# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:14:57 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: N-ethyl-2-{[5-(propan-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)CSc1oc(nn1)C(C)C
#
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
 RDJ  RDJ  N-ethyl-2-{[5-(propan-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetamide  ligand  30  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RDJ
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
 RDJ  C4   C  CR5   0   0.299  45.8623  6.6448  64.2926
 RDJ  C5   C  CR5   0   0.512  47.1104  6.9174  62.6118
 RDJ  C6   C  CH1   0  -0.365  48.1704  6.5789  61.6263
 RDJ  N1   N  N     0  -0.310  45.4819  7.7378  63.7369
 RDJ  C7   C  CH3   0  -0.653  48.2513  7.6480  60.5441
 RDJ  C8   C  CH3   0  -0.662  47.9253  5.1909  61.0260
 RDJ  N2   N  N     0  -0.314  46.3044  7.9147  62.6470
 RDJ  O    O  O     0  -0.479  44.3490  4.0978  63.5181
 RDJ  C2   C  C     0   0.568  45.3048  3.6517  64.1299
 RDJ  N    N  NH1   0  -0.626  46.0585  2.6374  63.6981
 RDJ  C1   C  CH2   0  -0.264  45.8084  1.9485  62.4454
 RDJ  C    C  CH3   0  -0.703  46.9652  1.0276  62.1099
 RDJ  C3   C  CH2   0  -0.716  45.7402  4.2125  65.4785
 RDJ  S    S  S2    0   0.121  45.2165  5.9221  65.7269
 RDJ  O1   O  O     0  -0.402  46.8889  6.0774  63.6481
 RDJ  H1   H  HCH1  0   0.281  49.1220  6.5547  62.1688
 RDJ  H2   H  HCH3  0   0.242  48.4302  8.6379  60.9618
 RDJ  H3   H  HCH3  0   0.244  49.0708  7.4186  59.8641
 RDJ  H4   H  HCH3  0   0.231  47.3312  7.6858  59.9603
 RDJ  H5   H  HCH3  0   0.242  47.9144  4.4077  61.7836
 RDJ  H6   H  HCH3  0   0.235  46.9767  5.1627  60.4876
 RDJ  H7   H  HCH3  0   0.248  48.7193  4.9562  60.3177
 RDJ  H8   H  HNH1  0   0.408  46.8216  2.3131  64.2715
 RDJ  H9   H  HCH2  0   0.238  45.6778  2.6888  61.6539
 RDJ  H10  H  HCH2  0   0.243  44.8785  1.3777  62.5070
 RDJ  H11  H  HCH3  0   0.249  46.7787  0.5279  61.1607
 RDJ  H12  H  HCH3  0   0.235  47.9001  1.5819  62.0191
 RDJ  H13  H  HCH3  0   0.237  47.0974  0.2579  62.8714
 RDJ  H14  H  HCH2  0   0.345  45.2418  3.6589  66.2780
 RDJ  H15  H  HCH2  0   0.318  46.8129  4.1136  65.6395

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
 RDJ  C8  C6   single    1.532  0.020  1.532
 RDJ  C7  C6   single    1.523  0.020  1.523
 RDJ  C6  C5   single    1.486  0.020  1.486
 RDJ  C   C1   single    1.516  0.020  1.516
 RDJ  C5  N2   aromatic  1.283  0.020  1.283
 RDJ  C5  O1   aromatic  1.352  0.020  1.352
 RDJ  N2  N1   aromatic  1.377  0.020  1.377
 RDJ  C1  N    single    1.451  0.020  1.451
 RDJ  O1  C4   aromatic  1.338  0.020  1.338
 RDJ  N1  C4   aromatic  1.284  0.020  1.284
 RDJ  N   C2   single    1.335  0.020  1.335
 RDJ  C4  S    single    1.731  0.020  1.731
 RDJ  O   C2   double    1.219  0.020  1.219
 RDJ  C2  C3   single    1.524  0.020  1.524
 RDJ  C3  S    single    1.805  0.020  1.805
 RDJ  C6  H1   single    0.970  0.020  1.090
 RDJ  C7  H2   single    0.970  0.020  1.090
 RDJ  C7  H3   single    0.970  0.020  1.090
 RDJ  C7  H4   single    0.970  0.020  1.090
 RDJ  C8  H5   single    0.970  0.020  1.090
 RDJ  C8  H6   single    0.970  0.020  1.090
 RDJ  C8  H7   single    0.970  0.020  1.090
 RDJ  N   H8   single    0.860  0.020  1.020
 RDJ  C1  H9   single    0.970  0.020  1.090
 RDJ  C1  H10  single    0.970  0.020  1.090
 RDJ  C   H11  single    0.970  0.020  1.090
 RDJ  C   H12  single    0.970  0.020  1.090
 RDJ  C   H13  single    0.970  0.020  1.090
 RDJ  C3  H14  single    0.970  0.020  1.090
 RDJ  C3  H15  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
 RDJ  O1   C4  S    120.54  3.000
 RDJ  S    C4  N1   127.13  3.000
 RDJ  O1   C4  N1   112.32  3.000
 RDJ  O1   C5  N2   111.04  3.000
 RDJ  O1   C5  C6   118.91  3.000
 RDJ  N2   C5  C6   130.04  3.000
 RDJ  H1   C6  C8   108.24  3.000
 RDJ  H1   C6  C7   108.74  3.000
 RDJ  C8   C6  C7   111.46  3.000
 RDJ  H1   C6  C5   107.22  3.000
 RDJ  C7   C6  C5   110.43  3.000
 RDJ  C8   C6  C5   110.61  3.000
 RDJ  N2   N1  C4   105.97  3.000
 RDJ  H4   C7  H3   107.93  3.000
 RDJ  H4   C7  H2   108.21  3.000
 RDJ  H3   C7  H2   107.89  3.000
 RDJ  H4   C7  C6   111.10  3.000
 RDJ  H3   C7  C6   109.61  3.000
 RDJ  H2   C7  C6   111.96  3.000
 RDJ  H7   C8  H6   107.89  3.000
 RDJ  H7   C8  H5   107.72  3.000
 RDJ  H6   C8  H5   108.41  3.000
 RDJ  H7   C8  C6   109.47  3.000
 RDJ  H6   C8  C6   110.85  3.000
 RDJ  H5   C8  C6   112.35  3.000
 RDJ  N1   N2  C5   107.29  3.000
 RDJ  C3   C2  N    113.85  3.000
 RDJ  C3   C2  O    122.23  3.000
 RDJ  N    C2  O    123.92  3.000
 RDJ  H8   N   C1   117.95  3.000
 RDJ  H8   N   C2   119.18  3.000
 RDJ  C1   N   C2   122.84  3.000
 RDJ  H10  C1  H9   107.06  3.000
 RDJ  H10  C1  C    110.14  3.000
 RDJ  H9   C1  C    110.04  3.000
 RDJ  H10  C1  N    110.24  3.000
 RDJ  H9   C1  N    108.94  3.000
 RDJ  C    C1  N    110.35  3.000
 RDJ  H13  C   H12  108.23  3.000
 RDJ  H13  C   H11  107.79  3.000
 RDJ  H12  C   H11  107.91  3.000
 RDJ  H13  C   C1   111.51  3.000
 RDJ  H12  C   C1   111.33  3.000
 RDJ  H11  C   C1   109.94  3.000
 RDJ  H15  C3  H14  107.15  3.000
 RDJ  H15  C3  S    110.57  3.000
 RDJ  H14  C3  S    104.29  3.000
 RDJ  H15  C3  C2   112.26  3.000
 RDJ  H14  C3  C2   109.31  3.000
 RDJ  S    C3  C2   112.79  3.000
 RDJ  C3   S   C4    99.97  3.000
 RDJ  C5   O1  C4   103.37  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
 RDJ  CONST_01  N2   C5  O1  C4     0.00   0.0  0
 RDJ  CONST_02  C5   N2  N1  C4     0.00   0.0  0
 RDJ  CONST_03  N1   C4  O1  C5     0.00   0.0  0
 RDJ  CONST_04  O1   C5  N2  N1     0.00   0.0  0
 RDJ  CONST_05  O1   C4  N1  N2     0.00   0.0  0
 RDJ  CONST_06  C6   C5  O1  C4   180.00   0.0  0
 RDJ  CONST_07  S    C4  O1  C5   180.00   0.0  0
 RDJ  CONST_08  N1   N2  C5  C6   180.00   0.0  0
 RDJ  CONST_09  S    C4  N1  N2   180.00   0.0  0
 RDJ  CONST_10  C1   N   C2  O      0.00   0.0  0
 RDJ  CONST_11  C3   C2  N   C1   180.00   0.0  0
 RDJ  CONST_12  H8   N   C2  O    180.00   0.0  0
 RDJ  Var_01    N2   C5  C6  C7     1.08  30.0  2
 RDJ  Var_02    O1   C4  S   C3   -23.44  30.0  2
 RDJ  Var_03    C2   C3  S   C4   -53.51  30.0  1
 RDJ  Var_04    H5   C8  C6  C5   -59.58  30.0  3
 RDJ  Var_05    H2   C7  C6  C5    56.90  30.0  3
 RDJ  Var_06    S    C3  C2  O    -24.18  30.0  3
 RDJ  Var_07    C    C1  N   C2   169.65  30.0  2
 RDJ  Var_08    H11  C   C1  N   -179.00  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
 RDJ  plan-1  C4  0.020
 RDJ  plan-1  C5  0.020
 RDJ  plan-1  C6  0.020
 RDJ  plan-1  N1  0.020
 RDJ  plan-1  N2  0.020
 RDJ  plan-1  S   0.020
 RDJ  plan-1  O1  0.020
 RDJ  plan-2  O   0.020
 RDJ  plan-2  C2  0.020
 RDJ  plan-2  N   0.020
 RDJ  plan-2  C1  0.020
 RDJ  plan-2  C3  0.020
 RDJ  plan-2  H8  0.020

