# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:33:02 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (5Z)-5-{2-[(3R)-3-aminopiperidin-1-yl]-3-(propan-2-yloxy)benzylidene}-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1cccc(\C=C2/SC(=O)NC2=O)c1N3CCC[C@@H](N)C3
#
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
 7LI  7LI  (5Z)-5-{2-[(3R)-3-aminopiperidin-1-yl]-3-(propan-2-yloxy)benzylidene}-1,3-thiazolidine-2,4-dione  ligand  48  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7LI
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
 7LI  C     C  CH3   0  -0.680   3.9344   3.2306  -1.2083
 7LI  N     N  NT    0  -0.505   1.4435  -0.7105   0.0490
 7LI  O     O  O2    0  -0.468   3.1532   1.4407   0.2329
 7LI  S     S  S2    0   0.099  -3.4599   0.8462  -0.5881
 7LI  C1    C  CH1   0  -0.002   4.1038   2.5025   0.1148
 7LI  N1    N  NH2   0  -0.793   3.4897  -3.4415   1.4867
 7LI  O1    O  O     0  -0.409  -2.8502  -2.8140   0.4086
 7LI  C2    C  CH3   0  -0.661   5.4685   1.8554   0.2413
 7LI  N2    N  NR15  0  -0.684  -4.4688  -1.5285  -0.5645
 7LI  O2    O  O     0  -0.396  -5.8214   0.0805  -1.4832
 7LI  C3    C  CR6   0   0.404   1.8625   1.6844   0.4997
 7LI  C4    C  CR16  0  -0.391   1.3492   2.9320   0.8474
 7LI  C5    C  CR16  0  -0.237  -0.0116   3.0880   1.0787
 7LI  C6    C  CR16  0  -0.353  -0.8771   2.0195   0.9571
 7LI  C7    C  CR6   0   0.069  -0.3731   0.7582   0.6233
 7LI  C8    C  CR6   0   0.164   1.0006   0.5755   0.4070
 7LI  C9    C  CH2   0  -0.284   1.4795  -1.0042  -1.3749
 7LI  C10   C  CH2   0  -0.440   1.3977  -2.5061  -1.5956
 7LI  C11   C  CH2   0  -0.447   2.4813  -3.2275  -0.8025
 7LI  C12   C  CH1   0  -0.095   2.4368  -2.8455   0.6769
 7LI  C13   C  CH2   0  -0.268   2.5126  -1.3266   0.8121
 7LI  C14   C  C1    0  -0.221  -1.2321  -0.4120   0.5172
 7LI  C15   C  CR5   0  -0.301  -2.4952  -0.4633   0.0782
 7LI  C16   C  CR5   0   0.633  -3.2418  -1.7400   0.0194
 7LI  C17   C  CR5   0   0.419  -4.7954  -0.2615  -0.9638
 7LI  H     H  HCH3  0   0.239   4.6781   4.0232  -1.2928
 7LI  HA    H  HCH3  0   0.232   4.0725   2.5442  -2.0452
 7LI  HB    H  HCH3  0   0.241   2.9518   3.6931  -1.3066
 7LI  H1    H  HCH1  0   0.230   3.9763   3.2056   0.9452
 7LI  HN1   H  HNH2  0   0.345   3.4367  -4.4504   1.4107
 7LI  HN1A  H  HNH2  0   0.334   4.3917  -3.1912   1.0959
 7LI  H2    H  HCH3  0   0.234   6.2462   2.6146   0.1650
 7LI  H2A   H  HCH3  0   0.239   5.5795   1.3553   1.2034
 7LI  H2B   H  HCH3  0   0.229   5.6316   1.1219  -0.5501
 7LI  HN2   H  HNR5  0   0.440  -5.1231  -2.2892  -0.7042
 7LI  H4    H  HCR6  0   0.283   1.9926   3.7968   0.9303
 7LI  H5    H  HCR6  0   0.265  -0.3912   4.0620   1.3568
 7LI  H6    H  HCR6  0   0.256  -1.9273   2.1587   1.1768
 7LI  H9    H  HCH2  0   0.241   0.6352  -0.5088  -1.8579
 7LI  H9A   H  HCH2  0   0.208   2.3969  -0.6102  -1.8413
 7LI  H10   H  HCH2  0   0.216   0.4109  -2.8597  -1.2802
 7LI  H10A  H  HCH2  0   0.231   1.4912  -2.7248  -2.6617
 7LI  H11   H  HCH2  0   0.231   2.3822  -4.3110  -0.9134
 7LI  H11A  H  HCH2  0   0.206   3.4671  -2.9570  -1.2017
 7LI  H12   H  HCH1  0   0.216   1.4761  -3.1716   1.0919
 7LI  H13   H  HCH2  0   0.203   3.5109  -1.0005   0.4841
 7LI  H13A  H  HCH2  0   0.237   2.4059  -1.0467   1.8618
 7LI  H14   H  H     0   0.289  -0.7837  -1.3584   0.7982

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
 7LI  C    C1    single    1.520  0.020  1.520
 7LI  N    C8    single    1.406  0.020  1.406
 7LI  N    C9    single    1.454  0.020  1.454
 7LI  N    C13   single    1.451  0.020  1.451
 7LI  O    C1    single    1.430  0.020  1.430
 7LI  O    C3    single    1.340  0.020  1.340
 7LI  S    C15   single    1.758  0.020  1.758
 7LI  S    C17   single    1.775  0.020  1.775
 7LI  C1   C2    single    1.516  0.020  1.516
 7LI  N1   C12   single    1.456  0.020  1.456
 7LI  O1   C16   double    1.208  0.020  1.208
 7LI  N2   C16   single    1.375  0.020  1.375
 7LI  N2   C17   single    1.368  0.020  1.368
 7LI  O2   C17   double    1.200  0.020  1.200
 7LI  C3   C4    aromatic  1.393  0.020  1.393
 7LI  C3   C8    aromatic  1.408  0.020  1.408
 7LI  C4   C5    aromatic  1.389  0.020  1.389
 7LI  C5   C6    aromatic  1.380  0.020  1.380
 7LI  C6   C7    aromatic  1.399  0.020  1.399
 7LI  C7   C8    aromatic  1.403  0.020  1.403
 7LI  C7   C14   single    1.456  0.020  1.456
 7LI  C9   C10   single    1.520  0.020  1.520
 7LI  C10  C11   single    1.524  0.020  1.524
 7LI  C11  C12   single    1.529  0.020  1.529
 7LI  C12  C13   single    1.527  0.020  1.527
 7LI  C14  C15   double    1.338  0.020  1.338
 7LI  C15  C16   single    1.480  0.020  1.480
 7LI  C    H     single    0.970  0.020  1.090
 7LI  C    HA    single    0.970  0.020  1.090
 7LI  C    HB    single    0.970  0.020  1.090
 7LI  C1   H1    single    0.970  0.020  1.090
 7LI  N1   HN1   single    0.890  0.020  1.040
 7LI  N1   HN1A  single    0.890  0.020  1.040
 7LI  C2   H2    single    0.970  0.020  1.090
 7LI  C2   H2A   single    0.970  0.020  1.090
 7LI  C2   H2B   single    0.970  0.020  1.090
 7LI  N2   HN2   single    0.860  0.020  1.020
 7LI  C4   H4    single    0.930  0.020  1.080
 7LI  C5   H5    single    0.930  0.020  1.080
 7LI  C6   H6    single    0.930  0.020  1.080
 7LI  C9   H9    single    0.970  0.020  1.090
 7LI  C9   H9A   single    0.970  0.020  1.090
 7LI  C10  H10   single    0.970  0.020  1.090
 7LI  C10  H10A  single    0.970  0.020  1.090
 7LI  C11  H11   single    0.970  0.020  1.090
 7LI  C11  H11A  single    0.970  0.020  1.090
 7LI  C12  H12   single    0.970  0.020  1.090
 7LI  C13  H13   single    0.970  0.020  1.090
 7LI  C13  H13A  single    0.970  0.020  1.090
 7LI  C14  H14   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
 7LI  HB    C    HA   108.16  3.000
 7LI  HB    C    H    107.42  3.000
 7LI  HA    C    H    108.15  3.000
 7LI  HB    C    C1   112.47  3.000
 7LI  HA    C    C1   110.62  3.000
 7LI  H     C    C1   109.87  3.000
 7LI  C13   N    C9   114.26  3.000
 7LI  C13   N    C8   119.11  3.000
 7LI  C9    N    C8   116.21  3.000
 7LI  C3    O    C1   121.44  3.000
 7LI  C17   S    C15   91.62  3.000
 7LI  H1    C1   C2   108.39  3.000
 7LI  H1    C1   O    109.66  3.000
 7LI  C2    C1   O    105.94  3.000
 7LI  H1    C1   C    109.84  3.000
 7LI  C2    C1   C    112.19  3.000
 7LI  O     C1   C    110.71  3.000
 7LI  HN1A  N1   HN1  105.26  3.000
 7LI  HN1A  N1   C12  109.14  3.000
 7LI  HN1   N1   C12  109.15  3.000
 7LI  H2B   C2   H2A  108.45  3.000
 7LI  H2B   C2   H2   108.12  3.000
 7LI  H2A   C2   H2   107.99  3.000
 7LI  H2B   C2   C1   111.16  3.000
 7LI  H2A   C2   C1   111.18  3.000
 7LI  H2    C2   C1   109.84  3.000
 7LI  HN2   N2   C17  120.07  3.000
 7LI  HN2   N2   C16  121.29  3.000
 7LI  C17   N2   C16  118.64  3.000
 7LI  C8    C3   C4   119.76  3.000
 7LI  C8    C3   O    115.68  3.000
 7LI  C4    C3   O    124.56  3.000
 7LI  H4    C4   C5   118.71  3.000
 7LI  H4    C4   C3   121.08  3.000
 7LI  C5    C4   C3   120.21  3.000
 7LI  H5    C5   C6   119.97  3.000
 7LI  H5    C5   C4   119.19  3.000
 7LI  C6    C5   C4   120.84  3.000
 7LI  H6    C6   C7   120.94  3.000
 7LI  H6    C6   C5   119.42  3.000
 7LI  C7    C6   C5   119.55  3.000
 7LI  C14   C7   C8   117.52  3.000
 7LI  C14   C7   C6   121.99  3.000
 7LI  C8    C7   C6   120.47  3.000
 7LI  C7    C8   C3   119.14  3.000
 7LI  C7    C8   N    117.82  3.000
 7LI  C3    C8   N    122.98  3.000
 7LI  H9A   C9   H9   107.12  3.000
 7LI  H9A   C9   C10  109.67  3.000
 7LI  H9    C9   C10  110.03  3.000
 7LI  H9A   C9   N    111.27  3.000
 7LI  H9    C9   N    108.81  3.000
 7LI  C10   C9   N    109.89  3.000
 7LI  H10A  C10  H10  107.08  3.000
 7LI  H10A  C10  C11  110.62  3.000
 7LI  H10   C10  C11  109.76  3.000
 7LI  H10A  C10  C9   109.57  3.000
 7LI  H10   C10  C9   109.02  3.000
 7LI  C11   C10  C9   110.72  3.000
 7LI  H11A  C11  H11  106.78  3.000
 7LI  H11A  C11  C12  108.45  3.000
 7LI  H11   C11  C12  110.07  3.000
 7LI  H11A  C11  C10  109.43  3.000
 7LI  H11   C11  C10  110.59  3.000
 7LI  C12   C11  C10  111.38  3.000
 7LI  H12   C12  C13  107.81  3.000
 7LI  H12   C12  C11  108.52  3.000
 7LI  C13   C12  C11  109.44  3.000
 7LI  H12   C12  N1   107.55  3.000
 7LI  C13   C12  N1   108.79  3.000
 7LI  C11   C12  N1   114.52  3.000
 7LI  H13A  C13  H13  107.41  3.000
 7LI  H13A  C13  C12  109.60  3.000
 7LI  H13   C13  C12  108.27  3.000
 7LI  H13A  C13  N    108.96  3.000
 7LI  H13   C13  N    112.71  3.000
 7LI  C12   C13  N    109.83  3.000
 7LI  H14   C14  C15  116.23  3.000
 7LI  H14   C14  C7   116.02  3.000
 7LI  C15   C14  C7   127.72  3.000
 7LI  C16   C15  C14  121.48  3.000
 7LI  C16   C15  S    110.53  3.000
 7LI  C14   C15  S    127.87  3.000
 7LI  C15   C16  N2   109.53  3.000
 7LI  C15   C16  O1   126.21  3.000
 7LI  N2    C16  O1   124.26  3.000
 7LI  O2    C17  N2   126.48  3.000
 7LI  O2    C17  S    123.86  3.000
 7LI  N2    C17  S    109.67  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
 7LI  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 7LI  CONST_02  C6   C7   C8   C3      0.00   0.0  0
 7LI  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 7LI  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 7LI  CONST_05  C8   C3   C4   C5      0.00   0.0  0
 7LI  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 7LI  CONST_07  C4   C3   C8   N     180.00   0.0  0
 7LI  CONST_08  C6   C7   C8   N     180.00   0.0  0
 7LI  CONST_09  C17  N2   C16  C15     0.00   0.0  0
 7LI  CONST_10  O    C3   C8   N       0.00   0.0  0
 7LI  CONST_11  C14  C7   C8   N       0.00   0.0  0
 7LI  CONST_12  C5   C4   C3   O     180.00   0.0  0
 7LI  CONST_13  C7   C8   C3   O     180.00   0.0  0
 7LI  CONST_14  C14  C7   C8   C3    180.00   0.0  0
 7LI  CONST_15  C14  C7   C6   C5    180.00   0.0  0
 7LI  CONST_16  C17  N2   C16  O1    180.00   0.0  0
 7LI  CONST_17  H5   C5   C4   C3    180.00   0.0  0
 7LI  CONST_18  H6   C6   C5   C4    180.00   0.0  0
 7LI  CONST_19  H4   C4   C5   C6    180.00   0.0  0
 7LI  CONST_20  HN2  N2   C16  C15   180.00   0.0  0
 7LI  Var_01    C11  C10  C9   N     -54.03  30.0  1
 7LI  Var_02    C9   N    C8   C3    -87.56  30.0  2
 7LI  Var_03    C10  C9   N    C8   -156.39  30.0  1
 7LI  Var_04    C12  C13  N    C8    156.12  30.0  1
 7LI  Var_05    C12  C11  C10  C9     53.76  30.0  1
 7LI  Var_06    C7   C14  C15  S       3.94  30.0  2
 7LI  Var_07    C15  C14  C7   C6     34.74  30.0  2
 7LI  Var_08    C4   C3   O    C1     -8.30  30.0  2
 7LI  Var_09    H1   C1   O    C3     46.29  30.0  3
 7LI  Var_10    H2   C2   C1   C      59.40  30.0  3
 7LI  Var_11    H    C    C1   O    -178.85  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
 7LI  chir_01  C12  N1  C11  C13  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
 7LI  plan-1  S    0.020
 7LI  plan-1  O1   0.020
 7LI  plan-1  N2   0.020
 7LI  plan-1  O2   0.020
 7LI  plan-1  C14  0.020
 7LI  plan-1  C15  0.020
 7LI  plan-1  C16  0.020
 7LI  plan-1  C17  0.020
 7LI  plan-1  HN2  0.020
 7LI  plan-2  N    0.020
 7LI  plan-2  O    0.020
 7LI  plan-2  C3   0.020
 7LI  plan-2  C4   0.020
 7LI  plan-2  C5   0.020
 7LI  plan-2  C6   0.020
 7LI  plan-2  C7   0.020
 7LI  plan-2  C8   0.020
 7LI  plan-2  C14  0.020
 7LI  plan-2  H4   0.020
 7LI  plan-2  H5   0.020
 7LI  plan-2  H6   0.020

