# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 19:05:44 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (4S)-6-bromo-3,4-dihydro-2H-thiochromen-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc2SCC[C@H](OC(=O)[C@H]3C[C@]4(CN3)C(=O)Nc5ccccc45)c2c1
#
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
 09D  09D  '(4S)-6-bromo-3,4-dihydro-2H-thiochromen-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate'  ligand  47  28  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_09D
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
 09D  C1   C   CR16  0  -0.262  -5.7364  -1.4067   2.6029
 09D  C2   C   CR16  0  -0.267  -6.7652  -0.4794   2.4995
 09D  C3   C   CR16  0  -0.350  -4.6382  -1.3390   1.7450
 09D  C4   C   CR16  0  -0.305  -6.7295   0.5371   1.5465
 09D  C5   C   CR16  0  -0.258   5.0753   1.1467   1.2432
 09D  C6   C   CR16  0  -0.229   5.1988  -0.2246   1.3494
 09D  C7   C   CR16  0  -0.258   3.1496  -0.4687   0.1076
 09D  C8   C   CR56  0   0.139  -4.5915  -0.3374   0.7979
 09D  C9   C   CR6   0   0.125   3.0118   0.9157   0.0101
 09D  C10  C   CR56  0   0.366  -5.6319   0.5859   0.7087
 09D  C11  C   CR6   0  -0.172   3.9961   1.7310   0.5764
 09D  C12  C   CR6   0  -0.111   4.2272  -1.0270   0.7698
 09D  C13  C   CR5   0   0.577  -4.1619   1.2264  -0.9119
 09D  C14  C   C     0   0.590  -0.1941   0.4310  -1.4515
 09D  C15  C   CH2   0  -0.474   1.4521   2.8952  -0.3420
 09D  C16  C   CH2   0  -0.463  -2.1286   0.1757   0.1813
 09D  C17  C   CH2   0  -0.300  -3.4423  -1.1367  -1.3495
 09D  C18  C   CH2   0  -0.579   2.6085   3.8459  -0.5635
 09D  C19  C   CH1   0  -0.003   1.8313   1.4816  -0.7495
 09D  C20  C   CH1   0  -0.196  -1.2799  -0.4856  -0.9527
 09D  C21  C   CR5   0  -0.333  -3.5855  -0.0318  -0.2649
 09D  N22  N   NR15  0  -0.743  -5.3528   1.4886  -0.3109
 09D  N23  N   NH1   0  -0.577  -2.1838  -0.8857  -2.0114
 09D  O24  O   O     0  -0.449  -3.6580   1.8682  -1.8114
 09D  O26  O   O2    0  -0.470   0.7225   0.6088  -0.5048
 09D  S27  S   S2    0   0.059   3.9872   3.4894   0.5530
 09D  BR2  BR  BR    0  -0.045   4.3775  -2.9054   0.8837
 09D  H1   H   HCR6  0   0.255  -5.7865  -2.1854   3.3519
 09D  H2   H   HCR6  0   0.259  -7.6127  -0.5430   3.1693
 09D  H3   H   HCR6  0   0.253  -3.8364  -2.0635   1.8280
 09D  H4   H   HCR6  0   0.268  -7.5331   1.2574   1.4690
 09D  H6   H   HCR6  0   0.285   6.0469  -0.6485   1.8695
 09D  H8   H   HCH2  0   0.266   1.1337   2.9174   0.7026
 09D  H9   H   HCH2  0   0.276   0.6095   3.2278  -0.9517
 09D  H10  H   HCH2  0   0.276  -1.9396  -0.3184   1.1333
 09D  H11  H   HCH2  0   0.272  -1.8998   1.2324   0.3256
 09D  H12  H   HCH2  0   0.254  -3.4163  -2.1079  -0.8464
 09D  H13  H   HCH2  0   0.271  -4.2681  -1.1569  -2.0606
 09D  H14  H   HCH2  0   0.287   2.9552   3.8135  -1.5971
 09D  H15  H   HCH2  0   0.306   2.3142   4.8709  -0.3424
 09D  H16  H   HCH1  0   0.277   2.0697   1.4699  -1.8178
 09D  H17  H   HCH1  0   0.288  -0.7983  -1.3761  -0.5361
 09D  H18  H   HNR5  0   0.412  -5.9481   2.2607  -0.5708
 09D  H19  H   HNH1  0   0.358  -2.2990  -0.1210  -2.6669
 09D  H7   H   HCR6  0   0.277   2.4038  -1.1117  -0.3397
 09D  O25  O   O     0  -0.429  -0.1622   0.9438  -2.5387
 09D  H5   H   HCR6  0   0.277   5.8395   1.7748   1.6843

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
 09D  N23  C20  single    1.448  0.020  1.448
 09D  N23  C17  single    1.444  0.020  1.444
 09D  C3   C1   aromatic  1.395  0.020  1.395
 09D  C3   C8   aromatic  1.379  0.020  1.379
 09D  C1   C2   aromatic  1.389  0.020  1.389
 09D  C20  C16  single    1.563  0.020  1.563
 09D  C20  C14  single    1.506  0.020  1.506
 09D  C17  C21  single    1.555  0.020  1.555
 09D  C16  C21  single    1.538  0.020  1.538
 09D  C8   C21  single    1.495  0.020  1.495
 09D  C8   C10  aromatic  1.394  0.020  1.394
 09D  O25  C14  double    1.202  0.020  1.202
 09D  C14  O26  single    1.330  0.020  1.330
 09D  C21  C13  single    1.528  0.020  1.528
 09D  C2   C4   aromatic  1.394  0.020  1.394
 09D  BR2  C12  single    1.888  0.020  1.888
 09D  O26  C19  single    1.432  0.020  1.432
 09D  C10  C4   aromatic  1.382  0.020  1.382
 09D  C10  N22  single    1.390  0.020  1.390
 09D  C7   C12  aromatic  1.383  0.020  1.383
 09D  C7   C9   aromatic  1.395  0.020  1.395
 09D  C13  O24  double    1.215  0.020  1.215
 09D  C13  N22  single    1.360  0.020  1.360
 09D  C12  C6   aromatic  1.387  0.020  1.387
 09D  C19  C9   single    1.513  0.020  1.513
 09D  C19  C15  single    1.519  0.020  1.519
 09D  C9   C11  aromatic  1.398  0.020  1.398
 09D  C15  C18  single    1.513  0.020  1.513
 09D  C6   C5   aromatic  1.381  0.020  1.381
 09D  C11  C5   aromatic  1.397  0.020  1.397
 09D  C11  S27  single    1.759  0.020  1.759
 09D  C18  S27  single    1.809  0.020  1.809
 09D  C1   H1   single    0.930  0.020  1.080
 09D  C2   H2   single    0.930  0.020  1.080
 09D  C3   H3   single    0.930  0.020  1.080
 09D  C4   H4   single    0.930  0.020  1.080
 09D  C5   H5   single    0.930  0.020  1.080
 09D  C6   H6   single    0.930  0.020  1.080
 09D  C15  H8   single    0.970  0.020  1.090
 09D  C15  H9   single    0.970  0.020  1.090
 09D  C16  H10  single    0.970  0.020  1.090
 09D  C16  H11  single    0.970  0.020  1.090
 09D  C17  H12  single    0.970  0.020  1.090
 09D  C17  H13  single    0.970  0.020  1.090
 09D  C18  H14  single    0.970  0.020  1.090
 09D  C18  H15  single    0.970  0.020  1.090
 09D  C19  H16  single    0.970  0.020  1.090
 09D  C20  H17  single    0.970  0.020  1.090
 09D  N22  H18  single    0.860  0.020  1.020
 09D  N23  H19  single    0.890  0.020  1.040
 09D  C7   H7   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
 09D  H1   C1   C3   119.82  3.000
 09D  H1   C1   C2   119.86  3.000
 09D  C3   C1   C2   120.32  3.000
 09D  H2   C2   C4   119.09  3.000
 09D  H2   C2   C1   119.66  3.000
 09D  C4   C2   C1   121.25  3.000
 09D  H3   C3   C8   120.87  3.000
 09D  H3   C3   C1   120.18  3.000
 09D  C8   C3   C1   118.95  3.000
 09D  H4   C4   C10  121.54  3.000
 09D  H4   C4   C2   121.03  3.000
 09D  C10  C4   C2   117.43  3.000
 09D  H5   C5   C11  119.80  3.000
 09D  H5   C5   C6   118.78  3.000
 09D  C11  C5   C6   121.42  3.000
 09D  H6   C6   C12  121.58  3.000
 09D  H6   C6   C5   119.75  3.000
 09D  C12  C6   C5   118.67  3.000
 09D  H7   C7   C12  119.70  3.000
 09D  H7   C7   C9   119.54  3.000
 09D  C12  C7   C9   120.76  3.000
 09D  C21  C8   C10  108.74  3.000
 09D  C10  C8   C3   119.98  3.000
 09D  C21  C8   C3   131.25  3.000
 09D  C19  C9   C11  122.30  3.000
 09D  C11  C9   C7   118.75  3.000
 09D  C19  C9   C7   118.91  3.000
 09D  N22  C10  C8   109.11  3.000
 09D  N22  C10  C4   128.84  3.000
 09D  C8   C10  C4   122.05  3.000
 09D  S27  C11  C9   125.04  3.000
 09D  S27  C11  C5   115.38  3.000
 09D  C9   C11  C5   119.57  3.000
 09D  BR2  C12  C7   119.52  3.000
 09D  C7   C12  C6   120.83  3.000
 09D  BR2  C12  C6   119.65  3.000
 09D  O24  C13  N22  126.08  3.000
 09D  N22  C13  C21  107.59  3.000
 09D  O24  C13  C21  126.32  3.000
 09D  O26  C14  O25  124.64  3.000
 09D  O26  C14  C20  110.03  3.000
 09D  O25  C14  C20  125.32  3.000
 09D  H9   C15  H8   107.63  3.000
 09D  H9   C15  C19  109.04  3.000
 09D  H8   C15  C19  110.38  3.000
 09D  H9   C15  C18  108.46  3.000
 09D  H8   C15  C18  110.48  3.000
 09D  C19  C15  C18  110.76  3.000
 09D  H11  C16  H10  106.70  3.000
 09D  H11  C16  C21  111.58  3.000
 09D  H10  C16  C21  110.91  3.000
 09D  H11  C16  C20  113.07  3.000
 09D  H10  C16  C20  110.36  3.000
 09D  C21  C16  C20  104.29  3.000
 09D  H13  C17  H12  107.55  3.000
 09D  H13  C17  N23  111.38  3.000
 09D  H12  C17  N23  110.14  3.000
 09D  H13  C17  C21  113.49  3.000
 09D  H12  C17  C21  108.19  3.000
 09D  N23  C17  C21  106.05  3.000
 09D  H15  C18  H14  107.83  3.000
 09D  H15  C18  S27  105.43  3.000
 09D  H14  C18  S27  109.68  3.000
 09D  H15  C18  C15  110.79  3.000
 09D  H14  C18  C15  111.28  3.000
 09D  S27  C18  C15  111.60  3.000
 09D  H16  C19  O26  109.20  3.000
 09D  H16  C19  C15  109.04  3.000
 09D  O26  C19  C15  109.14  3.000
 09D  H16  C19  C9   108.42  3.000
 09D  C15  C19  C9   114.08  3.000
 09D  O26  C19  C9   106.87  3.000
 09D  H17  C20  N23  109.15  3.000
 09D  H17  C20  C16  107.87  3.000
 09D  N23  C20  C16  107.95  3.000
 09D  H17  C20  C14  107.70  3.000
 09D  C16  C20  C14  111.98  3.000
 09D  N23  C20  C14  112.08  3.000
 09D  C17  C21  C16  102.18  3.000
 09D  C16  C21  C13  111.67  3.000
 09D  C17  C21  C13  108.94  3.000
 09D  C13  C21  C8   102.45  3.000
 09D  C16  C21  C8   117.31  3.000
 09D  C17  C21  C8   114.37  3.000
 09D  H18  N22  C13  123.41  3.000
 09D  H18  N22  C10  124.57  3.000
 09D  C13  N22  C10  112.01  3.000
 09D  H19  N23  C20  109.58  3.000
 09D  H19  N23  C17  109.17  3.000
 09D  C20  N23  C17  104.88  3.000
 09D  C19  O26  C14  119.57  3.000
 09D  C18  S27  C11  102.07  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
 09D  CONST_01  C10  C8   C3   C1      0.00   0.0  0
 09D  CONST_02  C10  C4   C2   C1      0.00   0.0  0
 09D  CONST_03  C8   C3   C1   C2      0.00   0.0  0
 09D  CONST_04  C8   C10  C4   C2      0.00   0.0  0
 09D  CONST_05  C4   C2   C1   C3      0.00   0.0  0
 09D  CONST_06  C4   C10  C8   C3      0.00   0.0  0
 09D  CONST_07  C7   C12  C6   C5      0.00   0.0  0
 09D  CONST_08  C7   C9   C11  C5      0.00   0.0  0
 09D  CONST_09  C9   C7   C12  C6      0.00   0.0  0
 09D  CONST_10  C9   C11  C5   C6      0.00   0.0  0
 09D  CONST_11  C12  C7   C9   C11     0.00   0.0  0
 09D  CONST_12  C12  C6   C5   C11     0.00   0.0  0
 09D  CONST_13  C21  C13  N22  C10     0.00   0.0  0
 09D  CONST_14  BR2  C12  C6   C5    180.00   0.0  0
 09D  CONST_15  BR2  C12  C7   C9    180.00   0.0  0
 09D  CONST_16  O24  C13  N22  C10   180.00   0.0  0
 09D  CONST_17  H4   C4   C2   C1    180.00   0.0  0
 09D  CONST_18  H3   C3   C1   C2    180.00   0.0  0
 09D  CONST_19  H2   C2   C1   C3    180.00   0.0  0
 09D  CONST_20  H1   C1   C2   C4    180.00   0.0  0
 09D  CONST_21  H7   C7   C12  C6    180.00   0.0  0
 09D  CONST_22  H6   C6   C12  C7    180.00   0.0  0
 09D  CONST_23  H5   C5   C11  C9    180.00   0.0  0
 09D  CONST_24  H18  N22  C13  C21   180.00   0.0  0
 09D  Var_01    C15  C18  S27  C11    39.34  30.0  1
 09D  Var_02    S27  C18  C15  C19   -67.09  30.0  1
 09D  Var_03    C21  C17  N23  C20    39.20  30.0  1
 09D  Var_04    C20  C14  O26  C19  -178.11  30.0  1

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
 09D  chir_01  C19  O26  C9   C15  positiv
 09D  chir_02  C20  N23  C16  C14  positiv
 09D  chir_03  C21  C16  C8   C13  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
 09D  plan-1  C5   0.020
 09D  plan-1  C6   0.020
 09D  plan-1  C7   0.020
 09D  plan-1  C9   0.020
 09D  plan-1  C11  0.020
 09D  plan-1  C12  0.020
 09D  plan-1  C19  0.020
 09D  plan-1  S27  0.020
 09D  plan-1  BR2  0.020
 09D  plan-1  H6   0.020
 09D  plan-1  H7   0.020
 09D  plan-1  H5   0.020
 09D  plan-2  C1   0.020
 09D  plan-2  C2   0.020
 09D  plan-2  C3   0.020
 09D  plan-2  C4   0.020
 09D  plan-2  C8   0.020
 09D  plan-2  C10  0.020
 09D  plan-2  C13  0.020
 09D  plan-2  C21  0.020
 09D  plan-2  N22  0.020
 09D  plan-2  O24  0.020
 09D  plan-2  H1   0.020
 09D  plan-2  H2   0.020
 09D  plan-2  H3   0.020
 09D  plan-2  H4   0.020
 09D  plan-2  H18  0.020
 09D  plan-3  C14  0.020
 09D  plan-3  C20  0.020
 09D  plan-3  O26  0.020
 09D  plan-3  O25  0.020

