# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 02:08:15 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCC(=O)Nc2sc(Cc3cccc4ccc(Br)cc34)cn2)n1
#
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
 5GN  5GN  N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide  ligand  49  30  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5GN
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
 5GN  C11  C   CR16  0  -0.306  -4.2975   0.4443  -0.3938
 5GN  C6   C   CR16  0  -0.314  -4.5522  -3.1625   0.4889
 5GN  C8   C   CR16  0  -0.328  -5.4768  -1.8670   2.2907
 5GN  C3   C   CR5   0  -0.159  -2.0511  -2.1257  -1.4303
 5GN  N2   N   N     0  -0.428   5.9696   1.1055   0.4716
 5GN  C10  C   CR66  0   0.085  -4.5693  -0.7603   0.3012
 5GN  C1   C   CR5   0   0.308   0.2922  -1.5971  -1.0444
 5GN  C7   C   CR16  0  -0.241  -5.1696  -3.0842   1.7517
 5GN  N3   N   N     0  -0.440   7.7279  -0.4495   0.1558
 5GN  C9   C   CR66  0   0.122  -5.1823  -0.6814   1.5808
 5GN  N1   N   N     0  -0.392   0.1743  -2.7814  -1.5346
 5GN  C2   C   CR15  0  -0.043  -1.1440  -3.0806  -1.7475
 5GN  C5   C   CR6   0   0.126  -4.2474  -2.0390  -0.2361
 5GN  C12  C   CR6   0  -0.114  -4.6050   1.6492   0.1735
 5GN  C13  C   CR16  0  -0.237  -5.2020   1.7401   1.4454
 5GN  C14  C   CR16  0  -0.306  -5.4863   0.5883   2.1232
 5GN  S    S   S2    0   0.200  -1.2063  -0.7505  -0.7978
 5GN  N    N   NH1   0  -0.711   1.4679  -0.9609  -0.7075
 5GN  C    C   C     0   0.567   2.7072  -1.5321  -0.6216
 5GN  O    O   O     0  -0.421   2.9427  -2.6963  -0.8452
 5GN  C15  C   CH2   0  -0.706   3.7717  -0.5422  -0.2049
 5GN  S1   S   S2    0   0.074   5.3639  -1.3916  -0.2584
 5GN  C16  C   CR6   0   0.220   6.4547  -0.0839   0.1749
 5GN  C20  C   CR6   0   0.285   8.6216   0.4873   0.4611
 5GN  C21  C   CH3   0  -0.720  10.0615   0.0933   0.4360
 5GN  C19  C   CR16  0  -0.400   8.2163   1.7783   0.7829
 5GN  C17  C   CR6   0   0.301   6.8575   2.0533   0.7816
 5GN  C18  C   CH3   0  -0.719   6.3195   3.3999   1.1356
 5GN  H1   H   HCR6  0   0.274  -3.8593   0.4127  -1.3825
 5GN  H2   H   HCR6  0   0.259  -4.3086  -4.1369   0.0828
 5GN  H3   H   HCR6  0   0.261  -5.9486  -1.7963   3.2631
 5GN  H4   H   HCH2  0   0.289  -3.8923  -1.4482  -2.2858
 5GN  H5   H   HCH2  0   0.299  -3.7824  -3.1599  -1.9869
 5GN  H6   H   HCR6  0   0.263  -5.3943  -3.9949   2.2909
 5GN  H7   H   HCR5  0   0.274  -1.4100  -4.0455  -2.1576
 5GN  H8   H   HCR6  0   0.282  -5.4366   2.7022   1.8798
 5GN  H9   H   HCR6  0   0.269  -5.9542   0.6439   3.0984
 5GN  H10  H   HNH1  0   0.437   1.4015   0.0198  -0.4764
 5GN  H11  H   HCH2  0   0.322   3.7762   0.3195  -0.8746
 5GN  H12  H   HCH2  0   0.326   3.5636  -0.1725   0.8012
 5GN  H13  H   HCH3  0   0.263  10.3385  -0.2620  -0.5571
 5GN  H14  H   HCH3  0   0.251  10.7114   0.9252   0.6986
 5GN  H15  H   HCH3  0   0.263  10.2448  -0.7243   1.1339
 5GN  H16  H   HCR6  0   0.273   8.9397   2.5443   1.0249
 5GN  H17  H   HCH3  0   0.264   5.7892   3.3522   2.0884
 5GN  H18  H   HCH3  0   0.251   7.1121   4.1394   1.2249
 5GN  H19  H   HCH3  0   0.260   5.6047   3.7377   0.3856
 5GN  C4   C   CH2   0  -0.643  -3.5394  -2.1853  -1.5610
 5GN  BR   BR  BR    0  -0.038  -4.2319   3.2445  -0.7643

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
 5GN  BR   C12  single    1.888  0.020  1.888
 5GN  S1   C16  single    1.757  0.020  1.757
 5GN  S1   C15  single    1.805  0.020  1.805
 5GN  N3   C16  aromatic  1.325  0.020  1.325
 5GN  N3   C20  aromatic  1.330  0.020  1.330
 5GN  C21  C20  single    1.493  0.020  1.493
 5GN  C16  N2   aromatic  1.318  0.020  1.318
 5GN  C15  C    single    1.512  0.020  1.512
 5GN  C20  C19  aromatic  1.391  0.020  1.391
 5GN  C12  C13  aromatic  1.408  0.020  1.408
 5GN  C12  C11  aromatic  1.367  0.020  1.367
 5GN  C13  C14  aromatic  1.366  0.020  1.366
 5GN  O    C    double    1.209  0.020  1.209
 5GN  C    N    single    1.367  0.020  1.367
 5GN  C11  C10  aromatic  1.417  0.020  1.417
 5GN  N2   C17  aromatic  1.335  0.020  1.335
 5GN  C19  C17  aromatic  1.386  0.020  1.386
 5GN  N    C1   single    1.379  0.020  1.379
 5GN  C14  C9   aromatic  1.414  0.020  1.414
 5GN  S    C1   aromatic  1.739  0.020  1.739
 5GN  S    C3   aromatic  1.733  0.020  1.733
 5GN  C17  C18  single    1.493  0.020  1.493
 5GN  C1   N1   aromatic  1.287  0.020  1.287
 5GN  C10  C9   aromatic  1.421  0.020  1.421
 5GN  C10  C5   aromatic  1.424  0.020  1.424
 5GN  C9   C8   aromatic  1.413  0.020  1.413
 5GN  N1   C2   aromatic  1.369  0.020  1.369
 5GN  C3   C4   single    1.495  0.020  1.495
 5GN  C3   C2   aromatic  1.355  0.020  1.355
 5GN  C4   C5   single    1.509  0.020  1.509
 5GN  C5   C6   aromatic  1.371  0.020  1.371
 5GN  C8   C7   aromatic  1.366  0.020  1.366
 5GN  C6   C7   aromatic  1.408  0.020  1.408
 5GN  C11  H1   single    0.930  0.020  1.080
 5GN  C6   H2   single    0.930  0.020  1.080
 5GN  C8   H3   single    0.930  0.020  1.080
 5GN  C4   H4   single    0.970  0.020  1.090
 5GN  C4   H5   single    0.970  0.020  1.090
 5GN  C7   H6   single    0.930  0.020  1.080
 5GN  C2   H7   single    0.930  0.020  1.080
 5GN  C13  H8   single    0.930  0.020  1.080
 5GN  C14  H9   single    0.930  0.020  1.080
 5GN  N    H10  single    0.860  0.020  1.020
 5GN  C15  H11  single    0.970  0.020  1.090
 5GN  C15  H12  single    0.970  0.020  1.090
 5GN  C21  H13  single    0.970  0.020  1.090
 5GN  C21  H14  single    0.970  0.020  1.090
 5GN  C21  H15  single    0.970  0.020  1.090
 5GN  C19  H16  single    0.930  0.020  1.080
 5GN  C18  H17  single    0.970  0.020  1.090
 5GN  C18  H18  single    0.970  0.020  1.090
 5GN  C18  H19  single    0.970  0.020  1.090

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
 5GN  H1   C11  C12  119.75  3.000
 5GN  H1   C11  C10  120.07  3.000
 5GN  C12  C11  C10  120.18  3.000
 5GN  H2   C6   C5   119.25  3.000
 5GN  H2   C6   C7   119.00  3.000
 5GN  C5   C6   C7   121.75  3.000
 5GN  H3   C8   C9   119.15  3.000
 5GN  H3   C8   C7   120.68  3.000
 5GN  C9   C8   C7   120.17  3.000
 5GN  S    C3   C2   108.56  3.000
 5GN  C2   C3   C4   128.16  3.000
 5GN  S    C3   C4   123.27  3.000
 5GN  C17  N2   C16  116.61  3.000
 5GN  C5   C10  C9   119.16  3.000
 5GN  C5   C10  C11  122.34  3.000
 5GN  C9   C10  C11  118.50  3.000
 5GN  N    C1   S    118.40  3.000
 5GN  S    C1   N1   115.03  3.000
 5GN  N    C1   N1   126.57  3.000
 5GN  H6   C7   C8   120.44  3.000
 5GN  H6   C7   C6   119.43  3.000
 5GN  C8   C7   C6   120.13  3.000
 5GN  C20  N3   C16  116.61  3.000
 5GN  C14  C9   C10  119.22  3.000
 5GN  C10  C9   C8   119.72  3.000
 5GN  C14  C9   C8   121.07  3.000
 5GN  C2   N1   C1   110.40  3.000
 5GN  H7   C2   N1   119.40  3.000
 5GN  H7   C2   C3   123.57  3.000
 5GN  N1   C2   C3   117.03  3.000
 5GN  C4   C5   C10  121.62  3.000
 5GN  C4   C5   C6   119.27  3.000
 5GN  C10  C5   C6   119.07  3.000
 5GN  C13  C12  BR   118.56  3.000
 5GN  C13  C12  C11  121.82  3.000
 5GN  BR   C12  C11  119.62  3.000
 5GN  H8   C13  C14  120.37  3.000
 5GN  H8   C13  C12  120.82  3.000
 5GN  C14  C13  C12  118.81  3.000
 5GN  H9   C14  C13  119.55  3.000
 5GN  H9   C14  C9   118.98  3.000
 5GN  C13  C14  C9   121.47  3.000
 5GN  C1   S    C3    88.97  3.000
 5GN  H10  N    C    116.80  3.000
 5GN  H10  N    C1   116.62  3.000
 5GN  C    N    C1   126.55  3.000
 5GN  C15  C    O    122.98  3.000
 5GN  O    C    N    124.57  3.000
 5GN  C15  C    N    112.45  3.000
 5GN  H12  C15  H11  107.39  3.000
 5GN  H12  C15  S1   110.78  3.000
 5GN  H11  C15  S1   110.47  3.000
 5GN  H12  C15  C    109.96  3.000
 5GN  H11  C15  C    110.52  3.000
 5GN  S1   C15  C    107.74  3.000
 5GN  C16  S1   C15  100.95  3.000
 5GN  S1   C16  N3   112.81  3.000
 5GN  N3   C16  N2   127.29  3.000
 5GN  S1   C16  N2   119.90  3.000
 5GN  C19  C20  C21  121.99  3.000
 5GN  C19  C20  N3   120.74  3.000
 5GN  C21  C20  N3   117.27  3.000
 5GN  H15  C21  H14  108.57  3.000
 5GN  H15  C21  H13  107.20  3.000
 5GN  H14  C21  H13  108.50  3.000
 5GN  H15  C21  C20  110.44  3.000
 5GN  H14  C21  C20  111.74  3.000
 5GN  H13  C21  C20  110.26  3.000
 5GN  H16  C19  C17  121.03  3.000
 5GN  H16  C19  C20  120.97  3.000
 5GN  C17  C19  C20  118.00  3.000
 5GN  C18  C17  C19  122.14  3.000
 5GN  C18  C17  N2   117.11  3.000
 5GN  C19  C17  N2   120.74  3.000
 5GN  H19  C18  H18  108.89  3.000
 5GN  H19  C18  H17  107.20  3.000
 5GN  H18  C18  H17  108.18  3.000
 5GN  H19  C18  C17  110.66  3.000
 5GN  H18  C18  C17  111.73  3.000
 5GN  H17  C18  C17  110.05  3.000
 5GN  H5   C4   H4   105.77  3.000
 5GN  H5   C4   C5   108.95  3.000
 5GN  H4   C4   C5   111.44  3.000
 5GN  H5   C4   C3   106.94  3.000
 5GN  H4   C4   C3   110.65  3.000
 5GN  C5   C4   C3   112.73  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
 5GN  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 5GN  CONST_02  C14  C9   C10  C11     0.00   0.0  0
 5GN  CONST_03  C8   C9   C10  C11   180.00   0.0  0
 5GN  CONST_04  C6   C5   C10  C11   180.00   0.0  0
 5GN  CONST_05  C9   C10  C5   C6      0.00   0.0  0
 5GN  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 5GN  CONST_07  C13  C14  C9   C8    180.00   0.0  0
 5GN  CONST_08  C5   C10  C9   C8      0.00   0.0  0
 5GN  CONST_09  C5   C6   C7   C8      0.00   0.0  0
 5GN  CONST_10  N1   C1   S    C3      0.00   0.0  0
 5GN  CONST_11  C1   N1   C2   C3      0.00   0.0  0
 5GN  CONST_12  C20  N3   C16  N2      0.00   0.0  0
 5GN  CONST_13  C20  C19  C17  N2      0.00   0.0  0
 5GN  CONST_14  C13  C12  C11  C10     0.00   0.0  0
 5GN  CONST_15  C13  C14  C9   C10     0.00   0.0  0
 5GN  CONST_16  C7   C8   C9   C10     0.00   0.0  0
 5GN  CONST_17  C7   C6   C5   C10     0.00   0.0  0
 5GN  CONST_18  C2   C3   S    C1      0.00   0.0  0
 5GN  CONST_19  C14  C9   C8   C7    180.00   0.0  0
 5GN  CONST_20  C17  N2   C16  N3      0.00   0.0  0
 5GN  CONST_21  C17  C19  C20  N3      0.00   0.0  0
 5GN  CONST_22  C12  C13  C14  C9      0.00   0.0  0
 5GN  CONST_23  C12  C11  C10  C9      0.00   0.0  0
 5GN  CONST_24  S    C3   C2   N1      0.00   0.0  0
 5GN  CONST_25  S    C1   N1   C2      0.00   0.0  0
 5GN  CONST_26  C12  C11  C10  C5    180.00   0.0  0
 5GN  CONST_27  C14  C9   C10  C5    180.00   0.0  0
 5GN  CONST_28  C19  C20  N3   C16     0.00   0.0  0
 5GN  CONST_29  C19  C17  N2   C16     0.00   0.0  0
 5GN  CONST_30  C4   C5   C10  C11     0.00   0.0  0
 5GN  CONST_31  N    C1   S    C3    180.00   0.0  0
 5GN  CONST_32  BR   C12  C11  C10   180.00   0.0  0
 5GN  CONST_33  C1   S    C3   C4    180.00   0.0  0
 5GN  CONST_34  N1   C2   C3   C4    180.00   0.0  0
 5GN  CONST_35  C9   C10  C5   C4    180.00   0.0  0
 5GN  CONST_36  C7   C6   C5   C4    180.00   0.0  0
 5GN  CONST_37  N    C1   N1   C2    180.00   0.0  0
 5GN  CONST_38  C14  C13  C12  BR    180.00   0.0  0
 5GN  CONST_39  C20  N3   C16  S1    180.00   0.0  0
 5GN  CONST_40  C17  N2   C16  S1    180.00   0.0  0
 5GN  CONST_41  C21  C20  N3   C16   180.00   0.0  0
 5GN  CONST_42  C18  C17  N2   C16   180.00   0.0  0
 5GN  CONST_43  C18  C17  C19  C20   180.00   0.0  0
 5GN  CONST_44  C17  C19  C20  C21   180.00   0.0  0
 5GN  CONST_45  H8   C13  C12  C11   180.00   0.0  0
 5GN  CONST_46  H3   C8   C7   C6    180.00   0.0  0
 5GN  CONST_47  H9   C14  C9   C8      0.00   0.0  0
 5GN  CONST_48  H2   C6   C7   C8    180.00   0.0  0
 5GN  CONST_49  H16  C19  C17  N2    180.00   0.0  0
 5GN  CONST_50  H7   C2   N1   C1    180.00   0.0  0
 5GN  CONST_51  H1   C11  C10  C9    180.00   0.0  0
 5GN  CONST_52  H6   C7   C8   C9    180.00   0.0  0
 5GN  CONST_53  C    N    C1   N1      0.00   0.0  0
 5GN  CONST_54  C    N    C1   S     180.00   0.0  0
 5GN  CONST_55  H10  N    C1   N1    180.00   0.0  0
 5GN  CONST_56  C15  C    N    C1    180.00   0.0  0
 5GN  CONST_57  O    C    N    C1      0.00   0.0  0
 5GN  Var_01    C3   C4   C5   C6    -91.33  30.0  2
 5GN  Var_02    C5   C4   C3   C2    118.79  30.0  2
 5GN  Var_03    H17  C18  C17  N2     68.42  30.0  2
 5GN  Var_04    H13  C21  C20  N3     59.24  30.0  2
 5GN  Var_05    H11  C15  S1   C16    56.68  30.0  3
 5GN  Var_06    S1   C15  C    N    -175.61  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
 5GN  plan-1  C3   0.020
 5GN  plan-1  C1   0.020
 5GN  plan-1  N1   0.020
 5GN  plan-1  C2   0.020
 5GN  plan-1  S    0.020
 5GN  plan-1  N    0.020
 5GN  plan-1  H7   0.020
 5GN  plan-1  C4   0.020
 5GN  plan-2  N2   0.020
 5GN  plan-2  N3   0.020
 5GN  plan-2  S1   0.020
 5GN  plan-2  C16  0.020
 5GN  plan-2  C20  0.020
 5GN  plan-2  C21  0.020
 5GN  plan-2  C19  0.020
 5GN  plan-2  C17  0.020
 5GN  plan-2  C18  0.020
 5GN  plan-2  H16  0.020
 5GN  plan-3  C11  0.020
 5GN  plan-3  C6   0.020
 5GN  plan-3  C8   0.020
 5GN  plan-3  C10  0.020
 5GN  plan-3  C7   0.020
 5GN  plan-3  C9   0.020
 5GN  plan-3  C5   0.020
 5GN  plan-3  C12  0.020
 5GN  plan-3  C13  0.020
 5GN  plan-3  C14  0.020
 5GN  plan-3  H1   0.020
 5GN  plan-3  H2   0.020
 5GN  plan-3  H3   0.020
 5GN  plan-3  H6   0.020
 5GN  plan-3  H8   0.020
 5GN  plan-3  H9   0.020
 5GN  plan-3  C4   0.020
 5GN  plan-3  BR   0.020
 5GN  plan-4  C1   0.020
 5GN  plan-4  N    0.020
 5GN  plan-4  C    0.020
 5GN  plan-4  O    0.020
 5GN  plan-4  C15  0.020
 5GN  plan-4  H10  0.020

