# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 20:03:14 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (4~{R},5~{R})-~{N}-(1,3-benzodioxol-4-ylmethyl)-4-methyl-5-[(3~{R})-1-methylpyrazolidin-3-yl]-1,3-thiazolidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N[C@H](NCc2cccc3OCOc23)S[C@H]1[C@H]4CCN(C)N4
#
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
 L9T  L9T  (4~{R},5~{R})-~{N}-(1,3-benzodioxol-4-ylmethyl)-4-methyl-5-[(3~{R})-1-methylpyrazolidin-3-yl]-1,3-thiazolidin-2-amine  ligand  47  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L9T
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
 L9T  C1   C  CR15  0  -0.109  -2.1519   1.8133  -0.3512
 L9T  C2   C  CR15  0  -0.011  -0.1179   0.8005   0.3192
 L9T  C3   C  CH2   0  -0.340   1.8487  -0.5037   0.7993
 L9T  C7   C  CR16  0  -0.355   5.7789  -1.5098  -0.7841
 L9T  C8   C  CR56  0   0.301   5.4116  -0.2173  -0.4971
 L9T  C9   C  CH2   0   0.067   5.3840   1.9477  -0.0177
 L9T  C10  C  CR56  0   0.287   4.1614   0.0980   0.0080
 L9T  C11  C  CR15  0  -0.376  -2.7160   0.3759  -0.2498
 L9T  C12  C  CR15  0  -0.039  -4.0861   0.2587   0.3905
 L9T  C13  C  CH2   0  -0.505  -5.1980   0.9841  -0.3936
 L9T  C14  C  CH2   0  -0.253  -6.3169  -0.0552  -0.4733
 L9T  N2   N  NR5   0  -0.319  -5.9658  -1.0229   0.5534
 L9T  N3   N  NR15  0  -0.497  -4.5348  -1.1342   0.3833
 L9T  S    S  S2    0  -0.122  -1.4517  -0.5369   0.6943
 L9T  N    N  NR15  0  -0.565  -0.7255   1.7057  -0.6041
 L9T  C    C  CH3   0  -0.674  -2.4155   2.6648   0.8829
 L9T  N1   N  NH1   0  -0.577   1.1022   0.2792  -0.1688
 L9T  C4   C  CR6   0  -0.014   3.2042  -0.8585   0.2655
 L9T  C5   C  CR16  0  -0.320   3.5719  -2.1799  -0.0272
 L9T  O2   O  O     0  -0.487   6.1303   0.9224  -0.6582
 L9T  O1   O  O     0  -0.479   4.0715   1.4402   0.1796
 L9T  C6   C  CR16  0  -0.262   4.8214  -2.4990  -0.5350
 L9T  H1   H  HCR5  0   0.264  -2.6006   2.3081  -1.2160
 L9T  H2   H  HCR5  0   0.272   0.0686   1.2834   1.2794
 L9T  H3   H  HCH2  0   0.254   1.9477   0.0927   1.7105
 L9T  H4   H  HCH2  0   0.234   1.3267  -1.4270   1.0863
 L9T  H6   H  HCH2  0   0.231   5.8386   2.1901   0.9495
 L9T  H7   H  HCR5  0   0.266  -2.7795  -0.0476  -1.2569
 L9T  H8   H  HCR5  0   0.236  -4.0429   0.6534   1.4128
 L9T  H9   H  HCH2  0   0.248  -5.5089   1.8884   0.1287
 L9T  H10  H  HCH2  0   0.246  -4.8705   1.2810  -1.3910
 L9T  H11  H  HCH2  0   0.239  -7.3076   0.3564  -0.2789
 L9T  H12  H  HCH2  0   0.198  -6.3338  -0.5158  -1.4724
 L9T  H13  H  HCH3  0   0.195  -6.3271  -2.7460  -0.6423
 L9T  H14  H  HCH3  0   0.233  -6.2809  -3.0127   1.1126
 L9T  H15  H  HCH3  0   0.233  -7.6651  -2.2003   0.3920
 L9T  H16  H  HNR5  0   0.352  -4.1858  -1.5923   1.2203
 L9T  H17  H  HNR5  0   0.359  -0.5727   1.3778  -1.5518
 L9T  H19  H  HCH3  0   0.230  -2.0803   2.1807   1.8015
 L9T  H20  H  HCH3  0   0.244  -1.8947   3.6176   0.7891
 L9T  H21  H  HCH3  0   0.239  -3.4779   2.8790   0.9936
 L9T  H22  H  HNH1  0   0.358   0.9499  -0.2684  -1.0088
 L9T  H24  H  HCR6  0   0.254   2.8543  -2.9702   0.1558
 L9T  H25  H  HCR6  0   0.259   5.0664  -3.5322  -0.7407
 L9T  H26  H  HCH2  0   0.246   5.3468   2.8311  -0.6543
 L9T  C15  C  CH3   0  -0.514  -6.5821  -2.3101   0.3339
 L9T  H5   H  HCR6  0   0.273   6.7549  -1.7528  -1.1816

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
 L9T  C14  C13  single    1.529  0.020  1.529
 L9T  C14  N2   single    1.454  0.020  1.454
 L9T  C    C1   single    1.522  0.020  1.522
 L9T  C13  C12  single    1.542  0.020  1.542
 L9T  C7   C6   aromatic  1.399  0.020  1.399
 L9T  C7   C8   aromatic  1.374  0.020  1.374
 L9T  C6   C5   aromatic  1.386  0.020  1.386
 L9T  N2   C15  single    1.444  0.020  1.444
 L9T  N2   N3   single    1.445  0.020  1.445
 L9T  C1   C11  single    1.548  0.020  1.548
 L9T  C1   N    single    1.453  0.020  1.453
 L9T  C12  N3   single    1.463  0.020  1.463
 L9T  C12  C11  single    1.517  0.020  1.517
 L9T  C8   O2   single    1.357  0.020  1.357
 L9T  C8   C10  aromatic  1.385  0.020  1.385
 L9T  C11  S    single    1.823  0.020  1.823
 L9T  O2   C9   single    1.421  0.020  1.421
 L9T  C5   C4   aromatic  1.402  0.020  1.402
 L9T  N    C2   single    1.429  0.020  1.429
 L9T  C2   N1   single    1.414  0.020  1.414
 L9T  C2   S    single    1.926  0.020  1.926
 L9T  C10  C4   aromatic  1.377  0.020  1.377
 L9T  C10  O1   single    1.356  0.020  1.356
 L9T  N1   C3   single    1.452  0.020  1.452
 L9T  C4   C3   single    1.499  0.020  1.499
 L9T  C9   O1   single    1.421  0.020  1.421
 L9T  C1   H1   single    0.970  0.020  1.090
 L9T  C2   H2   single    0.970  0.020  1.090
 L9T  C3   H3   single    0.970  0.020  1.090
 L9T  C3   H4   single    0.970  0.020  1.090
 L9T  C7   H5   single    0.930  0.020  1.080
 L9T  C9   H6   single    0.970  0.020  1.090
 L9T  C11  H7   single    0.970  0.020  1.090
 L9T  C12  H8   single    0.970  0.020  1.090
 L9T  C13  H9   single    0.970  0.020  1.090
 L9T  C13  H10  single    0.970  0.020  1.090
 L9T  C14  H11  single    0.970  0.020  1.090
 L9T  C14  H12  single    0.970  0.020  1.090
 L9T  C15  H13  single    0.970  0.020  1.090
 L9T  C15  H14  single    0.970  0.020  1.090
 L9T  C15  H15  single    0.970  0.020  1.090
 L9T  N3   H16  single    0.890  0.020  1.040
 L9T  N    H17  single    0.890  0.020  1.040
 L9T  C    H19  single    0.970  0.020  1.090
 L9T  C    H20  single    0.970  0.020  1.090
 L9T  C    H21  single    0.970  0.020  1.090
 L9T  N1   H22  single    0.890  0.020  1.040
 L9T  C5   H24  single    0.930  0.020  1.080
 L9T  C6   H25  single    0.930  0.020  1.080
 L9T  C9   H26  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
 L9T  H1   C1   C    108.50  3.000
 L9T  H1   C1   N    107.40  3.000
 L9T  C    C1   N    110.64  3.000
 L9T  H1   C1   C11  108.83  3.000
 L9T  N    C1   C11  107.49  3.000
 L9T  C    C1   C11  113.79  3.000
 L9T  H2   C2   N1   108.64  3.000
 L9T  H2   C2   N    111.16  3.000
 L9T  N1   C2   N    112.18  3.000
 L9T  H2   C2   S    104.74  3.000
 L9T  N1   C2   S    114.14  3.000
 L9T  N    C2   S    105.75  3.000
 L9T  H4   C3   H3   106.47  3.000
 L9T  H4   C3   C4   108.88  3.000
 L9T  H3   C3   C4   110.11  3.000
 L9T  H4   C3   N1   112.52  3.000
 L9T  H3   C3   N1   107.95  3.000
 L9T  C4   C3   N1   110.80  3.000
 L9T  H5   C7   C6   121.61  3.000
 L9T  H5   C7   C8   121.96  3.000
 L9T  C6   C7   C8   116.42  3.000
 L9T  O2   C8   C10  109.28  3.000
 L9T  C10  C8   C7   122.12  3.000
 L9T  O2   C8   C7   128.59  3.000
 L9T  H26  C9   H6   110.52  3.000
 L9T  H26  C9   O1   109.82  3.000
 L9T  H6   C9   O1   109.86  3.000
 L9T  H26  C9   O2   109.86  3.000
 L9T  H6   C9   O2   109.85  3.000
 L9T  O1   C9   O2   106.87  3.000
 L9T  O1   C10  C4   128.14  3.000
 L9T  O1   C10  C8   109.35  3.000
 L9T  C4   C10  C8   122.51  3.000
 L9T  H7   C11  S    108.85  3.000
 L9T  H7   C11  C12  107.83  3.000
 L9T  S    C11  C12  111.66  3.000
 L9T  H7   C11  C1   108.68  3.000
 L9T  S    C11  C1   104.25  3.000
 L9T  C12  C11  C1   115.38  3.000
 L9T  H8   C12  N3   111.05  3.000
 L9T  H8   C12  C13  109.46  3.000
 L9T  N3   C12  C13  102.96  3.000
 L9T  H8   C12  C11  109.28  3.000
 L9T  N3   C12  C11  110.39  3.000
 L9T  C13  C12  C11  113.60  3.000
 L9T  H10  C13  H9   107.34  3.000
 L9T  H10  C13  C14  110.92  3.000
 L9T  H9   C13  C14  112.35  3.000
 L9T  H10  C13  C12  112.12  3.000
 L9T  H9   C13  C12  110.64  3.000
 L9T  C14  C13  C12  103.55  3.000
 L9T  H12  C14  H11  107.81  3.000
 L9T  H12  C14  N2   111.49  3.000
 L9T  H11  C14  N2   110.17  3.000
 L9T  H12  C14  C13  110.06  3.000
 L9T  H11  C14  C13  113.52  3.000
 L9T  N2   C14  C13  103.82  3.000
 L9T  N3   N2   C15  109.64  3.000
 L9T  N3   N2   C14  101.96  3.000
 L9T  C15  N2   C14  112.51  3.000
 L9T  H16  N3   N2   106.13  3.000
 L9T  H16  N3   C12  108.65  3.000
 L9T  N2   N3   C12  103.28  3.000
 L9T  C11  S    C2    91.82  3.000
 L9T  H17  N    C2   109.57  3.000
 L9T  H17  N    C1   109.54  3.000
 L9T  C2   N    C1   110.61  3.000
 L9T  H21  C    H20  107.63  3.000
 L9T  H21  C    H19  107.53  3.000
 L9T  H20  C    H19  108.28  3.000
 L9T  H21  C    C1   111.17  3.000
 L9T  H20  C    C1   109.66  3.000
 L9T  H19  C    C1   112.40  3.000
 L9T  H22  N1   C3   109.78  3.000
 L9T  H22  N1   C2   110.82  3.000
 L9T  C3   N1   C2   114.36  3.000
 L9T  C5   C4   C10  115.66  3.000
 L9T  C10  C4   C3   122.03  3.000
 L9T  C5   C4   C3   122.30  3.000
 L9T  H24  C5   C6   119.42  3.000
 L9T  H24  C5   C4   118.59  3.000
 L9T  C6   C5   C4   121.99  3.000
 L9T  C9   O2   C8   105.92  3.000
 L9T  C10  O1   C9   105.94  3.000
 L9T  H25  C6   C5   119.59  3.000
 L9T  H25  C6   C7   119.12  3.000
 L9T  C5   C6   C7   121.29  3.000
 L9T  H15  C15  H14  107.53  3.000
 L9T  H15  C15  H13  108.53  3.000
 L9T  H14  C15  H13  108.33  3.000
 L9T  H15  C15  N2   109.03  3.000
 L9T  H14  C15  N2   110.34  3.000
 L9T  H13  C15  N2   112.92  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
 L9T  CONST_01  C4   C5   C6   C7      0.00   0.0  0
 L9T  CONST_02  C4   C10  C8   C7      0.00   0.0  0
 L9T  CONST_03  C5   C6   C7   C8      0.00   0.0  0
 L9T  CONST_04  C5   C4   C10  C8      0.00   0.0  0
 L9T  CONST_05  C6   C7   C8   C10     0.00   0.0  0
 L9T  CONST_06  C6   C5   C4   C10     0.00   0.0  0
 L9T  CONST_07  C6   C5   C4   C3    180.00   0.0  0
 L9T  CONST_08  C8   C10  C4   C3    180.00   0.0  0
 L9T  CONST_09  O1   C10  C4   C3      0.00   0.0  0
 L9T  CONST_10  H24  C5   C6   C7    180.00   0.0  0
 L9T  CONST_11  H25  C6   C7   C8    180.00   0.0  0
 L9T  CONST_12  H5   C7   C8   C10   180.00   0.0  0
 L9T  Var_01    O1   C9   O2   C8    -15.86  30.0  1
 L9T  Var_02    C10  C8   O2   C9     10.09  30.0  1
 L9T  Var_03    C4   C10  O1   C9    170.63  30.0  1
 L9T  Var_04    O2   C9   O1   C10    15.72  30.0  1
 L9T  Var_05    N2   C14  C13  C12    17.07  30.0  1
 L9T  Var_06    C14  N2   N3   C12    50.66  30.0  1
 L9T  Var_07    N3   N2   C14  C13   -41.14  30.0  1
 L9T  Var_08    C4   C3   N1   C2   -172.29  30.0  3
 L9T  Var_09    N1   C3   C4   C10    65.38  30.0  2
 L9T  Var_10    H13  C15  N2   C14    57.56  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
 L9T  chir_01  C1   C   C11  N    positiv
 L9T  chir_02  C2   S   N    N1   positiv
 L9T  chir_03  C11  S   C1   C12  positiv
 L9T  chir_04  C12  N3  C13  C11  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
 L9T  plan-1  C3   0.020
 L9T  plan-1  C7   0.020
 L9T  plan-1  C8   0.020
 L9T  plan-1  C10  0.020
 L9T  plan-1  C4   0.020
 L9T  plan-1  C5   0.020
 L9T  plan-1  O2   0.020
 L9T  plan-1  O1   0.020
 L9T  plan-1  C6   0.020
 L9T  plan-1  H24  0.020
 L9T  plan-1  H25  0.020
 L9T  plan-1  H5   0.020

