# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:36:30 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: (5S)-5-({6-[(2-fluorobenzyl)oxy]naphthalen-2-yl}methyl)-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccccc1COc2ccc3cc(C[C@@H]4SC(=O)NC4=O)ccc3c2
#
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
 MC5  MC5  (5S)-5-({6-[(2-fluorobenzyl)oxy]naphthalen-2-yl}methyl)-1,3-thiazolidine-2,4-dione  ligand  43  27  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MC5
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
 MC5  F     F  F     0  -0.313   6.6177   2.1330   0.8705
 MC5  N     N  NH1   0  -0.658  -7.0725   0.5860  -0.4175
 MC5  S     S  S2    0   0.087  -4.5832   0.9463  -1.0014
 MC5  C1    C  CR66  0   0.120  -0.5474  -0.1263   0.8254
 MC5  O1    O  O2    0  -0.484   3.5126  -0.4450  -0.0184
 MC5  C2    C  CR66  0   0.127  -0.0207  -1.2345   0.1145
 MC5  O2    O  O     0  -0.409  -7.1661  -1.5155   0.4567
 MC5  C3    C  CR16  0  -0.298   0.3414   0.8861   1.2408
 MC5  O3    O  O     0  -0.400  -6.5798   2.6419  -1.2971
 MC5  C4    C  CR16  0  -0.368  -1.9351  -0.0685   1.0968
 MC5  C5    C  CR6   0   0.107  -2.7816  -1.0642   0.6901
 MC5  C6    C  CR16  0  -0.437   1.3599  -1.2988  -0.1513
 MC5  C7    C  CR6   0   0.417   2.2030  -0.2976   0.2721
 MC5  C8    C  CR16  0  -0.302  -0.9153  -2.2521  -0.3041
 MC5  C9    C  CR16  0  -0.374   1.6834   0.8117   0.9777
 MC5  C10   C  CR16  0  -0.254   7.3623  -1.2841  -1.2367
 MC5  C11   C  CR16  0  -0.293  -2.2487  -2.1663  -0.0259
 MC5  C13   C  CH1   0  -0.556  -5.0473  -0.6675  -0.3053
 MC5  C14   C  C     0   0.624  -6.5394  -0.6134  -0.0378
 MC5  C15   C  CR16  0  -0.250   8.4077  -0.4271  -0.9280
 MC5  C16   C  C     0   0.404  -6.2408   1.5479  -0.9380
 MC5  C17   C  CR16  0  -0.403   8.1601   0.7368  -0.2118
 MC5  C19   C  CR6   0  -0.161   5.7931   0.1739  -0.1132
 MC5  C20   C  CR6   0   0.534   6.8648   1.0066   0.1753
 MC5  C21   C  CR16  0  -0.288   6.0668  -0.9850  -0.8322
 MC5  HN    H  HNH1  0   0.440  -8.0591   0.7832  -0.2946
 MC5  H3    H  HCR6  0   0.263  -0.0471   1.7421   1.7789
 MC5  H4    H  HCR6  0   0.252  -2.3231   0.7848   1.6418
 MC5  H6    H  HCR6  0   0.261   1.7616  -2.1493  -0.6897
 MC5  H8    H  HCR6  0   0.255  -0.5259  -3.1069  -0.8436
 MC5  H9    H  HCR6  0   0.287   2.3263   1.6118   1.3181
 MC5  H10   H  HCR6  0   0.262   7.5511  -2.1910  -1.7953
 MC5  H11   H  HCR6  0   0.256  -2.9134  -2.9585  -0.3516
 MC5  H12   H  HCH2  0   0.285  -4.6130  -1.9552   1.3405
 MC5  H12A  H  HCH2  0   0.281  -4.4647  -0.2422   1.7261
 MC5  H13   H  HCH1  0   0.355  -4.8742  -1.4347  -1.0643
 MC5  H15   H  HCR6  0   0.268   9.4171  -0.6577  -1.2409
 MC5  H17   H  HCR6  0   0.280   8.9573   1.4230   0.0426
 MC5  H18   H  HCH2  0   0.252   4.1333   1.5250  -0.0909
 MC5  H18A  H  HCH2  0   0.251   4.4205   0.7005   1.4432
 MC5  H21   H  HCR6  0   0.265   5.2653  -1.6655  -1.0823
 MC5  C18   C  CH2   0  -0.185   4.4190   0.5649   0.3554
 MC5  C12   C  CH2   0  -0.500  -4.2561  -0.9940   0.9628

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
 MC5  F    C20   single    1.346  0.020  1.346
 MC5  N    C14   single    1.366  0.020  1.366
 MC5  N    C16   single    1.374  0.020  1.374
 MC5  S    C13   single    1.818  0.020  1.818
 MC5  S    C16   single    1.765  0.020  1.765
 MC5  C1   C2    aromatic  1.418  0.020  1.418
 MC5  C1   C3    aromatic  1.410  0.020  1.410
 MC5  C1   C4    aromatic  1.415  0.020  1.415
 MC5  O1   C7    single    1.350  0.020  1.350
 MC5  O1   C18   single    1.408  0.020  1.408
 MC5  C2   C6    aromatic  1.407  0.020  1.407
 MC5  C2   C8    aromatic  1.418  0.020  1.418
 MC5  O2   C14   double    1.205  0.020  1.205
 MC5  C3   C9    aromatic  1.370  0.020  1.370
 MC5  O3   C16   double    1.200  0.020  1.200
 MC5  C4   C5    aromatic  1.369  0.020  1.369
 MC5  C5   C11   aromatic  1.418  0.020  1.418
 MC5  C5   C12   single    1.501  0.020  1.501
 MC5  C6   C7    aromatic  1.376  0.020  1.376
 MC5  C7   C9    aromatic  1.414  0.020  1.414
 MC5  C8   C11   aromatic  1.365  0.020  1.365
 MC5  C10  C15   aromatic  1.387  0.020  1.387
 MC5  C10  C21   aromatic  1.390  0.020  1.390
 MC5  C12  C13   single    1.530  0.020  1.530
 MC5  C13  C14   single    1.517  0.020  1.517
 MC5  C15  C17   aromatic  1.389  0.020  1.389
 MC5  C17  C20   aromatic  1.379  0.020  1.379
 MC5  C18  C19   single    1.503  0.020  1.503
 MC5  C19  C20   aromatic  1.388  0.020  1.388
 MC5  C19  C21   aromatic  1.391  0.020  1.391
 MC5  N    HN    single    0.860  0.020  1.020
 MC5  C3   H3    single    0.930  0.020  1.080
 MC5  C4   H4    single    0.930  0.020  1.080
 MC5  C6   H6    single    0.930  0.020  1.080
 MC5  C8   H8    single    0.930  0.020  1.080
 MC5  C9   H9    single    0.930  0.020  1.080
 MC5  C10  H10   single    0.930  0.020  1.080
 MC5  C11  H11   single    0.930  0.020  1.080
 MC5  C12  H12   single    0.970  0.020  1.090
 MC5  C12  H12A  single    0.970  0.020  1.090
 MC5  C13  H13   single    0.970  0.020  1.090
 MC5  C15  H15   single    0.930  0.020  1.080
 MC5  C17  H17   single    0.930  0.020  1.080
 MC5  C18  H18   single    0.970  0.020  1.090
 MC5  C18  H18A  single    0.970  0.020  1.090
 MC5  C21  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
 MC5  HN    N    C16  119.92  3.000
 MC5  HN    N    C14  121.13  3.000
 MC5  C16   N    C14  118.92  3.000
 MC5  C16   S    C13   92.81  3.000
 MC5  C4    C1   C3   122.17  3.000
 MC5  C4    C1   C2   119.49  3.000
 MC5  C3    C1   C2   118.34  3.000
 MC5  C18   O1   C7   119.30  3.000
 MC5  C8    C2   C6   122.02  3.000
 MC5  C8    C2   C1   118.32  3.000
 MC5  C6    C2   C1   119.66  3.000
 MC5  H3    C3   C9   119.33  3.000
 MC5  H3    C3   C1   119.20  3.000
 MC5  C9    C3   C1   121.48  3.000
 MC5  H4    C4   C5   120.03  3.000
 MC5  H4    C4   C1   118.65  3.000
 MC5  C5    C4   C1   121.32  3.000
 MC5  C12   C5   C11  119.81  3.000
 MC5  C12   C5   C4   121.30  3.000
 MC5  C11   C5   C4   118.88  3.000
 MC5  H6    C6   C7   119.79  3.000
 MC5  H6    C6   C2   119.56  3.000
 MC5  C7    C6   C2   120.65  3.000
 MC5  C9    C7   C6   119.97  3.000
 MC5  C9    C7   O1   123.35  3.000
 MC5  C6    C7   O1   116.68  3.000
 MC5  H8    C8   C11  120.15  3.000
 MC5  H8    C8   C2   119.12  3.000
 MC5  C11   C8   C2   120.73  3.000
 MC5  H9    C9   C7   121.28  3.000
 MC5  H9    C9   C3   118.81  3.000
 MC5  C7    C9   C3   119.91  3.000
 MC5  H10   C10  C21  119.56  3.000
 MC5  H10   C10  C15  120.11  3.000
 MC5  C21   C10  C15  120.33  3.000
 MC5  H11   C11  C8   119.46  3.000
 MC5  H11   C11  C5   119.28  3.000
 MC5  C8    C11  C5   121.26  3.000
 MC5  H13   C13  C14  107.65  3.000
 MC5  H13   C13  C12  110.11  3.000
 MC5  C14   C13  C12  111.72  3.000
 MC5  H13   C13  S    108.47  3.000
 MC5  C14   C13  S    106.68  3.000
 MC5  C12   C13  S    112.01  3.000
 MC5  C13   C14  O2   123.88  3.000
 MC5  C13   C14  N    111.48  3.000
 MC5  O2    C14  N    124.64  3.000
 MC5  H15   C15  C17  119.62  3.000
 MC5  H15   C15  C10  120.49  3.000
 MC5  C17   C15  C10  119.89  3.000
 MC5  O3    C16  S    124.43  3.000
 MC5  O3    C16  N    125.48  3.000
 MC5  S     C16  N    110.09  3.000
 MC5  H17   C17  C20  120.14  3.000
 MC5  H17   C17  C15  121.42  3.000
 MC5  C20   C17  C15  118.45  3.000
 MC5  C21   C19  C20  117.10  3.000
 MC5  C21   C19  C18  123.89  3.000
 MC5  C20   C19  C18  119.02  3.000
 MC5  C19   C20  C17  123.36  3.000
 MC5  C19   C20  F    117.88  3.000
 MC5  C17   C20  F    118.76  3.000
 MC5  H21   C21  C19  119.89  3.000
 MC5  H21   C21  C10  119.24  3.000
 MC5  C19   C21  C10  120.88  3.000
 MC5  H18A  C18  H18  107.22  3.000
 MC5  H18A  C18  C19  109.89  3.000
 MC5  H18   C18  C19  109.81  3.000
 MC5  H18A  C18  O1   110.68  3.000
 MC5  H18   C18  O1   110.63  3.000
 MC5  C19   C18  O1   108.61  3.000
 MC5  H12A  C12  H12  107.56  3.000
 MC5  H12A  C12  C13  109.51  3.000
 MC5  H12   C12  C13  107.78  3.000
 MC5  H12A  C12  C5   110.30  3.000
 MC5  H12   C12  C5   110.02  3.000
 MC5  C13   C12  C5   111.55  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
 MC5  CONST_01  C7   C6   C2   C1      0.00   0.0  0
 MC5  CONST_02  C11  C8   C2   C1      0.00   0.0  0
 MC5  CONST_03  C7   C9   C3   C1      0.00   0.0  0
 MC5  CONST_04  C11  C5   C4   C1      0.00   0.0  0
 MC5  CONST_05  C9   C3   C1   C2      0.00   0.0  0
 MC5  CONST_06  C5   C4   C1   C2      0.00   0.0  0
 MC5  CONST_07  C9   C7   C6   C2      0.00   0.0  0
 MC5  CONST_08  C5   C11  C8   C2      0.00   0.0  0
 MC5  CONST_09  C6   C2   C1   C3      0.00   0.0  0
 MC5  CONST_10  C8   C2   C1   C3    180.00   0.0  0
 MC5  CONST_11  C5   C4   C1   C3    180.00   0.0  0
 MC5  CONST_12  C6   C7   C9   C3      0.00   0.0  0
 MC5  CONST_13  C6   C2   C1   C4    180.00   0.0  0
 MC5  CONST_14  C8   C2   C1   C4      0.00   0.0  0
 MC5  CONST_15  C9   C3   C1   C4    180.00   0.0  0
 MC5  CONST_16  C8   C11  C5   C4      0.00   0.0  0
 MC5  CONST_17  C11  C8   C2   C6    180.00   0.0  0
 MC5  CONST_18  C8   C2   C6   C7    180.00   0.0  0
 MC5  CONST_19  C20  C17  C15  C10     0.00   0.0  0
 MC5  CONST_20  C20  C19  C21  C10     0.00   0.0  0
 MC5  CONST_21  C19  C21  C10  C15     0.00   0.0  0
 MC5  CONST_22  C19  C20  C17  C15     0.00   0.0  0
 MC5  CONST_23  C21  C10  C15  C17     0.00   0.0  0
 MC5  CONST_24  C21  C19  C20  C17     0.00   0.0  0
 MC5  CONST_25  C16  N    C14  C13     0.00   0.0  0
 MC5  CONST_26  C15  C17  C20  F     180.00   0.0  0
 MC5  CONST_27  C21  C19  C20  F     180.00   0.0  0
 MC5  CONST_28  C12  C5   C4   C1    180.00   0.0  0
 MC5  CONST_29  C2   C6   C7   O1    180.00   0.0  0
 MC5  CONST_30  C3   C9   C7   O1    180.00   0.0  0
 MC5  CONST_31  C12  C5   C11  C8    180.00   0.0  0
 MC5  CONST_32  C18  C19  C21  C10   180.00   0.0  0
 MC5  CONST_33  C18  C19  C20  C17   180.00   0.0  0
 MC5  CONST_34  C16  N    C14  O2    180.00   0.0  0
 MC5  CONST_35  H6   C6   C2   C1    180.00   0.0  0
 MC5  CONST_36  H8   C8   C2   C1    180.00   0.0  0
 MC5  CONST_37  H9   C9   C3   C1    180.00   0.0  0
 MC5  CONST_38  H3   C3   C1   C2    180.00   0.0  0
 MC5  CONST_39  H4   C4   C1   C2    180.00   0.0  0
 MC5  CONST_40  H11  C11  C8   C2    180.00   0.0  0
 MC5  CONST_41  H17  C17  C15  C10   180.00   0.0  0
 MC5  CONST_42  H21  C21  C10  C15   180.00   0.0  0
 MC5  CONST_43  H10  C10  C15  C17   180.00   0.0  0
 MC5  CONST_44  H15  C15  C17  C20   180.00   0.0  0
 MC5  CONST_45  HN   N    C14  C13   180.00   0.0  0
 MC5  Var_01    C14  N    C16  S       0.48  30.0  1
 MC5  Var_02    C13  C12  C5   C4    106.08  30.0  2
 MC5  Var_03    C20  C19  C18  O1   -178.31  30.0  2
 MC5  Var_04    C19  C18  O1   C7   -178.53  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
 MC5  chir_01  C13  S  C12  C14  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
 MC5  plan-1  F    0.020
 MC5  plan-1  C10  0.020
 MC5  plan-1  C15  0.020
 MC5  plan-1  C17  0.020
 MC5  plan-1  C19  0.020
 MC5  plan-1  C20  0.020
 MC5  plan-1  C21  0.020
 MC5  plan-1  H10  0.020
 MC5  plan-1  H15  0.020
 MC5  plan-1  H17  0.020
 MC5  plan-1  H21  0.020
 MC5  plan-1  C18  0.020
 MC5  plan-2  C1   0.020
 MC5  plan-2  O1   0.020
 MC5  plan-2  C2   0.020
 MC5  plan-2  C3   0.020
 MC5  plan-2  C4   0.020
 MC5  plan-2  C5   0.020
 MC5  plan-2  C6   0.020
 MC5  plan-2  C7   0.020
 MC5  plan-2  C8   0.020
 MC5  plan-2  C9   0.020
 MC5  plan-2  C11  0.020
 MC5  plan-2  H3   0.020
 MC5  plan-2  H4   0.020
 MC5  plan-2  H6   0.020
 MC5  plan-2  H8   0.020
 MC5  plan-2  H9   0.020
 MC5  plan-2  H11  0.020
 MC5  plan-2  C12  0.020
 MC5  plan-3  N    0.020
 MC5  plan-3  O2   0.020
 MC5  plan-3  C13  0.020
 MC5  plan-3  C14  0.020
 MC5  plan-3  C16  0.020
 MC5  plan-3  HN   0.020
 MC5  plan-4  N    0.020
 MC5  plan-4  S    0.020
 MC5  plan-4  O3   0.020
 MC5  plan-4  C16  0.020

