# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:21:10 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: methyl (3R,9bR)-5-oxo-9b-phenyl-2,3,5,9b-tetrahydro[1,3]thiazolo[2,3-a]isoindole-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H]1CS[C@]2(N1C(=O)c3ccccc23)c4ccccc4
#
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
 BM5  BM5  'methyl (3R,9bR)-5-oxo-9b-phenyl-2,3,5,9b-tetrahydro[1,3]thiazolo[2,3-a]isoindole-3-carboxylate'  ligand  38  23  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BM5
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
 BM5  S1    S  S2    0   0.091   0.4528   2.0089   0.3505
 BM5  C2    C  CH2   0  -0.599   1.3479   1.1380   1.6673
 BM5  C3    C  CR15  0  -0.167   0.5550  -0.1644   1.9168
 BM5  C5    C  C     0  -0.215   0.2578   0.3818  -0.4622
 BM5  N4    N  N     0  -0.493  -0.0452  -0.4985   0.6478
 BM5  C6    C  CR5   0   0.544  -1.2339  -1.1598   0.5114
 BM5  OE    O  O     0  -0.445  -1.7043  -1.9280   1.3240
 BM5  C7    C  CR56  0  -0.068  -1.7969  -0.7174  -0.7784
 BM5  C12   C  CR56  0   0.204  -0.9603   0.2393  -1.3318
 BM5  C8    C  CR16  0  -0.290  -2.9813  -1.0915  -1.3899
 BM5  C9    C  CR16  0  -0.256  -3.3109  -0.4757  -2.5889
 BM5  C10   C  CR16  0  -0.234  -2.4668   0.4825  -3.1499
 BM5  C11   C  CR16  0  -0.324  -1.2741   0.8456  -2.5335
 BM5  C13   C  CR6   0   0.214   1.5178  -0.0290  -1.2087
 BM5  C14   C  CR16  0  -0.286   2.1611   0.8754  -2.0494
 BM5  C15   C  CR16  0  -0.243   3.2707   0.4866  -2.7845
 BM5  C16   C  CR16  0  -0.261   3.7571  -0.8108  -2.6841
 BM5  C17   C  CR16  0  -0.236   3.1198  -1.7157  -1.8486
 BM5  C18   C  CR16  0  -0.292   2.0030  -1.3291  -1.1181
 BM5  CA    C  C     0   0.587  -0.5075   0.1145   2.9722
 BM5  OB    O  O     0  -0.427  -1.5357   0.6983   2.7593
 BM5  OC    O  O2    0  -0.444  -0.1023  -0.2947   4.1595
 BM5  CD    C  CH3   0  -0.427  -0.9423  -0.0033   5.2798
 BM5  H21   H  HCH2  0   0.319   1.4179   1.7698   2.5513
 BM5  H22   H  HCH2  0   0.314   2.3600   0.9031   1.3379
 BM5  H3    H  HCR5  0   0.317   1.2347  -0.9436   2.2650
 BM5  H81   H  HCR6  0   0.269  -3.6280  -1.8373  -0.9461
 BM5  H91   H  HCR6  0   0.271  -4.2295  -0.7397  -3.0957
 BM5  H101  H  HCR6  0   0.273  -2.7444   0.9510  -4.0847
 BM5  H111  H  HCR6  0   0.266  -0.6256   1.5837  -2.9873
 BM5  H141  H  HCR6  0   0.253   1.8080   1.8962  -2.1240
 BM5  H151  H  HCR6  0   0.260   3.7595   1.2014  -3.4334
 BM5  H161  H  HCR6  0   0.260   4.6288  -1.1114  -3.2506
 BM5  H171  H  HCR6  0   0.260   3.4895  -2.7289  -1.7603
 BM5  H181  H  HCR6  0   0.259   1.5175  -2.0501  -0.4742
 BM5  HD1   H  HCH3  0   0.256  -0.4422  -0.4277   6.1446
 BM5  HD2   H  HCH3  0   0.244  -1.0572   1.0713   5.4174
 BM5  HD3   H  HCH3  0   0.244  -1.9240  -0.4616   5.1663

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
 BM5  S1   C2    single    1.815  0.020  1.815
 BM5  S1   C5    single    1.829  0.020  1.829
 BM5  C2   C3    single    1.545  0.020  1.545
 BM5  C2   H21   single    0.970  0.020  1.090
 BM5  C2   H22   single    0.970  0.020  1.090
 BM5  C3   N4    single    1.443  0.020  1.443
 BM5  C3   CA    single    1.523  0.020  1.523
 BM5  C3   H3    single    0.970  0.020  1.090
 BM5  C5   N4    single    1.449  0.020  1.449
 BM5  C5   C12   single    1.503  0.020  1.503
 BM5  C5   C13   single    1.521  0.020  1.521
 BM5  N4   C6    single    1.367  0.020  1.367
 BM5  C6   OE    double    1.213  0.020  1.213
 BM5  C6   C7    single    1.475  0.020  1.475
 BM5  C7   C12   aromatic  1.386  0.020  1.386
 BM5  C7   C8    aromatic  1.384  0.020  1.384
 BM5  C12  C11   aromatic  1.382  0.020  1.382
 BM5  C8   C9    aromatic  1.388  0.020  1.388
 BM5  C8   H81   single    0.930  0.020  1.080
 BM5  C9   C10   aromatic  1.395  0.020  1.395
 BM5  C9   H91   single    0.930  0.020  1.080
 BM5  C10  C11   aromatic  1.391  0.020  1.391
 BM5  C10  H101  single    0.930  0.020  1.080
 BM5  C11  H111  single    0.930  0.020  1.080
 BM5  C13  C14   aromatic  1.392  0.020  1.392
 BM5  C13  C18   aromatic  1.391  0.020  1.391
 BM5  C14  C15   aromatic  1.387  0.020  1.387
 BM5  C14  H141  single    0.930  0.020  1.080
 BM5  C15  C16   aromatic  1.389  0.020  1.389
 BM5  C15  H151  single    0.930  0.020  1.080
 BM5  C16  C17   aromatic  1.387  0.020  1.387
 BM5  C16  H161  single    0.930  0.020  1.080
 BM5  C17  C18   aromatic  1.389  0.020  1.389
 BM5  C17  H171  single    0.930  0.020  1.080
 BM5  C18  H181  single    0.930  0.020  1.080
 BM5  CA   OB    double    1.201  0.020  1.201
 BM5  CA   OC    single    1.320  0.020  1.320
 BM5  OC   CD    single    1.430  0.020  1.430
 BM5  CD   HD1   single    0.970  0.020  1.090
 BM5  CD   HD2   single    0.970  0.020  1.090
 BM5  CD   HD3   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
 BM5  C5    S1   C2    87.02  3.000
 BM5  H22   C2   H21  108.10  3.000
 BM5  H22   C2   C3   110.10  3.000
 BM5  H21   C2   C3   113.01  3.000
 BM5  H22   C2   S1   110.01  3.000
 BM5  H21   C2   S1   110.02  3.000
 BM5  C3    C2   S1   105.58  3.000
 BM5  H3    C3   CA   110.13  3.000
 BM5  H3    C3   N4   111.99  3.000
 BM5  CA    C3   N4   111.19  3.000
 BM5  H3    C3   C2   109.51  3.000
 BM5  CA    C3   C2   108.39  3.000
 BM5  N4    C3   C2   105.46  3.000
 BM5  C13   C5   C12  111.21  3.000
 BM5  C13   C5   N4   112.66  3.000
 BM5  C12   C5   N4   102.48  3.000
 BM5  C13   C5   S1   111.71  3.000
 BM5  C12   C5   S1   115.32  3.000
 BM5  N4    C5   S1   102.85  3.000
 BM5  C6    N4   C5   113.54  3.000
 BM5  C6    N4   C3   124.16  3.000
 BM5  C5    N4   C3   116.49  3.000
 BM5  C7    C6   OE   128.87  3.000
 BM5  C7    C6   N4   105.90  3.000
 BM5  OE    C6   N4   125.21  3.000
 BM5  C8    C7   C12  121.77  3.000
 BM5  C8    C7   C6   129.17  3.000
 BM5  C12   C7   C6   109.01  3.000
 BM5  C11   C12  C7   120.85  3.000
 BM5  C11   C12  C5   130.19  3.000
 BM5  C7    C12  C5   108.88  3.000
 BM5  H81   C8   C9   121.21  3.000
 BM5  H81   C8   C7   121.08  3.000
 BM5  C9    C8   C7   117.70  3.000
 BM5  H91   C9   C10  119.55  3.000
 BM5  H91   C9   C8   119.88  3.000
 BM5  C10   C9   C8   120.57  3.000
 BM5  H101  C10  C11  119.33  3.000
 BM5  H101  C10  C9   119.33  3.000
 BM5  C11   C10  C9   121.34  3.000
 BM5  H111  C11  C10  120.41  3.000
 BM5  H111  C11  C12  121.85  3.000
 BM5  C10   C11  C12  117.74  3.000
 BM5  C18   C13  C14  119.04  3.000
 BM5  C18   C13  C5   120.63  3.000
 BM5  C14   C13  C5   120.24  3.000
 BM5  H141  C14  C15  119.26  3.000
 BM5  H141  C14  C13  120.22  3.000
 BM5  C15   C14  C13  120.51  3.000
 BM5  H151  C15  C16  120.14  3.000
 BM5  H151  C15  C14  119.61  3.000
 BM5  C16   C15  C14  120.25  3.000
 BM5  H161  C16  C17  120.28  3.000
 BM5  H161  C16  C15  120.24  3.000
 BM5  C17   C16  C15  119.48  3.000
 BM5  H171  C17  C18  119.49  3.000
 BM5  H171  C17  C16  120.21  3.000
 BM5  C18   C17  C16  120.31  3.000
 BM5  H181  C18  C17  119.23  3.000
 BM5  H181  C18  C13  120.35  3.000
 BM5  C17   C18  C13  120.42  3.000
 BM5  OC    CA   OB   124.96  3.000
 BM5  OC    CA   C3   110.64  3.000
 BM5  OB    CA   C3   124.27  3.000
 BM5  CD    OC   CA   117.47  3.000
 BM5  HD3   CD   HD2  109.46  3.000
 BM5  HD3   CD   HD1  109.49  3.000
 BM5  HD2   CD   HD1  109.49  3.000
 BM5  HD3   CD   OC   111.22  3.000
 BM5  HD2   CD   OC   111.21  3.000
 BM5  HD1   CD   OC   105.89  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
 BM5  CONST_01  C10   C11  C12  C7      0.00   0.0  0
 BM5  CONST_02  C10   C9   C8   C7      0.00   0.0  0
 BM5  CONST_03  C9    C8   C7   C12     0.00   0.0  0
 BM5  CONST_04  C9    C10  C11  C12     0.00   0.0  0
 BM5  CONST_05  C11   C12  C7   C8      0.00   0.0  0
 BM5  CONST_06  C11   C10  C9   C8      0.00   0.0  0
 BM5  CONST_07  C16   C15  C14  C13     0.00   0.0  0
 BM5  CONST_08  C16   C17  C18  C13     0.00   0.0  0
 BM5  CONST_09  C17   C18  C13  C14     0.00   0.0  0
 BM5  CONST_10  C17   C16  C15  C14     0.00   0.0  0
 BM5  CONST_11  C18   C13  C14  C15     0.00   0.0  0
 BM5  CONST_12  C18   C17  C16  C15     0.00   0.0  0
 BM5  CONST_13  C15   C14  C13  C5    180.00   0.0  0
 BM5  CONST_14  C17   C18  C13  C5    180.00   0.0  0
 BM5  CONST_16  C7    C6   N4   C5      0.00   0.0  0
 BM5  CONST_18  OE    C6   N4   C5    180.00   0.0  0
 BM5  CONST_19  H111  C11  C12  C5      0.00   0.0  0
 BM5  CONST_20  H141  C14  C13  C5      0.00   0.0  0
 BM5  CONST_21  H181  C18  C13  C5      0.00   0.0  0
 BM5  CONST_22  H81   C8   C7   C6      0.00   0.0  0
 BM5  CONST_23  H91   C9   C8   C7    180.00   0.0  0
 BM5  CONST_24  H101  C10  C11  C12   180.00   0.0  0
 BM5  CONST_25  H151  C15  C14  C13   180.00   0.0  0
 BM5  CONST_26  H171  C17  C18  C13   180.00   0.0  0
 BM5  CONST_27  H161  C16  C15  C14   180.00   0.0  0
 BM5  Var_01    H21   C2   S1   C5   -163.89  30.0  1
 BM5  Var_02    HD1   CD   OC   CA    179.39  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
 BM5  chir_01  C3  C2  N4   CA   positiv
 BM5  chir_02  C5  N4  C12  C13  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
 BM5  plan-1  C5    0.020
 BM5  plan-1  C13   0.020
 BM5  plan-1  C14   0.020
 BM5  plan-1  C15   0.020
 BM5  plan-1  C16   0.020
 BM5  plan-1  C17   0.020
 BM5  plan-1  C18   0.020
 BM5  plan-1  H141  0.020
 BM5  plan-1  H151  0.020
 BM5  plan-1  H161  0.020
 BM5  plan-1  H171  0.020
 BM5  plan-1  H181  0.020
 BM5  plan-2  C3    0.020
 BM5  plan-2  C5    0.020
 BM5  plan-2  N4    0.020
 BM5  plan-2  C6    0.020
 BM5  plan-2  OE    0.020
 BM5  plan-2  C7    0.020
 BM5  plan-2  C12   0.020
 BM5  plan-2  C8    0.020
 BM5  plan-2  C9    0.020
 BM5  plan-2  C10   0.020
 BM5  plan-2  C11   0.020
 BM5  plan-2  H81   0.020
 BM5  plan-2  H91   0.020
 BM5  plan-2  H101  0.020
 BM5  plan-2  H111  0.020
 BM5  plan-3  C3    0.020
 BM5  plan-3  CA    0.020
 BM5  plan-3  OB    0.020
 BM5  plan-3  OC    0.020

