# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:08:18 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 2-[[3-[[5-(3-iodanylphenyl)carbonylthiophen-2-yl]carbonylamino]phenyl]methyl]propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(Cc1cccc(NC(=O)c2sc(cc2)C(=O)c3cccc(I)c3)c1)C(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
 8VB  8VB  '2-[[3-[[5-(3-iodanylphenyl)carbonylthiophen-2-yl]carbonylamino]phenyl]methyl]propanedioic acid'  ligand  47  31  .  2021-08-06  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8VB
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
 8VB  OAA  O  O     0  -0.430  -8.1765  -2.6511   0.1749
 8VB  CAU  C  C     0   0.561  -7.2716  -2.1834  -0.4688
 8VB  OAE  O  OH1   0  -0.573  -6.1425  -2.8139  -0.7330
 8VB  CBE  C  CH1   0  -0.500  -7.3117  -0.7776  -1.0346
 8VB  CAV  C  C     0   0.586  -8.5419  -0.6366  -1.9099
 8VB  OAF  O  O     0  -0.419  -9.3446   0.2541  -1.8306
 8VB  OAB  O  OH1   0  -0.589  -8.6038  -1.6181  -2.7975
 8VB  CAR  C  CH2   0  -0.515  -7.3000   0.2496   0.1035
 8VB  CAZ  C  CR6   0   0.123  -6.0761   0.1058   0.9676
 8VB  CAP  C  CR16  0  -0.361  -4.8691   0.6568   0.5445
 8VB  CAK  C  CR16  0  -0.317  -6.1318  -0.6010   2.1629
 8VB  CAH  C  CR16  0  -0.228  -4.9832  -0.7622   2.9261
 8VB  CAL  C  CR16  0  -0.357  -3.7840  -0.2137   2.5106
 8VB  CBA  C  CR6   0   0.400  -3.7197   0.5055   1.3159
 8VB  NAS  N  NH1   0  -0.768  -2.4653   1.0133   0.9500
 8VB  CAW  C  C     0   0.550  -2.1997   2.0481   0.1154
 8VB  OAC  O  O     0  -0.443  -3.0439   2.7137  -0.4536
 8VB  CBC  C  CR5   0  -0.320  -0.7615   2.3539  -0.0748
 8VB  SAT  S  S2    0   0.300   0.5062   1.2351   0.2038
 8VB  CAN  C  CR15  0  -0.158  -0.2834   3.5576  -0.5244
 8VB  CAO  C  CR15  0  -0.156   1.1174   3.5753  -0.6338
 8VB  CBD  C  CR5   0  -0.310   1.6956   2.3862  -0.2643
 8VB  CAX  C  C     0   0.377   3.1287   2.0704  -0.3595
 8VB  OAD  O  O     0  -0.372   3.8669   2.7864  -1.0035
 8VB  CBB  C  CR6   0  -0.042   3.6479   0.8482   0.3135
 8VB  CAQ  C  CR16  0  -0.241   4.5940   0.0801  -0.3652
 8VB  CAY  C  CR6   0  -0.211   5.1188  -1.0433   0.2487
 8VB  IAG  I  I     0   0.074   6.5148  -2.2262  -0.7864
 8VB  CAJ  C  CR16  0  -0.218   4.7433  -1.4004   1.5381
 8VB  CAI  C  CR16  0  -0.230   3.8216  -0.6154   2.2145
 8VB  CAM  C  CR16  0  -0.277   3.2660   0.5011   1.6070
 8VB  H1   H  HOH1  0   0.486  -6.1493  -3.6952  -0.3277
 8VB  H2   H  HCH1  0   0.330  -6.4406  -0.6177  -1.6781
 8VB  H3   H  HOH1  0   0.489  -9.3918  -1.5267  -3.3554
 8VB  H4   H  HCH2  0   0.280  -7.3293   1.2470  -0.3368
 8VB  H5   H  HCH2  0   0.271  -8.2004   0.1394   0.7092
 8VB  H6   H  HCR6  0   0.273  -4.8421   1.2007  -0.3880
 8VB  H7   H  HCR6  0   0.255  -7.0705  -1.0224   2.5003
 8VB  H8   H  HCR6  0   0.262  -5.0223  -1.3131   3.8566
 8VB  H9   H  HCR6  0   0.273  -2.8934  -0.3360   3.1158
 8VB  H10  H  HNH1  0   0.420  -1.6997   0.6595   1.5049
 8VB  H12  H  HCR5  0   0.286  -0.9204   4.3971  -0.7606
 8VB  H14  H  HCR5  0   0.288   1.6858   4.4296  -0.9709
 8VB  H15  H  HCR6  0   0.290   4.8924   0.3585  -1.3671
 8VB  H16  H  HCR6  0   0.289   5.1617  -2.2732   2.0204
 8VB  H17  H  HCR6  0   0.281   3.5387  -0.8765   3.2249
 8VB  H18  H  HCR6  0   0.286   2.5694   1.1151   2.1623

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
 8VB  CAH  CAK  aromatic  1.388  0.020  1.388
 8VB  CAH  CAL  aromatic  1.383  0.020  1.383
 8VB  CAK  CAZ  aromatic  1.390  0.020  1.390
 8VB  CAL  CBA  aromatic  1.396  0.020  1.396
 8VB  OAC  CAW  double    1.216  0.020  1.216
 8VB  CAZ  CAR  single    1.505  0.020  1.505
 8VB  CAZ  CAP  aromatic  1.393  0.020  1.393
 8VB  CBA  CAP  aromatic  1.393  0.020  1.393
 8VB  CBA  NAS  single    1.402  0.020  1.402
 8VB  CAR  CBE  single    1.533  0.020  1.533
 8VB  CAW  NAS  single    1.356  0.020  1.356
 8VB  CAW  CBC  single    1.483  0.020  1.483
 8VB  OAF  CAV  double    1.202  0.020  1.202
 8VB  CBE  CAV  single    1.516  0.020  1.516
 8VB  CBE  CAU  single    1.516  0.020  1.516
 8VB  CAV  OAB  single    1.325  0.020  1.325
 8VB  CAN  CBC  aromatic  1.371  0.020  1.371
 8VB  CAN  CAO  aromatic  1.405  0.020  1.405
 8VB  CBC  SAT  aromatic  1.714  0.020  1.714
 8VB  OAA  CAU  double    1.205  0.020  1.205
 8VB  CAU  OAE  single    1.320  0.020  1.320
 8VB  CAO  CBD  aromatic  1.373  0.020  1.373
 8VB  SAT  CBD  aromatic  1.720  0.020  1.720
 8VB  CBD  CAX  single    1.471  0.020  1.471
 8VB  CAX  OAD  double    1.213  0.020  1.213
 8VB  CAX  CBB  single    1.489  0.020  1.489
 8VB  CBB  CAQ  aromatic  1.395  0.020  1.395
 8VB  CBB  CAM  aromatic  1.393  0.020  1.393
 8VB  CAQ  CAY  aromatic  1.384  0.020  1.384
 8VB  IAG  CAY  single    2.102  0.020  2.102
 8VB  CAM  CAI  aromatic  1.387  0.020  1.387
 8VB  CAY  CAJ  aromatic  1.390  0.020  1.390
 8VB  CAI  CAJ  aromatic  1.387  0.020  1.387
 8VB  OAE  H1   single    0.850  0.020  0.980
 8VB  CBE  H2   single    0.970  0.020  1.090
 8VB  OAB  H3   single    0.850  0.020  0.980
 8VB  CAR  H4   single    0.970  0.020  1.090
 8VB  CAR  H5   single    0.970  0.020  1.090
 8VB  CAP  H6   single    0.930  0.020  1.080
 8VB  CAK  H7   single    0.930  0.020  1.080
 8VB  CAH  H8   single    0.930  0.020  1.080
 8VB  CAL  H9   single    0.930  0.020  1.080
 8VB  NAS  H10  single    0.860  0.020  1.020
 8VB  CAN  H12  single    0.930  0.020  1.080
 8VB  CAO  H14  single    0.930  0.020  1.080
 8VB  CAQ  H15  single    0.930  0.020  1.080
 8VB  CAJ  H16  single    0.930  0.020  1.080
 8VB  CAI  H17  single    0.930  0.020  1.080
 8VB  CAM  H18  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
 8VB  CBE  CAU  OAE  113.01  3.000
 8VB  OAE  CAU  OAA  124.33  3.000
 8VB  CBE  CAU  OAA  122.65  3.000
 8VB  H1   OAE  CAU  110.14  3.000
 8VB  H2   CBE  CAR  109.41  3.000
 8VB  H2   CBE  CAV  107.02  3.000
 8VB  CAR  CBE  CAV  111.86  3.000
 8VB  H2   CBE  CAU  109.50  3.000
 8VB  CAV  CBE  CAU  108.86  3.000
 8VB  CAR  CBE  CAU  110.12  3.000
 8VB  OAB  CAV  OAF  124.21  3.000
 8VB  OAB  CAV  CBE  110.84  3.000
 8VB  OAF  CAV  CBE  124.95  3.000
 8VB  H3   OAB  CAV  110.70  3.000
 8VB  H5   CAR  H4   107.12  3.000
 8VB  H5   CAR  CAZ  110.04  3.000
 8VB  H4   CAR  CAZ  109.94  3.000
 8VB  H5   CAR  CBE  109.77  3.000
 8VB  H4   CAR  CBE  108.23  3.000
 8VB  CAZ  CAR  CBE  111.62  3.000
 8VB  CAK  CAZ  CAP  119.82  3.000
 8VB  CAP  CAZ  CAR  119.50  3.000
 8VB  CAK  CAZ  CAR  120.65  3.000
 8VB  H6   CAP  CBA  120.83  3.000
 8VB  H6   CAP  CAZ  118.90  3.000
 8VB  CBA  CAP  CAZ  120.27  3.000
 8VB  H7   CAK  CAH  120.05  3.000
 8VB  H7   CAK  CAZ  120.05  3.000
 8VB  CAH  CAK  CAZ  119.91  3.000
 8VB  H8   CAH  CAL  119.45  3.000
 8VB  H8   CAH  CAK  120.13  3.000
 8VB  CAL  CAH  CAK  120.42  3.000
 8VB  H9   CAL  CBA  119.88  3.000
 8VB  H9   CAL  CAH  120.02  3.000
 8VB  CBA  CAL  CAH  120.10  3.000
 8VB  NAS  CBA  CAL  116.82  3.000
 8VB  NAS  CBA  CAP  123.68  3.000
 8VB  CAL  CBA  CAP  119.48  3.000
 8VB  H10  NAS  CAW  117.21  3.000
 8VB  H10  NAS  CBA  114.09  3.000
 8VB  CAW  NAS  CBA  127.77  3.000
 8VB  CBC  CAW  OAC  120.03  3.000
 8VB  CBC  CAW  NAS  115.24  3.000
 8VB  OAC  CAW  NAS  124.73  3.000
 8VB  CAN  CBC  SAT  111.62  3.000
 8VB  SAT  CBC  CAW  124.20  3.000
 8VB  CAN  CBC  CAW  124.16  3.000
 8VB  CBD  SAT  CBC   91.74  3.000
 8VB  H12  CAN  CAO  124.14  3.000
 8VB  H12  CAN  CBC  123.26  3.000
 8VB  CAO  CAN  CBC  112.60  3.000
 8VB  H14  CAO  CBD  123.19  3.000
 8VB  H14  CAO  CAN  123.98  3.000
 8VB  CBD  CAO  CAN  112.83  3.000
 8VB  CAX  CBD  CAO  125.38  3.000
 8VB  CAX  CBD  SAT  123.21  3.000
 8VB  CAO  CBD  SAT  111.20  3.000
 8VB  CBB  CAX  OAD  120.81  3.000
 8VB  CBB  CAX  CBD  119.14  3.000
 8VB  OAD  CAX  CBD  120.03  3.000
 8VB  CAM  CBB  CAQ  120.04  3.000
 8VB  CAM  CBB  CAX  121.93  3.000
 8VB  CAQ  CBB  CAX  117.95  3.000
 8VB  H15  CAQ  CAY  121.01  3.000
 8VB  H15  CAQ  CBB  119.73  3.000
 8VB  CAY  CAQ  CBB  119.24  3.000
 8VB  CAJ  CAY  IAG  119.45  3.000
 8VB  CAJ  CAY  CAQ  121.19  3.000
 8VB  IAG  CAY  CAQ  119.36  3.000
 8VB  H16  CAJ  CAI  119.77  3.000
 8VB  H16  CAJ  CAY  121.11  3.000
 8VB  CAI  CAJ  CAY  119.12  3.000
 8VB  H17  CAI  CAM  119.92  3.000
 8VB  H17  CAI  CAJ  119.53  3.000
 8VB  CAM  CAI  CAJ  120.54  3.000
 8VB  H18  CAM  CAI  119.33  3.000
 8VB  H18  CAM  CBB  120.78  3.000
 8VB  CAI  CAM  CBB  119.84  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
 8VB  CONST_01  CAL  CAH  CAK  CAZ     0.00   0.0  0
 8VB  CONST_02  CAL  CBA  CAP  CAZ     0.00   0.0  0
 8VB  CONST_03  CAH  CAK  CAZ  CAP     0.00   0.0  0
 8VB  CONST_04  CAH  CAL  CBA  CAP     0.00   0.0  0
 8VB  CONST_05  CBA  CAL  CAH  CAK     0.00   0.0  0
 8VB  CONST_06  CBA  CAP  CAZ  CAK     0.00   0.0  0
 8VB  CONST_07  CBD  CAO  CAN  CBC     0.00   0.0  0
 8VB  CONST_08  CAO  CBD  SAT  CBC     0.00   0.0  0
 8VB  CONST_09  CAO  CAN  CBC  SAT     0.00   0.0  0
 8VB  CONST_10  CAN  CAO  CBD  SAT     0.00   0.0  0
 8VB  CONST_11  CBD  SAT  CBC  CAN     0.00   0.0  0
 8VB  CONST_12  CAJ  CAY  CAQ  CBB     0.00   0.0  0
 8VB  CONST_13  CAJ  CAI  CAM  CBB     0.00   0.0  0
 8VB  CONST_14  CAI  CAM  CBB  CAQ     0.00   0.0  0
 8VB  CONST_15  CAI  CAJ  CAY  CAQ     0.00   0.0  0
 8VB  CONST_16  CAM  CBB  CAQ  CAY     0.00   0.0  0
 8VB  CONST_17  CAM  CAI  CAJ  CAY     0.00   0.0  0
 8VB  CONST_18  CAH  CAK  CAZ  CAR   180.00   0.0  0
 8VB  CONST_19  CBA  CAP  CAZ  CAR   180.00   0.0  0
 8VB  CONST_20  NAS  CBA  CAP  CAZ   180.00   0.0  0
 8VB  CONST_21  NAS  CBA  CAL  CAH   180.00   0.0  0
 8VB  CONST_22  CAO  CAN  CBC  CAW   180.00   0.0  0
 8VB  CONST_23  CBD  SAT  CBC  CAW   180.00   0.0  0
 8VB  CONST_24  CAX  CBD  SAT  CBC   180.00   0.0  0
 8VB  CONST_25  CAX  CBD  CAO  CAN   180.00   0.0  0
 8VB  CONST_26  CAY  CAQ  CBB  CAX   180.00   0.0  0
 8VB  CONST_27  CAI  CAM  CBB  CAX   180.00   0.0  0
 8VB  CONST_28  IAG  CAY  CAQ  CBB   180.00   0.0  0
 8VB  CONST_29  CAI  CAJ  CAY  IAG   180.00   0.0  0
 8VB  CONST_30  H8   CAH  CAK  CAZ   180.00   0.0  0
 8VB  CONST_31  H7   CAK  CAZ  CAP   180.00   0.0  0
 8VB  CONST_32  H9   CAL  CBA  CAP   180.00   0.0  0
 8VB  CONST_33  H6   CAP  CAZ  CAK   180.00   0.0  0
 8VB  CONST_34  H14  CAO  CAN  CBC   180.00   0.0  0
 8VB  CONST_35  H12  CAN  CBC  SAT   180.00   0.0  0
 8VB  CONST_36  H17  CAI  CAM  CBB   180.00   0.0  0
 8VB  CONST_37  H18  CAM  CBB  CAQ   180.00   0.0  0
 8VB  CONST_38  H16  CAJ  CAY  CAQ   180.00   0.0  0
 8VB  CONST_39  H15  CAQ  CAY  CAJ   180.00   0.0  0
 8VB  CONST_40  CBC  CAW  NAS  CBA   180.00   0.0  0
 8VB  CONST_43  H10  NAS  CBA  CAP   180.00   0.0  0
 8VB  CONST_44  OAC  CAW  NAS  CBA     0.00   0.0  0
 8VB  CONST_45  H1   OAE  CAU  OAA     0.00   0.0  0
 8VB  CONST_46  H3   OAB  CAV  CBE   180.00   0.0  0
 8VB  Var_01    CBB  CAX  CBD  SAT   -17.23  30.0  2
 8VB  Var_02    CAQ  CBB  CAX  CBD   139.02  30.0  2
 8VB  Var_03    CAK  CAZ  CAR  CBE   -97.88  30.0  2
 8VB  Var_04    CAN  CBC  CAW  NAS  -159.47  30.0  2
 8VB  Var_05    CAZ  CAR  CBE  CAU    58.88  30.0  2
 8VB  Var_06    CAR  CBE  CAU  OAA    66.41  30.0  3
 8VB  Var_07    OAF  CAV  CBE  CAU   129.68  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
 8VB  plan-1  CAW  0.020
 8VB  plan-1  CBC  0.020
 8VB  plan-1  SAT  0.020
 8VB  plan-1  CAN  0.020
 8VB  plan-1  CAO  0.020
 8VB  plan-1  CBD  0.020
 8VB  plan-1  CAX  0.020
 8VB  plan-1  H12  0.020
 8VB  plan-1  H14  0.020
 8VB  plan-2  CAR  0.020
 8VB  plan-2  CAZ  0.020
 8VB  plan-2  CAP  0.020
 8VB  plan-2  CAK  0.020
 8VB  plan-2  CAH  0.020
 8VB  plan-2  CAL  0.020
 8VB  plan-2  CBA  0.020
 8VB  plan-2  NAS  0.020
 8VB  plan-2  H6   0.020
 8VB  plan-2  H7   0.020
 8VB  plan-2  H8   0.020
 8VB  plan-2  H9   0.020
 8VB  plan-3  CAX  0.020
 8VB  plan-3  CBB  0.020
 8VB  plan-3  CAQ  0.020
 8VB  plan-3  CAY  0.020
 8VB  plan-3  IAG  0.020
 8VB  plan-3  CAJ  0.020
 8VB  plan-3  CAI  0.020
 8VB  plan-3  CAM  0.020
 8VB  plan-3  H15  0.020
 8VB  plan-3  H16  0.020
 8VB  plan-3  H17  0.020
 8VB  plan-3  H18  0.020
 8VB  plan-4  CBA  0.020
 8VB  plan-4  NAS  0.020
 8VB  plan-4  CAW  0.020
 8VB  plan-4  OAC  0.020
 8VB  plan-4  CBC  0.020
 8VB  plan-4  H10  0.020
 8VB  plan-5  CBD  0.020
 8VB  plan-5  CAX  0.020
 8VB  plan-5  OAD  0.020
 8VB  plan-5  CBB  0.020
 8VB  plan-6  OAA  0.020
 8VB  plan-6  CAU  0.020
 8VB  plan-6  OAE  0.020
 8VB  plan-6  CBE  0.020
 8VB  plan-6  H1   0.020
 8VB  plan-7  CBE  0.020
 8VB  plan-7  CAV  0.020
 8VB  plan-7  OAF  0.020
 8VB  plan-7  OAB  0.020
 8VB  plan-7  H3   0.020

