# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:23:10 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (3R)-3-{3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl}-N-hydroxyheptanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](CC(=O)NO)c1onc(Cc2ccc(F)cc2)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
 SF7  SF7  (3R)-3-{3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl}-N-hydroxyheptanamide  ligand  43  23  .  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_SF7
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
 SF7  O4   O  O     0  -0.460   0.1243  -1.8748  -1.1308
 SF7  C3   C  C     0   0.561   1.2741  -2.2369  -1.3060
 SF7  N1   N  NH1   0  -0.383   1.6197  -3.5007  -1.6124
 SF7  O2   O  OH1   0  -0.543   0.6621  -4.3908  -1.9960
 SF7  C5   C  CH2   0  -0.611   2.4614  -1.3081  -1.1841
 SF7  C6   C  CH1   0  -0.379   2.2038  -0.1506  -0.2212
 SF7  C7   C  CH2   0  -0.417   3.4329   0.7675  -0.0888
 SF7  C8   C  CH2   0  -0.424   4.6113   0.1014   0.6112
 SF7  C9   C  CH2   0  -0.422   5.7932   1.0469   0.7877
 SF7  C10  C  CH3   0  -0.662   6.9647   0.3861   1.5009
 SF7  C12  C  CR5   0   0.568   1.0232   0.6636  -0.6194
 SF7  O13  O  O     0  -0.338   0.8716   1.0102  -1.8890
 SF7  N15  N  N     0  -0.159  -0.2517   1.7973  -1.9654
 SF7  C16  C  CR5   0   0.325  -0.6600   1.8687  -0.7374
 SF7  N14  N  N     0  -0.448   0.1168   1.1769   0.1439
 SF7  H1   H  HNH1  0   0.417   2.5579  -3.7422  -1.8989
 SF7  H2   H  HOH1  0   0.479   0.4804  -4.9379  -1.2212
 SF7  H3   H  HCH2  0   0.291   3.3400  -1.8618  -0.8516
 SF7  H4   H  HCH2  0   0.292   2.7053  -0.9293  -2.1817
 SF7  H5   H  HCH1  0   0.289   1.9697  -0.5498   0.7693
 SF7  H6   H  HCH2  0   0.236   3.7360   1.1179  -1.0801
 SF7  H7   H  HCH2  0   0.248   3.1441   1.6558   0.4802
 SF7  H8   H  HCH2  0   0.220   4.2874  -0.2641   1.5916
 SF7  H9   H  HCH2  0   0.224   4.9432  -0.7768   0.0494
 SF7  H10  H  HCH2  0   0.216   6.1168   1.4083  -0.1929
 SF7  H11  H  HCH2  0   0.216   5.4718   1.9308   1.3471
 SF7  H12  H  HCH3  0   0.228   7.8094   1.0683   1.6013
 SF7  H13  H  HCH3  0   0.218   6.6823   0.0590   2.5031
 SF7  H14  H  HCH3  0   0.217   7.3113  -0.4924   0.9537
 SF7  C1   C  CH2   0  -0.623  -1.8785   2.6216  -0.3332
 SF7  C2   C  CR6   0   0.117  -2.8891   1.7088   0.3134
 SF7  C4   C  CR16  0  -0.296  -3.0841   1.7149   1.6895
 SF7  C11  C  CR16  0  -0.397  -4.0011   0.8606   2.2879
 SF7  C13  C  CR6   0   0.512  -4.7171  -0.0043   1.4850
 SF7  C14  C  CR16  0  -0.397  -4.5485  -0.0418   0.1136
 SF7  C15  C  CR16  0  -0.262  -3.6292   0.8209  -0.4632
 SF7  F1   F  F     0  -0.317  -5.6073  -0.8355   2.0527
 SF7  H15  H  HCH2  0   0.289  -1.5857   3.4110   0.3623
 SF7  H16  H  HCH2  0   0.288  -2.3026   3.1078  -1.2126
 SF7  H17  H  HCR6  0   0.264  -2.5171   2.3962   2.3115
 SF7  H18  H  HCR6  0   0.280  -4.1533   0.8701   3.3593
 SF7  H19  H  HCR6  0   0.280  -5.1223  -0.7300  -0.4931
 SF7  H20  H  HCR6  0   0.263  -3.4887   0.7985  -1.5374

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
 SF7  C10  C9   single    1.522  0.020  1.522
 SF7  C9   C8   single    1.524  0.020  1.524
 SF7  C8   C7   single    1.524  0.020  1.524
 SF7  C7   C6   single    1.540  0.020  1.540
 SF7  C6   C12  single    1.488  0.020  1.488
 SF7  C6   C5   single    1.528  0.020  1.528
 SF7  O13  C12  aromatic  1.325  0.020  1.325
 SF7  O13  N15  aromatic  1.374  0.020  1.374
 SF7  O2   N1   single    1.363  0.020  1.363
 SF7  C12  N14  aromatic  1.291  0.020  1.291
 SF7  N1   C3   single    1.346  0.020  1.346
 SF7  N15  C16  aromatic  1.296  0.020  1.296
 SF7  N14  C16  aromatic  1.363  0.020  1.363
 SF7  C3   C5   single    1.512  0.020  1.512
 SF7  C3   O4   double    1.218  0.020  1.218
 SF7  N1   H1   single    0.890  0.020  1.040
 SF7  O2   H2   single    0.850  0.020  0.980
 SF7  C5   H3   single    0.970  0.020  1.090
 SF7  C5   H4   single    0.970  0.020  1.090
 SF7  C6   H5   single    0.970  0.020  1.090
 SF7  C7   H6   single    0.970  0.020  1.090
 SF7  C7   H7   single    0.970  0.020  1.090
 SF7  C8   H8   single    0.970  0.020  1.090
 SF7  C8   H9   single    0.970  0.020  1.090
 SF7  C9   H10  single    0.970  0.020  1.090
 SF7  C9   H11  single    0.970  0.020  1.090
 SF7  C10  H12  single    0.970  0.020  1.090
 SF7  C10  H13  single    0.970  0.020  1.090
 SF7  C10  H14  single    0.970  0.020  1.090
 SF7  C16  C1   single    1.488  0.020  1.488
 SF7  C1   C2   single    1.508  0.020  1.508
 SF7  C2   C4   aromatic  1.390  0.020  1.390
 SF7  C4   C11  aromatic  1.389  0.020  1.389
 SF7  C11  C13  aromatic  1.380  0.020  1.380
 SF7  C13  C14  aromatic  1.382  0.020  1.382
 SF7  C14  C15  aromatic  1.386  0.020  1.386
 SF7  C15  C2   aromatic  1.393  0.020  1.393
 SF7  C13  F1   single    1.344  0.020  1.344
 SF7  C1   H15  single    0.970  0.020  1.090
 SF7  C1   H16  single    0.970  0.020  1.090
 SF7  C4   H17  single    0.930  0.020  1.080
 SF7  C11  H18  single    0.930  0.020  1.080
 SF7  C14  H19  single    0.930  0.020  1.080
 SF7  C15  H20  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
 SF7  C5   C3   N1   113.18  3.000
 SF7  C5   C3   O4   123.15  3.000
 SF7  N1   C3   O4   123.67  3.000
 SF7  H1   N1   O2   114.63  3.000
 SF7  H1   N1   C3   121.84  3.000
 SF7  O2   N1   C3   119.81  3.000
 SF7  H2   O2   N1   106.04  3.000
 SF7  H4   C5   H3   105.91  3.000
 SF7  H4   C5   C6   110.48  3.000
 SF7  H3   C5   C6   109.17  3.000
 SF7  H4   C5   C3   108.30  3.000
 SF7  H3   C5   C3   110.20  3.000
 SF7  C6   C5   C3   112.57  3.000
 SF7  H5   C6   C12  105.80  3.000
 SF7  H5   C6   C7   108.11  3.000
 SF7  C12  C6   C7   109.27  3.000
 SF7  H5   C6   C5   109.30  3.000
 SF7  C12  C6   C5   112.31  3.000
 SF7  C7   C6   C5   111.80  3.000
 SF7  H7   C7   H6   106.52  3.000
 SF7  H7   C7   C8   108.68  3.000
 SF7  H6   C7   C8   109.99  3.000
 SF7  H7   C7   C6   108.56  3.000
 SF7  H6   C7   C6   109.52  3.000
 SF7  C8   C7   C6   113.33  3.000
 SF7  H9   C8   H8   106.35  3.000
 SF7  H9   C8   C9   108.79  3.000
 SF7  H8   C8   C9   109.44  3.000
 SF7  H9   C8   C7   110.46  3.000
 SF7  H8   C8   C7   109.17  3.000
 SF7  C9   C8   C7   112.44  3.000
 SF7  H11  C9   H10  106.15  3.000
 SF7  H11  C9   C10  109.71  3.000
 SF7  H10  C9   C10  109.61  3.000
 SF7  H11  C9   C8   109.42  3.000
 SF7  H10  C9   C8   109.30  3.000
 SF7  C10  C9   C8   112.45  3.000
 SF7  H14  C10  H13  107.53  3.000
 SF7  H14  C10  H12  107.68  3.000
 SF7  H13  C10  H12  107.66  3.000
 SF7  H14  C10  C9   111.03  3.000
 SF7  H13  C10  C9   111.17  3.000
 SF7  H12  C10  C9   111.58  3.000
 SF7  N14  C12  O13  112.46  3.000
 SF7  N14  C12  C6   128.03  3.000
 SF7  O13  C12  C6   119.36  3.000
 SF7  N15  O13  C12  107.27  3.000
 SF7  C16  N15  O13  103.68  3.000
 SF7  C1   C16  N14  123.21  3.000
 SF7  C1   C16  N15  122.90  3.000
 SF7  N14  C16  N15  113.89  3.000
 SF7  C16  N14  C12  102.69  3.000
 SF7  H16  C1   H15  107.19  3.000
 SF7  H16  C1   C2   110.80  3.000
 SF7  H15  C1   C2   110.13  3.000
 SF7  H16  C1   C16  108.96  3.000
 SF7  H15  C1   C16  108.61  3.000
 SF7  C2   C1   C16  111.04  3.000
 SF7  C15  C2   C4   118.71  3.000
 SF7  C15  C2   C1   120.21  3.000
 SF7  C4   C2   C1   121.07  3.000
 SF7  H17  C4   C11  119.03  3.000
 SF7  H17  C4   C2   119.87  3.000
 SF7  C11  C4   C2   121.10  3.000
 SF7  H18  C11  C13  120.56  3.000
 SF7  H18  C11  C4   120.93  3.000
 SF7  C13  C11  C4   118.51  3.000
 SF7  F1   C13  C14  118.90  3.000
 SF7  F1   C13  C11  119.04  3.000
 SF7  C14  C13  C11  122.06  3.000
 SF7  H19  C14  C15  120.94  3.000
 SF7  H19  C14  C13  120.59  3.000
 SF7  C15  C14  C13  118.48  3.000
 SF7  H20  C15  C14  119.05  3.000
 SF7  H20  C15  C2   119.81  3.000
 SF7  C14  C15  C2   121.14  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
 SF7  CONST_01  C16  N15  O13  C12     0.00   0.0  0
 SF7  CONST_02  N15  C16  N14  C12     0.00   0.0  0
 SF7  CONST_03  C16  N14  C12  O13     0.00   0.0  0
 SF7  CONST_04  N14  C16  N15  O13     0.00   0.0  0
 SF7  CONST_05  N14  C12  O13  N15     0.00   0.0  0
 SF7  CONST_06  C13  C11  C4   C2      0.00   0.0  0
 SF7  CONST_07  C13  C14  C15  C2      0.00   0.0  0
 SF7  CONST_08  C14  C15  C2   C4      0.00   0.0  0
 SF7  CONST_09  C14  C13  C11  C4      0.00   0.0  0
 SF7  CONST_10  C15  C2   C4   C11     0.00   0.0  0
 SF7  CONST_11  C15  C14  C13  C11     0.00   0.0  0
 SF7  CONST_12  N15  O13  C12  C6    180.00   0.0  0
 SF7  CONST_13  C16  N14  C12  C6    180.00   0.0  0
 SF7  CONST_14  C1   C16  N14  C12   180.00   0.0  0
 SF7  CONST_15  C1   C16  N15  O13   180.00   0.0  0
 SF7  CONST_16  C11  C4   C2   C1    180.00   0.0  0
 SF7  CONST_17  C14  C15  C2   C1    180.00   0.0  0
 SF7  CONST_18  F1   C13  C11  C4    180.00   0.0  0
 SF7  CONST_19  F1   C13  C14  C15   180.00   0.0  0
 SF7  CONST_20  H18  C11  C4   C2    180.00   0.0  0
 SF7  CONST_21  H19  C14  C15  C2    180.00   0.0  0
 SF7  CONST_22  H20  C15  C2   C4    180.00   0.0  0
 SF7  CONST_23  H17  C4   C11  C13   180.00   0.0  0
 SF7  CONST_24  O2   N1   C3   O4      0.00   0.0  0
 SF7  CONST_25  C5   C3   N1   O2    180.00   0.0  0
 SF7  CONST_26  H1   N1   C3   O4    180.00   0.0  0
 SF7  Var_01    C2   C1   C16  N15   119.78  30.0  2
 SF7  Var_02    C4   C2   C1   C16   104.54  30.0  2
 SF7  Var_03    C6   C5   C3   O4     27.62  30.0  3
 SF7  Var_04    C9   C8   C7   C6   -177.40  30.0  2
 SF7  Var_05    C10  C9   C8   C7    179.36  30.0  1
 SF7  Var_06    H12  C10  C9   C8    178.83  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
 SF7  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
 SF7  plan-1  C6   0.020
 SF7  plan-1  C12  0.020
 SF7  plan-1  O13  0.020
 SF7  plan-1  N15  0.020
 SF7  plan-1  C16  0.020
 SF7  plan-1  N14  0.020
 SF7  plan-1  C1   0.020
 SF7  plan-2  C1   0.020
 SF7  plan-2  C2   0.020
 SF7  plan-2  C4   0.020
 SF7  plan-2  C11  0.020
 SF7  plan-2  C13  0.020
 SF7  plan-2  C14  0.020
 SF7  plan-2  C15  0.020
 SF7  plan-2  F1   0.020
 SF7  plan-2  H17  0.020
 SF7  plan-2  H18  0.020
 SF7  plan-2  H19  0.020
 SF7  plan-2  H20  0.020
 SF7  plan-3  O4   0.020
 SF7  plan-3  C3   0.020
 SF7  plan-3  N1   0.020
 SF7  plan-3  O2   0.020
 SF7  plan-3  C5   0.020
 SF7  plan-3  H1   0.020

