# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 23:55:09 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (4-amino-2-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-nitrophenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N[C@H]2C[C@@H]3CC[C@H]2C3)sc1C(=O)c4ccccc4[N+]([O-])=O
#
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
 TO7  TO7  "(4-amino-2-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]amino}-1,3-thiazol-5-yl)(2-nitrophenyl)methanone"
  ligand  43  25  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TO7
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
 TO7  C1   C  CR16   0  -0.218  50.9841  -17.3252  -15.8882
 TO7  C5   C  CR6    0  -0.059  51.6052  -15.7587  -14.1536
 TO7  C4   C  CR16   0  -0.266  50.0319  -17.5580  -13.6987
 TO7  C3   C  CR16   0  -0.259  51.6999  -16.2140  -15.4636
 TO7  C2   C  CR16   0  -0.256  50.1515  -17.9979  -15.0069
 TO7  C6   C  CR6    0   0.219  50.7610  -16.4525  -13.2914
 TO7  C7   C  CR5    0  -0.440  53.7071  -14.4926  -13.7577
 TO7  C8   C  CR5    0   0.572  54.5598  -13.4054  -13.4926
 TO7  O1   O  O     -1  -0.368  49.6256  -16.2773  -11.3166
 TO7  O3   O  O      0  -0.369  51.6215  -15.5191  -11.3948
 TO7  O2   O  O      0  -0.457  51.6122  -13.4665  -13.5993
 TO7  C10  C  C      0   0.354  52.3000  -14.4721  -13.7902
 TO7  N4   N  N      1   0.328  50.6590  -16.0474  -11.8975
 TO7  S1   S  S2     0   0.150  54.6898  -15.9350  -13.9661
 TO7  C9   C  CR5    0   0.361  56.1020  -14.9515  -13.7084
 TO7  N1   N  N      0  -0.474  55.8806  -13.6784  -13.4734
 TO7  N2   N  NH2    0  -0.827  54.1469  -12.1619  -13.2592
 TO7  N3   N  NH1    0  -0.639  57.3190  -15.4755  -13.7694
 TO7  C17  C  CH1    0  -0.080  57.5948  -16.8864  -13.9573
 TO7  C16  C  CH1    0  -0.261  57.4429  -17.7176  -12.6677
 TO7  C13  C  CH2    0  -0.437  58.8221  -17.5492  -12.0230
 TO7  C12  C  CH2    0  -0.445  57.4631  -19.1965  -13.0751
 TO7  C14  C  CH2    0  -0.459  59.0786  -17.1155  -14.3413
 TO7  C15  C  CH1    0  -0.257  59.5865  -18.0627  -13.2472
 TO7  C11  C  CH2    0  -0.437  58.9452  -19.4398  -13.4631
 TO7  H1   H  HCR6   0   0.279  51.0751  -17.6612  -16.9124
 TO7  H2   H  HCR6   0   0.299  49.3926  -18.0853  -13.0048
 TO7  H3   H  HCR6   0   0.284  52.3324  -15.6831  -16.1640
 TO7  H4   H  HCR6   0   0.280  49.5960  -18.8666  -15.3319
 TO7  H5   H  HNH2   0   0.402  54.8168  -11.4258  -13.1188
 TO7  H6   H  HNH2   0   0.413  53.1654  -11.9436  -13.2895
 TO7  H7   H  HNH1   0   0.409  58.0823  -14.8474  -13.5615
 TO7  H8   H  HCH1   0   0.269  56.9257  -17.2538  -14.7428
 TO7  H9   H  HCH1   0   0.240  56.5774  -17.4335  -12.0682
 TO7  H10  H  HCH2   0   0.240  58.9556  -18.1706  -11.1350
 TO7  H11  H  HCH2   0   0.237  59.0623  -16.5159  -11.7598
 TO7  H12  H  HCH2   0   0.233  56.7692  -19.4080  -13.8912
 TO7  H13  H  HCH2   0   0.240  57.1663  -19.8243  -12.2337
 TO7  H14  H  HCH2   0   0.252  59.1827  -17.5305  -15.3439
 TO7  H15  H  HCH2   0   0.251  59.6337  -16.1740  -14.3257
 TO7  H16  H  HCH1   0   0.232  60.6732  -18.0850  -13.1667
 TO7  H17  H  HCH2   0   0.229  59.0605  -19.7884  -14.4909
 TO7  H18  H  HCH2   0   0.235  59.4046  -20.1880  -12.8151

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
 TO7  C1   C2   aromatic  1.387  0.020  1.387
 TO7  C1   C3   aromatic  1.388  0.020  1.388
 TO7  C2   C4   aromatic  1.385  0.020  1.385
 TO7  C3   C5   aromatic  1.390  0.020  1.390
 TO7  C4   C6   aromatic  1.386  0.020  1.386
 TO7  C14  C17  single    1.550  0.020  1.550
 TO7  C14  C15  single    1.534  0.020  1.534
 TO7  C5   C6   aromatic  1.392  0.020  1.392
 TO7  C5   C10  single    1.507  0.020  1.507
 TO7  N1   C8   aromatic  1.349  0.020  1.349
 TO7  N1   C9   aromatic  1.313  0.020  1.313
 TO7  N2   C8   single    1.331  0.020  1.331
 TO7  N3   C9   single    1.326  0.020  1.326
 TO7  N3   C17  single    1.450  0.020  1.450
 TO7  C8   C7   aromatic  1.407  0.020  1.407
 TO7  C9   S1   aromatic  1.740  0.020  1.740
 TO7  C6   N4   single    1.455  0.020  1.455
 TO7  C7   S1   aromatic  1.758  0.020  1.758
 TO7  C7   C10  single    1.408  0.020  1.408
 TO7  C17  C16  single    1.542  0.020  1.542
 TO7  C10  O2   double    1.233  0.020  1.233
 TO7  C15  C11  single    1.534  0.020  1.534
 TO7  C15  C13  single    1.532  0.020  1.532
 TO7  C11  C12  single    1.551  0.020  1.551
 TO7  N4   O3   double    1.208  0.020  1.208
 TO7  N4   O1   single    1.208  0.020  1.208
 TO7  C16  C12  single    1.534  0.020  1.534
 TO7  C16  C13  single    1.532  0.020  1.532
 TO7  C1   H1   single    0.930  0.020  1.080
 TO7  C4   H2   single    0.930  0.020  1.080
 TO7  C3   H3   single    0.930  0.020  1.080
 TO7  C2   H4   single    0.930  0.020  1.080
 TO7  N2   H5   single    0.860  0.020  1.020
 TO7  N2   H6   single    0.860  0.020  1.020
 TO7  N3   H7   single    0.860  0.020  1.020
 TO7  C17  H8   single    0.970  0.020  1.090
 TO7  C16  H9   single    0.970  0.020  1.090
 TO7  C13  H10  single    0.970  0.020  1.090
 TO7  C13  H11  single    0.970  0.020  1.090
 TO7  C12  H12  single    0.970  0.020  1.090
 TO7  C12  H13  single    0.970  0.020  1.090
 TO7  C14  H14  single    0.970  0.020  1.090
 TO7  C14  H15  single    0.970  0.020  1.090
 TO7  C15  H16  single    0.970  0.020  1.090
 TO7  C11  H17  single    0.970  0.020  1.090
 TO7  C11  H18  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
 TO7  H1   C1   C2   120.11  3.000
 TO7  H1   C1   C3   119.66  3.000
 TO7  C2   C1   C3   120.23  3.000
 TO7  C10  C5   C6   123.77  3.000
 TO7  C10  C5   C3   118.40  3.000
 TO7  C6   C5   C3   117.51  3.000
 TO7  H2   C4   C6   120.78  3.000
 TO7  H2   C4   C2   120.16  3.000
 TO7  C6   C4   C2   119.05  3.000
 TO7  H3   C3   C5   119.26  3.000
 TO7  H3   C3   C1   119.72  3.000
 TO7  C5   C3   C1   121.01  3.000
 TO7  H4   C2   C4   119.65  3.000
 TO7  H4   C2   C1   120.48  3.000
 TO7  C4   C2   C1   119.87  3.000
 TO7  N4   C6   C4   117.83  3.000
 TO7  N4   C6   C5   119.82  3.000
 TO7  C4   C6   C5   122.32  3.000
 TO7  S1   C7   C10  124.61  3.000
 TO7  C10  C7   C8   126.79  3.000
 TO7  S1   C7   C8   108.52  3.000
 TO7  N2   C8   N1   119.37  3.000
 TO7  N2   C8   C7   124.54  3.000
 TO7  N1   C8   C7   116.09  3.000
 TO7  O2   C10  C7   124.46  3.000
 TO7  O2   C10  C5   118.45  3.000
 TO7  C7   C10  C5   117.01  3.000
 TO7  O3   N4   O1   124.40  3.000
 TO7  O1   N4   C6   117.90  3.000
 TO7  O3   N4   C6   117.69  3.000
 TO7  C9   S1   C7    88.42  3.000
 TO7  N3   C9   N1   123.08  3.000
 TO7  N3   C9   S1   120.97  3.000
 TO7  N1   C9   S1   115.94  3.000
 TO7  C9   N1   C8   111.02  3.000
 TO7  H6   N2   H5   119.71  3.000
 TO7  H6   N2   C8   120.01  3.000
 TO7  H5   N2   C8   120.13  3.000
 TO7  H7   N3   C17  119.21  3.000
 TO7  H7   N3   C9   115.99  3.000
 TO7  C17  N3   C9   124.40  3.000
 TO7  H8   C17  C14  110.95  3.000
 TO7  H8   C17  C16  111.03  3.000
 TO7  C14  C17  C16  102.82  3.000
 TO7  H8   C17  N3   107.65  3.000
 TO7  C16  C17  N3   113.42  3.000
 TO7  C14  C17  N3   110.99  3.000
 TO7  H9   C16  C12  114.05  3.000
 TO7  H9   C16  C13  117.04  3.000
 TO7  C12  C16  C13  101.88  3.000
 TO7  H9   C16  C17  113.43  3.000
 TO7  C13  C16  C17  101.77  3.000
 TO7  C12  C16  C17  107.23  3.000
 TO7  H11  C13  H10  108.38  3.000
 TO7  H11  C13  C15  113.56  3.000
 TO7  H10  C13  C15  113.46  3.000
 TO7  H11  C13  C16  113.77  3.000
 TO7  H10  C13  C16  112.94  3.000
 TO7  C15  C13  C16   94.36  3.000
 TO7  H13  C12  H12  106.99  3.000
 TO7  H13  C12  C11  111.26  3.000
 TO7  H12  C12  C11  112.94  3.000
 TO7  H13  C12  C16  110.27  3.000
 TO7  H12  C12  C16  112.14  3.000
 TO7  C11  C12  C16  103.31  3.000
 TO7  H15  C14  H14  107.01  3.000
 TO7  H15  C14  C15  110.70  3.000
 TO7  H14  C14  C15  112.92  3.000
 TO7  H15  C14  C17  110.82  3.000
 TO7  H14  C14  C17  112.06  3.000
 TO7  C15  C14  C17  103.40  3.000
 TO7  H16  C15  C11  114.12  3.000
 TO7  H16  C15  C14  113.30  3.000
 TO7  C11  C15  C14  108.39  3.000
 TO7  H16  C15  C13  116.44  3.000
 TO7  C11  C15  C13  101.82  3.000
 TO7  C14  C15  C13  101.41  3.000
 TO7  H18  C11  H17  107.20  3.000
 TO7  H18  C11  C15  110.85  3.000
 TO7  H17  C11  C15  112.03  3.000
 TO7  H18  C11  C12  111.17  3.000
 TO7  H17  C11  C12  112.74  3.000
 TO7  C15  C11  C12  102.91  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
 TO7  CONST_01  C6   C4   C2   C1      0.00   0.0  0
 TO7  CONST_02  C6   C5   C3   C1      0.00   0.0  0
 TO7  CONST_03  C2   C1   C3   C5      0.00   0.0  0
 TO7  CONST_04  C2   C4   C6   C5      0.00   0.0  0
 TO7  CONST_05  C3   C1   C2   C4      0.00   0.0  0
 TO7  CONST_06  C3   C5   C6   C4      0.00   0.0  0
 TO7  CONST_07  C9   N1   C8   C7      0.00   0.0  0
 TO7  CONST_08  N1   C9   S1   C7      0.00   0.0  0
 TO7  CONST_09  S1   C9   N1   C8      0.00   0.0  0
 TO7  CONST_10  C9   S1   C7   C8      0.00   0.0  0
 TO7  CONST_11  N1   C8   C7   S1      0.00   0.0  0
 TO7  CONST_12  C10  C5   C3   C1    180.00   0.0  0
 TO7  CONST_13  C10  C5   C6   C4    180.00   0.0  0
 TO7  CONST_14  N4   C6   C5   C3    180.00   0.0  0
 TO7  CONST_15  N4   C6   C4   C2    180.00   0.0  0
 TO7  CONST_16  N3   C9   S1   C7    180.00   0.0  0
 TO7  CONST_17  N3   C9   N1   C8    180.00   0.0  0
 TO7  CONST_18  N1   C8   C7   C10   180.00   0.0  0
 TO7  CONST_19  C9   S1   C7   C10   180.00   0.0  0
 TO7  CONST_20  N2   C8   C7   S1    180.00   0.0  0
 TO7  CONST_21  N2   C8   N1   C9    180.00   0.0  0
 TO7  CONST_22  C17  N3   C9   S1      0.00   0.0  0
 TO7  CONST_23  C17  N3   C9   N1    180.00   0.0  0
 TO7  CONST_24  H2   C4   C2   C1    180.00   0.0  0
 TO7  CONST_25  H1   C1   C3   C5    180.00   0.0  0
 TO7  CONST_26  H2   C4   C6   C5    180.00   0.0  0
 TO7  CONST_27  H1   C1   C2   C4    180.00   0.0  0
 TO7  CONST_28  H4   C2   C1   C3    180.00   0.0  0
 TO7  CONST_29  H3   C3   C1   C2    180.00   0.0  0
 TO7  CONST_30  H4   C2   C4   C6    180.00   0.0  0
 TO7  CONST_31  H3   C3   C5   C6    180.00   0.0  0
 TO7  CONST_36  H5   N2   C8   C7    180.00   0.0  0
 TO7  CONST_37  H6   N2   C8   C7      0.00   0.0  0
 TO7  CONST_38  H7   N3   C9   S1    180.00   0.0  0
 TO7  CONST_39  H5   N2   C8   N1      0.00   0.0  0
 TO7  CONST_40  H6   N2   C8   N1    180.00   0.0  0
 TO7  CONST_41  H7   N3   C9   N1      0.00   0.0  0
 TO7  Var_01    C15  C11  C12  C16    -0.73  30.0  1
 TO7  Var_02    C8   C7   C10  C5    177.59  30.0  2
 TO7  Var_03    S1   C7   C10  C5     -5.81  30.0  2
 TO7  Var_04    C7   C10  C5   C3    -70.07  30.0  2
 TO7  Var_05    C7   C10  C5   C6    116.66  30.0  2
 TO7  Var_06    H17  C11  C12  C16  -121.61  30.0  1
 TO7  Var_07    H18  C11  C12  C16   117.98  30.0  1
 TO7  Var_08    H12  C12  C11  C15   120.64  30.0  1
 TO7  Var_09    H13  C12  C11  C15  -119.02  30.0  1
 TO7  Var_10    O2   C10  C5   C3    106.87  30.0  2
 TO7  Var_11    O2   C10  C5   C6    -66.40  30.0  2
 TO7  Var_12    O2   C10  C7   C8      0.85  30.0  2
 TO7  Var_13    S1   C7   C10  O2    177.45  30.0  2

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
 TO7  chir_01  C17  C14  N3   C16  positiv
 TO7  chir_02  C16  C17  C12  C13  negativ
 TO7  chir_03  C15  C13  C11  C14  negativ

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
 TO7  plan-1  C7   0.020
 TO7  plan-1  C8   0.020
 TO7  plan-1  C10  0.020
 TO7  plan-1  S1   0.020
 TO7  plan-1  C9   0.020
 TO7  plan-1  N1   0.020
 TO7  plan-1  N2   0.020
 TO7  plan-1  N3   0.020
 TO7  plan-2  C1   0.020
 TO7  plan-2  C5   0.020
 TO7  plan-2  C4   0.020
 TO7  plan-2  C3   0.020
 TO7  plan-2  C2   0.020
 TO7  plan-2  C6   0.020
 TO7  plan-2  C10  0.020
 TO7  plan-2  N4   0.020
 TO7  plan-2  H1   0.020
 TO7  plan-2  H2   0.020
 TO7  plan-2  H3   0.020
 TO7  plan-2  H4   0.020
 TO7  plan-3  C6   0.020
 TO7  plan-3  O1   0.020
 TO7  plan-3  O3   0.020
 TO7  plan-3  N4   0.020
 TO7  plan-4  C8   0.020
 TO7  plan-4  N2   0.020
 TO7  plan-4  H5   0.020
 TO7  plan-4  H6   0.020
 TO7  plan-5  C9   0.020
 TO7  plan-5  N3   0.020
 TO7  plan-5  C17  0.020
 TO7  plan-5  H7   0.020
 TO7  plan-6  C5   0.020
 TO7  plan-6  C7   0.020
 TO7  plan-6  O2   0.020
 TO7  plan-6  C10  0.020

