# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:18:43 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 4-{[2-(3-benzyl-1,2,4-oxadiazol-5-yl)-3-methyl-1-benzofuran-4-yl]oxy}piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(oc2cccc(OC3CCNCC3)c12)c4onc(Cc5ccccc5)n4
#
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
 X25  X25  4-{[2-(3-benzyl-1,2,4-oxadiazol-5-yl)-3-methyl-1-benzofuran-4-yl]oxy}piperidine  ligand  52  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X25
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
 X25  C     C  CH3   0  -0.756  -1.1333   1.8331   0.9757
 X25  C1    C  CR5   0   0.051  -0.7074   0.4317   0.7103
 X25  C2    C  CR5   0   0.232   0.5386  -0.1175   0.7657
 X25  O     O  O     0  -0.459   0.5339  -1.4432   0.4463
 X25  C14   C  CR5   0   0.455   1.8403   0.4056   1.0707
 X25  N1    N  N     0  -0.441   2.9669  -0.2326   1.0328
 X25  C15   C  CR5   0   0.325   3.8595   0.7277   1.4027
 X25  C16   C  CH2   0  -0.628   5.3258   0.4861   1.4827
 X25  C17   C  CR6   0   0.122   5.8845   0.1532   0.1213
 X25  C18   C  CR16  0  -0.286   6.1230   1.1702  -0.7994
 X25  C19   C  CR16  0  -0.241   6.6156   0.8774  -2.0632
 X25  C20   C  CR16  0  -0.267   6.8730  -0.4402  -2.4217
 X25  C21   C  CR16  0  -0.241   6.6349  -1.4593  -1.5097
 X25  C22   C  CR16  0  -0.308   6.1416  -1.1632  -0.2452
 X25  N2    N  N     0  -0.142   3.3208   1.8807   1.6526
 X25  O2    O  O     0  -0.344   1.9797   1.6728   1.4353
 X25  C3    C  CR56  0   0.381  -0.7399  -1.7726   0.1775
 X25  C13   C  CR56  0  -0.057  -1.5609  -0.6561   0.3207
 X25  C4    C  CR16  0  -0.370  -1.1934  -3.0299  -0.1911
 X25  C5    C  CR16  0  -0.255  -2.5528  -3.1223  -0.4186
 X25  C6    C  CR16  0  -0.399  -3.4210  -2.0289  -0.2885
 X25  C7    C  CR6   0   0.329  -2.9429  -0.7803   0.0850
 X25  O1    O  O2    0  -0.473  -3.6749   0.3244   0.2578
 X25  C8    C  CH1   0   0.022  -5.0720   0.3259  -0.0320
 X25  C9    C  CH2   0  -0.442  -5.6763   1.5297   0.6691
 X25  C10   C  CH2   0  -0.305  -7.1624   1.6159   0.3454
 X25  N     N  NH1   0  -0.595  -7.3508   1.7037  -1.0912
 X25  C11   C  CH2   0  -0.299  -6.8407   0.5269  -1.7695
 X25  C12   C  CH2   0  -0.465  -5.3413   0.3976  -1.5293
 X25  HC1   H  HCH3  0   0.258  -1.6188   2.2552   0.0963
 X25  HC2   H  HCH3  0   0.259  -1.8618   1.8642   1.7856
 X25  HC3   H  HCH3  0   0.254  -0.3037   2.4789   1.2448
 X25  H161  H  HCH2  0   0.291   5.8101   1.3739   1.8907
 X25  H162  H  HCH2  0   0.292   5.5064  -0.3345   2.1796
 X25  H18   H  HCR6  0   0.253   5.9248   2.1996  -0.5240
 X25  H22   H  HCR6  0   0.253   5.9619  -1.9634   0.4626
 X25  H19   H  HCR6  0   0.257   6.8008   1.6784  -2.7672
 X25  H20   H  HCR6  0   0.257   7.2596  -0.6715  -3.4057
 X25  H21   H  HCR6  0   0.257   6.8326  -2.4879  -1.7823
 X25  H4    H  HCR6  0   0.271  -0.5302  -3.8768  -0.2961
 X25  H5    H  HCR6  0   0.270  -2.9736  -4.0743  -0.7135
 X25  H6    H  HCR6  0   0.280  -4.4710  -2.1890  -0.4876
 X25  H8    H  HCH1  0   0.225  -5.5349  -0.5798   0.3822
 X25  H91C  H  HCH2  0   0.243  -5.5345   1.4506   1.7491
 X25  H92C  H  HCH2  0   0.230  -5.1756   2.4415   0.3308
 X25  H121  H  HCH2  0   0.233  -4.8259   1.2689  -1.9438
 X25  H122  H  HCH2  0   0.246  -4.9643  -0.4872  -2.0467
 X25  H101  H  HCH2  0   0.194  -7.6732   0.7425   0.7841
 X25  H102  H  HCH2  0   0.241  -7.5888   2.5030   0.8167
 X25  H     H  HNH1  0   0.355  -8.3348   1.8143  -1.2974
 X25  H111  H  HCH2  0   0.194  -7.3339  -0.4015  -1.4345
 X25  H112  H  HCH2  0   0.240  -7.0339   0.6194  -2.8395

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
 X25  C    C1    single    1.489  0.020  1.489
 X25  C1   C2    aromatic  1.363  0.020  1.363
 X25  C1   C13   aromatic  1.437  0.020  1.437
 X25  C2   O     aromatic  1.364  0.020  1.364
 X25  C2   C14   single    1.436  0.020  1.436
 X25  O    C3    aromatic  1.343  0.020  1.343
 X25  C14  N1    aromatic  1.295  0.020  1.295
 X25  C14  O2    aromatic  1.326  0.020  1.326
 X25  N1   C15   aromatic  1.362  0.020  1.362
 X25  C15  C16   single    1.488  0.020  1.488
 X25  C15  N2    aromatic  1.297  0.020  1.297
 X25  C16  C17   single    1.509  0.020  1.509
 X25  C17  C18   aromatic  1.392  0.020  1.392
 X25  C17  C22   aromatic  1.390  0.020  1.390
 X25  C18  C19   aromatic  1.388  0.020  1.388
 X25  C19  C20   aromatic  1.390  0.020  1.390
 X25  C20  C21   aromatic  1.388  0.020  1.388
 X25  C21  C22   aromatic  1.389  0.020  1.389
 X25  N2   O2    aromatic  1.374  0.020  1.374
 X25  C3   C13   aromatic  1.393  0.020  1.393
 X25  C3   C4    aromatic  1.386  0.020  1.386
 X25  C13  C7    aromatic  1.407  0.020  1.407
 X25  C4   C5    aromatic  1.381  0.020  1.381
 X25  C5   C6    aromatic  1.402  0.020  1.402
 X25  C6   C7    aromatic  1.388  0.020  1.388
 X25  C7   O1    single    1.336  0.020  1.336
 X25  O1   C8    single    1.427  0.020  1.427
 X25  C8   C9    single    1.518  0.020  1.518
 X25  C8   C12   single    1.523  0.020  1.523
 X25  C9   C10   single    1.523  0.020  1.523
 X25  C10  N     single    1.452  0.020  1.452
 X25  N    C11   single    1.451  0.020  1.451
 X25  C11  C12   single    1.524  0.020  1.524
 X25  C    HC1   single    0.970  0.020  1.090
 X25  C    HC2   single    0.970  0.020  1.090
 X25  C    HC3   single    0.970  0.020  1.090
 X25  C16  H161  single    0.970  0.020  1.090
 X25  C16  H162  single    0.970  0.020  1.090
 X25  C18  H18   single    0.930  0.020  1.080
 X25  C22  H22   single    0.930  0.020  1.080
 X25  C19  H19   single    0.930  0.020  1.080
 X25  C20  H20   single    0.930  0.020  1.080
 X25  C21  H21   single    0.930  0.020  1.080
 X25  C4   H4    single    0.930  0.020  1.080
 X25  C5   H5    single    0.930  0.020  1.080
 X25  C6   H6    single    0.930  0.020  1.080
 X25  C8   H8    single    0.970  0.020  1.090
 X25  C9   H91C  single    0.970  0.020  1.090
 X25  C9   H92C  single    0.970  0.020  1.090
 X25  C12  H121  single    0.970  0.020  1.090
 X25  C12  H122  single    0.970  0.020  1.090
 X25  C10  H101  single    0.970  0.020  1.090
 X25  C10  H102  single    0.970  0.020  1.090
 X25  N    H     single    0.860  0.020  1.020
 X25  C11  H111  single    0.970  0.020  1.090
 X25  C11  H112  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
 X25  HC3   C    HC2   108.05  3.000
 X25  HC3   C    HC1   108.07  3.000
 X25  HC2   C    HC1   106.91  3.000
 X25  HC3   C    C1    112.69  3.000
 X25  HC2   C    C1    110.53  3.000
 X25  HC1   C    C1    110.38  3.000
 X25  C13   C1   C2    104.43  3.000
 X25  C13   C1   C     126.24  3.000
 X25  C2    C1   C     129.33  3.000
 X25  C14   C2   O     114.02  3.000
 X25  C14   C2   C1    133.69  3.000
 X25  O     C2   C1    112.28  3.000
 X25  C3    O    C2    106.78  3.000
 X25  O2    C14  N1    112.80  3.000
 X25  O2    C14  C2    120.13  3.000
 X25  N1    C14  C2    127.07  3.000
 X25  C15   N1   C14   102.39  3.000
 X25  N2    C15  C16   122.91  3.000
 X25  N2    C15  N1    114.01  3.000
 X25  C16   C15  N1    123.07  3.000
 X25  H162  C16  H161  107.44  3.000
 X25  H162  C16  C17   110.42  3.000
 X25  H161  C16  C17   110.66  3.000
 X25  H162  C16  C15   108.63  3.000
 X25  H161  C16  C15   108.99  3.000
 X25  C17   C16  C15   110.62  3.000
 X25  C22   C17  C18   119.05  3.000
 X25  C22   C17  C16   121.01  3.000
 X25  C18   C17  C16   119.93  3.000
 X25  H18   C18  C19   119.78  3.000
 X25  H18   C18  C17   119.62  3.000
 X25  C19   C18  C17   120.59  3.000
 X25  H19   C19  C20   120.14  3.000
 X25  H19   C19  C18   119.81  3.000
 X25  C20   C19  C18   120.05  3.000
 X25  H20   C20  C21   120.11  3.000
 X25  H20   C20  C19   120.23  3.000
 X25  C21   C20  C19   119.66  3.000
 X25  H21   C21  C22   119.78  3.000
 X25  H21   C21  C20   120.06  3.000
 X25  C22   C21  C20   120.16  3.000
 X25  H22   C22  C21   119.75  3.000
 X25  H22   C22  C17   119.77  3.000
 X25  C21   C22  C17   120.49  3.000
 X25  O2    N2   C15   103.91  3.000
 X25  N2    O2   C14   106.89  3.000
 X25  C4    C3   C13   124.14  3.000
 X25  C4    C3   O     125.87  3.000
 X25  C13   C3   O     109.99  3.000
 X25  C7    C13  C3    119.39  3.000
 X25  C7    C13  C1    134.08  3.000
 X25  C3    C13  C1    106.53  3.000
 X25  H4    C4   C5    122.37  3.000
 X25  H4    C4   C3    122.39  3.000
 X25  C5    C4   C3    115.23  3.000
 X25  H5    C5   C6    118.07  3.000
 X25  H5    C5   C4    119.11  3.000
 X25  C6    C5   C4    122.81  3.000
 X25  H6    C6   C7    121.16  3.000
 X25  H6    C6   C5    117.97  3.000
 X25  C7    C6   C5    120.86  3.000
 X25  O1    C7   C6    126.13  3.000
 X25  O1    C7   C13   116.31  3.000
 X25  C6    C7   C13   117.56  3.000
 X25  C8    O1   C7    120.73  3.000
 X25  H8    C8   C12   109.58  3.000
 X25  H8    C8   C9    108.17  3.000
 X25  C12   C8   C9    110.26  3.000
 X25  H8    C8   O1    109.58  3.000
 X25  C12   C8   O1    111.89  3.000
 X25  C9    C8   O1    107.26  3.000
 X25  H92C  C9   H91C  107.86  3.000
 X25  H92C  C9   C10   109.49  3.000
 X25  H91C  C9   C10   109.93  3.000
 X25  H92C  C9   C8    109.62  3.000
 X25  H91C  C9   C8    110.33  3.000
 X25  C10   C9   C8    109.57  3.000
 X25  H102  C10  H101  106.92  3.000
 X25  H102  C10  N     109.12  3.000
 X25  H101  C10  N     112.43  3.000
 X25  H102  C10  C9    109.60  3.000
 X25  H101  C10  C9    108.81  3.000
 X25  N     C10  C9    109.90  3.000
 X25  H     N    C11   109.59  3.000
 X25  H     N    C10   109.55  3.000
 X25  C11   N    C10   111.59  3.000
 X25  H112  C11  H111  106.85  3.000
 X25  H112  C11  C12   109.63  3.000
 X25  H111  C11  C12   108.69  3.000
 X25  H112  C11  N     109.11  3.000
 X25  H111  C11  N     112.55  3.000
 X25  C12   C11  N     109.94  3.000
 X25  H122  C12  H121  107.65  3.000
 X25  H122  C12  C11   109.49  3.000
 X25  H121  C12  C11   109.65  3.000
 X25  H122  C12  C8    111.51  3.000
 X25  H121  C12  C8    109.07  3.000
 X25  C11   C12  C8    109.44  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
 X25  CONST_01  C3   O    C2   C1     0.00   0.0  0
 X25  CONST_02  N1   C14  C2   C1   180.00   0.0  0
 X25  CONST_03  O2   C14  C2   C1     0.00   0.0  0
 X25  CONST_04  O    C3   C13  C1     0.00   0.0  0
 X25  CONST_05  C4   C3   C13  C1   180.00   0.0  0
 X25  CONST_06  C6   C7   C13  C1   180.00   0.0  0
 X25  CONST_07  C3   C13  C1   C2     0.00   0.0  0
 X25  CONST_08  C7   C13  C1   C2   180.00   0.0  0
 X25  CONST_09  C13  C3   O    C2     0.00   0.0  0
 X25  CONST_10  C4   C3   O    C2   180.00   0.0  0
 X25  CONST_11  C15  N1   C14  C2   180.00   0.0  0
 X25  CONST_12  N2   O2   C14  C2   180.00   0.0  0
 X25  CONST_13  C13  C1   C2   O      0.00   0.0  0
 X25  CONST_14  N1   C14  C2   O      0.00   0.0  0
 X25  CONST_15  O2   C14  C2   O    180.00   0.0  0
 X25  CONST_16  C7   C13  C3   O    180.00   0.0  0
 X25  CONST_17  C5   C4   C3   O    180.00   0.0  0
 X25  CONST_18  C13  C1   C2   C14  180.00   0.0  0
 X25  CONST_19  C3   O    C2   C14  180.00   0.0  0
 X25  CONST_20  N2   C15  N1   C14    0.00   0.0  0
 X25  CONST_21  C15  N2   O2   C14    0.00   0.0  0
 X25  CONST_22  N2   O2   C14  N1     0.00   0.0  0
 X25  CONST_23  O2   N2   C15  N1     0.00   0.0  0
 X25  CONST_24  O2   C14  N1   C15    0.00   0.0  0
 X25  CONST_25  C20  C19  C18  C17    0.00   0.0  0
 X25  CONST_26  C20  C21  C22  C17    0.00   0.0  0
 X25  CONST_27  C21  C22  C17  C18    0.00   0.0  0
 X25  CONST_28  C21  C20  C19  C18    0.00   0.0  0
 X25  CONST_29  C22  C17  C18  C19    0.00   0.0  0
 X25  CONST_30  C22  C21  C20  C19    0.00   0.0  0
 X25  CONST_31  C6   C7   C13  C3     0.00   0.0  0
 X25  CONST_32  C6   C5   C4   C3     0.00   0.0  0
 X25  CONST_33  C5   C4   C3   C13    0.00   0.0  0
 X25  CONST_34  C5   C6   C7   C13    0.00   0.0  0
 X25  CONST_35  C7   C13  C3   C4     0.00   0.0  0
 X25  CONST_36  C7   C6   C5   C4     0.00   0.0  0
 X25  CONST_37  O    C2   C1   C    180.00   0.0  0
 X25  CONST_38  C14  C2   C1   C      0.00   0.0  0
 X25  CONST_39  C3   C13  C1   C    180.00   0.0  0
 X25  CONST_40  C7   C13  C1   C      0.00   0.0  0
 X25  CONST_41  O1   C7   C13  C1     0.00   0.0  0
 X25  CONST_42  C16  C15  N1   C14  180.00   0.0  0
 X25  CONST_43  O2   N2   C15  C16  180.00   0.0  0
 X25  CONST_44  C19  C18  C17  C16  180.00   0.0  0
 X25  CONST_45  C21  C22  C17  C16  180.00   0.0  0
 X25  CONST_46  O1   C7   C13  C3   180.00   0.0  0
 X25  CONST_47  O1   C7   C6   C5   180.00   0.0  0
 X25  CONST_48  H4   C4   C3   O      0.00   0.0  0
 X25  CONST_49  H19  C19  C18  C17  180.00   0.0  0
 X25  CONST_50  H21  C21  C22  C17  180.00   0.0  0
 X25  CONST_51  H22  C22  C17  C18  180.00   0.0  0
 X25  CONST_52  H20  C20  C19  C18  180.00   0.0  0
 X25  CONST_53  H18  C18  C19  C20  180.00   0.0  0
 X25  CONST_54  H5   C5   C4   C3   180.00   0.0  0
 X25  CONST_55  H6   C6   C7   C13  180.00   0.0  0
 X25  Var_01    N    C10  C9   C8   -57.86  30.0  1
 X25  Var_02    N    C11  C12  C8    57.77  30.0  1
 X25  Var_03    C11  N    C10  C9    61.68  30.0  1
 X25  Var_04    C12  C11  N    C10  -61.71  30.0  1
 X25  Var_05    C17  C16  C15  N1    63.49  30.0  2
 X25  Var_06    C18  C17  C16  C15   78.55  30.0  2
 X25  Var_07    HC1  C    C1   C2   121.19  30.0  2

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
 X25  chir_01  C8  O1  C9  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
 X25  plan-1  C2   0.020
 X25  plan-1  C14  0.020
 X25  plan-1  N1   0.020
 X25  plan-1  C15  0.020
 X25  plan-1  C16  0.020
 X25  plan-1  N2   0.020
 X25  plan-1  O2   0.020
 X25  plan-2  C16  0.020
 X25  plan-2  C17  0.020
 X25  plan-2  C18  0.020
 X25  plan-2  C19  0.020
 X25  plan-2  C20  0.020
 X25  plan-2  C21  0.020
 X25  plan-2  C22  0.020
 X25  plan-2  H18  0.020
 X25  plan-2  H22  0.020
 X25  plan-2  H19  0.020
 X25  plan-2  H20  0.020
 X25  plan-2  H21  0.020
 X25  plan-3  C    0.020
 X25  plan-3  C1   0.020
 X25  plan-3  C2   0.020
 X25  plan-3  O    0.020
 X25  plan-3  C14  0.020
 X25  plan-3  C3   0.020
 X25  plan-3  C13  0.020
 X25  plan-3  C4   0.020
 X25  plan-3  C5   0.020
 X25  plan-3  C6   0.020
 X25  plan-3  C7   0.020
 X25  plan-3  O1   0.020
 X25  plan-3  H4   0.020
 X25  plan-3  H5   0.020
 X25  plan-3  H6   0.020

