# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 23:15:12 2021
#   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  39  23  .  2022-03-22  2022-11-17
;
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  -0.440  24.0191  48.5167  41.9058
 LDK  CD   C  C     0   0.561  24.1200  48.0659  43.0190
 LDK  OE2  O  OH1   0  -0.594  25.1923  48.2416  43.7822
 LDK  CG   C  CH2   0  -0.598  23.0712  47.2471  43.7214
 LDK  CB   C  CH2   0  -0.476  21.8243  47.0530  42.8740
 LDK  CA   C  CH1   0  -0.156  20.8175  46.0875  43.5084
 LDK  C    C  C     0   0.548  20.3393  46.6355  44.8450
 LDK  OXT  O  OH1   0  -0.586  20.9742  46.0698  45.8595
 LDK  O    O  O     0  -0.428  19.5266  47.5141  44.9578
 LDK  N    N  NC1   0  -0.767  19.6781  45.9883  42.6099
 LDK  SAW  S  S     0   1.532  18.6297  44.7354  42.8076
 LDK  OAE  O  OS    0  -0.650  18.5983  44.5184  44.2437
 LDK  OAF  O  OS    0  -0.650  18.9096  43.5976  41.9466
 LDK  NAP  N  NC1   0  -0.773  17.2255  45.3542  42.2717
 LDK  CAV  C  CH1   0  -0.170  16.5068  44.8128  41.1402
 LDK  CAT  C  C     0   0.543  17.2394  44.9392  39.8131
 LDK  OAJ  O  OH1   0  -0.589  18.1957  45.8541  39.8212
 LDK  OAD  O  O     0  -0.431  16.9376  44.2854  38.8488
 LDK  CAN  C  CH2   0  -0.471  15.1245  45.4694  41.0413
 LDK  CAL  C  CH2   0  -0.602  15.1461  46.9505  40.6911
 LDK  CAR  C  C     0   0.564  13.7665  47.5538  40.6855
 LDK  OAH  O  O     0  -0.439  12.7453  46.9498  40.8969
 LDK  OAB  O  OH1   0  -0.594  13.8027  48.8524  40.4113
 LDK  H1   H  HOH1  0   0.481  25.8509  48.7738  43.3115
 LDK  H2   H  HCH2  0   0.291  22.8450  47.7446  44.6681
 LDK  H3   H  HCH2  0   0.293  23.5140  46.2834  43.9908
 LDK  H4   H  HCH2  0   0.265  21.3346  48.0108  42.6866
 LDK  H5   H  HCH2  0   0.275  22.1031  46.6359  41.9044
 LDK  H6   H  HCH1  0   0.289  21.3144  45.1244  43.6619
 LDK  H7   H  HOH1  0   0.485  20.6998  46.4761  46.6960
 LDK  H8   H  HNC1  0   0.424  19.8730  46.1922  41.6358
 LDK  H9   H  HNC1  0   0.431  16.9620  46.2493  42.6601
 LDK  H10  H  HCH1  0   0.321  16.3327  43.7468  41.2951
 LDK  H11  H  HOH1  0   0.490  18.6195  45.9054  38.9502
 LDK  H12  H  HCH2  0   0.280  14.6195  45.3081  41.9947
 LDK  H13  H  HCH2  0   0.278  14.5564  44.9198  40.2907
 LDK  H14  H  HCH2  0   0.295  15.5766  47.1212  39.6999
 LDK  H15  H  HCH2  0   0.285  15.7603  47.5360  41.3810
 LDK  H16  H  HOH1  0   0.482  12.9035  49.2132  40.3996

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  double  1.204  0.020  1.204
 LDK  OAH  CAR  double  1.205  0.020  1.205
 LDK  OAJ  CAT  single  1.324  0.020  1.324
 LDK  CAR  OAB  single  1.328  0.020  1.328
 LDK  CAR  CAL  single  1.506  0.020  1.506
 LDK  CAT  CAV  single  1.521  0.020  1.521
 LDK  CAL  CAN  single  1.522  0.020  1.522
 LDK  CAN  CAV  single  1.534  0.020  1.534
 LDK  CAV  NAP  single  1.446  0.020  1.446
 LDK  OAF  SAW  double  1.454  0.020  1.454
 LDK  NAP  SAW  single  1.625  0.020  1.625
 LDK  OE1  CD   double  1.205  0.020  1.205
 LDK  CG   CB   single  1.520  0.020  1.520
 LDK  CG   CD   single  1.505  0.020  1.505
 LDK  N    SAW  single  1.646  0.020  1.646
 LDK  N    CA   single  1.454  0.020  1.454
 LDK  CB   CA   single  1.532  0.020  1.532
 LDK  CD   OE2  single  1.328  0.020  1.328
 LDK  SAW  OAE  double  1.453  0.020  1.453
 LDK  CA   C    single  1.522  0.020  1.522
 LDK  C    O    double  1.202  0.020  1.202
 LDK  C    OXT  single  1.324  0.020  1.324
 LDK  OE2  H1   single  0.850  0.020  0.980
 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  OXT  H7   single  0.850  0.020  0.980
 LDK  N    H8   single  0.890  0.020  1.040
 LDK  NAP  H9   single  0.860  0.020  1.020
 LDK  CAV  H10  single  0.970  0.020  1.090
 LDK  OAJ  H11  single  0.850  0.020  0.980
 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
 LDK  OAB  H16  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
 LDK  CG   CD   OE2  111.50  3.000
 LDK  OE2  CD   OE1  123.30  3.000
 LDK  CG   CD   OE1  125.20  3.000
 LDK  H1   OE2  CD   110.02  3.000
 LDK  H3   CG   H2   105.75  3.000
 LDK  H3   CG   CB   110.90  3.000
 LDK  H2   CG   CB   111.79  3.000
 LDK  H3   CG   CD   108.19  3.000
 LDK  H2   CG   CD   107.50  3.000
 LDK  CB   CG   CD   112.40  3.000
 LDK  H5   CB   H4   107.29  3.000
 LDK  H5   CB   CA   107.15  3.000
 LDK  H4   CB   CA   109.21  3.000
 LDK  H5   CB   CG   109.54  3.000
 LDK  H4   CB   CG   110.58  3.000
 LDK  CA   CB   CG   112.87  3.000
 LDK  H6   CA   N    112.48  3.000
 LDK  H6   CA   C    109.65  3.000
 LDK  N    CA   C    108.72  3.000
 LDK  H6   CA   CB   108.31  3.000
 LDK  C    CA   CB   110.07  3.000
 LDK  N    CA   CB   107.57  3.000
 LDK  O    C    OXT  124.38  3.000
 LDK  OXT  C    CA   111.63  3.000
 LDK  O    C    CA   123.92  3.000
 LDK  H7   OXT  C    110.27  3.000
 LDK  H8   N    SAW  113.01  3.000
 LDK  H8   N    CA   115.41  3.000
 LDK  SAW  N    CA   118.47  3.000
 LDK  NAP  SAW  OAF  105.60  3.000
 LDK  NAP  SAW  OAE  111.35  3.000
 LDK  OAF  SAW  OAE  118.21  3.000
 LDK  OAE  SAW  N    104.26  3.000
 LDK  NAP  SAW  N    102.76  3.000
 LDK  OAF  SAW  N    113.70  3.000
 LDK  H9   NAP  CAV  120.19  3.000
 LDK  H9   NAP  SAW  115.83  3.000
 LDK  CAV  NAP  SAW  123.02  3.000
 LDK  H10  CAV  CAN  106.47  3.000
 LDK  H10  CAV  CAT  106.37  3.000
 LDK  CAN  CAV  CAT  110.01  3.000
 LDK  H10  CAV  NAP  109.52  3.000
 LDK  CAN  CAV  NAP  109.77  3.000
 LDK  CAT  CAV  NAP  114.35  3.000
 LDK  OAD  CAT  OAJ  124.17  3.000
 LDK  OAJ  CAT  CAV  113.58  3.000
 LDK  OAD  CAT  CAV  122.22  3.000
 LDK  H11  OAJ  CAT  110.29  3.000
 LDK  H13  CAN  H12  106.62  3.000
 LDK  H13  CAN  CAL  109.85  3.000
 LDK  H12  CAN  CAL  110.58  3.000
 LDK  H13  CAN  CAV  107.36  3.000
 LDK  H12  CAN  CAV  107.31  3.000
 LDK  CAL  CAN  CAV  114.75  3.000
 LDK  H15  CAL  H14  105.49  3.000
 LDK  H15  CAL  CAR  107.60  3.000
 LDK  H14  CAL  CAR  107.14  3.000
 LDK  H15  CAL  CAN  112.57  3.000
 LDK  H14  CAL  CAN  111.46  3.000
 LDK  CAR  CAL  CAN  112.19  3.000
 LDK  OAB  CAR  OAH  123.33  3.000
 LDK  OAB  CAR  CAL  111.57  3.000
 LDK  OAH  CAR  CAL  125.09  3.000
 LDK  H16  OAB  CAR  109.97  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  CONST_01  H1   OE2  CD   OE1     0.00   0.0  0
 LDK  CONST_02  H7   OXT  C    CA    180.00   0.0  0
 LDK  CONST_03  H11  OAJ  CAT  CAV   180.00   0.0  0
 LDK  CONST_04  H16  OAB  CAR  CAL   180.00   0.0  0
 LDK  Var_01    CB   CG   CD   OE1    -0.85  30.0  2
 LDK  Var_02    CA   CB   CG   CD    173.28  30.0  3
 LDK  Var_03    OAF  SAW  N    CA    -95.47  30.0  3
 LDK  Var_04    CAV  NAP  SAW  N     118.28  30.0  1
 LDK  Var_05    CAR  CAL  CAN  CAV  -176.76  30.0  1
 LDK  Var_06    OAH  CAR  CAL  CAN    -1.77  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-1  H1   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-2  H7   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-3  H11  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
 LDK  plan-4  H16  0.020

