# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:24:11 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-1,5-bis(oxidanyl)-1,5-bis(oxidanylidene)pentan-2-yl]sulfamoylamino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](N[S](=O)(=O)N[C@@H](CCC(O)=O)C(O)=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
 LDK  LDK  '(2~{S})-2-[[(2~{S})-1,5-bis(oxidanyl)-1,5-bis(oxidanylidene)pentan-2-yl]sulfamoylamino]pentanedioic acid'  ligand  35  23  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LDK
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
 LDK  OE1  O  O      0  -0.604  23.4657  48.5892  41.4246
 LDK  CD   C  C      0   0.411  23.9604  47.9813  42.3951
 LDK  OE2  O  OC    -1  -0.624  25.1428  48.0515  42.7906
 LDK  CG   C  CH2    0  -0.589  23.0455  47.0308  43.1960
 LDK  CB   C  CH2    0  -0.433  21.5668  47.1065  42.8553
 LDK  CA   C  CH1    0  -0.160  20.7204  46.0734  43.5954
 LDK  C    C  C      0   0.402  20.8544  46.2493  45.1292
 LDK  OXT  O  OC    -1  -0.608  21.3872  45.3050  45.7447
 LDK  O    O  O      0  -0.605  20.4596  47.3319  45.6014
 LDK  N    N  NC1    0  -0.796  19.3343  46.2609  43.1462
 LDK  SAW  S  S      0   1.488  18.2540  45.0711  43.5030
 LDK  OAE  O  OS     0  -0.674  17.9279  45.1728  44.9181
 LDK  OAF  O  OS     0  -0.685  18.6754  43.7580  43.0222
 LDK  NAP  N  NC1    0  -0.761  16.9344  45.4989  42.6317
 LDK  CAV  C  CH1    0  -0.193  16.6974  45.0133  41.2706
 LDK  CAT  C  C      0   0.436  17.7400  45.4160  40.1992
 LDK  OAJ  O  OC    -1  -0.597  18.6018  46.2775  40.4957
 LDK  OAD  O  O      0  -0.581  17.6102  44.8465  39.1059
 LDK  CAN  C  CH2    0  -0.430  15.2943  45.4596  40.8440
 LDK  CAL  C  CH2    0  -0.590  15.1150  46.9627  40.6701
 LDK  CAR  C  C      0   0.412  13.7215  47.3825  40.1519
 LDK  OAH  O  O      0  -0.606  13.1193  46.5701  39.4211
 LDK  OAB  O  OC    -1  -0.616  13.3283  48.5196  40.4810
 LDK  H2   H  HCH2   0   0.218  23.2020  47.2322  44.2596
 LDK  H3   H  HCH2   0   0.215  23.4058  46.0061  43.0431
 LDK  H4   H  HCH2   0   0.206  21.1773  48.1017  43.0843
 LDK  H5   H  HCH2   0   0.209  21.4365  46.9636  41.7790
 LDK  H6   H  HCH1   0   0.197  21.0856  45.0746  43.3222
 LDK  H8   H  HNC1   0   0.422  19.2440  46.4140  42.1261
 LDK  H9   H  HNC1   0   0.406  16.6511  46.4550  42.8110
 LDK  H10  H  HCH1   0   0.253  16.6804  43.9225  41.3190
 LDK  H12  H  HCH2   0   0.220  14.5759  45.0844  41.5787
 LDK  H13  H  HCH2   0   0.227  15.0620  44.9590  39.9054
 LDK  H14  H  HCH2   0   0.228  15.8536  47.3427  39.9536
 LDK  H15  H  HCH2   0   0.203  15.3116  47.4991  41.6030

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
 LDK  OAD  CAT  deloc   1.240  0.020  1.240
 LDK  OAH  CAR  deloc   1.248  0.020  1.248
 LDK  OAJ  CAT  deloc   1.254  0.020  1.254
 LDK  CAR  OAB  deloc   1.247  0.020  1.247
 LDK  CAR  CAL  single  1.545  0.020  1.545
 LDK  CAT  CAV  single  1.548  0.020  1.548
 LDK  CAL  CAN  single  1.524  0.020  1.524
 LDK  CAN  CAV  single  1.533  0.020  1.533
 LDK  CAV  NAP  single  1.464  0.020  1.464
 LDK  OAF  SAW  double  1.461  0.020  1.461
 LDK  NAP  SAW  single  1.638  0.020  1.638
 LDK  OE1  CD   deloc   1.247  0.020  1.247
 LDK  CG   CB   single  1.519  0.020  1.519
 LDK  CG   CD   single  1.543  0.020  1.543
 LDK  N    SAW  single  1.646  0.020  1.646
 LDK  N    CA   single  1.469  0.020  1.469
 LDK  CB   CA   single  1.527  0.020  1.527
 LDK  CD   OE2  deloc   1.249  0.020  1.249
 LDK  SAW  OAE  double  1.456  0.020  1.456
 LDK  CA   C    single  1.550  0.020  1.550
 LDK  C    O    deloc   1.245  0.020  1.245
 LDK  C    OXT  deloc   1.247  0.020  1.247
 LDK  CG   H2   single  0.970  0.020  1.090
 LDK  CG   H3   single  0.970  0.020  1.090
 LDK  CB   H4   single  0.970  0.020  1.090
 LDK  CB   H5   single  0.970  0.020  1.090
 LDK  CA   H6   single  0.970  0.020  1.090
 LDK  N    H8   single  0.890  0.020  1.040
 LDK  NAP  H9   single  0.890  0.020  1.040
 LDK  CAV  H10  single  0.970  0.020  1.090
 LDK  CAN  H12  single  0.970  0.020  1.090
 LDK  CAN  H13  single  0.970  0.020  1.090
 LDK  CAL  H14  single  0.970  0.020  1.090
 LDK  CAL  H15  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
 LDK  CG   CD   OE2  115.57  3.000
 LDK  OE2  CD   OE1  126.48  3.000
 LDK  CG   CD   OE1  117.95  3.000
 LDK  H3   CG   H2   105.10  3.000
 LDK  H3   CG   CB   109.57  3.000
 LDK  H2   CG   CB   110.37  3.000
 LDK  H3   CG   CD   107.95  3.000
 LDK  H2   CG   CD   107.85  3.000
 LDK  CB   CG   CD   115.47  3.000
 LDK  H5   CB   H4   106.42  3.000
 LDK  H5   CB   CA   108.82  3.000
 LDK  H4   CB   CA   108.48  3.000
 LDK  H5   CB   CG   109.27  3.000
 LDK  H4   CB   CG   110.19  3.000
 LDK  CA   CB   CG   113.40  3.000
 LDK  H6   CA   N    110.73  3.000
 LDK  H6   CA   C    108.71  3.000
 LDK  N    CA   C    111.70  3.000
 LDK  H6   CA   CB   108.09  3.000
 LDK  C    CA   CB   110.79  3.000
 LDK  N    CA   CB   106.77  3.000
 LDK  O    C    OXT  127.35  3.000
 LDK  OXT  C    CA   116.08  3.000
 LDK  O    C    CA   116.53  3.000
 LDK  H8   N    SAW  105.25  3.000
 LDK  H8   N    CA   113.73  3.000
 LDK  SAW  N    CA   117.43  3.000
 LDK  NAP  SAW  OAF  106.98  3.000
 LDK  NAP  SAW  OAE  108.57  3.000
 LDK  OAF  SAW  OAE  116.58  3.000
 LDK  OAE  SAW  N    107.89  3.000
 LDK  NAP  SAW  N    102.98  3.000
 LDK  OAF  SAW  N    112.90  3.000
 LDK  H9   NAP  CAV  115.60  3.000
 LDK  H9   NAP  SAW  112.18  3.000
 LDK  CAV  NAP  SAW  122.56  3.000
 LDK  H10  CAV  CAN  106.79  3.000
 LDK  H10  CAV  CAT  107.52  3.000
 LDK  CAN  CAV  CAT  110.37  3.000
 LDK  H10  CAV  NAP  107.01  3.000
 LDK  CAN  CAV  NAP  108.07  3.000
 LDK  CAT  CAV  NAP  116.61  3.000
 LDK  OAD  CAT  OAJ  126.59  3.000
 LDK  OAJ  CAT  CAV  118.55  3.000
 LDK  OAD  CAT  CAV  114.86  3.000
 LDK  H13  CAN  H12  106.33  3.000
 LDK  H13  CAN  CAL  109.27  3.000
 LDK  H12  CAN  CAL  109.74  3.000
 LDK  H13  CAN  CAV  107.54  3.000
 LDK  H12  CAN  CAV  108.32  3.000
 LDK  CAL  CAN  CAV  115.25  3.000
 LDK  H15  CAL  H14  105.44  3.000
 LDK  H15  CAL  CAR  108.35  3.000
 LDK  H14  CAL  CAR  107.11  3.000
 LDK  H15  CAL  CAN  111.42  3.000
 LDK  H14  CAL  CAN  109.70  3.000
 LDK  CAR  CAL  CAN  114.36  3.000
 LDK  OAB  CAR  OAH  126.59  3.000
 LDK  OAB  CAR  CAL  116.33  3.000
 LDK  OAH  CAR  CAL  117.06  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
 LDK  Var_01  CB   CG   CD   OE1   -9.66  30.0  2
 LDK  Var_02  CA   CB   CG   CD   175.53  30.0  3
 LDK  Var_03  OAF  SAW  N    CA   -55.29  30.0  3
 LDK  Var_04  CAV  NAP  SAW  N     91.64  30.0  1
 LDK  Var_05  CAR  CAL  CAN  CAV  176.23  30.0  1
 LDK  Var_06  OAH  CAR  CAL  CAN  -29.47  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
 LDK  chir_01  CA   N    CB   C    negativ
 LDK  chir_02  CAV  NAP  CAT  CAN  positiv

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
 LDK  plan-1  OE1  0.020
 LDK  plan-1  CD   0.020
 LDK  plan-1  OE2  0.020
 LDK  plan-1  CG   0.020
 LDK  plan-2  CA   0.020
 LDK  plan-2  C    0.020
 LDK  plan-2  OXT  0.020
 LDK  plan-2  O    0.020
 LDK  plan-3  CAV  0.020
 LDK  plan-3  CAT  0.020
 LDK  plan-3  OAJ  0.020
 LDK  plan-3  OAD  0.020
 LDK  plan-4  CAL  0.020
 LDK  plan-4  CAR  0.020
 LDK  plan-4  OAH  0.020
 LDK  plan-4  OAB  0.020

