# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 13:56:49 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  30  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   0.556   1.6281  -4.0573  -2.6964
 DSB  O2    O  O     0  -0.444   2.0960  -4.4175  -1.6451
 DSB  C2    C  CH2   0  -0.583   1.1158  -2.6758  -2.9949
 DSB  C3    C  CH2   0  -0.553   1.2131  -1.7434  -1.8040
 DSB  C5    C  CH2   0  -0.554   0.6693   0.5696  -0.8891
 DSB  O1    O  OH1   0  -0.597   1.5053  -4.8610  -3.7481
 DSB  C6    C  CH2   0  -0.555   0.1770   1.9673  -1.2056
 DSB  C8    C  CH2   0  -0.553  -0.2567   4.3070  -0.2925
 DSB  C9    C  CH2   0  -0.582  -0.4803   5.1358   0.9574
 DSB  C10   C  C     0   0.555  -0.8321   6.5653   0.6535
 DSB  O11   O  OH1   0  -0.597  -1.0573   7.2598   1.7643
 DSB  O12   O  O     0  -0.444  -0.9057   7.0472  -0.4494
 DSB  C7    C  C     0   0.414   0.1118   2.8734  -0.0024
 DSB  C4    C  C     0   0.412   0.6898  -0.3556  -2.0792
 DSB  O4    O  O     0  -0.408   0.3126  -0.0117  -3.1764
 DSB  O7    O  O     0  -0.408   0.3390   2.4800   1.1191
 DSB  H21   H  HCH2  0   0.288   1.6764  -2.2837  -3.8476
 DSB  H22   H  HCH2  0   0.287   0.0818  -2.7636  -3.3387
 DSB  H31   H  HCH2  0   0.282   2.2496  -1.6431  -1.4670
 DSB  H32   H  HCH2  0   0.277   0.6711  -2.1443  -0.9427
 DSB  H51   H  HCH2  0   0.277   1.6772   0.5946  -0.4636
 DSB  H52   H  HCH2  0   0.279   0.0497   0.1017  -0.1180
 DSB  H11   H  HOH1  0   0.479   1.8416  -5.7431  -3.5305
 DSB  H61   H  HCH2  0   0.280  -0.8256   1.9383  -1.6442
 DSB  H62   H  HCH2  0   0.276   0.8030   2.4476  -1.9634
 DSB  H81   H  HCH2  0   0.283   0.5454   4.7320  -0.9041
 DSB  H82   H  HCH2  0   0.276  -1.1411   4.3138  -0.9357
 DSB  H91   H  HCH2  0   0.287  -1.2798   4.7097   1.5692
 DSB  H92   H  HCH2  0   0.288   0.4090   5.1329   1.5931
 DSB  H111  H  HOH1  0   0.479  -1.2819   8.1757   1.5420

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    double  1.206  0.020  1.206
 DSB  C1   C2    single  1.503  0.020  1.503
 DSB  C1   O1    single  1.329  0.020  1.329
 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  1.508  0.020  1.508
 DSB  C3   H31   single  0.970  0.020  1.090
 DSB  C3   H32   single  0.970  0.020  1.090
 DSB  C5   C6    single  1.515  0.020  1.515
 DSB  C5   C4    single  1.508  0.020  1.508
 DSB  C5   H51   single  0.970  0.020  1.090
 DSB  C5   H52   single  0.970  0.020  1.090
 DSB  O1   H11   single  0.850  0.020  0.980
 DSB  C6   C7    single  1.508  0.020  1.508
 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  1.508  0.020  1.508
 DSB  C8   H81   single  0.970  0.020  1.090
 DSB  C8   H82   single  0.970  0.020  1.090
 DSB  C9   C10   single  1.503  0.020  1.503
 DSB  C9   H91   single  0.970  0.020  1.090
 DSB  C9   H92   single  0.970  0.020  1.090
 DSB  C10  O11   single  1.329  0.020  1.329
 DSB  C10  O12   double  1.206  0.020  1.206
 DSB  O11  H111  single  0.850  0.020  0.980
 DSB  C7   O7    double  1.210  0.020  1.210
 DSB  C4   O4    double  1.210  0.020  1.210

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   111.53  3.000
 DSB  O1    C1   O2   123.03  3.000
 DSB  C2    C1   O2   125.44  3.000
 DSB  H22   C2   H21  105.58  3.000
 DSB  H22   C2   C3   110.93  3.000
 DSB  H21   C2   C3   111.06  3.000
 DSB  H22   C2   C1   108.12  3.000
 DSB  H21   C2   C1   108.04  3.000
 DSB  C3    C2   C1   112.80  3.000
 DSB  H32   C3   H31  105.09  3.000
 DSB  H32   C3   C4   108.00  3.000
 DSB  H31   C3   C4   107.48  3.000
 DSB  H32   C3   C2   111.19  3.000
 DSB  H31   C3   C2   111.05  3.000
 DSB  C4    C3   C2   113.60  3.000
 DSB  H52   C5   H51  104.91  3.000
 DSB  H52   C5   C4   107.55  3.000
 DSB  H51   C5   C4   107.96  3.000
 DSB  H52   C5   C6   110.96  3.000
 DSB  H51   C5   C6   111.06  3.000
 DSB  C4    C5   C6   113.93  3.000
 DSB  H11   O1   C1   109.92  3.000
 DSB  H62   C6   H61  104.96  3.000
 DSB  H62   C6   C7   108.28  3.000
 DSB  H61   C6   C7   107.22  3.000
 DSB  H62   C6   C5   111.33  3.000
 DSB  H61   C6   C5   110.91  3.000
 DSB  C7    C6   C5   113.68  3.000
 DSB  H82   C8   H81  105.16  3.000
 DSB  H82   C8   C7   108.46  3.000
 DSB  H81   C8   C7   107.31  3.000
 DSB  H82   C8   C9   111.23  3.000
 DSB  H81   C8   C9   110.88  3.000
 DSB  C7    C8   C9   113.39  3.000
 DSB  H92   C9   H91  105.58  3.000
 DSB  H92   C9   C10  108.09  3.000
 DSB  H91   C9   C10  108.22  3.000
 DSB  H92   C9   C8   110.97  3.000
 DSB  H91   C9   C8   110.86  3.000
 DSB  C10   C9   C8   112.81  3.000
 DSB  O12   C10  O11  123.04  3.000
 DSB  O12   C10  C9   125.39  3.000
 DSB  O11   C10  C9   111.57  3.000
 DSB  H111  O11  C10  109.96  3.000
 DSB  O7    C7   C8   122.22  3.000
 DSB  O7    C7   C6   122.42  3.000
 DSB  C8    C7   C6   115.36  3.000
 DSB  O4    C4   C5   122.49  3.000
 DSB  O4    C4   C3   122.34  3.000
 DSB  C5    C4   C3   115.17  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  CONST_01  H11   O1   C1   O2      0.00   0.0  0
 DSB  CONST_02  H111  O11  C10  C9    180.00   0.0  0
 DSB  Var_01    C4    C3   C2   C1   -179.37  30.0  3
 DSB  Var_02    C3    C2   C1   O2     -1.31  30.0  3
 DSB  Var_03    C5    C4   C3   C2    175.41  30.0  3
 DSB  Var_04    C6    C5   C4   C3    178.31  30.0  1
 DSB  Var_05    C8    C7   C6   C5    174.84  30.0  3
 DSB  Var_06    C9    C8   C7   C6    172.73  30.0  1
 DSB  Var_07    O11   C10  C9   C8    178.34  30.0  3
 DSB  Var_08    C7    C8   C9   C10   179.38  30.0  1
 DSB  Var_09    C4    C5   C6   C7    177.92  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-3  H11   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
 DSB  plan-4  H111  0.020

