# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 09:39:50 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-cyclohexyl-4-(1H-imidazol-5-yl)piperidine-1-carbothioamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=C(NC1CCCCC1)N2CCC(CC2)c3[nH]cnc3
#
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
 FJZ  FJZ  N-cyclohexyl-4-(1H-imidazol-5-yl)piperidine-1-carbothioamide  ligand  44  20  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FJZ
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
 FJZ  C1    C  CR15  0  -0.280  -3.3504  -1.7537  -0.9468
 FJZ  N1    N  N     0  -0.443  -4.4272  -2.0253  -1.7470
 FJZ  S1    S  S1    0  -0.453   1.4455   2.5751  -0.2645
 FJZ  C2    C  CR15  0   0.075  -5.2790  -1.0607  -1.5186
 FJZ  N2    N  NR15  0  -0.616  -4.7995  -0.1843  -0.6119
 FJZ  C3    C  CR5   0   0.354  -3.5578  -0.6090  -0.2252
 FJZ  N3    N  NT    0  -0.426  -0.1430   1.2823   1.4502
 FJZ  C4    C  CH1   0  -0.342  -2.7099   0.1410   0.7456
 FJZ  N4    N  NH1   0  -0.634   1.8309   0.2348   0.8994
 FJZ  C5    C  CH2   0  -0.418  -1.5443  -0.7142   1.2466
 FJZ  C6    C  CH2   0  -0.416  -2.1937   1.4577   0.1426
 FJZ  C7    C  CH2   0  -0.384  -0.6465   0.1117   2.1594
 FJZ  C8    C  CH2   0  -0.324  -1.2408   2.1706   1.0940
 FJZ  C10   C  CH1   0  -0.046   3.0896   0.0222   0.2052
 FJZ  C11   C  CH2   0  -0.446   4.0158  -0.8114   1.0850
 FJZ  C12   C  CH2   0  -0.419   2.8664  -0.6465  -1.1498
 FJZ  C13   C  CH2   0  -0.435   5.3386  -1.0899   0.3767
 FJZ  C14   C  CH2   0  -0.440   4.1918  -0.9194  -1.8539
 FJZ  C15   C  CH2   0  -0.432   5.1195  -1.7539  -0.9783
 FJZ  H1    H  HCR5  0   0.249  -2.4818  -2.3942  -0.9302
 FJZ  H2    H  HCR5  0   0.274  -6.2512  -0.9466  -1.9729
 FJZ  HN2   H  HNR5  0   0.415  -5.2859   0.6289  -0.2671
 FJZ  H4    H  HCH1  0   0.252  -3.3259   0.3966   1.6180
 FJZ  HN4   H  HNH1  0   0.404   1.5100  -0.5602   1.4289
 FJZ  H5    H  HCH2  0   0.256  -1.9187  -1.5847   1.7887
 FJZ  H5A   H  HCH2  0   0.234  -0.9576  -1.0885   0.4017
 FJZ  H6    H  HCH2  0   0.233  -1.6683   1.2515  -0.7950
 FJZ  H6A   H  HCH2  0   0.244  -3.0289   2.1211  -0.0941
 FJZ  H7    H  HCH2  0   0.269   0.1552  -0.4842   2.5914
 FJZ  H7A   H  HCH2  0   0.272  -1.2197   0.4745   3.0163
 FJZ  H8    H  HCH2  0   0.249  -1.7567   2.4537   2.0151
 FJZ  H8A   H  HCH2  0   0.271  -0.8472   3.0763   0.6437
 FJZ  H10   H  HCH1  0   0.239   3.5428   1.0023   0.0419
 FJZ  H11   H  HCH2  0   0.241   4.1932  -0.2945   2.0314
 FJZ  H11A  H  HCH2  0   0.218   3.5288  -1.7632   1.3291
 FJZ  H12   H  HCH2  0   0.210   2.3293  -1.5899  -0.9984
 FJZ  H12A  H  HCH2  0   0.234   2.2275  -0.0073  -1.7634
 FJZ  H13   H  HCH2  0   0.215   5.8799  -0.1479   0.2382
 FJZ  H13A  H  HCH2  0   0.233   5.9682  -1.7176   1.0112
 FJZ  H14   H  HCH2  0   0.231   4.0087  -1.4230  -2.8058
 FJZ  H14A  H  HCH2  0   0.214   4.6769   0.0323  -2.0960
 FJZ  H15   H  HCH2  0   0.230   6.0769  -1.9118  -1.4805
 FJZ  H15A  H  HCH2  0   0.211   4.6792  -2.7456  -0.8268
 FJZ  C9    C  C     0   0.427   1.0135   1.2832   0.7446

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
 FJZ  C1   N1    aromatic  1.369  0.020  1.369
 FJZ  C1   C3    aromatic  1.369  0.020  1.369
 FJZ  N1   C2    aromatic  1.307  0.020  1.307
 FJZ  S1   C9    double    1.695  0.020  1.695
 FJZ  C2   N2    aromatic  1.349  0.020  1.349
 FJZ  N2   C3    aromatic  1.368  0.020  1.368
 FJZ  C3   C4    single    1.491  0.020  1.491
 FJZ  N3   C7    single    1.458  0.020  1.458
 FJZ  N3   C8    single    1.456  0.020  1.456
 FJZ  N3   C9    single    1.355  0.020  1.355
 FJZ  C4   C5    single    1.530  0.020  1.530
 FJZ  C4   C6    single    1.537  0.020  1.537
 FJZ  N4   C9    single    1.338  0.020  1.338
 FJZ  N4   C10   single    1.453  0.020  1.453
 FJZ  C5   C7    single    1.524  0.020  1.524
 FJZ  C6   C8    single    1.524  0.020  1.524
 FJZ  C10  C11   single    1.525  0.020  1.525
 FJZ  C10  C12   single    1.527  0.020  1.527
 FJZ  C11  C13   single    1.526  0.020  1.526
 FJZ  C12  C14   single    1.525  0.020  1.525
 FJZ  C13  C15   single    1.525  0.020  1.525
 FJZ  C14  C15   single    1.524  0.020  1.524
 FJZ  C1   H1    single    0.930  0.020  1.080
 FJZ  C2   H2    single    0.930  0.020  1.080
 FJZ  N2   HN2   single    0.860  0.020  1.020
 FJZ  C4   H4    single    0.970  0.020  1.090
 FJZ  N4   HN4   single    0.860  0.020  1.020
 FJZ  C5   H5    single    0.970  0.020  1.090
 FJZ  C5   H5A   single    0.970  0.020  1.090
 FJZ  C6   H6    single    0.970  0.020  1.090
 FJZ  C6   H6A   single    0.970  0.020  1.090
 FJZ  C7   H7    single    0.970  0.020  1.090
 FJZ  C7   H7A   single    0.970  0.020  1.090
 FJZ  C8   H8    single    0.970  0.020  1.090
 FJZ  C8   H8A   single    0.970  0.020  1.090
 FJZ  C10  H10   single    0.970  0.020  1.090
 FJZ  C11  H11   single    0.970  0.020  1.090
 FJZ  C11  H11A  single    0.970  0.020  1.090
 FJZ  C12  H12   single    0.970  0.020  1.090
 FJZ  C12  H12A  single    0.970  0.020  1.090
 FJZ  C13  H13   single    0.970  0.020  1.090
 FJZ  C13  H13A  single    0.970  0.020  1.090
 FJZ  C14  H14   single    0.970  0.020  1.090
 FJZ  C14  H14A  single    0.970  0.020  1.090
 FJZ  C15  H15   single    0.970  0.020  1.090
 FJZ  C15  H15A  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
 FJZ  H1    C1   C3   127.59  3.000
 FJZ  H1    C1   N1   121.63  3.000
 FJZ  C3    C1   N1   110.78  3.000
 FJZ  C2    N1   C1   105.32  3.000
 FJZ  H2    C2   N2   122.31  3.000
 FJZ  H2    C2   N1   126.27  3.000
 FJZ  N2    C2   N1   111.42  3.000
 FJZ  HN2   N2   C3   126.27  3.000
 FJZ  HN2   N2   C2   125.61  3.000
 FJZ  C3    N2   C2   108.11  3.000
 FJZ  C4    C3   N2   122.95  3.000
 FJZ  C4    C3   C1   132.65  3.000
 FJZ  N2    C3   C1   104.37  3.000
 FJZ  C9    N3   C8   121.05  3.000
 FJZ  C9    N3   C7   123.26  3.000
 FJZ  C8    N3   C7   110.38  3.000
 FJZ  H4    C4   C6   107.49  3.000
 FJZ  H4    C4   C5   107.30  3.000
 FJZ  C6    C4   C5   110.57  3.000
 FJZ  H4    C4   C3   108.38  3.000
 FJZ  C6    C4   C3   111.49  3.000
 FJZ  C5    C4   C3   111.42  3.000
 FJZ  HN4   N4   C10  114.30  3.000
 FJZ  HN4   N4   C9   118.97  3.000
 FJZ  C10   N4   C9   126.04  3.000
 FJZ  H5A   C5   H5   107.13  3.000
 FJZ  H5A   C5   C7   109.38  3.000
 FJZ  H5    C5   C7   109.68  3.000
 FJZ  H5A   C5   C4   110.29  3.000
 FJZ  H5    C5   C4   110.30  3.000
 FJZ  C7    C5   C4   110.01  3.000
 FJZ  H6A   C6   H6   107.21  3.000
 FJZ  H6A   C6   C8   109.22  3.000
 FJZ  H6    C6   C8   108.84  3.000
 FJZ  H6A   C6   C4   110.38  3.000
 FJZ  H6    C6   C4   109.62  3.000
 FJZ  C8    C6   C4   111.46  3.000
 FJZ  H7A   C7   H7   104.89  3.000
 FJZ  H7A   C7   C5   109.91  3.000
 FJZ  H7    C7   C5   112.03  3.000
 FJZ  H7A   C7   N3   107.21  3.000
 FJZ  H7    C7   N3   112.22  3.000
 FJZ  C5    C7   N3   110.31  3.000
 FJZ  H8A   C8   H8   107.74  3.000
 FJZ  H8A   C8   C6   110.99  3.000
 FJZ  H8    C8   C6   110.63  3.000
 FJZ  H8A   C8   N3   109.69  3.000
 FJZ  H8    C8   N3   107.91  3.000
 FJZ  C6    C8   N3   109.80  3.000
 FJZ  H10   C10  C12  108.71  3.000
 FJZ  H10   C10  C11  108.95  3.000
 FJZ  C12   C10  C11  111.17  3.000
 FJZ  H10   C10  N4   107.43  3.000
 FJZ  C12   C10  N4   111.18  3.000
 FJZ  C11   C10  N4   109.29  3.000
 FJZ  H11A  C11  H11  106.84  3.000
 FJZ  H11A  C11  C13  109.26  3.000
 FJZ  H11   C11  C13  110.33  3.000
 FJZ  H11A  C11  C10  109.45  3.000
 FJZ  H11   C11  C10  109.85  3.000
 FJZ  C13   C11  C10  111.00  3.000
 FJZ  H12A  C12  H12  107.14  3.000
 FJZ  H12A  C12  C14  110.71  3.000
 FJZ  H12   C12  C14  109.60  3.000
 FJZ  H12A  C12  C10  109.13  3.000
 FJZ  H12   C12  C10  109.02  3.000
 FJZ  C14   C12  C10  111.15  3.000
 FJZ  H13A  C13  H13  106.44  3.000
 FJZ  H13A  C13  C15  110.41  3.000
 FJZ  H13   C13  C15  109.46  3.000
 FJZ  H13A  C13  C11  109.57  3.000
 FJZ  H13   C13  C11  109.28  3.000
 FJZ  C15   C13  C11  111.55  3.000
 FJZ  H14A  C14  H14  106.39  3.000
 FJZ  H14A  C14  C15  109.46  3.000
 FJZ  H14   C14  C15  110.50  3.000
 FJZ  H14A  C14  C12  109.35  3.000
 FJZ  H14   C14  C12  109.82  3.000
 FJZ  C15   C14  C12  111.20  3.000
 FJZ  H15A  C15  H15  106.56  3.000
 FJZ  H15A  C15  C14  109.29  3.000
 FJZ  H15   C15  C14  110.39  3.000
 FJZ  H15A  C15  C13  109.21  3.000
 FJZ  H15   C15  C13  110.21  3.000
 FJZ  C14   C15  C13  111.07  3.000
 FJZ  N4    C9   N3   117.43  3.000
 FJZ  N4    C9   S1   120.68  3.000
 FJZ  N3    C9   S1   121.87  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
 FJZ  CONST_01  N2   C2   N1   C1     0.00   0.0  0
 FJZ  CONST_02  C2   N2   C3   C1     0.00   0.0  0
 FJZ  CONST_03  N2   C3   C1   N1     0.00   0.0  0
 FJZ  CONST_04  C3   N2   C2   N1     0.00   0.0  0
 FJZ  CONST_05  C3   C1   N1   C2     0.00   0.0  0
 FJZ  CONST_06  C4   C3   C1   N1   180.00   0.0  0
 FJZ  CONST_07  C4   C3   N2   C2   180.00   0.0  0
 FJZ  CONST_08  H2   C2   N1   C1   180.00   0.0  0
 FJZ  CONST_09  HN2  N2   C3   C1   180.00   0.0  0
 FJZ  CONST_10  H1   C1   N1   C2   180.00   0.0  0
 FJZ  CONST_11  C7   N3   C9   S1   180.00   0.0  0
 FJZ  CONST_13  C10  N4   C9   N3   180.00   0.0  0
 FJZ  CONST_14  C7   N3   C9   N4     0.00   0.0  0
 FJZ  CONST_16  C10  N4   C9   S1     0.00   0.0  0
 FJZ  CONST_17  HN4  N4   C9   N3     0.00   0.0  0
 FJZ  Var_01    C4   C5   C7   N3   -58.25  30.0  1
 FJZ  Var_02    C4   C6   C8   N3    56.05  30.0  1
 FJZ  Var_03    C8   N3   C7   C5    64.31  30.0  1
 FJZ  Var_04    C7   N3   C8   C6   -62.61  30.0  1
 FJZ  Var_05    C15  C13  C11  C10  -55.37  30.0  1
 FJZ  Var_06    C15  C14  C12  C10   55.75  30.0  1
 FJZ  Var_07    C14  C15  C13  C11   55.39  30.0  1
 FJZ  Var_08    C13  C15  C14  C12  -55.46  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
 FJZ  chir_01  C4   C3  C5   C6   negativ
 FJZ  chir_02  C10  N4  C11  C12  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
 FJZ  plan-1  C1   0.020
 FJZ  plan-1  N1   0.020
 FJZ  plan-1  C2   0.020
 FJZ  plan-1  N2   0.020
 FJZ  plan-1  C3   0.020
 FJZ  plan-1  C4   0.020
 FJZ  plan-1  H1   0.020
 FJZ  plan-1  H2   0.020
 FJZ  plan-1  HN2  0.020
 FJZ  plan-2  S1   0.020
 FJZ  plan-2  N3   0.020
 FJZ  plan-2  N4   0.020
 FJZ  plan-2  C7   0.020
 FJZ  plan-2  C8   0.020
 FJZ  plan-2  C10  0.020
 FJZ  plan-2  HN4  0.020
 FJZ  plan-2  C9   0.020

