# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 19:30:44 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: ~{S}-[5-[(~{E})-2-phenylethenyl]-1,3,4-oxadiazol-2-yl] 5-nitrothiophene-2-carbothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1sc(cc1)C(=O)Sc2oc(\C=C\c3ccccc3)nn2
#
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
 E9B  E9B  "S-[5-[(E)-2-phenylethenyl]-1,3,4-oxadiazol-2-yl] 5-nitrothiophene-2-carbothioate"  ligand  33  24  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E9B
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
 E9B  CAA  C  CR15   0  -0.174  -11.6452  17.2221  -15.4754
 E9B  CAB  C  CR15   0  -0.177  -11.3104  15.9294  -15.9176
 E9B  CAC  C  CR5    0  -0.248  -12.0078  14.9555  -15.2476
 E9B  CAD  C  C      0   0.249  -11.9773  13.5031  -15.3919
 E9B  CAE  C  CR5    0   0.250  -11.1632  11.2221  -16.4782
 E9B  CAF  C  CR5    0   0.520  -12.1769   9.3987  -16.7481
 E9B  CAG  C  C1     0  -0.394  -13.2190   8.5139  -17.1979
 E9B  CAH  C  C1     0  -0.231  -13.2177   7.2100  -16.8859
 E9B  CAI  C  CR6    0   0.150  -14.2147   6.2236  -17.2793
 E9B  CAJ  C  CR16   0  -0.311  -15.3111   6.5257  -18.0955
 E9B  CAK  C  CR16   0  -0.230  -16.2287   5.5466  -18.4308
 E9B  CAL  C  CR16   0  -0.256  -16.0730   4.2465  -17.9592
 E9B  CAM  C  CR16   0  -0.238  -14.9902   3.9326  -17.1505
 E9B  CAN  C  CR16   0  -0.301  -14.0689   4.9132  -16.8153
 E9B  CAU  C  CR5    0   0.019  -12.5857  17.1619  -14.4879
 E9B  NAO  N  N      0  -0.236  -10.4614  10.3270  -15.8819
 E9B  NAP  N  N      0  -0.315  -11.1098   9.1458  -16.0542
 E9B  NAV  N  N      1   0.355  -13.1715  18.2727  -13.8044
 E9B  OAS  O  O      0  -0.336  -12.6618  12.7629  -14.7428
 E9B  OAT  O  O      0  -0.382  -12.2562  10.7024  -17.0551
 E9B  OAW  O  O      0  -0.370  -13.9877  18.0135  -12.9496
 E9B  OAX  O  O     -1  -0.362  -12.8181  19.3795  -14.1246
 E9B  SAQ  S  S2     0   0.389  -13.0817  15.5862  -14.0680
 E9B  SAR  S  S2     0   0.113  -10.8181  12.9118  -16.6330
 E9B  H1   H  HCR5   0   0.325  -11.2189  18.1336  -15.8663
 E9B  H3   H  HCR5   0   0.309  -10.5868  15.7411  -16.6989
 E9B  H5   H  H      0   0.298  -14.0008   8.9674  -17.7942
 E9B  H7   H  H      0   0.277  -12.4043   6.8293  -16.2756
 E9B  H9   H  HCR6   0   0.259  -15.4536   7.5288  -18.4765
 E9B  H10  H  HCR6   0   0.263  -17.0704   5.7955  -19.0638
 E9B  H11  H  HCR6   0   0.263  -16.7943   3.4841  -18.2232
 E9B  H12  H  HCR6   0   0.262  -14.8615   2.9241  -16.7802
 E9B  H13  H  HCR6   0   0.262  -13.2251   4.6636  -16.1831

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
 E9B  CAA  CAB  aromatic  1.407  0.020  1.407
 E9B  CAA  CAU  aromatic  1.365  0.020  1.365
 E9B  CAB  CAC  aromatic  1.372  0.020  1.372
 E9B  CAC  CAD  single    1.460  0.020  1.460
 E9B  CAC  SAQ  aromatic  1.715  0.020  1.715
 E9B  CAD  OAS  double    1.199  0.020  1.199
 E9B  CAD  SAR  single    1.798  0.020  1.798
 E9B  CAE  NAO  aromatic  1.284  0.020  1.284
 E9B  CAE  OAT  aromatic  1.341  0.020  1.341
 E9B  CAE  SAR  single    1.732  0.020  1.732
 E9B  CAF  CAG  single    1.439  0.020  1.439
 E9B  CAF  NAP  aromatic  1.298  0.020  1.298
 E9B  CAF  OAT  aromatic  1.342  0.020  1.342
 E9B  CAG  CAH  double    1.341  0.020  1.341
 E9B  CAH  CAI  single    1.457  0.020  1.457
 E9B  CAI  CAJ  aromatic  1.400  0.020  1.400
 E9B  CAI  CAN  aromatic  1.398  0.020  1.398
 E9B  CAJ  CAK  aromatic  1.383  0.020  1.383
 E9B  CAK  CAL  aromatic  1.392  0.020  1.392
 E9B  CAL  CAM  aromatic  1.387  0.020  1.387
 E9B  CAM  CAN  aromatic  1.387  0.020  1.387
 E9B  CAU  NAV  single    1.430  0.020  1.430
 E9B  CAU  SAQ  aromatic  1.704  0.020  1.704
 E9B  NAO  NAP  aromatic  1.358  0.020  1.358
 E9B  NAV  OAW  double    1.210  0.020  1.210
 E9B  NAV  OAX  single    1.205  0.020  1.205
 E9B  CAA  H1   single    0.930  0.020  1.080
 E9B  CAB  H3   single    0.930  0.020  1.080
 E9B  CAG  H5   single    0.930  0.020  1.080
 E9B  CAH  H7   single    0.930  0.020  1.080
 E9B  CAJ  H9   single    0.930  0.020  1.080
 E9B  CAK  H10  single    0.930  0.020  1.080
 E9B  CAL  H11  single    0.930  0.020  1.080
 E9B  CAM  H12  single    0.930  0.020  1.080
 E9B  CAN  H13  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
 E9B  H1   CAA  CAU  124.84  3.000
 E9B  H1   CAA  CAB  124.61  3.000
 E9B  CAU  CAA  CAB  110.54  3.000
 E9B  H3   CAB  CAC  124.69  3.000
 E9B  H3   CAB  CAA  123.12  3.000
 E9B  CAC  CAB  CAA  112.19  3.000
 E9B  SAQ  CAC  CAD  116.54  3.000
 E9B  SAQ  CAC  CAB  113.14  3.000
 E9B  CAD  CAC  CAB  130.32  3.000
 E9B  SAR  CAD  OAS  122.59  3.000
 E9B  SAR  CAD  CAC  114.13  3.000
 E9B  OAS  CAD  CAC  123.28  3.000
 E9B  SAR  CAE  OAT  120.15  3.000
 E9B  SAR  CAE  NAO  127.79  3.000
 E9B  OAT  CAE  NAO  112.03  3.000
 E9B  OAT  CAF  NAP  111.12  3.000
 E9B  OAT  CAF  CAG  118.89  3.000
 E9B  NAP  CAF  CAG  129.99  3.000
 E9B  H5   CAG  CAH  122.43  3.000
 E9B  H5   CAG  CAF  115.94  3.000
 E9B  CAH  CAG  CAF  121.63  3.000
 E9B  H7   CAH  CAI  115.29  3.000
 E9B  H7   CAH  CAG  118.20  3.000
 E9B  CAI  CAH  CAG  126.52  3.000
 E9B  CAN  CAI  CAJ  118.53  3.000
 E9B  CAN  CAI  CAH  118.28  3.000
 E9B  CAJ  CAI  CAH  123.19  3.000
 E9B  H9   CAJ  CAK  118.90  3.000
 E9B  H9   CAJ  CAI  120.56  3.000
 E9B  CAK  CAJ  CAI  120.54  3.000
 E9B  H10  CAK  CAL  120.01  3.000
 E9B  H10  CAK  CAJ  119.67  3.000
 E9B  CAL  CAK  CAJ  120.33  3.000
 E9B  H11  CAL  CAM  120.20  3.000
 E9B  H11  CAL  CAK  120.06  3.000
 E9B  CAM  CAL  CAK  119.75  3.000
 E9B  H12  CAM  CAN  119.83  3.000
 E9B  H12  CAM  CAL  120.21  3.000
 E9B  CAN  CAM  CAL  119.96  3.000
 E9B  H13  CAN  CAM  119.71  3.000
 E9B  H13  CAN  CAI  119.40  3.000
 E9B  CAM  CAN  CAI  120.89  3.000
 E9B  SAQ  CAU  NAV  118.77  3.000
 E9B  SAQ  CAU  CAA  114.80  3.000
 E9B  NAV  CAU  CAA  126.43  3.000
 E9B  NAP  NAO  CAE  106.64  3.000
 E9B  NAO  NAP  CAF  106.91  3.000
 E9B  OAX  NAV  OAW  125.60  3.000
 E9B  OAX  NAV  CAU  117.80  3.000
 E9B  OAW  NAV  CAU  116.60  3.000
 E9B  CAF  OAT  CAE  103.30  3.000
 E9B  CAU  SAQ  CAC   89.33  3.000
 E9B  CAE  SAR  CAD   97.51  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
 E9B  CONST_01  SAQ  CAC  CAB  CAA     0.00   0.0  0
 E9B  CONST_02  CAC  SAQ  CAU  CAA     0.00   0.0  0
 E9B  CONST_03  SAQ  CAU  CAA  CAB     0.00   0.0  0
 E9B  CONST_04  CAU  SAQ  CAC  CAB     0.00   0.0  0
 E9B  CONST_05  CAU  CAA  CAB  CAC     0.00   0.0  0
 E9B  CONST_06  CAF  NAP  NAO  CAE     0.00   0.0  0
 E9B  CONST_07  NAP  CAF  OAT  CAE     0.00   0.0  0
 E9B  CONST_08  NAO  CAE  OAT  CAF     0.00   0.0  0
 E9B  CONST_09  CAL  CAK  CAJ  CAI     0.00   0.0  0
 E9B  CONST_10  CAL  CAM  CAN  CAI     0.00   0.0  0
 E9B  CONST_11  CAM  CAN  CAI  CAJ     0.00   0.0  0
 E9B  CONST_12  CAM  CAL  CAK  CAJ     0.00   0.0  0
 E9B  CONST_13  CAN  CAI  CAJ  CAK     0.00   0.0  0
 E9B  CONST_14  CAN  CAM  CAL  CAK     0.00   0.0  0
 E9B  CONST_15  OAT  CAF  NAP  NAO     0.00   0.0  0
 E9B  CONST_16  OAT  CAE  NAO  NAP     0.00   0.0  0
 E9B  CONST_17  CAD  CAC  CAB  CAA   180.00   0.0  0
 E9B  CONST_18  NAV  CAU  CAA  CAB   180.00   0.0  0
 E9B  CONST_19  NAV  CAU  SAQ  CAC   180.00   0.0  0
 E9B  CONST_20  CAU  SAQ  CAC  CAD   180.00   0.0  0
 E9B  CONST_21  CAG  CAF  OAT  CAE   180.00   0.0  0
 E9B  CONST_22  SAR  CAE  OAT  CAF   180.00   0.0  0
 E9B  CONST_23  NAO  NAP  CAF  CAG   180.00   0.0  0
 E9B  CONST_24  CAK  CAJ  CAI  CAH   180.00   0.0  0
 E9B  CONST_25  CAM  CAN  CAI  CAH   180.00   0.0  0
 E9B  CONST_26  SAR  CAE  NAO  NAP   180.00   0.0  0
 E9B  CONST_27  H1   CAA  CAB  CAC   180.00   0.0  0
 E9B  CONST_28  H10  CAK  CAJ  CAI   180.00   0.0  0
 E9B  CONST_29  H12  CAM  CAN  CAI   180.00   0.0  0
 E9B  CONST_30  H13  CAN  CAI  CAJ   180.00   0.0  0
 E9B  CONST_31  H11  CAL  CAK  CAJ   180.00   0.0  0
 E9B  CONST_32  H12  CAM  CAL  CAK   180.00   0.0  0
 E9B  CONST_33  H9   CAJ  CAK  CAL   180.00   0.0  0
 E9B  CONST_34  H13  CAN  CAM  CAL   180.00   0.0  0
 E9B  CONST_35  H10  CAK  CAL  CAM   180.00   0.0  0
 E9B  CONST_36  H9   CAJ  CAI  CAN   180.00   0.0  0
 E9B  CONST_37  H11  CAL  CAM  CAN   180.00   0.0  0
 E9B  CONST_38  H3   CAB  CAA  CAU   180.00   0.0  0
 E9B  CONST_39  H3   CAB  CAC  SAQ   180.00   0.0  0
 E9B  CONST_40  H1   CAA  CAU  SAQ   180.00   0.0  0
 E9B  CONST_41  OAW  NAV  CAU  CAA   180.00   0.0  0
 E9B  CONST_42  OAX  NAV  CAU  CAA     0.00   0.0  0
 E9B  CONST_43  SAQ  CAU  NAV  OAW     0.00   0.0  0
 E9B  CONST_44  SAQ  CAU  NAV  OAX   180.00   0.0  0
 E9B  Var_01    CAI  CAH  CAG  CAF   179.86   0.0  2
 E9B  Var_02    OAS  CAD  CAC  CAB  -179.02  30.0  2
 E9B  Var_03    SAR  CAD  CAC  CAB     1.01  30.0  2
 E9B  Var_04    CAE  SAR  CAD  CAC  -178.38  30.0  3
 E9B  Var_05    NAO  CAE  SAR  CAD  -103.35  30.0  1
 E9B  Var_06    OAT  CAE  SAR  CAD    78.79  30.0  1
 E9B  Var_07    CAJ  CAI  CAH  CAG     2.13  30.0  2
 E9B  Var_08    CAN  CAI  CAH  CAG  -177.71  30.0  2
 E9B  Var_09    NAP  CAF  CAG  CAH     2.07  30.0  2
 E9B  Var_10    OAT  CAF  CAG  CAH  -177.80  30.0  2
 E9B  Var_11    SAQ  CAC  CAD  OAS     0.57  30.0  2
 E9B  Var_12    SAR  CAD  CAC  SAQ  -179.39  30.0  2
 E9B  Var_13    H7   CAH  CAI  CAJ  -178.18  30.0  2
 E9B  Var_14    H7   CAH  CAI  CAN     1.98  30.0  2
 E9B  Var_15    H5   CAG  CAF  NAP  -178.32  30.0  2
 E9B  Var_16    H5   CAG  CAF  OAT     1.82  30.0  2
 E9B  Var_17    OAS  CAD  SAR  CAE     1.65  30.0  1
 E9B  Var_18    H7   CAH  CAG  CAF     0.17   0.0  2
 E9B  Var_19    H5   CAG  CAH  CAI     0.26   0.0  2
 E9B  Var_20    H7   CAH  CAG  H5   -179.42   0.0  2

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
 E9B  plan-1  CAA  0.020
 E9B  plan-1  CAB  0.020
 E9B  plan-1  CAC  0.020
 E9B  plan-1  CAD  0.020
 E9B  plan-1  CAU  0.020
 E9B  plan-1  NAV  0.020
 E9B  plan-1  SAQ  0.020
 E9B  plan-1  H1   0.020
 E9B  plan-1  H3   0.020
 E9B  plan-2  CAE  0.020
 E9B  plan-2  CAF  0.020
 E9B  plan-2  CAG  0.020
 E9B  plan-2  NAO  0.020
 E9B  plan-2  NAP  0.020
 E9B  plan-2  OAT  0.020
 E9B  plan-2  SAR  0.020
 E9B  plan-3  CAH  0.020
 E9B  plan-3  CAI  0.020
 E9B  plan-3  CAJ  0.020
 E9B  plan-3  CAK  0.020
 E9B  plan-3  CAL  0.020
 E9B  plan-3  CAM  0.020
 E9B  plan-3  CAN  0.020
 E9B  plan-3  H9   0.020
 E9B  plan-3  H10  0.020
 E9B  plan-3  H11  0.020
 E9B  plan-3  H12  0.020
 E9B  plan-3  H13  0.020
 E9B  plan-4  CAU  0.020
 E9B  plan-4  NAV  0.020
 E9B  plan-4  OAW  0.020
 E9B  plan-4  OAX  0.020
 E9B  plan-5  CAC  0.020
 E9B  plan-5  CAD  0.020
 E9B  plan-5  OAS  0.020
 E9B  plan-5  SAR  0.020
 E9B  plan-6  CAF  0.020
 E9B  plan-6  CAG  0.020
 E9B  plan-6  CAH  0.020
 E9B  plan-6  CAI  0.020
 E9B  plan-6  H5   0.020
 E9B  plan-6  H7   0.020

