# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:21:56 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: ~{N}-butyl-4-methyl-piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCNC(=O)N1CCC(C)CC1
#
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
 8YH  8YH  ~{N}-butyl-4-methyl-piperidine-1-carboxamide  ligand  36  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8YH
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
 8YH  CAE  C  CH2   0  -0.340  -1.4246  -0.5743  -1.3942
 8YH  CAH  C  CH2   0  -0.407  -2.2067  -1.4259  -0.4008
 8YH  CAI  C  CH1   0  -0.239  -3.4899  -0.7250   0.0458
 8YH  CAK  C  CH3   0  -0.654  -4.2295  -1.5268   1.1071
 8YH  CAG  C  CH2   0  -0.415  -3.1744   0.6912   0.5270
 8YH  CAD  C  CH2   0  -0.318  -2.3570   1.4592  -0.5047
 8YH  NAB  N  NT    0  -0.485  -1.1382   0.7422  -0.8443
 8YH  CAA  C  C     0   0.730   0.0056   1.0436  -0.1511
 8YH  OAC  O  O     0  -0.548   0.0656   1.9927   0.6260
 8YH  NAF  N  NH1   0  -0.685   1.0861   0.2446  -0.3720
 8YH  CAJ  C  CH2   0  -0.234   2.3852   0.5952   0.1640
 8YH  CAL  C  CH2   0  -0.453   3.3575  -0.5637   0.0119
 8YH  CAM  C  CH2   0  -0.425   4.7488  -0.2122   0.5238
 8YH  CAN  C  CH3   0  -0.660   5.7325  -1.3663   0.3947
 8YH  H1   H  HCH2  0   0.251  -0.5194  -1.0883  -1.7104
 8YH  H2   H  HCH2  0   0.234  -2.4429  -2.3900  -0.8595
 8YH  H3   H  HCH3  0   0.215  -3.6216  -1.6410   2.0075
 8YH  H4   H  HCH3  0   0.226  -5.1592  -1.0338   1.3965
 8YH  H5   H  HCH3  0   0.226  -4.4814  -2.5258   0.7470
 8YH  H6   H  HCH2  0   0.230  -4.1008   1.2324   0.7386
 8YH  H7   H  HCH2  0   0.233  -2.9393   1.5756  -1.4242
 8YH  H8   H  HNH1  0   0.388   1.1069  -0.3153  -1.2080
 8YH  H9   H  HCH2  0   0.214   2.7941   1.4851  -0.3299
 8YH  H10  H  HCH2  0   0.231   2.2787   0.8433   1.2205
 8YH  H11  H  HCH2  0   0.224   2.9731  -1.4343   0.5524
 8YH  H12  H  HCH2  0   0.220   3.4240  -0.8555  -1.0422
 8YH  H13  H  HCH2  0   0.217   5.1272   0.6559  -0.0241
 8YH  H14  H  HCH2  0   0.216   4.6820   0.0953   1.5715
 8YH  H15  H  HCH3  0   0.218   5.3929  -2.2397   0.9545
 8YH  H16  H  HCH3  0   0.218   5.8517  -1.6701  -0.6468
 8YH  H17  H  HCH3  0   0.228   6.7175  -1.0936   0.7744
 8YH  H18  H  HCH2  0   0.242  -2.0149  -0.4327  -2.3045
 8YH  H19  H  HCH2  0   0.217  -1.5754  -1.6351   0.4704
 8YH  H20  H  HCH1  0   0.214  -4.1420  -0.6400  -0.8334
 8YH  H21  H  HCH2  0   0.216  -2.6129   0.6438   1.4668
 8YH  H22  H  HCH2  0   0.256  -2.1127   2.4577  -0.1528

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
 8YH  CAN  CAM  single  1.522  0.020  1.522
 8YH  OAC  CAA  double  1.228  0.020  1.228
 8YH  CAJ  CAL  single  1.520  0.020  1.520
 8YH  CAJ  NAF  single  1.448  0.020  1.448
 8YH  CAM  CAL  single  1.524  0.020  1.524
 8YH  CAA  NAF  single  1.362  0.020  1.362
 8YH  CAA  NAB  single  1.371  0.020  1.371
 8YH  CAD  CAG  single  1.524  0.020  1.524
 8YH  CAD  NAB  single  1.454  0.020  1.454
 8YH  CAG  CAI  single  1.529  0.020  1.529
 8YH  NAB  CAE  single  1.455  0.020  1.455
 8YH  CAI  CAK  single  1.522  0.020  1.522
 8YH  CAI  CAH  single  1.529  0.020  1.529
 8YH  CAE  CAH  single  1.524  0.020  1.524
 8YH  CAE  H1   single  0.970  0.020  1.090
 8YH  CAH  H2   single  0.970  0.020  1.090
 8YH  CAK  H3   single  0.970  0.020  1.090
 8YH  CAK  H4   single  0.970  0.020  1.090
 8YH  CAK  H5   single  0.970  0.020  1.090
 8YH  CAG  H6   single  0.970  0.020  1.090
 8YH  CAD  H7   single  0.970  0.020  1.090
 8YH  NAF  H8   single  0.890  0.020  1.040
 8YH  CAJ  H9   single  0.970  0.020  1.090
 8YH  CAJ  H10  single  0.970  0.020  1.090
 8YH  CAL  H11  single  0.970  0.020  1.090
 8YH  CAL  H12  single  0.970  0.020  1.090
 8YH  CAM  H13  single  0.970  0.020  1.090
 8YH  CAM  H14  single  0.970  0.020  1.090
 8YH  CAN  H15  single  0.970  0.020  1.090
 8YH  CAN  H16  single  0.970  0.020  1.090
 8YH  CAN  H17  single  0.970  0.020  1.090
 8YH  CAE  H18  single  0.970  0.020  1.090
 8YH  CAH  H19  single  0.970  0.020  1.090
 8YH  CAI  H20  single  0.970  0.020  1.090
 8YH  CAG  H21  single  0.970  0.020  1.090
 8YH  CAD  H22  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
 8YH  H18  CAE  H1   105.56  3.000
 8YH  H18  CAE  NAB  107.67  3.000
 8YH  H1   CAE  NAB  111.93  3.000
 8YH  H18  CAE  CAH  109.73  3.000
 8YH  H1   CAE  CAH  110.63  3.000
 8YH  NAB  CAE  CAH  111.10  3.000
 8YH  H19  CAH  H2   106.83  3.000
 8YH  H19  CAH  CAI  109.80  3.000
 8YH  H2   CAH  CAI  110.21  3.000
 8YH  H19  CAH  CAE  109.21  3.000
 8YH  H2   CAH  CAE  109.27  3.000
 8YH  CAI  CAH  CAE  111.40  3.000
 8YH  H20  CAI  CAG  107.64  3.000
 8YH  H20  CAI  CAK  108.09  3.000
 8YH  CAG  CAI  CAK  111.65  3.000
 8YH  H20  CAI  CAH  107.46  3.000
 8YH  CAK  CAI  CAH  111.72  3.000
 8YH  CAG  CAI  CAH  110.09  3.000
 8YH  H5   CAK  H4   107.72  3.000
 8YH  H5   CAK  H3   107.74  3.000
 8YH  H4   CAK  H3   107.62  3.000
 8YH  H5   CAK  CAI  111.37  3.000
 8YH  H4   CAK  CAI  111.16  3.000
 8YH  H3   CAK  CAI  111.06  3.000
 8YH  H21  CAG  H6   106.84  3.000
 8YH  H21  CAG  CAD  109.12  3.000
 8YH  H6   CAG  CAD  109.63  3.000
 8YH  H21  CAG  CAI  109.61  3.000
 8YH  H6   CAG  CAI  110.16  3.000
 8YH  CAD  CAG  CAI  111.37  3.000
 8YH  H22  CAD  H7   107.09  3.000
 8YH  H22  CAD  NAB  109.90  3.000
 8YH  H7   CAD  NAB  107.58  3.000
 8YH  H22  CAD  CAG  111.37  3.000
 8YH  H7   CAD  CAG  109.70  3.000
 8YH  NAB  CAD  CAG  111.05  3.000
 8YH  CAA  NAB  CAD  118.21  3.000
 8YH  CAD  NAB  CAE  111.68  3.000
 8YH  CAA  NAB  CAE  123.66  3.000
 8YH  NAF  CAA  OAC  121.15  3.000
 8YH  NAF  CAA  NAB  116.80  3.000
 8YH  OAC  CAA  NAB  122.05  3.000
 8YH  H8   NAF  CAJ  115.06  3.000
 8YH  H8   NAF  CAA  118.53  3.000
 8YH  CAJ  NAF  CAA  120.63  3.000
 8YH  H10  CAJ  H9   106.75  3.000
 8YH  H10  CAJ  CAL  109.44  3.000
 8YH  H9   CAJ  CAL  109.57  3.000
 8YH  H10  CAJ  NAF  109.02  3.000
 8YH  H9   CAJ  NAF  111.35  3.000
 8YH  CAL  CAJ  NAF  110.61  3.000
 8YH  H12  CAL  H11  106.54  3.000
 8YH  H12  CAL  CAM  109.22  3.000
 8YH  H11  CAL  CAM  109.78  3.000
 8YH  H12  CAL  CAJ  109.76  3.000
 8YH  H11  CAL  CAJ  109.41  3.000
 8YH  CAM  CAL  CAJ  111.99  3.000
 8YH  H14  CAM  H13  106.12  3.000
 8YH  H14  CAM  CAN  109.51  3.000
 8YH  H13  CAM  CAN  109.61  3.000
 8YH  H14  CAM  CAL  109.32  3.000
 8YH  H13  CAM  CAL  109.31  3.000
 8YH  CAN  CAM  CAL  112.75  3.000
 8YH  H17  CAN  H16  107.66  3.000
 8YH  H17  CAN  H15  107.62  3.000
 8YH  H16  CAN  H15  107.50  3.000
 8YH  H17  CAN  CAM  111.39  3.000
 8YH  H16  CAN  CAM  111.26  3.000
 8YH  H15  CAN  CAM  111.23  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
 8YH  CONST_02  OAC  CAA  NAB  CAD    0.00   0.0  0
 8YH  CONST_04  NAF  CAA  NAB  CAD  180.00   0.0  0
 8YH  CONST_05  CAJ  NAF  CAA  NAB  180.00   0.0  0
 8YH  CONST_07  CAJ  NAF  CAA  OAC    0.00   0.0  0
 8YH  Var_01    CAG  CAD  NAB  CAE   59.65  30.0  1
 8YH  Var_02    CAD  NAB  CAE  CAH  -59.52  30.0  1
 8YH  Var_03    NAB  CAD  CAG  CAI  -55.82  30.0  1
 8YH  Var_04    NAB  CAE  CAH  CAI   55.55  30.0  1
 8YH  Var_05    CAL  CAJ  NAF  CAA  169.33  30.0  1
 8YH  Var_06    CAM  CAL  CAJ  NAF  178.08  30.0  3
 8YH  Var_07    CAN  CAM  CAL  CAJ  179.33  30.0  1
 8YH  Var_08    H15  CAN  CAM  CAL  -59.48  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
 8YH  chir_01  CAI  CAG  CAK  CAH  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
 8YH  plan-1  CAE  0.020
 8YH  plan-1  CAD  0.020
 8YH  plan-1  NAB  0.020
 8YH  plan-1  CAA  0.020
 8YH  plan-1  OAC  0.020
 8YH  plan-1  NAF  0.020
 8YH  plan-1  CAJ  0.020
 8YH  plan-1  H8   0.020

