# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:33:52 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-(2,6-difluorophenyl)-N-[(2Z)-5-[(1R)-1-hydroxy-1-(4-methyl-1,3-thiazol-2-yl)ethyl]-1,3,4-thiadiazol-2(3H)-ylidene]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1csc(n1)[C@](C)(O)C2=NNC(S2)=NC(=O)Cc3c(F)cccc3F
#
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
 IBH  IBH  2-(2,6-difluorophenyl)-N-[(2Z)-5-[(1R)-1-hydroxy-1-(4-methyl-1,3-thiazol-2-yl)ethyl]-1,3,4-thiadiazol-2(3H)-ylidene]acetamide  ligand  40  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IBH
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
 IBH  F1    F  F     0  -0.306  -4.4437   0.1808  -1.6960
 IBH  C11   C  CR6   0   0.553  -5.0175   0.4932  -0.5242
 IBH  C12   C  CR16  0  -0.420  -5.9955   1.4652  -0.4992
 IBH  C13   C  CR16  0  -0.238  -6.5767   1.7775   0.7224
 IBH  C14   C  CR16  0  -0.419  -6.1782   1.1295   1.8810
 IBH  C15   C  CR6   0   0.525  -5.1898   0.1665   1.7915
 IBH  F     F  F     0  -0.307  -4.8055  -0.4556   2.9164
 IBH  C10   C  CR6   0  -0.250  -4.5798  -0.1927   0.6003
 IBH  C9    C  CH2   0  -0.639  -3.5147  -1.2373   0.4919
 IBH  C8    C  C     0   0.492  -2.1611  -0.6611   0.1387
 IBH  O     O  O     0  -0.459  -1.8947   0.5205   0.3092
 IBH  N3    N  N     0  -0.525  -1.2921  -1.5842  -0.3544
 IBH  C7    C  CR5   0   0.382  -0.1089  -1.1538  -0.6759
 IBH  N2    N  NR15  0  -0.463   0.8347  -1.9541  -1.1892
 IBH  N1    N  N     0  -0.175   2.0224  -1.4223  -1.5118
 IBH  S1    S  S2    0   0.243   0.5595   0.4600  -0.5668
 IBH  C6    C  CR5   0   0.050   2.0325  -0.1750  -1.2408
 IBH  C4    C  CT    0   0.122   3.2114   0.7404  -1.4852
 IBH  C5    C  CH3   0  -0.650   3.5981   0.7092  -2.9622
 IBH  O1    O  OH1   0  -0.658   2.8242   2.0294  -1.1080
 IBH  C3    C  CR5   0   0.058   4.3663   0.3046  -0.6093
 IBH  S     S  S2    0   0.272   5.2205  -1.1719  -0.7800
 IBH  C2    C  CR15  0  -0.543   6.2227  -0.7040   0.5322
 IBH  N     N  N     0  -0.430   4.7896   1.0664   0.3424
 IBH  C1    C  CR5   0   0.354   5.8514   0.5126   1.0107
 IBH  C     C  CH3   0  -0.704   6.4800   1.2425   2.1468
 IBH  H12   H  HCR6  0   0.283  -6.2937   1.9661  -1.4102
 IBH  H13   H  HCR6  0   0.279  -7.3473   2.5341   0.7697
 IBH  H14   H  HCR6  0   0.283  -6.6241   1.3636   2.8381
 IBH  H91C  H  HCH2  0   0.309  -3.4026  -1.7787   1.4341
 IBH  H92C  H  HCH2  0   0.292  -3.7804  -1.9959  -0.2467
 IBH  H2    H  HNR5  0   0.442   0.6831  -2.9396  -1.3550
 IBH  H51C  H  HCH3  0   0.261   2.7673   1.0634  -3.5726
 IBH  H52C  H  HCH3  0   0.262   4.4603   1.3526  -3.1352
 IBH  H53C  H  HCH3  0   0.244   3.8458  -0.3014  -3.2847
 IBH  H1    H  HOH1  0   0.456   3.3455   2.2717  -0.3245
 IBH  HA    H  HCR5  0   0.286   7.0185  -1.3421   0.8820
 IBH  HC1   H  HCH3  0   0.248   6.8046   2.2367   1.8391
 IBH  HC2   H  HCH3  0   0.249   5.7748   1.3686   2.9691
 IBH  HC3   H  HCH3  0   0.240   7.3468   0.7049   2.5243

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
 IBH  F1   C11   single    1.342  0.020  1.342
 IBH  C11  C12   aromatic  1.379  0.020  1.379
 IBH  C11  C10   aromatic  1.388  0.020  1.388
 IBH  C12  C13   aromatic  1.388  0.020  1.388
 IBH  C13  C14   aromatic  1.386  0.020  1.386
 IBH  C14  C15   aromatic  1.383  0.020  1.383
 IBH  C15  F     single    1.342  0.020  1.342
 IBH  C15  C10   aromatic  1.386  0.020  1.386
 IBH  C10  C9    single    1.496  0.020  1.496
 IBH  C9   C8    single    1.513  0.020  1.513
 IBH  C8   O     double    1.223  0.020  1.223
 IBH  C8   N3    single    1.360  0.020  1.360
 IBH  N3   C7    double    1.299  0.020  1.299
 IBH  C7   N2    single    1.340  0.020  1.340
 IBH  C7   S1    single    1.750  0.020  1.750
 IBH  N2   N1    single    1.341  0.020  1.341
 IBH  N1   C6    double    1.276  0.020  1.276
 IBH  S1   C6    single    1.740  0.020  1.740
 IBH  C6   C4    single    1.512  0.020  1.512
 IBH  C4   C5    single    1.527  0.020  1.527
 IBH  C4   O1    single    1.398  0.020  1.398
 IBH  C4   C3    single    1.514  0.020  1.514
 IBH  C3   S     aromatic  1.714  0.020  1.714
 IBH  C3   N     aromatic  1.290  0.020  1.290
 IBH  S    C2    aromatic  1.716  0.020  1.716
 IBH  C2   C1    aromatic  1.359  0.020  1.359
 IBH  N    C1    aromatic  1.371  0.020  1.371
 IBH  C1   C     single    1.490  0.020  1.490
 IBH  C12  H12   single    0.930  0.020  1.080
 IBH  C13  H13   single    0.930  0.020  1.080
 IBH  C14  H14   single    0.930  0.020  1.080
 IBH  C9   H91C  single    0.970  0.020  1.090
 IBH  C9   H92C  single    0.970  0.020  1.090
 IBH  N2   H2    single    0.860  0.020  1.020
 IBH  C5   H51C  single    0.970  0.020  1.090
 IBH  C5   H52C  single    0.970  0.020  1.090
 IBH  C5   H53C  single    0.970  0.020  1.090
 IBH  O1   H1    single    0.850  0.020  0.980
 IBH  C2   HA    single    0.930  0.020  1.080
 IBH  C    HC1   single    0.970  0.020  1.090
 IBH  C    HC2   single    0.970  0.020  1.090
 IBH  C    HC3   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
 IBH  C10   C11  C12   123.87  3.000
 IBH  C10   C11  F1    117.24  3.000
 IBH  C12   C11  F1    118.90  3.000
 IBH  H12   C12  C13   121.43  3.000
 IBH  H12   C12  C11   120.44  3.000
 IBH  C13   C12  C11   118.12  3.000
 IBH  H13   C13  C14   119.71  3.000
 IBH  H13   C13  C12   119.63  3.000
 IBH  C14   C13  C12   120.66  3.000
 IBH  H14   C14  C15   120.18  3.000
 IBH  H14   C14  C13   121.33  3.000
 IBH  C15   C14  C13   118.49  3.000
 IBH  C10   C15  F     118.33  3.000
 IBH  C10   C15  C14   123.42  3.000
 IBH  F     C15  C14   118.25  3.000
 IBH  C9    C10  C15   123.83  3.000
 IBH  C9    C10  C11   120.73  3.000
 IBH  C15   C10  C11   115.44  3.000
 IBH  H92C  C9   H91C  105.32  3.000
 IBH  H92C  C9   C8    108.94  3.000
 IBH  H91C  C9   C8    107.36  3.000
 IBH  H92C  C9   C10   111.16  3.000
 IBH  H91C  C9   C10   110.89  3.000
 IBH  C8    C9   C10   112.83  3.000
 IBH  N3    C8   O     124.54  3.000
 IBH  N3    C8   C9    113.44  3.000
 IBH  O     C8   C9    122.02  3.000
 IBH  C7    N3   C8    116.53  3.000
 IBH  S1    C7   N2    107.80  3.000
 IBH  S1    C7   N3    129.62  3.000
 IBH  N2    C7   N3    122.57  3.000
 IBH  H2    N2   N1    118.69  3.000
 IBH  H2    N2   C7    122.66  3.000
 IBH  N1    N2   C7    118.64  3.000
 IBH  C6    N1   N2    110.09  3.000
 IBH  C6    S1   C7     87.86  3.000
 IBH  C4    C6   S1    120.11  3.000
 IBH  C4    C6   N1    124.28  3.000
 IBH  S1    C6   N1    115.61  3.000
 IBH  C3    C4   O1    108.71  3.000
 IBH  C3    C4   C5    111.14  3.000
 IBH  O1    C4   C5    110.48  3.000
 IBH  C3    C4   C6    109.09  3.000
 IBH  O1    C4   C6    107.37  3.000
 IBH  C5    C4   C6    109.95  3.000
 IBH  H53C  C5   H52C  108.71  3.000
 IBH  H53C  C5   H51C  107.99  3.000
 IBH  H52C  C5   H51C  108.80  3.000
 IBH  H53C  C5   C4    111.28  3.000
 IBH  H52C  C5   C4    109.99  3.000
 IBH  H51C  C5   C4    110.00  3.000
 IBH  H1    O1   C4    107.38  3.000
 IBH  N     C3   S     114.74  3.000
 IBH  N     C3   C4    120.47  3.000
 IBH  S     C3   C4    124.79  3.000
 IBH  C2    S    C3     88.85  3.000
 IBH  HA    C2   C1    128.11  3.000
 IBH  HA    C2   S     121.18  3.000
 IBH  C1    C2   S     110.71  3.000
 IBH  C1    N    C3    112.02  3.000
 IBH  C     C1   N     120.04  3.000
 IBH  C     C1   C2    126.29  3.000
 IBH  N     C1   C2    113.67  3.000
 IBH  HC3   C    HC2   108.11  3.000
 IBH  HC3   C    HC1   108.15  3.000
 IBH  HC2   C    HC1   107.45  3.000
 IBH  HC3   C    C1    111.03  3.000
 IBH  HC2   C    C1    111.03  3.000
 IBH  HC1   C    C1    110.93  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
 IBH  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 IBH  CONST_02  C14  C15  C10  C11    0.00   0.0  0
 IBH  CONST_03  C15  C10  C11  C12    0.00   0.0  0
 IBH  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 IBH  CONST_05  C10  C11  C12  C13    0.00   0.0  0
 IBH  CONST_06  C10  C15  C14  C13    0.00   0.0  0
 IBH  CONST_07  C1   C2   S    C3     0.00   0.0  0
 IBH  CONST_08  C2   C1   N    C3     0.00   0.0  0
 IBH  CONST_09  C1   N    C3   S      0.00   0.0  0
 IBH  CONST_10  N    C1   C2   S      0.00   0.0  0
 IBH  CONST_11  N    C3   S    C2     0.00   0.0  0
 IBH  CONST_12  S1   C7   N2   N1     0.00   0.0  0
 IBH  CONST_13  C13  C12  C11  F1   180.00   0.0  0
 IBH  CONST_14  C15  C10  C11  F1   180.00   0.0  0
 IBH  CONST_15  F    C15  C10  C11  180.00   0.0  0
 IBH  CONST_16  C9   C10  C11  C12  180.00   0.0  0
 IBH  CONST_17  F    C15  C14  C13  180.00   0.0  0
 IBH  CONST_18  C9   C10  C15  C14  180.00   0.0  0
 IBH  CONST_19  C2   S    C3   C4   180.00   0.0  0
 IBH  CONST_20  C1   N    C3   C4   180.00   0.0  0
 IBH  CONST_21  C    C1   N    C3   180.00   0.0  0
 IBH  CONST_22  C    C1   C2   S    180.00   0.0  0
 IBH  CONST_23  N1   N2   C7   N3   180.00   0.0  0
 IBH  CONST_24  H13  C13  C12  C11  180.00   0.0  0
 IBH  CONST_25  H14  C14  C13  C12  180.00   0.0  0
 IBH  CONST_26  H12  C12  C13  C14  180.00   0.0  0
 IBH  CONST_27  HA   C2   S    C3   180.00   0.0  0
 IBH  CONST_28  H2   N2   C7   S1   180.00   0.0  0
 IBH  CONST_29  N2   C7   N3   C8   180.00   0.0  0
 IBH  CONST_30  S1   C7   N3   C8     0.00   0.0  0
 IBH  CONST_31  C7   N3   C8   C9   180.00   0.0  0
 IBH  CONST_32  C7   N3   C8   O      0.00   0.0  0
 IBH  Var_01    C8   C9   C10  C11   68.26  30.0  2
 IBH  Var_02    HC1  C    C1   C2   124.30  30.0  2
 IBH  Var_03    O    C8   C9   C10   19.77  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
 IBH  chir_01  C4  C6  O1  C3  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
 IBH  plan-1  C4   0.020
 IBH  plan-1  C3   0.020
 IBH  plan-1  S    0.020
 IBH  plan-1  C2   0.020
 IBH  plan-1  N    0.020
 IBH  plan-1  C1   0.020
 IBH  plan-1  C    0.020
 IBH  plan-1  HA   0.020
 IBH  plan-2  F1   0.020
 IBH  plan-2  C11  0.020
 IBH  plan-2  C12  0.020
 IBH  plan-2  C13  0.020
 IBH  plan-2  C14  0.020
 IBH  plan-2  C15  0.020
 IBH  plan-2  F    0.020
 IBH  plan-2  C10  0.020
 IBH  plan-2  C9   0.020
 IBH  plan-2  H12  0.020
 IBH  plan-2  H13  0.020
 IBH  plan-2  H14  0.020
 IBH  plan-3  C9   0.020
 IBH  plan-3  C8   0.020
 IBH  plan-3  O    0.020
 IBH  plan-3  N3   0.020
 IBH  plan-3  C7   0.020
 IBH  plan-3  N2   0.020
 IBH  plan-3  N1   0.020
 IBH  plan-3  S1   0.020
 IBH  plan-3  C6   0.020
 IBH  plan-3  C4   0.020
 IBH  plan-3  H2   0.020

