# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 07:12:57 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N-{6-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]imidazo[1,2-a]pyridin-2-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cn2cc(ccc2n1)\C=C3/SC(=O)NC3=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
 ZW3  ZW3  N-{6-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]imidazo[1,2-a]pyridin-2-yl}acetamide  ligand  31  21  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZW3
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
 ZW3  C1    C  CH3   0  -0.805   6.7505   1.6619   0.1162
 ZW3  C2    C  C     0   0.582   5.2568   1.4967   0.1977
 ZW3  O3    O  O     0  -0.577   4.4922   2.3903   0.5099
 ZW3  N4    N  NH1   0  -0.681   4.8199   0.2457  -0.1096
 ZW3  C5    C  CR5   0   0.322   3.5096  -0.1852  -0.0855
 ZW3  C6    C  CR15  0  -0.122   2.3608   0.5004   0.2327
 ZW3  N7    N  N     0  -0.442   1.3617  -0.4369   0.0855
 ZW3  C8    C  CR16  0   0.023   0.0270  -0.3204   0.2741
 ZW3  C9    C  CR6   0  -0.112  -0.7921  -1.3989   0.0667
 ZW3  C10   C  C1    0  -0.206  -2.2315  -1.3435   0.2357
 ZW3  C11   C  CR5   0  -0.306  -3.0550  -0.2870   0.1976
 ZW3  S12   S  S2    0   0.092  -2.6590   1.3907  -0.1249
 ZW3  C13   C  CR5   0   0.423  -4.3712   1.8669  -0.0523
 ZW3  O14   O  O     0  -0.363  -4.7576   2.9881  -0.2195
 ZW3  N15   N  NR15  0  -0.667  -5.1378   0.7677   0.2184
 ZW3  C16   C  CR5   0   0.609  -4.5172  -0.4493   0.3795
 ZW3  O17   O  O     0  -0.482  -5.0958  -1.4809   0.6176
 ZW3  C18   C  CR16  0  -0.150  -0.2015  -2.6396  -0.3156
 ZW3  C19   C  CR16  0  -0.434   1.1411  -2.7511  -0.5056
 ZW3  C20   C  CR56  0   0.570   1.9598  -1.6228  -0.3060
 ZW3  N21   N  N     0  -0.427   3.2633  -1.4761  -0.4120
 ZW3  H11C  H  HCH3  0   0.308   7.0304   2.6808   0.3675
 ZW3  H12C  H  HCH3  0   0.268   7.2498   0.9802   0.8063
 ZW3  H13C  H  HCH3  0   0.277   7.1123   1.4336  -0.8871
 ZW3  H4    H  HNH1  0   0.430   5.4978  -0.4585  -0.3613
 ZW3  H6    H  HCR5  0   0.323   2.1553   1.5114   0.5281
 ZW3  H8    H  HCR6  0   0.265  -0.3043   0.6430   0.6328
 ZW3  H10   H  H     0   0.315  -2.7157  -2.3029   0.3871
 ZW3  H18   H  HCR6  0   0.281  -0.8421  -3.4991  -0.4631
 ZW3  H15   H  HNR5  0   0.426  -6.1439   0.8578   0.2918
 ZW3  H19   H  HCR6  0   0.260   1.5990  -3.6835  -0.8015

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
 ZW3  C1   C2    single    1.505  0.020  1.505
 ZW3  C2   O3    double    1.217  0.020  1.217
 ZW3  C2   N4    single    1.360  0.020  1.360
 ZW3  N4   C5    single    1.380  0.020  1.380
 ZW3  C5   C6    aromatic  1.375  0.020  1.375
 ZW3  C5   N21   aromatic  1.354  0.020  1.354
 ZW3  C6   N7    aromatic  1.378  0.020  1.378
 ZW3  N7   C8    aromatic  1.353  0.020  1.353
 ZW3  N7   C20   aromatic  1.385  0.020  1.385
 ZW3  C8   C9    aromatic  1.370  0.020  1.370
 ZW3  C9   C10   single    1.450  0.020  1.450
 ZW3  C9   C18   aromatic  1.426  0.020  1.426
 ZW3  C10  C11   double    1.340  0.020  1.340
 ZW3  C11  S12   single    1.754  0.020  1.754
 ZW3  C11  C16   single    1.482  0.020  1.482
 ZW3  S12  C13   single    1.779  0.020  1.779
 ZW3  C13  O14   double    1.198  0.020  1.198
 ZW3  C13  N15   single    1.367  0.020  1.367
 ZW3  N15  C16   single    1.376  0.020  1.376
 ZW3  C16  O17   double    1.206  0.020  1.206
 ZW3  C18  C19   aromatic  1.361  0.020  1.361
 ZW3  C19  C20   aromatic  1.408  0.020  1.408
 ZW3  C20  N21   aromatic  1.316  0.020  1.316
 ZW3  C1   H11C  single    0.970  0.020  1.090
 ZW3  C1   H12C  single    0.970  0.020  1.090
 ZW3  C1   H13C  single    0.970  0.020  1.090
 ZW3  N4   H4    single    0.860  0.020  1.020
 ZW3  C6   H6    single    0.930  0.020  1.080
 ZW3  C8   H8    single    0.930  0.020  1.080
 ZW3  C10  H10   single    0.930  0.020  1.080
 ZW3  C18  H18   single    0.930  0.020  1.080
 ZW3  N15  H15   single    0.860  0.020  1.020
 ZW3  C19  H19   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
 ZW3  H13C  C1   H12C  107.41  3.000
 ZW3  H13C  C1   H11C  108.89  3.000
 ZW3  H12C  C1   H11C  108.77  3.000
 ZW3  H13C  C1   C2    110.86  3.000
 ZW3  H12C  C1   C2    110.58  3.000
 ZW3  H11C  C1   C2    110.25  3.000
 ZW3  N4    C2   O3    122.11  3.000
 ZW3  N4    C2   C1    114.05  3.000
 ZW3  O3    C2   C1    123.85  3.000
 ZW3  H4    N4   C5    115.10  3.000
 ZW3  H4    N4   C2    118.84  3.000
 ZW3  C5    N4   C2    126.04  3.000
 ZW3  N21   C5   C6    112.28  3.000
 ZW3  N21   C5   N4    117.80  3.000
 ZW3  C6    C5   N4    129.92  3.000
 ZW3  H6    C6   N7    122.11  3.000
 ZW3  H6    C6   C5    133.89  3.000
 ZW3  N7    C6   C5    103.99  3.000
 ZW3  C20   N7   C8    122.63  3.000
 ZW3  C20   N7   C6    107.44  3.000
 ZW3  C8    N7   C6    129.93  3.000
 ZW3  H8    C8   C9    124.68  3.000
 ZW3  H8    C8   N7    115.19  3.000
 ZW3  C9    C8   N7    120.06  3.000
 ZW3  C18   C9   C10   118.39  3.000
 ZW3  C18   C9   C8    118.54  3.000
 ZW3  C10   C9   C8    123.07  3.000
 ZW3  H10   C10  C11   115.26  3.000
 ZW3  H10   C10  C9    115.16  3.000
 ZW3  C11   C10  C9    129.55  3.000
 ZW3  C16   C11  S12   110.49  3.000
 ZW3  C16   C11  C10   121.09  3.000
 ZW3  S12   C11  C10   128.37  3.000
 ZW3  C13   S12  C11    91.79  3.000
 ZW3  N15   C13  O14   126.83  3.000
 ZW3  N15   C13  S12   109.43  3.000
 ZW3  O14   C13  S12   123.75  3.000
 ZW3  H15   N15  C16   121.23  3.000
 ZW3  H15   N15  C13   119.99  3.000
 ZW3  C16   N15  C13   118.78  3.000
 ZW3  O17   C16  N15   124.28  3.000
 ZW3  O17   C16  C11   126.22  3.000
 ZW3  N15   C16  C11   109.50  3.000
 ZW3  H18   C18  C19   120.00  3.000
 ZW3  H18   C18  C9    118.84  3.000
 ZW3  C19   C18  C9    121.16  3.000
 ZW3  H19   C19  C20   118.95  3.000
 ZW3  H19   C19  C18   121.83  3.000
 ZW3  C20   C19  C18   119.22  3.000
 ZW3  N21   C20  C19   130.83  3.000
 ZW3  N21   C20  N7    110.80  3.000
 ZW3  C19   C20  N7    118.37  3.000
 ZW3  C20   N21  C5    105.49  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
 ZW3  CONST_01  C8    N7   C6   C5   180.00   0.0  0
 ZW3  CONST_02  C20   N7   C6   C5     0.00   0.0  0
 ZW3  CONST_03  N7    C20  N21  C5     0.00   0.0  0
 ZW3  CONST_04  C19   C20  N21  C5   180.00   0.0  0
 ZW3  CONST_05  C20   N21  C5   C6     0.00   0.0  0
 ZW3  CONST_06  C9    C8   N7   C6   180.00   0.0  0
 ZW3  CONST_07  C19   C20  N7   C6   180.00   0.0  0
 ZW3  CONST_08  N21   C20  N7   C6     0.00   0.0  0
 ZW3  CONST_09  N21   C5   C6   N7     0.00   0.0  0
 ZW3  CONST_10  C18   C9   C8   N7     0.00   0.0  0
 ZW3  CONST_11  C18   C19  C20  N7     0.00   0.0  0
 ZW3  CONST_12  C19   C20  N7   C8     0.00   0.0  0
 ZW3  CONST_13  N21   C20  N7   C8   180.00   0.0  0
 ZW3  CONST_14  C19   C18  C9   C8     0.00   0.0  0
 ZW3  CONST_15  C20   N7   C8   C9     0.00   0.0  0
 ZW3  CONST_16  C20   C19  C18  C9     0.00   0.0  0
 ZW3  CONST_17  N21   C20  C19  C18  180.00   0.0  0
 ZW3  CONST_18  C13   N15  C16  C11    0.00   0.0  0
 ZW3  CONST_19  N7    C6   C5   N4   180.00   0.0  0
 ZW3  CONST_20  C20   N21  C5   N4   180.00   0.0  0
 ZW3  CONST_21  C10   C9   C8   N7   180.00   0.0  0
 ZW3  CONST_22  C19   C18  C9   C10  180.00   0.0  0
 ZW3  CONST_23  O17   C16  N15  C13  180.00   0.0  0
 ZW3  CONST_24  H8    C8   N7   C6     0.00   0.0  0
 ZW3  CONST_25  H19   C19  C20  N7   180.00   0.0  0
 ZW3  CONST_26  H6    C6   N7   C8     0.00   0.0  0
 ZW3  CONST_27  H18   C18  C9   C8   180.00   0.0  0
 ZW3  CONST_28  H15   N15  C16  C11  180.00   0.0  0
 ZW3  CONST_29  C6    C5   N4   C2     0.00   0.0  0
 ZW3  CONST_30  N21   C5   N4   C2   180.00   0.0  0
 ZW3  CONST_31  H4    N4   C5   C6   180.00   0.0  0
 ZW3  CONST_32  C5    N4   C2   C1   180.00   0.0  0
 ZW3  CONST_33  C5    N4   C2   O3     0.00   0.0  0
 ZW3  Var_01    C11   C10  C9   C8    22.66  30.0  2
 ZW3  Var_02    S12   C11  C10  C9     2.19  30.0  2
 ZW3  Var_03    H11C  C1   C2   O3    -0.36  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
 ZW3  plan-1  C10  0.020
 ZW3  plan-1  C11  0.020
 ZW3  plan-1  S12  0.020
 ZW3  plan-1  C13  0.020
 ZW3  plan-1  O14  0.020
 ZW3  plan-1  N15  0.020
 ZW3  plan-1  C16  0.020
 ZW3  plan-1  O17  0.020
 ZW3  plan-1  H15  0.020
 ZW3  plan-2  N4   0.020
 ZW3  plan-2  C5   0.020
 ZW3  plan-2  C6   0.020
 ZW3  plan-2  N7   0.020
 ZW3  plan-2  C8   0.020
 ZW3  plan-2  C9   0.020
 ZW3  plan-2  C10  0.020
 ZW3  plan-2  C18  0.020
 ZW3  plan-2  C19  0.020
 ZW3  plan-2  C20  0.020
 ZW3  plan-2  N21  0.020
 ZW3  plan-2  H6   0.020
 ZW3  plan-2  H8   0.020
 ZW3  plan-2  H18  0.020
 ZW3  plan-2  H19  0.020
 ZW3  plan-3  C1   0.020
 ZW3  plan-3  C2   0.020
 ZW3  plan-3  O3   0.020
 ZW3  plan-3  N4   0.020
 ZW3  plan-3  C5   0.020
 ZW3  plan-3  H4   0.020

