# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:44:58 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: [(1~{R},3~{R})-1-(4-methanoyl-1,3-thiazol-2-yl)-4-methyl-3-(methylamino)pentyl] ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](C[C@@H](OC(C)=O)c1scc(C=O)n1)C(C)C
#
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
 O9K  O9K  '[(1~{R},3~{R})-1-(4-methanoyl-1,3-thiazol-2-yl)-4-methyl-3-(methylamino)pentyl] ethanoate'  ligand  39  19  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_O9K
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
 O9K  N1   N  NH1   0  -0.598  -2.9835  31.7717  16.4901
 O9K  C4   C  CH2   0  -0.482  -3.4683  29.3031  16.5333
 O9K  C5   C  CH1   0  -0.050  -2.9562  30.5510  17.2799
 O9K  C6   C  CH1   0  -0.244  -3.7077  30.7299  18.6133
 O9K  C7   C  CH3   0  -0.642  -3.2912  32.0171  19.3190
 O9K  C8   C  CH3   0  -0.660  -3.4827  29.5393  19.5446
 O9K  C22  C  CR5   0   0.023  -3.4242  27.8804  14.5025
 O9K  C24  C  CR15  0  -0.510  -4.8666  26.3946  13.2598
 O9K  O1   O  O     0  -0.434  -0.9688  28.8985  13.2491
 O9K  C2   C  CH3   0  -0.769   0.8111  28.4894  14.8191
 O9K  O2   O  O2    0  -0.456  -1.4237  28.8131  15.4335
 O9K  C3   C  CH1   0  -0.024  -2.8000  29.0637  15.1852
 O9K  C9   C  CH3   0  -0.531  -4.2626  32.1633  15.9372
 O9K  N4   N  N     0  -0.366  -3.0443  26.6613  14.6545
 O9K  C23  C  CR5   0   0.227  -3.8479  25.8067  13.9506
 O9K  S1   S  S2    0   0.294  -4.8121  28.0807  13.4792
 O9K  C25  C  C1    0   0.111  -3.6158  24.3614  13.9420
 O9K  O5   O  O     0  -0.371  -2.7070  23.8188  14.5227
 O9K  H1   H  HNH1  0   0.351  -2.2823  31.7392  15.7631
 O9K  H3   H  HCH2  0   0.250  -4.5455  29.3892  16.3635
 O9K  H4   H  HCH2  0   0.263  -3.3290  28.4084  17.1430
 O9K  H5   H  HCH1  0   0.229  -1.9034  30.3859  17.5358
 O9K  H6   H  HCH1  0   0.214  -4.7831  30.7871  18.4042
 O9K  H7   H  HCH3  0   0.217  -3.8021  32.1076  20.2790
 O9K  H8   H  HCH3  0   0.208  -2.2163  32.0218  19.5163
 O9K  H9   H  HCH3  0   0.232  -3.5225  32.9028  18.7303
 O9K  H10  H  HCH3  0   0.230  -3.9560  29.7169  20.5114
 O9K  H11  H  HCH3  0   0.230  -3.8957  28.6091  19.1553
 O9K  H12  H  HCH3  0   0.215  -2.4163  29.3814  19.7248
 O9K  H13  H  HCR5  0   0.328  -5.6160  25.9171  12.6463
 O9K  H14  H  HCH3  0   0.264   1.4681  28.4225  13.9570
 O9K  H15  H  HCH3  0   0.275   1.1615  29.2878  15.4742
 O9K  H16  H  HCH3  0   0.274   0.8657  27.5592  15.3852
 O9K  H17  H  HCH1  0   0.272  -2.9108  29.9435  14.5433
 O9K  H18  H  HCH3  0   0.234  -4.1374  33.0883  15.3746
 O9K  H19  H  HCH3  0   0.196  -4.7326  31.4342  15.2626
 O9K  H20  H  HCH3  0   0.227  -4.9757  32.3702  16.7368
 O9K  H21  H  H     0   0.201  -4.3493  23.7903  13.3487
 O9K  C1   C  C     0   0.572  -0.5972  28.7530  14.3839

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
 O9K  C24  S1   aromatic  1.701  0.020  1.701
 O9K  C24  C23  aromatic  1.364  0.020  1.364
 O9K  S1   C22  aromatic  1.736  0.020  1.736
 O9K  O1   C1   double    1.203  0.020  1.203
 O9K  C23  C25  single    1.464  0.020  1.464
 O9K  C23  N4   aromatic  1.368  0.020  1.368
 O9K  C25  O5   double    1.207  0.020  1.207
 O9K  C22  N4   aromatic  1.286  0.020  1.286
 O9K  C22  C3   single    1.502  0.020  1.502
 O9K  C1   C2   single    1.497  0.020  1.497
 O9K  C1   O2   single    1.337  0.020  1.337
 O9K  C3   O2   single    1.421  0.020  1.421
 O9K  C3   C4   single    1.524  0.020  1.524
 O9K  C9   N1   single    1.447  0.020  1.447
 O9K  N1   C5   single    1.454  0.020  1.454
 O9K  C4   C5   single    1.542  0.020  1.542
 O9K  C5   C6   single    1.541  0.020  1.541
 O9K  C6   C7   single    1.526  0.020  1.526
 O9K  C6   C8   single    1.528  0.020  1.528
 O9K  N1   H1   single    0.890  0.020  1.040
 O9K  C4   H3   single    0.970  0.020  1.090
 O9K  C4   H4   single    0.970  0.020  1.090
 O9K  C5   H5   single    0.970  0.020  1.090
 O9K  C6   H6   single    0.970  0.020  1.090
 O9K  C7   H7   single    0.970  0.020  1.090
 O9K  C7   H8   single    0.970  0.020  1.090
 O9K  C7   H9   single    0.970  0.020  1.090
 O9K  C8   H10  single    0.970  0.020  1.090
 O9K  C8   H11  single    0.970  0.020  1.090
 O9K  C8   H12  single    0.970  0.020  1.090
 O9K  C24  H13  single    0.930  0.020  1.080
 O9K  C2   H14  single    0.970  0.020  1.090
 O9K  C2   H15  single    0.970  0.020  1.090
 O9K  C2   H16  single    0.970  0.020  1.090
 O9K  C3   H17  single    0.970  0.020  1.090
 O9K  C9   H18  single    0.970  0.020  1.090
 O9K  C9   H19  single    0.970  0.020  1.090
 O9K  C9   H20  single    0.970  0.020  1.090
 O9K  C25  H21  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
 O9K  H1   N1   C9   110.31  3.000
 O9K  H1   N1   C5   110.53  3.000
 O9K  C9   N1   C5   116.82  3.000
 O9K  H4   C4   H3   106.08  3.000
 O9K  H4   C4   C3   108.03  3.000
 O9K  H3   C4   C3   107.88  3.000
 O9K  H4   C4   C5   110.52  3.000
 O9K  H3   C4   C5   109.78  3.000
 O9K  C3   C4   C5   114.20  3.000
 O9K  H5   C5   C6   106.49  3.000
 O9K  H5   C5   C4   108.07  3.000
 O9K  C6   C5   C4   110.55  3.000
 O9K  H5   C5   N1   105.74  3.000
 O9K  C6   C5   N1   111.31  3.000
 O9K  C4   C5   N1   114.22  3.000
 O9K  H6   C6   C8   107.53  3.000
 O9K  H6   C6   C7   108.16  3.000
 O9K  C8   C6   C7   109.58  3.000
 O9K  H6   C6   C5   108.61  3.000
 O9K  C8   C6   C5   111.41  3.000
 O9K  C7   C6   C5   111.40  3.000
 O9K  H9   C7   H8   107.65  3.000
 O9K  H9   C7   H7   107.99  3.000
 O9K  H8   C7   H7   107.53  3.000
 O9K  H9   C7   C6   112.24  3.000
 O9K  H8   C7   C6   110.83  3.000
 O9K  H7   C7   C6   110.43  3.000
 O9K  H12  C8   H11  107.78  3.000
 O9K  H12  C8   H10  107.50  3.000
 O9K  H11  C8   H10  106.93  3.000
 O9K  H12  C8   C6   110.90  3.000
 O9K  H11  C8   C6   113.04  3.000
 O9K  H10  C8   C6   110.44  3.000
 O9K  S1   C22  N4   114.54  3.000
 O9K  N4   C22  C3   124.77  3.000
 O9K  S1   C22  C3   120.62  3.000
 O9K  H13  C24  S1   122.26  3.000
 O9K  H13  C24  C23  127.98  3.000
 O9K  S1   C24  C23  109.75  3.000
 O9K  H16  C2   H15  107.26  3.000
 O9K  H16  C2   H14  109.23  3.000
 O9K  H15  C2   H14  109.12  3.000
 O9K  H16  C2   C1   110.37  3.000
 O9K  H15  C2   C1   110.36  3.000
 O9K  H14  C2   C1   110.43  3.000
 O9K  C3   O2   C1   118.00  3.000
 O9K  H17  C3   O2   110.01  3.000
 O9K  H17  C3   C22  108.94  3.000
 O9K  O2   C3   C22  110.07  3.000
 O9K  H17  C3   C4   110.37  3.000
 O9K  O2   C3   C4   107.34  3.000
 O9K  C22  C3   C4   110.10  3.000
 O9K  H20  C9   H19  107.22  3.000
 O9K  H20  C9   H18  107.00  3.000
 O9K  H19  C9   H18  107.18  3.000
 O9K  H20  C9   N1   110.42  3.000
 O9K  H19  C9   N1   115.65  3.000
 O9K  H18  C9   N1   108.98  3.000
 O9K  C23  N4   C22  110.97  3.000
 O9K  C25  C23  N4   121.78  3.000
 O9K  N4   C23  C24  115.47  3.000
 O9K  C25  C23  C24  122.75  3.000
 O9K  C24  S1   C22   89.27  3.000
 O9K  H21  C25  O5   121.78  3.000
 O9K  H21  C25  C23  114.14  3.000
 O9K  O5   C25  C23  124.07  3.000
 O9K  O2   C1   C2   111.17  3.000
 O9K  O2   C1   O1   122.96  3.000
 O9K  C2   C1   O1   125.87  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
 O9K  CONST_01  C23  C24  S1   C22     0.00   0.0  0
 O9K  CONST_02  C24  C23  N4   C22     0.00   0.0  0
 O9K  CONST_03  N4   C22  S1   C24     0.00   0.0  0
 O9K  CONST_04  S1   C24  C23  N4      0.00   0.0  0
 O9K  CONST_05  S1   C22  N4   C23     0.00   0.0  0
 O9K  CONST_06  C25  C23  N4   C22   180.00   0.0  0
 O9K  CONST_07  C3   C22  S1   C24   180.00   0.0  0
 O9K  CONST_08  C23  N4   C22  C3    180.00   0.0  0
 O9K  CONST_09  C25  C23  C24  S1    180.00   0.0  0
 O9K  CONST_10  H13  C24  S1   C22   180.00   0.0  0
 O9K  Var_01    O5   C25  C23  C24   178.48  30.0  2
 O9K  Var_02    H18  C9   N1   C5    179.93  30.0  3
 O9K  Var_03    H7   C7   C6   C5   -177.71  30.0  3
 O9K  Var_04    H10  C8   C6   C5    175.56  30.0  3
 O9K  Var_05    H14  C2   C1   O1     -1.29  30.0  3

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
 O9K  chir_01  C5  N1  C4   C6  positiv
 O9K  chir_02  C3  O2  C22  C4  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
 O9K  plan-1  C22  0.020
 O9K  plan-1  C24  0.020
 O9K  plan-1  C3   0.020
 O9K  plan-1  N4   0.020
 O9K  plan-1  C23  0.020
 O9K  plan-1  S1   0.020
 O9K  plan-1  C25  0.020
 O9K  plan-1  H13  0.020
 O9K  plan-2  O1   0.020
 O9K  plan-2  C2   0.020
 O9K  plan-2  O2   0.020
 O9K  plan-2  C1   0.020
 O9K  plan-3  C23  0.020
 O9K  plan-3  C25  0.020
 O9K  plan-3  O5   0.020
 O9K  plan-3  H21  0.020

