# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 12:46:19 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: 1-[(4S)-5-(2,4-difluorophenyl)imidazo[2,1-b][1,3,4]thiadiazol-2-yl]-4-methylpiperidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(N)CCN(CC1)c2sc3ncc(n3n2)c4ccc(F)cc4F
#
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
 A5G  A5G  "1-[(4S)-5-(2,4-difluorophenyl)imidazo[2,1-b][1,3,4]thiadiazol-2-yl]-4-methylpiperidin-4-amine"
  ligand  41  24  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A5G
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
 A5G  C1   C  CT    0   0.071  22.4673  14.5925   -9.3709
 A5G  C2   C  CH2   0  -0.423  21.2909  14.4264  -10.3537
 A5G  C3   C  CH2   0  -0.362  21.6328  14.8533  -11.7759
 A5G  C11  C  CR16  0  -0.262  26.3552  10.8516  -14.0871
 A5G  C12  C  CR16  0  -0.411  27.7029  10.5847  -13.9143
 A5G  C13  C  CR6   0   0.538  28.1246   9.2702  -13.9387
 A5G  C14  C  CR16  0  -0.553  27.2444   8.2233  -14.1262
 A5G  C15  C  CR6   0   0.527  25.9086   8.5305  -14.2873
 A5G  N    N  NH2   0  -0.787  22.2065  13.9360   -8.0935
 A5G  C    C  CH3   0  -0.653  22.7163  16.0707   -9.0756
 A5G  C10  C  CR6   0  -0.162  25.4150   9.8331  -14.2768
 A5G  C4   C  CH2   0  -0.351  23.9894  14.4037  -11.4065
 A5G  C5   C  CH2   0  -0.423  23.7196  13.9448   -9.9785
 A5G  C6   C  CR5   0   0.392  22.7496  13.0200  -12.9467
 A5G  C7   C  CR5   0   0.350  23.9990  10.1118  -14.4680
 A5G  C8   C  CR15  0  -0.278  23.0038   9.4739  -15.1831
 A5G  C9   C  CR55  0   0.277  22.0811  11.1785  -14.3727
 A5G  F1   F  F     0  -0.298  25.0585   7.5112  -14.4559
 A5G  N1   N  NT    0  -0.458  22.8217  14.1602  -12.2456
 A5G  N2   N  N     0  -0.316  23.7534  12.2209  -13.1395
 A5G  N3   N  N     0  -0.359  23.3605  11.2159  -13.9564
 A5G  N4   N  N     0  -0.445  21.8163  10.1428  -15.1198
 A5G  S    S  S2    0   0.149  21.2288  12.5433  -13.7310
 A5G  H6   H  HCH2  0   0.241  20.4286  15.0000  -10.0017
 A5G  H5   H  HCH2  0   0.234  20.9873  13.3739  -10.3693
 A5G  H7   H  HCH2  0   0.270  21.8345  15.9254  -11.8301
 A5G  H8   H  HCH2  0   0.275  20.7928  14.6781  -12.4501
 A5G  H14  H  HCR6  0   0.278  26.0285  11.8813  -14.0783
 A5G  H15  H  HCR6  0   0.286  28.4104  11.3899  -13.7704
 A5G  H16  H  HCR6  0   0.304  27.5813   7.1948  -14.1407
 A5G  H3   H  HNH2  0   0.338  21.3796  14.3429   -7.6691
 A5G  H4   H  HNH2  0   0.338  21.9771  12.9608   -8.2550
 A5G  H    H  HCH3  0   0.230  21.8370  16.5218   -8.6103
 A5G  H2   H  HCH3  0   0.232  23.5562  16.1844   -8.3891
 A5G  H1   H  HCH3  0   0.228  22.9395  16.6489   -9.9717
 A5G  H10  H  HCH2  0   0.280  24.8525  13.8924  -11.8254
 A5G  H9   H  HCH2  0   0.263  24.2022  15.4742  -11.4451
 A5G  H12  H  HCH2  0   0.236  23.5992  12.8558   -9.9792
 A5G  H11  H  HCH2  0   0.243  24.5892  14.1670   -9.3553
 A5G  H13  H  HCR5  0   0.265  23.0968   8.5727  -15.7673
 A5G  F    F  F     0  -0.306  29.4238   8.9947  -13.7779

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
 A5G  N4   C8   aromatic  1.364  0.020  1.364
 A5G  N4   C9   aromatic  1.304  0.020  1.304
 A5G  C8   C7   aromatic  1.382  0.020  1.382
 A5G  F1   C15  single    1.338  0.020  1.338
 A5G  C9   N3   aromatic  1.346  0.020  1.346
 A5G  C9   S    aromatic  1.732  0.020  1.732
 A5G  C7   C10  single    1.456  0.020  1.456
 A5G  C7   N3   aromatic  1.374  0.020  1.374
 A5G  C15  C10  aromatic  1.393  0.020  1.393
 A5G  C15  C14  aromatic  1.380  0.020  1.380
 A5G  C10  C11  aromatic  1.399  0.020  1.399
 A5G  N3   N2   aromatic  1.353  0.020  1.353
 A5G  C14  C13  aromatic  1.381  0.020  1.381
 A5G  S    C6   aromatic  1.776  0.020  1.776
 A5G  C11  C12  aromatic  1.385  0.020  1.385
 A5G  N2   C6   aromatic  1.298  0.020  1.298
 A5G  C13  C12  aromatic  1.381  0.020  1.381
 A5G  C13  F    single    1.338  0.020  1.338
 A5G  C6   N1   single    1.340  0.020  1.340
 A5G  N1   C4   single    1.458  0.020  1.458
 A5G  N1   C3   single    1.454  0.020  1.454
 A5G  C4   C5   single    1.524  0.020  1.524
 A5G  C3   C2   single    1.524  0.020  1.524
 A5G  C5   C1   single    1.535  0.020  1.535
 A5G  C2   C1   single    1.542  0.020  1.542
 A5G  C1   C    single    1.528  0.020  1.528
 A5G  C1   N    single    1.460  0.020  1.460
 A5G  C2   H6   single    0.970  0.020  1.090
 A5G  C2   H5   single    0.970  0.020  1.090
 A5G  C3   H7   single    0.970  0.020  1.090
 A5G  C3   H8   single    0.970  0.020  1.090
 A5G  C11  H14  single    0.930  0.020  1.080
 A5G  C12  H15  single    0.930  0.020  1.080
 A5G  C14  H16  single    0.930  0.020  1.080
 A5G  N    H3   single    0.890  0.020  1.040
 A5G  N    H4   single    0.890  0.020  1.040
 A5G  C    H    single    0.970  0.020  1.090
 A5G  C    H2   single    0.970  0.020  1.090
 A5G  C    H1   single    0.970  0.020  1.090
 A5G  C4   H10  single    0.970  0.020  1.090
 A5G  C4   H9   single    0.970  0.020  1.090
 A5G  C5   H12  single    0.970  0.020  1.090
 A5G  C5   H11  single    0.970  0.020  1.090
 A5G  C8   H13  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
 A5G  C5   C1   C    110.60  3.000
 A5G  C    C1   N    107.17  3.000
 A5G  C5   C1   N    107.60  3.000
 A5G  N    C1   C2   111.90  3.000
 A5G  C    C1   C2   110.60  3.000
 A5G  C5   C1   C2   108.94  3.000
 A5G  H5   C2   H6   106.85  3.000
 A5G  H5   C2   C3   108.55  3.000
 A5G  H6   C2   C3   109.29  3.000
 A5G  H5   C2   C1   108.91  3.000
 A5G  H6   C2   C1   109.87  3.000
 A5G  C3   C2   C1   113.18  3.000
 A5G  H8   C3   H7   105.61  3.000
 A5G  H8   C3   N1   110.69  3.000
 A5G  H7   C3   N1   107.51  3.000
 A5G  H8   C3   C2   111.04  3.000
 A5G  H7   C3   C2   111.27  3.000
 A5G  N1   C3   C2   110.57  3.000
 A5G  H14  C11  C10  119.46  3.000
 A5G  H14  C11  C12  118.49  3.000
 A5G  C10  C11  C12  122.05  3.000
 A5G  H15  C12  C13  120.75  3.000
 A5G  H15  C12  C11  120.65  3.000
 A5G  C13  C12  C11  118.60  3.000
 A5G  F    C13  C14  118.64  3.000
 A5G  F    C13  C12  119.38  3.000
 A5G  C14  C13  C12  121.98  3.000
 A5G  H16  C14  C15  120.75  3.000
 A5G  H16  C14  C13  121.59  3.000
 A5G  C15  C14  C13  117.66  3.000
 A5G  F1   C15  C10  119.22  3.000
 A5G  C10  C15  C14  123.38  3.000
 A5G  F1   C15  C14  117.40  3.000
 A5G  H4   N    H3   105.53  3.000
 A5G  H4   N    C1   109.48  3.000
 A5G  H3   N    C1   109.35  3.000
 A5G  H1   C    H2   107.73  3.000
 A5G  H1   C    H    107.22  3.000
 A5G  H2   C    H    107.98  3.000
 A5G  H1   C    C1   112.82  3.000
 A5G  H2   C    C1   110.37  3.000
 A5G  H    C    C1   110.53  3.000
 A5G  C7   C10  C15  121.51  3.000
 A5G  C15  C10  C11  116.34  3.000
 A5G  C7   C10  C11  122.15  3.000
 A5G  H9   C4   H10  107.02  3.000
 A5G  H9   C4   N1   107.42  3.000
 A5G  H10  C4   N1   109.60  3.000
 A5G  H9   C4   C5   111.27  3.000
 A5G  H10  C4   C5   111.10  3.000
 A5G  N1   C4   C5   110.31  3.000
 A5G  H11  C5   H12  106.86  3.000
 A5G  H11  C5   C4   109.41  3.000
 A5G  H12  C5   C4   108.55  3.000
 A5G  H11  C5   C1   109.73  3.000
 A5G  H12  C5   C1   109.27  3.000
 A5G  C4   C5   C1   112.84  3.000
 A5G  S    C6   N2   115.56  3.000
 A5G  N2   C6   N1   124.06  3.000
 A5G  S    C6   N1   120.35  3.000
 A5G  N3   C7   C8   103.24  3.000
 A5G  N3   C7   C10  123.84  3.000
 A5G  C8   C7   C10  132.86  3.000
 A5G  H13  C8   N4   120.67  3.000
 A5G  H13  C8   C7   127.18  3.000
 A5G  N4   C8   C7   112.12  3.000
 A5G  S    C9   N4   137.56  3.000
 A5G  S    C9   N3   109.34  3.000
 A5G  N4   C9   N3   113.09  3.000
 A5G  C6   N1   C4   119.08  3.000
 A5G  C4   N1   C3   112.91  3.000
 A5G  C6   N1   C3   122.03  3.000
 A5G  N3   N2   C6   108.81  3.000
 A5G  N2   N3   C9   118.90  3.000
 A5G  N2   N3   C7   133.35  3.000
 A5G  C9   N3   C7   107.71  3.000
 A5G  C9   N4   C8   103.84  3.000
 A5G  C9   S    C6    87.35  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
 A5G  CONST_03  C14  C15  C10  C11     0.00   0.0  0
 A5G  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 A5G  CONST_05  C7   C10  C11  C12   180.00   0.0  0
 A5G  CONST_06  C15  C10  C11  C12     0.00   0.0  0
 A5G  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 A5G  CONST_08  C10  C15  C14  C13     0.00   0.0  0
 A5G  CONST_09  C10  C11  C12  C13     0.00   0.0  0
 A5G  CONST_10  C7   C10  C15  C14   180.00   0.0  0
 A5G  CONST_13  N4   C8   C7   C10   180.00   0.0  0
 A5G  CONST_14  C9   N3   C7   C10   180.00   0.0  0
 A5G  CONST_15  N2   N3   C7   C10     0.00   0.0  0
 A5G  CONST_16  N4   C9   S    C6    180.00   0.0  0
 A5G  CONST_17  N3   C9   S    C6      0.00   0.0  0
 A5G  CONST_18  C9   N3   N2   C6      0.00   0.0  0
 A5G  CONST_19  C7   N3   N2   C6    180.00   0.0  0
 A5G  CONST_20  C9   N4   C8   C7      0.00   0.0  0
 A5G  CONST_21  N4   C9   N3   C7      0.00   0.0  0
 A5G  CONST_22  S    C9   N3   C7    180.00   0.0  0
 A5G  CONST_23  N3   C9   N4   C8      0.00   0.0  0
 A5G  CONST_24  S    C9   N4   C8    180.00   0.0  0
 A5G  CONST_25  C9   N3   C7   C8      0.00   0.0  0
 A5G  CONST_26  N2   N3   C7   C8    180.00   0.0  0
 A5G  CONST_27  N2   C6   S    C9      0.00   0.0  0
 A5G  CONST_28  N4   C9   N3   N2    180.00   0.0  0
 A5G  CONST_29  S    C9   N3   N2      0.00   0.0  0
 A5G  CONST_30  N4   C8   C7   N3      0.00   0.0  0
 A5G  CONST_31  S    C6   N2   N3      0.00   0.0  0
 A5G  CONST_32  N1   C6   S    C9    180.00   0.0  0
 A5G  CONST_33  N3   N2   C6   N1    180.00   0.0  0
 A5G  CONST_34  F1   C15  C10  C11   180.00   0.0  0
 A5G  CONST_35  F    C13  C12  C11   180.00   0.0  0
 A5G  CONST_36  F1   C15  C14  C13   180.00   0.0  0
 A5G  CONST_37  F    C13  C14  C15   180.00   0.0  0
 A5G  CONST_38  F1   C15  C10  C7      0.00   0.0  0
 A5G  CONST_39  H16  C14  C13  C12   180.00   0.0  0
 A5G  CONST_40  H14  C11  C12  C13   180.00   0.0  0
 A5G  CONST_41  H15  C12  C13  C14   180.00   0.0  0
 A5G  CONST_42  H14  C11  C10  C15   180.00   0.0  0
 A5G  CONST_43  H13  C8   C7   C10     0.00   0.0  0
 A5G  CONST_44  H16  C14  C15  C10   180.00   0.0  0
 A5G  CONST_45  H15  C12  C11  C10   180.00   0.0  0
 A5G  CONST_46  H14  C11  C10  C7      0.00   0.0  0
 A5G  CONST_47  H13  C8   N4   C9    180.00   0.0  0
 A5G  CONST_48  H13  C8   C7   N3    180.00   0.0  0
 A5G  Var_01    N1   C4   C5   C1    -55.49  30.0  1
 A5G  Var_02    N1   C3   C2   C1     54.09  30.0  1
 A5G  Var_03    C6   N1   C3   C2     93.72  30.0  1
 A5G  Var_04    C4   N1   C3   C2    -58.75  30.0  1
 A5G  Var_05    S    C6   N1   C3     17.56  30.0  1
 A5G  Var_06    N2   C6   N1   C3   -164.59  30.0  1
 A5G  Var_07    C5   C4   N1   C3     59.46  30.0  1
 A5G  Var_08    S    C6   N1   C4    168.41  30.0  1
 A5G  Var_09    N2   C6   N1   C4    -13.74  30.0  1
 A5G  Var_10    C6   N1   C4   C5    -93.90  30.0  1
 A5G  Var_11    H10  C4   C5   C1   -177.24  30.0  1
 A5G  Var_12    H9   C4   C5   C1     63.63  30.0  1
 A5G  Var_13    H7   C3   C2   C1    -65.31  30.0  1
 A5G  Var_14    H8   C3   C2   C1    177.36  30.0  1
 A5G  Var_15    H10  C4   N1   C3   -177.90  30.0  1
 A5G  Var_16    H9   C4   N1   C3    -61.97  30.0  1
 A5G  Var_17    H7   C3   N1   C4     62.89  30.0  1
 A5G  Var_18    H8   C3   N1   C4    177.77  30.0  1
 A5G  Var_19    H10  C4   N1   C6     28.73  30.0  1
 A5G  Var_20    H9   C4   N1   C6    144.66  30.0  1
 A5G  Var_21    H7   C3   N1   C6   -144.64  30.0  1
 A5G  Var_22    H8   C3   N1   C6    -29.75  30.0  1
 A5G  Var_23    H12  C5   C4   N1     65.78  30.0  1
 A5G  Var_24    H11  C5   C4   N1   -177.95  30.0  1
 A5G  Var_25    H6   C2   C3   N1    176.87  30.0  1
 A5G  Var_26    H5   C2   C3   N1    -66.94  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 A5G  chir_01  C1  C2  C5  N  positiv

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
 A5G  plan-1  C11  0.020
 A5G  plan-1  C12  0.020
 A5G  plan-1  C13  0.020
 A5G  plan-1  C14  0.020
 A5G  plan-1  C15  0.020
 A5G  plan-1  C10  0.020
 A5G  plan-1  C7   0.020
 A5G  plan-1  F1   0.020
 A5G  plan-1  H14  0.020
 A5G  plan-1  H15  0.020
 A5G  plan-1  H16  0.020
 A5G  plan-1  F    0.020
 A5G  plan-2  C10  0.020
 A5G  plan-2  C7   0.020
 A5G  plan-2  C8   0.020
 A5G  plan-2  C9   0.020
 A5G  plan-2  N2   0.020
 A5G  plan-2  N3   0.020
 A5G  plan-2  N4   0.020
 A5G  plan-2  S    0.020
 A5G  plan-2  H13  0.020

