# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 20:54:47 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-(3-chlorophenyl)-5-(1,5-naphthyridin-2-yl)-1,3-thiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1sc(c2ccc3ncccc3n2)c(n1)c4cccc(Cl)c4
#
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
 5G9  5G9  4-(3-chlorophenyl)-5-(1,5-naphthyridin-2-yl)-1,3-thiazol-2-amine  ligand  34  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5G9
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
 5G9  N1   N   N     0  -0.436   1.3795  -0.0688   0.4597
 5G9  N3   N   NH2   0  -0.819  -3.4355  -3.7003   0.6140
 5G9  C4   C   CR16  0  -0.087   5.2837   1.1032   0.4278
 5G9  C5   C   CR6   0   0.168   1.0876  -1.2802   0.0512
 5G9  C6   C   CR5   0  -0.337  -0.3192  -1.6685   0.0517
 5G9  C7   C   CR5   0   0.290  -2.4487  -2.8297   0.3468
 5G9  C8   C   CR5   0   0.378  -1.4514  -0.9204  -0.1252
 5G9  C10  C   CR16  0  -0.253  -2.4549   1.3254   0.0777
 5G9  C13  C   CR16  0  -0.249  -0.8036   2.3347  -1.9104
 5G9  C15  C   CR16  0  -0.190   3.3923  -1.8225  -0.3683
 5G9  C11  C   CR6   0  -0.026  -2.5407   2.6527  -0.3086
 5G9  C12  C   CR16  0  -0.224  -1.7242   3.1748  -1.2981
 5G9  C14  C   CR16  0  -0.270  -0.6963   1.0075  -1.5313
 5G9  C9   C   CR6   0   0.054  -1.5132   0.4950  -0.5257
 5G9  N2   N   N     0  -0.447  -2.6350  -1.5763   0.0515
 5G9  S    S   S2    0   0.190  -0.7798  -3.3064   0.4349
 5G9  C16  C   CR16  0  -0.315   2.0835  -2.2020  -0.3740
 5G9  C    C   CR66  0   0.191   3.7278  -0.5139   0.0443
 5G9  C1   C   CR66  0   0.177   2.6656   0.3297   0.4456
 5G9  C2   C   CR16  0  -0.197   2.9915   1.6419   0.8557
 5G9  C3   C   CR16  0  -0.318   4.3016   2.0274   0.8451
 5G9  N    N   N     0  -0.426   5.0188  -0.1176   0.0421
 5G9  H1   H   HNH2  0   0.409  -4.3736  -3.4168   0.3810
 5G9  H2   H   HNH2  0   0.413  -3.2597  -4.6898   0.5790
 5G9  H3   H   HCR6  0   0.269   6.3261   1.4026   0.4185
 5G9  H4   H   HCR6  0   0.273  -3.1065   0.9364   0.8486
 5G9  H5   H   HCR6  0   0.268  -0.1719   2.7239  -2.6977
 5G9  H6   H   HCR6  0   0.279   4.1765  -2.4974  -0.6868
 5G9  H7   H   HCR6  0   0.280  -1.8073   4.2117  -1.5936
 5G9  H8   H   HCR6  0   0.257   0.0127   0.3645  -2.0341
 5G9  H9   H   HCR6  0   0.275   1.8022  -3.1889  -0.7179
 5G9  H10  H   HCR6  0   0.276   2.1994   2.3114   1.1661
 5G9  H11  H   HCR6  0   0.278   4.5990   3.0210   1.1504
 5G9  CL   CL  CL    0  -0.132  -3.7053   3.6818   0.4634

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
 5G9  N3   C7   single    1.343  0.020  1.343
 5G9  S    C7   aromatic  1.738  0.020  1.738
 5G9  S    C6   aromatic  1.744  0.020  1.744
 5G9  C7   N2   aromatic  1.301  0.020  1.301
 5G9  C6   C5   single    1.459  0.020  1.459
 5G9  C6   C8   aromatic  1.369  0.020  1.369
 5G9  C2   C1   aromatic  1.413  0.020  1.413
 5G9  C2   C3   aromatic  1.366  0.020  1.366
 5G9  C1   N1   aromatic  1.346  0.020  1.346
 5G9  C1   C    aromatic  1.415  0.020  1.415
 5G9  N1   C5   aromatic  1.311  0.020  1.311
 5G9  C3   C4   aromatic  1.412  0.020  1.412
 5G9  C5   C16  aromatic  1.422  0.020  1.422
 5G9  C    N    aromatic  1.350  0.020  1.350
 5G9  C    C15  aromatic  1.413  0.020  1.413
 5G9  N2   C8   aromatic  1.365  0.020  1.365
 5G9  C4   N    aromatic  1.307  0.020  1.307
 5G9  C16  C15  aromatic  1.363  0.020  1.363
 5G9  C8   C9   single    1.472  0.020  1.472
 5G9  C10  C9   aromatic  1.393  0.020  1.393
 5G9  C10  C11  aromatic  1.385  0.020  1.385
 5G9  C9   C14  aromatic  1.393  0.020  1.393
 5G9  CL   C11  single    1.735  0.020  1.735
 5G9  C11  C12  aromatic  1.385  0.020  1.385
 5G9  C14  C13  aromatic  1.384  0.020  1.384
 5G9  C12  C13  aromatic  1.389  0.020  1.389
 5G9  N3   H1   single    0.890  0.020  1.040
 5G9  N3   H2   single    0.890  0.020  1.040
 5G9  C4   H3   single    0.930  0.020  1.080
 5G9  C10  H4   single    0.930  0.020  1.080
 5G9  C13  H5   single    0.930  0.020  1.080
 5G9  C15  H6   single    0.930  0.020  1.080
 5G9  C12  H7   single    0.930  0.020  1.080
 5G9  C14  H8   single    0.930  0.020  1.080
 5G9  C16  H9   single    0.930  0.020  1.080
 5G9  C2   H10  single    0.930  0.020  1.080
 5G9  C3   H11  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
 5G9  C1   N1   C5   118.87  3.000
 5G9  H2   N3   H1   115.58  3.000
 5G9  H2   N3   C7   120.17  3.000
 5G9  H1   N3   C7   117.12  3.000
 5G9  H3   C4   N    116.74  3.000
 5G9  H3   C4   C3   119.37  3.000
 5G9  N    C4   C3   123.89  3.000
 5G9  C16  C5   C6   120.18  3.000
 5G9  C16  C5   N1   122.41  3.000
 5G9  C6   C5   N1   117.41  3.000
 5G9  S    C6   C8   108.86  3.000
 5G9  C8   C6   C5   130.69  3.000
 5G9  S    C6   C5   120.30  3.000
 5G9  S    C7   N2   114.41  3.000
 5G9  N2   C7   N3   124.37  3.000
 5G9  S    C7   N3   121.18  3.000
 5G9  N2   C8   C9   117.44  3.000
 5G9  C9   C8   C6   126.54  3.000
 5G9  N2   C8   C6   115.98  3.000
 5G9  H4   C10  C9   120.10  3.000
 5G9  H4   C10  C11  120.41  3.000
 5G9  C9   C10  C11  119.49  3.000
 5G9  H5   C13  C14  119.93  3.000
 5G9  H5   C13  C12  119.36  3.000
 5G9  C14  C13  C12  120.71  3.000
 5G9  H6   C15  C    119.43  3.000
 5G9  H6   C15  C16  121.40  3.000
 5G9  C    C15  C16  119.17  3.000
 5G9  C12  C11  CL   119.33  3.000
 5G9  C12  C11  C10  121.60  3.000
 5G9  CL   C11  C10  119.07  3.000
 5G9  H7   C12  C11  120.76  3.000
 5G9  H7   C12  C13  120.70  3.000
 5G9  C11  C12  C13  118.54  3.000
 5G9  H8   C14  C9   120.09  3.000
 5G9  H8   C14  C13  119.58  3.000
 5G9  C9   C14  C13  120.32  3.000
 5G9  C14  C9   C10  119.33  3.000
 5G9  C14  C9   C8   121.69  3.000
 5G9  C10  C9   C8   118.92  3.000
 5G9  C8   N2   C7   111.61  3.000
 5G9  C7   S    C6    89.14  3.000
 5G9  H9   C16  C15  120.32  3.000
 5G9  H9   C16  C5   120.27  3.000
 5G9  C15  C16  C5   119.40  3.000
 5G9  N    C    C1   122.91  3.000
 5G9  N    C    C15  119.90  3.000
 5G9  C1   C    C15  117.19  3.000
 5G9  C2   C1   C    117.58  3.000
 5G9  C    C1   N1   122.93  3.000
 5G9  C2   C1   N1   119.48  3.000
 5G9  H10  C2   C3   121.98  3.000
 5G9  H10  C2   C1   119.26  3.000
 5G9  C3   C2   C1   118.76  3.000
 5G9  H11  C3   C2   121.40  3.000
 5G9  H11  C3   C4   119.59  3.000
 5G9  C2   C3   C4   119.01  3.000
 5G9  C    N    C4   117.86  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
 5G9  CONST_01  C3   C2   C1   N1   180.00  0.0  0
 5G9  CONST_02  N    C    C1   N1   180.00  0.0  0
 5G9  CONST_03  C15  C    C1   N1     0.00  0.0  0
 5G9  CONST_06  C15  C16  C5   N1     0.00  0.0  0
 5G9  CONST_07  C1   C2   C3   C4     0.00  0.0  0
 5G9  CONST_08  C1   C    N    C4     0.00  0.0  0
 5G9  CONST_09  C15  C    N    C4   180.00  0.0  0
 5G9  CONST_10  C7   S    C6   C5   180.00  0.0  0
 5G9  CONST_11  N2   C8   C6   C5   180.00  0.0  0
 5G9  CONST_12  C9   C8   C6   C5     0.00  0.0  0
 5G9  CONST_13  C2   C1   N1   C5   180.00  0.0  0
 5G9  CONST_14  C    C1   N1   C5     0.00  0.0  0
 5G9  CONST_15  C    C15  C16  C5     0.00  0.0  0
 5G9  CONST_16  N2   C7   S    C6     0.00  0.0  0
 5G9  CONST_17  C1   N1   C5   C6   180.00  0.0  0
 5G9  CONST_18  C15  C16  C5   C6   180.00  0.0  0
 5G9  CONST_19  C7   N2   C8   C6     0.00  0.0  0
 5G9  CONST_22  C8   C6   S    C7     0.00  0.0  0
 5G9  CONST_23  C9   C8   N2   C7   180.00  0.0  0
 5G9  CONST_25  S    C7   N2   C8     0.00  0.0  0
 5G9  CONST_26  C11  C10  C9   C8   180.00  0.0  0
 5G9  CONST_27  C13  C14  C9   C8   180.00  0.0  0
 5G9  CONST_29  C13  C14  C9   C10    0.00  0.0  0
 5G9  CONST_30  C13  C12  C11  C10    0.00  0.0  0
 5G9  CONST_31  C2   C1   C    C15  180.00  0.0  0
 5G9  CONST_32  C14  C9   C10  C11    0.00  0.0  0
 5G9  CONST_33  C14  C13  C12  C11    0.00  0.0  0
 5G9  CONST_34  C9   C10  C11  C12    0.00  0.0  0
 5G9  CONST_35  C9   C14  C13  C12    0.00  0.0  0
 5G9  CONST_37  S    C6   C8   C9   180.00  0.0  0
 5G9  CONST_38  S    C6   C8   N2     0.00  0.0  0
 5G9  CONST_40  C1   N1   C5   C16    0.00  0.0  0
 5G9  CONST_41  C1   C    C15  C16    0.00  0.0  0
 5G9  CONST_42  N    C    C15  C16  180.00  0.0  0
 5G9  CONST_43  C3   C2   C1   C      0.00  0.0  0
 5G9  CONST_44  C3   C4   N    C      0.00  0.0  0
 5G9  CONST_45  N    C    C1   C2     0.00  0.0  0
 5G9  CONST_46  N    C4   C3   C2     0.00  0.0  0
 5G9  CONST_47  C6   S    C7   N3   180.00  0.0  0
 5G9  CONST_48  C8   N2   C7   N3   180.00  0.0  0
 5G9  CONST_49  CL   C11  C12  C13  180.00  0.0  0
 5G9  CONST_50  C9   C10  C11  CL   180.00  0.0  0
 5G9  CONST_51  H10  C2   C1   N1     0.00  0.0  0
 5G9  CONST_52  H9   C16  C5   N1   180.00  0.0  0
 5G9  CONST_53  H6   C15  C16  C5   180.00  0.0  0
 5G9  CONST_54  H4   C10  C9   C8     0.00  0.0  0
 5G9  CONST_55  H8   C14  C9   C8     0.00  0.0  0
 5G9  CONST_56  H7   C12  C11  C10  180.00  0.0  0
 5G9  CONST_57  H5   C13  C12  C11  180.00  0.0  0
 5G9  CONST_58  H3   C4   N    C    180.00  0.0  0
 5G9  CONST_59  H11  C3   C2   C1   180.00  0.0  0
 5G9  CONST_60  H1   N3   C7   N2     0.00  0.0  0

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
 5G9  plan-1  N3   0.020
 5G9  plan-1  C5   0.020
 5G9  plan-1  C6   0.020
 5G9  plan-1  C7   0.020
 5G9  plan-1  C8   0.020
 5G9  plan-1  C9   0.020
 5G9  plan-1  N2   0.020
 5G9  plan-1  S    0.020
 5G9  plan-2  C8   0.020
 5G9  plan-2  C10  0.020
 5G9  plan-2  C13  0.020
 5G9  plan-2  C11  0.020
 5G9  plan-2  C12  0.020
 5G9  plan-2  C14  0.020
 5G9  plan-2  C9   0.020
 5G9  plan-2  H4   0.020
 5G9  plan-2  H5   0.020
 5G9  plan-2  H7   0.020
 5G9  plan-2  H8   0.020
 5G9  plan-2  CL   0.020
 5G9  plan-3  N1   0.020
 5G9  plan-3  C4   0.020
 5G9  plan-3  C5   0.020
 5G9  plan-3  C6   0.020
 5G9  plan-3  C15  0.020
 5G9  plan-3  C16  0.020
 5G9  plan-3  C    0.020
 5G9  plan-3  C1   0.020
 5G9  plan-3  C2   0.020
 5G9  plan-3  C3   0.020
 5G9  plan-3  N    0.020
 5G9  plan-3  H3   0.020
 5G9  plan-3  H6   0.020
 5G9  plan-3  H9   0.020
 5G9  plan-3  H10  0.020
 5G9  plan-3  H11  0.020
 5G9  plan-4  N3   0.020
 5G9  plan-4  C7   0.020
 5G9  plan-4  H1   0.020
 5G9  plan-4  H2   0.020

