# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 15:34:55 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: N-[(4-fluorophenyl)methyl]-5-(methoxymethyl)-1,2,4-oxadiazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1onc(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
 LHS  LHS  N-[(4-fluorophenyl)methyl]-5-(methoxymethyl)-1,2,4-oxadiazole-3-carboxamide  ligand  31  19  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LHS
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
 LHS  N1   N  N     0  -0.403   2.5454  -0.5465  -0.6864
 LHS  N3   N  NH1   0  -0.520  -0.5896  -1.3309   1.0129
 LHS  C4   C  CR5   0   0.195   1.5868  -0.6800   0.2671
 LHS  C5   C  C     0   0.482   0.2363  -1.2484  -0.0330
 LHS  C6   C  CH2   0  -0.302  -1.9451  -1.8286   0.8831
 LHS  C7   C  CR6   0   0.031  -2.8766  -0.8307   0.2424
 LHS  C8   C  CR16  0  -0.318  -3.3139   0.2823   0.9561
 LHS  C10  C  CR6   0   0.425  -4.5708   1.0151  -0.9264
 LHS  C1   C  CH3   0  -0.429   6.7334   1.6460  -0.0903
 LHS  C11  C  CR16  0  -0.287  -4.1595  -0.0757  -1.6654
 LHS  C12  C  CR16  0  -0.297  -3.3060  -0.9950  -1.0694
 LHS  C2   C  CH2   0  -0.247   4.8810   0.3041  -0.5164
 LHS  C3   C  CR5   0   0.464   3.5211  -0.0312  -0.0207
 LHS  C9   C  CR16  0  -0.297  -4.1634   1.2145   0.3797
 LHS  F1   F  F     0  -0.358  -5.3979   1.9105  -1.4912
 LHS  N2   N  N     0  -0.018   1.9472  -0.2661   1.4405
 LHS  O1   O  O2    0  -0.542   5.4073   1.3283   0.2682
 LHS  O2   O  O     0  -0.307   3.2244   0.1602   1.2585
 LHS  O3   O  O     0  -0.635  -0.0323  -1.6022  -1.1657
 LHS  H1   H  HNH1  0   0.420  -0.2862  -0.9982   1.9145
 LHS  H2   H  HCH2  0   0.260  -1.9369  -2.7576   0.3117
 LHS  H3   H  HCH2  0   0.304  -2.2863  -2.0721   1.8882
 LHS  H4   H  HCR6  0   0.267  -2.9949   0.4272   1.9814
 LHS  H5   H  HCH3  0   0.248   7.4025   0.7876   0.0329
 LHS  H6   H  HCH3  0   0.246   6.8034   1.9898  -1.1278
 LHS  H7   H  HCH3  0   0.270   7.0680   2.4471   0.5656
 LHS  H8   H  HCR6  0   0.295  -4.4942  -0.2080  -2.6858
 LHS  H9   H  HCR6  0   0.248  -2.9708  -1.8516  -1.6398
 LHS  H10  H  HCH2  0   0.258   5.4953  -0.6081  -0.4716
 LHS  H11  H  HCH2  0   0.263   4.7989   0.5749  -1.5762
 LHS  H12  H  HCR6  0   0.283  -4.5083   2.0758   0.9371

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
 LHS  C1   O1   single    1.410  0.020  1.410
 LHS  O1   C2   single    1.393  0.020  1.393
 LHS  C2   C3   single    1.486  0.020  1.486
 LHS  O2   C3   aromatic  1.327  0.020  1.327
 LHS  O2   N2   aromatic  1.359  0.020  1.359
 LHS  C3   N1   aromatic  1.289  0.020  1.289
 LHS  N2   C4   aromatic  1.295  0.020  1.295
 LHS  N1   C4   aromatic  1.359  0.020  1.359
 LHS  C4   C5   single    1.496  0.020  1.496
 LHS  C5   N3   single    1.335  0.020  1.335
 LHS  C5   O3   double    1.217  0.020  1.217
 LHS  N3   C6   single    1.450  0.020  1.450
 LHS  C6   C7   single    1.508  0.020  1.508
 LHS  C7   C12  aromatic  1.390  0.020  1.390
 LHS  C7   C8   aromatic  1.393  0.020  1.393
 LHS  C12  C11  aromatic  1.389  0.020  1.389
 LHS  C8   C9   aromatic  1.387  0.020  1.387
 LHS  C11  C10  aromatic  1.380  0.020  1.380
 LHS  C9   C10  aromatic  1.383  0.020  1.383
 LHS  C10  F1   single    1.343  0.020  1.343
 LHS  N3   H1   single    0.860  0.020  1.020
 LHS  C6   H2   single    0.970  0.020  1.090
 LHS  C6   H3   single    0.970  0.020  1.090
 LHS  C8   H4   single    0.930  0.020  1.080
 LHS  C1   H5   single    0.970  0.020  1.090
 LHS  C1   H6   single    0.970  0.020  1.090
 LHS  C1   H7   single    0.970  0.020  1.090
 LHS  C11  H8   single    0.930  0.020  1.080
 LHS  C12  H9   single    0.930  0.020  1.080
 LHS  C2   H10  single    0.970  0.020  1.090
 LHS  C2   H11  single    0.970  0.020  1.090
 LHS  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
 LHS  C3   N1   C4   102.18  3.000
 LHS  H1   N3   C6   118.35  3.000
 LHS  H1   N3   C5   119.62  3.000
 LHS  C6   N3   C5   121.97  3.000
 LHS  N2   C4   C5   123.67  3.000
 LHS  C5   C4   N1   122.25  3.000
 LHS  N2   C4   N1   114.08  3.000
 LHS  O3   C5   C4   119.77  3.000
 LHS  O3   C5   N3   125.08  3.000
 LHS  C4   C5   N3   115.14  3.000
 LHS  H3   C6   H2   107.19  3.000
 LHS  H3   C6   C7   110.27  3.000
 LHS  H2   C6   C7   110.22  3.000
 LHS  H3   C6   N3   106.68  3.000
 LHS  H2   C6   N3   109.41  3.000
 LHS  C7   C6   N3   112.86  3.000
 LHS  C12  C7   C8   118.76  3.000
 LHS  C8   C7   C6   120.34  3.000
 LHS  C12  C7   C6   120.90  3.000
 LHS  H4   C8   C9   118.93  3.000
 LHS  H4   C8   C7   119.96  3.000
 LHS  C9   C8   C7   121.11  3.000
 LHS  F1   C10  C9   118.84  3.000
 LHS  F1   C10  C11  119.02  3.000
 LHS  C9   C10  C11  122.14  3.000
 LHS  H7   C1   H6   108.68  3.000
 LHS  H7   C1   H5   108.74  3.000
 LHS  H6   C1   H5   108.27  3.000
 LHS  H7   C1   O1   107.57  3.000
 LHS  H6   C1   O1   111.82  3.000
 LHS  H5   C1   O1   111.68  3.000
 LHS  H8   C11  C12  120.92  3.000
 LHS  H8   C11  C10  120.62  3.000
 LHS  C12  C11  C10  118.45  3.000
 LHS  H9   C12  C11  119.21  3.000
 LHS  H9   C12  C7   119.68  3.000
 LHS  C11  C12  C7   121.10  3.000
 LHS  H11  C2   H10  106.60  3.000
 LHS  H11  C2   O1   113.01  3.000
 LHS  H10  C2   O1   112.05  3.000
 LHS  H11  C2   C3   108.03  3.000
 LHS  H10  C2   C3   108.07  3.000
 LHS  O1   C2   C3   108.89  3.000
 LHS  O2   C3   C2   119.58  3.000
 LHS  O2   C3   N1   112.73  3.000
 LHS  C2   C3   N1   127.66  3.000
 LHS  H12  C9   C10  120.49  3.000
 LHS  H12  C9   C8   121.07  3.000
 LHS  C10  C9   C8   118.43  3.000
 LHS  O2   N2   C4   103.91  3.000
 LHS  C2   O1   C1   112.19  3.000
 LHS  N2   O2   C3   107.10  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
 LHS  CONST_01  N2   O2   C3   N1     0.00   0.0  0
 LHS  CONST_02  O2   N2   C4   N1     0.00   0.0  0
 LHS  CONST_03  C3   O2   N2   C4     0.00   0.0  0
 LHS  CONST_04  O2   C3   N1   C4     0.00   0.0  0
 LHS  CONST_05  C10  C11  C12  C7     0.00   0.0  0
 LHS  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 LHS  CONST_07  C11  C12  C7   C8     0.00   0.0  0
 LHS  CONST_08  C11  C10  C9   C8     0.00   0.0  0
 LHS  CONST_09  C9   C8   C7   C12    0.00   0.0  0
 LHS  CONST_10  C9   C10  C11  C12    0.00   0.0  0
 LHS  CONST_11  N2   C4   N1   C3     0.00   0.0  0
 LHS  CONST_12  C2   C3   N1   C4   180.00   0.0  0
 LHS  CONST_13  O2   N2   C4   C5   180.00   0.0  0
 LHS  CONST_14  C3   N1   C4   C5   180.00   0.0  0
 LHS  CONST_15  C11  C12  C7   C6   180.00   0.0  0
 LHS  CONST_16  C9   C8   C7   C6   180.00   0.0  0
 LHS  CONST_17  F1   C10  C9   C8   180.00   0.0  0
 LHS  CONST_18  F1   C10  C11  C12  180.00   0.0  0
 LHS  CONST_19  N2   O2   C3   C2   180.00   0.0  0
 LHS  CONST_20  H8   C11  C12  C7   180.00   0.0  0
 LHS  CONST_21  H12  C9   C8   C7   180.00   0.0  0
 LHS  CONST_22  H9   C12  C7   C8   180.00   0.0  0
 LHS  CONST_23  H4   C8   C9   C10  180.00   0.0  0
 LHS  CONST_24  C6   N3   C5   C4   180.00   0.0  0
 LHS  CONST_25  H1   N3   C5   C4     0.00   0.0  0
 LHS  CONST_26  O3   C5   N3   C6     0.00   0.0  0
 LHS  Var_01    O1   C2   C3   N1   153.96  30.0  2
 LHS  Var_02    N3   C5   C4   N1   179.16  30.0  2
 LHS  Var_03    C12  C7   C6   N3   105.73  30.0  2
 LHS  Var_04    C7   C6   N3   C5   -75.39  30.0  3
 LHS  Var_05    C3   C2   O1   C1   176.32  30.0  3
 LHS  Var_06    H5   C1   O1   C2   -60.68  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
 LHS  plan-1  N1   0.020
 LHS  plan-1  C4   0.020
 LHS  plan-1  C5   0.020
 LHS  plan-1  C2   0.020
 LHS  plan-1  C3   0.020
 LHS  plan-1  N2   0.020
 LHS  plan-1  O2   0.020
 LHS  plan-2  C6   0.020
 LHS  plan-2  C7   0.020
 LHS  plan-2  C8   0.020
 LHS  plan-2  C10  0.020
 LHS  plan-2  C11  0.020
 LHS  plan-2  C12  0.020
 LHS  plan-2  C9   0.020
 LHS  plan-2  F1   0.020
 LHS  plan-2  H4   0.020
 LHS  plan-2  H8   0.020
 LHS  plan-2  H9   0.020
 LHS  plan-2  H12  0.020
 LHS  plan-3  N3   0.020
 LHS  plan-3  C4   0.020
 LHS  plan-3  C5   0.020
 LHS  plan-3  C6   0.020
 LHS  plan-3  O3   0.020
 LHS  plan-3  H1   0.020

