# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:27:57 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-{[(3S,5S)-5-(1,3-thiazolidin-3-ylcarbonyl)pyrrolidin-3-yl]methyl}-1,3-thiazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC[C@@H]1CN[C@@H](C1)C(=O)N2CCSC2)c3cscn3
#
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
 AIL  AIL  N-{[(3S,5S)-5-(1,3-thiazolidin-3-ylcarbonyl)pyrrolidin-3-yl]methyl}-1,3-thiazole-4-carboxamide  ligand  39  21  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AIL
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
 AIL  C1    C  CH2   0  -0.261   3.2963   2.5465   0.0516
 AIL  N2    N  NH1   0  -0.604   1.8447   2.6149   0.0640
 AIL  C3    C  CH1   0  -0.203   1.3363   1.5982  -0.8402
 AIL  C4    C  CH2   0  -0.472   2.5124   1.2839  -1.8000
 AIL  C5    C  CH1   0  -0.260   3.5966   2.2942  -1.4187
 AIL  C6    C  CH2   0  -0.296   5.0160   1.8090  -1.6683
 AIL  C7    C  C     0   0.535   0.8630   0.3418  -0.1112
 AIL  O8    O  O     0  -0.493   0.9933   0.2161   1.0991
 AIL  N9    N  NR5   0  -0.462   0.2929  -0.6277  -0.8546
 AIL  C10   C  CH2   0  -0.238  -0.2020  -1.8389  -0.2051
 AIL  C11   C  CH2   0  -0.606  -0.7595  -2.7370  -1.2996
 AIL  S12   S  S2    0  -0.002  -1.4111  -1.5993  -2.5533
 AIL  C13   C  CH2   0  -0.403   0.0400  -0.5514  -2.2808
 AIL  N14   N  NH1   0  -0.640   5.2591   1.4173  -3.0389
 AIL  C15   C  C     0   0.522   5.4981   2.2914  -4.0230
 AIL  O16   O  O     0  -0.489   5.5638   3.5040  -3.8687
 AIL  N17   N  N     0  -0.383   5.6255   0.3234  -5.5357
 AIL  C18   C  CR15  0  -0.218   5.8277   0.0035  -6.7697
 AIL  S19   S  S2    0   0.252   6.1202   1.3375  -7.8155
 AIL  C20   C  CR15  0  -0.505   5.9565   2.3943  -6.4887
 AIL  C21   C  CR5   0   0.205   5.6960   1.6764  -5.3617
 AIL  H11   H  HCH2  0   0.197   3.7031   1.7256   0.6619
 AIL  H12   H  HCH2  0   0.233   3.7347   3.4773   0.4172
 AIL  HN2   H  HNH1  0   0.351   1.4698   2.5002   0.9965
 AIL  H3    H  HCH1  0   0.266   0.4821   2.0015  -1.3969
 AIL  H41   H  HCH2  0   0.244   2.8801   0.2651  -1.6428
 AIL  H42   H  HCH2  0   0.260   2.2184   1.3609  -2.8458
 AIL  H5    H  HCH1  0   0.251   3.4332   3.2240  -1.9704
 AIL  H61   H  HCH2  0   0.252   5.2246   0.9379  -1.0449
 AIL  H62   H  HCH2  0   0.255   5.7300   2.5838  -1.3820
 AIL  H101  H  HCH2  0   0.254  -0.9816  -1.5833   0.5150
 AIL  H102  H  HCH2  0   0.261   0.5989  -2.3483   0.3323
 AIL  H111  H  HCH2  0   0.283   0.0154  -3.3649  -1.7406
 AIL  H112  H  HCH2  0   0.301  -1.5584  -3.3759  -0.9290
 AIL  H131  H  HCH2  0   0.296  -0.1853   0.4603  -2.6130
 AIL  H132  H  HCH2  0   0.282   0.8851  -0.9306  -2.8594
 AIL  HN14  H  HNH1  0   0.407   5.2132   0.4390  -3.2778
 AIL  H20   H  HCR5  0   0.318   6.0541   3.4629  -6.5943
 AIL  H18   H  HCR5  0   0.309   5.8202  -1.0102  -7.1448

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
 AIL  C1   N2    single    1.453  0.020  1.453
 AIL  C1   C5    single    1.522  0.020  1.522
 AIL  C1   H11   single    0.970  0.020  1.090
 AIL  C1   H12   single    0.970  0.020  1.090
 AIL  N2   C3    single    1.452  0.020  1.452
 AIL  N2   HN2   single    0.890  0.020  1.040
 AIL  C3   C7    single    1.528  0.020  1.528
 AIL  C3   C4    single    1.550  0.020  1.550
 AIL  C3   H3    single    0.970  0.020  1.090
 AIL  C4   C5    single    1.530  0.020  1.530
 AIL  C4   H41   single    0.970  0.020  1.090
 AIL  C4   H42   single    0.970  0.020  1.090
 AIL  C5   C6    single    1.521  0.020  1.521
 AIL  C5   H5    single    0.970  0.020  1.090
 AIL  C6   N14   single    1.446  0.020  1.446
 AIL  C6   H61   single    0.970  0.020  1.090
 AIL  C6   H62   single    0.970  0.020  1.090
 AIL  C7   N9    single    1.348  0.020  1.348
 AIL  C7   O8    double    1.224  0.020  1.224
 AIL  N9   C10   single    1.461  0.020  1.461
 AIL  N9   C13   single    1.450  0.020  1.450
 AIL  C10  C11   single    1.522  0.020  1.522
 AIL  C10  H101  single    0.970  0.020  1.090
 AIL  C10  H102  single    0.970  0.020  1.090
 AIL  C11  S12   single    1.814  0.020  1.814
 AIL  C11  H111  single    0.970  0.020  1.090
 AIL  C11  H112  single    0.970  0.020  1.090
 AIL  S12  C13   single    1.811  0.020  1.811
 AIL  C13  H131  single    0.970  0.020  1.090
 AIL  C13  H132  single    0.970  0.020  1.090
 AIL  N14  C15   single    1.338  0.020  1.338
 AIL  N14  HN14  single    0.860  0.020  1.020
 AIL  C15  C21   single    1.486  0.020  1.486
 AIL  C15  O16   double    1.224  0.020  1.224
 AIL  N17  C21   aromatic  1.366  0.020  1.366
 AIL  N17  C18   aromatic  1.291  0.020  1.291
 AIL  C18  S19   aromatic  1.720  0.020  1.720
 AIL  C18  H18   single    0.930  0.020  1.080
 AIL  S19  C20   aromatic  1.704  0.020  1.704
 AIL  C20  C21   aromatic  1.361  0.020  1.361
 AIL  C20  H20   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
 AIL  H12   C1   H11   107.56  3.000
 AIL  H12   C1   C5    112.68  3.000
 AIL  H11   C1   C5    109.82  3.000
 AIL  H12   C1   N2    110.99  3.000
 AIL  H11   C1   N2    113.54  3.000
 AIL  C5    C1   N2    102.31  3.000
 AIL  HN2   N2   C3    111.39  3.000
 AIL  HN2   N2   C1    111.88  3.000
 AIL  C3    N2   C1    108.14  3.000
 AIL  H3    C3   C7    107.66  3.000
 AIL  H3    C3   C4    110.56  3.000
 AIL  C7    C3   C4    111.33  3.000
 AIL  H3    C3   N2    109.34  3.000
 AIL  C4    C3   N2    105.18  3.000
 AIL  C7    C3   N2    112.77  3.000
 AIL  H42   C4   H41   107.12  3.000
 AIL  H42   C4   C5    112.58  3.000
 AIL  H41   C4   C5    109.92  3.000
 AIL  H42   C4   C3    112.05  3.000
 AIL  H41   C4   C3    110.77  3.000
 AIL  C5    C4   C3    104.45  3.000
 AIL  H5    C5   C6    109.15  3.000
 AIL  H5    C5   C4    109.26  3.000
 AIL  C6    C5   C4    114.20  3.000
 AIL  H5    C5   C1    108.48  3.000
 AIL  C6    C5   C1    113.31  3.000
 AIL  C4    C5   C1    102.14  3.000
 AIL  H62   C6   H61   106.95  3.000
 AIL  H62   C6   N14   109.32  3.000
 AIL  H61   C6   N14   107.04  3.000
 AIL  H62   C6   C5    109.94  3.000
 AIL  H61   C6   C5    109.84  3.000
 AIL  N14   C6   C5    113.51  3.000
 AIL  N9    C7   O8    121.10  3.000
 AIL  O8    C7   C3    121.56  3.000
 AIL  N9    C7   C3    117.34  3.000
 AIL  C13   N9   C10   114.95  3.000
 AIL  C13   N9   C7    125.31  3.000
 AIL  C10   N9   C7    119.63  3.000
 AIL  H102  C10  H101  107.98  3.000
 AIL  H102  C10  C11   110.35  3.000
 AIL  H101  C10  C11   110.55  3.000
 AIL  H102  C10  N9    110.95  3.000
 AIL  H101  C10  N9    109.95  3.000
 AIL  C11   C10  N9    107.08  3.000
 AIL  H112  C11  H111  108.75  3.000
 AIL  H112  C11  S12   109.87  3.000
 AIL  H111  C11  S12   109.69  3.000
 AIL  H112  C11  C10   111.75  3.000
 AIL  H111  C11  C10   111.74  3.000
 AIL  S12   C11  C10   104.98  3.000
 AIL  C13   S12  C11    88.34  3.000
 AIL  H132  C13  H131  108.74  3.000
 AIL  H132  C13  S12   109.84  3.000
 AIL  H131  C13  S12   109.03  3.000
 AIL  H132  C13  N9    111.57  3.000
 AIL  H131  C13  N9    112.66  3.000
 AIL  S12   C13  N9    104.91  3.000
 AIL  HN14  N14  C15   117.89  3.000
 AIL  HN14  N14  C6    118.68  3.000
 AIL  C15   N14  C6    123.39  3.000
 AIL  C21   C15  O16   121.08  3.000
 AIL  O16   C15  N14   124.34  3.000
 AIL  C21   C15  N14   114.58  3.000
 AIL  C21   N17  C18   111.05  3.000
 AIL  H18   C18  S19   121.17  3.000
 AIL  H18   C18  N17   124.27  3.000
 AIL  S19   C18  N17   114.57  3.000
 AIL  C20   S19  C18    89.50  3.000
 AIL  H20   C20  C21   128.39  3.000
 AIL  H20   C20  S19   121.98  3.000
 AIL  C21   C20  S19   109.63  3.000
 AIL  C20   C21  N17   115.26  3.000
 AIL  C20   C21  C15   123.57  3.000
 AIL  N17   C21  C15   121.17  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
 AIL  CONST_01  S19   C20  C21  N17    0.00   0.0  0
 AIL  CONST_02  C20   S19  C18  N17    0.00   0.0  0
 AIL  CONST_03  C20   C21  N17  C18    0.00   0.0  0
 AIL  CONST_04  C21   C20  S19  C18    0.00   0.0  0
 AIL  CONST_05  C21   N17  C18  S19    0.00   0.0  0
 AIL  CONST_06  C18   N17  C21  C15  180.00   0.0  0
 AIL  CONST_07  S19   C20  C21  C15  180.00   0.0  0
 AIL  CONST_08  C10   N9   C7   C3   180.00   0.0  0
 AIL  CONST_09  C13   N9   C7   C3     0.00   0.0  0
 AIL  CONST_10  H20   C20  C21  N17  180.00   0.0  0
 AIL  CONST_11  H18   C18  S19  C20  180.00   0.0  0
 AIL  CONST_12  C10   N9   C7   O8     0.00   0.0  0
 AIL  CONST_13  C13   N9   C7   O8   180.00   0.0  0
 AIL  CONST_14  C21   C15  N14  C6   180.00   0.0  0
 AIL  CONST_15  HN14  N14  C15  C21    0.00   0.0  0
 AIL  CONST_16  O16   C15  N14  C6     0.00   0.0  0
 AIL  Var_01    C5    C1   N2   C3    39.65  30.0  1
 AIL  Var_02    S12   C11  C10  N9   -32.18  30.0  1
 AIL  Var_03    S12   C13  N9   C10   25.16  30.0  1
 AIL  Var_04    C13   N9   C10  C11    4.57  30.0  1
 AIL  Var_05    N17   C21  C15  N14    0.31  30.0  2
 AIL  Var_06    C15   N14  C6   C5    79.42  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
 AIL  chir_01  C3  N2  C7  C4  positiv
 AIL  chir_02  C5  C1  C4  C6  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
 AIL  plan-1  C3    0.020
 AIL  plan-1  C7    0.020
 AIL  plan-1  O8    0.020
 AIL  plan-1  N9    0.020
 AIL  plan-1  C10   0.020
 AIL  plan-1  C13   0.020
 AIL  plan-2  C15   0.020
 AIL  plan-2  N17   0.020
 AIL  plan-2  C18   0.020
 AIL  plan-2  S19   0.020
 AIL  plan-2  C20   0.020
 AIL  plan-2  C21   0.020
 AIL  plan-2  H20   0.020
 AIL  plan-2  H18   0.020
 AIL  plan-3  C6    0.020
 AIL  plan-3  N14   0.020
 AIL  plan-3  C15   0.020
 AIL  plan-3  O16   0.020
 AIL  plan-3  C21   0.020
 AIL  plan-3  HN14  0.020

