# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 21:13:01 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 3-chloro-N-[(2E)-4-methoxy-4-oxobut-2-enoyl]-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)\C=C\C(=O)N[C@@H](Cc1ccc(O)c(Cl)c1)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
 PMX  PMX  3-chloro-N-[(2E)-4-methoxy-4-oxobut-2-enoyl]-L-tyrosine  ligand  36  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PMX
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
 PMX  C     C   C     0   0.554   1.0267  -4.2464   0.8593
 PMX  N     N   NH1   0  -0.641  -0.3396  -2.3043   0.4128
 PMX  O     O   O     0  -0.426   0.1743  -4.7019   1.5759
 PMX  CL    CL  CL    0  -0.113  -0.1947   2.7176   0.8763
 PMX  CA    C   CH1   0  -0.207   0.9532  -2.8883   0.1908
 PMX  CB    C   CH2   0  -0.525   2.0841  -1.9577   0.7054
 PMX  CG    C   CR6   0   0.100   1.9379  -0.5836   0.1211
 PMX  OAA   O   O     0  -0.463  -0.6484  -1.5290  -1.6971
 PMX  CAC   C   CR16  0  -0.329   2.2804   0.9646  -1.7065
 PMX  CAD   C   C1    0  -0.337  -2.4648   0.3781  -0.6260
 PMX  CAE   C   C1    0  -0.317  -2.0391  -0.6899   0.0398
 PMX  CAF   C   C     0   0.564  -0.9571  -1.5451  -0.5181
 PMX  CAK   C   CR6   0   0.400   1.4417   1.9030  -1.1089
 PMX  OAL   O   OH1   0  -0.614   1.2267   3.0633  -1.7465
 PMX  OAM   O   O     0  -0.444  -4.0113   1.1283   1.0288
 PMX  CAN   C   C     0   0.591  -3.4639   1.2947  -0.0338
 PMX  CAS   C   CR6   0  -0.142   0.8761   1.5778   0.1219
 PMX  OAU   O   O2    0  -0.454  -3.6792   2.3323  -0.8255
 PMX  CAV   C   CH3   0  -0.426  -4.6119   3.3172  -0.3807
 PMX  CD1   C   CR16  0  -0.276   1.1266   0.3621   0.7353
 PMX  CD2   C   CR16  0  -0.267   2.5133  -0.2575  -1.1039
 PMX  OXT   O   OH1   0  -0.587   2.1605  -4.8627   0.5667
 PMX  HN    H   HNH1  0   0.407  -0.6458  -2.2237   1.3709
 PMX  HA    H   HCH1  0   0.312   1.0827  -3.0304  -0.8840
 PMX  HB    H   HCH2  0   0.271   2.0414  -1.9159   1.7964
 PMX  HBA   H   HCH2  0   0.277   3.0490  -2.3859   0.4324
 PMX  HAC   H   HCR6  0   0.273   2.7365   1.2021  -2.6594
 PMX  HAD   H   H     0   0.291  -2.0662   0.6210  -1.6032
 PMX  HAE   H   H     0   0.294  -2.4225  -0.9139   1.0295
 PMX  HOAL  H   HOH1  0   0.468   0.6395   3.6384  -1.2397
 PMX  HAV   H   HCH3  0   0.255  -4.6333   4.0786  -1.1540
 PMX  HAVA  H   HCH3  0   0.243  -5.6086   2.8935  -0.2610
 PMX  HAVB  H   HCH3  0   0.241  -4.2969   3.7656   0.5612
 PMX  HD1   H   HCR6  0   0.282   0.6720   0.1519   1.6953
 PMX  HD2   H   HCR6  0   0.256   3.1522  -0.9741  -1.6054
 PMX  HOXT  H   HOH1  0   0.489   2.2052  -5.7175   1.0214

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
 PMX  C    O     double    1.203  0.020  1.203
 PMX  C    CA    single    1.516  0.020  1.516
 PMX  C    OXT   single    1.323  0.020  1.323
 PMX  N    CA    single    1.436  0.020  1.436
 PMX  N    CAF   single    1.351  0.020  1.351
 PMX  CL   CAS   single    1.736  0.020  1.736
 PMX  CA   CB    single    1.552  0.020  1.552
 PMX  CB   CG    single    1.500  0.020  1.500
 PMX  CG   CD1   aromatic  1.389  0.020  1.389
 PMX  CG   CD2   aromatic  1.392  0.020  1.392
 PMX  OAA  CAF   double    1.219  0.020  1.219
 PMX  CAC  CAK   aromatic  1.393  0.020  1.393
 PMX  CAC  CD2   aromatic  1.382  0.020  1.382
 PMX  CAD  CAE   double    1.329  0.020  1.329
 PMX  CAD  CAN   single    1.480  0.020  1.480
 PMX  CAE  CAF   single    1.488  0.020  1.488
 PMX  CAK  OAL   single    1.341  0.020  1.341
 PMX  CAK  CAS   aromatic  1.393  0.020  1.393
 PMX  OAM  CAN   double    1.207  0.020  1.207
 PMX  CAN  OAU   single    1.323  0.020  1.323
 PMX  CAS  CD1   aromatic  1.385  0.020  1.385
 PMX  OAU  CAV   single    1.427  0.020  1.427
 PMX  N    HN    single    0.860  0.020  1.020
 PMX  CA   HA    single    0.970  0.020  1.090
 PMX  CB   HB    single    0.970  0.020  1.090
 PMX  CB   HBA   single    0.970  0.020  1.090
 PMX  CAC  HAC   single    0.930  0.020  1.080
 PMX  CAD  HAD   single    0.930  0.020  1.080
 PMX  CAE  HAE   single    0.930  0.020  1.080
 PMX  OAL  HOAL  single    0.850  0.020  0.980
 PMX  CAV  HAV   single    0.970  0.020  1.090
 PMX  CAV  HAVA  single    0.970  0.020  1.090
 PMX  CAV  HAVB  single    0.970  0.020  1.090
 PMX  CD1  HD1   single    0.930  0.020  1.080
 PMX  CD2  HD2   single    0.930  0.020  1.080
 PMX  OXT  HOXT  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
 PMX  OXT   C    CA    111.19  3.000
 PMX  OXT   C    O     124.23  3.000
 PMX  CA    C    O     124.58  3.000
 PMX  HN    N    CAF   118.08  3.000
 PMX  HN    N    CA    116.91  3.000
 PMX  CAF   N    CA    122.25  3.000
 PMX  HA    CA   CB    108.54  3.000
 PMX  HA    CA   N     108.17  3.000
 PMX  CB    CA   N     111.15  3.000
 PMX  HA    CA   C     108.17  3.000
 PMX  CB    CA   C     110.83  3.000
 PMX  N     CA   C     109.87  3.000
 PMX  HBA   CB   HB    107.43  3.000
 PMX  HBA   CB   CG    110.39  3.000
 PMX  HB    CB   CG    110.49  3.000
 PMX  HBA   CB   CA    109.05  3.000
 PMX  HB    CB   CA    108.99  3.000
 PMX  CG    CB   CA    110.42  3.000
 PMX  CD2   CG   CD1   118.10  3.000
 PMX  CD2   CG   CB    121.12  3.000
 PMX  CD1   CG   CB    120.55  3.000
 PMX  HAC   CAC  CD2   120.44  3.000
 PMX  HAC   CAC  CAK   118.90  3.000
 PMX  CD2   CAC  CAK   120.65  3.000
 PMX  HAD   CAD  CAN   118.08  3.000
 PMX  HAD   CAD  CAE   120.97  3.000
 PMX  CAN   CAD  CAE   120.92  3.000
 PMX  HAE   CAE  CAF   118.72  3.000
 PMX  HAE   CAE  CAD   120.66  3.000
 PMX  CAF   CAE  CAD   120.48  3.000
 PMX  CAE   CAF  OAA   122.64  3.000
 PMX  CAE   CAF  N     113.40  3.000
 PMX  OAA   CAF  N     123.94  3.000
 PMX  CAS   CAK  OAL   123.84  3.000
 PMX  CAS   CAK  CAC   117.79  3.000
 PMX  OAL   CAK  CAC   118.38  3.000
 PMX  HOAL  OAL  CAK   111.30  3.000
 PMX  OAU   CAN  OAM   124.14  3.000
 PMX  OAU   CAN  CAD   110.88  3.000
 PMX  OAM   CAN  CAD   124.98  3.000
 PMX  CD1   CAS  CAK   121.53  3.000
 PMX  CD1   CAS  CL    119.70  3.000
 PMX  CAK   CAS  CL    118.75  3.000
 PMX  CAV   OAU  CAN   117.46  3.000
 PMX  HAVB  CAV  HAVA  109.24  3.000
 PMX  HAVB  CAV  HAV   109.43  3.000
 PMX  HAVA  CAV  HAV   109.45  3.000
 PMX  HAVB  CAV  OAU   111.37  3.000
 PMX  HAVA  CAV  OAU   111.32  3.000
 PMX  HAV   CAV  OAU   105.96  3.000
 PMX  HD1   CD1  CAS   119.16  3.000
 PMX  HD1   CD1  CG    120.34  3.000
 PMX  CAS   CD1  CG    120.50  3.000
 PMX  HD2   CD2  CAC   118.84  3.000
 PMX  HD2   CD2  CG    119.75  3.000
 PMX  CAC   CD2  CG    121.40  3.000
 PMX  HOXT  OXT  C     110.28  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
 PMX  CONST_01  CAK   CAS  CD1  CG      0.00   0.0  0
 PMX  CONST_02  CAK   CAC  CD2  CG      0.00   0.0  0
 PMX  CONST_03  CD1   CAS  CAK  CAC     0.00   0.0  0
 PMX  CONST_04  CD1   CG   CD2  CAC     0.00   0.0  0
 PMX  CONST_05  CD2   CAC  CAK  CAS     0.00   0.0  0
 PMX  CONST_06  CD2   CG   CD1  CAS     0.00   0.0  0
 PMX  CONST_07  CAC   CAK  CAS  CL    180.00   0.0  0
 PMX  CONST_08  CG    CD1  CAS  CL    180.00   0.0  0
 PMX  CONST_09  CAS   CD1  CG   CB    180.00   0.0  0
 PMX  CONST_10  CAC   CD2  CG   CB    180.00   0.0  0
 PMX  CONST_11  CD2   CAC  CAK  OAL   180.00   0.0  0
 PMX  CONST_12  CD1   CAS  CAK  OAL   180.00   0.0  0
 PMX  CONST_13  HAC   CAC  CD2  CG    180.00   0.0  0
 PMX  CONST_14  HD2   CD2  CAC  CAK   180.00   0.0  0
 PMX  CONST_15  HD1   CD1  CAS  CAK   180.00   0.0  0
 PMX  CONST_18  HN    N    CAF  OAA   180.00   0.0  0
 PMX  CONST_19  HOXT  OXT  C    O       0.00   0.0  0
 PMX  Var_01    CD1   CG   CB   CA     86.58  30.0  2
 PMX  Var_02    CAN   CAD  CAE  CAF  -175.16   0.0  2
 PMX  Var_03    CAD   CAE  CAF  N     159.80  30.0  2
 PMX  Var_04    OAM   CAN  CAD  CAE    -3.92  30.0  2
 PMX  Var_05    HAV   CAV  OAU  CAN   179.20  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
 PMX  chir_01  CA  C  N  CB  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
 PMX  plan-1  CL    0.020
 PMX  plan-1  CB    0.020
 PMX  plan-1  CG    0.020
 PMX  plan-1  CAC   0.020
 PMX  plan-1  CAK   0.020
 PMX  plan-1  OAL   0.020
 PMX  plan-1  CAS   0.020
 PMX  plan-1  CD1   0.020
 PMX  plan-1  CD2   0.020
 PMX  plan-1  HAC   0.020
 PMX  plan-1  HD1   0.020
 PMX  plan-1  HD2   0.020
 PMX  plan-2  N     0.020
 PMX  plan-2  CA    0.020
 PMX  plan-2  OAA   0.020
 PMX  plan-2  CAE   0.020
 PMX  plan-2  CAF   0.020
 PMX  plan-2  HN    0.020
 PMX  plan-3  C     0.020
 PMX  plan-3  O     0.020
 PMX  plan-3  CA    0.020
 PMX  plan-3  OXT   0.020
 PMX  plan-3  HOXT  0.020
 PMX  plan-4  CAD   0.020
 PMX  plan-4  CAE   0.020
 PMX  plan-4  CAF   0.020
 PMX  plan-4  CAN   0.020
 PMX  plan-4  HAD   0.020
 PMX  plan-4  HAE   0.020
 PMX  plan-5  CAD   0.020
 PMX  plan-5  OAM   0.020
 PMX  plan-5  CAN   0.020
 PMX  plan-5  OAU   0.020

