# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 11:21:18 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-ethyl-N-[(4-fluorophenyl)methyl]-1,2,4-oxadiazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1noc(n1)C(=O)NCc2ccc(F)cc2
#
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
 LD7  LD7  3-ethyl-N-[(4-fluorophenyl)methyl]-1,2,4-oxadiazole-5-carboxamide  ligand  30  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LD7
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
 LD7  N1   N  N     0  -0.132   3.1967  -1.7055   0.3458
 LD7  N3   N  NH1   0  -0.633  -0.0675   0.6945  -0.2736
 LD7  C4   C  CR5   0   0.429   2.2531   0.2207   0.0888
 LD7  C5   C  C     0   0.493   1.1466   1.2140  -0.0900
 LD7  C6   C  CH2   0  -0.324  -1.2374   1.5324  -0.4813
 LD7  C7   C  CR6   0   0.041  -2.4917   0.7372  -0.2542
 LD7  C8   C  CR16  0  -0.273  -3.2460   0.2759  -1.3269
 LD7  C10  C  CR6   0   0.520  -4.7861  -0.7411   0.1735
 LD7  C1   C  CH3   0  -0.668   6.2797  -0.4906  -0.8122
 LD7  C11  C  CR16  0  -0.396  -4.0595  -0.3031   1.2656
 LD7  C12  C  CR16  0  -0.263  -2.9095   0.4369   1.0403
 LD7  C2   C  CH2   0  -0.526   5.5333  -0.9673   0.4313
 LD7  C3   C  CR5   0   0.326   4.0697  -0.7443   0.3168
 LD7  C9   C  CR16  0  -0.397  -4.4023  -0.4656  -1.1233
 LD7  F1   F  F     0  -0.314  -5.9037  -1.4541   0.3831
 LD7  N2   N  N     0  -0.423   3.5078   0.4919   0.1550
 LD7  O1   O  O     0  -0.329   1.9947  -1.0712   0.1970
 LD7  O2   O  O     0  -0.453   1.4098   2.4009  -0.0543
 LD7  H1   H  HNH1  0   0.421  -0.1864  -0.3028  -0.3690
 LD7  H2   H  HCH2  0   0.273  -1.1922   2.3729   0.2124
 LD7  H3   H  HCH2  0   0.271  -1.2276   1.9478  -1.4922
 LD7  H4   H  HCR6  0   0.269  -2.9337   0.4970  -2.3400
 LD7  H5   H  HCH3  0   0.247   7.3480  -0.6674  -0.6977
 LD7  H6   H  HCH3  0   0.236   5.9441  -1.0224  -1.7025
 LD7  H7   H  HCH3  0   0.236   6.1323   0.5759  -0.9780
 LD7  H8   H  HCR6  0   0.283  -4.3880  -0.5298   2.2712
 LD7  H9   H  HCR6  0   0.269  -2.3352   0.7895   1.8884
 LD7  H10  H  HCH2  0   0.266   5.7155  -2.0272   0.6073
 LD7  H11  H  HCH2  0   0.269   5.8947  -0.4284   1.3098
 LD7  H12  H  HCR6  0   0.282  -4.9920  -0.8181  -1.9594

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
 LD7  C2   C1   single    1.527  0.020  1.527
 LD7  C2   C3   single    1.485  0.020  1.485
 LD7  C3   N1   aromatic  1.299  0.020  1.299
 LD7  C3   N2   aromatic  1.368  0.020  1.368
 LD7  N1   O1   aromatic  1.367  0.020  1.367
 LD7  N2   C4   aromatic  1.285  0.020  1.285
 LD7  O1   C4   aromatic  1.322  0.020  1.322
 LD7  C4   C5   single    1.498  0.020  1.498
 LD7  C5   O2   double    1.216  0.020  1.216
 LD7  C5   N3   single    1.333  0.020  1.333
 LD7  N3   C6   single    1.454  0.020  1.454
 LD7  C6   C7   single    1.502  0.020  1.502
 LD7  C7   C12  aromatic  1.393  0.020  1.393
 LD7  C7   C8   aromatic  1.390  0.020  1.390
 LD7  C12  C11  aromatic  1.386  0.020  1.386
 LD7  C8   C9   aromatic  1.389  0.020  1.389
 LD7  C11  C10  aromatic  1.383  0.020  1.383
 LD7  C9   C10  aromatic  1.380  0.020  1.380
 LD7  C10  F1   single    1.342  0.020  1.342
 LD7  N3   H1   single    0.860  0.020  1.020
 LD7  C6   H2   single    0.970  0.020  1.090
 LD7  C6   H3   single    0.970  0.020  1.090
 LD7  C8   H4   single    0.930  0.020  1.080
 LD7  C1   H5   single    0.970  0.020  1.090
 LD7  C1   H6   single    0.970  0.020  1.090
 LD7  C1   H7   single    0.970  0.020  1.090
 LD7  C11  H8   single    0.930  0.020  1.080
 LD7  C12  H9   single    0.930  0.020  1.080
 LD7  C2   H10  single    0.970  0.020  1.090
 LD7  C2   H11  single    0.970  0.020  1.090
 LD7  C9   H12  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
 LD7  O1   N1   C3   104.19  3.000
 LD7  H1   N3   C6   117.47  3.000
 LD7  H1   N3   C5   120.37  3.000
 LD7  C6   N3   C5   121.86  3.000
 LD7  O1   C4   N2   113.13  3.000
 LD7  O1   C4   C5   120.90  3.000
 LD7  N2   C4   C5   125.97  3.000
 LD7  O2   C5   C4   118.94  3.000
 LD7  O2   C5   N3   125.54  3.000
 LD7  C4   C5   N3   115.52  3.000
 LD7  H3   C6   H2   107.16  3.000
 LD7  H3   C6   C7   110.39  3.000
 LD7  H2   C6   C7   110.26  3.000
 LD7  H3   C6   N3   110.12  3.000
 LD7  H2   C6   N3   108.66  3.000
 LD7  C7   C6   N3   110.19  3.000
 LD7  C12  C7   C8   118.87  3.000
 LD7  C8   C7   C6   120.80  3.000
 LD7  C12  C7   C6   120.33  3.000
 LD7  H4   C8   C9   119.10  3.000
 LD7  H4   C8   C7   119.84  3.000
 LD7  C9   C8   C7   121.06  3.000
 LD7  F1   C10  C9   118.97  3.000
 LD7  F1   C10  C11  118.84  3.000
 LD7  C9   C10  C11  122.19  3.000
 LD7  H7   C1   H6   108.16  3.000
 LD7  H7   C1   H5   107.92  3.000
 LD7  H6   C1   H5   107.98  3.000
 LD7  H7   C1   C2   111.32  3.000
 LD7  H6   C1   C2   111.25  3.000
 LD7  H5   C1   C2   110.08  3.000
 LD7  H8   C11  C12  120.99  3.000
 LD7  H8   C11  C10  120.54  3.000
 LD7  C12  C11  C10  118.47  3.000
 LD7  H9   C12  C11  119.10  3.000
 LD7  H9   C12  C7   119.89  3.000
 LD7  C11  C12  C7   121.00  3.000
 LD7  H11  C2   H10  107.13  3.000
 LD7  H11  C2   C3   108.30  3.000
 LD7  H10  C2   C3   108.86  3.000
 LD7  H11  C2   C1   109.84  3.000
 LD7  H10  C2   C1   110.70  3.000
 LD7  C3   C2   C1   111.85  3.000
 LD7  N2   C3   C2   123.36  3.000
 LD7  N2   C3   N1   113.29  3.000
 LD7  C2   C3   N1   123.35  3.000
 LD7  H12  C9   C10  120.63  3.000
 LD7  H12  C9   C8   120.96  3.000
 LD7  C10  C9   C8   118.42  3.000
 LD7  C3   N2   C4   102.50  3.000
 LD7  C4   O1   N1   106.89  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
 LD7  CONST_01  C4   N2   C3   N1      0.00   0.0  0
 LD7  CONST_02  N2   C4   O1   N1      0.00   0.0  0
 LD7  CONST_03  C3   N1   O1   C4      0.00   0.0  0
 LD7  CONST_04  C10  C11  C12  C7      0.00   0.0  0
 LD7  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 LD7  CONST_06  C11  C12  C7   C8      0.00   0.0  0
 LD7  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 LD7  CONST_08  C9   C8   C7   C12     0.00   0.0  0
 LD7  CONST_09  C9   C10  C11  C12     0.00   0.0  0
 LD7  CONST_10  O1   C4   N2   C3      0.00   0.0  0
 LD7  CONST_11  O1   N1   C3   N2      0.00   0.0  0
 LD7  CONST_12  C5   C4   O1   N1    180.00   0.0  0
 LD7  CONST_13  C2   C3   N2   C4    180.00   0.0  0
 LD7  CONST_14  C3   N2   C4   C5    180.00   0.0  0
 LD7  CONST_15  C11  C12  C7   C6    180.00   0.0  0
 LD7  CONST_16  C9   C8   C7   C6    180.00   0.0  0
 LD7  CONST_17  F1   C10  C9   C8    180.00   0.0  0
 LD7  CONST_18  F1   C10  C11  C12   180.00   0.0  0
 LD7  CONST_19  O1   N1   C3   C2    180.00   0.0  0
 LD7  CONST_20  H8   C11  C12  C7    180.00   0.0  0
 LD7  CONST_21  H12  C9   C8   C7    180.00   0.0  0
 LD7  CONST_22  H9   C12  C7   C8    180.00   0.0  0
 LD7  CONST_23  H4   C8   C9   C10   180.00   0.0  0
 LD7  CONST_24  C6   N3   C5   C4    180.00   0.0  0
 LD7  CONST_25  H1   N3   C5   C4      0.00   0.0  0
 LD7  CONST_26  O2   C5   N3   C6      0.00   0.0  0
 LD7  Var_01    C1   C2   C3   N1    118.78  30.0  2
 LD7  Var_02    N2   C4   C5   N3    173.14  30.0  2
 LD7  Var_03    C12  C7   C6   N3     76.44  30.0  2
 LD7  Var_04    C7   C6   N3   C5   -163.28  30.0  3
 LD7  Var_05    H5   C1   C2   C3   -180.00  30.0  3

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
 LD7  plan-1  N1   0.020
 LD7  plan-1  C4   0.020
 LD7  plan-1  C5   0.020
 LD7  plan-1  C2   0.020
 LD7  plan-1  C3   0.020
 LD7  plan-1  N2   0.020
 LD7  plan-1  O1   0.020
 LD7  plan-2  C6   0.020
 LD7  plan-2  C7   0.020
 LD7  plan-2  C8   0.020
 LD7  plan-2  C10  0.020
 LD7  plan-2  C11  0.020
 LD7  plan-2  C12  0.020
 LD7  plan-2  C9   0.020
 LD7  plan-2  F1   0.020
 LD7  plan-2  H4   0.020
 LD7  plan-2  H8   0.020
 LD7  plan-2  H9   0.020
 LD7  plan-2  H12  0.020
 LD7  plan-3  N3   0.020
 LD7  plan-3  C4   0.020
 LD7  plan-3  C5   0.020
 LD7  plan-3  C6   0.020
 LD7  plan-3  O2   0.020
 LD7  plan-3  H1   0.020

