# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:00:53 2022
#   Inital geometry file: a 148 line input string
#   Ligand name: 1-acetyl-4-(4-{4-[(2-ethoxyphenyl)sulfanyl]-3-nitrophenyl}pyridin-2-yl)piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccccc1Sc2ccc(cc2[N+]([O-])=O)c3ccnc(c3)N4CCN(CC4)C(C)=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
 L08  L08  1-acetyl-4-(4-{4-[(2-ethoxyphenyl)sulfanyl]-3-nitrophenyl}pyridin-2-yl)piperazine  ligand  60  34  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L08
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
 L08  O4    O  O      0  -0.378   3.2777   3.9003  -0.4380
 L08  N3    N  N      1   0.332   3.4862   2.8145  -0.9265
 L08  C11   C  CR6    0   0.287   2.5688   1.7357  -0.6435
 L08  C10   C  CR6    0  -0.131   2.9429   0.4039  -0.8645
 L08  C15   C  CR16   0  -0.208   1.9719  -0.5617  -0.5928
 L08  C14   C  CR16   0  -0.281   0.7200  -0.2198  -0.1290
 L08  C13   C  CR6    0   0.091   0.3636   1.1118   0.0991
 L08  C12   C  CR16   0  -0.352   1.3129   2.0839  -0.1613
 L08  C16   C  CR6    0   0.208  -0.9776   1.4814   0.5890
 L08  C8    C  CR16   0  -0.424  -1.1512   2.5579   1.4621
 L08  C35   C  CR16   0  -0.051  -2.4350   2.8308   1.8883
 L08  N20   N  N      0  -0.476  -3.5076   2.1469   1.5171
 L08  C18   C  CR6    0   0.572  -3.3641   1.1275   0.6692
 L08  N1    N  NT     0  -0.520  -4.5106   0.4845   0.2723
 L08  C19   C  CH2    0  -0.292  -5.7180   0.6318   1.0706
 L08  C20   C  CH2    0  -0.318  -6.9609   0.4095   0.2281
 L08  N2    N  NT     0  -0.444  -6.8888  -0.8664  -0.4535
 L08  C21   C  CH2    0  -0.316  -5.7126  -0.9686  -1.2872
 L08  C22   C  CH2    0  -0.292  -4.4457  -0.7585  -0.4718
 L08  C23   C  C      0   0.516  -7.7847  -1.8534  -0.2252
 L08  O2    O  O      0  -0.505  -8.7391  -1.7018   0.5268
 L08  C24   C  CH3    0  -0.807  -7.5690  -3.1611  -0.9512
 L08  C17   C  CR16   0  -0.489  -2.0911   0.7604   0.1920
 L08  S1    S  S2     0   0.162   4.5481  -0.0541  -1.4304
 L08  C1    C  CR6    0  -0.320   4.6226  -1.7647  -0.9970
 L08  C2    C  CR6    0   0.478   4.6803  -2.1498   0.3534
 L08  C3    C  CR16   0  -0.385   4.8421  -3.4975   0.6653
 L08  C4    C  CR16   0  -0.234   4.9641  -4.4352  -0.3532
 L08  C5    C  CR16   0  -0.279   4.9200  -4.0559  -1.6854
 L08  C6    C  CR16   0  -0.211   4.7436  -2.7152  -2.0007
 L08  O7    O  O2     0  -0.448   4.5515  -1.1711   1.2521
 L08  C9    C  CH2    0  -0.191   4.4560  -1.4954   2.6346
 L08  C33   C  CH3    0  -0.677   4.2019  -0.2145   3.3911
 L08  O3    O  O     -1  -0.378   4.4271   2.5707  -1.6500
 L08  H15   H  HCR6   0   0.287   2.1953  -1.6068  -0.7512
 L08  H14   H  HCR6   0   0.276   0.0120  -1.0137   0.0703
 L08  H12   H  HCR6   0   0.298   1.0696   3.1278  -0.0228
 L08  H8    H  HCR6   0   0.262  -0.3185   3.1444   1.8248
 L08  H35   H  HCR6   0   0.260  -2.6100   3.6487   2.5792
 L08  H191  H  HCH2   0   0.228  -5.7124  -0.0833   1.9047
 L08  H192  H  HCH2   0   0.271  -5.7485   1.6305   1.4955
 L08  H201  H  HCH2   0   0.270  -7.8417   0.4417   0.8632
 L08  H202  H  HCH2   0   0.247  -7.0515   1.2070  -0.5167
 L08  H211  H  HCH2   0   0.283  -5.6586  -1.9359  -1.7785
 L08  H212  H  HCH2   0   0.253  -5.7663  -0.2070  -2.0717
 L08  H221  H  HCH2   0   0.267  -3.6163  -0.7388  -1.1745
 L08  H222  H  HCH2   0   0.234  -4.2933  -1.6123   0.2022
 L08  H241  H  HCH3   0   0.264  -6.6065  -3.6101  -0.7040
 L08  H242  H  HCH3   0   0.270  -8.3539  -3.8568  -0.6672
 L08  H243  H  HCH3   0   0.267  -7.6008  -3.0306  -2.0336
 L08  H17   H  HCR6   0   0.270  -1.9657  -0.0616  -0.4963
 L08  H3    H  HCR6   0   0.285   4.8844  -3.8304   1.6935
 L08  H4    H  HCR6   0   0.268   5.0946  -5.4771  -0.0913
 L08  H5    H  HCR6   0   0.261   5.0139  -4.7915  -2.4721
 L08  H6    H  HCR6   0   0.273   4.6936  -2.4002  -3.0351
 L08  H91   H  HCH2   0   0.229   5.3820  -1.9697   2.9754
 L08  H92   H  HCH2   0   0.228   3.6388  -2.2056   2.7948
 L08  H331  H  HCH3   0   0.234   3.2730   0.2568   3.0695
 L08  H332  H  HCH3   0   0.238   4.1183  -0.4343   4.4550
 L08  H333  H  HCH3   0   0.236   5.0176   0.4957   3.2580

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
 L08  O4   N3    double    1.209  0.020  1.209
 L08  N3   C11   single    1.444  0.020  1.444
 L08  N3   O3    single    1.212  0.020  1.212
 L08  C11  C10   aromatic  1.401  0.020  1.401
 L08  C11  C12   aromatic  1.390  0.020  1.390
 L08  C10  C15   aromatic  1.396  0.020  1.396
 L08  C10  S1    single    1.762  0.020  1.762
 L08  C15  C14   aromatic  1.378  0.020  1.378
 L08  C15  H15   single    0.930  0.020  1.080
 L08  C14  C13   aromatic  1.397  0.020  1.397
 L08  C14  H14   single    0.930  0.020  1.080
 L08  C13  C12   aromatic  1.384  0.020  1.384
 L08  C13  C16   single    1.475  0.020  1.475
 L08  C12  H12   single    0.930  0.020  1.080
 L08  C16  C8    aromatic  1.397  0.020  1.397
 L08  C16  C17   aromatic  1.385  0.020  1.385
 L08  C8   C35   aromatic  1.380  0.020  1.380
 L08  C8   H8    single    0.930  0.020  1.080
 L08  C35  N20   aromatic  1.325  0.020  1.325
 L08  C35  H35   single    0.930  0.020  1.080
 L08  N20  C18   aromatic  1.334  0.020  1.334
 L08  C18  N1    single    1.373  0.020  1.373
 L08  C18  C17   aromatic  1.408  0.020  1.408
 L08  N1   C19   single    1.455  0.020  1.455
 L08  N1   C22   single    1.450  0.020  1.450
 L08  C19  C20   single    1.518  0.020  1.518
 L08  C19  H191  single    0.970  0.020  1.090
 L08  C19  H192  single    0.970  0.020  1.090
 L08  C20  N2    single    1.448  0.020  1.448
 L08  C20  H201  single    0.970  0.020  1.090
 L08  C20  H202  single    0.970  0.020  1.090
 L08  N2   C21   single    1.445  0.020  1.445
 L08  N2   C23   single    1.352  0.020  1.352
 L08  C21  C22   single    1.521  0.020  1.521
 L08  C21  H211  single    0.970  0.020  1.090
 L08  C21  H212  single    0.970  0.020  1.090
 L08  C22  H221  single    0.970  0.020  1.090
 L08  C22  H222  single    0.970  0.020  1.090
 L08  C23  O2    double    1.225  0.020  1.225
 L08  C23  C24   single    1.511  0.020  1.511
 L08  C24  H241  single    0.970  0.020  1.090
 L08  C24  H242  single    0.970  0.020  1.090
 L08  C24  H243  single    0.970  0.020  1.090
 L08  C17  H17   single    0.930  0.020  1.080
 L08  S1   C1    single    1.766  0.020  1.766
 L08  C1   C2    aromatic  1.405  0.020  1.405
 L08  C1   C6    aromatic  1.388  0.020  1.388
 L08  C2   C3    aromatic  1.393  0.020  1.393
 L08  C2   O7    single    1.335  0.020  1.335
 L08  C3   C4    aromatic  1.390  0.020  1.390
 L08  C3   H3    single    0.930  0.020  1.080
 L08  C4   C5    aromatic  1.386  0.020  1.386
 L08  C4   H4    single    0.930  0.020  1.080
 L08  C5   C6    aromatic  1.389  0.020  1.389
 L08  C5   H5    single    0.930  0.020  1.080
 L08  C6   H6    single    0.930  0.020  1.080
 L08  O7   C9    single    1.423  0.020  1.423
 L08  C9   C33   single    1.509  0.020  1.509
 L08  C9   H91   single    0.970  0.020  1.090
 L08  C9   H92   single    0.970  0.020  1.090
 L08  C33  H331  single    0.970  0.020  1.090
 L08  C33  H332  single    0.970  0.020  1.090
 L08  C33  H333  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
 L08  O3    N3   C11   117.38  3.000
 L08  O3    N3   O4    123.78  3.000
 L08  C11   N3   O4    118.84  3.000
 L08  C12   C11  C10   122.30  3.000
 L08  C12   C11  N3    117.06  3.000
 L08  C10   C11  N3    120.64  3.000
 L08  S1    C10  C15   121.08  3.000
 L08  S1    C10  C11   122.74  3.000
 L08  C15   C10  C11   116.17  3.000
 L08  H15   C15  C14   118.50  3.000
 L08  H15   C15  C10   119.78  3.000
 L08  C14   C15  C10   121.72  3.000
 L08  H14   C14  C13   120.14  3.000
 L08  H14   C14  C15   118.31  3.000
 L08  C13   C14  C15   121.54  3.000
 L08  C16   C13  C12   120.69  3.000
 L08  C16   C13  C14   121.67  3.000
 L08  C12   C13  C14   117.64  3.000
 L08  H12   C12  C13   120.00  3.000
 L08  H12   C12  C11   119.34  3.000
 L08  C13   C12  C11   120.62  3.000
 L08  C17   C16  C8    118.72  3.000
 L08  C17   C16  C13   120.36  3.000
 L08  C8    C16  C13   120.92  3.000
 L08  H8    C8   C35   120.37  3.000
 L08  H8    C8   C16   122.14  3.000
 L08  C35   C8   C16   117.46  3.000
 L08  H35   C35  N20   115.90  3.000
 L08  H35   C35  C8    119.73  3.000
 L08  N20   C35  C8    124.37  3.000
 L08  C18   N20  C35   119.04  3.000
 L08  C17   C18  N1    122.33  3.000
 L08  C17   C18  N20   120.79  3.000
 L08  N1    C18  N20   116.87  3.000
 L08  C22   N1   C19   113.92  3.000
 L08  C22   N1   C18   120.82  3.000
 L08  C19   N1   C18   119.14  3.000
 L08  H192  C19  H191  107.57  3.000
 L08  H192  C19  C20   109.21  3.000
 L08  H191  C19  C20   109.28  3.000
 L08  H192  C19  N1    109.33  3.000
 L08  H191  C19  N1    110.26  3.000
 L08  C20   C19  N1    111.11  3.000
 L08  H202  C20  H201  107.99  3.000
 L08  H202  C20  N2    109.00  3.000
 L08  H201  C20  N2    109.97  3.000
 L08  H202  C20  C19   109.80  3.000
 L08  H201  C20  C19   109.58  3.000
 L08  N2    C20  C19   110.46  3.000
 L08  C23   N2   C21   125.79  3.000
 L08  C23   N2   C20   122.04  3.000
 L08  C21   N2   C20   111.98  3.000
 L08  H212  C21  H211  107.33  3.000
 L08  H212  C21  C22   109.20  3.000
 L08  H211  C21  C22   108.91  3.000
 L08  H212  C21  N2    108.92  3.000
 L08  H211  C21  N2    111.37  3.000
 L08  C22   C21  N2    111.03  3.000
 L08  H222  C22  H221  107.75  3.000
 L08  H222  C22  C21   109.70  3.000
 L08  H221  C22  C21   106.94  3.000
 L08  H222  C22  N1    110.95  3.000
 L08  H221  C22  N1    110.50  3.000
 L08  C21   C22  N1    110.87  3.000
 L08  C24   C23  O2    120.89  3.000
 L08  C24   C23  N2    117.13  3.000
 L08  O2    C23  N2    121.98  3.000
 L08  H243  C24  H242  108.36  3.000
 L08  H243  C24  H241  107.46  3.000
 L08  H242  C24  H241  108.34  3.000
 L08  H243  C24  C23   111.65  3.000
 L08  H242  C24  C23   108.99  3.000
 L08  H241  C24  C23   111.93  3.000
 L08  H17   C17  C18   121.31  3.000
 L08  H17   C17  C16   119.07  3.000
 L08  C18   C17  C16   119.61  3.000
 L08  C1    S1   C10   102.20  3.000
 L08  C6    C1   C2    120.25  3.000
 L08  C6    C1   S1    119.31  3.000
 L08  C2    C1   S1    120.19  3.000
 L08  O7    C2   C3    124.74  3.000
 L08  O7    C2   C1    116.23  3.000
 L08  C3    C2   C1    119.02  3.000
 L08  H3    C3   C4    119.05  3.000
 L08  H3    C3   C2    121.01  3.000
 L08  C4    C3   C2    119.93  3.000
 L08  H4    C4   C5    119.99  3.000
 L08  H4    C4   C3    118.87  3.000
 L08  C5    C4   C3    121.13  3.000
 L08  H5    C5   C6    120.18  3.000
 L08  H5    C5   C4    120.70  3.000
 L08  C6    C5   C4    119.12  3.000
 L08  H6    C6   C5    120.25  3.000
 L08  H6    C6   C1    119.20  3.000
 L08  C5    C6   C1    120.54  3.000
 L08  C9    O7   C2    119.57  3.000
 L08  H92   C9   H91   107.75  3.000
 L08  H92   C9   C33   110.59  3.000
 L08  H91   C9   C33   110.74  3.000
 L08  H92   C9   O7    109.89  3.000
 L08  H91   C9   O7    110.14  3.000
 L08  C33   C9   O7    107.75  3.000
 L08  H333  C33  H332  107.95  3.000
 L08  H333  C33  H331  108.67  3.000
 L08  H332  C33  H331  108.06  3.000
 L08  H333  C33  C9    111.46  3.000
 L08  H332  C33  C9    109.34  3.000
 L08  H331  C33  C9    111.25  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
 L08  CONST_01  C14   C15  C10  C11     0.00   0.0  0
 L08  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 L08  CONST_03  C16   C13  C12  C11   180.00   0.0  0
 L08  CONST_04  C13   C12  C11  C10     0.00   0.0  0
 L08  CONST_05  C13   C14  C15  C10     0.00   0.0  0
 L08  CONST_06  C12   C11  C10  C15     0.00   0.0  0
 L08  CONST_07  C12   C13  C14  C15     0.00   0.0  0
 L08  CONST_08  C16   C13  C14  C15   180.00   0.0  0
 L08  CONST_11  C35   C8   C16  C13   180.00   0.0  0
 L08  CONST_12  C18   C17  C16  C13   180.00   0.0  0
 L08  CONST_15  N20   C35  C8   C16     0.00   0.0  0
 L08  CONST_16  N20   C18  C17  C16     0.00   0.0  0
 L08  CONST_17  C18   C17  C16  C8      0.00   0.0  0
 L08  CONST_18  C18   N20  C35  C8      0.00   0.0  0
 L08  CONST_19  C17   C16  C8   C35     0.00   0.0  0
 L08  CONST_20  C17   C18  N20  C35     0.00   0.0  0
 L08  CONST_21  C4    C3   C2   C1      0.00   0.0  0
 L08  CONST_22  C4    C5   C6   C1      0.00   0.0  0
 L08  CONST_23  C5    C6   C1   C2      0.00   0.0  0
 L08  CONST_24  C5    C4   C3   C2      0.00   0.0  0
 L08  CONST_25  C6    C1   C2   C3      0.00   0.0  0
 L08  CONST_26  C6    C5   C4   C3      0.00   0.0  0
 L08  CONST_27  N1    C18  C17  C16   180.00   0.0  0
 L08  CONST_28  N1    C18  N20  C35   180.00   0.0  0
 L08  CONST_29  C15   C10  C11  N3    180.00   0.0  0
 L08  CONST_30  C13   C12  C11  N3    180.00   0.0  0
 L08  CONST_31  S1    C10  C15  C14   180.00   0.0  0
 L08  CONST_32  S1    C10  C11  C12   180.00   0.0  0
 L08  CONST_33  C3    C2   C1   S1    180.00   0.0  0
 L08  CONST_34  C5    C6   C1   S1    180.00   0.0  0
 L08  CONST_35  O7    C2   C3   C4    180.00   0.0  0
 L08  CONST_36  O7    C2   C1   C6    180.00   0.0  0
 L08  CONST_37  H15   C15  C10  C11   180.00   0.0  0
 L08  CONST_38  H12   C12  C11  C10   180.00   0.0  0
 L08  CONST_39  H14   C14  C15  C10   180.00   0.0  0
 L08  CONST_40  H8    C8   C16  C13     0.00   0.0  0
 L08  CONST_41  H17   C17  C16  C13     0.00   0.0  0
 L08  CONST_42  H35   C35  C8   C16   180.00   0.0  0
 L08  CONST_43  H3    C3   C2   C1    180.00   0.0  0
 L08  CONST_44  H5    C5   C6   C1    180.00   0.0  0
 L08  CONST_45  H6    C6   C1   C2    180.00   0.0  0
 L08  CONST_46  H4    C4   C3   C2    180.00   0.0  0
 L08  CONST_47  O2    C23  N2   C20     0.00   0.0  0
 L08  CONST_48  C24   C23  N2   C20   180.00   0.0  0
 L08  CONST_49  O2    C23  N2   C21   180.00   0.0  0
 L08  CONST_50  C24   C23  N2   C21     0.00   0.0  0
 L08  Var_01    C19   N1   C18  N20   -19.27  30.0  2
 L08  Var_02    C20   C19  N1   C18   154.81  30.0  1
 L08  Var_03    C21   C22  N1   C18  -155.90  30.0  1
 L08  Var_04    N2    C20  C19  N1     53.94  30.0  1
 L08  Var_05    N2    C21  C22  N1    -53.33  30.0  1
 L08  Var_06    C21   N2   C20  C19   -57.52  30.0  1
 L08  Var_07    C22   C21  N2   C20    57.36  30.0  1
 L08  Var_08    C2    C1   S1   C10   -68.75  30.0  2
 L08  Var_09    C33   C9   O7   C2   -175.24  30.0  3
 L08  Var_10    H241  C24  C23  N2     59.73  30.0  3
 L08  Var_11    H331  C33  C9   O7     60.40  30.0  3

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
 L08  plan-1  N3   0.020
 L08  plan-1  C11  0.020
 L08  plan-1  C10  0.020
 L08  plan-1  C15  0.020
 L08  plan-1  C14  0.020
 L08  plan-1  C13  0.020
 L08  plan-1  C12  0.020
 L08  plan-1  C16  0.020
 L08  plan-1  S1   0.020
 L08  plan-1  H15  0.020
 L08  plan-1  H14  0.020
 L08  plan-1  H12  0.020
 L08  plan-2  C13  0.020
 L08  plan-2  C16  0.020
 L08  plan-2  C8   0.020
 L08  plan-2  C35  0.020
 L08  plan-2  N20  0.020
 L08  plan-2  C18  0.020
 L08  plan-2  N1   0.020
 L08  plan-2  C17  0.020
 L08  plan-2  H8   0.020
 L08  plan-2  H35  0.020
 L08  plan-2  H17  0.020
 L08  plan-3  S1   0.020
 L08  plan-3  C1   0.020
 L08  plan-3  C2   0.020
 L08  plan-3  C3   0.020
 L08  plan-3  C4   0.020
 L08  plan-3  C5   0.020
 L08  plan-3  C6   0.020
 L08  plan-3  O7   0.020
 L08  plan-3  H3   0.020
 L08  plan-3  H4   0.020
 L08  plan-3  H5   0.020
 L08  plan-3  H6   0.020
 L08  plan-4  O4   0.020
 L08  plan-4  N3   0.020
 L08  plan-4  C11  0.020
 L08  plan-4  O3   0.020
 L08  plan-5  C20  0.020
 L08  plan-5  N2   0.020
 L08  plan-5  C21  0.020
 L08  plan-5  C23  0.020
 L08  plan-5  O2   0.020
 L08  plan-5  C24  0.020

