# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:20:59 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (1E)-5-(1-piperidin-4-yl-3-pyridin-4-yl-1H-pyrazol-4-yl)-2,3-dihydro-1H-inden-1-one oxime
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O/N=C/1CCc2cc(ccc/12)c3cn(nc3c4ccncc4)C5CCNCC5
#
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
 SM5  SM5  '(1E)-5-(1-piperidin-4-yl-3-pyridin-4-yl-1H-pyrazol-4-yl)-2,3-dihydro-1H-inden-1-one oxime'  ligand  51  28  .  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_SM5
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
 SM5  C18   C  CH1   0  -0.079  -4.1004   0.5410  -0.0817
 SM5  N4    N  NR5   0  -0.285  -2.7189   0.0817  -0.1280
 SM5  C14   C  CR16  0  -0.279   3.0598   0.0028   1.0760
 SM5  C13   C  CR16  0  -0.317   1.7321  -0.3566   0.9392
 SM5  C12   C  CR6   0   0.030   0.8794   0.3380   0.0692
 SM5  C17   C  CR16  0  -0.379   1.3791   1.4174  -0.6603
 SM5  C16   C  CR56  0   0.080   2.7072   1.7859  -0.5200
 SM5  C15   C  CR56  0   0.073   3.5424   1.0789   0.3382
 SM5  C11   C  CR16  0  -0.378   0.6920  -2.8459  -0.9202
 SM5  N3    N  N     0  -0.298  -2.4527  -1.2125  -0.1899
 SM5  C10   C  CR16  0  -0.059   1.2146  -4.1271  -0.9887
 SM5  C8    C  CR16  0  -0.061  -0.5242  -4.9987   0.1759
 SM5  C22   C  CH2   0  -0.321  -5.8139   2.1310  -0.9471
 SM5  C7    C  CR16  0  -0.361  -1.1307  -3.7603   0.3049
 SM5  C5    C  CR15  0   0.047  -1.6047   0.8263  -0.0413
 SM5  C6    C  CR6   0   0.121  -0.5124  -2.6415  -0.2504
 SM5  C1    C  CR5   0  -0.195  -0.5309  -0.0399  -0.0523
 SM5  C19   C  CH2   0  -0.441  -4.5136   0.9265   1.3352
 SM5  C20   C  CH2   0  -0.322  -5.9672   1.4026   1.3395
 SM5  C2    C  CR5   0   0.291  -1.1321  -1.3178  -0.1532
 SM5  N9    N  N     0  -0.409   0.6300  -5.1927  -0.4532
 SM5  N21   N  NH1   0  -0.573  -6.2393   2.4746   0.3981
 SM5  C23   C  CH2   0  -0.457  -4.3502   1.6949  -1.0454
 SM5  C24   C  CH2   0  -0.507   3.4405   2.9049  -1.2046
 SM5  C25   C  CH2   0  -0.530   4.8886   2.8011  -0.6865
 SM5  C26   C  CR5   0   0.149   4.8829   1.6552   0.2938
 SM5  N27   N  N     0  -0.157   5.8372   1.2015   0.9990
 SM5  O28   O  OH1   0  -0.556   7.0046   1.8886   0.7994
 SM5  H18   H  HCH1  0   0.267  -4.6912  -0.3203  -0.4036
 SM5  H13   H  HCR6  0   0.254   1.3411  -1.1820   1.5203
 SM5  H17   H  HCR6  0   0.248   0.7296   1.9522  -1.3435
 SM5  H11   H  HCR6  0   0.269   1.2158  -2.0307  -1.3997
 SM5  H10   H  HCR6  0   0.265   2.1512  -4.2971  -1.5080
 SM5  H8    H  HCR6  0   0.264  -0.9942  -5.8755   0.6077
 SM5  H122  H  HCH2  0   0.224  -6.4528   1.3190  -1.3106
 SM5  H222  H  HCH2  0   0.246  -5.9890   2.9839  -1.6045
 SM5  H7    H  HCR6  0   0.265  -2.0657  -3.6692   0.8406
 SM5  H5    H  HCR5  0   0.301  -1.6320   1.8998   0.0523
 SM5  H119  H  HCH2  0   0.246  -4.3920   0.0747   2.0086
 SM5  H219  H  HCH2  0   0.230  -3.8656   1.7297   1.7017
 SM5  H120  H  HCH2  0   0.223  -6.6237   0.5599   1.0975
 SM5  H220  H  HCH2  0   0.245  -6.2439   1.7326   2.3421
 SM5  H123  H  HCH2  0   0.230  -3.7066   2.5451  -0.7979
 SM5  H223  H  HCH2  0   0.251  -4.1126   1.3935  -2.0684
 SM5  H24   H  HCH2  0   0.264   3.3883   2.8066  -2.2903
 SM5  H25   H  HCH2  0   0.275   5.5978   2.6074  -1.4937
 SM5  HO28  H  HOH1  0   0.475   7.6333   1.4604   1.3896
 SM5  H121  H  HNH1  0   0.343  -5.7498   3.3102   0.6975
 SM5  H22   H  HCH2  0   0.264   2.9949   3.8705  -0.9581
 SM5  H23   H  HCH2  0   0.274   5.2178   3.7229  -0.2037
 SM5  H14   H  HCR6  0   0.253   3.7065  -0.5411   1.7524

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
 SM5  C18  H18   single    0.970  0.020  1.090
 SM5  N4   C18   single    1.457  0.020  1.457
 SM5  N4   C5    aromatic  1.343  0.020  1.343
 SM5  C14  H14   single    0.930  0.020  1.080
 SM5  C13  C14   aromatic  1.382  0.020  1.382
 SM5  C13  H13   single    0.930  0.020  1.080
 SM5  C12  C13   aromatic  1.402  0.020  1.402
 SM5  C17  C16   aromatic  1.385  0.020  1.385
 SM5  C17  C12   aromatic  1.395  0.020  1.395
 SM5  C17  H17   single    0.930  0.020  1.080
 SM5  C16  C15   aromatic  1.391  0.020  1.391
 SM5  C15  C26   single    1.460  0.020  1.460
 SM5  C15  C14   aromatic  1.391  0.020  1.391
 SM5  C11  H11   single    0.930  0.020  1.080
 SM5  N3   C2    aromatic  1.325  0.020  1.325
 SM5  N3   N4    aromatic  1.323  0.020  1.323
 SM5  C10  C11   aromatic  1.385  0.020  1.385
 SM5  C10  H10   single    0.930  0.020  1.080
 SM5  C8   C7    aromatic  1.385  0.020  1.385
 SM5  C8   N9    aromatic  1.329  0.020  1.329
 SM5  C8   H8    single    0.930  0.020  1.080
 SM5  C22  H122  single    0.970  0.020  1.090
 SM5  C22  H222  single    0.970  0.020  1.090
 SM5  C7   C6    aromatic  1.394  0.020  1.394
 SM5  C7   H7    single    0.930  0.020  1.080
 SM5  C5   H5    single    0.930  0.020  1.080
 SM5  C6   C2    single    1.465  0.020  1.465
 SM5  C6   C11   aromatic  1.393  0.020  1.393
 SM5  C1   C5    aromatic  1.380  0.020  1.380
 SM5  C1   C12   single    1.465  0.020  1.465
 SM5  C19  C20   single    1.530  0.020  1.530
 SM5  C19  C18   single    1.526  0.020  1.526
 SM5  C19  H119  single    0.970  0.020  1.090
 SM5  C19  H219  single    0.970  0.020  1.090
 SM5  C20  H120  single    0.970  0.020  1.090
 SM5  C20  H220  single    0.970  0.020  1.090
 SM5  C2   C1    aromatic  1.416  0.020  1.416
 SM5  N9   C10   aromatic  1.328  0.020  1.328
 SM5  N21  C22   single    1.452  0.020  1.452
 SM5  N21  C20   single    1.452  0.020  1.452
 SM5  C23  C22   single    1.530  0.020  1.530
 SM5  C23  C18   single    1.524  0.020  1.524
 SM5  C23  H123  single    0.970  0.020  1.090
 SM5  C23  H223  single    0.970  0.020  1.090
 SM5  C24  C16   single    1.503  0.020  1.503
 SM5  C24  C25   single    1.542  0.020  1.542
 SM5  C24  H24   single    0.970  0.020  1.090
 SM5  C25  C26   single    1.508  0.020  1.508
 SM5  C25  H25   single    0.970  0.020  1.090
 SM5  C26  N27   double    1.270  0.020  1.270
 SM5  N27  O28   single    1.369  0.020  1.369
 SM5  O28  HO28  single    0.850  0.020  0.980
 SM5  N21  H121  single    0.890  0.020  1.040
 SM5  C24  H22   single    0.970  0.020  1.090
 SM5  C25  H23   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
 SM5  H18   C18  C23   108.78  3.000
 SM5  C23   C18  C19   110.58  3.000
 SM5  H18   C18  C19   109.04  3.000
 SM5  C23   C18  N4    111.97  3.000
 SM5  C19   C18  N4    111.47  3.000
 SM5  H18   C18  N4    104.77  3.000
 SM5  C5    N4   N3    112.24  3.000
 SM5  N3    N4   C18   120.06  3.000
 SM5  C5    N4   C18   127.60  3.000
 SM5  H14   C14  C15   120.85  3.000
 SM5  C15   C14  C13   118.81  3.000
 SM5  H14   C14  C13   120.34  3.000
 SM5  H13   C13  C12   119.42  3.000
 SM5  C12   C13  C14   121.11  3.000
 SM5  H13   C13  C14   119.47  3.000
 SM5  C1    C12  C17   120.06  3.000
 SM5  C1    C12  C13   120.59  3.000
 SM5  C17   C12  C13   119.33  3.000
 SM5  H17   C17  C16   120.46  3.000
 SM5  H17   C17  C12   119.79  3.000
 SM5  C16   C17  C12   119.74  3.000
 SM5  C24   C16  C15   111.51  3.000
 SM5  C24   C16  C17   128.29  3.000
 SM5  C15   C16  C17   120.20  3.000
 SM5  C26   C15  C16   109.39  3.000
 SM5  C26   C15  C14   129.80  3.000
 SM5  C16   C15  C14   120.81  3.000
 SM5  H11   C11  C6    121.42  3.000
 SM5  C6    C11  C10   119.05  3.000
 SM5  H11   C11  C10   119.52  3.000
 SM5  C2    N3   N4    106.08  3.000
 SM5  H10   C10  N9    116.58  3.000
 SM5  N9    C10  C11   123.78  3.000
 SM5  H10   C10  C11   119.64  3.000
 SM5  H8    C8   N9    116.55  3.000
 SM5  H8    C8   C7    119.74  3.000
 SM5  N9    C8   C7    123.71  3.000
 SM5  H222  C22  H122  106.62  3.000
 SM5  H222  C22  C23   109.73  3.000
 SM5  H122  C22  C23   108.98  3.000
 SM5  C23   C22  N21   114.02  3.000
 SM5  H222  C22  N21   109.04  3.000
 SM5  H122  C22  N21   108.18  3.000
 SM5  H7    C7   C6    120.88  3.000
 SM5  H7    C7   C8    120.00  3.000
 SM5  C6    C7   C8    119.11  3.000
 SM5  H5    C5   C1    130.21  3.000
 SM5  C1    C5   N4    107.29  3.000
 SM5  H5    C5   N4    122.47  3.000
 SM5  C2    C6   C7    120.75  3.000
 SM5  C2    C6   C11   122.02  3.000
 SM5  C7    C6   C11   117.21  3.000
 SM5  C2    C1   C5    103.69  3.000
 SM5  C2    C1   C12   130.35  3.000
 SM5  C5    C1   C12   125.92  3.000
 SM5  H219  C19  H119  107.44  3.000
 SM5  H219  C19  C20   109.46  3.000
 SM5  H119  C19  C20   110.29  3.000
 SM5  H219  C19  C18   109.63  3.000
 SM5  H119  C19  C18   110.20  3.000
 SM5  C20   C19  C18   109.80  3.000
 SM5  H220  C20  H120  106.48  3.000
 SM5  H220  C20  N21   108.95  3.000
 SM5  H120  C20  N21   108.20  3.000
 SM5  N21   C20  C19   113.95  3.000
 SM5  H220  C20  C19   109.74  3.000
 SM5  H120  C20  C19   109.24  3.000
 SM5  C1    C2   C6    129.84  3.000
 SM5  C1    C2   N3    110.69  3.000
 SM5  C6    C2   N3    119.44  3.000
 SM5  C8    N9   C10   117.13  3.000
 SM5  H121  N21  C20   109.06  3.000
 SM5  H121  N21  C22   109.10  3.000
 SM5  C20   N21  C22   111.77  3.000
 SM5  H223  C23  H123  107.34  3.000
 SM5  H223  C23  C22   110.29  3.000
 SM5  H123  C23  C22   109.05  3.000
 SM5  H223  C23  C18   110.34  3.000
 SM5  H123  C23  C18   110.41  3.000
 SM5  C22   C23  C18   109.39  3.000
 SM5  H22   C24  H24   106.55  3.000
 SM5  H22   C24  C25   111.54  3.000
 SM5  H24   C24  C25   111.91  3.000
 SM5  H22   C24  C16   110.89  3.000
 SM5  H24   C24  C16   111.27  3.000
 SM5  C25   C24  C16   104.78  3.000
 SM5  H23   C25  H25   106.32  3.000
 SM5  H23   C25  C26   110.81  3.000
 SM5  H25   C25  C26   110.38  3.000
 SM5  H23   C25  C24   112.03  3.000
 SM5  H25   C25  C24   111.94  3.000
 SM5  C26   C25  C24   105.43  3.000
 SM5  N27   C26  C25   129.01  3.000
 SM5  N27   C26  C15   122.13  3.000
 SM5  C25   C26  C15   108.86  3.000
 SM5  O28   N27  C26   112.35  3.000
 SM5  HO28  O28  N27   104.14  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
 SM5  CONST_01  C12  C1   C5   N4    180.00   0.0  0
 SM5  CONST_02  C2   C1   C5   N4      0.00   0.0  0
 SM5  CONST_03  C6   C2   N3   N4    180.00   0.0  0
 SM5  CONST_04  C1   C2   N3   N4      0.00   0.0  0
 SM5  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 SM5  CONST_06  C1   C12  C13  C14   180.00   0.0  0
 SM5  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 SM5  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 SM5  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 SM5  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 SM5  CONST_13  C15  C16  C17  C12     0.00   0.0  0
 SM5  CONST_14  N3   C2   C1   C12   180.00   0.0  0
 SM5  CONST_15  C6   C2   C1   C12     0.00   0.0  0
 SM5  CONST_18  C1   C12  C17  C16   180.00   0.0  0
 SM5  CONST_19  C8   N9   C10  C11     0.00   0.0  0
 SM5  CONST_20  C8   C7   C6   C11     0.00   0.0  0
 SM5  CONST_24  C5   C1   C2   N3      0.00   0.0  0
 SM5  CONST_25  C1   C5   N4   N3      0.00   0.0  0
 SM5  CONST_26  C7   C6   C11  C10     0.00   0.0  0
 SM5  CONST_27  C2   C6   C11  C10   180.00   0.0  0
 SM5  CONST_28  C7   C8   N9   C10     0.00   0.0  0
 SM5  CONST_29  C2   C6   C7   C8    180.00   0.0  0
 SM5  CONST_31  C2   N3   N4   C5      0.00   0.0  0
 SM5  CONST_32  C6   C2   C1   C5    180.00   0.0  0
 SM5  CONST_33  N9   C8   C7   C6      0.00   0.0  0
 SM5  CONST_34  N9   C10  C11  C6      0.00   0.0  0
 SM5  CONST_35  C1   C5   N4   C18   180.00   0.0  0
 SM5  CONST_36  C2   N3   N4   C18   180.00   0.0  0
 SM5  CONST_37  H5   C5   N4   C18     0.00   0.0  0
 SM5  CONST_38  H17  C17  C12  C13   180.00   0.0  0
 SM5  CONST_39  H14  C14  C13  C12   180.00   0.0  0
 SM5  CONST_40  H13  C13  C12  C17   180.00   0.0  0
 SM5  CONST_41  H7   C7   C6   C11   180.00   0.0  0
 SM5  CONST_42  H8   C8   N9   C10   180.00   0.0  0
 SM5  CONST_43  H10  C10  N9   C8    180.00   0.0  0
 SM5  CONST_44  H11  C11  C6   C7    180.00   0.0  0
 SM5  Var_01    N21  C20  C19  C18   -54.26  30.0  1
 SM5  Var_02    N21  C22  C23  C18    55.04  30.0  1
 SM5  Var_03    C25  C26  C15  C14   179.10  30.0  1
 SM5  Var_04    C25  C24  C16  C17  -178.40  30.0  1
 SM5  Var_05    C26  C25  C24  C16    -1.67  30.0  1
 SM5  Var_06    C24  C25  C26  C15     1.61  30.0  1
 SM5  Var_07    C19  C20  N21  C22    53.47  30.0  1
 SM5  Var_08    C23  C22  N21  C20   -53.98  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
 SM5  chir_01  C18  N4  C19  C23  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
 SM5  plan-1  C18  0.020
 SM5  plan-1  N4   0.020
 SM5  plan-1  C12  0.020
 SM5  plan-1  N3   0.020
 SM5  plan-1  C5   0.020
 SM5  plan-1  C6   0.020
 SM5  plan-1  C1   0.020
 SM5  plan-1  C2   0.020
 SM5  plan-1  H5   0.020
 SM5  plan-2  C11  0.020
 SM5  plan-2  C10  0.020
 SM5  plan-2  C8   0.020
 SM5  plan-2  C7   0.020
 SM5  plan-2  C6   0.020
 SM5  plan-2  C2   0.020
 SM5  plan-2  N9   0.020
 SM5  plan-2  H11  0.020
 SM5  plan-2  H10  0.020
 SM5  plan-2  H8   0.020
 SM5  plan-2  H7   0.020
 SM5  plan-3  C14  0.020
 SM5  plan-3  C13  0.020
 SM5  plan-3  C12  0.020
 SM5  plan-3  C17  0.020
 SM5  plan-3  C16  0.020
 SM5  plan-3  C15  0.020
 SM5  plan-3  C1   0.020
 SM5  plan-3  C24  0.020
 SM5  plan-3  C26  0.020
 SM5  plan-3  H13  0.020
 SM5  plan-3  H17  0.020
 SM5  plan-3  H14  0.020

