# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:57:53 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 1-[4-(4-ethylpiperazin-1-yl)piperidin-1-yl]-2-(4-phenylphenoxy)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCN(CC1)C2CCN(CC2)C(=O)COc3ccc(cc3)c4ccccc4
#
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
 SOF  SOF  1-[4-(4-ethylpiperazin-1-yl)piperidin-1-yl]-2-(4-phenylphenoxy)ethanone  ligand  63  30  .  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_SOF
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
 SOF  O01   O  O2    0  -0.462   1.7012  -1.8442  -0.3402
 SOF  C02   C  CH2   0  -0.328   0.6352  -1.4851   0.4958
 SOF  C03   C  C     0   0.528  -0.5061  -2.4591   0.2232
 SOF  O04   O  O     0  -0.485  -0.3675  -3.3664  -0.5798
 SOF  N05   N  NT    0  -0.447  -1.6334  -2.2554   0.9311
 SOF  C06   C  CH2   0  -0.321  -2.8342  -3.0298   0.6628
 SOF  C07   C  CH2   0  -0.433  -3.8878  -2.1594  -0.0132
 SOF  C08   C  CH1   0  -0.062  -4.1919  -0.9157   0.8234
 SOF  N09   N  NT    0  -0.431  -5.2538  -0.1209   0.2281
 SOF  C10   C  CH2   0  -0.292  -5.9252   0.7644   1.1617
 SOF  C11   C  CH2   0  -0.323  -7.1829   1.3315   0.5126
 SOF  N12   N  NT    0  -0.408  -6.9305   2.0379  -0.7321
 SOF  C13   C  CH2   0  -0.323  -6.1729   1.1719  -1.6216
 SOF  C14   C  CH2   0  -0.302  -4.9109   0.5898  -0.9912
 SOF  C15   C  CH2   0  -0.282  -6.3524   3.3615  -0.5415
 SOF  C16   C  CH3   0  -0.668  -6.4939   4.2427  -1.7725
 SOF  C17   C  CH2   0  -0.444  -2.8903  -0.1658   1.1395
 SOF  C18   C  CH2   0  -0.336  -1.8804  -1.1067   1.7869
 SOF  C19   C  CR6   0   0.374   2.8597  -1.1647  -0.2186
 SOF  C20   C  CR16  0  -0.333   3.9040  -1.5766  -1.0484
 SOF  C21   C  CR16  0  -0.292   5.1304  -0.9448  -0.9901
 SOF  C22   C  CR6   0   0.065   5.3646   0.1134  -0.1063
 SOF  C23   C  CR16  0  -0.298   4.3110   0.5140   0.7096
 SOF  C24   C  CR16  0  -0.360   3.0698  -0.1074   0.6622
 SOF  C25   C  CR6   0   0.094   6.6798   0.7793  -0.0401
 SOF  C26   C  CR16  0  -0.314   7.1991   1.2184   1.1798
 SOF  C27   C  CR16  0  -0.240   8.4330   1.8489   1.2432
 SOF  C28   C  CR16  0  -0.269   9.1764   2.0509   0.0876
 SOF  C29   C  CR16  0  -0.240   8.6732   1.6158  -1.1315
 SOF  C30   C  CR16  0  -0.316   7.4378   0.9879  -1.1945
 SOF  H021  H  HCH2  0   0.266   0.9252  -1.5413   1.5520
 SOF  H022  H  HCH2  0   0.262   0.3093  -0.4565   0.2968
 SOF  H061  H  HCH2  0   0.267  -2.5832  -3.8890   0.0471
 SOF  H062  H  HCH2  0   0.244  -3.2143  -3.4097   1.6163
 SOF  H181  H  HCH2  0   0.255  -2.2691  -1.4730   2.7423
 SOF  H182  H  HCH2  0   0.275  -0.9566  -0.5835   2.0211
 SOF  H071  H  HCH2  0   0.229  -3.5233  -1.8817  -1.0060
 SOF  H072  H  HCH2  0   0.241  -4.8037  -2.7373  -0.1523
 SOF  H08   H  HCH1  0   0.224  -4.5946  -1.2727   1.7808
 SOF  H171  H  HCH2  0   0.230  -2.4526   0.2500   0.2264
 SOF  H172  H  HCH2  0   0.245  -3.0776   0.6689   1.8191
 SOF  H101  H  HCH2  0   0.233  -6.2089   0.1968   2.0522
 SOF  H102  H  HCH2  0   0.193  -5.2840   1.5936   1.5054
 SOF  H141  H  HCH2  0   0.198  -4.1751   1.3913  -0.8179
 SOF  H142  H  HCH2  0   0.238  -4.4537  -0.0958  -1.7073
 SOF  H111  H  HCH2  0   0.224  -7.8693   0.5030   0.3057
 SOF  H112  H  HCH2  0   0.233  -7.6916   2.0002   1.2110
 SOF  H131  H  HCH2  0   0.226  -6.8196   0.3415  -1.9243
 SOF  H132  H  HCH2  0   0.236  -5.9090   1.7129  -2.5317
 SOF  HA1   H  HCH2  0   0.225  -6.8921   3.8327   0.2838
 SOF  HB2   H  HCH2  0   0.197  -5.2968   3.3397  -0.2339
 SOF  H161  H  HCH3  0   0.223  -5.9264   3.8651  -2.6240
 SOF  H162  H  HCH3  0   0.220  -7.5387   4.3230  -2.0744
 SOF  H163  H  HCH3  0   0.228  -6.1239   5.2459  -1.5588
 SOF  H20   H  HCR6  0   0.265   3.7503  -2.4028  -1.7312
 SOF  H24   H  HCR6  0   0.280   2.2866   0.2570   1.3126
 SOF  H21   H  HCR6  0   0.256   5.9278  -1.2985  -1.6318
 SOF  H23   H  HCR6  0   0.259   4.4413   1.3446   1.3921
 SOF  H26   H  HCR6  0   0.252   6.6424   1.0499   2.0936
 SOF  H30   H  HCR6  0   0.253   7.0503   0.6763  -2.1568
 SOF  H27   H  HCR6  0   0.257   8.8189   2.1734   2.2009
 SOF  H28   H  HCR6  0   0.256  10.1390   2.5435   0.1367
 SOF  H29   H  HCR6  0   0.256   9.2400   1.7728  -2.0402

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
 SOF  O01  C02   single    1.401  0.020  1.401
 SOF  O01  C19   single    1.349  0.020  1.349
 SOF  C02  C03   single    1.525  0.020  1.525
 SOF  C03  O04   double    1.219  0.020  1.219
 SOF  C03  N05   single    1.347  0.020  1.347
 SOF  N05  C06   single    1.454  0.020  1.454
 SOF  N05  C18   single    1.454  0.020  1.454
 SOF  C06  C07   single    1.525  0.020  1.525
 SOF  C07  C08   single    1.529  0.020  1.529
 SOF  C08  N09   single    1.454  0.020  1.454
 SOF  C08  C17   single    1.535  0.020  1.535
 SOF  N09  C10   single    1.451  0.020  1.451
 SOF  N09  C14   single    1.452  0.020  1.452
 SOF  C10  C11   single    1.525  0.020  1.525
 SOF  C11  N12   single    1.453  0.020  1.453
 SOF  N12  C13   single    1.454  0.020  1.454
 SOF  N12  C15   single    1.457  0.020  1.457
 SOF  C13  C14   single    1.526  0.020  1.526
 SOF  C15  C16   single    1.520  0.020  1.520
 SOF  C17  C18   single    1.525  0.020  1.525
 SOF  C19  C20   aromatic  1.396  0.020  1.396
 SOF  C19  C24   aromatic  1.392  0.020  1.392
 SOF  C20  C21   aromatic  1.381  0.020  1.381
 SOF  C21  C22   aromatic  1.398  0.020  1.398
 SOF  C22  C23   aromatic  1.391  0.020  1.391
 SOF  C22  C25   single    1.476  0.020  1.476
 SOF  C23  C24   aromatic  1.389  0.020  1.389
 SOF  C25  C26   aromatic  1.397  0.020  1.397
 SOF  C25  C30   aromatic  1.397  0.020  1.397
 SOF  C26  C27   aromatic  1.387  0.020  1.387
 SOF  C27  C28   aromatic  1.389  0.020  1.389
 SOF  C28  C29   aromatic  1.389  0.020  1.389
 SOF  C29  C30   aromatic  1.387  0.020  1.387
 SOF  C02  H021  single    0.970  0.020  1.090
 SOF  C02  H022  single    0.970  0.020  1.090
 SOF  C06  H061  single    0.970  0.020  1.090
 SOF  C06  H062  single    0.970  0.020  1.090
 SOF  C18  H181  single    0.970  0.020  1.090
 SOF  C18  H182  single    0.970  0.020  1.090
 SOF  C07  H071  single    0.970  0.020  1.090
 SOF  C07  H072  single    0.970  0.020  1.090
 SOF  C08  H08   single    0.970  0.020  1.090
 SOF  C17  H171  single    0.970  0.020  1.090
 SOF  C17  H172  single    0.970  0.020  1.090
 SOF  C10  H101  single    0.970  0.020  1.090
 SOF  C10  H102  single    0.970  0.020  1.090
 SOF  C14  H141  single    0.970  0.020  1.090
 SOF  C14  H142  single    0.970  0.020  1.090
 SOF  C11  H111  single    0.970  0.020  1.090
 SOF  C11  H112  single    0.970  0.020  1.090
 SOF  C13  H131  single    0.970  0.020  1.090
 SOF  C13  H132  single    0.970  0.020  1.090
 SOF  C15  HA1   single    0.970  0.020  1.090
 SOF  C15  HB2   single    0.970  0.020  1.090
 SOF  C16  H161  single    0.970  0.020  1.090
 SOF  C16  H162  single    0.970  0.020  1.090
 SOF  C16  H163  single    0.970  0.020  1.090
 SOF  C20  H20   single    0.930  0.020  1.080
 SOF  C24  H24   single    0.930  0.020  1.080
 SOF  C21  H21   single    0.930  0.020  1.080
 SOF  C23  H23   single    0.930  0.020  1.080
 SOF  C26  H26   single    0.930  0.020  1.080
 SOF  C30  H30   single    0.930  0.020  1.080
 SOF  C27  H27   single    0.930  0.020  1.080
 SOF  C28  H28   single    0.930  0.020  1.080
 SOF  C29  H29   single    0.930  0.020  1.080

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
 SOF  C19   O01  C02   118.07  3.000
 SOF  H022  C02  H021  107.53  3.000
 SOF  H022  C02  C03   110.12  3.000
 SOF  H021  C02  C03   109.72  3.000
 SOF  H022  C02  O01   110.97  3.000
 SOF  H021  C02  O01   111.11  3.000
 SOF  C03   C02  O01   107.40  3.000
 SOF  N05   C03  O04   123.63  3.000
 SOF  N05   C03  C02   115.85  3.000
 SOF  O04   C03  C02   120.52  3.000
 SOF  C18   N05  C06   112.91  3.000
 SOF  C18   N05  C03   124.84  3.000
 SOF  C06   N05  C03   120.92  3.000
 SOF  H062  C06  H061  107.42  3.000
 SOF  H062  C06  C07   110.14  3.000
 SOF  H061  C06  C07   111.09  3.000
 SOF  H062  C06  N05   108.12  3.000
 SOF  H061  C06  N05   109.58  3.000
 SOF  C07   C06  N05   110.40  3.000
 SOF  H072  C07  H071  107.36  3.000
 SOF  H072  C07  C08   109.47  3.000
 SOF  H071  C07  C08   110.88  3.000
 SOF  H072  C07  C06   109.51  3.000
 SOF  H071  C07  C06   108.49  3.000
 SOF  C08   C07  C06   111.05  3.000
 SOF  H08   C08  C17   106.87  3.000
 SOF  H08   C08  N09   105.48  3.000
 SOF  C17   C08  N09   115.88  3.000
 SOF  H08   C08  C07   106.58  3.000
 SOF  C17   C08  C07   109.96  3.000
 SOF  N09   C08  C07   111.46  3.000
 SOF  C14   N09  C10   110.54  3.000
 SOF  C14   N09  C08   116.03  3.000
 SOF  C10   N09  C08   114.08  3.000
 SOF  H102  C10  H101  106.69  3.000
 SOF  H102  C10  C11   109.42  3.000
 SOF  H101  C10  C11   109.01  3.000
 SOF  H102  C10  N09   112.96  3.000
 SOF  H101  C10  N09   109.11  3.000
 SOF  C11   C10  N09   109.55  3.000
 SOF  H112  C11  H111  106.96  3.000
 SOF  H112  C11  N12   109.32  3.000
 SOF  H111  C11  N12   108.34  3.000
 SOF  H112  C11  C10   109.85  3.000
 SOF  H111  C11  C10   108.41  3.000
 SOF  N12   C11  C10   113.72  3.000
 SOF  C15   N12  C13   114.48  3.000
 SOF  C15   N12  C11   113.48  3.000
 SOF  C13   N12  C11   108.96  3.000
 SOF  H132  C13  H131  106.75  3.000
 SOF  H132  C13  C14   109.49  3.000
 SOF  H131  C13  C14   108.25  3.000
 SOF  H132  C13  N12   109.94  3.000
 SOF  H131  C13  N12   108.24  3.000
 SOF  C14   C13  N12   113.91  3.000
 SOF  H142  C14  H141  106.28  3.000
 SOF  H142  C14  C13   108.35  3.000
 SOF  H141  C14  C13   109.86  3.000
 SOF  H142  C14  N09   110.02  3.000
 SOF  H141  C14  N09   112.44  3.000
 SOF  C13   C14  N09   109.77  3.000
 SOF  HB2   C15  HA1   105.74  3.000
 SOF  HB2   C15  C16   109.10  3.000
 SOF  HA1   C15  C16   108.40  3.000
 SOF  HB2   C15  N12   113.54  3.000
 SOF  HA1   C15  N12   107.13  3.000
 SOF  C16   C15  N12   112.56  3.000
 SOF  H163  C16  H162  108.16  3.000
 SOF  H163  C16  H161  107.16  3.000
 SOF  H162  C16  H161  107.93  3.000
 SOF  H163  C16  C15   110.06  3.000
 SOF  H162  C16  C15   110.85  3.000
 SOF  H161  C16  C15   112.52  3.000
 SOF  H172  C17  H171  107.29  3.000
 SOF  H172  C17  C18   108.72  3.000
 SOF  H171  C17  C18   108.89  3.000
 SOF  H172  C17  C08   110.85  3.000
 SOF  H171  C17  C08   110.66  3.000
 SOF  C18   C17  C08   110.34  3.000
 SOF  H182  C18  H181  105.95  3.000
 SOF  H182  C18  C17   110.94  3.000
 SOF  H181  C18  C17   110.00  3.000
 SOF  H182  C18  N05   111.27  3.000
 SOF  H181  C18  N05   108.04  3.000
 SOF  C17   C18  N05   110.51  3.000
 SOF  C24   C19  C20   119.16  3.000
 SOF  C24   C19  O01   124.71  3.000
 SOF  C20   C19  O01   116.13  3.000
 SOF  H20   C20  C21   120.12  3.000
 SOF  H20   C20  C19   119.59  3.000
 SOF  C21   C20  C19   120.29  3.000
 SOF  H21   C21  C22   119.89  3.000
 SOF  H21   C21  C20   118.65  3.000
 SOF  C22   C21  C20   121.44  3.000
 SOF  C25   C22  C23   121.24  3.000
 SOF  C25   C22  C21   121.26  3.000
 SOF  C23   C22  C21   117.49  3.000
 SOF  H23   C23  C24   118.18  3.000
 SOF  H23   C23  C22   119.95  3.000
 SOF  C24   C23  C22   121.86  3.000
 SOF  H24   C24  C23   118.42  3.000
 SOF  H24   C24  C19   121.82  3.000
 SOF  C23   C24  C19   119.76  3.000
 SOF  C30   C25  C26   118.24  3.000
 SOF  C30   C25  C22   120.93  3.000
 SOF  C26   C25  C22   120.82  3.000
 SOF  H26   C26  C27   119.30  3.000
 SOF  H26   C26  C25   119.79  3.000
 SOF  C27   C26  C25   120.90  3.000
 SOF  H27   C27  C28   120.12  3.000
 SOF  H27   C27  C26   119.60  3.000
 SOF  C28   C27  C26   120.28  3.000
 SOF  H28   C28  C29   120.31  3.000
 SOF  H28   C28  C27   120.30  3.000
 SOF  C29   C28  C27   119.40  3.000
 SOF  H29   C29  C30   119.60  3.000
 SOF  H29   C29  C28   120.11  3.000
 SOF  C30   C29  C28   120.29  3.000
 SOF  H30   C30  C29   119.28  3.000
 SOF  H30   C30  C25   119.81  3.000
 SOF  C29   C30  C25   120.89  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
 SOF  CONST_01  C22   C21  C20  C19     0.00   0.0  0
 SOF  CONST_02  C22   C23  C24  C19     0.00   0.0  0
 SOF  CONST_03  C23   C24  C19  C20     0.00   0.0  0
 SOF  CONST_04  C23   C22  C21  C20     0.00   0.0  0
 SOF  CONST_05  C25   C22  C21  C20   180.00   0.0  0
 SOF  CONST_06  C24   C19  C20  C21     0.00   0.0  0
 SOF  CONST_07  C24   C23  C22  C21     0.00   0.0  0
 SOF  CONST_10  C27   C26  C25  C22   180.00   0.0  0
 SOF  CONST_11  C29   C30  C25  C22   180.00   0.0  0
 SOF  CONST_14  C25   C22  C23  C24   180.00   0.0  0
 SOF  CONST_15  C28   C27  C26  C25     0.00   0.0  0
 SOF  CONST_16  C28   C29  C30  C25     0.00   0.0  0
 SOF  CONST_17  C29   C30  C25  C26     0.00   0.0  0
 SOF  CONST_18  C29   C28  C27  C26     0.00   0.0  0
 SOF  CONST_19  C30   C25  C26  C27     0.00   0.0  0
 SOF  CONST_20  C30   C29  C28  C27     0.00   0.0  0
 SOF  CONST_21  C21   C20  C19  O01   180.00   0.0  0
 SOF  CONST_22  C23   C24  C19  O01   180.00   0.0  0
 SOF  CONST_23  H21   C21  C20  C19   180.00   0.0  0
 SOF  CONST_24  H23   C23  C24  C19   180.00   0.0  0
 SOF  CONST_25  H24   C24  C19  C20   180.00   0.0  0
 SOF  CONST_26  H20   C20  C21  C22   180.00   0.0  0
 SOF  CONST_27  H26   C26  C25  C22     0.00   0.0  0
 SOF  CONST_28  H30   C30  C25  C22     0.00   0.0  0
 SOF  CONST_29  H27   C27  C26  C25   180.00   0.0  0
 SOF  CONST_30  H29   C29  C30  C25   180.00   0.0  0
 SOF  CONST_31  H28   C28  C27  C26   180.00   0.0  0
 SOF  CONST_32  C06   N05  C03  C02   180.00   0.0  0
 SOF  CONST_33  C18   N05  C03  C02     0.00   0.0  0
 SOF  CONST_34  C06   N05  C03  O04     0.00   0.0  0
 SOF  CONST_35  C18   N05  C03  O04   180.00   0.0  0
 SOF  Var_01    C08   C07  C06  N05   -55.53  30.0  1
 SOF  Var_02    C08   C17  C18  N05    56.48  30.0  1
 SOF  Var_03    C17   C18  N05  C06   -59.86  30.0  1
 SOF  Var_04    C18   N05  C06  C07    59.11  30.0  1
 SOF  Var_05    C11   C10  N09  C08  -168.68  30.0  1
 SOF  Var_06    C13   C14  N09  C08   170.19  30.0  1
 SOF  Var_07    N12   C11  C10  N09   -57.04  30.0  1
 SOF  Var_08    N12   C13  C14  N09    55.92  30.0  1
 SOF  Var_09    C13   N12  C11  C10    52.97  30.0  1
 SOF  Var_10    C14   C13  N12  C11   -52.43  30.0  1
 SOF  Var_11    C20   C19  O01  C02   178.52  30.0  2
 SOF  Var_12    C16   C15  N12  C11  -162.12  30.0  3
 SOF  Var_13    N05   C03  C02  O01  -179.17  30.0  3
 SOF  Var_14    H161  C16  C15  N12   -65.25  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
 SOF  chir_01  C08  C07  N09  C17  positiv

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
 SOF  plan-1  O01  0.020
 SOF  plan-1  C19  0.020
 SOF  plan-1  C20  0.020
 SOF  plan-1  C21  0.020
 SOF  plan-1  C22  0.020
 SOF  plan-1  C23  0.020
 SOF  plan-1  C24  0.020
 SOF  plan-1  C25  0.020
 SOF  plan-1  H20  0.020
 SOF  plan-1  H24  0.020
 SOF  plan-1  H21  0.020
 SOF  plan-1  H23  0.020
 SOF  plan-2  C22  0.020
 SOF  plan-2  C25  0.020
 SOF  plan-2  C26  0.020
 SOF  plan-2  C27  0.020
 SOF  plan-2  C28  0.020
 SOF  plan-2  C29  0.020
 SOF  plan-2  C30  0.020
 SOF  plan-2  H26  0.020
 SOF  plan-2  H30  0.020
 SOF  plan-2  H27  0.020
 SOF  plan-2  H28  0.020
 SOF  plan-2  H29  0.020
 SOF  plan-3  C02  0.020
 SOF  plan-3  C03  0.020
 SOF  plan-3  O04  0.020
 SOF  plan-3  N05  0.020
 SOF  plan-3  C06  0.020
 SOF  plan-3  C18  0.020

