# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 17:48:37 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  48  34  .  2021-08-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.150    4.8266   2.6347   0.7681
 IDB  I2    I  I     0   0.128    5.5396  -2.5832  -2.1692
 IDB  I3    I  I     0   0.141   10.2232  -0.1007   0.6024
 IDB  O1    O  O     0  -0.456    3.4459  -0.9342   0.9362
 IDB  O2    O  OH1   0  -0.558    7.8904   1.9504   2.5941
 IDB  O3    O  O     0  -0.391    8.4846   3.1307   0.7826
 IDB  N1    N  NH1   0  -0.741    4.1359   0.0487  -0.9670
 IDB  C1    C  CR6   0   0.099    7.3950   1.0363   0.5118
 IDB  C2    C  CR6   0  -0.265    6.0512   1.0456   0.1556
 IDB  C3    C  CR6   0   0.419    5.4914   0.0241  -0.6127
 IDB  C4    C  CR6   0  -0.245    6.3229  -1.0178  -1.0189
 IDB  C5    C  CR16  0  -0.228    7.6662  -1.0499  -0.6799
 IDB  C6    C  CR6   0  -0.242    8.1897  -0.0217   0.0866
 IDB  C7    C  C     0   0.558    3.1747  -0.4692  -0.1530
 IDB  C8    C  CH2   0  -0.594    1.7830  -0.4312  -0.7329
 IDB  C10   C  CH2   0  -0.419    0.6863  -0.4360   0.3205
 IDB  C11   C  CH2   0  -0.419   -0.6980  -0.4397  -0.3151
 IDB  O4    O  O     0  -0.456   -3.4564  -0.9499  -0.9282
 IDB  O5    O  OH1   0  -0.558   -7.9137   1.9715  -2.5673
 IDB  O6    O  O     0  -0.391   -8.5089   3.1257  -0.7396
 IDB  N2    N  NH1   0  -0.742   -4.1486   0.0409   0.9701
 IDB  C12   C  CR6   0   0.099   -7.4117   1.0322  -0.4975
 IDB  C13   C  CR6   0  -0.265   -6.0676   1.0420  -0.1423
 IDB  C14   C  CR6   0   0.419   -5.5038   0.0143   0.6145
 IDB  C15   C  CR6   0  -0.245   -6.3311  -1.0355   1.0090
 IDB  C16   C  CR16  0  -0.228   -7.6739  -1.0698   0.6684
 IDB  C17   C  CR6   0  -0.242   -8.2021  -0.0339  -0.0848
 IDB  C18   C  C     0   0.558   -3.1863  -0.4790   0.1587
 IDB  C19   C  CH2   0  -0.594   -1.7947  -0.4356   0.7384
 IDB  H2    H  HOH1  0   0.499    8.2743   2.6879   3.0959
 IDB  H1    H  HNH1  0   0.423    3.8822   0.4147  -1.8735
 IDB  H5    H  HCR6  0   0.312    8.2941  -1.8668  -1.0057
 IDB  H8C1  H  HCH2  0   0.263    1.6780   0.4371  -1.3885
 IDB  H8C2  H  HCH2  0   0.279    1.6806  -1.3077  -1.3831
 IDB  H101  H  HCH2  0   0.233    0.7945  -1.3105   0.9663
 IDB  H102  H  HCH2  0   0.230    0.7923   0.4407   0.9662
 IDB  H111  H  HCH2  0   0.230   -0.8074   0.4342  -0.9641
 IDB  H112  H  HCH2  0   0.233   -0.8030  -1.3171  -0.9576
 IDB  HA    H  HOH1  0   0.499   -8.2997   2.7148  -3.0589
 IDB  HB    H  HNH1  0   0.423   -3.8949   0.4185   1.8717
 IDB  H16   H  HCR6  0   0.312   -8.2986  -1.8932   0.9837
 IDB  H191  H  HCH2  0   0.280   -1.6902  -1.3105   1.3905
 IDB  H192  H  HCH2  0   0.263   -1.6917   0.4344   1.3922
 IDB  C9    C  C     0   0.407    7.9876   2.1679   1.2990
 IDB  C20   C  C     0   0.407   -8.0092   2.1717  -1.2695
 IDB  I4    I  I     0   0.150   -4.8481   2.6401  -0.7408
 IDB  I5    I  I     0   0.128   -5.5427  -2.6082   2.1458
 IDB  I6    I  I     0   0.141  -10.2355  -0.1143  -0.6000

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    2.098  0.020  2.098
 IDB  I2   C4    single    2.095  0.020  2.095
 IDB  I3   C6    single    2.099  0.020  2.099
 IDB  O1   C7    double    1.215  0.020  1.215
 IDB  O2   C9    single    1.317  0.020  1.317
 IDB  O2   H2    single    0.850  0.020  0.980
 IDB  O3   C9    double    1.200  0.020  1.200
 IDB  N1   C3    single    1.401  0.020  1.401
 IDB  N1   C7    single    1.362  0.020  1.362
 IDB  N1   H1    single    0.860  0.020  1.020
 IDB  C1   C2    aromatic  1.390  0.020  1.390
 IDB  C1   C6    aromatic  1.390  0.020  1.390
 IDB  C1   C9    single    1.500  0.020  1.500
 IDB  C2   C3    aromatic  1.395  0.020  1.395
 IDB  C3   C4    aromatic  1.394  0.020  1.394
 IDB  C4   C5    aromatic  1.386  0.020  1.386
 IDB  C5   C6    aromatic  1.385  0.020  1.385
 IDB  C5   H5    single    0.930  0.020  1.080
 IDB  C7   C8    single    1.508  0.020  1.508
 IDB  C8   C10   single    1.521  0.020  1.521
 IDB  C8   H8C1  single    0.970  0.020  1.090
 IDB  C8   H8C2  single    0.970  0.020  1.090
 IDB  C10  C11   single    1.523  0.020  1.523
 IDB  C10  H101  single    0.970  0.020  1.090
 IDB  C10  H102  single    0.970  0.020  1.090
 IDB  C11  C19   single    1.521  0.020  1.521
 IDB  C11  H111  single    0.970  0.020  1.090
 IDB  C11  H112  single    0.970  0.020  1.090
 IDB  I4   C13   single    2.098  0.020  2.098
 IDB  I5   C15   single    2.095  0.020  2.095
 IDB  I6   C17   single    2.099  0.020  2.099
 IDB  O4   C18   double    1.215  0.020  1.215
 IDB  O5   C20   single    1.317  0.020  1.317
 IDB  O5   HA    single    0.850  0.020  0.980
 IDB  O6   C20   double    1.200  0.020  1.200
 IDB  N2   C14   single    1.401  0.020  1.401
 IDB  N2   C18   single    1.362  0.020  1.362
 IDB  N2   HB    single    0.860  0.020  1.020
 IDB  C12  C13   aromatic  1.390  0.020  1.390
 IDB  C12  C17   aromatic  1.390  0.020  1.390
 IDB  C12  C20   single    1.501  0.020  1.501
 IDB  C13  C14   aromatic  1.395  0.020  1.395
 IDB  C14  C15   aromatic  1.394  0.020  1.394
 IDB  C15  C16   aromatic  1.386  0.020  1.386
 IDB  C16  C17   aromatic  1.385  0.020  1.385
 IDB  C16  H16   single    0.930  0.020  1.080
 IDB  C18  C19   single    1.508  0.020  1.508
 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  H2    O2   C9    110.71  3.000
 IDB  H1    N1   C7    119.80  3.000
 IDB  H1    N1   C3    118.44  3.000
 IDB  C7    N1   C3    121.67  3.000
 IDB  C9    C1   C6    120.58  3.000
 IDB  C9    C1   C2    120.74  3.000
 IDB  C6    C1   C2    118.65  3.000
 IDB  C3    C2   C1    121.60  3.000
 IDB  C3    C2   I1    118.76  3.000
 IDB  C1    C2   I1    119.64  3.000
 IDB  C4    C3   C2    117.94  3.000
 IDB  C4    C3   N1    121.10  3.000
 IDB  C2    C3   N1    120.96  3.000
 IDB  C5    C4   C3    121.63  3.000
 IDB  C5    C4   I2    118.65  3.000
 IDB  C3    C4   I2    119.72  3.000
 IDB  H5    C5   C6    120.55  3.000
 IDB  H5    C5   C4    120.47  3.000
 IDB  C6    C5   C4    118.98  3.000
 IDB  C5    C6   C1    121.21  3.000
 IDB  C5    C6   I3    118.30  3.000
 IDB  C1    C6   I3    120.49  3.000
 IDB  C8    C7   N1    114.33  3.000
 IDB  C8    C7   O1    124.08  3.000
 IDB  N1    C7   O1    121.59  3.000
 IDB  H8C2  C8   H8C1  105.69  3.000
 IDB  H8C2  C8   C10   109.94  3.000
 IDB  H8C1  C8   C10   110.41  3.000
 IDB  H8C2  C8   C7    107.10  3.000
 IDB  H8C1  C8   C7    109.83  3.000
 IDB  C10   C8   C7    113.52  3.000
 IDB  H102  C10  H101  106.44  3.000
 IDB  H102  C10  C11   109.65  3.000
 IDB  H101  C10  C11   109.56  3.000
 IDB  H102  C10  C8    109.66  3.000
 IDB  H101  C10  C8    109.91  3.000
 IDB  C11   C10  C8    111.49  3.000
 IDB  H112  C11  H111  106.44  3.000
 IDB  H112  C11  C19   109.89  3.000
 IDB  H111  C11  C19   109.67  3.000
 IDB  H112  C11  C10   109.55  3.000
 IDB  H111  C11  C10   109.66  3.000
 IDB  C19   C11  C10   111.49  3.000
 IDB  HA    O5   C20   110.71  3.000
 IDB  HB    N2   C18   119.81  3.000
 IDB  HB    N2   C14   118.46  3.000
 IDB  C18   N2   C14   121.67  3.000
 IDB  C20   C12  C17   120.58  3.000
 IDB  C20   C12  C13   120.74  3.000
 IDB  C17   C12  C13   118.65  3.000
 IDB  C14   C13  C12   121.61  3.000
 IDB  C14   C13  I4    118.75  3.000
 IDB  C12   C13  I4    119.64  3.000
 IDB  C15   C14  C13   117.93  3.000
 IDB  C15   C14  N2    121.10  3.000
 IDB  C13   C14  N2    120.96  3.000
 IDB  C16   C15  C14   121.62  3.000
 IDB  C16   C15  I5    118.65  3.000
 IDB  C14   C15  I5    119.72  3.000
 IDB  H16   C16  C17   120.53  3.000
 IDB  H16   C16  C15   120.49  3.000
 IDB  C17   C16  C15   118.98  3.000
 IDB  C16   C17  C12   121.21  3.000
 IDB  C16   C17  I6    118.30  3.000
 IDB  C12   C17  I6    120.49  3.000
 IDB  C19   C18  N2    114.33  3.000
 IDB  C19   C18  O4    124.07  3.000
 IDB  N2    C18  O4    121.59  3.000
 IDB  H192  C19  H191  105.69  3.000
 IDB  H192  C19  C18   109.86  3.000
 IDB  H191  C19  C18   107.08  3.000
 IDB  H192  C19  C11   110.40  3.000
 IDB  H191  C19  C11   109.95  3.000
 IDB  C18   C19  C11   113.52  3.000
 IDB  C1    C9   O3    122.87  3.000
 IDB  C1    C9   O2    111.24  3.000
 IDB  O3    C9   O2    125.89  3.000
 IDB  C12   C20  O6    122.84  3.000
 IDB  C12   C20  O5    111.27  3.000
 IDB  O6    C20  O5    125.89  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  CONST_45  H2   O2   C9   C1    180.00   0.0  0
 IDB  CONST_46  HA   O5   C20  C12   180.00   0.0  0
 IDB  Var_01    C2   C1   C9   O2     89.76  30.0  2
 IDB  Var_02    C13  C12  C20  O5     89.81  30.0  2
 IDB  Var_03    C10  C8   C7   O1     25.60  30.0  3
 IDB  Var_04    C11  C10  C8   C7   -178.27  30.0  3
 IDB  Var_05    C19  C11  C10  C8   -179.64  30.0  3
 IDB  Var_06    C18  C19  C11  C10  -178.34  30.0  3
 IDB  Var_07    O4   C18  C19  C11    25.77  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  HA   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  C20  0.020
 IDB  plan-3  I4   0.020
 IDB  plan-3  I5   0.020
 IDB  plan-3  I6   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  H2   0.020
 IDB  plan-6  C9   0.020

