# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 11:24:29 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 1-[(3S)-1-benzylpiperidin-3-yl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H]1CCCN(C1)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
 531  531  1-[(3S)-1-benzylpiperidin-3-yl]ethanone  ligand  35  16  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_531
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
 531  C1    C  CH2   0  -0.317  -0.9493  -0.5753  -1.0761
 531  C2    C  CR6   0   0.084  -2.3220  -0.3673  -0.4897
 531  C3    C  CR16  0  -0.315  -3.3745   0.0824  -1.2797
 531  C4    C  CR16  0  -0.241  -4.6498   0.2357  -0.7477
 531  C5    C  CR16  0  -0.272  -4.8856  -0.0538   0.5887
 531  C6    C  CR16  0  -0.242  -3.8379  -0.4981   1.3881
 531  C7    C  CR16  0  -0.282  -2.5680  -0.6534   0.8524
 531  N8    N  NT    0  -0.421   0.1045  -0.0585  -0.2277
 531  C9    C  CH2   0  -0.247   1.4092  -0.5208  -0.6666
 531  C10   C  CH1   0  -0.388   2.4862  -0.1080   0.3293
 531  C11   C  CH2   0  -0.435   2.4887   1.4193   0.5008
 531  C12   C  CH2   0  -0.436   1.0901   1.8933   0.8707
 531  C13   C  CH2   0  -0.277   0.0641   1.3901  -0.1297
 531  C14   C  C     0   0.413   3.8644  -0.5803  -0.0706
 531  O15   O  O     0  -0.405   4.1456  -0.8536  -1.2173
 531  C16   C  CH3   0  -0.773   4.8678  -0.7014   1.0433
 531  H12   H  HCH2  0   0.251  -0.7830  -1.6506  -1.1979
 531  H11   H  HCH2  0   0.211  -0.9161  -0.1461  -2.0916
 531  H31   H  HCR6  0   0.247  -3.1982   0.3175  -2.3231
 531  H41   H  HCR6  0   0.252  -5.4574   0.5866  -1.3777
 531  H51   H  HCR6  0   0.253  -5.8768   0.0680   1.0064
 531  H61   H  HCR6  0   0.252  -4.0130  -0.7241   2.4324
 531  H71   H  HCR6  0   0.242  -1.7520  -0.9897   1.4803
 531  H91   H  HCH2  0   0.242   1.3811  -1.6105  -0.7463
 531  H92   H  HCH2  0   0.195   1.6598  -0.1338  -1.6678
 531  H101  H  HCH1  0   0.256   2.2496  -0.5509   1.3046
 531  H112  H  HCH2  0   0.246   3.2075   1.7260   1.2629
 531  H111  H  HCH2  0   0.229   2.7988   1.8884  -0.4387
 531  H122  H  HCH2  0   0.222   0.8297   1.5290   1.8684
 531  H121  H  HCH2  0   0.238   1.0582   2.9840   0.9073
 531  H132  H  HCH2  0   0.189   0.2509   1.8597  -1.1127
 531  H131  H  HCH2  0   0.242  -0.9351   1.6983   0.1827
 531  H161  H  HCH3  0   0.273   4.6546  -1.6183   1.5994
 531  H163  H  HCH3  0   0.260   5.8859  -0.7568   0.6635
 531  H162  H  HCH3  0   0.257   4.7858   0.1198   1.7546

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
 531  C7   C6    aromatic  1.387  0.020  1.387
 531  C7   C2    aromatic  1.394  0.020  1.394
 531  C6   C5    aromatic  1.391  0.020  1.391
 531  C13  C12   single    1.519  0.020  1.519
 531  C13  N8    single    1.452  0.020  1.452
 531  C12  C11   single    1.522  0.020  1.522
 531  C11  C10   single    1.537  0.020  1.537
 531  C1   C2    single    1.507  0.020  1.507
 531  C1   N8    single    1.448  0.020  1.448
 531  C2   C3    aromatic  1.391  0.020  1.391
 531  N8   C9    single    1.452  0.020  1.452
 531  C5   C4    aromatic  1.388  0.020  1.388
 531  C9   C10   single    1.524  0.020  1.524
 531  C16  C14   single    1.504  0.020  1.504
 531  C10  C14   single    1.511  0.020  1.511
 531  C3   C4    aromatic  1.390  0.020  1.390
 531  C14  O15   double    1.212  0.020  1.212
 531  C1   H12   single    0.970  0.020  1.090
 531  C1   H11   single    0.970  0.020  1.090
 531  C3   H31   single    0.930  0.020  1.080
 531  C4   H41   single    0.930  0.020  1.080
 531  C5   H51   single    0.930  0.020  1.080
 531  C6   H61   single    0.930  0.020  1.080
 531  C7   H71   single    0.930  0.020  1.080
 531  C9   H91   single    0.970  0.020  1.090
 531  C9   H92   single    0.970  0.020  1.090
 531  C10  H101  single    0.970  0.020  1.090
 531  C11  H112  single    0.970  0.020  1.090
 531  C11  H111  single    0.970  0.020  1.090
 531  C12  H122  single    0.970  0.020  1.090
 531  C12  H121  single    0.970  0.020  1.090
 531  C13  H132  single    0.970  0.020  1.090
 531  C13  H131  single    0.970  0.020  1.090
 531  C16  H161  single    0.970  0.020  1.090
 531  C16  H163  single    0.970  0.020  1.090
 531  C16  H162  single    0.970  0.020  1.090

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
 531  H11   C1   H12   105.97  3.000
 531  H11   C1   N8    112.24  3.000
 531  H12   C1   N8    107.77  3.000
 531  H11   C1   C2    109.39  3.000
 531  H12   C1   C2    108.49  3.000
 531  N8    C1   C2    112.68  3.000
 531  C7    C2   C3    118.66  3.000
 531  C3    C2   C1    120.86  3.000
 531  C7    C2   C1    120.46  3.000
 531  H31   C3   C4    119.58  3.000
 531  H31   C3   C2    119.59  3.000
 531  C4    C3   C2    120.83  3.000
 531  H41   C4   C5    120.09  3.000
 531  H41   C4   C3    119.82  3.000
 531  C5    C4   C3    120.09  3.000
 531  H51   C5   C6    120.26  3.000
 531  H51   C5   C4    120.25  3.000
 531  C6    C5   C4    119.49  3.000
 531  H61   C6   C7    119.82  3.000
 531  H61   C6   C5    119.95  3.000
 531  C7    C6   C5    120.23  3.000
 531  H71   C7   C6    120.05  3.000
 531  H71   C7   C2    119.26  3.000
 531  C6    C7   C2    120.69  3.000
 531  C13   N8   C9    111.28  3.000
 531  C9    N8   C1    111.29  3.000
 531  C13   N8   C1    112.04  3.000
 531  H92   C9   H91   106.83  3.000
 531  H92   C9   C10   109.75  3.000
 531  H91   C9   C10   109.63  3.000
 531  H92   C9   N8    111.53  3.000
 531  H91   C9   N8    108.44  3.000
 531  C10   C9   N8    110.57  3.000
 531  H101  C10  C14   107.82  3.000
 531  H101  C10  C11   107.60  3.000
 531  C14   C10  C11   109.80  3.000
 531  H101  C10  C9    108.62  3.000
 531  C14   C10  C9    112.77  3.000
 531  C11   C10  C9    110.07  3.000
 531  H111  C11  H112  106.99  3.000
 531  H111  C11  C12   109.59  3.000
 531  H112  C11  C12   110.35  3.000
 531  H111  C11  C10   109.30  3.000
 531  H112  C11  C10   110.99  3.000
 531  C12   C11  C10   109.58  3.000
 531  H121  C12  H122  107.17  3.000
 531  H121  C12  C13   109.47  3.000
 531  H122  C12  C13   109.25  3.000
 531  H121  C12  C11   110.25  3.000
 531  H122  C12  C11   109.68  3.000
 531  C13   C12  C11   110.94  3.000
 531  H131  C13  H132  106.81  3.000
 531  H131  C13  C12   109.66  3.000
 531  H132  C13  C12   109.32  3.000
 531  H131  C13  N8    109.05  3.000
 531  H132  C13  N8    111.04  3.000
 531  C12   C13  N8    110.86  3.000
 531  C16   C14  O15   121.86  3.000
 531  O15   C14  C10   122.18  3.000
 531  C16   C14  C10   115.96  3.000
 531  H162  C16  H163  109.67  3.000
 531  H162  C16  H161  106.57  3.000
 531  H163  C16  H161  108.50  3.000
 531  H162  C16  C14   111.88  3.000
 531  H163  C16  C14   111.71  3.000
 531  H161  C16  C14   108.31  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
 531  CONST_01  C5    C6   C7   C2     0.00   0.0  0
 531  CONST_02  C5    C4   C3   C2     0.00   0.0  0
 531  CONST_03  C6    C7   C2   C3     0.00   0.0  0
 531  CONST_04  C6    C5   C4   C3     0.00   0.0  0
 531  CONST_05  C7    C6   C5   C4     0.00   0.0  0
 531  CONST_06  C7    C2   C3   C4     0.00   0.0  0
 531  CONST_07  C6    C7   C2   C1   180.00   0.0  0
 531  CONST_08  C4    C3   C2   C1   180.00   0.0  0
 531  CONST_09  H61   C6   C7   C2   180.00   0.0  0
 531  CONST_10  H41   C4   C3   C2   180.00   0.0  0
 531  CONST_11  H71   C7   C2   C3   180.00   0.0  0
 531  CONST_12  H51   C5   C4   C3   180.00   0.0  0
 531  CONST_13  H31   C3   C4   C5   180.00   0.0  0
 531  Var_01    C11   C12  C13  N8    56.66  30.0  1
 531  Var_02    C12   C13  N8   C9   -60.28  30.0  1
 531  Var_03    C13   C12  C11  C10  -53.49  30.0  1
 531  Var_04    C13   N8   C9   C10   61.07  30.0  1
 531  Var_05    N8    C1   C2   C3   136.05  30.0  2
 531  Var_06    H161  C16  C14  C10   77.28  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
 531  chir_01  C10  C11  C9  C14  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
 531  plan-1  C1   0.020
 531  plan-1  C2   0.020
 531  plan-1  C3   0.020
 531  plan-1  C4   0.020
 531  plan-1  C5   0.020
 531  plan-1  C6   0.020
 531  plan-1  C7   0.020
 531  plan-1  H31  0.020
 531  plan-1  H41  0.020
 531  plan-1  H51  0.020
 531  plan-1  H61  0.020
 531  plan-1  H71  0.020
 531  plan-2  C10  0.020
 531  plan-2  C14  0.020
 531  plan-2  O15  0.020
 531  plan-2  C16  0.020

