# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:00:56 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 1-[4-(piperidine-1-carbonyl)piperidin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC(CC1)C(=O)N2CCCCC2
#
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
 T7S  T7S  1-[4-(piperidine-1-carbonyl)piperidin-1-yl]ethan-1-one  ligand  39  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T7S
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
 T7S  N1   N  NT    0  -0.456  -2.3384  -0.5403  -0.3099
 T7S  C4   C  CH1   0  -0.428   0.1203  -0.4746  -0.5178
 T7S  C5   C  CH2   0  -0.423   0.5745   0.7516   0.2847
 T7S  C6   C  CH2   0  -0.312   1.8873   1.2971  -0.2632
 T7S  C7   C  C     0   0.590  -1.1528  -1.0644   0.0706
 T7S  C8   C  CH2   0  -0.311  -3.5864  -1.0708   0.2216
 T7S  C10  C  CH2   0  -0.445  -4.5677   1.2373   0.1840
 T7S  N    N  NT    0  -0.442   2.9107   0.2679  -0.2859
 T7S  C    C  CH3   0  -0.779   4.4161   1.4014   1.3268
 T7S  O    O  O     0  -0.521   4.8204  -0.7197   0.3891
 T7S  C1   C  C     0   0.524   4.0512   0.2359   0.4369
 T7S  C11  C  CH2   0  -0.433  -3.2537   1.7345  -0.4064
 T7S  C12  C  CH2   0  -0.316  -2.5376   0.6210  -1.1633
 T7S  C2   C  CH2   0  -0.323   2.5229  -0.8777  -1.0959
 T7S  C3   C  CH2   0  -0.408   1.2446  -1.5072  -0.5586
 T7S  C9   C  CH2   0  -0.434  -4.3353  -0.0141   1.0226
 T7S  O1   O  O     0  -0.508  -1.0834  -1.9895   0.8733
 T7S  H6   H  HCH1  0   0.261  -0.0565  -0.1555  -1.5490
 T7S  H7   H  HCH2  0   0.255  -0.1741   1.5459   0.2497
 T7S  H8   H  HCH2  0   0.242   0.7038   0.4784   1.3357
 T7S  H9   H  HCH2  0   0.245   1.7355   1.6533  -1.2877
 T7S  H10  H  HCH2  0   0.267   2.2026   2.1561   0.3190
 T7S  H12  H  HCH2  0   0.233  -4.2025  -1.3974  -0.6239
 T7S  H11  H  HCH2  0   0.262  -3.3757  -1.9464   0.8281
 T7S  H15  H  HCH2  0   0.239  -5.0369   2.0196   0.7840
 T7S  H16  H  HCH2  0   0.217  -5.2664   1.0071  -0.6275
 T7S  H    H  HCH3  0   0.251   3.7354   2.2445   1.3470
 T7S  H21  H  HCH3  0   0.267   4.5164   1.0297   2.3467
 T7S  H1   H  HCH3  0   0.267   5.3967   1.7683   1.0236
 T7S  H18  H  HCH2  0   0.240  -3.4243   2.5704  -1.0879
 T7S  H17  H  HCH2  0   0.225  -2.6029   2.1017   0.3940
 T7S  H20  H  HCH2  0   0.263  -1.5951   0.9847  -1.5608
 T7S  H19  H  HCH2  0   0.243  -3.1424   0.3156  -2.0244
 T7S  H2   H  HCH2  0   0.239   2.3723  -0.5374  -2.1260
 T7S  H3   H  HCH2  0   0.267   3.3306  -1.6027  -1.1087
 T7S  H4   H  HCH2  0   0.233   1.4342  -1.9078   0.4389
 T7S  H5   H  HCH2  0   0.246   0.9658  -2.3475  -1.1984
 T7S  H14  H  HCH2  0   0.238  -5.2841  -0.4322   1.3653
 T7S  H13  H  HCH2  0   0.223  -3.7561   0.2382   1.9159

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
 T7S  C1   C    single  1.511  0.020  1.511
 T7S  C1   O    double  1.228  0.020  1.228
 T7S  N    C1   single  1.351  0.020  1.351
 T7S  C2   N    single  1.456  0.020  1.456
 T7S  C3   C2   single  1.523  0.020  1.523
 T7S  C4   C3   single  1.527  0.020  1.527
 T7S  C4   C5   single  1.534  0.020  1.534
 T7S  C5   C6   single  1.524  0.020  1.524
 T7S  C6   N    single  1.452  0.020  1.452
 T7S  C7   C4   single  1.522  0.020  1.522
 T7S  O1   C7   double  1.227  0.020  1.227
 T7S  C7   N1   single  1.351  0.020  1.351
 T7S  N1   C8   single  1.457  0.020  1.457
 T7S  C9   C8   single  1.523  0.020  1.523
 T7S  C10  C9   single  1.524  0.020  1.524
 T7S  C11  C10  single  1.524  0.020  1.524
 T7S  C12  C11  single  1.525  0.020  1.525
 T7S  N1   C12  single  1.455  0.020  1.455
 T7S  C4   H6   single  0.970  0.020  1.090
 T7S  C5   H7   single  0.970  0.020  1.090
 T7S  C5   H8   single  0.970  0.020  1.090
 T7S  C6   H9   single  0.970  0.020  1.090
 T7S  C6   H10  single  0.970  0.020  1.090
 T7S  C8   H12  single  0.970  0.020  1.090
 T7S  C8   H11  single  0.970  0.020  1.090
 T7S  C10  H15  single  0.970  0.020  1.090
 T7S  C10  H16  single  0.970  0.020  1.090
 T7S  C    H    single  0.970  0.020  1.090
 T7S  C    H21  single  0.970  0.020  1.090
 T7S  C    H1   single  0.970  0.020  1.090
 T7S  C11  H18  single  0.970  0.020  1.090
 T7S  C11  H17  single  0.970  0.020  1.090
 T7S  C12  H20  single  0.970  0.020  1.090
 T7S  C12  H19  single  0.970  0.020  1.090
 T7S  C2   H2   single  0.970  0.020  1.090
 T7S  C2   H3   single  0.970  0.020  1.090
 T7S  C3   H4   single  0.970  0.020  1.090
 T7S  C3   H5   single  0.970  0.020  1.090
 T7S  C9   H14  single  0.970  0.020  1.090
 T7S  C9   H13  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
 T7S  C12  N1   C8   112.80  3.000
 T7S  C12  N1   C7   126.52  3.000
 T7S  C8   N1   C7   120.52  3.000
 T7S  H6   C4   C3   106.92  3.000
 T7S  H6   C4   C7   110.03  3.000
 T7S  C3   C4   C7   111.36  3.000
 T7S  H6   C4   C5   107.92  3.000
 T7S  C7   C4   C5   110.81  3.000
 T7S  C3   C4   C5   109.66  3.000
 T7S  H8   C5   H7   107.07  3.000
 T7S  H8   C5   C6   109.46  3.000
 T7S  H7   C5   C6   108.59  3.000
 T7S  H8   C5   C4   109.75  3.000
 T7S  H7   C5   C4   111.20  3.000
 T7S  C6   C5   C4   110.68  3.000
 T7S  H10  C6   H9   106.55  3.000
 T7S  H10  C6   N    111.41  3.000
 T7S  H9   C6   N    108.28  3.000
 T7S  H10  C6   C5   109.94  3.000
 T7S  H9   C6   C5   109.47  3.000
 T7S  N    C6   C5   111.06  3.000
 T7S  O1   C7   C4   119.87  3.000
 T7S  O1   C7   N1   121.77  3.000
 T7S  C4   C7   N1   118.36  3.000
 T7S  H11  C8   H12  107.44  3.000
 T7S  H11  C8   C9   111.17  3.000
 T7S  H12  C8   C9   109.64  3.000
 T7S  H11  C8   N1   109.35  3.000
 T7S  H12  C8   N1   107.98  3.000
 T7S  C9   C8   N1   111.13  3.000
 T7S  H16  C10  H15  106.48  3.000
 T7S  H16  C10  C9   109.41  3.000
 T7S  H15  C10  C9   110.57  3.000
 T7S  H16  C10  C11  109.36  3.000
 T7S  H15  C10  C11  110.47  3.000
 T7S  C9   C10  C11  110.46  3.000
 T7S  C2   N    C1   120.28  3.000
 T7S  C2   N    C6   112.27  3.000
 T7S  C1   N    C6   127.13  3.000
 T7S  H1   C    H21  107.00  3.000
 T7S  H1   C    H    107.97  3.000
 T7S  H21  C    H    107.79  3.000
 T7S  H1   C    C1   108.24  3.000
 T7S  H21  C    C1   108.07  3.000
 T7S  H    C    C1   117.34  3.000
 T7S  O    C1   C    118.16  3.000
 T7S  O    C1   N    121.78  3.000
 T7S  C    C1   N    120.06  3.000
 T7S  H17  C11  H18  107.00  3.000
 T7S  H17  C11  C12  109.19  3.000
 T7S  H18  C11  C12  108.82  3.000
 T7S  H17  C11  C10  109.80  3.000
 T7S  H18  C11  C10  110.90  3.000
 T7S  C12  C11  C10  111.04  3.000
 T7S  H19  C12  H20  106.55  3.000
 T7S  H19  C12  C11  109.54  3.000
 T7S  H20  C12  C11  110.17  3.000
 T7S  H19  C12  N1   108.30  3.000
 T7S  H20  C12  N1   111.30  3.000
 T7S  C11  C12  N1   110.85  3.000
 T7S  H3   C2   H2   107.39  3.000
 T7S  H3   C2   C3   110.66  3.000
 T7S  H2   C2   C3   110.17  3.000
 T7S  H3   C2   N    109.51  3.000
 T7S  H2   C2   N    108.39  3.000
 T7S  C3   C2   N    110.65  3.000
 T7S  H5   C3   H4   107.29  3.000
 T7S  H5   C3   C2   109.00  3.000
 T7S  H4   C3   C2   109.16  3.000
 T7S  H5   C3   C4   110.36  3.000
 T7S  H4   C3   C4   110.59  3.000
 T7S  C2   C3   C4   110.36  3.000
 T7S  H13  C9   H14  106.98  3.000
 T7S  H13  C9   C10  109.91  3.000
 T7S  H14  C9   C10  110.76  3.000
 T7S  H13  C9   C8   109.21  3.000
 T7S  H14  C9   C8   109.07  3.000
 T7S  C10  C9   C8   110.81  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
 T7S  CONST_01  C8   N1   C7   C4   180.00   0.0  0
 T7S  CONST_02  C12  N1   C7   C4     0.00   0.0  0
 T7S  CONST_03  C    C1   N    C6     0.00   0.0  0
 T7S  CONST_04  O    C1   N    C6   180.00   0.0  0
 T7S  CONST_05  O1   C7   N1   C8     0.00   0.0  0
 T7S  CONST_06  C2   N    C1   C    180.00   0.0  0
 T7S  CONST_07  C2   N    C1   O      0.00   0.0  0
 T7S  CONST_08  O1   C7   N1   C12  180.00   0.0  0
 T7S  Var_01    C10  C9   C8   N1    55.22  30.0  1
 T7S  Var_02    C10  C11  C12  N1   -55.23  30.0  1
 T7S  Var_03    N    C2   C3   C4    57.33  30.0  1
 T7S  Var_04    N    C6   C5   C4   -55.61  30.0  1
 T7S  Var_05    C2   N    C6   C5    58.80  30.0  1
 T7S  Var_06    C3   C2   N    C6   -59.62  30.0  1
 T7S  Var_07    C11  C12  N1   C8    58.08  30.0  1
 T7S  Var_08    C11  C10  C9   C8   -53.12  30.0  1
 T7S  Var_09    C9   C10  C11  C12   53.23  30.0  1
 T7S  Var_10    C9   C8   N1   C12  -58.25  30.0  1
 T7S  Var_11    H    C    C1   N     -0.45  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
 T7S  chir_01  C4  C3  C5  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
 T7S  plan-1  N1   0.020
 T7S  plan-1  C4   0.020
 T7S  plan-1  C7   0.020
 T7S  plan-1  C8   0.020
 T7S  plan-1  C12  0.020
 T7S  plan-1  O1   0.020
 T7S  plan-2  C6   0.020
 T7S  plan-2  N    0.020
 T7S  plan-2  C    0.020
 T7S  plan-2  O    0.020
 T7S  plan-2  C1   0.020
 T7S  plan-2  C2   0.020

