# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:23:12 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-{[4-(5-methyl-3-oxohex-4-en-1-yl)phenyl]amino}-5-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CC(=O)CCc1ccc(NC(=O)CCCC(O)=O)cc1
#
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
 DIK  DIK  '5-{[4-(5-methyl-3-oxohex-4-en-1-yl)phenyl]amino}-5-oxopentanoic acid'  ligand  46  23  .  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_DIK
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
 DIK  C1    C  CH3   0  -0.721  -8.5781  -0.6180   0.3346
 DIK  C2    C  C     0   0.156  -7.5501  -1.3993  -0.4271
 DIK  C3    C  C1    0  -0.386  -6.2435  -1.0881  -0.5038
 DIK  C4    C  C     0   0.377  -5.5802   0.0578   0.1290
 DIK  O1    O  O     0  -0.427  -6.1683   0.9363   0.7336
 DIK  C5    C  CH2   0  -0.561  -4.0761   0.0803  -0.0264
 DIK  C6    C  CH2   0  -0.506  -3.3911   1.2775   0.6218
 DIK  C7    C  CR6   0   0.115  -1.9013   1.2259   0.4289
 DIK  C8    C  CR16  0  -0.302  -1.0722   0.6048   1.3557
 DIK  C9    C  CR16  0  -0.300   0.3029   0.5180   1.1811
 DIK  C10   C  CR16  0  -0.298  -1.3008   1.7671  -0.7052
 DIK  C11   C  CR16  0  -0.334   0.0666   1.6910  -0.8989
 DIK  C12   C  CR6   0   0.351   0.8902   1.0668   0.0410
 DIK  N1    N  NH1   0  -0.747   2.2624   1.0554  -0.2334
 DIK  C13   C  C     0   0.559   3.2767   0.4638   0.4473
 DIK  O2    O  O     0  -0.471   3.1186  -0.2182   1.4444
 DIK  C14   C  CH2   0  -0.593   4.6472   0.7580  -0.1251
 DIK  C15   C  CH2   0  -0.420   5.6330  -0.3859   0.0653
 DIK  C16   C  CH2   0  -0.582   7.0090   0.0078  -0.4458
 DIK  C17   C  C     0   0.551   8.0418  -1.0727  -0.2850
 DIK  O3    O  O     0  -0.444   7.8447  -2.1573   0.2028
 DIK  O4    O  OH1   0  -0.597   9.2288  -0.6915  -0.7489
 DIK  H1    H  HCH3  0   0.255  -8.8007   0.3241  -0.1694
 DIK  H1A   H  HCH3  0   0.241  -9.5086  -1.1795   0.4081
 DIK  H1B   H  HCH3  0   0.254  -8.2465  -0.3662   1.3396
 DIK  C18   C  CH3   0  -0.725  -8.0713  -2.6035  -1.1433
 DIK  H3    H  H     0   0.244  -5.5966  -1.7406  -1.0811
 DIK  H5    H  HCH2  0   0.273  -3.6793  -0.8567   0.3807
 DIK  H5A   H  HCH2  0   0.272  -3.8459   0.0393  -1.0973
 DIK  H6    H  HCH2  0   0.247  -3.7876   2.2009   0.1944
 DIK  H6A   H  HCH2  0   0.247  -3.6251   1.3025   1.6882
 DIK  H8    H  HCR6  0   0.248  -1.5039   0.1757   2.2525
 DIK  H9    H  HCR6  0   0.276   0.8987   0.0301   1.9346
 DIK  H10   H  HCR6  0   0.250  -1.9082   2.2632  -1.4533
 DIK  H11   H  HCR6  0   0.267   0.5023   2.1254  -1.7911
 DIK  HN1   H  HNH1  0   0.414   2.5282   1.5648  -1.0623
 DIK  H14   H  HCH2  0   0.260   4.5739   1.0213  -1.1831
 DIK  H14A  H  HCH2  0   0.279   5.0183   1.6558   0.3827
 DIK  H15   H  HCH2  0   0.242   5.6912  -0.6515   1.1209
 DIK  H15A  H  HCH2  0   0.242   5.2762  -1.2712  -0.4654
 DIK  H16   H  HCH2  0   0.280   6.9674   0.2853  -1.5037
 DIK  H16A  H  HCH2  0   0.280   7.3687   0.9013   0.0755
 DIK  HO4   H  HOH1  0   0.479   9.8757  -1.4022  -0.6263
 DIK  H21   H  HCH3  0   0.254  -8.8608  -2.3134  -1.8412
 DIK  H22   H  HCH3  0   0.247  -7.2984  -3.1341  -1.6961
 DIK  H23   H  HCH3  0   0.253  -8.5319  -3.2949  -0.4337

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
 DIK  C1   C2    single    1.499  0.020  1.499
 DIK  C1   H1    single    0.970  0.020  1.090
 DIK  C1   H1A   single    0.970  0.020  1.090
 DIK  C1   H1B   single    0.970  0.020  1.090
 DIK  C2   C3    double    1.345  0.020  1.345
 DIK  C2   C18   single    1.495  0.020  1.495
 DIK  C3   C4    single    1.467  0.020  1.467
 DIK  C3   H3    single    0.930  0.020  1.080
 DIK  C4   O1    double    1.218  0.020  1.218
 DIK  C4   C5    single    1.512  0.020  1.512
 DIK  C5   H5    single    0.970  0.020  1.090
 DIK  C5   H5A   single    0.970  0.020  1.090
 DIK  C6   C5    single    1.524  0.020  1.524
 DIK  C6   C7    single    1.503  0.020  1.503
 DIK  C6   H6    single    0.970  0.020  1.090
 DIK  C6   H6A   single    0.970  0.020  1.090
 DIK  C7   C10   aromatic  1.393  0.020  1.393
 DIK  C8   C7    aromatic  1.390  0.020  1.390
 DIK  C8   C9    aromatic  1.389  0.020  1.389
 DIK  C8   H8    single    0.930  0.020  1.080
 DIK  C9   C12   aromatic  1.395  0.020  1.395
 DIK  C9   H9    single    0.930  0.020  1.080
 DIK  C10  C11   aromatic  1.383  0.020  1.383
 DIK  C10  H10   single    0.930  0.020  1.080
 DIK  C11  H11   single    0.930  0.020  1.080
 DIK  C12  C11   aromatic  1.397  0.020  1.397
 DIK  C12  N1    single    1.399  0.020  1.399
 DIK  N1   HN1   single    0.860  0.020  1.020
 DIK  C13  N1    single    1.357  0.020  1.357
 DIK  C13  C14   single    1.514  0.020  1.514
 DIK  O2   C13   double    1.218  0.020  1.218
 DIK  C14  C15   single    1.522  0.020  1.522
 DIK  C14  H14   single    0.970  0.020  1.090
 DIK  C14  H14A  single    0.970  0.020  1.090
 DIK  C15  C16   single    1.520  0.020  1.520
 DIK  C15  H15   single    0.970  0.020  1.090
 DIK  C15  H15A  single    0.970  0.020  1.090
 DIK  C16  C17   single    1.503  0.020  1.503
 DIK  C16  H16   single    0.970  0.020  1.090
 DIK  C16  H16A  single    0.970  0.020  1.090
 DIK  C17  O3    double    1.205  0.020  1.205
 DIK  C17  O4    single    1.330  0.020  1.330
 DIK  O4   HO4   single    0.850  0.020  0.980
 DIK  C18  H21   single    0.970  0.020  1.090
 DIK  C18  H22   single    0.970  0.020  1.090
 DIK  C18  H23   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
 DIK  H1B   C1   H1A  108.51  3.000
 DIK  H1B   C1   H1   106.80  3.000
 DIK  H1A   C1   H1   107.57  3.000
 DIK  H1B   C1   C2   112.39  3.000
 DIK  H1A   C1   C2   110.58  3.000
 DIK  H1    C1   C2   110.79  3.000
 DIK  C18   C2   C3   119.84  3.000
 DIK  C18   C2   C1   115.09  3.000
 DIK  C3    C2   C1   125.06  3.000
 DIK  H3    C3   C4   115.43  3.000
 DIK  H3    C3   C2   118.05  3.000
 DIK  C4    C3   C2   126.52  3.000
 DIK  C5    C4   O1   121.37  3.000
 DIK  C5    C4   C3   114.64  3.000
 DIK  O1    C4   C3   123.99  3.000
 DIK  H5A   C5   H5   104.77  3.000
 DIK  H5A   C5   C6   110.53  3.000
 DIK  H5    C5   C6   110.54  3.000
 DIK  C6    C5   C4   114.52  3.000
 DIK  H5A   C5   C4   107.98  3.000
 DIK  H5    C5   C4   108.01  3.000
 DIK  H6A   C6   H6   106.57  3.000
 DIK  H6A   C6   C7   109.78  3.000
 DIK  H6    C6   C7   109.80  3.000
 DIK  H6A   C6   C5   109.70  3.000
 DIK  H6    C6   C5   109.54  3.000
 DIK  C7    C6   C5   111.34  3.000
 DIK  C10   C7   C8   117.35  3.000
 DIK  C8    C7   C6   121.40  3.000
 DIK  C10   C7   C6   121.23  3.000
 DIK  H8    C8   C9   118.27  3.000
 DIK  H8    C8   C7   119.40  3.000
 DIK  C9    C8   C7   122.33  3.000
 DIK  H9    C9   C12  121.13  3.000
 DIK  H9    C9   C8   119.21  3.000
 DIK  C12   C9   C8   119.66  3.000
 DIK  H10   C10  C11  118.85  3.000
 DIK  H10   C10  C7   119.89  3.000
 DIK  C11   C10  C7   121.26  3.000
 DIK  H11   C11  C12  119.73  3.000
 DIK  C12   C11  C10  120.88  3.000
 DIK  H11   C11  C10  119.38  3.000
 DIK  N1    C12  C11  116.74  3.000
 DIK  N1    C12  C9   124.73  3.000
 DIK  C11   C12  C9   118.52  3.000
 DIK  HN1   N1   C13  115.81  3.000
 DIK  C13   N1   C12  129.65  3.000
 DIK  HN1   N1   C12  114.55  3.000
 DIK  C14   C13  O2   122.38  3.000
 DIK  O2    C13  N1   123.88  3.000
 DIK  C14   C13  N1   113.72  3.000
 DIK  H14A  C14  H14  105.90  3.000
 DIK  H14A  C14  C15  109.78  3.000
 DIK  H14   C14  C15  110.22  3.000
 DIK  H14A  C14  C13  106.89  3.000
 DIK  H14   C14  C13  110.62  3.000
 DIK  C15   C14  C13  113.14  3.000
 DIK  H15A  C15  H15  106.89  3.000
 DIK  H15A  C15  C16  110.02  3.000
 DIK  H15   C15  C16  109.91  3.000
 DIK  H15A  C15  C14  109.68  3.000
 DIK  H15   C15  C14  109.80  3.000
 DIK  C16   C15  C14  110.46  3.000
 DIK  H16A  C16  H16  105.41  3.000
 DIK  H16A  C16  C17  108.05  3.000
 DIK  H16   C16  C17  108.16  3.000
 DIK  H16A  C16  C15  110.40  3.000
 DIK  H16   C16  C15  110.88  3.000
 DIK  C17   C16  C15  113.57  3.000
 DIK  O4    C17  O3   123.01  3.000
 DIK  O4    C17  C16  111.70  3.000
 DIK  O3    C17  C16  125.28  3.000
 DIK  HO4   O4   C17  109.97  3.000
 DIK  H23   C18  H22  108.70  3.000
 DIK  H23   C18  H21  106.15  3.000
 DIK  H22   C18  H21  108.54  3.000
 DIK  H23   C18  C2   110.22  3.000
 DIK  H22   C18  C2   112.86  3.000
 DIK  H21   C18  C2   110.12  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
 DIK  CONST_01  C12  C11  C10  C7      0.00   0.0  0
 DIK  CONST_02  C12  C9   C8   C7      0.00   0.0  0
 DIK  CONST_03  C11  C10  C7   C8      0.00   0.0  0
 DIK  CONST_04  C11  C12  C9   C8      0.00   0.0  0
 DIK  CONST_05  C10  C7   C8   C9      0.00   0.0  0
 DIK  CONST_06  C10  C11  C12  C9      0.00   0.0  0
 DIK  CONST_07  C11  C10  C7   C6    180.00   0.0  0
 DIK  CONST_08  C9   C8   C7   C6    180.00   0.0  0
 DIK  CONST_09  N1   C12  C9   C8    180.00   0.0  0
 DIK  CONST_10  N1   C12  C11  C10   180.00   0.0  0
 DIK  CONST_11  H11  C11  C10  C7    180.00   0.0  0
 DIK  CONST_12  H9   C9   C8   C7    180.00   0.0  0
 DIK  CONST_13  H10  C10  C7   C8    180.00   0.0  0
 DIK  CONST_14  H8   C8   C7   C10   180.00   0.0  0
 DIK  CONST_15  C13  N1   C12  C9      0.00   0.0  0
 DIK  CONST_16  C13  N1   C12  C11   180.00   0.0  0
 DIK  CONST_17  HN1  N1   C12  C9    180.00   0.0  0
 DIK  CONST_18  C14  C13  N1   C12   180.00   0.0  0
 DIK  CONST_19  O2   C13  N1   C12     0.00   0.0  0
 DIK  CONST_20  HO4  O4   C17  C16   180.00   0.0  0
 DIK  Var_01    C10  C7   C6   C5     87.41  30.0  2
 DIK  Var_02    C7   C6   C5   C4    179.80  30.0  2
 DIK  Var_03    C4   C3   C2   C1     -0.14   0.0  2
 DIK  Var_04    O1   C4   C3   C2     -5.66  30.0  2
 DIK  Var_05    C6   C5   C4   C3    179.52  30.0  3
 DIK  Var_06    C15  C14  C13  N1   -148.30  30.0  3
 DIK  Var_07    C16  C15  C14  C13  -176.22  30.0  3
 DIK  Var_08    C17  C16  C15  C14   179.72  30.0  3
 DIK  Var_09    O3   C17  C16  C15    -0.41  30.0  3
 DIK  Var_10    H21  C18  C2   C1     57.64  30.0  3
 DIK  Var_11    H1   C1   C2   C3     72.36  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
 DIK  plan-1  C6   0.020
 DIK  plan-1  C7   0.020
 DIK  plan-1  C8   0.020
 DIK  plan-1  C9   0.020
 DIK  plan-1  C10  0.020
 DIK  plan-1  C11  0.020
 DIK  plan-1  C12  0.020
 DIK  plan-1  N1   0.020
 DIK  plan-1  H8   0.020
 DIK  plan-1  H9   0.020
 DIK  plan-1  H10  0.020
 DIK  plan-1  H11  0.020
 DIK  plan-2  C12  0.020
 DIK  plan-2  N1   0.020
 DIK  plan-2  C13  0.020
 DIK  plan-2  O2   0.020
 DIK  plan-2  C14  0.020
 DIK  plan-2  HN1  0.020
 DIK  plan-3  C3   0.020
 DIK  plan-3  C4   0.020
 DIK  plan-3  O1   0.020
 DIK  plan-3  C5   0.020
 DIK  plan-4  C16  0.020
 DIK  plan-4  C17  0.020
 DIK  plan-4  O3   0.020
 DIK  plan-4  O4   0.020
 DIK  plan-4  HO4  0.020
 DIK  plan-5  C1   0.020
 DIK  plan-5  C2   0.020
 DIK  plan-5  C3   0.020
 DIK  plan-5  C4   0.020
 DIK  plan-5  C18  0.020
 DIK  plan-5  H3   0.020

