# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:45:43 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-[(1R)-1-carboxy-2-(4-hydroxyphenyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1ccc(O)cc1)N2C(=O)c3ccc(cc3C2=O)C(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
 DK2  DK2  '2-[(1R)-1-carboxy-2-(4-hydroxyphenyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid'  ligand  39  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DK2
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
 DK2  O11   O  O     0  -0.390   0.4914   2.1075   1.9120
 DK2  C7    C  CR5   0   0.597   0.0522   1.5172   0.9598
 DK2  C5    C  CR56  0  -0.015  -1.2836   0.8948   0.7918
 DK2  C4    C  CR56  0  -0.011  -1.3235   0.2997  -0.4573
 DK2  C3    C  CR16  0  -0.307  -2.4364  -0.3716  -0.9047
 DK2  C6    C  CR16  0  -0.280  -2.3588   0.8470   1.6498
 DK2  C1    C  CR16  0  -0.244  -3.4947   0.1709   1.2128
 DK2  C2    C  CR6   0  -0.075  -3.5372  -0.4326  -0.0457
 DK2  C23   C  C     0   0.553  -4.7449  -1.1615  -0.5253
 DK2  O24   O  OH1   0  -0.588  -5.7252  -1.1733   0.3607
 DK2  O25   O  O     0  -0.426  -4.8119  -1.6839  -1.6101
 DK2  N8    N  NR5   0  -0.605   0.7361   1.2696  -0.2195
 DK2  C9    C  CR5   0   0.596  -0.0223   0.5361  -1.1237
 DK2  O10   O  O     0  -0.385   0.3368   0.1856  -2.2163
 DK2  C12   C  CH1   0  -0.237   2.1076   1.6465  -0.4428
 DK2  C13   C  C     0   0.571   2.2310   3.1618  -0.3910
 DK2  O14   O  OH1   0  -0.583   3.4916   3.5403  -0.2800
 DK2  O15   O  O     0  -0.423   1.3000   3.9153  -0.4909
 DK2  C16   C  CH2   0  -0.532   3.0791   0.8775   0.4721
 DK2  C17   C  CR6   0   0.107   2.8028  -0.5986   0.4198
 DK2  C18   C  CR16  0  -0.275   3.2032  -1.3619  -0.6752
 DK2  C19   C  CR16  0  -0.323   2.9212  -2.7141  -0.7565
 DK2  C20   C  CR6   0   0.341   2.2165  -3.3402   0.2703
 DK2  O26   O  OH1   0  -0.634   1.9656  -4.6596   0.1468
 DK2  C21   C  CR16  0  -0.367   1.8083  -2.5940   1.3710
 DK2  C22   C  CR16  0  -0.303   2.1019  -1.2387   1.4352
 DK2  H3    H  HCR6  0   0.284  -2.4620  -0.8363  -1.8812
 DK2  H6    H  HCR6  0   0.284  -2.3335   1.3126   2.6254
 DK2  H1    H  HCR6  0   0.291  -4.3510   0.1206   1.8699
 DK2  HO24  H  HOH1  0   0.494  -6.4881  -1.6579   0.0109
 DK2  H12   H  HCH1  0   0.335   2.3349   1.3679  -1.4778
 DK2  HO14  H  HOH1  0   0.491   3.5567   4.5077  -0.2998
 DK2  H161  H  HCH2  0   0.280   4.0949   1.0807   0.1325
 DK2  H162  H  HCH2  0   0.271   3.0053   1.2395   1.4977
 DK2  H18   H  HCR6  0   0.251   3.7524  -0.8941  -1.4844
 DK2  H19   H  HCR6  0   0.262   3.2488  -3.2900  -1.6132
 DK2  HO26  H  HOH1  0   0.473   1.5013  -4.9881   0.9246
 DK2  H21   H  HCR6  0   0.270   1.2639  -3.0650   2.1818
 DK2  H22   H  HCR6  0   0.253   1.7819  -0.6779   2.3058

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
 DK2  O11  C7    double    1.203  0.020  1.203
 DK2  C7   N8    single    1.386  0.020  1.386
 DK2  C7   C5    single    1.483  0.020  1.483
 DK2  C5   C4    aromatic  1.384  0.020  1.384
 DK2  C5   C6    aromatic  1.376  0.020  1.376
 DK2  C4   C9    single    1.481  0.020  1.481
 DK2  C4   C3    aromatic  1.374  0.020  1.374
 DK2  C3   C2    aromatic  1.398  0.020  1.398
 DK2  C3   H3    single    0.930  0.020  1.080
 DK2  C6   C1    aromatic  1.392  0.020  1.392
 DK2  C6   H6    single    0.930  0.020  1.080
 DK2  C1   C2    aromatic  1.396  0.020  1.396
 DK2  C1   H1    single    0.930  0.020  1.080
 DK2  C2   C23   single    1.490  0.020  1.490
 DK2  C23  O25   double    1.206  0.020  1.206
 DK2  C23  O24   single    1.321  0.020  1.321
 DK2  O24  HO24  single    0.850  0.020  0.980
 DK2  N8   C12   single    1.440  0.020  1.440
 DK2  N8   C9    single    1.390  0.020  1.390
 DK2  C9   O10   double    1.202  0.020  1.202
 DK2  C12  C13   single    1.521  0.020  1.521
 DK2  C12  C16   single    1.540  0.020  1.540
 DK2  C12  H12   single    0.970  0.020  1.090
 DK2  C13  O15   double    1.202  0.020  1.202
 DK2  C13  O14   single    1.321  0.020  1.321
 DK2  O14  HO14  single    0.850  0.020  0.980
 DK2  C16  C17   single    1.503  0.020  1.503
 DK2  C16  H161  single    0.970  0.020  1.090
 DK2  C16  H162  single    0.970  0.020  1.090
 DK2  C17  C18   aromatic  1.394  0.020  1.394
 DK2  C17  C22   aromatic  1.390  0.020  1.390
 DK2  C18  C19   aromatic  1.384  0.020  1.384
 DK2  C18  H18   single    0.930  0.020  1.080
 DK2  C19  C20   aromatic  1.394  0.020  1.394
 DK2  C19  H19   single    0.930  0.020  1.080
 DK2  C20  O26   single    1.349  0.020  1.349
 DK2  C20  C21   aromatic  1.391  0.020  1.391
 DK2  O26  HO26  single    0.850  0.020  0.980
 DK2  C21  C22   aromatic  1.388  0.020  1.388
 DK2  C21  H21   single    0.930  0.020  1.080
 DK2  C22  H22   single    0.930  0.020  1.080

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
 DK2  N8    C7   C5    105.85  3.000
 DK2  C5    C7   O11   128.62  3.000
 DK2  N8    C7   O11   125.52  3.000
 DK2  C6    C5   C4    121.67  3.000
 DK2  C6    C5   C7    130.35  3.000
 DK2  C4    C5   C7    107.98  3.000
 DK2  C9    C4   C3    130.01  3.000
 DK2  C3    C4   C5    121.81  3.000
 DK2  C9    C4   C5    108.18  3.000
 DK2  H3    C3   C2    121.16  3.000
 DK2  H3    C3   C4    121.52  3.000
 DK2  C2    C3   C4    117.32  3.000
 DK2  H6    C6   C1    120.76  3.000
 DK2  H6    C6   C5    121.95  3.000
 DK2  C1    C6   C5    117.29  3.000
 DK2  H1    C1   C2    120.25  3.000
 DK2  H1    C1   C6    118.58  3.000
 DK2  C2    C1   C6    121.17  3.000
 DK2  C23   C2   C1    121.75  3.000
 DK2  C23   C2   C3    117.51  3.000
 DK2  C1    C2   C3    120.74  3.000
 DK2  O25   C23  O24   123.92  3.000
 DK2  O24   C23  C2    112.95  3.000
 DK2  O25   C23  C2    123.13  3.000
 DK2  HO24  O24  C23   110.27  3.000
 DK2  C12   N8   C9    123.86  3.000
 DK2  C9    N8   C7    112.26  3.000
 DK2  C12   N8   C7    123.74  3.000
 DK2  O10   C9   N8    125.61  3.000
 DK2  O10   C9   C4    128.67  3.000
 DK2  N8    C9   C4    105.73  3.000
 DK2  H12   C12  C16   107.66  3.000
 DK2  H12   C12  C13   105.59  3.000
 DK2  C16   C12  C13   115.21  3.000
 DK2  H12   C12  N8    106.11  3.000
 DK2  C16   C12  N8    112.21  3.000
 DK2  C13   C12  N8    109.44  3.000
 DK2  O15   C13  O14   124.52  3.000
 DK2  O14   C13  C12   111.45  3.000
 DK2  O15   C13  C12   123.97  3.000
 DK2  HO14  O14  C13   110.38  3.000
 DK2  H162  C16  H161  107.11  3.000
 DK2  H162  C16  C17   110.27  3.000
 DK2  H161  C16  C17   110.10  3.000
 DK2  H162  C16  C12   110.51  3.000
 DK2  H161  C16  C12   108.04  3.000
 DK2  C17   C16  C12   110.72  3.000
 DK2  C22   C17  C18   117.82  3.000
 DK2  C22   C17  C16   121.31  3.000
 DK2  C18   C17  C16   120.83  3.000
 DK2  H18   C18  C19   118.75  3.000
 DK2  H18   C18  C17   119.72  3.000
 DK2  C19   C18  C17   121.53  3.000
 DK2  H19   C19  C20   119.79  3.000
 DK2  H19   C19  C18   120.30  3.000
 DK2  C20   C19  C18   119.91  3.000
 DK2  C21   C20  O26   122.86  3.000
 DK2  C21   C20  C19   119.36  3.000
 DK2  O26   C20  C19   117.78  3.000
 DK2  HO26  O26  C20   110.45  3.000
 DK2  H21   C21  C22   119.72  3.000
 DK2  H21   C21  C20   120.40  3.000
 DK2  C22   C21  C20   119.89  3.000
 DK2  H22   C22  C21   118.68  3.000
 DK2  H22   C22  C17   119.83  3.000
 DK2  C21   C22  C17   121.50  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
 DK2  CONST_01  C2    C3   C4   C5     0.00   0.0  0
 DK2  CONST_02  C2    C1   C6   C5     0.00   0.0  0
 DK2  CONST_03  C1    C6   C5   C4     0.00   0.0  0
 DK2  CONST_04  C1    C2   C3   C4     0.00   0.0  0
 DK2  CONST_05  C6    C5   C4   C3     0.00   0.0  0
 DK2  CONST_06  C6    C1   C2   C3     0.00   0.0  0
 DK2  CONST_07  C20   C19  C18  C17    0.00   0.0  0
 DK2  CONST_08  C20   C21  C22  C17    0.00   0.0  0
 DK2  CONST_09  C21   C22  C17  C18    0.00   0.0  0
 DK2  CONST_10  C21   C20  C19  C18    0.00   0.0  0
 DK2  CONST_11  C22   C17  C18  C19    0.00   0.0  0
 DK2  CONST_12  C22   C21  C20  C19    0.00   0.0  0
 DK2  CONST_13  C9    N8   C7   C5     0.00   0.0  0
 DK2  CONST_14  C23   C2   C3   C4   180.00   0.0  0
 DK2  CONST_15  C23   C2   C1   C6   180.00   0.0  0
 DK2  CONST_16  C19   C18  C17  C16  180.00   0.0  0
 DK2  CONST_17  C21   C22  C17  C16  180.00   0.0  0
 DK2  CONST_18  O26   C20  C19  C18  180.00   0.0  0
 DK2  CONST_19  C22   C21  C20  O26  180.00   0.0  0
 DK2  CONST_20  C9    N8   C7   O11  180.00   0.0  0
 DK2  CONST_21  C12   N8   C7   C5   180.00   0.0  0
 DK2  CONST_22  H6    C6   C5   C7     0.00   0.0  0
 DK2  CONST_23  H3    C3   C4   C5   180.00   0.0  0
 DK2  CONST_24  H1    C1   C6   C5   180.00   0.0  0
 DK2  CONST_25  H19   C19  C18  C17  180.00   0.0  0
 DK2  CONST_26  H21   C21  C22  C17  180.00   0.0  0
 DK2  CONST_27  H22   C22  C17  C18  180.00   0.0  0
 DK2  CONST_28  H18   C18  C19  C20  180.00   0.0  0
 DK2  CONST_29  C12   N8   C7   O11    0.00   0.0  0
 DK2  CONST_30  HO24  O24  C23  C2   180.00   0.0  0
 DK2  CONST_31  HO14  O14  C13  C12  180.00   0.0  0
 DK2  Var_01    O25   C23  C2   C3    -0.52  30.0  2
 DK2  Var_02    C18   C17  C16  C12   76.07  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DK2  chir_01  C12  N8  C13  C16  negativ

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
 DK2  plan-1  C16   0.020
 DK2  plan-1  C17   0.020
 DK2  plan-1  C18   0.020
 DK2  plan-1  C19   0.020
 DK2  plan-1  C20   0.020
 DK2  plan-1  O26   0.020
 DK2  plan-1  C21   0.020
 DK2  plan-1  C22   0.020
 DK2  plan-1  H18   0.020
 DK2  plan-1  H19   0.020
 DK2  plan-1  H21   0.020
 DK2  plan-1  H22   0.020
 DK2  plan-2  O11   0.020
 DK2  plan-2  C7    0.020
 DK2  plan-2  C5    0.020
 DK2  plan-2  C4    0.020
 DK2  plan-2  C3    0.020
 DK2  plan-2  C6    0.020
 DK2  plan-2  C1    0.020
 DK2  plan-2  C2    0.020
 DK2  plan-2  C23   0.020
 DK2  plan-2  N8    0.020
 DK2  plan-2  C9    0.020
 DK2  plan-2  O10   0.020
 DK2  plan-2  C12   0.020
 DK2  plan-2  H3    0.020
 DK2  plan-2  H6    0.020
 DK2  plan-2  H1    0.020
 DK2  plan-3  C2    0.020
 DK2  plan-3  C23   0.020
 DK2  plan-3  O24   0.020
 DK2  plan-3  O25   0.020
 DK2  plan-3  HO24  0.020
 DK2  plan-4  C12   0.020
 DK2  plan-4  C13   0.020
 DK2  plan-4  O14   0.020
 DK2  plan-4  O15   0.020
 DK2  plan-4  HO14  0.020

