# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:21:17 2021
#   Inital geometry file: a 98 line input string
#   Ligand name: 3,5,6,8-tetrakis(oxidanyl)-2-pentanoyl-naphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(=O)C1=C(O)C(=O)c2c(O)c(O)cc(O)c2C1=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
 OOH  OOH  3,5,6,8-tetrakis(oxidanyl)-2-pentanoyl-naphthalene-1,4-dione  ligand  36  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OOH
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
 OOH  O6   O  OH1   0  -0.596  23.2052  16.2884  6.0773
 OOH  C    C  CR6   0   0.335  24.4665  16.6791  5.9202
 OOH  O    O  OH1   0  -0.590  24.7599  14.6118  4.8635
 OOH  C1   C  CR16  0  -0.465  24.9643  17.8797  6.3540
 OOH  C2   C  CR6   0   0.380  26.3144  18.2244  6.1484
 OOH  C3   C  CR66  0  -0.232  27.1614  17.3358  5.4927
 OOH  O1   O  O     0  -0.441  27.1579  14.0617  3.9463
 OOH  C4   C  CR66  0  -0.163  26.6454  16.0901  5.0463
 OOH  O5   O  OH1   0  -0.614  26.7165  19.4039  6.5987
 OOH  C14  C  CH3   0  -0.673  32.6583  19.7914  5.3264
 OOH  C13  C  CH2   0  -0.425  32.8646  19.8107  3.8181
 OOH  C6   C  CR6   0   0.323  27.5175  15.1576  4.3680
 OOH  C5   C  CR6   0   0.295  25.3169  15.7486  5.2484
 OOH  C8   C  CR6   0  -0.314  29.4149  16.7284  4.5892
 OOH  C7   C  CR6   0   0.340  28.9406  15.5412  4.1686
 OOH  C9   C  CR6   0   0.462  28.5532  17.6792  5.2756
 OOH  O2   O  O     0  -0.474  29.0235  18.7562  5.6661
 OOH  C10  C  C     0   0.402  30.8650  17.0875  4.4029
 OOH  C11  C  CH2   0  -0.579  31.1609  17.9805  3.2355
 OOH  C12  C  CH2   0  -0.433  32.5954  18.4856  3.1088
 OOH  O3   O  O     0  -0.366  31.6969  16.6091  5.1332
 OOH  O4   O  OH1   0  -0.578  29.7055  14.6665  3.5449
 OOH  H1   H  HOH1  0   0.491  22.6876  16.9676  6.5277
 OOH  H2   H  HOH1  0   0.491  25.4364  14.0624  4.4192
 OOH  H3   H  HCR6  0   0.307  24.3183  18.5838  6.8665
 OOH  H4   H  HOH1  0   0.484  27.6750  19.4922  6.3831
 OOH  H5   H  HCH3  0   0.225  32.9288  20.7530  5.7647
 OOH  H6   H  HCH3  0   0.224  31.6193  19.5958  5.5930
 OOH  H7   H  HCH3  0   0.216  33.2723  19.0249  5.8010
 OOH  H8   H  HCH2  0   0.223  33.8937  20.1097  3.6017
 OOH  H9   H  HCH2  0   0.214  32.2291  20.5849  3.3768
 OOH  H10  H  HCH2  0   0.277  30.4433  18.8077  3.2375
 OOH  H11  H  HCH2  0   0.293  30.8859  17.3853  2.3550
 OOH  H12  H  HCH2  0   0.229  33.2902  17.7222  3.4681
 OOH  H13  H  HCH2  0   0.239  32.8141  18.6170  2.0473
 OOH  H14  H  HOH1  0   0.491  29.1835  13.8843  3.3016

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
 OOH  O4   C7   single    1.319  0.020  1.319
 OOH  O1   C6   double    1.228  0.020  1.228
 OOH  C11  C12  single    1.526  0.020  1.526
 OOH  C11  C10  single    1.499  0.020  1.499
 OOH  C13  C12  single    1.527  0.020  1.527
 OOH  C13  C14  single    1.522  0.020  1.522
 OOH  C7   C6   single    1.487  0.020  1.487
 OOH  C7   C8   double    1.346  0.020  1.346
 OOH  C6   C4   single    1.446  0.020  1.446
 OOH  O    C5   single    1.323  0.020  1.323
 OOH  C10  C8   single    1.505  0.020  1.505
 OOH  C10  O3   double    1.206  0.020  1.206
 OOH  C8   C9   single    1.455  0.020  1.455
 OOH  C4   C5   aromatic  1.386  0.020  1.386
 OOH  C4   C3   aromatic  1.420  0.020  1.420
 OOH  C5   C    aromatic  1.428  0.020  1.428
 OOH  C9   C3   single    1.450  0.020  1.450
 OOH  C9   O2   double    1.238  0.020  1.238
 OOH  C3   C2   aromatic  1.392  0.020  1.392
 OOH  C    O6   single    1.330  0.020  1.330
 OOH  C    C1   aromatic  1.370  0.020  1.370
 OOH  C2   C1   aromatic  1.409  0.020  1.409
 OOH  C2   O5   single    1.325  0.020  1.325
 OOH  O6   H1   single    0.850  0.020  0.980
 OOH  O    H2   single    0.850  0.020  0.980
 OOH  C1   H3   single    0.930  0.020  1.080
 OOH  O5   H4   single    0.850  0.020  0.980
 OOH  C14  H5   single    0.970  0.020  1.090
 OOH  C14  H6   single    0.970  0.020  1.090
 OOH  C14  H7   single    0.970  0.020  1.090
 OOH  C13  H8   single    0.970  0.020  1.090
 OOH  C13  H9   single    0.970  0.020  1.090
 OOH  C11  H10  single    0.970  0.020  1.090
 OOH  C11  H11  single    0.970  0.020  1.090
 OOH  C12  H12  single    0.970  0.020  1.090
 OOH  C12  H13  single    0.970  0.020  1.090
 OOH  O4   H14  single    0.850  0.020  0.980

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
 OOH  H1   O6   C    110.91  3.000
 OOH  C5   C    C1   120.22  3.000
 OOH  C1   C    O6   124.37  3.000
 OOH  C5   C    O6   115.40  3.000
 OOH  H2   O    C5   108.88  3.000
 OOH  H3   C1   C2   118.76  3.000
 OOH  H3   C1   C    120.15  3.000
 OOH  C2   C1   C    121.09  3.000
 OOH  O5   C2   C3   122.95  3.000
 OOH  O5   C2   C1   117.33  3.000
 OOH  C3   C2   C1   119.72  3.000
 OOH  C9   C3   C4   120.62  3.000
 OOH  C9   C3   C2   120.23  3.000
 OOH  C4   C3   C2   119.15  3.000
 OOH  C5   C4   C6   119.18  3.000
 OOH  C5   C4   C3   121.22  3.000
 OOH  C6   C4   C3   119.61  3.000
 OOH  H4   O5   C2   107.47  3.000
 OOH  H7   C14  H6   107.70  3.000
 OOH  H7   C14  H5   107.76  3.000
 OOH  H6   C14  H5   107.22  3.000
 OOH  H7   C14  C13  111.33  3.000
 OOH  H6   C14  C13  111.94  3.000
 OOH  H5   C14  C13  110.69  3.000
 OOH  H9   C13  H8   105.86  3.000
 OOH  H9   C13  C12  108.91  3.000
 OOH  H8   C13  C12  108.14  3.000
 OOH  H9   C13  C14  109.26  3.000
 OOH  H8   C13  C14  109.09  3.000
 OOH  C12  C13  C14  115.17  3.000
 OOH  C7   C6   C4   118.28  3.000
 OOH  C4   C6   O1   124.06  3.000
 OOH  C7   C6   O1   117.66  3.000
 OOH  C4   C5   O    124.93  3.000
 OOH  C4   C5   C    118.60  3.000
 OOH  O    C5   C    116.48  3.000
 OOH  C10  C8   C9   118.22  3.000
 OOH  C9   C8   C7   121.00  3.000
 OOH  C10  C8   C7   120.75  3.000
 OOH  O4   C7   C8   121.90  3.000
 OOH  C8   C7   C6   121.52  3.000
 OOH  O4   C7   C6   116.57  3.000
 OOH  O2   C9   C8   119.48  3.000
 OOH  O2   C9   C3   121.55  3.000
 OOH  C8   C9   C3   118.97  3.000
 OOH  O3   C10  C11  124.86  3.000
 OOH  O3   C10  C8   119.67  3.000
 OOH  C11  C10  C8   115.37  3.000
 OOH  H11  C11  H10  104.29  3.000
 OOH  H11  C11  C12  110.39  3.000
 OOH  H10  C11  C12  111.48  3.000
 OOH  H11  C11  C10  104.60  3.000
 OOH  H10  C11  C10  108.61  3.000
 OOH  C12  C11  C10  116.57  3.000
 OOH  H13  C12  H12  106.04  3.000
 OOH  H13  C12  C11  107.99  3.000
 OOH  H12  C12  C11  109.82  3.000
 OOH  H13  C12  C13  108.17  3.000
 OOH  H12  C12  C13  109.96  3.000
 OOH  C11  C12  C13  114.48  3.000
 OOH  H14  O4   C7   109.93  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
 OOH  CONST_01  C3   C4   C5   C      0.00   0.0  0
 OOH  CONST_02  C3   C2   C1   C      0.00   0.0  0
 OOH  CONST_03  C4   C5   C    C1     0.00   0.0  0
 OOH  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 OOH  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 OOH  CONST_06  C5   C    C1   C2     0.00   0.0  0
 OOH  CONST_07  C4   C5   C    O6   180.00   0.0  0
 OOH  CONST_08  C2   C1   C    O6   180.00   0.0  0
 OOH  CONST_09  O5   C2   C1   C    180.00   0.0  0
 OOH  CONST_10  C6   C4   C5   O      0.00   0.0  0
 OOH  CONST_11  C3   C4   C5   O    180.00   0.0  0
 OOH  CONST_12  C1   C    C5   O    180.00   0.0  0
 OOH  CONST_13  O5   C2   C3   C4   180.00   0.0  0
 OOH  CONST_14  C9   C3   C2   O5     0.00   0.0  0
 OOH  CONST_15  H3   C1   C2   C3   180.00   0.0  0
 OOH  Var_01    C11  C10  C8   C7    99.83  30.0  2
 OOH  Var_02    C12  C11  C10  C8   173.53  30.0  2
 OOH  Var_03    C11  C12  C13  C14   61.74  30.0  3
 OOH  Var_04    C10  C11  C12  C13  -90.33  30.0  2
 OOH  Var_05    H5   C14  C13  C12  176.51  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
 OOH  plan-1  O6   0.020
 OOH  plan-1  C    0.020
 OOH  plan-1  O    0.020
 OOH  plan-1  C1   0.020
 OOH  plan-1  C2   0.020
 OOH  plan-1  C3   0.020
 OOH  plan-1  O1   0.020
 OOH  plan-1  C4   0.020
 OOH  plan-1  O5   0.020
 OOH  plan-1  C6   0.020
 OOH  plan-1  C5   0.020
 OOH  plan-1  C8   0.020
 OOH  plan-1  C7   0.020
 OOH  plan-1  C9   0.020
 OOH  plan-1  O2   0.020
 OOH  plan-1  C10  0.020
 OOH  plan-1  O4   0.020
 OOH  plan-1  H3   0.020
 OOH  plan-2  C8   0.020
 OOH  plan-2  C10  0.020
 OOH  plan-2  C11  0.020
 OOH  plan-2  O3   0.020

