# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:04:48 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  35  22  .  2021-08-19  2021-08-19  
;
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   0.418   0.4501  -3.8172   0.3848
 PMX  N     N   NH1    0  -0.627  -0.2651  -1.4281   0.3348
 PMX  O     O   O      0  -0.588  -0.6509  -4.0307   0.9149
 PMX  CL    CL  CL     0  -0.118   2.2187   3.2806   1.3247
 PMX  CA    C   CH1    0  -0.199   0.7841  -2.3509  -0.0136
 PMX  CB    C   CH2    0  -0.550   2.1097  -1.8880   0.6040
 PMX  CG    C   CR6    0   0.136   2.5230  -0.5269   0.1233
 PMX  OAA   O   O      0  -0.497  -1.3848  -1.5065  -1.6328
 PMX  CAC   C   CR16   0  -0.372   3.5278   0.8837  -1.5708
 PMX  CAD   C   C1     0  -0.347  -3.3679   0.1799  -0.5270
 PMX  CAE   C   C1     0  -0.331  -2.2981  -0.2250   0.1501
 PMX  CAF   C   C      0   0.571  -1.2849  -1.1226  -0.4739
 PMX  CAK   C   CR6    0   0.392   3.2360   2.0283  -0.8341
 PMX  OAL   O   OH1    0  -0.614   3.5543   3.2694  -1.2359
 PMX  OAM   O   O      0  -0.445  -4.3019   1.5215   1.2123
 PMX  CAN   C   C      0   0.595  -4.3643   1.0828   0.0894
 PMX  CAS   C   CR6    0  -0.124   2.5851   1.8708   0.3872
 PMX  OAU   O   O2     0  -0.457  -5.3437   1.3550  -0.7588
 PMX  CAV   C   CH3    0  -0.425  -6.3776   2.2321  -0.3122
 PMX  CD1   C   CR16   0  -0.276   2.2332   0.6168   0.8587
 PMX  CD2   C   CR16   0  -0.288   3.1745  -0.3690  -1.0965
 PMX  OXT   O   OC    -1  -0.609   1.3408  -4.6454   0.1151
 PMX  HN    H   HNH1   0   0.396  -0.3360  -1.1597   1.3039
 PMX  HA    H   HCH1   0   0.257   0.8927  -2.3241  -1.1006
 PMX  HB    H   HCH2   0   0.251   2.0280  -1.8924   1.6954
 PMX  HBA   H   HCH2   0   0.261   2.8707  -2.6237   0.3447
 PMX  HAC   H   HCR6   0   0.278   4.0417   0.9763  -2.5210
 PMX  HAD   H   H      0   0.287  -3.5333  -0.1383  -1.5490
 PMX  HAE   H   H      0   0.286  -2.1407   0.0979   1.1735
 PMX  HOAL  H   HOH1   0   0.480   3.9986   3.2378  -2.0909
 PMX  HAV   H   HCH3   0   0.254  -7.0737   2.3189  -1.1408
 PMX  HAVA  H   HCH3   0   0.242  -6.8962   1.8264   0.5560
 PMX  HAVB  H   HCH3   0   0.242  -5.9822   3.2174  -0.0668
 PMX  HD1   H   HCR6   0   0.266   1.7351   0.5364   1.8175
 PMX  HD2   H   HCR6   0   0.256   3.4173  -1.2414  -1.6919

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     deloc     1.241  0.020  1.241
 PMX  C    CA    single    1.556  0.020  1.556
 PMX  C    OXT   deloc     1.246  0.020  1.246
 PMX  N    CA    single    1.440  0.020  1.440
 PMX  N    CAF   single    1.337  0.020  1.337
 PMX  CL   CAS   single    1.732  0.020  1.732
 PMX  CA   CB    single    1.534  0.020  1.534
 PMX  CB   CG    single    1.502  0.020  1.502
 PMX  CG   CD1   aromatic  1.390  0.020  1.390
 PMX  CG   CD2   aromatic  1.392  0.020  1.392
 PMX  OAA  CAF   double    1.225  0.020  1.225
 PMX  CAC  CAK   aromatic  1.392  0.020  1.392
 PMX  CAC  CD2   aromatic  1.385  0.020  1.385
 PMX  CAD  CAE   double    1.329  0.020  1.329
 PMX  CAD  CAN   single    1.479  0.020  1.479
 PMX  CAE  CAF   single    1.490  0.020  1.490
 PMX  CAK  OAL   single    1.343  0.020  1.343
 PMX  CAK  CAS   aromatic  1.393  0.020  1.393
 PMX  OAM  CAN   double    1.207  0.020  1.207
 PMX  CAN  OAU   single    1.324  0.020  1.324
 PMX  CAS  CD1   aromatic  1.385  0.020  1.385
 PMX  OAU  CAV   single    1.428  0.020  1.428
 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

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    114.69  3.000
 PMX  OXT   C    O     127.78  3.000
 PMX  CA    C    O     117.53  3.000
 PMX  HN    N    CAF   117.84  3.000
 PMX  HN    N    CA    117.03  3.000
 PMX  CAF   N    CA    123.77  3.000
 PMX  HA    CA   CB    107.89  3.000
 PMX  HA    CA   N     107.30  3.000
 PMX  CB    CA   N     109.81  3.000
 PMX  HA    CA   C     107.41  3.000
 PMX  CB    CA   C     111.52  3.000
 PMX  N     CA   C     112.68  3.000
 PMX  HBA   CB   HB    106.66  3.000
 PMX  HBA   CB   CG    110.09  3.000
 PMX  HB    CB   CG    110.09  3.000
 PMX  HBA   CB   CA    107.70  3.000
 PMX  HB    CB   CA    109.62  3.000
 PMX  CG    CB   CA    112.49  3.000
 PMX  CD2   CG   CD1   117.89  3.000
 PMX  CD2   CG   CB    120.82  3.000
 PMX  CD1   CG   CB    121.26  3.000
 PMX  HAC   CAC  CD2   119.88  3.000
 PMX  HAC   CAC  CAK   119.53  3.000
 PMX  CD2   CAC  CAK   120.59  3.000
 PMX  HAD   CAD  CAN   118.01  3.000
 PMX  HAD   CAD  CAE   120.93  3.000
 PMX  CAN   CAD  CAE   121.05  3.000
 PMX  HAE   CAE  CAF   118.40  3.000
 PMX  HAE   CAE  CAD   120.44  3.000
 PMX  CAF   CAE  CAD   121.15  3.000
 PMX  CAE   CAF  OAA   121.96  3.000
 PMX  CAE   CAF  N     113.76  3.000
 PMX  OAA   CAF  N     124.26  3.000
 PMX  CAS   CAK  OAL   118.53  3.000
 PMX  CAS   CAK  CAC   117.97  3.000
 PMX  OAL   CAK  CAC   123.50  3.000
 PMX  HOAL  OAL  CAK   110.14  3.000
 PMX  OAU   CAN  OAM   124.02  3.000
 PMX  OAU   CAN  CAD   110.90  3.000
 PMX  OAM   CAN  CAD   125.07  3.000
 PMX  CD1   CAS  CAK   121.30  3.000
 PMX  CD1   CAS  CL    119.92  3.000
 PMX  CAK   CAS  CL    118.78  3.000
 PMX  CAV   OAU  CAN   117.50  3.000
 PMX  HAVB  CAV  HAVA  109.26  3.000
 PMX  HAVB  CAV  HAV   109.41  3.000
 PMX  HAVA  CAV  HAV   109.44  3.000
 PMX  HAVB  CAV  OAU   111.30  3.000
 PMX  HAVA  CAV  OAU   111.42  3.000
 PMX  HAV   CAV  OAU   105.95  3.000
 PMX  HD1   CD1  CAS   119.02  3.000
 PMX  HD1   CD1  CG    120.20  3.000
 PMX  CAS   CD1  CG    120.78  3.000
 PMX  HD2   CD2  CAC   118.86  3.000
 PMX  HD2   CD2  CG    119.67  3.000
 PMX  CAC   CD2  CG    121.47  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_16  OAA  CAF  N    CA      0.00   0.0  0
 PMX  CONST_17  CAE  CAF  N    CA    180.00   0.0  0
 PMX  CONST_18  HN   N    CAF  OAA   180.00   0.0  0
 PMX  Var_01    CD1  CG   CB   CA     96.00  30.0  2
 PMX  Var_02    CAN  CAD  CAE  CAF  -179.31   0.0  2
 PMX  Var_03    CAD  CAE  CAF  N     179.47  30.0  2
 PMX  Var_04    OAM  CAN  CAD  CAE     0.26  30.0  2
 PMX  Var_05    HAV  CAV  OAU  CAN  -179.67  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-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

