# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 16:16:42 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-{[4-amino-5-(pyridin-3-ylcarbonyl)-1,3-thiazol-2-yl]amino}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(Nc2sc(c(N)n2)C(=O)c3cccnc3)cc1
#
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
 08Z  08Z  4-{[4-amino-5-(pyridin-3-ylcarbonyl)-1,3-thiazol-2-yl]amino}benzamide  ligand  37  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_08Z
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
 08Z  C1    C  CR6   0   0.366   2.5390   0.6358  -0.1435
 08Z  N2    N  NH1   0  -0.760   1.1763   0.9095  -0.2301
 08Z  C3    C  CR5   0   0.363   0.1249   0.0823  -0.0874
 08Z  N4    N  N     0  -0.480   0.1986  -1.1968   0.1414
 08Z  C5    C  CR5   0   0.620  -1.0363  -1.7508   0.2347
 08Z  C6    C  CR5   0  -0.476  -2.1155  -0.8656   0.0934
 08Z  S7    S  S2    0   0.178  -1.4770   0.7426  -0.2080
 08Z  N8    N  NH2   0  -0.823  -1.1352  -3.0590   0.4471
 08Z  C9    C  C     0   0.368  -3.4912  -1.2135   0.1286
 08Z  C10   C  CR6   0  -0.131  -4.5057  -0.1213   0.0481
 08Z  C11   C  CR16  0  -0.180  -4.4623   1.0051   0.8618
 08Z  C12   C  CR16  0  -0.314  -5.4760   1.9444   0.7592
 08Z  C13   C  CR16  0  -0.059  -6.4903   1.7250  -0.1594
 08Z  N14   N  N     0  -0.400  -6.5475   0.6499  -0.9394
 08Z  C15   C  CR16  0  -0.071  -5.5845  -0.2519  -0.8245
 08Z  O16   O  O     0  -0.463  -3.8782  -2.3827   0.2103
 08Z  C17   C  CR16  0  -0.339   3.4034   1.7264  -0.2868
 08Z  C18   C  CR16  0  -0.258   4.7693   1.5535  -0.2176
 08Z  C19   C  CR6   0  -0.052   5.3222   0.2939   0.0121
 08Z  C20   C  CR16  0  -0.271   4.4547  -0.7861   0.1439
 08Z  C21   C  CR16  0  -0.293   3.0797  -0.6324   0.0679
 08Z  C22   C  C     0   0.492   6.8088   0.1714   0.0674
 08Z  O23   O  O     0  -0.485   7.5298   1.0666  -0.3558
 08Z  N24   N  NH2   0  -0.819   7.3028  -0.9587   0.5960
 08Z  HN2   H  HNH1  0   0.432   0.9551   1.8783  -0.4087
 08Z  HN8   H  HNH2  0   0.407  -0.3068  -3.6068   0.6022
 08Z  HN8A  H  HNH2  0   0.416  -2.0407  -3.4876   0.5371
 08Z  H11   H  HCR6  0   0.286  -3.6688   1.1401   1.5865
 08Z  H12   H  HCR6  0   0.279  -5.4845   2.8273   1.3827
 08Z  H13   H  HCR6  0   0.272  -7.2939   2.4446  -0.2671
 08Z  H15   H  HCR6  0   0.270  -5.6573  -1.1230  -1.4667
 08Z  H17   H  HCR6  0   0.280   2.9987   2.7170  -0.4571
 08Z  H18   H  HCR6  0   0.267   5.4142   2.4134  -0.3366
 08Z  H20   H  HCR6  0   0.259   4.8296  -1.7910   0.2908
 08Z  H21   H  HCR6  0   0.300   2.4410  -1.4945   0.1671
 08Z  HN24  H  HNH2  0   0.413   6.7324  -1.6486   1.0514
 08Z  HN2A  H  HNH2  0   0.405   8.3001  -1.0835   0.6555

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
 08Z  C1   N2    single    1.393  0.020  1.393
 08Z  C1   C17   aromatic  1.399  0.020  1.399
 08Z  C1   C21   aromatic  1.395  0.020  1.395
 08Z  N2   C3    single    1.345  0.020  1.345
 08Z  C3   N4    aromatic  1.301  0.020  1.301
 08Z  C3   S7    aromatic  1.737  0.020  1.737
 08Z  N4   C5    aromatic  1.357  0.020  1.357
 08Z  C5   C6    aromatic  1.403  0.020  1.403
 08Z  C5   N8    single    1.329  0.020  1.329
 08Z  C6   S7    aromatic  1.756  0.020  1.756
 08Z  C6   C9    single    1.419  0.020  1.419
 08Z  C9   C10   single    1.493  0.020  1.493
 08Z  C9   O16   double    1.234  0.020  1.234
 08Z  C10  C11   aromatic  1.390  0.020  1.390
 08Z  C10  C15   aromatic  1.394  0.020  1.394
 08Z  C11  C12   aromatic  1.386  0.020  1.386
 08Z  C12  C13   aromatic  1.386  0.020  1.386
 08Z  C13  N14   aromatic  1.330  0.020  1.330
 08Z  N14  C15   aromatic  1.324  0.020  1.324
 08Z  C17  C18   aromatic  1.379  0.020  1.379
 08Z  C18  C19   aromatic  1.395  0.020  1.395
 08Z  C19  C20   aromatic  1.392  0.020  1.392
 08Z  C19  C22   single    1.493  0.020  1.493
 08Z  C20  C21   aromatic  1.386  0.020  1.386
 08Z  C22  O23   double    1.225  0.020  1.225
 08Z  C22  N24   single    1.342  0.020  1.342
 08Z  N2   HN2   single    0.860  0.020  1.020
 08Z  N8   HN8   single    0.860  0.020  1.020
 08Z  N8   HN8A  single    0.860  0.020  1.020
 08Z  C11  H11   single    0.930  0.020  1.080
 08Z  C12  H12   single    0.930  0.020  1.080
 08Z  C13  H13   single    0.930  0.020  1.080
 08Z  C15  H15   single    0.930  0.020  1.080
 08Z  C17  H17   single    0.930  0.020  1.080
 08Z  C18  H18   single    0.930  0.020  1.080
 08Z  C20  H20   single    0.930  0.020  1.080
 08Z  C21  H21   single    0.930  0.020  1.080
 08Z  N24  HN24  single    0.860  0.020  1.020
 08Z  N24  HN2A  single    0.860  0.020  1.020

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
 08Z  C21   C1   C17   119.00  3.000
 08Z  C21   C1   N2    124.57  3.000
 08Z  C17   C1   N2    116.42  3.000
 08Z  HN2   N2   C3    115.95  3.000
 08Z  HN2   N2   C1    114.45  3.000
 08Z  C3    N2   C1    129.59  3.000
 08Z  S7    C3   N4    115.98  3.000
 08Z  S7    C3   N2    118.66  3.000
 08Z  N4    C3   N2    125.36  3.000
 08Z  C5    N4   C3    111.22  3.000
 08Z  N8    C5   C6    125.45  3.000
 08Z  N8    C5   N4    118.73  3.000
 08Z  C6    C5   N4    115.82  3.000
 08Z  C9    C6   S7    125.52  3.000
 08Z  C9    C6   C5    126.04  3.000
 08Z  S7    C6   C5    108.38  3.000
 08Z  C6    S7   C3     88.58  3.000
 08Z  HN8A  N8   HN8   119.72  3.000
 08Z  HN8A  N8   C5    120.05  3.000
 08Z  HN8   N8   C5    119.99  3.000
 08Z  O16   C9   C10   118.92  3.000
 08Z  O16   C9   C6    122.53  3.000
 08Z  C10   C9   C6    118.55  3.000
 08Z  C15   C10  C11   117.82  3.000
 08Z  C15   C10  C9    119.42  3.000
 08Z  C11   C10  C9    122.68  3.000
 08Z  H11   C11  C12   120.06  3.000
 08Z  H11   C11  C10   121.03  3.000
 08Z  C12   C11  C10   118.88  3.000
 08Z  H12   C12  C13   120.39  3.000
 08Z  H12   C12  C11   121.11  3.000
 08Z  C13   C12  C11   118.50  3.000
 08Z  H13   C13  N14   116.53  3.000
 08Z  H13   C13  C12   120.22  3.000
 08Z  N14   C13  C12   123.25  3.000
 08Z  C15   N14  C13   117.94  3.000
 08Z  H15   C15  N14   116.53  3.000
 08Z  H15   C15  C10   119.86  3.000
 08Z  N14   C15  C10   123.60  3.000
 08Z  H17   C17  C18   119.51  3.000
 08Z  H17   C17  C1    119.87  3.000
 08Z  C18   C17  C1    120.62  3.000
 08Z  H18   C18  C19   119.99  3.000
 08Z  H18   C18  C17   119.05  3.000
 08Z  C19   C18  C17   120.95  3.000
 08Z  C22   C19  C20   123.62  3.000
 08Z  C22   C19  C18   118.36  3.000
 08Z  C20   C19  C18   118.00  3.000
 08Z  H20   C20  C21   117.01  3.000
 08Z  H20   C20  C19   121.16  3.000
 08Z  C21   C20  C19   121.82  3.000
 08Z  H21   C21  C20   119.63  3.000
 08Z  H21   C21  C1    120.78  3.000
 08Z  C20   C21  C1    119.59  3.000
 08Z  N24   C22  O23   122.34  3.000
 08Z  N24   C22  C19   116.77  3.000
 08Z  O23   C22  C19   120.89  3.000
 08Z  HN2A  N24  HN24  116.79  3.000
 08Z  HN2A  N24  C22   119.49  3.000
 08Z  HN24  N24  C22   123.23  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
 08Z  CONST_01  C19   C18  C17  C1      0.00   0.0  0
 08Z  CONST_02  C19   C20  C21  C1      0.00   0.0  0
 08Z  CONST_03  C6    C5   N4   C3      0.00   0.0  0
 08Z  CONST_04  C5    C6   S7   C3      0.00   0.0  0
 08Z  CONST_05  C6    S7   C3   N4      0.00   0.0  0
 08Z  CONST_06  S7    C6   C5   N4      0.00   0.0  0
 08Z  CONST_07  S7    C3   N4   C5      0.00   0.0  0
 08Z  CONST_08  C13   C12  C11  C10     0.00   0.0  0
 08Z  CONST_09  C13   N14  C15  C10     0.00   0.0  0
 08Z  CONST_10  N14   C15  C10  C11     0.00   0.0  0
 08Z  CONST_11  N14   C13  C12  C11     0.00   0.0  0
 08Z  CONST_12  C15   C10  C11  C12     0.00   0.0  0
 08Z  CONST_13  C15   N14  C13  C12     0.00   0.0  0
 08Z  CONST_14  C20   C21  C1   C17     0.00   0.0  0
 08Z  CONST_15  C20   C19  C18  C17     0.00   0.0  0
 08Z  CONST_16  C21   C1   C17  C18     0.00   0.0  0
 08Z  CONST_17  C21   C20  C19  C18     0.00   0.0  0
 08Z  CONST_18  C18   C17  C1   N2    180.00   0.0  0
 08Z  CONST_19  C20   C21  C1   N2    180.00   0.0  0
 08Z  CONST_20  C5    N4   C3   N2    180.00   0.0  0
 08Z  CONST_21  C6    S7   C3   N2    180.00   0.0  0
 08Z  CONST_22  N8    C5   N4   C3    180.00   0.0  0
 08Z  CONST_23  C9    C6   S7   C3    180.00   0.0  0
 08Z  CONST_24  C9    C6   C5   N4    180.00   0.0  0
 08Z  CONST_25  N8    C5   C6   S7    180.00   0.0  0
 08Z  CONST_26  C12   C11  C10  C9    180.00   0.0  0
 08Z  CONST_27  N14   C15  C10  C9    180.00   0.0  0
 08Z  CONST_28  C22   C19  C18  C17   180.00   0.0  0
 08Z  CONST_29  C22   C19  C20  C21   180.00   0.0  0
 08Z  CONST_30  H18   C18  C17  C1    180.00   0.0  0
 08Z  CONST_31  H20   C20  C21  C1    180.00   0.0  0
 08Z  CONST_32  H12   C12  C11  C10   180.00   0.0  0
 08Z  CONST_33  H15   C15  C10  C11   180.00   0.0  0
 08Z  CONST_34  H13   C13  C12  C11   180.00   0.0  0
 08Z  CONST_35  H11   C11  C12  C13   180.00   0.0  0
 08Z  CONST_36  H21   C21  C1   C17   180.00   0.0  0
 08Z  CONST_37  H17   C17  C18  C19   180.00   0.0  0
 08Z  CONST_38  HN8   N8   C5   N4      0.00   0.0  0
 08Z  CONST_39  HN8A  N8   C5   N4    180.00   0.0  0
 08Z  CONST_40  HN24  N24  C22  C19     0.00   0.0  0
 08Z  CONST_41  HN2A  N24  C22  C19   180.00   0.0  0
 08Z  Var_01    N4    C3   N2   C1     -1.63  30.0  2
 08Z  Var_02    C17   C1   N2   C3   -177.46  30.0  2
 08Z  Var_03    C10   C9   C6   C5    176.09  30.0  2
 08Z  Var_04    C11   C10  C9   C6    -50.28  30.0  2
 08Z  Var_05    O23   C22  C19  C18   -15.53  30.0  2

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
 08Z  plan-1  N2    0.020
 08Z  plan-1  C3    0.020
 08Z  plan-1  N4    0.020
 08Z  plan-1  C5    0.020
 08Z  plan-1  C6    0.020
 08Z  plan-1  S7    0.020
 08Z  plan-1  N8    0.020
 08Z  plan-1  C9    0.020
 08Z  plan-2  C1    0.020
 08Z  plan-2  N2    0.020
 08Z  plan-2  C17   0.020
 08Z  plan-2  C18   0.020
 08Z  plan-2  C19   0.020
 08Z  plan-2  C20   0.020
 08Z  plan-2  C21   0.020
 08Z  plan-2  C22   0.020
 08Z  plan-2  H17   0.020
 08Z  plan-2  H18   0.020
 08Z  plan-2  H20   0.020
 08Z  plan-2  H21   0.020
 08Z  plan-3  C9    0.020
 08Z  plan-3  C10   0.020
 08Z  plan-3  C11   0.020
 08Z  plan-3  C12   0.020
 08Z  plan-3  C13   0.020
 08Z  plan-3  N14   0.020
 08Z  plan-3  C15   0.020
 08Z  plan-3  H11   0.020
 08Z  plan-3  H12   0.020
 08Z  plan-3  H13   0.020
 08Z  plan-3  H15   0.020
 08Z  plan-4  C19   0.020
 08Z  plan-4  C22   0.020
 08Z  plan-4  O23   0.020
 08Z  plan-4  N24   0.020
 08Z  plan-4  HN24  0.020
 08Z  plan-4  HN2A  0.020
 08Z  plan-5  C5    0.020
 08Z  plan-5  N8    0.020
 08Z  plan-5  HN8   0.020
 08Z  plan-5  HN8A  0.020
 08Z  plan-6  C6    0.020
 08Z  plan-6  C9    0.020
 08Z  plan-6  C10   0.020
 08Z  plan-6  O16   0.020

