# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 06:10:21 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-{4-[5-(4-chlorophenyl)-4-pyrimidin-4-yl-1H-pyrazol-3-yl]piperidin-1-yl}-2-oxoethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(=O)N1CCC(CC1)c2n[nH]c(c3ccc(Cl)cc3)c2c4ccncn4
#
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
 I47  I47  2-{4-[5-(4-chlorophenyl)-4-pyrimidin-4-yl-1H-pyrazol-3-yl]piperidin-1-yl}-2-oxoethanol  ligand  48  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_I47
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
 I47  C1    C   CR5   0   0.468  -1.4422  -0.9961   0.2298
 I47  N2    N   NR15  0  -0.497  -0.7176  -2.0962   0.4759
 I47  N3    N   N     0  -0.279   0.5796  -1.8553   0.6282
 I47  C4    C   CR5   0   0.334   0.7238  -0.5544   0.4753
 I47  C5    C   CR5   0  -0.239  -0.5347   0.0556   0.2235
 I47  C6    C   CR6   0   0.014  -2.8850  -1.0562  -0.0082
 I47  C7    C   CR6   0   0.180  -0.8254   1.4762   0.0771
 I47  C8    C   CH1   0  -0.347   2.0688   0.0917   0.5828
 I47  C9    C   CR16  0  -0.295  -3.4459  -0.4020  -1.1044
 I47  C10   C   CR16  0  -0.192  -4.8085  -0.4577  -1.3409
 I47  C11   C   CR6   0  -0.046  -5.6159  -1.1812  -0.4754
 I47  C12   C   CR16  0  -0.197  -5.0814  -1.8462   0.6166
 I47  C13   C   CR16  0  -0.295  -3.7161  -1.7785   0.8461
 I47  C14   C   CR16  0  -0.357  -1.9990   2.0513   0.5674
 I47  C15   C   CR16  0  -0.029  -2.1674   3.4069   0.3729
 I47  N16   N   N     0  -0.403  -1.2576   4.1616  -0.2382
 I47  C17   C   CR16  0   0.048  -0.1695   3.5286  -0.6460
 I47  N18   N   N     0  -0.414   0.0900   2.2373  -0.5265
 I47  C19   C   CH2   0  -0.410   2.9912  -0.6220   1.5735
 I47  C20   C   CH2   0  -0.323   4.3535   0.0600   1.6210
 I47  N21   N   NT    0  -0.445   4.9423   0.1194   0.2943
 I47  C22   C   CH2   0  -0.340   4.1189   0.8372  -0.6635
 I47  C23   C   CH2   0  -0.408   2.7481   0.1866  -0.7885
 I47  CL24  CL  CL    0  -0.119  -7.3204  -1.2550  -0.7657
 I47  C25   C   C     0   0.512   6.0145  -0.6358  -0.0221
 I47  O26   O   O     0  -0.498   6.6146  -1.3167   0.7947
 I47  C27   C   CH2   0  -0.280   6.4711  -0.5946  -1.4749
 I47  O28   O   OH1   0  -0.658   7.6138  -1.3898  -1.5944
 I47  H8    H   HCH1  0   0.243   1.9194   1.1163   0.9389
 I47  H9    H   HCR6  0   0.274  -2.8149   0.1496  -1.7891
 I47  H10   H   HCR6  0   0.287  -5.2335   0.0504  -2.1954
 I47  H12   H   HCR6  0   0.287  -5.7182  -2.4051   1.2883
 I47  H13   H   HCR6  0   0.274  -3.3046  -2.2798   1.7128
 I47  H14   H   HCR6  0   0.277  -2.7445   1.4747   1.0947
 I47  H15   H   HCR6  0   0.280  -3.0609   3.9062   0.7304
 I47  H17   H   HCR6  0   0.260   0.5904   4.1287  -1.1351
 I47  H19   H   HCH2  0   0.242   2.5522  -0.6178   2.5737
 I47  H19A  H   HCH2  0   0.231   3.1233  -1.6671   1.2830
 I47  H20   H   HCH2  0   0.240   4.2460   1.0827   1.9978
 I47  H20A  H   HCH2  0   0.265   5.0277  -0.4646   2.2924
 I47  H22   H   HCH2  0   0.249   4.0059   1.8688  -0.3142
 I47  H22A  H   HCH2  0   0.271   4.6037   0.8970  -1.6343
 I47  H23   H   HCH2  0   0.227   2.8584  -0.8144  -1.2177
 I47  H23A  H   HCH2  0   0.254   2.1292   0.7749  -1.4667
 I47  H27   H   HCH2  0   0.233   5.6522  -0.9523  -2.1148
 I47  H27A  H   HCH2  0   0.236   6.6619   0.4474  -1.7636
 I47  HO28  H   HOH1  0   0.459   7.8864  -1.3634  -2.5158
 I47  HN2   H   HNR5  0   0.425  -1.0536  -3.0472   0.4964

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
 I47  C6    C1    single    1.464  0.020  1.464
 I47  C1    N2    aromatic  1.340  0.020  1.340
 I47  C1    C5    aromatic  1.389  0.020  1.389
 I47  N2    N3    aromatic  1.328  0.020  1.328
 I47  N3    C4    aromatic  1.318  0.020  1.318
 I47  C5    C4    aromatic  1.421  0.020  1.421
 I47  C4    C8    single    1.496  0.020  1.496
 I47  C5    C7    single    1.457  0.020  1.457
 I47  C9    C6    aromatic  1.394  0.020  1.394
 I47  C6    C13   aromatic  1.394  0.020  1.394
 I47  N18   C7    aromatic  1.335  0.020  1.335
 I47  C7    C14   aromatic  1.396  0.020  1.396
 I47  C8    C19   single    1.530  0.020  1.530
 I47  C8    C23   single    1.533  0.020  1.533
 I47  C8    H8    single    0.970  0.020  1.090
 I47  C10   C9    aromatic  1.384  0.020  1.384
 I47  C9    H9    single    0.930  0.020  1.080
 I47  C10   C11   aromatic  1.387  0.020  1.387
 I47  C10   H10   single    0.930  0.020  1.080
 I47  CL24  C11   single    1.731  0.020  1.731
 I47  C11   C12   aromatic  1.386  0.020  1.386
 I47  C12   C13   aromatic  1.386  0.020  1.386
 I47  C12   H12   single    0.930  0.020  1.080
 I47  C13   H13   single    0.930  0.020  1.080
 I47  C14   C15   aromatic  1.380  0.020  1.380
 I47  C14   H14   single    0.930  0.020  1.080
 I47  N16   C15   aromatic  1.331  0.020  1.331
 I47  C15   H15   single    0.930  0.020  1.080
 I47  C17   N16   aromatic  1.323  0.020  1.323
 I47  N18   C17   aromatic  1.323  0.020  1.323
 I47  C17   H17   single    0.930  0.020  1.080
 I47  C19   C20   single    1.524  0.020  1.524
 I47  C19   H19   single    0.970  0.020  1.090
 I47  C19   H19A  single    0.970  0.020  1.090
 I47  C20   N21   single    1.453  0.020  1.453
 I47  C20   H20   single    0.970  0.020  1.090
 I47  C20   H20A  single    0.970  0.020  1.090
 I47  C22   N21   single    1.453  0.020  1.453
 I47  N21   C25   single    1.349  0.020  1.349
 I47  C23   C22   single    1.522  0.020  1.522
 I47  C22   H22   single    0.970  0.020  1.090
 I47  C22   H22A  single    0.970  0.020  1.090
 I47  C23   H23   single    0.970  0.020  1.090
 I47  C23   H23A  single    0.970  0.020  1.090
 I47  O26   C25   double    1.221  0.020  1.221
 I47  C25   C27   single    1.523  0.020  1.523
 I47  C27   O28   single    1.397  0.020  1.397
 I47  C27   H27   single    0.970  0.020  1.090
 I47  C27   H27A  single    0.970  0.020  1.090
 I47  O28   HO28  single    0.850  0.020  0.980
 I47  N2    HN2   single    0.860  0.020  1.020

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
 I47  C6    C1   C5   132.41  3.000
 I47  C5    C1   N2   105.61  3.000
 I47  C6    C1   N2   121.95  3.000
 I47  HN2   N2   N3   119.60  3.000
 I47  HN2   N2   C1   126.69  3.000
 I47  N3    N2   C1   113.60  3.000
 I47  C4    N3   N2   105.82  3.000
 I47  C8    C4   C5   128.58  3.000
 I47  C8    C4   N3   121.09  3.000
 I47  C5    C4   N3   110.33  3.000
 I47  C7    C5   C4   127.80  3.000
 I47  C7    C5   C1   127.46  3.000
 I47  C4    C5   C1   104.64  3.000
 I47  C13   C6   C9   119.03  3.000
 I47  C13   C6   C1   120.63  3.000
 I47  C9    C6   C1   120.34  3.000
 I47  N18   C7   C14  120.03  3.000
 I47  C14   C7   C5   122.28  3.000
 I47  N18   C7   C5   117.68  3.000
 I47  H8    C8   C23  107.06  3.000
 I47  H8    C8   C19  107.94  3.000
 I47  C23   C8   C19  109.93  3.000
 I47  H8    C8   C4   107.75  3.000
 I47  C23   C8   C4   111.15  3.000
 I47  C19   C8   C4   112.77  3.000
 I47  H9    C9   C10  119.11  3.000
 I47  H9    C9   C6   120.13  3.000
 I47  C10   C9   C6   120.76  3.000
 I47  H10   C10  C11  120.63  3.000
 I47  H10   C10  C9   120.20  3.000
 I47  C11   C10  C9   119.17  3.000
 I47  CL24  C11  C12  119.45  3.000
 I47  C12   C11  C10  121.16  3.000
 I47  CL24  C11  C10  119.39  3.000
 I47  H12   C12  C13  120.17  3.000
 I47  H12   C12  C11  120.69  3.000
 I47  C13   C12  C11  119.14  3.000
 I47  H13   C13  C12  118.97  3.000
 I47  H13   C13  C6   120.28  3.000
 I47  C12   C13  C6   120.74  3.000
 I47  H14   C14  C15  120.61  3.000
 I47  H14   C14  C7   122.13  3.000
 I47  C15   C14  C7   117.25  3.000
 I47  H15   C15  N16  116.98  3.000
 I47  H15   C15  C14  120.43  3.000
 I47  N16   C15  C14  122.58  3.000
 I47  C17   N16  C15  115.62  3.000
 I47  H17   C17  N18  116.32  3.000
 I47  H17   C17  N16  116.76  3.000
 I47  N18   C17  N16  126.91  3.000
 I47  C17   N18  C7   117.58  3.000
 I47  H19A  C19  H19  107.20  3.000
 I47  H19A  C19  C20  109.16  3.000
 I47  H19   C19  C20  109.21  3.000
 I47  H19A  C19  C8   110.29  3.000
 I47  H19   C19  C8   110.41  3.000
 I47  C20   C19  C8   110.50  3.000
 I47  H20A  C20  H20  107.41  3.000
 I47  H20A  C20  N21  109.42  3.000
 I47  H20   C20  N21  108.41  3.000
 I47  H20A  C20  C19  110.97  3.000
 I47  H20   C20  C19  109.93  3.000
 I47  N21   C20  C19  110.62  3.000
 I47  C25   N21  C22  124.92  3.000
 I47  C25   N21  C20  120.89  3.000
 I47  C22   N21  C20  113.11  3.000
 I47  H22A  C22  H22  106.21  3.000
 I47  H22A  C22  C23  110.60  3.000
 I47  H22   C22  C23  109.63  3.000
 I47  H22A  C22  N21  111.30  3.000
 I47  H22   C22  N21  108.28  3.000
 I47  C23   C22  N21  110.69  3.000
 I47  H23A  C23  H23  107.86  3.000
 I47  H23A  C23  C22  109.36  3.000
 I47  H23   C23  C22  109.40  3.000
 I47  H23A  C23  C8   109.77  3.000
 I47  H23   C23  C8   109.80  3.000
 I47  C22   C23  C8   110.60  3.000
 I47  C27   C25  O26  120.38  3.000
 I47  C27   C25  N21  116.53  3.000
 I47  O26   C25  N21  123.09  3.000
 I47  H27A  C27  H27  106.57  3.000
 I47  H27A  C27  O28  112.05  3.000
 I47  H27   C27  O28  111.98  3.000
 I47  H27A  C27  C25  109.18  3.000
 I47  H27   C27  C25  108.85  3.000
 I47  O28   C27  C25  108.14  3.000
 I47  HO28  O28  C27  107.35  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
 I47  CONST_01  C10   C9   C6   C1   180.00   0.0  0
 I47  CONST_02  C12   C13  C6   C1   180.00   0.0  0
 I47  CONST_03  C4    N3   N2   C1     0.00   0.0  0
 I47  CONST_04  N3    C4   C5   C1     0.00   0.0  0
 I47  CONST_09  C4    C5   C1   N2     0.00   0.0  0
 I47  CONST_10  C7    C5   C1   N2   180.00   0.0  0
 I47  CONST_11  C5    C4   N3   N2     0.00   0.0  0
 I47  CONST_12  C6    C1   N2   N3   180.00   0.0  0
 I47  CONST_13  C5    C1   N2   N3     0.00   0.0  0
 I47  CONST_14  C7    C5   C4   N3   180.00   0.0  0
 I47  CONST_15  C6    C1   C5   C4   180.00   0.0  0
 I47  CONST_20  C17   N18  C7   C5   180.00   0.0  0
 I47  CONST_21  C15   C14  C7   C5   180.00   0.0  0
 I47  CONST_22  C7    C5   C1   C6     0.00   0.0  0
 I47  CONST_23  C11   C10  C9   C6     0.00   0.0  0
 I47  CONST_24  C11   C12  C13  C6     0.00   0.0  0
 I47  CONST_25  N16   C17  N18  C7     0.00   0.0  0
 I47  CONST_26  N16   C15  C14  C7     0.00   0.0  0
 I47  CONST_27  C12   C13  C6   C9     0.00   0.0  0
 I47  CONST_28  C12   C11  C10  C9     0.00   0.0  0
 I47  CONST_29  C13   C6   C9   C10    0.00   0.0  0
 I47  CONST_30  C13   C12  C11  C10    0.00   0.0  0
 I47  CONST_31  C17   N18  C7   C14    0.00   0.0  0
 I47  CONST_32  C17   N16  C15  C14    0.00   0.0  0
 I47  CONST_33  N18   C7   C14  C15    0.00   0.0  0
 I47  CONST_34  N18   C17  N16  C15    0.00   0.0  0
 I47  CONST_35  C8    C4   C5   C1   180.00   0.0  0
 I47  CONST_36  C8    C4   N3   N2   180.00   0.0  0
 I47  CONST_37  C8    C4   C5   C7     0.00   0.0  0
 I47  CONST_38  CL24  C11  C10  C9   180.00   0.0  0
 I47  CONST_39  CL24  C11  C12  C13  180.00   0.0  0
 I47  CONST_40  H9    C9   C6   C1     0.00   0.0  0
 I47  CONST_41  H13   C13  C6   C1     0.00   0.0  0
 I47  CONST_42  HN2   N2   N3   C4   180.00   0.0  0
 I47  CONST_43  H14   C14  C7   C5     0.00   0.0  0
 I47  CONST_44  H10   C10  C9   C6   180.00   0.0  0
 I47  CONST_45  H12   C12  C13  C6   180.00   0.0  0
 I47  CONST_46  H17   C17  N18  C7   180.00   0.0  0
 I47  CONST_47  H15   C15  C14  C7   180.00   0.0  0
 I47  CONST_48  O26   C25  N21  C20    0.00   0.0  0
 I47  CONST_49  C27   C25  N21  C20  180.00   0.0  0
 I47  CONST_50  O26   C25  N21  C22  180.00   0.0  0
 I47  CONST_51  C27   C25  N21  C22    0.00   0.0  0
 I47  Var_01    N21   C20  C19  C8   -56.07  30.0  1
 I47  Var_02    N21   C22  C23  C8    55.70  30.0  1
 I47  Var_03    C22   N21  C20  C19   58.92  30.0  1
 I47  Var_04    C23   C22  N21  C20  -58.76  30.0  1
 I47  Var_05    O28   C27  C25  N21  177.69  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
 I47  chir_01  C8  C4  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
 I47  plan-1  C1    0.020
 I47  plan-1  N2    0.020
 I47  plan-1  N3    0.020
 I47  plan-1  C4    0.020
 I47  plan-1  C5    0.020
 I47  plan-1  C6    0.020
 I47  plan-1  C7    0.020
 I47  plan-1  C8    0.020
 I47  plan-1  HN2   0.020
 I47  plan-2  C1    0.020
 I47  plan-2  C6    0.020
 I47  plan-2  C9    0.020
 I47  plan-2  C10   0.020
 I47  plan-2  C11   0.020
 I47  plan-2  C12   0.020
 I47  plan-2  C13   0.020
 I47  plan-2  CL24  0.020
 I47  plan-2  H9    0.020
 I47  plan-2  H10   0.020
 I47  plan-2  H12   0.020
 I47  plan-2  H13   0.020
 I47  plan-3  C5    0.020
 I47  plan-3  C7    0.020
 I47  plan-3  C14   0.020
 I47  plan-3  C15   0.020
 I47  plan-3  N16   0.020
 I47  plan-3  C17   0.020
 I47  plan-3  N18   0.020
 I47  plan-3  H14   0.020
 I47  plan-3  H15   0.020
 I47  plan-3  H17   0.020
 I47  plan-4  C20   0.020
 I47  plan-4  N21   0.020
 I47  plan-4  C22   0.020
 I47  plan-4  C25   0.020
 I47  plan-4  O26   0.020
 I47  plan-4  C27   0.020

