# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:04:12 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 3,3'-[(1,6-dioxohexane-1,6-diyl)diimino]bis(2,4,6-triiodobenzoic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(I)cc(I)c(NC(=O)CCCCC(=O)Nc2c(I)cc(I)c(C(O)=O)c2I)c1I
#
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
 IDB  IDB  '3,3'-[(1,6-dioxohexane-1,6-diyl)diimino]bis(2,4,6-triiodobenzoic acid)'  ligand  46  34  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IDB
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
 IDB  I1    I  I      0   0.090    5.0847   2.8893  -0.0735
 IDB  I2    I  I      0   0.096    5.3680  -3.0241  -1.2339
 IDB  I3    I  I      0   0.080   10.2313  -0.1911   0.7807
 IDB  O1    O  O      0  -0.458    3.4077  -0.7078   1.0631
 IDB  O2    O  OC    -1  -0.565    8.1533   2.6407   1.9161
 IDB  O3    O  O      0  -0.568    8.7666   3.0432  -0.2027
 IDB  N1    N  NH1    0  -0.740    4.1887  -0.0382  -0.9396
 IDB  C1    C  CR6    0   0.073    7.5263   1.1144   0.2553
 IDB  C2    C  CR6    0  -0.286    6.1895   1.0961  -0.1271
 IDB  C3    C  CR6    0   0.423    5.5363  -0.0623  -0.5505
 IDB  C4    C  CR6    0  -0.263    6.2700  -1.2465  -0.5809
 IDB  C5    C  CR16   0  -0.224    7.6009  -1.2768  -0.1982
 IDB  C6    C  CR6    0  -0.261    8.2035  -0.0979   0.2118
 IDB  C7    C  C      0   0.560    3.1865  -0.3805  -0.0864
 IDB  C8    C  CH2    0  -0.596    1.8097  -0.3421  -0.7041
 IDB  C10   C  CH2    0  -0.417    0.6813  -0.3445   0.3142
 IDB  C11   C  CH2    0  -0.418   -0.6832  -0.3441  -0.3640
 IDB  O4    O  O      0  -0.458   -3.4125  -0.7219  -1.1053
 IDB  O5    O  OC    -1  -0.565   -8.1962   2.6918  -1.8730
 IDB  O6    O  O      0  -0.568   -8.7719   3.0557   0.2635
 IDB  N2    N  NH1    0  -0.740   -4.1874  -0.0301   0.8931
 IDB  C12   C  CR6    0   0.072   -7.5373   1.1375  -0.2510
 IDB  C13   C  CR6    0  -0.287   -6.1969   1.1145   0.1179
 IDB  C14   C  CR6    0   0.424   -5.5366  -0.0507   0.5109
 IDB  C15   C  CR6    0  -0.264   -6.2666  -1.2377   0.5214
 IDB  C16   C  CR16   0  -0.225   -7.6002  -1.2637   0.1478
 IDB  C17   C  CR6    0  -0.260   -8.2101  -0.0778  -0.2297
 IDB  C18   C  C      0   0.560   -3.1883  -0.3831   0.0401
 IDB  C19   C  CH2    0  -0.596   -1.8105  -0.3433   0.6555
 IDB  H1    H  HNH1   0   0.417    3.9641   0.2632  -1.8766
 IDB  H5    H  HCR6   0   0.299    8.1584  -2.2024  -0.2238
 IDB  H8C1  H  HCH2   0   0.262    1.7286   0.5293  -1.3606
 IDB  H8C2  H  HCH2   0   0.276    1.7226  -1.2143  -1.3623
 IDB  H101  H  HCH2   0   0.230    0.7671  -1.2209   0.9612
 IDB  H102  H  HCH2   0   0.229    0.7693   0.5301   0.9652
 IDB  H111  H  HCH2   0   0.229   -0.7716   0.5315  -1.0136
 IDB  H112  H  HCH2   0   0.231   -0.7693  -1.2197  -1.0120
 IDB  HB    H  HNH1   0   0.416   -3.9565   0.2964   1.8201
 IDB  H16   H  HCR6   0   0.299   -8.1543  -2.1917   0.1563
 IDB  H191  H  HCH2   0   0.276   -1.7223  -1.2162   1.3125
 IDB  H192  H  HCH2   0   0.261   -1.7287   0.5276   1.3124
 IDB  I4    I  I      0   0.090   -5.0976   2.9120   0.0881
 IDB  I5    I  I      0   0.095   -5.3603  -3.0254   1.1396
 IDB  I6    I  I      0   0.080  -10.2439  -0.1647  -0.7789
 IDB  C9    C  C      0   0.344    8.2202   2.4036   0.7042
 IDB  C20   C  C      0   0.348   -8.2406   2.4334  -0.6645

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
 IDB  I1   C2    single    2.107  0.020  2.107
 IDB  I2   C4    single    2.098  0.020  2.098
 IDB  I3   C6    single    2.108  0.020  2.108
 IDB  O1   C7    double    1.215  0.020  1.215
 IDB  O2   C9    deloc     1.237  0.020  1.237
 IDB  O3   C9    deloc     1.237  0.020  1.237
 IDB  N1   C3    single    1.403  0.020  1.403
 IDB  N1   C7    single    1.360  0.020  1.360
 IDB  N1   H1    single    0.860  0.020  1.020
 IDB  C1   C2    aromatic  1.391  0.020  1.391
 IDB  C1   C6    aromatic  1.389  0.020  1.389
 IDB  C1   C9    single    1.531  0.020  1.531
 IDB  C2   C3    aromatic  1.396  0.020  1.396
 IDB  C3   C4    aromatic  1.393  0.020  1.393
 IDB  C4   C5    aromatic  1.385  0.020  1.385
 IDB  C5   C6    aromatic  1.386  0.020  1.386
 IDB  C5   H5    single    0.930  0.020  1.080
 IDB  C7   C8    single    1.510  0.020  1.510
 IDB  C8   C10   single    1.520  0.020  1.520
 IDB  C8   H8C1  single    0.970  0.020  1.090
 IDB  C8   H8C2  single    0.970  0.020  1.090
 IDB  C10  C11   single    1.524  0.020  1.524
 IDB  C10  H101  single    0.970  0.020  1.090
 IDB  C10  H102  single    0.970  0.020  1.090
 IDB  C11  C19   single    1.520  0.020  1.520
 IDB  C11  H111  single    0.970  0.020  1.090
 IDB  C11  H112  single    0.970  0.020  1.090
 IDB  I4   C13   single    2.107  0.020  2.107
 IDB  I5   C15   single    2.097  0.020  2.097
 IDB  I6   C17   single    2.108  0.020  2.108
 IDB  O4   C18   double    1.215  0.020  1.215
 IDB  O5   C20   deloc     1.237  0.020  1.237
 IDB  O6   C20   deloc     1.237  0.020  1.237
 IDB  N2   C14   single    1.402  0.020  1.402
 IDB  N2   C18   single    1.360  0.020  1.360
 IDB  N2   HB    single    0.860  0.020  1.020
 IDB  C12  C13   aromatic  1.390  0.020  1.390
 IDB  C12  C17   aromatic  1.389  0.020  1.389
 IDB  C12  C20   single    1.531  0.020  1.531
 IDB  C13  C14   aromatic  1.396  0.020  1.396
 IDB  C14  C15   aromatic  1.394  0.020  1.394
 IDB  C15  C16   aromatic  1.385  0.020  1.385
 IDB  C16  C17   aromatic  1.386  0.020  1.386
 IDB  C16  H16   single    0.930  0.020  1.080
 IDB  C18  C19   single    1.509  0.020  1.509
 IDB  C19  H191  single    0.970  0.020  1.090
 IDB  C19  H192  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
 IDB  H1    N1   C7    119.57  3.000
 IDB  H1    N1   C3    118.44  3.000
 IDB  C7    N1   C3    121.98  3.000
 IDB  C9    C1   C6    121.53  3.000
 IDB  C9    C1   C2    121.82  3.000
 IDB  C6    C1   C2    116.64  3.000
 IDB  C3    C2   C1    122.98  3.000
 IDB  C3    C2   I1    117.95  3.000
 IDB  C1    C2   I1    119.07  3.000
 IDB  C4    C3   C2    117.75  3.000
 IDB  C4    C3   N1    120.95  3.000
 IDB  C2    C3   N1    121.30  3.000
 IDB  C5    C4   C3    121.23  3.000
 IDB  C5    C4   I2    118.73  3.000
 IDB  C3    C4   I2    120.04  3.000
 IDB  H5    C5   C6    120.74  3.000
 IDB  H5    C5   C4    120.52  3.000
 IDB  C6    C5   C4    118.74  3.000
 IDB  C5    C6   C1    122.65  3.000
 IDB  C5    C6   I3    117.42  3.000
 IDB  C1    C6   I3    119.93  3.000
 IDB  C8    C7   N1    114.14  3.000
 IDB  C8    C7   O1    124.05  3.000
 IDB  N1    C7   O1    121.80  3.000
 IDB  H8C2  C8   H8C1  105.52  3.000
 IDB  H8C2  C8   C10   110.00  3.000
 IDB  H8C1  C8   C10   110.38  3.000
 IDB  H8C2  C8   C7    107.33  3.000
 IDB  H8C1  C8   C7    109.48  3.000
 IDB  C10   C8   C7    113.76  3.000
 IDB  H102  C10  H101  106.41  3.000
 IDB  H102  C10  C11   109.67  3.000
 IDB  H101  C10  C11   109.51  3.000
 IDB  H102  C10  C8    109.75  3.000
 IDB  H101  C10  C8    109.86  3.000
 IDB  C11   C10  C8    111.51  3.000
 IDB  H112  C11  H111  106.43  3.000
 IDB  H112  C11  C19   109.87  3.000
 IDB  H111  C11  C19   109.75  3.000
 IDB  H112  C11  C10   109.53  3.000
 IDB  H111  C11  C10   109.68  3.000
 IDB  C19   C11  C10   111.45  3.000
 IDB  HB    N2   C18   119.45  3.000
 IDB  HB    N2   C14   118.36  3.000
 IDB  C18   N2   C14   122.13  3.000
 IDB  C20   C12  C17   121.47  3.000
 IDB  C20   C12  C13   121.90  3.000
 IDB  C17   C12  C13   116.63  3.000
 IDB  C14   C13  C12   123.00  3.000
 IDB  C14   C13  I4    117.99  3.000
 IDB  C12   C13  I4    119.01  3.000
 IDB  C15   C14  C13   117.74  3.000
 IDB  C15   C14  N2    120.95  3.000
 IDB  C13   C14  N2    121.31  3.000
 IDB  C16   C15  C14   121.22  3.000
 IDB  C16   C15  I5    118.65  3.000
 IDB  C14   C15  I5    120.12  3.000
 IDB  H16   C16  C17   120.74  3.000
 IDB  H16   C16  C15   120.50  3.000
 IDB  C17   C16  C15   118.76  3.000
 IDB  C16   C17  C12   122.65  3.000
 IDB  C16   C17  I6    117.40  3.000
 IDB  C12   C17  I6    119.95  3.000
 IDB  C19   C18  N2    114.08  3.000
 IDB  C19   C18  O4    124.05  3.000
 IDB  N2    C18  O4    121.86  3.000
 IDB  H192  C19  H191  105.54  3.000
 IDB  H192  C19  C18   109.52  3.000
 IDB  H191  C19  C18   107.26  3.000
 IDB  H192  C19  C11   110.35  3.000
 IDB  H191  C19  C11   110.00  3.000
 IDB  C18   C19  C11   113.80  3.000
 IDB  C1    C9   O3    114.87  3.000
 IDB  C1    C9   O2    115.10  3.000
 IDB  O3    C9   O2    130.03  3.000
 IDB  C12   C20  O6    114.86  3.000
 IDB  C12   C20  O5    115.10  3.000
 IDB  O6    C20  O5    130.04  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
 IDB  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 IDB  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 IDB  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 IDB  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 IDB  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 IDB  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 IDB  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 IDB  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 IDB  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 IDB  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 IDB  CONST_11  C17  C12  C13  C14     0.00   0.0  0
 IDB  CONST_12  C17  C16  C15  C14     0.00   0.0  0
 IDB  CONST_13  C6   C1   C2   I1    180.00   0.0  0
 IDB  CONST_14  C4   C3   C2   I1    180.00   0.0  0
 IDB  CONST_15  C2   C3   C4   I2    180.00   0.0  0
 IDB  CONST_16  C6   C5   C4   I2    180.00   0.0  0
 IDB  CONST_17  C2   C1   C6   I3    180.00   0.0  0
 IDB  CONST_18  C4   C5   C6   I3    180.00   0.0  0
 IDB  CONST_19  C1   C2   C3   N1    180.00   0.0  0
 IDB  CONST_20  C5   C4   C3   N1    180.00   0.0  0
 IDB  CONST_21  C9   C1   C2   C3    180.00   0.0  0
 IDB  CONST_22  C9   C1   C6   C5    180.00   0.0  0
 IDB  CONST_23  C17  C12  C13  I4    180.00   0.0  0
 IDB  CONST_24  C15  C14  C13  I4    180.00   0.0  0
 IDB  CONST_25  C13  C14  C15  I5    180.00   0.0  0
 IDB  CONST_26  C17  C16  C15  I5    180.00   0.0  0
 IDB  CONST_27  C13  C12  C17  I6    180.00   0.0  0
 IDB  CONST_28  C15  C16  C17  I6    180.00   0.0  0
 IDB  CONST_29  C12  C13  C14  N2    180.00   0.0  0
 IDB  CONST_30  C16  C15  C14  N2    180.00   0.0  0
 IDB  CONST_31  C20  C12  C13  C14   180.00   0.0  0
 IDB  CONST_32  C20  C12  C17  C16   180.00   0.0  0
 IDB  CONST_33  H5   C5   C6   C1    180.00   0.0  0
 IDB  CONST_34  H16  C16  C17  C12   180.00   0.0  0
 IDB  CONST_41  C3   N1   C7   O1      0.00   0.0  0
 IDB  CONST_42  C8   C7   N1   C3    180.00   0.0  0
 IDB  CONST_43  C14  N2   C18  O4      0.00   0.0  0
 IDB  CONST_44  C19  C18  N2   C14   180.00   0.0  0
 IDB  Var_01    C2   C1   C9   O2     89.73  30.0  2
 IDB  Var_02    C13  C12  C20  O5     90.30  30.0  2
 IDB  Var_03    C10  C8   C7   O1     17.19  30.0  3
 IDB  Var_04    C11  C10  C8   C7   -178.42  30.0  3
 IDB  Var_05    C19  C11  C10  C8   -179.87  30.0  3
 IDB  Var_06    C18  C19  C11  C10  -178.33  30.0  3
 IDB  Var_07    O4   C18  C19  C11    17.89  30.0  1

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
 IDB  plan-1  I1   0.020
 IDB  plan-1  I2   0.020
 IDB  plan-1  I3   0.020
 IDB  plan-1  N1   0.020
 IDB  plan-1  C1   0.020
 IDB  plan-1  C2   0.020
 IDB  plan-1  C3   0.020
 IDB  plan-1  C4   0.020
 IDB  plan-1  C5   0.020
 IDB  plan-1  C6   0.020
 IDB  plan-1  H5   0.020
 IDB  plan-1  C9   0.020
 IDB  plan-2  O5   0.020
 IDB  plan-2  O6   0.020
 IDB  plan-2  C12  0.020
 IDB  plan-2  C20  0.020
 IDB  plan-3  N2   0.020
 IDB  plan-3  C12  0.020
 IDB  plan-3  C13  0.020
 IDB  plan-3  C14  0.020
 IDB  plan-3  C15  0.020
 IDB  plan-3  C16  0.020
 IDB  plan-3  C17  0.020
 IDB  plan-3  H16  0.020
 IDB  plan-3  I4   0.020
 IDB  plan-3  I5   0.020
 IDB  plan-3  I6   0.020
 IDB  plan-3  C20  0.020
 IDB  plan-4  O1   0.020
 IDB  plan-4  N1   0.020
 IDB  plan-4  C3   0.020
 IDB  plan-4  C7   0.020
 IDB  plan-4  C8   0.020
 IDB  plan-4  H1   0.020
 IDB  plan-5  O4   0.020
 IDB  plan-5  N2   0.020
 IDB  plan-5  C14  0.020
 IDB  plan-5  C18  0.020
 IDB  plan-5  C19  0.020
 IDB  plan-5  HB   0.020
 IDB  plan-6  O2   0.020
 IDB  plan-6  O3   0.020
 IDB  plan-6  C1   0.020
 IDB  plan-6  C9   0.020

