# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 04:31:05 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: N-[(3-hydroxypyridin-2-yl)carbonyl]-S-(pyridin-2-ylmethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CSCc1ccccn1)NC(=O)c2ncccc2O
#
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
 6YT  6YT  N-[(3-hydroxypyridin-2-yl)carbonyl]-S-(pyridin-2-ylmethyl)-L-cysteine  ligand  38  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6YT
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
 6YT  CAK   C  CR16  0  -0.318  -4.0773  -1.3802   0.9611
 6YT  CAF   C  CR16  0  -0.150  -4.9401  -2.4118   0.6309
 6YT  CAE   C  CR16  0  -0.324  -5.9117  -2.1854  -0.3330
 6YT  CAH   C  CR16  0  -0.075  -5.9713  -0.9309  -0.9199
 6YT  NAN   N  N     0  -0.408  -5.1475   0.0634  -0.6084
 6YT  CAU   C  CR6   0   0.240  -4.2194  -0.1539   0.3177
 6YT  CAL   C  CH2   0  -0.615  -3.2875   0.9786   0.6308
 6YT  SAQ   S  S2    0   0.001  -1.7744   0.7473  -0.3567
 6YT  CB    C  CH2   0  -0.583  -0.7602   2.0824   0.3425
 6YT  CA    C  CH1   0  -0.179   0.6557   1.9918  -0.2227
 6YT  C     C  C     0   0.548   1.4969   3.1171   0.3730
 6YT  OXT   O  OH1   0  -0.584   1.3021   4.2504  -0.2784
 6YT  O     O  O     0  -0.423   2.2127   2.9904   1.3294
 6YT  N     N  NH1   0  -0.644   1.2340   0.7160   0.0913
 6YT  CAS   C  C     0   0.621   2.4213   0.3503  -0.3891
 6YT  OAB   O  O     0  -0.525   3.0853   1.0741  -1.1406
 6YT  CAV   C  CR6   0  -0.053   2.9114  -0.9877   0.0201
 6YT  NAO   N  N     0  -0.418   2.1354  -1.7040   0.8306
 6YT  CAI   C  CR16  0  -0.091   2.5322  -2.8973   1.2183
 6YT  CAG   C  CR16  0  -0.298   3.7487  -3.4430   0.8050
 6YT  CAJ   C  CR16  0  -0.242   4.5644  -2.7158  -0.0323
 6YT  CAT   C  CR6   0   0.347   4.1504  -1.4467  -0.4477
 6YT  OAD   O  OH1   0  -0.622   4.9351  -0.7389  -1.2547
 6YT  HAK   H  HCR6  0   0.272  -3.3049  -1.5166   1.7069
 6YT  HAF   H  HCR6  0   0.276  -4.8569  -3.3745   1.1178
 6YT  HAE   H  HCR6  0   0.273  -6.6084  -2.9588  -0.6249
 6YT  HAH   H  HCR6  0   0.265  -6.7191  -0.7177  -1.6758
 6YT  HAL1  H  HCH2  0   0.292  -3.7495   1.9328   0.3797
 6YT  HAL2  H  HCH2  0   0.290  -3.0157   0.9811   1.6872
 6YT  HB1C  H  HCH2  0   0.306  -1.1930   3.0490   0.0866
 6YT  HB2C  H  HCH2  0   0.291  -0.7430   1.9893   1.4310
 6YT  HA    H  HCH1  0   0.308   0.6142   2.1277  -1.3075
 6YT  H     H  HNH1  0   0.414   0.7665   0.0826   0.7254
 6YT  HB    H  HOH1  0   0.489   1.8063   4.9692   0.1328
 6YT  HAI   H  HCR6  0   0.270   1.8734  -3.4479   1.8782
 6YT  HAG   H  HCR6  0   0.282   4.0428  -4.4270   1.1429
 6YT  HAJ   H  HCR6  0   0.289   5.5145  -3.1085  -0.3719
 6YT  HAD   H  HOH1  0   0.480   4.4798   0.1159  -1.4337

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
 6YT  CAK  CAF   aromatic  1.385  0.020  1.385
 6YT  CAK  CAU   aromatic  1.392  0.020  1.392
 6YT  CAF  CAE   aromatic  1.387  0.020  1.387
 6YT  CAE  CAH   aromatic  1.386  0.020  1.386
 6YT  CAH  NAN   aromatic  1.328  0.020  1.328
 6YT  NAN  CAU   aromatic  1.329  0.020  1.329
 6YT  CAU  CAL   single    1.500  0.020  1.500
 6YT  CAL  SAQ   single    1.822  0.020  1.822
 6YT  SAQ  CB    single    1.817  0.020  1.817
 6YT  CB   CA    single    1.527  0.020  1.527
 6YT  CA   C     single    1.526  0.020  1.526
 6YT  CA   N     single    1.435  0.020  1.435
 6YT  C    OXT   single    1.322  0.020  1.322
 6YT  C    O     double    1.201  0.020  1.201
 6YT  N    CAS   single    1.332  0.020  1.332
 6YT  CAS  OAB   double    1.237  0.020  1.237
 6YT  CAS  CAV   single    1.483  0.020  1.483
 6YT  CAV  NAO   aromatic  1.331  0.020  1.331
 6YT  CAV  CAT   aromatic  1.402  0.020  1.402
 6YT  NAO  CAI   aromatic  1.316  0.020  1.316
 6YT  CAI  CAG   aromatic  1.396  0.020  1.396
 6YT  CAG  CAJ   aromatic  1.377  0.020  1.377
 6YT  CAJ  CAT   aromatic  1.398  0.020  1.398
 6YT  CAT  OAD   single    1.330  0.020  1.330
 6YT  CAK  HAK   single    0.930  0.020  1.080
 6YT  CAF  HAF   single    0.930  0.020  1.080
 6YT  CAE  HAE   single    0.930  0.020  1.080
 6YT  CAH  HAH   single    0.930  0.020  1.080
 6YT  CAL  HAL1  single    0.970  0.020  1.090
 6YT  CAL  HAL2  single    0.970  0.020  1.090
 6YT  CB   HB1C  single    0.970  0.020  1.090
 6YT  CB   HB2C  single    0.970  0.020  1.090
 6YT  CA   HA    single    0.970  0.020  1.090
 6YT  N    H     single    0.860  0.020  1.020
 6YT  OXT  HB    single    0.850  0.020  0.980
 6YT  CAI  HAI   single    0.930  0.020  1.080
 6YT  CAG  HAG   single    0.930  0.020  1.080
 6YT  CAJ  HAJ   single    0.930  0.020  1.080
 6YT  OAD  HAD   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
 6YT  HAK   CAK  CAU   120.15  3.000
 6YT  HAK   CAK  CAF   121.01  3.000
 6YT  CAU   CAK  CAF   118.84  3.000
 6YT  HAF   CAF  CAE   120.78  3.000
 6YT  HAF   CAF  CAK   120.50  3.000
 6YT  CAE   CAF  CAK   118.72  3.000
 6YT  HAE   CAE  CAH   120.35  3.000
 6YT  HAE   CAE  CAF   121.48  3.000
 6YT  CAH   CAE  CAF   118.16  3.000
 6YT  HAH   CAH  NAN   116.36  3.000
 6YT  HAH   CAH  CAE   120.17  3.000
 6YT  NAN   CAH  CAE   123.46  3.000
 6YT  CAU   NAN  CAH   118.31  3.000
 6YT  CAL   CAU  NAN   117.13  3.000
 6YT  CAL   CAU  CAK   120.35  3.000
 6YT  NAN   CAU  CAK   122.51  3.000
 6YT  HAL2  CAL  HAL1  109.08  3.000
 6YT  HAL2  CAL  SAQ   108.56  3.000
 6YT  HAL1  CAL  SAQ   109.78  3.000
 6YT  HAL2  CAL  CAU   111.03  3.000
 6YT  HAL1  CAL  CAU   110.48  3.000
 6YT  SAQ   CAL  CAU   107.88  3.000
 6YT  CB    SAQ  CAL    99.31  3.000
 6YT  HB2C  CB   HB1C  108.41  3.000
 6YT  HB2C  CB   CA    110.43  3.000
 6YT  HB1C  CB   CA    109.51  3.000
 6YT  HB2C  CB   SAQ   109.25  3.000
 6YT  HB1C  CB   SAQ   109.87  3.000
 6YT  CA    CB   SAQ   109.36  3.000
 6YT  HA    CA   N     110.03  3.000
 6YT  HA    CA   C     108.44  3.000
 6YT  N     CA   C     110.35  3.000
 6YT  HA    CA   CB    108.93  3.000
 6YT  N     CA   CB    110.20  3.000
 6YT  C     CA   CB    108.83  3.000
 6YT  O     C    OXT   124.80  3.000
 6YT  O     C    CA    124.16  3.000
 6YT  OXT   C    CA    111.02  3.000
 6YT  HB    OXT  C     110.49  3.000
 6YT  H     N    CAS   117.80  3.000
 6YT  H     N    CA    120.52  3.000
 6YT  CAS   N    CA    121.62  3.000
 6YT  CAV   CAS  OAB   121.22  3.000
 6YT  CAV   CAS  N     116.29  3.000
 6YT  OAB   CAS  N     122.48  3.000
 6YT  CAT   CAV  NAO   122.84  3.000
 6YT  CAT   CAV  CAS   119.71  3.000
 6YT  NAO   CAV  CAS   117.45  3.000
 6YT  CAI   NAO  CAV   119.44  3.000
 6YT  HAI   CAI  CAG   120.79  3.000
 6YT  HAI   CAI  NAO   117.20  3.000
 6YT  CAG   CAI  NAO   122.01  3.000
 6YT  HAG   CAG  CAJ   120.64  3.000
 6YT  HAG   CAG  CAI   120.02  3.000
 6YT  CAJ   CAG  CAI   119.34  3.000
 6YT  HAJ   CAJ  CAT   119.73  3.000
 6YT  HAJ   CAJ  CAG   121.27  3.000
 6YT  CAT   CAJ  CAG   119.00  3.000
 6YT  OAD   CAT  CAJ   119.26  3.000
 6YT  OAD   CAT  CAV   123.36  3.000
 6YT  CAJ   CAT  CAV   117.38  3.000
 6YT  HAD   OAD  CAT   107.43  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
 6YT  CONST_01  CAH  CAE  CAF  CAK    0.00   0.0  0
 6YT  CONST_02  CAH  NAN  CAU  CAK    0.00   0.0  0
 6YT  CONST_03  NAN  CAU  CAK  CAF    0.00   0.0  0
 6YT  CONST_04  NAN  CAH  CAE  CAF    0.00   0.0  0
 6YT  CONST_05  CAU  CAK  CAF  CAE    0.00   0.0  0
 6YT  CONST_06  CAU  NAN  CAH  CAE    0.00   0.0  0
 6YT  CONST_07  CAG  CAI  NAO  CAV    0.00   0.0  0
 6YT  CONST_08  CAG  CAJ  CAT  CAV    0.00   0.0  0
 6YT  CONST_09  CAJ  CAT  CAV  NAO    0.00   0.0  0
 6YT  CONST_10  CAJ  CAG  CAI  NAO    0.00   0.0  0
 6YT  CONST_11  CAT  CAV  NAO  CAI    0.00   0.0  0
 6YT  CONST_12  CAT  CAJ  CAG  CAI    0.00   0.0  0
 6YT  CONST_13  CAL  CAU  CAK  CAF  180.00   0.0  0
 6YT  CONST_14  CAL  CAU  NAN  CAH  180.00   0.0  0
 6YT  CONST_15  CAI  NAO  CAV  CAS  180.00   0.0  0
 6YT  CONST_16  CAJ  CAT  CAV  CAS  180.00   0.0  0
 6YT  CONST_17  OAD  CAT  CAV  NAO  180.00   0.0  0
 6YT  CONST_18  OAD  CAT  CAJ  CAG  180.00   0.0  0
 6YT  CONST_19  HAE  CAE  CAF  CAK  180.00   0.0  0
 6YT  CONST_20  HAH  CAH  CAE  CAF  180.00   0.0  0
 6YT  CONST_21  HAK  CAK  CAF  CAE  180.00   0.0  0
 6YT  CONST_22  HAF  CAF  CAE  CAH  180.00   0.0  0
 6YT  CONST_23  HAI  CAI  NAO  CAV  180.00   0.0  0
 6YT  CONST_24  HAJ  CAJ  CAT  CAV  180.00   0.0  0
 6YT  CONST_25  HAG  CAG  CAI  NAO  180.00   0.0  0
 6YT  CONST_26  CAV  CAS  N    CA   180.00   0.0  0
 6YT  CONST_27  H    N    CAS  CAV    0.00   0.0  0
 6YT  CONST_28  OAB  CAS  N    CA     0.00   0.0  0
 6YT  CONST_29  HB   OXT  C    CA   180.00   0.0  0
 6YT  Var_01    SAQ  CAL  CAU  CAK   82.92  30.0  2
 6YT  Var_02    NAO  CAV  CAS  N     -0.29  30.0  2
 6YT  Var_03    CA   CB   SAQ  CAL  173.29  30.0  3

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
 6YT  chir_01  CA  CB  C  N  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
 6YT  plan-1  CAK  0.020
 6YT  plan-1  CAF  0.020
 6YT  plan-1  CAE  0.020
 6YT  plan-1  CAH  0.020
 6YT  plan-1  NAN  0.020
 6YT  plan-1  CAU  0.020
 6YT  plan-1  CAL  0.020
 6YT  plan-1  HAK  0.020
 6YT  plan-1  HAF  0.020
 6YT  plan-1  HAE  0.020
 6YT  plan-1  HAH  0.020
 6YT  plan-2  CAS  0.020
 6YT  plan-2  CAV  0.020
 6YT  plan-2  NAO  0.020
 6YT  plan-2  CAI  0.020
 6YT  plan-2  CAG  0.020
 6YT  plan-2  CAJ  0.020
 6YT  plan-2  CAT  0.020
 6YT  plan-2  OAD  0.020
 6YT  plan-2  HAI  0.020
 6YT  plan-2  HAG  0.020
 6YT  plan-2  HAJ  0.020
 6YT  plan-3  CA   0.020
 6YT  plan-3  N    0.020
 6YT  plan-3  CAS  0.020
 6YT  plan-3  OAB  0.020
 6YT  plan-3  CAV  0.020
 6YT  plan-3  H    0.020
 6YT  plan-4  CA   0.020
 6YT  plan-4  C    0.020
 6YT  plan-4  OXT  0.020
 6YT  plan-4  O    0.020
 6YT  plan-4  HB   0.020

