# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 04:26:00 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2S,3S)-3-formyl-2-({[(4-nitrophenyl)sulfonyl]amino}methyl)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C=O)[C@@H](CN[S](=O)(=O)c1ccc(cc1)[N+]([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
 TPY  TPY  '(2S,3S)-3-formyl-2-({[(4-nitrophenyl)sulfonyl]amino}methyl)pentanoic acid'  ligand  38  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TPY
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
 TPY  C    C  C1     0   0.186   3.8826   0.7891   1.6659
 TPY  CA   C  CH1    0  -0.337   3.3790   1.0063   0.2678
 TPY  CB   C  CH1    0  -0.423   2.5938  -0.2262  -0.1998
 TPY  CC   C  C      0   0.481   1.9086  -0.0377  -1.5805
 TPY  CD   C  CH2    0  -0.437   4.6133   1.2517  -0.6179
 TPY  CE   C  CH3    0  -0.670   5.3552   2.5399  -0.2869
 TPY  O    O  O      0  -0.377   3.6890   1.5163   2.6094
 TPY  OA   O  OC    -1  -0.609   1.4210  -1.0912  -2.0712
 TPY  OB   O  O      0  -0.556   1.8533   1.0909  -2.0798
 TPY  OC   O  OS     0  -0.657  -0.9463  -3.5280   0.3793
 TPY  OD   O  OS     0  -0.657  -0.4626  -2.2034   2.4664
 TPY  S    S  S      0   1.382  -0.5442  -2.2857   1.0170
 TPY  CK   C  CH2    0  -0.275   1.5224  -0.6254   0.8288
 TPY  CF   C  CR6    0  -0.189  -1.6840  -1.0209   0.4807
 TPY  CG1  C  CR16   0  -0.221  -2.0168  -0.9578  -0.8669
 TPY  CG2  C  CR16   0  -0.230  -2.1936  -0.1114   1.3933
 TPY  CH1  C  CR16   0  -0.257  -2.8798   0.0273  -1.3085
 TPY  CH2  C  CR16   0  -0.254  -3.0590   0.8792   0.9563
 TPY  CI   C  CR6    0   0.268  -3.3891   0.9313  -0.3870
 TPY  NJ   N  N      1   0.333  -4.3039   1.9712  -0.8500
 TPY  OE   O  O     -1  -0.368  -4.6008   1.9804  -2.0196
 TPY  OF   O  O      0  -0.368  -4.7135   2.7644  -0.0380
 TPY  H    H  H      0   0.182   4.5035  -0.1228   1.7780
 TPY  HA   H  HCH1   0   0.246   2.7344   1.8893   0.2548
 TPY  HB   H  HCH1   0   0.254   3.2936  -1.0678  -0.2838
 TPY  HD2  H  HCH2   0   0.221   5.2908   0.3961  -0.5301
 TPY  HD1  H  HCH2   0   0.254   4.2845   1.2806  -1.6553
 TPY  HE3  H  HCH3   0   0.223   5.7850   2.5294   0.7162
 TPY  HE2  H  HCH3   0   0.224   4.6909   3.4036  -0.3504
 TPY  HE1  H  HCH3   0   0.236   6.1748   2.7016  -0.9871
 TPY  HN1  H  HNC1   0   0.423   0.9494  -1.9426  -0.6391
 TPY  HK2  H  HCH2   0   0.241   0.7964   0.1941   0.9205
 TPY  HK1  H  HCH2   0   0.267   1.9617  -0.7769   1.8161
 TPY  HG1  H  HCR6   0   0.298  -1.6149  -1.6646  -1.5800
 TPY  HG2  H  HCR6   0   0.300  -1.9310  -0.1637   2.4402
 TPY  HH1  H  HCR6   0   0.311  -3.1434   0.0792  -2.3543
 TPY  HH2  H  HCR6   0   0.311  -3.4606   1.5885   1.6645
 TPY  N    N  NC1    0  -0.757   0.8997  -1.8767   0.3979

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
 TPY  C    CA   single    1.502  0.020  1.502
 TPY  C    O    double    1.207  0.020  1.207
 TPY  C    H    single    0.930  0.020  1.080
 TPY  CA   CB   single    1.534  0.020  1.534
 TPY  CA   CD   single    1.539  0.020  1.539
 TPY  CA   HA   single    0.970  0.020  1.090
 TPY  CB   CC   single    1.553  0.020  1.553
 TPY  CB   CK   single    1.538  0.020  1.538
 TPY  CB   HB   single    0.970  0.020  1.090
 TPY  CC   OA   deloc     1.260  0.020  1.260
 TPY  CC   OB   deloc     1.235  0.020  1.235
 TPY  CD   CE   single    1.523  0.020  1.523
 TPY  CD   HD2  single    0.970  0.020  1.090
 TPY  CD   HD1  single    0.970  0.020  1.090
 TPY  CE   HE3  single    0.970  0.020  1.090
 TPY  CE   HE2  single    0.970  0.020  1.090
 TPY  CE   HE1  single    0.970  0.020  1.090
 TPY  OC   S    double    1.453  0.020  1.453
 TPY  OD   S    double    1.454  0.020  1.454
 TPY  S    N    single    1.623  0.020  1.623
 TPY  S    CF   single    1.785  0.020  1.785
 TPY  N    CK   single    1.463  0.020  1.463
 TPY  N    HN1  single    0.890  0.020  1.040
 TPY  CK   HK2  single    0.970  0.020  1.090
 TPY  CK   HK1  single    0.970  0.020  1.090
 TPY  CF   CG1  aromatic  1.390  0.020  1.390
 TPY  CF   CG2  aromatic  1.385  0.020  1.385
 TPY  CG1  CH1  aromatic  1.382  0.020  1.382
 TPY  CG1  HG1  single    0.930  0.020  1.080
 TPY  CG2  CH2  aromatic  1.386  0.020  1.386
 TPY  CG2  HG2  single    0.930  0.020  1.080
 TPY  CH1  CI   aromatic  1.388  0.020  1.388
 TPY  CH1  HH1  single    0.930  0.020  1.080
 TPY  CH2  CI   aromatic  1.384  0.020  1.384
 TPY  CH2  HH2  single    0.930  0.020  1.080
 TPY  CI   NJ   single    1.460  0.020  1.460
 TPY  NJ   OE   single    1.207  0.020  1.207
 TPY  NJ   OF   double    1.207  0.020  1.207

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
 TPY  H    C    O    120.42  3.000
 TPY  H    C    CA   113.63  3.000
 TPY  O    C    CA   125.93  3.000
 TPY  HA   CA   CD   109.71  3.000
 TPY  HA   CA   CB   110.08  3.000
 TPY  CD   CA   CB   111.29  3.000
 TPY  HA   CA   C    109.00  3.000
 TPY  CD   CA   C    106.85  3.000
 TPY  CB   CA   C    109.83  3.000
 TPY  HB   CB   CK   107.23  3.000
 TPY  HB   CB   CC   107.84  3.000
 TPY  CK   CB   CC   108.59  3.000
 TPY  HB   CB   CA   108.24  3.000
 TPY  CK   CB   CA   111.17  3.000
 TPY  CC   CB   CA   113.53  3.000
 TPY  OB   CC   OA   126.09  3.000
 TPY  OB   CC   CB   119.34  3.000
 TPY  OA   CC   CB   114.55  3.000
 TPY  HD1  CD   HD2  106.50  3.000
 TPY  HD1  CD   CE   109.38  3.000
 TPY  HD2  CD   CE   110.00  3.000
 TPY  HD1  CD   CA   108.09  3.000
 TPY  HD2  CD   CA   109.00  3.000
 TPY  CE   CD   CA   113.61  3.000
 TPY  HE1  CE   HE2  107.63  3.000
 TPY  HE1  CE   HE3  107.20  3.000
 TPY  HE2  CE   HE3  107.50  3.000
 TPY  HE1  CE   CD   110.62  3.000
 TPY  HE2  CE   CD   111.11  3.000
 TPY  HE3  CE   CD   112.55  3.000
 TPY  CF   S    N    105.95  3.000
 TPY  CF   S    OD   107.17  3.000
 TPY  N    S    OD   108.42  3.000
 TPY  CF   S    OC   107.29  3.000
 TPY  N    S    OC   107.11  3.000
 TPY  OD   S    OC   120.09  3.000
 TPY  HK1  CK   HK2  107.10  3.000
 TPY  HK1  CK   N    108.62  3.000
 TPY  HK2  CK   N    112.42  3.000
 TPY  HK1  CK   CB   111.14  3.000
 TPY  HK2  CK   CB   108.81  3.000
 TPY  N    CK   CB   108.76  3.000
 TPY  CG2  CF   CG1  121.40  3.000
 TPY  CG2  CF   S    120.14  3.000
 TPY  CG1  CF   S    118.45  3.000
 TPY  HG1  CG1  CH1  119.15  3.000
 TPY  HG1  CG1  CF   121.39  3.000
 TPY  CH1  CG1  CF   119.46  3.000
 TPY  HG2  CG2  CH2  119.45  3.000
 TPY  HG2  CG2  CF   121.13  3.000
 TPY  CH2  CG2  CF   119.41  3.000
 TPY  HH1  CH1  CI   121.48  3.000
 TPY  HH1  CH1  CG1  119.75  3.000
 TPY  CI   CH1  CG1  118.77  3.000
 TPY  HH2  CH2  CI   121.54  3.000
 TPY  HH2  CH2  CG2  119.66  3.000
 TPY  CI   CH2  CG2  118.80  3.000
 TPY  NJ   CI   CH2  118.94  3.000
 TPY  NJ   CI   CH1  118.90  3.000
 TPY  CH2  CI   CH1  122.16  3.000
 TPY  OF   NJ   OE   124.31  3.000
 TPY  OF   NJ   CI   117.86  3.000
 TPY  OE   NJ   CI   117.83  3.000
 TPY  HN1  N    CK   109.12  3.000
 TPY  HN1  N    S    114.00  3.000
 TPY  CK   N    S    118.81  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
 TPY  CONST_01  CI   CH1  CG1  CF      0.00   0.0  0
 TPY  CONST_02  CI   CH2  CG2  CF      0.00   0.0  0
 TPY  CONST_03  CH2  CG2  CF   CG1     0.00   0.0  0
 TPY  CONST_04  CH2  CI   CH1  CG1     0.00   0.0  0
 TPY  CONST_05  CH1  CG1  CF   CG2     0.00   0.0  0
 TPY  CONST_06  CH1  CI   CH2  CG2     0.00   0.0  0
 TPY  CONST_07  CH1  CG1  CF   S     180.00   0.0  0
 TPY  CONST_08  CH2  CG2  CF   S     180.00   0.0  0
 TPY  CONST_09  NJ   CI   CH1  CG1   180.00   0.0  0
 TPY  CONST_10  NJ   CI   CH2  CG2   180.00   0.0  0
 TPY  CONST_11  HH1  CH1  CG1  CF    180.00   0.0  0
 TPY  CONST_12  HH2  CH2  CG2  CF    180.00   0.0  0
 TPY  CONST_13  HG2  CG2  CF   CG1   180.00   0.0  0
 TPY  CONST_14  HG1  CG1  CF   CG2   180.00   0.0  0
 TPY  CONST_15  OE   NJ   CI   CH1     0.00   0.0  0
 TPY  CONST_16  OF   NJ   CI   CH1   180.00   0.0  0
 TPY  CONST_17  OE   NJ   CI   CH2   180.00   0.0  0
 TPY  CONST_18  OF   NJ   CI   CH2     0.00   0.0  0
 TPY  Var_01    CG1  CF   S    OC    -44.90  30.0  2
 TPY  Var_02    CF   S    N    CK     63.33  30.0  2
 TPY  Var_03    S    N    CK   CB   -161.13  30.0  1
 TPY  Var_04    HE3  CE   CD   CA     64.21  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
 TPY  chir_01  CA  C   CB  CD  positiv
 TPY  chir_02  CB  CA  CC  CK  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
 TPY  plan-1  S    0.020
 TPY  plan-1  CF   0.020
 TPY  plan-1  CG1  0.020
 TPY  plan-1  CG2  0.020
 TPY  plan-1  CH1  0.020
 TPY  plan-1  CH2  0.020
 TPY  plan-1  CI   0.020
 TPY  plan-1  NJ   0.020
 TPY  plan-1  HG1  0.020
 TPY  plan-1  HG2  0.020
 TPY  plan-1  HH1  0.020
 TPY  plan-1  HH2  0.020
 TPY  plan-2  CI   0.020
 TPY  plan-2  NJ   0.020
 TPY  plan-2  OE   0.020
 TPY  plan-2  OF   0.020
 TPY  plan-3  CB   0.020
 TPY  plan-3  CC   0.020
 TPY  plan-3  OA   0.020
 TPY  plan-3  OB   0.020
 TPY  plan-4  C    0.020
 TPY  plan-4  CA   0.020
 TPY  plan-4  O    0.020
 TPY  plan-4  H    0.020

