# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 08:38:01 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (3R)-3-{3-[(2H-1,3-benzodioxol-5-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(Cc3ccc4OCOc4c3)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
 7JT  7JT  (3R)-3-{3-[(2H-1,3-benzodioxol-5-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 OK
;

data_comp_7JT
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
 7JT  N1   N  NH1   0  -0.370   5.9325   0.0800  -0.0697
 7JT  O2   O  OH1   0  -0.541   6.9401  -0.7144  -0.5202
 7JT  C3   C  C     0   0.521   4.8794   0.3518  -0.8580
 7JT  O4   O  O     0  -0.473   4.8095   0.0254  -2.0298
 7JT  C5   C  CH2   0  -0.577   3.7926   1.1443  -0.1631
 7JT  C6   C  CH1   0  -0.383   2.4216   0.4895  -0.3782
 7JT  C7   C  CH2   0  -0.437   2.3295  -0.8668   0.3422
 7JT  C12  C  CR5   0   0.561   1.3343   1.4120   0.0386
 7JT  O13  O  O     0  -0.334   1.3417   1.9114   1.2678
 7JT  N14  N  N     0  -0.439   0.2991   1.7830  -0.6359
 7JT  N15  N  N     0  -0.147   0.1947   2.6538   1.4136
 7JT  C16  C  CR5   0   0.318  -0.3946   2.5385   0.2654
 7JT  C17  C  CR15  0  -0.216   1.0682  -1.6878   0.0774
 7JT  C18  C  CH2   0  -0.442   1.2386  -3.1550   0.5607
 7JT  C19  C  CH2   0  -0.456  -0.2214  -1.1971   0.7632
 7JT  C20  C  CH2   0  -0.441  -1.0389  -2.4656   0.9794
 7JT  C21  C  CH2   0  -0.441   0.0097  -3.4812   1.4220
 7JT  H1   H  HNH1  0   0.417   5.9258   0.2426   0.9268
 7JT  H2   H  HOH1  0   0.479   7.6336  -0.1195  -0.8343
 7JT  H3   H  HCH2  0   0.271   3.9975   1.2592   0.9036
 7JT  H4   H  HCH2  0   0.300   3.8018   2.1476  -0.5968
 7JT  H5   H  HCH1  0   0.291   2.2757   0.3249  -1.4481
 7JT  H6   H  HCH2  0   0.254   3.1879  -1.4548   0.0049
 7JT  H7   H  HCH2  0   0.236   2.4655  -0.7247   1.4194
 7JT  H9   H  HCH2  0   0.229   1.2969  -3.8255  -0.2983
 7JT  H10  H  HCH2  0   0.211   0.0151  -0.7431   1.7319
 7JT  H11  H  HCH2  0   0.253  -0.7641  -0.4572   0.1759
 7JT  H12  H  HCH2  0   0.227  -1.8492  -2.3350   1.6985
 7JT  H13  H  HCH2  0   0.228  -0.3186  -4.5160   1.3131
 7JT  C2   C  CH2   0  -0.618  -1.7641   3.0545  -0.0078
 7JT  H8   H  HCR5  0   0.228   0.8986  -1.6958  -1.0049
 7JT  H14  H  HCH2  0   0.227   2.1670  -3.2865   1.1210
 7JT  H15  H  HCH2  0   0.212  -1.4925  -2.7795   0.0332
 7JT  H16  H  HCH2  0   0.218   0.2391  -3.3271   2.4796
 7JT  H19  H  HCH2  0   0.288  -2.0358   3.7913   0.7475
 7JT  H20  H  HCH2  0   0.291  -1.7779   3.5499  -0.9799
 7JT  C4   C  CR16  0  -0.367  -2.8746   1.0944  -1.1329
 7JT  C8   C  CR56  0   0.309  -3.6491  -0.0316  -1.0198
 7JT  C9   C  CR56  0   0.292  -4.2583  -0.3915   0.1724
 7JT  C10  C  CR16  0  -0.329  -4.1264   0.3688   1.3068
 7JT  C11  C  CR16  0  -0.301  -3.3320   1.5169   1.2071
 7JT  C14  C  CR6   0   0.088  -2.7139   1.8799   0.0189
 7JT  H27  H  HCR6  0   0.272  -4.6072   0.0969   2.2366
 7JT  H30  H  HCR6  0   0.254  -3.1889   2.1293   2.0886
 7JT  O1   O  O     0  -0.485  -3.9717  -0.9383  -1.9770
 7JT  O3   O  O     0  -0.485  -4.9724  -1.5301  -0.0165
 7JT  C15  C  CH2   0   0.060  -4.5663  -2.0260  -1.2837
 7JT  H22  H  HCH2  0   0.252  -5.4315  -2.3895  -1.8357
 7JT  H23  H  HCH2  0   0.228  -3.8287  -2.8269  -1.1492
 7JT  H21  H  HCR6  0   0.268  -2.3975   1.3630  -2.0664

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
 7JT  C20  C21  single    1.525  0.020  1.525
 7JT  C20  C19  single    1.525  0.020  1.525
 7JT  C21  C18  single    1.536  0.020  1.536
 7JT  C19  C17  single    1.541  0.020  1.541
 7JT  C18  C17  single    1.554  0.020  1.554
 7JT  C17  C7   single    1.528  0.020  1.528
 7JT  C7   C6   single    1.539  0.020  1.539
 7JT  C6   C12  single    1.486  0.020  1.486
 7JT  C6   C5   single    1.535  0.020  1.535
 7JT  N14  C16  aromatic  1.365  0.020  1.365
 7JT  N14  C12  aromatic  1.290  0.020  1.290
 7JT  C16  N15  aromatic  1.296  0.020  1.296
 7JT  C12  O13  aromatic  1.327  0.020  1.327
 7JT  N15  O13  aromatic  1.374  0.020  1.374
 7JT  O2   N1   single    1.360  0.020  1.360
 7JT  N1   C3   single    1.343  0.020  1.343
 7JT  C3   C5   single    1.514  0.020  1.514
 7JT  C3   O4   double    1.218  0.020  1.218
 7JT  N1   H1   single    0.860  0.020  1.020
 7JT  O2   H2   single    0.850  0.020  0.980
 7JT  C5   H3   single    0.970  0.020  1.090
 7JT  C5   H4   single    0.970  0.020  1.090
 7JT  C6   H5   single    0.970  0.020  1.090
 7JT  C7   H6   single    0.970  0.020  1.090
 7JT  C7   H7   single    0.970  0.020  1.090
 7JT  C18  H9   single    0.970  0.020  1.090
 7JT  C19  H10  single    0.970  0.020  1.090
 7JT  C19  H11  single    0.970  0.020  1.090
 7JT  C20  H12  single    0.970  0.020  1.090
 7JT  C21  H13  single    0.970  0.020  1.090
 7JT  C17  H8   single    0.970  0.020  1.090
 7JT  C18  H14  single    0.970  0.020  1.090
 7JT  C20  H15  single    0.970  0.020  1.090
 7JT  C21  H16  single    0.970  0.020  1.090
 7JT  C2   H19  single    0.970  0.020  1.090
 7JT  C2   H20  single    0.970  0.020  1.090
 7JT  C2   C14  single    1.511  0.020  1.511
 7JT  C14  C4   aromatic  1.403  0.020  1.403
 7JT  C4   C8   aromatic  1.371  0.020  1.371
 7JT  C8   C9   aromatic  1.386  0.020  1.386
 7JT  C9   C10  aromatic  1.372  0.020  1.372
 7JT  C10  C11  aromatic  1.400  0.020  1.400
 7JT  C11  C14  aromatic  1.388  0.020  1.388
 7JT  C4   H21  single    0.930  0.020  1.080
 7JT  C10  H27  single    0.930  0.020  1.080
 7JT  C11  H30  single    0.930  0.020  1.080
 7JT  C8   O1   single    1.357  0.020  1.357
 7JT  C9   O3   single    1.357  0.020  1.357
 7JT  O1   C15  single    1.420  0.020  1.420
 7JT  O3   C15  single    1.420  0.020  1.420
 7JT  C15  H22  single    0.970  0.020  1.090
 7JT  C15  H23  single    0.970  0.020  1.090
 7JT  C16  C2   single    1.489  0.020  1.489

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
 7JT  H1   N1   C3   122.78  3.000
 7JT  H1   N1   O2   115.21  3.000
 7JT  C3   N1   O2   120.31  3.000
 7JT  H2   O2   N1   106.25  3.000
 7JT  C5   C3   O4   122.72  3.000
 7JT  O4   C3   N1   123.73  3.000
 7JT  C5   C3   N1   113.54  3.000
 7JT  H4   C5   H3   106.82  3.000
 7JT  H4   C5   C6   110.09  3.000
 7JT  H3   C5   C6   110.45  3.000
 7JT  H4   C5   C3   107.00  3.000
 7JT  H3   C5   C3   111.63  3.000
 7JT  C6   C5   C3   110.71  3.000
 7JT  H5   C6   C12  105.70  3.000
 7JT  H5   C6   C7   108.53  3.000
 7JT  C12  C6   C7   111.86  3.000
 7JT  H5   C6   C5   108.72  3.000
 7JT  C12  C6   C5   110.47  3.000
 7JT  C7   C6   C5   111.35  3.000
 7JT  H7   C7   H6   106.01  3.000
 7JT  H7   C7   C17  110.04  3.000
 7JT  H6   C7   C17  107.79  3.000
 7JT  H7   C7   C6   109.80  3.000
 7JT  H6   C7   C6   106.41  3.000
 7JT  C17  C7   C6   116.22  3.000
 7JT  N14  C12  O13  112.37  3.000
 7JT  O13  C12  C6   119.31  3.000
 7JT  N14  C12  C6   128.26  3.000
 7JT  N15  O13  C12  107.28  3.000
 7JT  C16  N14  C12  102.81  3.000
 7JT  C16  N15  O13  103.74  3.000
 7JT  C2   C16  N15  123.38  3.000
 7JT  C2   C16  N14  122.54  3.000
 7JT  N15  C16  N14  113.77  3.000
 7JT  H8   C17  C19  108.21  3.000
 7JT  H8   C17  C18  108.50  3.000
 7JT  C19  C17  C18  104.72  3.000
 7JT  H8   C17  C7   107.63  3.000
 7JT  C18  C17  C7   111.27  3.000
 7JT  C19  C17  C7   116.27  3.000
 7JT  H14  C18  H9   106.53  3.000
 7JT  H14  C18  C21  111.52  3.000
 7JT  H9   C18  C21  110.71  3.000
 7JT  H14  C18  C17  111.50  3.000
 7JT  H9   C18  C17  109.95  3.000
 7JT  C21  C18  C17  106.69  3.000
 7JT  H11  C19  H10  107.62  3.000
 7JT  H11  C19  C20  111.99  3.000
 7JT  H10  C19  C20  109.58  3.000
 7JT  H11  C19  C17  113.16  3.000
 7JT  H10  C19  C17  110.17  3.000
 7JT  C20  C19  C17  104.29  3.000
 7JT  H15  C20  H12  107.22  3.000
 7JT  H15  C20  C21  110.16  3.000
 7JT  H12  C20  C21  113.51  3.000
 7JT  H15  C20  C19  109.76  3.000
 7JT  H12  C20  C19  113.08  3.000
 7JT  C21  C20  C19  103.09  3.000
 7JT  H16  C21  H13  107.07  3.000
 7JT  H16  C21  C20  109.34  3.000
 7JT  H13  C21  C20  113.30  3.000
 7JT  H16  C21  C18  110.17  3.000
 7JT  H13  C21  C18  112.72  3.000
 7JT  C20  C21  C18  104.23  3.000
 7JT  C14  C2   H20  111.15  3.000
 7JT  C14  C2   H19  110.90  3.000
 7JT  H20  C2   H19  107.91  3.000
 7JT  C14  C2   C16  107.79  3.000
 7JT  H20  C2   C16  109.42  3.000
 7JT  H19  C2   C16  109.66  3.000
 7JT  H21  C4   C14  121.24  3.000
 7JT  H21  C4   C8   121.59  3.000
 7JT  C14  C4   C8   117.16  3.000
 7JT  O1   C8   C9   109.19  3.000
 7JT  O1   C8   C4   128.65  3.000
 7JT  C9   C8   C4   122.15  3.000
 7JT  O3   C9   C10  129.09  3.000
 7JT  O3   C9   C8   109.22  3.000
 7JT  C10  C9   C8   121.67  3.000
 7JT  H27  C10  C11  121.32  3.000
 7JT  H27  C10  C9   121.92  3.000
 7JT  C11  C10  C9   116.76  3.000
 7JT  H30  C11  C14  119.36  3.000
 7JT  H30  C11  C10  118.74  3.000
 7JT  C14  C11  C10  121.89  3.000
 7JT  C11  C14  C4   120.36  3.000
 7JT  C11  C14  C2   119.91  3.000
 7JT  C4   C14  C2   119.51  3.000
 7JT  C15  O1   C8   105.47  3.000
 7JT  C15  O3   C9   105.47  3.000
 7JT  H23  C15  H22  110.65  3.000
 7JT  H23  C15  O3   109.74  3.000
 7JT  H22  C15  O3   109.99  3.000
 7JT  H23  C15  O1   109.72  3.000
 7JT  H22  C15  O1   109.93  3.000
 7JT  O3   C15  O1   106.73  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
 7JT  CONST_01  N15  C16  N14  C12     0.00   0.0  0
 7JT  CONST_02  C16  N15  O13  C12     0.00   0.0  0
 7JT  CONST_03  C16  N14  C12  O13     0.00   0.0  0
 7JT  CONST_04  N14  C16  N15  O13     0.00   0.0  0
 7JT  CONST_05  N15  O13  C12  N14     0.00   0.0  0
 7JT  CONST_06  C10  C11  C14  C4      0.00   0.0  0
 7JT  CONST_07  C10  C9   C8   C4      0.00   0.0  0
 7JT  CONST_08  C11  C14  C4   C8      0.00   0.0  0
 7JT  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 7JT  CONST_10  C14  C4   C8   C9      0.00   0.0  0
 7JT  CONST_11  C14  C11  C10  C9      0.00   0.0  0
 7JT  CONST_12  C16  N14  C12  C6    180.00   0.0  0
 7JT  CONST_13  N15  O13  C12  C6    180.00   0.0  0
 7JT  CONST_14  C2   C16  N14  C12   180.00   0.0  0
 7JT  CONST_15  C2   C16  N15  O13   180.00   0.0  0
 7JT  CONST_16  C8   C4   C14  C2    180.00   0.0  0
 7JT  CONST_17  C10  C11  C14  C2    180.00   0.0  0
 7JT  CONST_18  H30  C11  C14  C4    180.00   0.0  0
 7JT  CONST_19  H27  C10  C9   C8    180.00   0.0  0
 7JT  CONST_20  H21  C4   C8   C9    180.00   0.0  0
 7JT  CONST_21  C5   C3   N1   O2    180.00   0.0  0
 7JT  CONST_22  O4   C3   N1   O2      0.00   0.0  0
 7JT  CONST_23  H1   N1   C3   O4    180.00   0.0  0
 7JT  Var_01    C21  C20  C19  C17    40.83  30.0  1
 7JT  Var_02    C20  C21  C18  C17    21.34  30.0  1
 7JT  Var_03    C19  C20  C21  C18   -38.28  30.0  1
 7JT  Var_04    O3   C15  O1   C8     19.24  30.0  1
 7JT  Var_05    O1   C15  O3   C9    -19.22  30.0  1
 7JT  Var_06    C14  C2   C16  N14    70.84  30.0  2
 7JT  Var_07    C4   C14  C2   C16   -83.87  30.0  2
 7JT  Var_08    C6   C5   C3   N1   -130.34  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
 7JT  chir_01  C6   C7  C12  C5   negativ
 7JT  chir_02  C17  C7  C18  C19  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
 7JT  plan-1  C6   0.020
 7JT  plan-1  C12  0.020
 7JT  plan-1  O13  0.020
 7JT  plan-1  N14  0.020
 7JT  plan-1  N15  0.020
 7JT  plan-1  C16  0.020
 7JT  plan-1  C2   0.020
 7JT  plan-2  C2   0.020
 7JT  plan-2  C4   0.020
 7JT  plan-2  C8   0.020
 7JT  plan-2  C9   0.020
 7JT  plan-2  C10  0.020
 7JT  plan-2  C11  0.020
 7JT  plan-2  C14  0.020
 7JT  plan-2  H27  0.020
 7JT  plan-2  H30  0.020
 7JT  plan-2  O1   0.020
 7JT  plan-2  O3   0.020
 7JT  plan-2  H21  0.020
 7JT  plan-3  N1   0.020
 7JT  plan-3  O2   0.020
 7JT  plan-3  C3   0.020
 7JT  plan-3  O4   0.020
 7JT  plan-3  C5   0.020
 7JT  plan-3  H1   0.020

