# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:49:34 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: {[5-(5-nitrofuran-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1oc(nn1)c2oc(cc2)[N+]([O-])=O
#
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
 LIT  LIT  '{[5-(5-nitrofuran-2-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}acetic acid'  ligand  22  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 PERFECT
;

data_comp_LIT
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
 LIT  C1    C  CR5    0   0.469   0.6913  -1.5192  -0.6704
 LIT  C2    C  CR15   0  -0.261  -0.5879  -1.1478  -0.9341
 LIT  C3    C  CR15   0  -0.336  -0.7331  -1.3109  -2.3299
 LIT  C4    C  CR5    0   0.377   0.4722  -1.7665  -2.7806
 LIT  C5    C  CR5    0   0.391   0.9350  -2.1149  -4.0920
 LIT  N6    N  N      0  -0.284   2.0865  -2.5488  -4.4630
 LIT  N7    N  N      0  -0.320   2.0184  -2.7241  -5.8142
 LIT  C8    C  CR5    0   0.331   0.8219  -2.3860  -6.1733
 LIT  S9    S  S2     0   0.076   0.1867  -2.4321  -7.7790
 LIT  C10   C  CH2    0  -0.705  -1.4621  -1.7092  -7.5372
 LIT  C11   C  C      0   0.456  -2.1328  -1.6824  -8.9259
 LIT  O12   O  OC    -1  -0.592  -3.2799  -1.2162  -8.9530
 LIT  O13   O  O      0  -0.590  -1.4507  -2.1314  -9.8645
 LIT  O14   O  O      0  -0.397   0.0839  -1.9896  -5.1237
 LIT  O15   O  O      0  -0.393   1.3454  -1.8945  -1.7721
 LIT  N16   N  N      1   0.326   1.4046  -1.5669   0.5501
 LIT  O17   O  O     -1  -0.382   0.7986  -1.2256   1.5408
 LIT  O18   O  O      0  -0.380   2.5538  -1.9398   0.5231
 LIT  H101  H  HCH2   0   0.297  -1.3755  -0.7010  -7.1305
 LIT  H102  H  HCH2   0   0.296  -2.0434  -2.3141  -6.8405
 LIT  H3    H  HCR5   0   0.301  -1.6140  -1.1154  -2.9189
 LIT  H2    H  HCR5   0   0.320  -1.3300  -0.8048  -0.2329

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
 LIT  C1   C2    aromatic  1.358  0.020  1.358
 LIT  C1   O15   aromatic  1.335  0.020  1.335
 LIT  C1   N16   single    1.414  0.020  1.414
 LIT  C2   C3    aromatic  1.413  0.020  1.413
 LIT  C2   H2    single    0.930  0.020  1.080
 LIT  C3   C4    aromatic  1.365  0.020  1.365
 LIT  C3   H3    single    0.930  0.020  1.080
 LIT  C4   C5    single    1.434  0.020  1.434
 LIT  C4   O15   aromatic  1.340  0.020  1.340
 LIT  C5   N6    aromatic  1.285  0.020  1.285
 LIT  C5   O14   aromatic  1.343  0.020  1.343
 LIT  N6   N7    aromatic  1.364  0.020  1.364
 LIT  N7   C8    aromatic  1.294  0.020  1.294
 LIT  C8   S9    single    1.727  0.020  1.727
 LIT  C8   O14   aromatic  1.343  0.020  1.343
 LIT  S9   C10   single    1.816  0.020  1.816
 LIT  C10  C11   single    1.542  0.020  1.542
 LIT  C10  H101  single    0.970  0.020  1.090
 LIT  C10  H102  single    0.970  0.020  1.090
 LIT  C11  O12   deloc     1.239  0.020  1.239
 LIT  C11  O13   deloc     1.244  0.020  1.244
 LIT  N16  O17   single    1.210  0.020  1.210
 LIT  N16  O18   double    1.208  0.020  1.208

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
 LIT  N16   C1   O15   117.10  3.000
 LIT  N16   C1   C2    130.68  3.000
 LIT  O15   C1   C2    112.22  3.000
 LIT  H2    C2   C3    127.52  3.000
 LIT  H2    C2   C1    127.57  3.000
 LIT  C3    C2   C1    104.90  3.000
 LIT  H3    C3   C4    127.01  3.000
 LIT  H3    C3   C2    127.10  3.000
 LIT  C4    C3   C2    105.90  3.000
 LIT  O15   C4   C5    117.05  3.000
 LIT  O15   C4   C3    111.03  3.000
 LIT  C5    C4   C3    131.92  3.000
 LIT  O14   C5   N6    112.17  3.000
 LIT  O14   C5   C4    118.38  3.000
 LIT  N6    C5   C4    129.44  3.000
 LIT  N7    N6   C5    106.53  3.000
 LIT  C8    N7   N6    106.71  3.000
 LIT  O14   C8   S9    122.16  3.000
 LIT  O14   C8   N7    111.61  3.000
 LIT  S9    C8   N7    126.23  3.000
 LIT  C10   S9   C8    101.50  3.000
 LIT  H102  C10  H101  108.47  3.000
 LIT  H102  C10  C11   110.68  3.000
 LIT  H101  C10  C11   110.75  3.000
 LIT  H102  C10  S9    110.37  3.000
 LIT  H101  C10  S9    110.21  3.000
 LIT  C11   C10  S9    106.36  3.000
 LIT  O13   C11  O12   128.84  3.000
 LIT  O13   C11  C10   115.76  3.000
 LIT  O12   C11  C10   115.40  3.000
 LIT  C8    O14  C5    102.98  3.000
 LIT  C4    O15  C1    105.96  3.000
 LIT  O18   N16  O17   125.55  3.000
 LIT  O18   N16  C1    118.08  3.000
 LIT  O17   N16  C1    116.38  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
 LIT  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 LIT  CONST_02  C3   C4   O15  C1     0.00   0.0  0
 LIT  CONST_03  C5   C4   O15  C1   180.00   0.0  0
 LIT  CONST_04  C4   O15  C1   C2     0.00   0.0  0
 LIT  CONST_05  C5   C4   C3   C2   180.00   0.0  0
 LIT  CONST_06  O15  C4   C3   C2     0.00   0.0  0
 LIT  CONST_07  O15  C1   C2   C3     0.00   0.0  0
 LIT  CONST_08  N6   C5   C4   C3   180.00   0.0  0
 LIT  CONST_09  O14  C5   C4   C3     0.00   0.0  0
 LIT  CONST_10  N7   N6   C5   C4   180.00   0.0  0
 LIT  CONST_11  C8   O14  C5   C4   180.00   0.0  0
 LIT  CONST_12  C8   N7   N6   C5     0.00   0.0  0
 LIT  CONST_13  N7   C8   O14  C5     0.00   0.0  0
 LIT  CONST_14  O15  C4   C5   N6     0.00   0.0  0
 LIT  CONST_15  C8   O14  C5   N6     0.00   0.0  0
 LIT  CONST_16  O14  C8   N7   N6     0.00   0.0  0
 LIT  CONST_17  O14  C5   N6   N7     0.00   0.0  0
 LIT  CONST_18  O15  C4   C5   O14  180.00   0.0  0
 LIT  CONST_19  N16  C1   C2   C3   180.00   0.0  0
 LIT  CONST_20  N16  C1   O15  C4   180.00   0.0  0
 LIT  CONST_21  S9   C8   O14  C5   180.00   0.0  0
 LIT  CONST_22  S9   C8   N7   N6   180.00   0.0  0
 LIT  CONST_23  H3   C3   C2   C1   180.00   0.0  0
 LIT  CONST_24  H2   C2   C3   C4   180.00   0.0  0
 LIT  CONST_25  O17  N16  C1   C2     0.00   0.0  0
 LIT  CONST_26  O18  N16  C1   C2   180.00   0.0  0
 LIT  CONST_27  O17  N16  C1   O15  180.00   0.0  0
 LIT  CONST_28  O18  N16  C1   O15    0.00   0.0  0
 LIT  Var_01    O14  C8   S9   C10    4.92  30.0  1
 LIT  Var_02    C11  C10  S9   C8   179.40  30.0  3
 LIT  Var_03    O12  C11  C10  S9   179.92  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
 LIT  plan-1  C1   0.020
 LIT  plan-1  C2   0.020
 LIT  plan-1  C3   0.020
 LIT  plan-1  C4   0.020
 LIT  plan-1  C5   0.020
 LIT  plan-1  O15  0.020
 LIT  plan-1  N16  0.020
 LIT  plan-1  H3   0.020
 LIT  plan-1  H2   0.020
 LIT  plan-2  C4   0.020
 LIT  plan-2  C5   0.020
 LIT  plan-2  N6   0.020
 LIT  plan-2  N7   0.020
 LIT  plan-2  C8   0.020
 LIT  plan-2  S9   0.020
 LIT  plan-2  O14  0.020
 LIT  plan-3  C1   0.020
 LIT  plan-3  N16  0.020
 LIT  plan-3  O17  0.020
 LIT  plan-3  O18  0.020
 LIT  plan-4  C10  0.020
 LIT  plan-4  C11  0.020
 LIT  plan-4  O12  0.020
 LIT  plan-4  O13  0.020

