PI  C31   C4   C3    119.25  3.000
 4PI  H5    C5   C6    119.42  3.000
 4PI  H5    C5   C4    120.16  3.000
 4PI  C6    C5   C4    120.42  3.000
 4PI  H6    C6   C5    119.28  3.000
 4PI  H6    C6   C1    119.64  3.000
 4PI  C5    C6   C1    121.09  3.000
 4PI  C4    C31  O32   119.02  3.000
 4PI  C4    C31  N12   117.83  3.000
 4PI  O32   C31  N12   123.10  3.000
 4PI  H372  C37  H371  106.57  3.000
 4PI  H372  C37  C21   109.32  3.000
 4PI  H371  C37  C21   110.01  3.000
 4PI  H372  C37  C9    108.49  3.000
 4PI  H371  C37  C9    108.99  3.000
 4PI  C21   C37  C9    113.23  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
 4PI  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 4PI  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 4PI  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 4PI  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 4PI  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 4PI  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 4PI  CONST_07  C24   C25  C26  C21     0.00   0.0  0
 4PI  CONST_08  C24   C23  C22  C21     0.00   0.0  0
 4PI  CONST_09  C25   C26  C21  C22     0.00   0.0  0
 4PI  CONST_10  C25   C24  C23  C22     0.00   0.0  0
 4PI  CONST_11  C26   C21  C22  C23     0.00   0.0  0
 4PI  CONST_12  C26   C25  C24  C23     0.00   0.0  0
 4PI  CONST_13  C31   C4   C3   C2    180.00   0.0  0
 4PI  CONST_14  C27   C1   C2   C3    180.00   0.0  0
 4PI  CONST_15  C5    C6   C1   C27   180.00   0.0  0
 4PI  CONST_16  C6    C5   C4   C31   180.00   0.0  0
 4PI  CONST_17  C37   C21  C22  C23   180.00   0.0  0
 4PI  CONST_18  C37   C21  C26  C25   180.00   0.0  0
 4PI  CONST_19  C4    C31  N12  C7    180.00   0.0  0
 4PI  CONST_21  H5    C5   C6   C1    180.00   0.0  0
 4PI  CONST_22  H3    C3   C2   C1    180.00   0.0  0
 4PI  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 4PI  CONST_24  H25   C25  C26  C21   180.00   0.0  0
 4PI  CONST_25  H23   C23  C22  C21   180.00   0.0  0
 4PI  CONST_26  H26   C26  C21  C22   180.00   0.0  0
 4PI  CONST_27  H24   C24  C23  C22   180.00   0.0  0
 4PI  CONST_28  H22   C22  C23  C24   180.00   0.0  0
 4PI  CONST_29  H2    C2   C3   C4    180.00   0.0  0
 4PI  CONST_30  O32   C31  N12  C7      0.00   0.0  0
 4PI  Var_01    C10   C11  N12  C7     56.83  30.0  1
 4PI  Var_02    C11   N12  C7   C8    -57.61  30.0  1
 4PI  Var_03    N12   C7   C8   C9     55.45  30.0  1
 4PI  Var_04    N12   C11  C10  C9    -54.83  30.0  1
 4PI  Var_05    N12   C31  C4   C3    132.56  30.0  2
 4PI  Var_06    C26   C21  C37  C9     75.44  30.0  2
 4PI  Var_07    H271  C27  C1   C2   -165.19  30.0  2

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
 4PI  chir_01  C9  C8  C10  C37  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
 4PI  plan-1  C1   0.020
 4PI  plan-1  C2   0.020
 4PI  plan-1  C3   0.020
 4PI  plan-1  C27  0.020
 4PI  plan-1  C4   0.020
 4PI  plan-1  C5   0.020
 4PI  plan-1  C6   0.020
 4PI  plan-1  H2   0.020
 4PI  plan-1  H3   0.020
 4PI  plan-1  H5   0.020
 4PI  plan-1  H6   0.020
 4PI  plan-1  C31  0.020
 4PI  plan-2  C21  0.020
 4PI  plan-2  C22  0.020
 4PI  plan-2  C24  0.020
 4PI  plan-2  C23  0.020
 4PI  plan-2  C25  0.020
 4PI  plan-2  C26  0.020
 4PI  plan-2  H22  0.020
 4PI  plan-2  H24  0.020
 4PI  plan-2  H23  0.020
 4PI  plan-2  H25  0.020
 4PI  plan-2  H26  0.020
 4PI  plan-2  C37  0.020
 4PI  plan-3  C7   0.020
 4PI  plan-3  C11  0.020
 4PI  plan-3  N12  0.020
 4PI  plan-3  O32  0.020
 4PI  plan-3  C4   0.020
 4PI  plan-3  C31  0.020

