# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:09:43 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC[C@@H](CC1)COC(=O)N[C@H]2CCC(=O)NC2=O
#
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
 JPW  JPW  '(4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate'  ligand  41  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JPW
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
 JPW  C4   C  CH1   0  -0.288  -3.1625   0.6598   0.1117
 JPW  C5   C  CH2   0  -0.431  -4.3671   1.2377  -0.6324
 JPW  C6   C  CH2   0  -0.425  -5.6889   0.7243  -0.0749
 JPW  C11  C  C     0   0.555   5.4766  -0.5976   0.2044
 JPW  C7   C  CH1   0  -0.074  -5.7520  -0.7987  -0.0750
 JPW  C8   C  CH2   0  -0.442  -4.5478  -1.3724   0.6729
 JPW  C9   C  CH2   0  -0.419  -3.2221  -0.8671   0.1130
 JPW  C10  C  C     0   0.573   3.0963  -0.8569  -0.4333
 JPW  C12  C  CH2   0  -0.593   5.1511   0.6917   0.9028
 JPW  C13  C  CH2   0  -0.470   3.7102   0.7613   1.3783
 JPW  N1   N  NH1   0  -0.657   1.3993   0.5528   0.5888
 JPW  N2   N  NH2   0  -0.794  -7.0421  -1.2398   0.4396
 JPW  C3   C  CH2   0  -0.139  -1.8957   1.1939  -0.5267
 JPW  N3   N  NH1   0  -0.686   4.4159  -1.2446  -0.3987
 JPW  C1   C  CH1   0  -0.211   2.7772   0.4875   0.2083
 JPW  C2   C  C     0   0.758   0.4404   0.9573  -0.2745
 JPW  O1   O  O2    0  -0.485  -0.7710   0.7549   0.2398
 JPW  O2   O  O     0  -0.514   0.6500   1.4664  -1.3552
 JPW  O4   O  O     0  -0.432   6.5901  -1.0656   0.1364
 JPW  H1   H  HCH1  0   0.227  -3.2072   1.0110   1.1507
 JPW  H2   H  HCH2  0   0.234  -4.3445   2.3300  -0.5890
 JPW  H3   H  HCH2  0   0.214  -4.2945   0.9699  -1.6932
 JPW  H4   H  HCH2  0   0.208  -5.8203   1.0870   0.9523
 JPW  H5   H  HCH2  0   0.230  -6.5220   1.1268  -0.6563
 JPW  H6   H  HCH1  0   0.208  -5.6912  -1.1331  -1.1185
 JPW  H7   H  HCH2  0   0.206  -4.6287  -1.0950   1.7314
 JPW  H8   H  HCH2  0   0.226  -4.5775  -2.4654   0.6353
 JPW  H9   H  HCH2  0   0.208  -3.0958  -1.2290  -0.9148
 JPW  H10  H  HCH2  0   0.235  -2.3938  -1.2838   0.6899
 JPW  H11  H  HCH2  0   0.298   5.8527   0.8209   1.7255
 JPW  H12  H  HCH2  0   0.293   5.3476   1.5002   0.1900
 JPW  H13  H  HCH2  0   0.261   3.5384   0.0353   2.1773
 JPW  H14  H  HCH2  0   0.282   3.4999   1.7503   1.7828
 JPW  H15  H  HNH1  0   0.403   1.1158   0.0452   1.4136
 JPW  H16  H  HNH2  0   0.340  -7.0878  -2.2517   0.4063
 JPW  H17  H  HNH2  0   0.331  -7.1024  -1.0037   1.4246
 JPW  H19  H  HCH2  0   0.225  -1.8141   0.8362  -1.5568
 JPW  H20  H  HCH2  0   0.236  -1.9140   2.2874  -0.5523
 JPW  H21  H  HNH1  0   0.417   4.6339  -2.1209  -0.8607
 JPW  H22  H  HCH1  0   0.311   2.9583   1.2468  -0.5596
 JPW  O3   O  O     0  -0.417   2.2584  -1.5497  -0.9587

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
 JPW  O4   C11  double  1.210  0.020  1.210
 JPW  C11  C12  single  1.502  0.020  1.502
 JPW  C11  N3   single  1.381  0.020  1.381
 JPW  C12  C13  single  1.519  0.020  1.519
 JPW  N3   C10  single  1.376  0.020  1.376
 JPW  C13  C1   single  1.521  0.020  1.521
 JPW  C10  C1   single  1.523  0.020  1.523
 JPW  C10  O3   double  1.207  0.020  1.207
 JPW  C1   N1   single  1.431  0.020  1.431
 JPW  N1   C2   single  1.352  0.020  1.352
 JPW  O2   C2   double  1.213  0.020  1.213
 JPW  C2   O1   single  1.331  0.020  1.331
 JPW  O1   C3   single  1.430  0.020  1.430
 JPW  C3   C4   single  1.516  0.020  1.516
 JPW  C9   C4   single  1.528  0.020  1.528
 JPW  C9   C8   single  1.525  0.020  1.525
 JPW  C4   C5   single  1.529  0.020  1.529
 JPW  C8   C7   single  1.529  0.020  1.529
 JPW  C5   C6   single  1.524  0.020  1.524
 JPW  N2   C7   single  1.457  0.020  1.457
 JPW  C7   C6   single  1.524  0.020  1.524
 JPW  C4   H1   single  0.970  0.020  1.090
 JPW  C5   H2   single  0.970  0.020  1.090
 JPW  C5   H3   single  0.970  0.020  1.090
 JPW  C6   H4   single  0.970  0.020  1.090
 JPW  C6   H5   single  0.970  0.020  1.090
 JPW  C7   H6   single  0.970  0.020  1.090
 JPW  C8   H7   single  0.970  0.020  1.090
 JPW  C8   H8   single  0.970  0.020  1.090
 JPW  C9   H9   single  0.970  0.020  1.090
 JPW  C9   H10  single  0.970  0.020  1.090
 JPW  C12  H11  single  0.970  0.020  1.090
 JPW  C12  H12  single  0.970  0.020  1.090
 JPW  C13  H13  single  0.970  0.020  1.090
 JPW  C13  H14  single  0.970  0.020  1.090
 JPW  N1   H15  single  0.860  0.020  1.020
 JPW  N2   H16  single  0.890  0.020  1.040
 JPW  N2   H17  single  0.890  0.020  1.040
 JPW  C3   H19  single  0.970  0.020  1.090
 JPW  C3   H20  single  0.970  0.020  1.090
 JPW  N3   H21  single  0.860  0.020  1.020
 JPW  C1   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
 JPW  H1   C4   C3   108.66  3.000
 JPW  H1   C4   C9   108.50  3.000
 JPW  C3   C4   C9   112.64  3.000
 JPW  H1   C4   C5   107.92  3.000
 JPW  C9   C4   C5   110.32  3.000
 JPW  C3   C4   C5   108.68  3.000
 JPW  H3   C5   H2   106.32  3.000
 JPW  H3   C5   C6   109.22  3.000
 JPW  H2   C5   C6   109.87  3.000
 JPW  H3   C5   C4   109.05  3.000
 JPW  H2   C5   C4   109.99  3.000
 JPW  C6   C5   C4   112.21  3.000
 JPW  H5   C6   H4   106.56  3.000
 JPW  H5   C6   C7   109.66  3.000
 JPW  H4   C6   C7   108.99  3.000
 JPW  H5   C6   C5   110.03  3.000
 JPW  H4   C6   C5   109.58  3.000
 JPW  C7   C6   C5   111.87  3.000
 JPW  O4   C11  N3   120.08  3.000
 JPW  N3   C11  C12  116.03  3.000
 JPW  O4   C11  C12  123.89  3.000
 JPW  H6   C7   N2   107.01  3.000
 JPW  H6   C7   C8   107.88  3.000
 JPW  N2   C7   C8   114.26  3.000
 JPW  H6   C7   C6   107.60  3.000
 JPW  N2   C7   C6   109.82  3.000
 JPW  C8   C7   C6   110.01  3.000
 JPW  H8   C8   H7   106.48  3.000
 JPW  H8   C8   C9   110.00  3.000
 JPW  H7   C8   C9   109.54  3.000
 JPW  H8   C8   C7   109.67  3.000
 JPW  H7   C8   C7   108.59  3.000
 JPW  C9   C8   C7   112.37  3.000
 JPW  H10  C9   H9   106.37  3.000
 JPW  H10  C9   C8   109.81  3.000
 JPW  H9   C9   C8   109.56  3.000
 JPW  H10  C9   C4   110.62  3.000
 JPW  H9   C9   C4   108.93  3.000
 JPW  C8   C9   C4   111.42  3.000
 JPW  O3   C10  C1   122.97  3.000
 JPW  O3   C10  N3   120.98  3.000
 JPW  C1   C10  N3   116.04  3.000
 JPW  H12  C12  H11  106.77  3.000
 JPW  H12  C12  C13  109.88  3.000
 JPW  H11  C12  C13  111.67  3.000
 JPW  H12  C12  C11  106.98  3.000
 JPW  H11  C12  C11  108.27  3.000
 JPW  C13  C12  C11  112.98  3.000
 JPW  H14  C13  H13  107.54  3.000
 JPW  H14  C13  C1   109.31  3.000
 JPW  H13  C13  C1   110.26  3.000
 JPW  H14  C13  C12  109.94  3.000
 JPW  H13  C13  C12  110.33  3.000
 JPW  C1   C13  C12  109.44  3.000
 JPW  H15  N1   C2   118.24  3.000
 JPW  H15  N1   C1   117.70  3.000
 JPW  C2   N1   C1   121.79  3.000
 JPW  H17  N2   H16  105.15  3.000
 JPW  H17  N2   C7   108.97  3.000
 JPW  H16  N2   C7   109.31  3.000
 JPW  H20  C3   H19  107.83  3.000
 JPW  H20  C3   O1   109.42  3.000
 JPW  H19  C3   O1   110.23  3.000
 JPW  H20  C3   C4   110.37  3.000
 JPW  H19  C3   C4   110.11  3.000
 JPW  O1   C3   C4   108.87  3.000
 JPW  H21  N3   C10  115.99  3.000
 JPW  H21  N3   C11  116.01  3.000
 JPW  C10  N3   C11  127.99  3.000
 JPW  H22  C1   N1   108.31  3.000
 JPW  H22  C1   C13  108.25  3.000
 JPW  N1   C1   C13  112.20  3.000
 JPW  H22  C1   C10  106.37  3.000
 JPW  N1   C1   C10  110.73  3.000
 JPW  C13  C1   C10  110.75  3.000
 JPW  O2   C2   O1   124.41  3.000
 JPW  O1   C2   N1   110.68  3.000
 JPW  O2   C2   N1   124.88  3.000
 JPW  C2   O1   C3   117.51  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
 JPW  CONST_01  C12  C11  N3   C10    0.00   0.0  0
 JPW  CONST_02  O4   C11  N3   C10  180.00   0.0  0
 JPW  CONST_03  H21  N3   C11  C12  180.00   0.0  0
 JPW  Var_01    C7   C8   C9   C4    55.82  30.0  1
 JPW  Var_02    C7   C6   C5   C4   -55.58  30.0  1
 JPW  Var_03    C1   C13  C12  C11  -54.09  30.0  1
 JPW  Var_04    C1   C10  N3   C11    3.56  30.0  1
 JPW  Var_05    N3   C11  C12  C13   26.29  30.0  1
 JPW  Var_06    O2   C2   N1   C1   -10.59  30.0  2
 JPW  Var_07    H19  C3   O1   C2    49.39  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
 JPW  chir_01  C4  C3   C9   C5  positiv
 JPW  chir_02  C7  N2   C8   C6  positiv
 JPW  chir_03  C1  C13  C10  N1  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
 JPW  plan-1  C10  0.020
 JPW  plan-1  N3   0.020
 JPW  plan-1  C1   0.020
 JPW  plan-1  O3   0.020
 JPW  plan-2  C11  0.020
 JPW  plan-2  C10  0.020
 JPW  plan-2  C12  0.020
 JPW  plan-2  N3   0.020
 JPW  plan-2  O4   0.020
 JPW  plan-2  H21  0.020
 JPW  plan-3  N1   0.020
 JPW  plan-3  C2   0.020
 JPW  plan-3  O1   0.020
 JPW  plan-3  O2   0.020

