# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 18:05:57 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: methyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](CC(=O)NO)c1onc(Cc2ccc(cc2)C(=O)OC)n1
#
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
 SF5  SF5  'methyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate'  ligand  49  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SF5
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
 SF5  N1   N  NH1   0  -0.372   6.3425  -0.3880  -0.0117
 SF5  O2   O  OH1   0  -0.541   7.4372  -1.0240  -0.5122
 SF5  C3   C  C     0   0.526   5.3166  -0.0823  -0.8249
 SF5  O4   O  O     0  -0.471   5.2085  -0.5041  -1.9624
 SF5  C5   C  CH2   0  -0.582   4.2909   0.8304  -0.1879
 SF5  C6   C  CH1   0  -0.381   2.8763   0.2760  -0.3801
 SF5  C7   C  CH2   0  -0.428   2.6397  -0.9890   0.4621
 SF5  C8   C  CH2   0  -0.414   1.3097  -1.6783   0.1835
 SF5  C9   C  CH2   0  -0.420   1.0782  -2.8870   1.0816
 SF5  C10  C  CH3   0  -0.659  -0.2427  -3.5847   0.7887
 SF5  C12  C  CR5   0   0.553   1.8468   1.2982  -0.0543
 SF5  O13  O  O     0  -0.331   1.9415   1.9748   1.0834
 SF5  N14  N  N     0  -0.431   0.7828   1.6033  -0.7183
 SF5  N15  N  N     0  -0.143   0.8373   2.7847   1.1711
 SF5  C16  C  CR5   0   0.324   0.1792   2.5266   0.0855
 SF5  H1   H  HNH1  0   0.417   6.4890   0.0754   0.8737
 SF5  H2   H  HOH1  0   0.479   7.3287  -1.9588  -0.2947
 SF5  H3   H  HCH2  0   0.272   4.4999   0.9884   0.8724
 SF5  H4   H  HCH2  0   0.302   4.3880   1.8034  -0.6779
 SF5  H5   H  HCH1  0   0.293   2.7316   0.0315  -1.4347
 SF5  H6   H  HCH2  0   0.249   3.4520  -1.6930   0.2592
 SF5  H7   H  HCH2  0   0.234   2.7189  -0.7352   1.5238
 SF5  H8   H  HCH2  0   0.224   0.4786  -0.9781   0.3141
 SF5  H9   H  HCH2  0   0.219   1.2789  -1.9887  -0.8661
 SF5  H10  H  HCH2  0   0.216   1.9039  -3.5948   0.9632
 SF5  H11  H  HCH2  0   0.215   1.1006  -2.5656   2.1274
 SF5  H12  H  HCH3  0   0.213  -1.0847  -2.8993   0.9071
 SF5  H13  H  HCH3  0   0.218  -0.2697  -3.9638  -0.2345
 SF5  H14  H  HCH3  0   0.228  -0.4079  -4.4287   1.4589
 SF5  C1   C  CH2   0  -0.612  -1.1473   3.1248  -0.2269
 SF5  C2   C  CR6   0   0.135  -2.2036   2.0504  -0.1639
 SF5  C4   C  CR16  0  -0.257  -2.8025   1.7292   1.0510
 SF5  C11  C  CR16  0  -0.222  -3.7341   0.7091   1.1290
 SF5  C13  C  CR6   0  -0.093  -4.0820  -0.0147  -0.0099
 SF5  C14  C  CR16  0  -0.231  -3.4857   0.3055  -1.2283
 SF5  C15  C  CR16  0  -0.256  -2.5557   1.3298  -1.2998
 SF5  C17  C  C     0   0.595  -5.0856  -1.0998   0.1259
 SF5  O1   O  O     0  -0.451  -5.6373  -1.3778   1.1642
 SF5  O3   O  O2    0  -0.448  -5.3121  -1.7336  -1.0128
 SF5  C20  C  CH3   0  -0.400  -6.2700  -2.7922  -1.0015
 SF5  H15  H  HCH2  0   0.280  -1.3622   3.9194   0.4873
 SF5  H16  H  HCH2  0   0.283  -1.1121   3.5694  -1.2229
 SF5  H17  H  HCR6  0   0.239  -2.5393   2.2823   1.9447
 SF5  H18  H  HCR6  0   0.245  -4.1918   0.4755   2.0809
 SF5  H19  H  HCR6  0   0.249  -3.7392  -0.2362  -2.1290
 SF5  H20  H  HCR6  0   0.240  -2.1000   1.5699  -2.2521
 SF5  H21  H  HCH3  0   0.228  -5.9696  -3.5936  -0.3269
 SF5  H22  H  HCH3  0   0.227  -7.2578  -2.4314  -0.7160
 SF5  H23  H  HCH3  0   0.240  -6.3051  -3.1721  -2.0181

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
 SF5  C10  C9   single    1.522  0.020  1.522
 SF5  C9   C8   single    1.524  0.020  1.524
 SF5  C8   C7   single    1.524  0.020  1.524
 SF5  C7   C6   single    1.538  0.020  1.538
 SF5  C16  N14  aromatic  1.365  0.020  1.365
 SF5  C16  N15  aromatic  1.295  0.020  1.295
 SF5  N14  C12  aromatic  1.291  0.020  1.291
 SF5  C6   C12  single    1.487  0.020  1.487
 SF5  C6   C5   single    1.532  0.020  1.532
 SF5  N15  O13  aromatic  1.372  0.020  1.372
 SF5  C12  O13  aromatic  1.327  0.020  1.327
 SF5  O2   N1   single    1.361  0.020  1.361
 SF5  N1   C3   single    1.344  0.020  1.344
 SF5  C3   C5   single    1.514  0.020  1.514
 SF5  C3   O4   double    1.218  0.020  1.218
 SF5  N1   H1   single    0.860  0.020  1.020
 SF5  O2   H2   single    0.850  0.020  0.980
 SF5  C5   H3   single    0.970  0.020  1.090
 SF5  C5   H4   single    0.970  0.020  1.090
 SF5  C6   H5   single    0.970  0.020  1.090
 SF5  C7   H6   single    0.970  0.020  1.090
 SF5  C7   H7   single    0.970  0.020  1.090
 SF5  C8   H8   single    0.970  0.020  1.090
 SF5  C8   H9   single    0.970  0.020  1.090
 SF5  C9   H10  single    0.970  0.020  1.090
 SF5  C9   H11  single    0.970  0.020  1.090
 SF5  C10  H12  single    0.970  0.020  1.090
 SF5  C10  H13  single    0.970  0.020  1.090
 SF5  C10  H14  single    0.970  0.020  1.090
 SF5  C16  C1   single    1.488  0.020  1.488
 SF5  C1   C2   single    1.508  0.020  1.508
 SF5  C2   C4   aromatic  1.392  0.020  1.392
 SF5  C4   C11  aromatic  1.384  0.020  1.384
 SF5  C11  C13  aromatic  1.394  0.020  1.394
 SF5  C13  C14  aromatic  1.394  0.020  1.394
 SF5  C14  C15  aromatic  1.385  0.020  1.385
 SF5  C15  C2   aromatic  1.391  0.020  1.391
 SF5  C13  C17  single    1.484  0.020  1.484
 SF5  C17  O1   double    1.208  0.020  1.208
 SF5  C17  O3   single    1.323  0.020  1.323
 SF5  O3   C20  single    1.428  0.020  1.428
 SF5  C1   H15  single    0.970  0.020  1.090
 SF5  C1   H16  single    0.970  0.020  1.090
 SF5  C4   H17  single    0.930  0.020  1.080
 SF5  C11  H18  single    0.930  0.020  1.080
 SF5  C14  H19  single    0.930  0.020  1.080
 SF5  C15  H20  single    0.930  0.020  1.080
 SF5  C20  H21  single    0.970  0.020  1.090
 SF5  C20  H22  single    0.970  0.020  1.090
 SF5  C20  H23  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
 SF5  H1   N1   C3   122.46  3.000
 SF5  H1   N1   O2   114.83  3.000
 SF5  C3   N1   O2   119.84  3.000
 SF5  H2   O2   N1   106.20  3.000
 SF5  C5   C3   O4   122.81  3.000
 SF5  O4   C3   N1   123.63  3.000
 SF5  C5   C3   N1   113.56  3.000
 SF5  H4   C5   H3   106.82  3.000
 SF5  H4   C5   C6   110.35  3.000
 SF5  H3   C5   C6   110.54  3.000
 SF5  H4   C5   C3   106.72  3.000
 SF5  H3   C5   C3   111.48  3.000
 SF5  C6   C5   C3   110.78  3.000
 SF5  H5   C6   C12  105.88  3.000
 SF5  H5   C6   C7   108.92  3.000
 SF5  C12  C6   C7   109.82  3.000
 SF5  H5   C6   C5   108.94  3.000
 SF5  C12  C6   C5   111.29  3.000
 SF5  C7   C6   C5   111.79  3.000
 SF5  H7   C7   H6   105.99  3.000
 SF5  H7   C7   C8   110.21  3.000
 SF5  H6   C7   C8   108.85  3.000
 SF5  H7   C7   C6   109.22  3.000
 SF5  H6   C7   C6   108.27  3.000
 SF5  C8   C7   C6   113.97  3.000
 SF5  H9   C8   H8   105.93  3.000
 SF5  H9   C8   C9   109.62  3.000
 SF5  H8   C8   C9   108.77  3.000
 SF5  H9   C8   C7   109.16  3.000
 SF5  H8   C8   C7   110.59  3.000
 SF5  C9   C8   C7   112.56  3.000
 SF5  H11  C9   H10  106.14  3.000
 SF5  H11  C9   C10  109.65  3.000
 SF5  H10  C9   C10  109.73  3.000
 SF5  H11  C9   C8   109.10  3.000
 SF5  H10  C9   C8   109.56  3.000
 SF5  C10  C9   C8   112.46  3.000
 SF5  H14  C10  H13  107.68  3.000
 SF5  H14  C10  H12  107.60  3.000
 SF5  H13  C10  H12  107.49  3.000
 SF5  H14  C10  C9   111.59  3.000
 SF5  H13  C10  C9   111.16  3.000
 SF5  H12  C10  C9   111.13  3.000
 SF5  N14  C12  O13  112.30  3.000
 SF5  O13  C12  C6   119.27  3.000
 SF5  N14  C12  C6   128.35  3.000
 SF5  N15  O13  C12  107.35  3.000
 SF5  C16  N14  C12  102.79  3.000
 SF5  C16  N15  O13  103.75  3.000
 SF5  C1   C16  N15  123.27  3.000
 SF5  C1   C16  N14  122.85  3.000
 SF5  N15  C16  N14  113.81  3.000
 SF5  H16  C1   H15  107.90  3.000
 SF5  H16  C1   C2   110.55  3.000
 SF5  H15  C1   C2   110.73  3.000
 SF5  H16  C1   C16  109.06  3.000
 SF5  H15  C1   C16  109.34  3.000
 SF5  C2   C1   C16  109.22  3.000
 SF5  C15  C2   C4   118.98  3.000
 SF5  C15  C2   C1   120.82  3.000
 SF5  C4   C2   C1   120.15  3.000
 SF5  H17  C4   C11  119.56  3.000
 SF5  H17  C4   C2   119.84  3.000
 SF5  C11  C4   C2   120.59  3.000
 SF5  H18  C11  C13  120.09  3.000
 SF5  H18  C11  C4   119.58  3.000
 SF5  C13  C11  C4   120.33  3.000
 SF5  C17  C13  C14  122.49  3.000
 SF5  C17  C13  C11  118.28  3.000
 SF5  C14  C13  C11  119.23  3.000
 SF5  H19  C14  C15  119.00  3.000
 SF5  H19  C14  C13  120.85  3.000
 SF5  C15  C14  C13  120.15  3.000
 SF5  H20  C15  C14  119.47  3.000
 SF5  H20  C15  C2   119.80  3.000
 SF5  C14  C15  C2   120.73  3.000
 SF5  O3   C17  O1   123.46  3.000
 SF5  O3   C17  C13  112.79  3.000
 SF5  O1   C17  C13  123.75  3.000
 SF5  C20  O3   C17  117.60  3.000
 SF5  H23  C20  H22  109.39  3.000
 SF5  H23  C20  H21  109.34  3.000
 SF5  H22  C20  H21  109.34  3.000
 SF5  H23  C20  O3   105.88  3.000
 SF5  H22  C20  O3   111.39  3.000
 SF5  H21  C20  O3   111.42  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
 SF5  CONST_01  N15  C16  N14  C12     0.00   0.0  0
 SF5  CONST_02  C16  N15  O13  C12     0.00   0.0  0
 SF5  CONST_03  N14  C16  N15  O13     0.00   0.0  0
 SF5  CONST_04  C16  N14  C12  O13     0.00   0.0  0
 SF5  CONST_05  N15  O13  C12  N14     0.00   0.0  0
 SF5  CONST_06  C13  C11  C4   C2      0.00   0.0  0
 SF5  CONST_07  C13  C14  C15  C2      0.00   0.0  0
 SF5  CONST_08  C14  C15  C2   C4      0.00   0.0  0
 SF5  CONST_09  C14  C13  C11  C4      0.00   0.0  0
 SF5  CONST_10  C15  C2   C4   C11     0.00   0.0  0
 SF5  CONST_11  C15  C14  C13  C11     0.00   0.0  0
 SF5  CONST_12  C16  N14  C12  C6    180.00   0.0  0
 SF5  CONST_13  N15  O13  C12  C6    180.00   0.0  0
 SF5  CONST_14  C1   C16  N14  C12   180.00   0.0  0
 SF5  CONST_15  C1   C16  N15  O13   180.00   0.0  0
 SF5  CONST_16  C11  C4   C2   C1    180.00   0.0  0
 SF5  CONST_17  C14  C15  C2   C1    180.00   0.0  0
 SF5  CONST_18  C17  C13  C11  C4    180.00   0.0  0
 SF5  CONST_19  C17  C13  C14  C15   180.00   0.0  0
 SF5  CONST_20  H18  C11  C4   C2    180.00   0.0  0
 SF5  CONST_21  H19  C14  C15  C2    180.00   0.0  0
 SF5  CONST_22  H20  C15  C2   C4    180.00   0.0  0
 SF5  CONST_23  H17  C4   C11  C13   180.00   0.0  0
 SF5  CONST_24  C5   C3   N1   O2    180.00   0.0  0
 SF5  CONST_25  O4   C3   N1   O2      0.00   0.0  0
 SF5  CONST_26  H1   N1   C3   O4    180.00   0.0  0
 SF5  Var_01    C2   C1   C16  N14    65.73  30.0  2
 SF5  Var_02    C4   C2   C1   C16    85.94  30.0  2
 SF5  Var_03    O1   C17  C13  C11     1.33  30.0  2
 SF5  Var_04    C6   C5   C3   N1   -130.51  30.0  3
 SF5  Var_05    C9   C8   C7   C6   -177.20  30.0  1
 SF5  Var_06    C10  C9   C8   C7   -179.24  30.0  2
 SF5  Var_07    H12  C10  C9   C8    -58.18  30.0  3
 SF5  Var_08    H21  C20  O3   C17   -61.24  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
 SF5  chir_01  C6  C7  C12  C5  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
 SF5  plan-1  C6   0.020
 SF5  plan-1  C12  0.020
 SF5  plan-1  O13  0.020
 SF5  plan-1  N14  0.020
 SF5  plan-1  N15  0.020
 SF5  plan-1  C16  0.020
 SF5  plan-1  C1   0.020
 SF5  plan-2  C1   0.020
 SF5  plan-2  C2   0.020
 SF5  plan-2  C4   0.020
 SF5  plan-2  C11  0.020
 SF5  plan-2  C13  0.020
 SF5  plan-2  C14  0.020
 SF5  plan-2  C15  0.020
 SF5  plan-2  C17  0.020
 SF5  plan-2  H17  0.020
 SF5  plan-2  H18  0.020
 SF5  plan-2  H19  0.020
 SF5  plan-2  H20  0.020
 SF5  plan-3  N1   0.020
 SF5  plan-3  O2   0.020
 SF5  plan-3  C3   0.020
 SF5  plan-3  O4   0.020
 SF5  plan-3  C5   0.020
 SF5  plan-3  H1   0.020
 SF5  plan-4  C13  0.020
 SF5  plan-4  C17  0.020
 SF5  plan-4  O1   0.020
 SF5  plan-4  O3   0.020

