# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 21:09:47 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: N-(5-chloranyl-2-oxidanyl-phenyl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(Cl)cc1NC(=O)C2CCNCC2
#
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
 FY8  FY8  N-(5-chloranyl-2-oxidanyl-phenyl)piperidine-4-carboxamide  ligand  32  17  .  2021-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_FY8
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
 FY8  CL    CL  CL    0  -0.137   4.2953   1.9663   0.1322
 FY8  C1    C   C     0   0.576  -1.0581   0.4589  -0.1759
 FY8  O1    O   O     0  -0.466  -0.7294   1.5970   0.1089
 FY8  C2    C   CR6   0   0.298   1.2149  -0.5445  -0.2300
 FY8  N2    N   NH1   0  -0.574  -5.3488   0.3058   0.4021
 FY8  O2    O   OH1   0  -0.633   1.0675  -2.8822  -0.3148
 FY8  C3    C   CR16  0  -0.275   1.9832   0.6103  -0.1281
 FY8  C4    C   CR6   0   0.292   1.8581  -1.7959  -0.2076
 FY8  C5    C   CH1   0  -0.408  -2.5079   0.0331  -0.2901
 FY8  C6    C   CR16  0  -0.376   3.2349  -1.8681  -0.0825
 FY8  C7    C   CR6   0  -0.051   3.3612   0.5079   0.0012
 FY8  C8    C   CR16  0  -0.227   4.0009  -0.7153   0.0252
 FY8  C9    C   CH2   0  -0.320  -4.8460   0.6890  -0.9072
 FY8  C10   C   CH2   0  -0.316  -4.5189  -0.7136   1.0205
 FY8  C11   C   CH2   0  -0.425  -3.3808   1.1221  -0.9086
 FY8  C12   C   CH2   0  -0.426  -3.0384  -0.3453   1.1016
 FY8  HN1   H   HNH1  0   0.416  -0.5749  -1.4513  -0.6022
 FY8  HO2   H   HOH1  0   0.486   1.5915  -3.6910  -0.3269
 FY8  H3    H   HCR6  0   0.299   1.5146   1.5800  -0.1511
 FY8  H5    H   HCH1  0   0.255  -2.5704  -0.8594  -0.9250
 FY8  H6    H   HCR6  0   0.285   3.7238  -2.8352  -0.0626
 FY8  H8    H   HCR6  0   0.281   5.0749  -0.7851   0.1248
 FY8  H9    H   HCH2  0   0.217  -4.9731  -0.1635  -1.5836
 FY8  H9A   H   HCH2  0   0.239  -5.4710   1.4928  -1.3012
 FY8  H10   H   HCH2  0   0.240  -4.9043  -0.9242   2.0200
 FY8  H10A  H   HCH2  0   0.218  -4.6267  -1.6383   0.4429
 FY8  H11   H   HCH2  0   0.225  -3.2774   2.0492  -0.3382
 FY8  H11A  H   HCH2  0   0.238  -3.0574   1.3358  -1.9308
 FY8  H12   H   HCH2  0   0.239  -2.4675  -1.1818   1.5135
 FY8  H12A  H   HCH2  0   0.230  -2.9094   0.5010   1.7838
 FY8  N1    N   NH1   0  -0.739  -0.1737  -0.5547  -0.3728
 FY8  HN2   H   HNH1  0   0.339  -5.3630   1.1251   0.9995

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
 FY8  CL   C7    single    1.737  0.020  1.737
 FY8  C1   N1    single    1.360  0.020  1.360
 FY8  C1   O1    double    1.218  0.020  1.218
 FY8  C1   C5    single    1.515  0.020  1.515
 FY8  N1   C2    single    1.396  0.020  1.396
 FY8  C2   C3    aromatic  1.391  0.020  1.391
 FY8  C2   C4    aromatic  1.407  0.020  1.407
 FY8  N2   C9    single    1.454  0.020  1.454
 FY8  N2   C10   single    1.453  0.020  1.453
 FY8  O2   C4    single    1.348  0.020  1.348
 FY8  C3   C7    aromatic  1.388  0.020  1.388
 FY8  C4   C6    aromatic  1.384  0.020  1.384
 FY8  C5   C11   single    1.527  0.020  1.527
 FY8  C5   C12   single    1.537  0.020  1.537
 FY8  C6   C8    aromatic  1.388  0.020  1.388
 FY8  C7   C8    aromatic  1.381  0.020  1.381
 FY8  C9   C11   single    1.528  0.020  1.528
 FY8  C10  C12   single    1.528  0.020  1.528
 FY8  N1   HN1   single    0.860  0.020  1.020
 FY8  N2   HN2   single    0.890  0.020  1.040
 FY8  O2   HO2   single    0.850  0.020  0.980
 FY8  C3   H3    single    0.930  0.020  1.080
 FY8  C5   H5    single    0.970  0.020  1.090
 FY8  C6   H6    single    0.930  0.020  1.080
 FY8  C8   H8    single    0.930  0.020  1.080
 FY8  C9   H9    single    0.970  0.020  1.090
 FY8  C9   H9A   single    0.970  0.020  1.090
 FY8  C10  H10   single    0.970  0.020  1.090
 FY8  C10  H10A  single    0.970  0.020  1.090
 FY8  C11  H11   single    0.970  0.020  1.090
 FY8  C11  H11A  single    0.970  0.020  1.090
 FY8  C12  H12   single    0.970  0.020  1.090
 FY8  C12  H12A  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
 FY8  C5    C1   O1   122.57  3.000
 FY8  C5    C1   N1   113.70  3.000
 FY8  O1    C1   N1   123.69  3.000
 FY8  C4    C2   C3   119.00  3.000
 FY8  C4    C2   N1   116.73  3.000
 FY8  C3    C2   N1   124.27  3.000
 FY8  HN2   N2   C10  108.92  3.000
 FY8  HN2   N2   C9   108.81  3.000
 FY8  C10   N2   C9   111.76  3.000
 FY8  HO2   O2   C4   111.01  3.000
 FY8  H3    C3   C7   120.03  3.000
 FY8  H3    C3   C2   120.37  3.000
 FY8  C7    C3   C2   119.60  3.000
 FY8  C6    C4   O2   123.27  3.000
 FY8  C6    C4   C2   120.16  3.000
 FY8  O2    C4   C2   116.57  3.000
 FY8  H5    C5   C12  107.70  3.000
 FY8  H5    C5   C11  108.26  3.000
 FY8  C12   C5   C11  110.19  3.000
 FY8  H5    C5   C1   109.07  3.000
 FY8  C12   C5   C1   109.34  3.000
 FY8  C11   C5   C1   112.16  3.000
 FY8  H6    C6   C8   119.38  3.000
 FY8  H6    C6   C4   119.79  3.000
 FY8  C8    C6   C4   120.83  3.000
 FY8  C8    C7   C3   121.81  3.000
 FY8  C8    C7   CL   119.57  3.000
 FY8  C3    C7   CL   118.62  3.000
 FY8  H8    C8   C7   121.28  3.000
 FY8  H8    C8   C6   120.12  3.000
 FY8  C7    C8   C6   118.60  3.000
 FY8  H9A   C9   H9   106.48  3.000
 FY8  H9A   C9   C11  109.87  3.000
 FY8  H9    C9   C11  109.34  3.000
 FY8  H9A   C9   N2   108.73  3.000
 FY8  H9    C9   N2   108.11  3.000
 FY8  C11   C9   N2   114.03  3.000
 FY8  H10A  C10  H10  106.57  3.000
 FY8  H10A  C10  C12  109.07  3.000
 FY8  H10   C10  C12  109.88  3.000
 FY8  H10A  C10  N2   108.16  3.000
 FY8  H10   C10  N2   108.87  3.000
 FY8  C12   C10  N2   114.02  3.000
 FY8  H11A  C11  H11  107.10  3.000
 FY8  H11A  C11  C9   109.88  3.000
 FY8  H11   C11  C9   109.31  3.000
 FY8  H11A  C11  C5   110.43  3.000
 FY8  H11   C11  C5   109.84  3.000
 FY8  C9    C11  C5   110.22  3.000
 FY8  H12A  C12  H12  107.17  3.000
 FY8  H12A  C12  C10  109.49  3.000
 FY8  H12   C12  C10  109.98  3.000
 FY8  H12A  C12  C5   109.47  3.000
 FY8  H12   C12  C5   110.45  3.000
 FY8  C10   C12  C5   110.23  3.000
 FY8  HN1   N1   C2   115.18  3.000
 FY8  HN1   N1   C1   115.91  3.000
 FY8  C2    N1   C1   128.82  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
 FY8  CONST_01  C8   C7   C3   C2     0.00   0.0  0
 FY8  CONST_02  C8   C6   C4   C2     0.00   0.0  0
 FY8  CONST_03  C6   C4   C2   C3     0.00   0.0  0
 FY8  CONST_04  C6   C8   C7   C3     0.00   0.0  0
 FY8  CONST_05  C7   C3   C2   C4     0.00   0.0  0
 FY8  CONST_06  C7   C8   C6   C4     0.00   0.0  0
 FY8  CONST_07  C2   C3   C7   CL   180.00   0.0  0
 FY8  CONST_08  C6   C8   C7   CL   180.00   0.0  0
 FY8  CONST_09  C7   C3   C2   N1   180.00   0.0  0
 FY8  CONST_10  C6   C4   C2   N1   180.00   0.0  0
 FY8  CONST_11  C3   C2   C4   O2   180.00   0.0  0
 FY8  CONST_12  C8   C6   C4   O2   180.00   0.0  0
 FY8  CONST_13  H6   C6   C4   C2   180.00   0.0  0
 FY8  CONST_14  H8   C8   C7   C3   180.00   0.0  0
 FY8  CONST_15  H3   C3   C2   C4   180.00   0.0  0
 FY8  CONST_16  C5   C1   N1   C2   180.00   0.0  0
 FY8  CONST_17  C3   C2   N1   C1     0.00   0.0  0
 FY8  CONST_18  C4   C2   N1   C1   180.00   0.0  0
 FY8  CONST_19  HN1  N1   C2   C3   180.00   0.0  0
 FY8  CONST_20  C2   N1   C1   O1     0.00   0.0  0
 FY8  Var_01    C5   C11  C9   N2    54.65  30.0  1
 FY8  Var_02    C5   C12  C10  N2   -54.16  30.0  1
 FY8  Var_03    C12  C10  N2   C9    53.74  30.0  1
 FY8  Var_04    C11  C9   N2   C10  -53.93  30.0  1

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
 FY8  chir_01  C5  C1  C11  C12  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
 FY8  plan-1  CL   0.020
 FY8  plan-1  C2   0.020
 FY8  plan-1  O2   0.020
 FY8  plan-1  C3   0.020
 FY8  plan-1  C4   0.020
 FY8  plan-1  C6   0.020
 FY8  plan-1  C7   0.020
 FY8  plan-1  C8   0.020
 FY8  plan-1  H3   0.020
 FY8  plan-1  H6   0.020
 FY8  plan-1  H8   0.020
 FY8  plan-1  N1   0.020
 FY8  plan-2  C1   0.020
 FY8  plan-2  O1   0.020
 FY8  plan-2  C2   0.020
 FY8  plan-2  C5   0.020
 FY8  plan-2  HN1  0.020
 FY8  plan-2  N1   0.020

