# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 11:56:20 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (3R)-3-{3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl}-4-cyclopentyl-N-hydroxybutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)C[C@@H](CC1CCCC1)c2onc(Cc3coc4ccccc34)n2
#
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
 6JT  6JT  (3R)-3-{3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl}-4-cyclopentyl-N-hydroxybutanamide  ligand  50  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6JT
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
 6JT  N1   N  NH1   0  -0.371  -3.5135   3.5580  -1.0409
 6JT  O2   O  OH1   0  -0.541  -4.4659   4.3962  -0.5512
 6JT  C3   C  C     0   0.527  -2.7232   2.8650  -0.2057
 6JT  O4   O  O     0  -0.474  -2.7232   3.0096   1.0040
 6JT  C5   C  CH2   0  -0.576  -1.7864   1.9115  -0.9178
 6JT  C6   C  CH1   0  -0.391  -1.7936   0.5338  -0.2431
 6JT  C7   C  CH2   0  -0.418  -3.1303  -0.1894  -0.4523
 6JT  C12  C  CR5   0   0.556  -0.6562  -0.2848  -0.7406
 6JT  O13  O  O     0  -0.331  -0.6183  -0.6244  -2.0224
 6JT  N14  N  N     0  -0.440   0.3523  -0.7490  -0.0815
 6JT  N15  N  N     0  -0.143   0.5116  -1.3773  -2.2135
 6JT  C16  C  CR5   0   0.311   1.0560  -1.4225  -1.0388
 6JT  C17  C  CH1   0  -0.252  -3.1946  -1.5837   0.1533
 6JT  C18  C  CH2   0  -0.427  -4.5558  -2.2576  -0.0447
 6JT  C19  C  CH2   0  -0.431  -3.0084  -1.6444   1.6686
 6JT  C20  C  CH2   0  -0.450  -3.4975  -3.0468   2.0331
 6JT  C21  C  CH2   0  -0.445  -4.6334  -3.3562   1.0325
 6JT  H1   H  HNH1  0   0.418  -3.5952   3.3418  -2.0238
 6JT  H2   H  HOH1  0   0.479  -4.0753   5.2800  -0.5508
 6JT  H3   H  HCH2  0   0.273  -2.0390   1.8156  -1.9759
 6JT  H4   H  HCH2  0   0.302  -0.7865   2.3509  -0.8679
 6JT  H5   H  HCH1  0   0.295  -1.6140   0.6720   0.8247
 6JT  H6   H  HCH2  0   0.244  -3.9205   0.4205  -0.0031
 6JT  H7   H  HCH2  0   0.242  -3.3497  -0.2369  -1.5233
 6JT  H9   H  HCH2  0   0.217  -5.3464  -1.5171   0.1111
 6JT  H10  H  HCH2  0   0.231  -1.9809  -1.4614   1.9905
 6JT  H11  H  HCH2  0   0.223  -2.6816  -3.7614   1.9060
 6JT  H12  H  HCH2  0   0.226  -5.6086  -3.3552   1.5210
 6JT  H13  H  HCH2  0   0.227  -4.5063  -4.3486   0.5977
 6JT  C1   C  CH2   0  -0.641   2.3401  -2.1296  -0.7727
 6JT  C2   C  CR5   0   0.025   3.4758  -1.1732  -0.6011
 6JT  C4   C  CR56  0   0.029   3.7427  -0.3015   0.5153
 6JT  C8   C  CR56  0   0.367   4.9212   0.3716   0.1873
 6JT  O1   O  O     0  -0.437   5.3638  -0.0277  -1.0258
 6JT  C10  C  CR15  0  -0.026   4.4797  -0.9546  -1.4751
 6JT  H8   H  HCH1  0   0.228  -2.4288  -2.2202  -0.3101
 6JT  H14  H  HCH2  0   0.233  -4.6831  -2.6439  -1.0573
 6JT  H15  H  HCH2  0   0.215  -3.6384  -0.8815   2.1395
 6JT  H16  H  HCH2  0   0.229  -3.8205  -3.1205   3.0721
 6JT  H17  H  HCH2  0   0.292   2.2225  -2.7398   0.1259
 6JT  H18  H  HCH2  0   0.292   2.5468  -2.8085  -1.5998
 6JT  H26  H  HCR5  0   0.293   4.6915  -1.3857  -2.4415
 6JT  C9   C  CR16  0  -0.340   5.5272   1.3022   1.0138
 6JT  C11  C  CR16  0  -0.270   4.9004   1.5488   2.2249
 6JT  C13  C  CR16  0  -0.260   3.7179   0.8879   2.5826
 6JT  C14  C  CR16  0  -0.355   3.1263  -0.0364   1.7392
 6JT  H19  H  HCR6  0   0.272   6.4417   1.8074   0.7325
 6JT  H20  H  HCR6  0   0.260   5.3350   2.2670   2.9075
 6JT  H21  H  HCR6  0   0.256   3.2595   1.1095   3.5375
 6JT  H22  H  HCR6  0   0.252   2.2052  -0.5302   2.0174

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
 6JT  C21  C20  single    1.545  0.020  1.545
 6JT  C21  C18  single    1.541  0.020  1.541
 6JT  C20  C19  single    1.529  0.020  1.529
 6JT  C18  C17  single    1.532  0.020  1.532
 6JT  C19  C17  single    1.528  0.020  1.528
 6JT  C17  C7   single    1.522  0.020  1.522
 6JT  C7   C6   single    1.534  0.020  1.534
 6JT  C6   C12  single    1.487  0.020  1.487
 6JT  C6   C5   single    1.534  0.020  1.534
 6JT  O13  N15  aromatic  1.371  0.020  1.371
 6JT  O13  C12  aromatic  1.327  0.020  1.327
 6JT  N15  C16  aromatic  1.295  0.020  1.295
 6JT  C12  N14  aromatic  1.291  0.020  1.291
 6JT  O2   N1   single    1.360  0.020  1.360
 6JT  C16  N14  aromatic  1.366  0.020  1.366
 6JT  N1   C3   single    1.343  0.020  1.343
 6JT  C3   C5   single    1.514  0.020  1.514
 6JT  C3   O4   double    1.218  0.020  1.218
 6JT  N1   H1   single    0.860  0.020  1.020
 6JT  O2   H2   single    0.850  0.020  0.980
 6JT  C5   H3   single    0.970  0.020  1.090
 6JT  C5   H4   single    0.970  0.020  1.090
 6JT  C6   H5   single    0.970  0.020  1.090
 6JT  C7   H6   single    0.970  0.020  1.090
 6JT  C7   H7   single    0.970  0.020  1.090
 6JT  C18  H9   single    0.970  0.020  1.090
 6JT  C19  H10  single    0.970  0.020  1.090
 6JT  C20  H11  single    0.970  0.020  1.090
 6JT  C21  H12  single    0.970  0.020  1.090
 6JT  C21  H13  single    0.970  0.020  1.090
 6JT  C16  C1   single    1.490  0.020  1.490
 6JT  C1   C2   single    1.495  0.020  1.495
 6JT  C2   C4   aromatic  1.441  0.020  1.441
 6JT  C4   C8   aromatic  1.396  0.020  1.396
 6JT  C8   O1   aromatic  1.352  0.020  1.352
 6JT  O1   C10  aromatic  1.357  0.020  1.357
 6JT  C10  C2   aromatic  1.349  0.020  1.349
 6JT  C17  H8   single    0.970  0.020  1.090
 6JT  C18  H14  single    0.970  0.020  1.090
 6JT  C19  H15  single    0.970  0.020  1.090
 6JT  C20  H16  single    0.970  0.020  1.090
 6JT  C1   H17  single    0.970  0.020  1.090
 6JT  C1   H18  single    0.970  0.020  1.090
 6JT  C10  H26  single    0.930  0.020  1.080
 6JT  C8   C9   aromatic  1.384  0.020  1.384
 6JT  C9   C11  aromatic  1.386  0.020  1.386
 6JT  C11  C13  aromatic  1.401  0.020  1.401
 6JT  C13  C14  aromatic  1.384  0.020  1.384
 6JT  C14  C4   aromatic  1.396  0.020  1.396
 6JT  C9   H19  single    0.930  0.020  1.080
 6JT  C11  H20  single    0.930  0.020  1.080
 6JT  C13  H21  single    0.930  0.020  1.080
 6JT  C14  H22  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
 6JT  H1   N1   C3   122.86  3.000
 6JT  H1   N1   O2   115.21  3.000
 6JT  C3   N1   O2   120.42  3.000
 6JT  H2   O2   N1   106.30  3.000
 6JT  C5   C3   O4   122.79  3.000
 6JT  O4   C3   N1   123.81  3.000
 6JT  C5   C3   N1   113.37  3.000
 6JT  H4   C5   H3   106.92  3.000
 6JT  H4   C5   C6   110.19  3.000
 6JT  H3   C5   C6   110.25  3.000
 6JT  H4   C5   C3   106.93  3.000
 6JT  H3   C5   C3   111.58  3.000
 6JT  C6   C5   C3   110.84  3.000
 6JT  H5   C6   C12  105.74  3.000
 6JT  H5   C6   C7   109.66  3.000
 6JT  C12  C6   C7   111.18  3.000
 6JT  H5   C6   C5   108.40  3.000
 6JT  C12  C6   C5   110.10  3.000
 6JT  C7   C6   C5   111.56  3.000
 6JT  H7   C7   H6   106.32  3.000
 6JT  H7   C7   C17  109.95  3.000
 6JT  H6   C7   C17  108.47  3.000
 6JT  H7   C7   C6   109.19  3.000
 6JT  H6   C7   C6   108.09  3.000
 6JT  C17  C7   C6   114.49  3.000
 6JT  N14  C12  O13  112.27  3.000
 6JT  N14  C12  C6   128.65  3.000
 6JT  O13  C12  C6   119.09  3.000
 6JT  N15  O13  C12  107.38  3.000
 6JT  C16  N14  C12  102.82  3.000
 6JT  C16  N15  O13  103.84  3.000
 6JT  C1   C16  N15  122.73  3.000
 6JT  C1   C16  N14  123.57  3.000
 6JT  N15  C16  N14  113.70  3.000
 6JT  H8   C17  C19  108.09  3.000
 6JT  H8   C17  C18  108.07  3.000
 6JT  C19  C17  C18  102.65  3.000
 6JT  H8   C17  C7   109.49  3.000
 6JT  C19  C17  C7   115.21  3.000
 6JT  C18  C17  C7   112.91  3.000
 6JT  H14  C18  H9   106.70  3.000
 6JT  H14  C18  C21  112.98  3.000
 6JT  H9   C18  C21  110.28  3.000
 6JT  H14  C18  C17  112.29  3.000
 6JT  H9   C18  C17  109.02  3.000
 6JT  C21  C18  C17  105.55  3.000
 6JT  H15  C19  H10  107.31  3.000
 6JT  H15  C19  C20  110.62  3.000
 6JT  H10  C19  C20  112.60  3.000
 6JT  H15  C19  C17  109.17  3.000
 6JT  H10  C19  C17  113.59  3.000
 6JT  C20  C19  C17  103.52  3.000
 6JT  H16  C20  H11  106.73  3.000
 6JT  H16  C20  C21  112.69  3.000
 6JT  H11  C20  C21  110.05  3.000
 6JT  H16  C20  C19  112.57  3.000
 6JT  H11  C20  C19  109.47  3.000
 6JT  C21  C20  C19  105.33  3.000
 6JT  H13  C21  H12  106.47  3.000
 6JT  H13  C21  C20  110.78  3.000
 6JT  H12  C21  C20  111.53  3.000
 6JT  H13  C21  C18  111.36  3.000
 6JT  H12  C21  C18  110.94  3.000
 6JT  C20  C21  C18  105.84  3.000
 6JT  H18  C1   H17  107.26  3.000
 6JT  H18  C1   C2   109.97  3.000
 6JT  H17  C1   C2   110.17  3.000
 6JT  H18  C1   C16  108.88  3.000
 6JT  H17  C1   C16  108.62  3.000
 6JT  C2   C1   C16  111.82  3.000
 6JT  C10  C2   C4   105.43  3.000
 6JT  C10  C2   C1   126.50  3.000
 6JT  C4   C2   C1   128.07  3.000
 6JT  C14  C4   C8   119.15  3.000
 6JT  C14  C4   C2   135.42  3.000
 6JT  C8   C4   C2   105.42  3.000
 6JT  C9   C8   O1   126.24  3.000
 6JT  C9   C8   C4   123.60  3.000
 6JT  O1   C8   C4   110.17  3.000
 6JT  C10  O1   C8   106.59  3.000
 6JT  H26  C10  O1   116.19  3.000
 6JT  H26  C10  C2   131.42  3.000
 6JT  O1   C10  C2   112.39  3.000
 6JT  H19  C9   C11  121.77  3.000
 6JT  H19  C9   C8   121.91  3.000
 6JT  C11  C9   C8   116.32  3.000
 6JT  H20  C11  C13  119.41  3.000
 6JT  H20  C11  C9   119.19  3.000
 6JT  C13  C11  C9   121.39  3.000
 6JT  H21  C13  C14  119.57  3.000
 6JT  H21  C13  C11  119.09  3.000
 6JT  C14  C13  C11  121.34  3.000
 6JT  H22  C14  C13  120.81  3.000
 6JT  H22  C14  C4   120.99  3.000
 6JT  C13  C14  C4   118.20  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
 6JT  CONST_01  C16  N15  O13  C12     0.00   0.0  0
 6JT  CONST_02  N15  C16  N14  C12     0.00   0.0  0
 6JT  CONST_03  N14  C16  N15  O13     0.00   0.0  0
 6JT  CONST_04  C16  N14  C12  O13     0.00   0.0  0
 6JT  CONST_05  N15  O13  C12  N14     0.00   0.0  0
 6JT  CONST_06  O1   C8   C4   C2      0.00   0.0  0
 6JT  CONST_07  C9   C8   C4   C2    180.00   0.0  0
 6JT  CONST_08  C13  C14  C4   C2    180.00   0.0  0
 6JT  CONST_09  C8   O1   C10  C2      0.00   0.0  0
 6JT  CONST_10  O1   C10  C2   C4      0.00   0.0  0
 6JT  CONST_11  C10  O1   C8   C4      0.00   0.0  0
 6JT  CONST_12  C11  C9   C8   C4      0.00   0.0  0
 6JT  CONST_13  C11  C13  C14  C4      0.00   0.0  0
 6JT  CONST_14  C10  C2   C4   C8      0.00   0.0  0
 6JT  CONST_15  C13  C14  C4   C8      0.00   0.0  0
 6JT  CONST_16  C13  C11  C9   C8      0.00   0.0  0
 6JT  CONST_17  C14  C4   C8   O1    180.00   0.0  0
 6JT  CONST_18  C11  C9   C8   O1    180.00   0.0  0
 6JT  CONST_19  C9   C8   O1   C10   180.00   0.0  0
 6JT  CONST_20  C14  C4   C2   C10   180.00   0.0  0
 6JT  CONST_21  C14  C4   C8   C9      0.00   0.0  0
 6JT  CONST_22  C14  C13  C11  C9      0.00   0.0  0
 6JT  CONST_23  N15  O13  C12  C6    180.00   0.0  0
 6JT  CONST_24  C16  N14  C12  C6    180.00   0.0  0
 6JT  CONST_25  C1   C16  N14  C12   180.00   0.0  0
 6JT  CONST_26  C1   C16  N15  O13   180.00   0.0  0
 6JT  CONST_27  C8   C4   C2   C1    180.00   0.0  0
 6JT  CONST_28  C14  C4   C2   C1      0.00   0.0  0
 6JT  CONST_29  O1   C10  C2   C1    180.00   0.0  0
 6JT  CONST_30  H22  C14  C4   C2      0.00   0.0  0
 6JT  CONST_31  H26  C10  C2   C4    180.00   0.0  0
 6JT  CONST_32  H19  C9   C8   C4    180.00   0.0  0
 6JT  CONST_33  H21  C13  C14  C4    180.00   0.0  0
 6JT  CONST_34  H20  C11  C9   C8    180.00   0.0  0
 6JT  CONST_35  C5   C3   N1   O2    180.00   0.0  0
 6JT  CONST_36  O4   C3   N1   O2      0.00   0.0  0
 6JT  CONST_37  H1   N1   C3   O4    180.00   0.0  0
 6JT  Var_01    C20  C21  C18  C17    14.24  30.0  1
 6JT  Var_02    C21  C20  C19  C17   -33.07  30.0  1
 6JT  Var_03    C19  C20  C21  C18    11.58  30.0  1
 6JT  Var_04    C2   C1   C16  N14   -74.24  30.0  2
 6JT  Var_05    C4   C2   C1   C16    72.62  30.0  2
 6JT  Var_06    C6   C5   C3   N1   -133.76  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
 6JT  chir_01  C6   C7  C12  C5   negativ
 6JT  chir_02  C17  C7  C19  C18  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
 6JT  plan-1  C6   0.020
 6JT  plan-1  C12  0.020
 6JT  plan-1  O13  0.020
 6JT  plan-1  N14  0.020
 6JT  plan-1  N15  0.020
 6JT  plan-1  C16  0.020
 6JT  plan-1  C1   0.020
 6JT  plan-2  C1   0.020
 6JT  plan-2  C2   0.020
 6JT  plan-2  C4   0.020
 6JT  plan-2  C8   0.020
 6JT  plan-2  O1   0.020
 6JT  plan-2  C10  0.020
 6JT  plan-2  H26  0.020
 6JT  plan-2  C9   0.020
 6JT  plan-2  C11  0.020
 6JT  plan-2  C13  0.020
 6JT  plan-2  C14  0.020
 6JT  plan-2  H19  0.020
 6JT  plan-2  H20  0.020
 6JT  plan-2  H21  0.020
 6JT  plan-2  H22  0.020
 6JT  plan-3  N1   0.020
 6JT  plan-3  O2   0.020
 6JT  plan-3  C3   0.020
 6JT  plan-3  O4   0.020
 6JT  plan-3  C5   0.020
 6JT  plan-3  H1   0.020

