# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 12:47:41 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4,7-dioxodecanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)CCC(=O)CCC(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
 DSB  DSB  '4,7-dioxodecanedioic acid'  ligand  28  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DSB
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
 DSB  C1   C  C      0   0.417   1.8168  -4.0574  -2.7586
 DSB  O2   O  O      0  -0.608   2.4758  -4.2074  -1.7110
 DSB  C2   C  CH2    0  -0.586   1.1112  -2.7072  -2.9829
 DSB  C3   C  CH2    0  -0.547   1.2373  -1.7206  -1.8387
 DSB  C5   C  CH2    0  -0.554   0.5189   0.5220  -0.8663
 DSB  O1   O  OC    -1  -0.630   1.6707  -4.9006  -3.6679
 DSB  C6   C  CH2    0  -0.553   0.0696   1.9363  -1.1746
 DSB  C8   C  CH2    0  -0.545  -0.2428   4.2893  -0.2395
 DSB  C9   C  CH2    0  -0.585  -0.5185   5.1415   0.9841
 DSB  C10  C  C      0   0.417  -0.7447   6.6375   0.6980
 DSB  O11  O  OC    -1  -0.631  -0.9372   7.3557   1.7013
 DSB  O12  O  O      0  -0.607  -0.7252   7.0167  -0.4893
 DSB  C7   C  C      0   0.410  -0.0299   2.8249   0.0425
 DSB  C4   C  C      0   0.411   0.5874  -0.3822  -2.0734
 DSB  O4   O  O      0  -0.417   0.1489  -0.0454  -3.1516
 DSB  O7   O  O      0  -0.417   0.0541   2.3800   1.1664
 DSB  H21  H  HCH2   0   0.230   1.5109  -2.2681  -3.9023
 DSB  H22  H  HCH2   0   0.228   0.0556  -2.9023  -3.1965
 DSB  H31  H  HCH2   0   0.261   2.2910  -1.5231  -1.6122
 DSB  H32  H  HCH2   0   0.252   0.8355  -2.1364  -0.9094
 DSB  H51  H  HCH2   0   0.266   1.4966   0.5174  -0.3756
 DSB  H52  H  HCH2   0   0.275  -0.1573   0.0469  -0.1480
 DSB  H61  H  HCH2   0   0.275  -0.9159   1.9355  -1.6521
 DSB  H62  H  HCH2   0   0.266   0.7333   2.4142  -1.9008
 DSB  H81  H  HCH2   0   0.260   0.6514   4.6433  -0.7645
 DSB  H82  H  HCH2   0   0.253  -1.0466   4.3815  -0.9761
 DSB  H91  H  HCH2   0   0.229  -1.3984   4.7609   1.5124
 DSB  H92  H  HCH2   0   0.229   0.3046   5.0505   1.6987

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
 DSB  C1   O2   deloc   1.247  0.020  1.247
 DSB  C1   C2   single  1.540  0.020  1.540
 DSB  C1   O1   deloc   1.249  0.020  1.249
 DSB  C2   C3   single  1.516  0.020  1.516
 DSB  C2   H21  single  0.970  0.020  1.090
 DSB  C2   H22  single  0.970  0.020  1.090
 DSB  C3   C4   single  1.506  0.020  1.506
 DSB  C3   H31  single  0.970  0.020  1.090
 DSB  C3   H32  single  0.970  0.020  1.090
 DSB  C5   C6   single  1.516  0.020  1.516
 DSB  C5   C4   single  1.510  0.020  1.510
 DSB  C5   H51  single  0.970  0.020  1.090
 DSB  C5   H52  single  0.970  0.020  1.090
 DSB  C6   C7   single  1.510  0.020  1.510
 DSB  C6   H61  single  0.970  0.020  1.090
 DSB  C6   H62  single  0.970  0.020  1.090
 DSB  C8   C9   single  1.516  0.020  1.516
 DSB  C8   C7   single  1.506  0.020  1.506
 DSB  C8   H81  single  0.970  0.020  1.090
 DSB  C8   H82  single  0.970  0.020  1.090
 DSB  C9   C10  single  1.540  0.020  1.540
 DSB  C9   H91  single  0.970  0.020  1.090
 DSB  C9   H92  single  0.970  0.020  1.090
 DSB  C10  O11  deloc   1.249  0.020  1.249
 DSB  C10  O12  deloc   1.247  0.020  1.247
 DSB  C7   O7   double  1.212  0.020  1.212
 DSB  C4   O4   double  1.212  0.020  1.212

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
 DSB  O1   C1   C2   115.62  3.000
 DSB  O1   C1   O2   126.34  3.000
 DSB  C2   C1   O2   118.04  3.000
 DSB  H22  C2   H21  105.06  3.000
 DSB  H22  C2   C3   110.09  3.000
 DSB  H21  C2   C3   110.03  3.000
 DSB  H22  C2   C1   108.30  3.000
 DSB  H21  C2   C1   107.86  3.000
 DSB  C3   C2   C1   115.00  3.000
 DSB  H32  C3   H31  104.23  3.000
 DSB  H32  C3   C4   108.15  3.000
 DSB  H31  C3   C4   106.68  3.000
 DSB  H32  C3   C2   111.29  3.000
 DSB  H31  C3   C2   110.69  3.000
 DSB  C4   C3   C2   115.14  3.000
 DSB  H52  C5   H51  104.82  3.000
 DSB  H52  C5   C4   107.02  3.000
 DSB  H51  C5   C4   108.40  3.000
 DSB  H52  C5   C6   110.81  3.000
 DSB  H51  C5   C6   111.11  3.000
 DSB  C4   C5   C6   114.18  3.000
 DSB  H62  C6   H61  104.88  3.000
 DSB  H62  C6   C7   108.54  3.000
 DSB  H61  C6   C7   107.01  3.000
 DSB  H62  C6   C5   111.28  3.000
 DSB  H61  C6   C5   110.78  3.000
 DSB  C7   C6   C5   113.87  3.000
 DSB  H82  C8   H81  104.46  3.000
 DSB  H82  C8   C7   108.16  3.000
 DSB  H81  C8   C7   106.77  3.000
 DSB  H82  C8   C9   111.24  3.000
 DSB  H81  C8   C9   110.70  3.000
 DSB  C7   C8   C9   114.89  3.000
 DSB  H92  C9   H91  105.11  3.000
 DSB  H92  C9   C10  108.23  3.000
 DSB  H91  C9   C10  108.02  3.000
 DSB  H92  C9   C8   110.09  3.000
 DSB  H91  C9   C8   109.89  3.000
 DSB  C10  C9   C8   115.01  3.000
 DSB  O12  C10  O11  126.35  3.000
 DSB  O12  C10  C9   118.05  3.000
 DSB  O11  C10  C9   115.60  3.000
 DSB  O7   C7   C8   122.71  3.000
 DSB  O7   C7   C6   121.79  3.000
 DSB  C8   C7   C6   115.50  3.000
 DSB  O4   C4   C5   121.91  3.000
 DSB  O4   C4   C3   122.80  3.000
 DSB  C5   C4   C3   115.29  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
 DSB  Var_01  C4   C3   C2  C1    178.05  30.0  3
 DSB  Var_02  C3   C2   C1  O2     -3.43  30.0  3
 DSB  Var_03  C5   C4   C3  C2    170.76  30.0  3
 DSB  Var_04  C6   C5   C4  C3    170.61  30.0  1
 DSB  Var_05  C8   C7   C6  C5    170.01  30.0  3
 DSB  Var_06  C9   C8   C7  C6    172.49  30.0  1
 DSB  Var_07  O11  C10  C9  C8   -178.15  30.0  3
 DSB  Var_08  C7   C8   C9  C10  -179.66  30.0  1
 DSB  Var_09  C4   C5   C6  C7    178.54  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
 DSB  plan-1  C6   0.020
 DSB  plan-1  C8   0.020
 DSB  plan-1  C7   0.020
 DSB  plan-1  O7   0.020
 DSB  plan-2  C3   0.020
 DSB  plan-2  C5   0.020
 DSB  plan-2  C4   0.020
 DSB  plan-2  O4   0.020
 DSB  plan-3  C1   0.020
 DSB  plan-3  O2   0.020
 DSB  plan-3  C2   0.020
 DSB  plan-3  O1   0.020
 DSB  plan-4  C9   0.020
 DSB  plan-4  C10  0.020
 DSB  plan-4  O11  0.020
 DSB  plan-4  O12  0.020

