# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 00:47:43 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2R)-2-{4-hydroxy-5-methoxy-2-[3-(4-methylpiperazin-1-yl)propyl]phenyl}-3-(pyridin-3-yl)-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc([C@H]2SCC(=O)N2c3cccnc3)c(CCCN4CCN(C)CC4)cc1O
#
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
 096  096  (2R)-2-{4-hydroxy-5-methoxy-2-[3-(4-methylpiperazin-1-yl)propyl]phenyl}-3-(pyridin-3-yl)-1,3-thiazolidin-4-one  ligand  61  31  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_096
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
 096  S     S  S2    0   0.040  -2.7940  -1.3436   2.6593
 096  C1    C  CH3   0  -0.433  -5.4377   1.5362  -0.9325
 096  N1    N  NT    0  -0.549  -1.5891  -1.6980   0.3670
 096  C2    C  CR6   0   0.291  -3.3650   2.1977   0.0196
 096  N2    N  N     0  -0.403  -0.1242  -0.4681  -2.7637
 096  O2    O  O     0  -0.456  -2.2702  -3.7607  -0.2962
 096  C3    C  CR16  0  -0.387  -3.0377   0.9316   0.4528
 096  N3    N  NT    0  -0.410   3.8012   0.2476   0.4327
 096  C4    C  CR6   0   0.089  -1.8055   0.6661   1.0616
 096  N4    N  NT    0  -0.410   6.1830  -0.1652  -1.0933
 096  C5    C  CH1   0  -0.349  -1.5227  -0.7535   1.4756
 096  C6    C  CH2   0  -0.674  -2.9299  -2.9634   1.8752
 096  C7    C  C     0   0.552  -2.2487  -2.8726   0.5295
 096  C8    C  CR6   0   0.203  -0.6762  -1.5365  -0.7043
 096  C9    C  CR16  0  -0.156   0.5454  -2.1950  -0.6938
 096  C10   C  CR16  0  -0.309   1.4274  -1.9664  -1.7353
 096  C11   C  CR16  0  -0.064   1.0494  -1.0890  -2.7406
 096  C12   C  CR16  0  -0.049  -0.9692  -0.6923  -1.7671
 096  C13   C  CR6   0   0.117  -0.8919   1.6981   1.2553
 096  C14   C  CH2   0  -0.550   0.4844   1.5095   1.8390
 096  C15   C  CH2   0  -0.448   1.4935   1.0822   0.7734
 096  C16   C  CH2   0  -0.249   2.9056   0.9556   1.3257
 096  C17   C  CH2   0  -0.284   5.0723  -0.0280   1.0715
 096  C18   C  CH2   0  -0.283   5.9623  -0.8524   0.1628
 096  C19   C  CH3   0  -0.518   7.0650  -0.9097  -1.9607
 096  C20   C  CH2   0  -0.284   4.9146   0.1161  -1.7336
 096  C21   C  CH2   0  -0.286   4.0149   0.9327  -0.8261
 096  C22   C  CR16  0  -0.401  -1.2424   2.9828   0.8276
 096  C23   C  CR6   0   0.297  -2.4499   3.2478   0.2151
 096  H1    H  HCH3  0   0.231  -5.8242   1.0225  -0.0488
 096  H1A   H  HCH3  0   0.265  -6.2628   2.0236  -1.4451
 096  H1B   H  HCH3  0   0.230  -4.9900   0.7983  -1.6037
 096  H3    H  HCR6  0   0.280  -3.7404   0.1169   0.3294
 096  HO3   H  HOH1  0   0.474  -3.5950   4.5301  -0.6103
 096  H5    H  HCH1  0   0.301  -0.5406  -0.8302   1.9444
 096  H6    H  HCH2  0   0.311  -2.4383  -3.7433   2.4596
 096  H6A   H  HCH2  0   0.315  -3.9760  -3.2397   1.7491
 096  H9    H  HCR6  0   0.287   0.8050  -2.8591   0.1210
 096  H10   H  HCR6  0   0.273   2.3934  -2.4501  -1.7659
 096  H11   H  HCR6  0   0.271   1.7243  -0.8820  -3.5636
 096  H12   H  HCR6  0   0.273  -1.9247  -0.1808  -1.8067
 096  H14   H  HCH2  0   0.254   0.8072   2.4541   2.2846
 096  H14A  H  HCH2  0   0.245   0.4796   0.7861   2.6578
 096  H15   H  HCH2  0   0.242   1.2030   0.1185   0.3518
 096  H15A  H  HCH2  0   0.233   1.4592   1.7999  -0.0504
 096  H16   H  HCH2  0   0.222   2.8670   0.3904   2.2626
 096  H16A  H  HCH2  0   0.186   3.2930   1.9571   1.5870
 096  H17   H  HCH2  0   0.185   5.6016   0.9002   1.3519
 096  H17A  H  HCH2  0   0.233   4.8923  -0.5825   1.9961
 096  H18   H  HCH2  0   0.186   5.5013  -1.8440   0.0068
 096  H18A  H  HCH2  0   0.233   6.9241  -1.0201   0.6542
 096  H19   H  HCH3  0   0.232   7.2536  -0.3484  -2.8774
 096  H19A  H  HCH3  0   0.232   8.0233  -1.0764  -1.4663
 096  H19B  H  HCH3  0   0.190   6.6604  -1.8933  -2.2476
 096  H20   H  HCH2  0   0.233   5.0942   0.6727  -2.6568
 096  H20A  H  HCH2  0   0.189   4.3889  -0.8139  -2.0158
 096  H21   H  HCH2  0   0.237   3.0606   1.0780  -1.3351
 096  H21A  H  HCH2  0   0.186   4.4574   1.9339  -0.6740
 096  H22   H  HCR6  0   0.257  -0.5441   3.8000   0.9702
 096  O1    O  O2    0  -0.489  -4.5175   2.5526  -0.5886
 096  O3    O  OH1   0  -0.627  -2.7314   4.5027  -0.1801

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
 096  S    C6    single    1.805  0.020  1.805
 096  S    C5    single    1.835  0.020  1.835
 096  C1   O1    single    1.414  0.020  1.414
 096  C1   H1    single    0.970  0.020  1.090
 096  C1   H1A   single    0.970  0.020  1.090
 096  C1   H1B   single    0.970  0.020  1.090
 096  C8   N1    single    1.417  0.020  1.417
 096  N1   C7    single    1.357  0.020  1.357
 096  N1   C5    single    1.458  0.020  1.458
 096  O1   C2    single    1.351  0.020  1.351
 096  C2   C23   aromatic  1.407  0.020  1.407
 096  C2   C3    aromatic  1.378  0.020  1.378
 096  C11  N2    aromatic  1.328  0.020  1.328
 096  N2   C12   aromatic  1.326  0.020  1.326
 096  O2   C7    double    1.213  0.020  1.213
 096  C3   C4    aromatic  1.400  0.020  1.400
 096  C3   H3    single    0.930  0.020  1.080
 096  C21  N3    single    1.449  0.020  1.449
 096  C17  N3    single    1.449  0.020  1.449
 096  N3   C16   single    1.449  0.020  1.449
 096  O3   C23   single    1.345  0.020  1.345
 096  O3   HO3   single    0.850  0.020  0.980
 096  C4   C13   aromatic  1.392  0.020  1.392
 096  C4   C5    single    1.506  0.020  1.506
 096  C19  N4    single    1.444  0.020  1.444
 096  C18  N4    single    1.449  0.020  1.449
 096  N4   C20   single    1.448  0.020  1.448
 096  C5   H5    single    0.970  0.020  1.090
 096  C7   C6    single    1.511  0.020  1.511
 096  C6   H6    single    0.970  0.020  1.090
 096  C6   H6A   single    0.970  0.020  1.090
 096  C9   C8    aromatic  1.388  0.020  1.388
 096  C8   C12   aromatic  1.389  0.020  1.389
 096  C10  C9    aromatic  1.384  0.020  1.384
 096  C9   H9    single    0.930  0.020  1.080
 096  C10  C11   aromatic  1.387  0.020  1.387
 096  C10  H10   single    0.930  0.020  1.080
 096  C11  H11   single    0.930  0.020  1.080
 096  C12  H12   single    0.930  0.020  1.080
 096  C22  C13   aromatic  1.399  0.020  1.399
 096  C13  C14   single    1.507  0.020  1.507
 096  C15  C14   single    1.528  0.020  1.528
 096  C14  H14   single    0.970  0.020  1.090
 096  C14  H14A  single    0.970  0.020  1.090
 096  C15  C16   single    1.521  0.020  1.521
 096  C15  H15   single    0.970  0.020  1.090
 096  C15  H15A  single    0.970  0.020  1.090
 096  C16  H16   single    0.970  0.020  1.090
 096  C16  H16A  single    0.970  0.020  1.090
 096  C18  C17   single    1.516  0.020  1.516
 096  C17  H17   single    0.970  0.020  1.090
 096  C17  H17A  single    0.970  0.020  1.090
 096  C18  H18   single    0.970  0.020  1.090
 096  C18  H18A  single    0.970  0.020  1.090
 096  C19  H19   single    0.970  0.020  1.090
 096  C19  H19A  single    0.970  0.020  1.090
 096  C19  H19B  single    0.970  0.020  1.090
 096  C21  C20   single    1.517  0.020  1.517
 096  C20  H20   single    0.970  0.020  1.090
 096  C20  H20A  single    0.970  0.020  1.090
 096  C21  H21   single    0.970  0.020  1.090
 096  C21  H21A  single    0.970  0.020  1.090
 096  C23  C22   aromatic  1.380  0.020  1.380
 096  C22  H22   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
 096  C6    S    C5     93.47  3.000
 096  H1B   C1   H1A   108.91  3.000
 096  H1B   C1   H1    108.91  3.000
 096  H1A   C1   H1    108.89  3.000
 096  H1B   C1   O1    111.59  3.000
 096  H1A   C1   O1    106.65  3.000
 096  H1    C1   O1    111.80  3.000
 096  C8    N1   C7    120.16  3.000
 096  C7    N1   C5    119.47  3.000
 096  C8    N1   C5    118.16  3.000
 096  C23   C2   C3    119.20  3.000
 096  C3    C2   O1    125.86  3.000
 096  C23   C2   O1    114.94  3.000
 096  C12   N2   C11   118.11  3.000
 096  H3    C3   C4    118.56  3.000
 096  H3    C3   C2    120.09  3.000
 096  C4    C3   C2    121.35  3.000
 096  C21   N3   C17   110.09  3.000
 096  C17   N3   C16   111.30  3.000
 096  C21   N3   C16   113.29  3.000
 096  C13   C4   C5    122.52  3.000
 096  C5    C4   C3    117.63  3.000
 096  C13   C4   C3    119.85  3.000
 096  C20   N4   C19   111.69  3.000
 096  C20   N4   C18   110.00  3.000
 096  C19   N4   C18   111.67  3.000
 096  H5    C5   C4    110.70  3.000
 096  H5    C5   N1    108.80  3.000
 096  C4    C5   N1    113.16  3.000
 096  H5    C5   S     108.90  3.000
 096  C4    C5   S     110.52  3.000
 096  N1    C5   S     104.52  3.000
 096  H6A   C6   H6    108.25  3.000
 096  H6A   C6   C7    110.19  3.000
 096  H6    C6   C7    108.47  3.000
 096  H6A   C6   S     110.50  3.000
 096  H6    C6   S     112.01  3.000
 096  C7    C6   S     107.40  3.000
 096  C6    C7   O2    123.66  3.000
 096  C6    C7   N1    112.20  3.000
 096  O2    C7   N1    124.12  3.000
 096  C12   C8   C9    118.69  3.000
 096  C12   C8   N1    120.80  3.000
 096  C9    C8   N1    120.49  3.000
 096  H9    C9   C10   120.98  3.000
 096  H9    C9   C8    120.52  3.000
 096  C10   C9   C8    118.49  3.000
 096  H10   C10  C11   120.42  3.000
 096  H10   C10  C9    121.14  3.000
 096  C11   C10  C9    118.45  3.000
 096  H11   C11  C10   120.09  3.000
 096  H11   C11  N2    116.59  3.000
 096  C10   C11  N2    123.32  3.000
 096  H12   C12  C8    120.04  3.000
 096  H12   C12  N2    117.03  3.000
 096  C8    C12  N2    122.93  3.000
 096  C22   C13  C14   117.54  3.000
 096  C14   C13  C4    124.10  3.000
 096  C22   C13  C4    118.30  3.000
 096  H14A  C14  H14   105.54  3.000
 096  H14A  C14  C15   109.89  3.000
 096  H14   C14  C15   109.32  3.000
 096  H14A  C14  C13   111.66  3.000
 096  H14   C14  C13   108.63  3.000
 096  C15   C14  C13   111.59  3.000
 096  H15A  C15  H15   106.28  3.000
 096  H15A  C15  C16   110.94  3.000
 096  H15   C15  C16   108.29  3.000
 096  H15A  C15  C14   108.73  3.000
 096  H15   C15  C14   109.90  3.000
 096  C16   C15  C14   112.52  3.000
 096  H16A  C16  H16   106.13  3.000
 096  H16A  C16  C15   109.62  3.000
 096  H16   C16  C15   108.71  3.000
 096  H16A  C16  N3    111.82  3.000
 096  H16   C16  N3    107.27  3.000
 096  C15   C16  N3    112.99  3.000
 096  H17A  C17  H17   106.89  3.000
 096  H17A  C17  C18   109.14  3.000
 096  H17   C17  C18   109.14  3.000
 096  H17A  C17  N3    108.96  3.000
 096  H17   C17  N3    111.86  3.000
 096  C18   C17  N3    110.74  3.000
 096  H18A  C18  H18   107.04  3.000
 096  H18A  C18  C17   109.31  3.000
 096  H18   C18  C17   109.14  3.000
 096  H18A  C18  N4    109.19  3.000
 096  H18   C18  N4    111.53  3.000
 096  C17   C18  N4    110.57  3.000
 096  H19B  C19  H19A  107.71  3.000
 096  H19B  C19  H19   107.70  3.000
 096  H19A  C19  H19   107.90  3.000
 096  H19B  C19  N4    113.11  3.000
 096  H19A  C19  N4    110.06  3.000
 096  H19   C19  N4    110.18  3.000
 096  H20A  C20  H20   106.93  3.000
 096  H20A  C20  C21   108.89  3.000
 096  H20   C20  C21   109.20  3.000
 096  H20A  C20  N4    111.48  3.000
 096  H20   C20  N4    109.17  3.000
 096  C21   C20  N4    111.07  3.000
 096  H21A  C21  H21   107.08  3.000
 096  H21A  C21  C20   109.43  3.000
 096  H21   C21  C20   108.14  3.000
 096  H21A  C21  N3    111.59  3.000
 096  H21   C21  N3    109.83  3.000
 096  C20   C21  N3    110.66  3.000
 096  H22   C22  C23   118.51  3.000
 096  H22   C22  C13   119.38  3.000
 096  C23   C22  C13   122.11  3.000
 096  C22   C23  O3    119.52  3.000
 096  C22   C23  C2    119.20  3.000
 096  O3    C23  C2    121.29  3.000
 096  C2    O1   C1    118.43  3.000
 096  HO3   O3   C23   110.16  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
 096  CONST_01  C13  C22  C23  C2      0.00   0.0  0
 096  CONST_02  C13  C4   C3   C2      0.00   0.0  0
 096  CONST_03  C9   C10  C11  N2      0.00   0.0  0
 096  CONST_04  C9   C8   C12  N2      0.00   0.0  0
 096  CONST_05  C22  C23  C2   C3      0.00   0.0  0
 096  CONST_06  C22  C13  C4   C3      0.00   0.0  0
 096  CONST_07  C23  C2   C3   C4      0.00   0.0  0
 096  CONST_08  C23  C22  C13  C4      0.00   0.0  0
 096  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 096  CONST_10  C11  N2   C12  C8      0.00   0.0  0
 096  CONST_11  C12  C8   C9   C10     0.00   0.0  0
 096  CONST_12  C12  N2   C11  C10     0.00   0.0  0
 096  CONST_13  C10  C9   C8   N1    180.00   0.0  0
 096  CONST_14  N2   C12  C8   N1    180.00   0.0  0
 096  CONST_15  C5   C4   C3   C2    180.00   0.0  0
 096  CONST_16  C22  C13  C4   C5    180.00   0.0  0
 096  CONST_17  C6   C7   N1   C5      0.00   0.0  0
 096  CONST_18  C8   N1   C7   C6    180.00   0.0  0
 096  CONST_19  C22  C23  C2   O1    180.00   0.0  0
 096  CONST_20  C4   C3   C2   O1    180.00   0.0  0
 096  CONST_21  O3   C23  C2   C3    180.00   0.0  0
 096  CONST_22  C14  C13  C4   C3    180.00   0.0  0
 096  CONST_23  C13  C22  C23  O3    180.00   0.0  0
 096  CONST_24  C14  C13  C4   C5      0.00   0.0  0
 096  CONST_25  C23  C22  C13  C14   180.00   0.0  0
 096  CONST_26  C8   N1   C7   O2      0.00   0.0  0
 096  CONST_27  C5   N1   C7   O2    180.00   0.0  0
 096  CONST_28  H9   C9   C8   N1      0.00   0.0  0
 096  CONST_29  H12  C12  C8   N1      0.00   0.0  0
 096  CONST_30  H22  C22  C23  C2    180.00   0.0  0
 096  CONST_31  H10  C10  C11  N2    180.00   0.0  0
 096  CONST_32  H3   C3   C4   C5      0.00   0.0  0
 096  CONST_33  H11  C11  C10  C9    180.00   0.0  0
 096  Var_01    N1   C7   C6   S       8.18  30.0  1
 096  Var_02    N4   C20  C21  N3    -57.16  30.0  1
 096  Var_03    N4   C18  C17  N3     58.05  30.0  1
 096  Var_04    C7   C6   S    C5    -13.93  30.0  1
 096  Var_05    C9   C8   N1   C5     91.67  30.0  3
 096  Var_06    C20  C21  N3   C17    56.88  30.0  1
 096  Var_07    C20  N4   C18  C17   -57.33  30.0  1
 096  Var_08    C21  C20  N4   C18    57.06  30.0  1
 096  Var_09    C21  N3   C17  C18   -57.49  30.0  1
 096  Var_10    C23  C2   O1   C1    174.29  30.0  2
 096  Var_11    C15  C14  C13  C4     84.25  30.0  2
 096  Var_12    H19  C19  N4   C18  -177.20  30.0  3
 096  Var_13    C14  C15  C16  N3    165.80  30.0  1
 096  Var_14    C16  C15  C14  C13   177.03  30.0  1
 096  Var_15    H1   C1   O1   C2     63.62  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
 096  chir_01  C5  S  N1  C4  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
 096  plan-1  C2   0.020
 096  plan-1  C3   0.020
 096  plan-1  C4   0.020
 096  plan-1  C5   0.020
 096  plan-1  C13  0.020
 096  plan-1  C14  0.020
 096  plan-1  C22  0.020
 096  plan-1  C23  0.020
 096  plan-1  H3   0.020
 096  plan-1  H22  0.020
 096  plan-1  O1   0.020
 096  plan-1  O3   0.020
 096  plan-2  N1   0.020
 096  plan-2  N2   0.020
 096  plan-2  C8   0.020
 096  plan-2  C9   0.020
 096  plan-2  C10  0.020
 096  plan-2  C11  0.020
 096  plan-2  C12  0.020
 096  plan-2  H9   0.020
 096  plan-2  H10  0.020
 096  plan-2  H11  0.020
 096  plan-2  H12  0.020
 096  plan-3  N1   0.020
 096  plan-3  O2   0.020
 096  plan-3  C5   0.020
 096  plan-3  C6   0.020
 096  plan-3  C7   0.020
 096  plan-3  C8   0.020

