# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 21:25:38 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-(3-methylphenyl)-5-(1,5-naphthyridin-2-yl)-1,3-thiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)c2nc(N)sc2c3ccc4ncccc4n3
#
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
 5GB  5GB  4-(3-methylphenyl)-5-(1,5-naphthyridin-2-yl)-1,3-thiazol-2-amine  ligand  37  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_5GB
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
 5GB  N1   N  N     0  -0.435  -1.1935   0.3217   0.4594
 5GB  N3   N  NH2   0  -0.819   4.6146   1.9729   0.6114
 5GB  C4   C  CR16  0  -0.087  -5.2532   0.6578   0.2887
 5GB  C5   C  CR6   0   0.170  -0.4634   1.3018  -0.0160
 5GB  C6   C  CR5   0  -0.342   0.9870   1.1518   0.0360
 5GB  C7   C  CR5   0   0.287   3.3842   1.4937   0.3576
 5GB  C8   C  CR5   0   0.373   1.7746   0.0333  -0.0270
 5GB  C10  C  CR16  0  -0.347   1.8871  -2.4022   0.3892
 5GB  C13  C  CR16  0  -0.229   0.0408  -2.9150  -1.5991
 5GB  C15  C  CR16  0  -0.298   0.4066  -1.6074  -1.3268
 5GB  C17  C  CR16  0  -0.316  -1.0393   2.4829  -0.5617
 5GB  S    S  S2    0   0.184   2.0007   2.5433   0.3221
 5GB  N2   N  N     0  -0.446   3.1118   0.2372   0.1631
 5GB  C9   C  CR6   0   0.079   1.3294  -1.3394  -0.3183
 5GB  C12  C  CR16  0  -0.310   0.5874  -3.9644  -0.8719
 5GB  C11  C  CR6   0   0.113   1.5189  -3.7202   0.1339
 5GB  C14  C  CH3   0  -0.724   2.1005  -4.8462   0.9391
 5GB  C16  C  CR16  0  -0.191  -2.3953   2.6083  -0.6061
 5GB  C    C  CR66  0   0.190  -3.2009   1.5546  -0.1210
 5GB  C1   C  CR66  0   0.177  -2.5350   0.4203   0.3996
 5GB  C2   C  CR16  0  -0.198  -3.3327  -0.6411   0.8822
 5GB  C3   C  CR16  0  -0.318  -4.6920  -0.5211   0.8251
 5GB  N    N  N     0  -0.426  -4.5465   1.6586  -0.1680
 5GB  H1   H  HNH2  0   0.408   5.3915   1.3644   0.4089
 5GB  H2   H  HNH2  0   0.411   4.7993   2.9563   0.5100
 5GB  H3   H  HCR6  0   0.269  -6.3319   0.7606   0.2423
 5GB  H4   H  HCR6  0   0.241   2.6219  -2.1985   1.1597
 5GB  H5   H  HCR6  0   0.252  -0.6666  -3.1191  -2.3925
 5GB  H6   H  HCR6  0   0.246  -0.0091  -0.8002  -1.9153
 5GB  H7   H  HCR6  0   0.273  -0.4078   3.2689  -0.9556
 5GB  H8   H  HCR6  0   0.247   0.2952  -4.9835  -1.0968
 5GB  H9   H  HCH3  0   0.248   1.4841  -5.0604   1.8149
 5GB  H10  H  HCH3  0   0.243   2.1626  -5.7652   0.3569
 5GB  H11  H  HCH3  0   0.243   3.1002  -4.6057   1.2997
 5GB  H12  H  HCR6  0   0.278  -2.8658   3.4919  -1.0173
 5GB  H13  H  HCR6  0   0.277  -2.8519  -1.5237   1.2836
 5GB  H14  H  HCR6  0   0.277  -5.3419  -1.3086   1.1811

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
 5GB  N3   C7   single    1.344  0.020  1.344
 5GB  S    C7   aromatic  1.737  0.020  1.737
 5GB  S    C6   aromatic  1.745  0.020  1.745
 5GB  C7   N2   aromatic  1.300  0.020  1.300
 5GB  C6   C5   single    1.459  0.020  1.459
 5GB  C6   C8   aromatic  1.369  0.020  1.369
 5GB  N2   C8   aromatic  1.366  0.020  1.366
 5GB  C5   N1   aromatic  1.311  0.020  1.311
 5GB  C5   C17  aromatic  1.423  0.020  1.423
 5GB  N1   C1   aromatic  1.346  0.020  1.346
 5GB  C2   C1   aromatic  1.413  0.020  1.413
 5GB  C2   C3   aromatic  1.366  0.020  1.366
 5GB  C1   C    aromatic  1.415  0.020  1.415
 5GB  C17  C16  aromatic  1.362  0.020  1.362
 5GB  C3   C4   aromatic  1.412  0.020  1.412
 5GB  C    C16  aromatic  1.412  0.020  1.412
 5GB  C    N    aromatic  1.350  0.020  1.350
 5GB  C4   N    aromatic  1.308  0.020  1.308
 5GB  C8   C9   single    1.472  0.020  1.472
 5GB  C10  C9   aromatic  1.393  0.020  1.393
 5GB  C10  C11  aromatic  1.392  0.020  1.392
 5GB  C9   C15  aromatic  1.393  0.020  1.393
 5GB  C14  C11  single    1.502  0.020  1.502
 5GB  C11  C12  aromatic  1.392  0.020  1.392
 5GB  C15  C13  aromatic  1.385  0.020  1.385
 5GB  C12  C13  aromatic  1.389  0.020  1.389
 5GB  N3   H1   single    0.890  0.020  1.040
 5GB  N3   H2   single    0.890  0.020  1.040
 5GB  C4   H3   single    0.930  0.020  1.080
 5GB  C10  H4   single    0.930  0.020  1.080
 5GB  C13  H5   single    0.930  0.020  1.080
 5GB  C15  H6   single    0.930  0.020  1.080
 5GB  C17  H7   single    0.930  0.020  1.080
 5GB  C12  H8   single    0.930  0.020  1.080
 5GB  C14  H9   single    0.970  0.020  1.090
 5GB  C14  H10  single    0.970  0.020  1.090
 5GB  C14  H11  single    0.970  0.020  1.090
 5GB  C16  H12  single    0.930  0.020  1.080
 5GB  C2   H13  single    0.930  0.020  1.080
 5GB  C3   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
 5GB  C1   N1   C5   118.94  3.000
 5GB  H2   N3   H1   115.38  3.000
 5GB  H2   N3   C7   119.84  3.000
 5GB  H1   N3   C7   116.91  3.000
 5GB  H3   C4   N    116.75  3.000
 5GB  H3   C4   C3   119.39  3.000
 5GB  N    C4   C3   123.86  3.000
 5GB  C17  C5   C6   120.09  3.000
 5GB  C17  C5   N1   122.29  3.000
 5GB  C6   C5   N1   117.62  3.000
 5GB  S    C6   C8   108.95  3.000
 5GB  C8   C6   C5   130.85  3.000
 5GB  S    C6   C5   120.08  3.000
 5GB  N2   C7   S    114.45  3.000
 5GB  N2   C7   N3   124.35  3.000
 5GB  S    C7   N3   121.16  3.000
 5GB  C9   C8   N2   117.57  3.000
 5GB  C9   C8   C6   126.64  3.000
 5GB  N2   C8   C6   115.77  3.000
 5GB  H4   C10  C11  119.18  3.000
 5GB  H4   C10  C9   119.27  3.000
 5GB  C11  C10  C9   121.55  3.000
 5GB  H5   C13  C12  119.90  3.000
 5GB  H5   C13  C15  119.65  3.000
 5GB  C12  C13  C15  120.44  3.000
 5GB  H6   C15  C9   120.31  3.000
 5GB  H6   C15  C13  119.74  3.000
 5GB  C9   C15  C13  119.93  3.000
 5GB  H7   C17  C16  120.13  3.000
 5GB  H7   C17  C5   120.41  3.000
 5GB  C16  C17  C5   119.45  3.000
 5GB  C7   S    C6    89.10  3.000
 5GB  C8   N2   C7   111.72  3.000
 5GB  C15  C9   C10  119.08  3.000
 5GB  C15  C9   C8   121.53  3.000
 5GB  C10  C9   C8   119.32  3.000
 5GB  H8   C12  C11  119.68  3.000
 5GB  H8   C12  C13  119.72  3.000
 5GB  C11  C12  C13  120.59  3.000
 5GB  C14  C11  C12  121.00  3.000
 5GB  C12  C11  C10  118.39  3.000
 5GB  C14  C11  C10  120.61  3.000
 5GB  H11  C14  H10  108.10  3.000
 5GB  H11  C14  H9   107.20  3.000
 5GB  H10  C14  H9   107.17  3.000
 5GB  H11  C14  C11  111.55  3.000
 5GB  H10  C14  C11  111.59  3.000
 5GB  H9   C14  C11  111.01  3.000
 5GB  H12  C16  C    119.45  3.000
 5GB  H12  C16  C17  121.34  3.000
 5GB  C    C16  C17  119.20  3.000
 5GB  N    C    C1   122.93  3.000
 5GB  N    C    C16  119.93  3.000
 5GB  C1   C    C16  117.14  3.000
 5GB  C2   C1   C    117.54  3.000
 5GB  C    C1   N1   122.96  3.000
 5GB  C2   C1   N1   119.50  3.000
 5GB  H13  C2   C3   121.96  3.000
 5GB  H13  C2   C1   119.25  3.000
 5GB  C3   C2   C1   118.80  3.000
 5GB  H14  C3   C2   121.36  3.000
 5GB  H14  C3   C4   119.63  3.000
 5GB  C2   C3   C4   119.01  3.000
 5GB  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
 5GB  CONST_03  C16  C17  C5   N1     0.00   0.0  0
 5GB  CONST_04  C3   C2   C1   N1   180.00   0.0  0
 5GB  CONST_05  C16  C    C1   N1     0.00   0.0  0
 5GB  CONST_06  N    C    C1   N1   180.00   0.0  0
 5GB  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 5GB  CONST_08  C1   C    N    C4     0.00   0.0  0
 5GB  CONST_09  C16  C    N    C4   180.00   0.0  0
 5GB  CONST_10  C7   S    C6   C5   180.00   0.0  0
 5GB  CONST_11  N2   C8   C6   C5   180.00   0.0  0
 5GB  CONST_12  C9   C8   C6   C5     0.00   0.0  0
 5GB  CONST_13  C2   C1   N1   C5   180.00   0.0  0
 5GB  CONST_14  C    C1   N1   C5     0.00   0.0  0
 5GB  CONST_15  C    C16  C17  C5     0.00   0.0  0
 5GB  CONST_16  N2   C7   S    C6     0.00   0.0  0
 5GB  CONST_17  C1   N1   C5   C6   180.00   0.0  0
 5GB  CONST_18  C16  C17  C5   C6   180.00   0.0  0
 5GB  CONST_19  C7   N2   C8   C6     0.00   0.0  0
 5GB  CONST_22  C8   C6   S    C7     0.00   0.0  0
 5GB  CONST_23  C9   C8   N2   C7   180.00   0.0  0
 5GB  CONST_25  S    C7   N2   C8     0.00   0.0  0
 5GB  CONST_26  C11  C10  C9   C8   180.00   0.0  0
 5GB  CONST_27  C13  C15  C9   C8   180.00   0.0  0
 5GB  CONST_29  C13  C15  C9   C10    0.00   0.0  0
 5GB  CONST_30  C13  C12  C11  C10    0.00   0.0  0
 5GB  CONST_32  C11  C10  C9   C15    0.00   0.0  0
 5GB  CONST_33  C11  C12  C13  C15    0.00   0.0  0
 5GB  CONST_35  C1   N1   C5   C17    0.00   0.0  0
 5GB  CONST_36  C1   C    C16  C17    0.00   0.0  0
 5GB  CONST_37  N    C    C16  C17  180.00   0.0  0
 5GB  CONST_38  N2   C8   C6   S      0.00   0.0  0
 5GB  CONST_39  C9   C8   C6   S    180.00   0.0  0
 5GB  CONST_40  C12  C11  C10  C9     0.00   0.0  0
 5GB  CONST_41  C12  C13  C15  C9     0.00   0.0  0
 5GB  CONST_42  C2   C1   C    C16  180.00   0.0  0
 5GB  CONST_43  C3   C2   C1   C      0.00   0.0  0
 5GB  CONST_44  C3   C4   N    C      0.00   0.0  0
 5GB  CONST_45  N    C    C1   C2     0.00   0.0  0
 5GB  CONST_46  N    C4   C3   C2     0.00   0.0  0
 5GB  CONST_47  C6   S    C7   N3   180.00   0.0  0
 5GB  CONST_48  C8   N2   C7   N3   180.00   0.0  0
 5GB  CONST_49  C14  C11  C12  C13  180.00   0.0  0
 5GB  CONST_50  C14  C11  C10  C9   180.00   0.0  0
 5GB  CONST_51  H7   C17  C5   N1   180.00   0.0  0
 5GB  CONST_52  H13  C2   C1   N1     0.00   0.0  0
 5GB  CONST_53  H12  C16  C17  C5   180.00   0.0  0
 5GB  CONST_54  H4   C10  C9   C8     0.00   0.0  0
 5GB  CONST_55  H6   C15  C9   C8     0.00   0.0  0
 5GB  CONST_56  H8   C12  C11  C10  180.00   0.0  0
 5GB  CONST_57  H5   C13  C15  C9   180.00   0.0  0
 5GB  CONST_58  H3   C4   N    C    180.00   0.0  0
 5GB  CONST_59  H14  C3   C2   C1   180.00   0.0  0
 5GB  CONST_60  H1   N3   C7   S    180.00   0.0  0
 5GB  Var_01    H9   C14  C11  C10   90.38  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
 5GB  plan-1  N3   0.020
 5GB  plan-1  C5   0.020
 5GB  plan-1  C6   0.020
 5GB  plan-1  C7   0.020
 5GB  plan-1  C8   0.020
 5GB  plan-1  S    0.020
 5GB  plan-1  N2   0.020
 5GB  plan-1  C9   0.020
 5GB  plan-2  C8   0.020
 5GB  plan-2  C10  0.020
 5GB  plan-2  C13  0.020
 5GB  plan-2  C15  0.020
 5GB  plan-2  C9   0.020
 5GB  plan-2  C12  0.020
 5GB  plan-2  C11  0.020
 5GB  plan-2  C14  0.020
 5GB  plan-2  H4   0.020
 5GB  plan-2  H5   0.020
 5GB  plan-2  H6   0.020
 5GB  plan-2  H8   0.020
 5GB  plan-3  N1   0.020
 5GB  plan-3  C4   0.020
 5GB  plan-3  C5   0.020
 5GB  plan-3  C6   0.020
 5GB  plan-3  C17  0.020
 5GB  plan-3  C16  0.020
 5GB  plan-3  C    0.020
 5GB  plan-3  C1   0.020
 5GB  plan-3  C2   0.020
 5GB  plan-3  C3   0.020
 5GB  plan-3  N    0.020
 5GB  plan-3  H3   0.020
 5GB  plan-3  H7   0.020
 5GB  plan-3  H12  0.020
 5GB  plan-3  H13  0.020
 5GB  plan-3  H14  0.020
 5GB  plan-4  N3   0.020
 5GB  plan-4  C7   0.020
 5GB  plan-4  H1   0.020
 5GB  plan-4  H2   0.020

