# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 17:33:13 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2E)-4-{2-[(4-benzylpyridin-3-yl)carbonyl]hydrazinyl}-4-oxobut-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)\C=C\C(=O)NNC(=O)c1cnccc1Cc2ccccc2
#
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
 6MK  6MK  '(2E)-4-{2-[(4-benzylpyridin-3-yl)carbonyl]hydrazinyl}-4-oxobut-2-enoic acid'  ligand  38  24  .  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_6MK
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
 6MK  OAA   O  O      0  -0.591   6.8996  -1.9988  -0.1427
 6MK  CAS   C  C      0   0.404   6.8892  -0.8975   0.4367
 6MK  OAD   O  OC    -1  -0.602   7.8303  -0.3478   1.0409
 6MK  CAE   C  C1     0  -0.351   5.5918  -0.1101   0.4183
 6MK  CAF   C  C1     0  -0.354   4.4917  -0.5273  -0.2030
 6MK  CAT   C  C      0   0.557   3.2482   0.2722  -0.2030
 6MK  OAB   O  O      0  -0.464   3.1179   1.3550   0.3377
 6MK  NAQ   N  NH1    0  -0.520   2.2304  -0.3182  -0.8880
 6MK  NAR   N  NH1    0  -0.477   1.0063   0.2641  -0.9359
 6MK  CAU   C  C      0   0.490   0.1793   0.2313   0.1385
 6MK  OAC   O  O      0  -0.441   0.3713  -0.4722   1.1091
 6MK  CAX   C  CR6    0  -0.180  -0.9902   1.1497   0.0210
 6MK  CAN   C  CR16   0  -0.061  -0.7567   2.4997  -0.2153
 6MK  NAP   N  N      0  -0.405  -1.7124   3.4173  -0.2657
 6MK  CAJ   C  CR16   0  -0.050  -2.9572   2.9980  -0.0860
 6MK  CAM   C  CR16   0  -0.362  -3.2968   1.6744   0.1519
 6MK  CAW   C  CR6    0   0.221  -2.3033   0.7070   0.2196
 6MK  CAO   C  CH2    0  -0.574  -2.6169  -0.7446   0.4926
 6MK  CAV   C  CR6    0   0.095  -4.0551  -1.1166   0.2635
 6MK  CAK   C  CR16   0  -0.285  -4.5327  -1.3063  -1.0320
 6MK  CAH   C  CR16   0  -0.241  -5.8607  -1.6374  -1.2567
 6MK  CAG   C  CR16   0  -0.267  -6.7336  -1.7844  -0.1849
 6MK  CAI   C  CR16   0  -0.241  -6.2678  -1.5986   1.1089
 6MK  CAL   C  CR16   0  -0.302  -4.9365  -1.2661   1.3292
 6MK  HAE   H  H      0   0.247   5.5804   0.8408   0.9426
 6MK  HAF   H  H      0   0.262   4.4921  -1.4750  -0.7309
 6MK  HAQ   H  HNH1   0   0.419   2.3191  -1.2445  -1.2774
 6MK  HAR   H  HNH1   0   0.423   0.8229   0.8871  -1.7091
 6MK  HAN   H  HCR6   0   0.274   0.2604   2.8558  -0.3484
 6MK  HAJ   H  HCR6   0   0.273  -3.7354   3.7511  -0.1343
 6MK  HAM   H  HCR6   0   0.272  -4.3378   1.4126   0.2813
 6MK  HAO1  H  HCH2   0   0.273  -1.9770  -1.3708  -0.1332
 6MK  HAO2  H  HCH2   0   0.289  -2.3293  -0.9671   1.5230
 6MK  HAK   H  HCR6   0   0.251  -3.8577  -1.1944  -1.8728
 6MK  HAL   H  HCR6   0   0.251  -4.5813  -1.1202   2.3426
 6MK  HAH   H  HCR6   0   0.256  -6.2149  -1.7844  -2.2689
 6MK  HAG   H  HCR6   0   0.256  -7.7699  -2.0433  -0.3594
 6MK  HAI   H  HCR6   0   0.256  -6.9393  -1.7130   1.9500

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
 6MK  OAA  CAS   deloc     1.244  0.020  1.244
 6MK  CAS  OAD   deloc     1.246  0.020  1.246
 6MK  CAS  CAE   single    1.518  0.020  1.518
 6MK  CAE  CAF   double    1.331  0.020  1.331
 6MK  CAF  CAT   single    1.478  0.020  1.478
 6MK  CAT  OAB   double    1.217  0.020  1.217
 6MK  CAT  NAQ   single    1.362  0.020  1.362
 6MK  NAQ  NAR   single    1.356  0.020  1.356
 6MK  NAR  CAU   single    1.356  0.020  1.356
 6MK  CAU  OAC   double    1.214  0.020  1.214
 6MK  CAU  CAX   single    1.492  0.020  1.492
 6MK  CAX  CAN   aromatic  1.390  0.020  1.390
 6MK  CAX  CAW   aromatic  1.400  0.020  1.400
 6MK  CAN  NAP   aromatic  1.326  0.020  1.326
 6MK  NAP  CAJ   aromatic  1.326  0.020  1.326
 6MK  CAJ  CAM   aromatic  1.387  0.020  1.387
 6MK  CAM  CAW   aromatic  1.388  0.020  1.388
 6MK  CAW  CAO   single    1.510  0.020  1.510
 6MK  CAO  CAV   single    1.503  0.020  1.503
 6MK  CAV  CAK   aromatic  1.394  0.020  1.394
 6MK  CAV  CAL   aromatic  1.391  0.020  1.391
 6MK  CAK  CAH   aromatic  1.387  0.020  1.387
 6MK  CAH  CAG   aromatic  1.390  0.020  1.390
 6MK  CAG  CAI   aromatic  1.388  0.020  1.388
 6MK  CAI  CAL   aromatic  1.390  0.020  1.390
 6MK  CAE  HAE   single    0.930  0.020  1.080
 6MK  CAF  HAF   single    0.930  0.020  1.080
 6MK  NAQ  HAQ   single    0.860  0.020  1.020
 6MK  NAR  HAR   single    0.860  0.020  1.020
 6MK  CAN  HAN   single    0.930  0.020  1.080
 6MK  CAJ  HAJ   single    0.930  0.020  1.080
 6MK  CAM  HAM   single    0.930  0.020  1.080
 6MK  CAO  HAO1  single    0.970  0.020  1.090
 6MK  CAO  HAO2  single    0.970  0.020  1.090
 6MK  CAK  HAK   single    0.930  0.020  1.080
 6MK  CAL  HAL   single    0.930  0.020  1.080
 6MK  CAH  HAH   single    0.930  0.020  1.080
 6MK  CAG  HAG   single    0.930  0.020  1.080
 6MK  CAI  HAI   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
 6MK  CAE   CAS  OAD   115.00  3.000
 6MK  CAE   CAS  OAA   117.42  3.000
 6MK  OAD   CAS  OAA   127.58  3.000
 6MK  HAE   CAE  CAF   119.43  3.000
 6MK  HAE   CAE  CAS   117.22  3.000
 6MK  CAF   CAE  CAS   123.35  3.000
 6MK  HAF   CAF  CAT   118.22  3.000
 6MK  HAF   CAF  CAE   120.06  3.000
 6MK  CAT   CAF  CAE   121.73  3.000
 6MK  NAQ   CAT  OAB   121.95  3.000
 6MK  NAQ   CAT  CAF   113.22  3.000
 6MK  OAB   CAT  CAF   124.83  3.000
 6MK  HAQ   NAQ  NAR   117.38  3.000
 6MK  HAQ   NAQ  CAT   121.79  3.000
 6MK  NAR   NAQ  CAT   120.41  3.000
 6MK  HAR   NAR  CAU   120.71  3.000
 6MK  HAR   NAR  NAQ   117.12  3.000
 6MK  CAU   NAR  NAQ   120.80  3.000
 6MK  CAX   CAU  OAC   122.94  3.000
 6MK  CAX   CAU  NAR   113.63  3.000
 6MK  OAC   CAU  NAR   123.43  3.000
 6MK  CAW   CAX  CAN   119.26  3.000
 6MK  CAW   CAX  CAU   121.97  3.000
 6MK  CAN   CAX  CAU   118.66  3.000
 6MK  HAN   CAN  NAP   116.33  3.000
 6MK  HAN   CAN  CAX   119.77  3.000
 6MK  NAP   CAN  CAX   123.88  3.000
 6MK  CAJ   NAP  CAN   116.93  3.000
 6MK  HAJ   CAJ  CAM   119.66  3.000
 6MK  HAJ   CAJ  NAP   116.64  3.000
 6MK  CAM   CAJ  NAP   123.70  3.000
 6MK  HAM   CAM  CAW   120.96  3.000
 6MK  HAM   CAM  CAJ   119.17  3.000
 6MK  CAW   CAM  CAJ   119.87  3.000
 6MK  CAO   CAW  CAM   122.01  3.000
 6MK  CAO   CAW  CAX   121.63  3.000
 6MK  CAM   CAW  CAX   116.36  3.000
 6MK  HAO2  CAO  HAO1  105.62  3.000
 6MK  HAO2  CAO  CAV   110.19  3.000
 6MK  HAO1  CAO  CAV   109.35  3.000
 6MK  HAO2  CAO  CAW   108.15  3.000
 6MK  HAO1  CAO  CAW   109.02  3.000
 6MK  CAV   CAO  CAW   114.15  3.000
 6MK  CAL   CAV  CAK   118.71  3.000
 6MK  CAL   CAV  CAO   121.07  3.000
 6MK  CAK   CAV  CAO   120.22  3.000
 6MK  HAK   CAK  CAH   119.68  3.000
 6MK  HAK   CAK  CAV   119.57  3.000
 6MK  CAH   CAK  CAV   120.74  3.000
 6MK  HAH   CAH  CAG   120.07  3.000
 6MK  HAH   CAH  CAK   119.82  3.000
 6MK  CAG   CAH  CAK   120.11  3.000
 6MK  HAG   CAG  CAI   120.25  3.000
 6MK  HAG   CAG  CAH   120.15  3.000
 6MK  CAI   CAG  CAH   119.60  3.000
 6MK  HAI   CAI  CAL   119.77  3.000
 6MK  HAI   CAI  CAG   120.14  3.000
 6MK  CAL   CAI  CAG   120.09  3.000
 6MK  HAL   CAL  CAI   119.63  3.000
 6MK  HAL   CAL  CAV   119.63  3.000
 6MK  CAI   CAL  CAV   120.74  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
 6MK  CONST_01  CAJ  NAP  CAN  CAX     0.00   0.0  0
 6MK  CONST_02  CAJ  CAM  CAW  CAX     0.00   0.0  0
 6MK  CONST_03  CAM  CAW  CAX  CAN     0.00   0.0  0
 6MK  CONST_04  CAM  CAJ  NAP  CAN     0.00   0.0  0
 6MK  CONST_05  CAW  CAX  CAN  NAP     0.00   0.0  0
 6MK  CONST_06  CAW  CAM  CAJ  NAP     0.00   0.0  0
 6MK  CONST_07  CAG  CAH  CAK  CAV     0.00   0.0  0
 6MK  CONST_08  CAG  CAI  CAL  CAV     0.00   0.0  0
 6MK  CONST_09  CAI  CAL  CAV  CAK     0.00   0.0  0
 6MK  CONST_10  CAI  CAG  CAH  CAK     0.00   0.0  0
 6MK  CONST_11  CAL  CAV  CAK  CAH     0.00   0.0  0
 6MK  CONST_12  CAL  CAI  CAG  CAH     0.00   0.0  0
 6MK  CONST_13  NAP  CAN  CAX  CAU   180.00   0.0  0
 6MK  CONST_14  CAM  CAW  CAX  CAU   180.00   0.0  0
 6MK  CONST_15  CAO  CAW  CAX  CAN   180.00   0.0  0
 6MK  CONST_16  CAO  CAW  CAM  CAJ   180.00   0.0  0
 6MK  CONST_17  CAH  CAK  CAV  CAO   180.00   0.0  0
 6MK  CONST_18  CAI  CAL  CAV  CAO   180.00   0.0  0
 6MK  CONST_19  HAM  CAM  CAW  CAX   180.00   0.0  0
 6MK  CONST_20  HAJ  CAJ  NAP  CAN   180.00   0.0  0
 6MK  CONST_21  HAN  CAN  NAP  CAJ   180.00   0.0  0
 6MK  CONST_22  HAH  CAH  CAK  CAV   180.00   0.0  0
 6MK  CONST_23  HAI  CAI  CAL  CAV   180.00   0.0  0
 6MK  CONST_24  HAL  CAL  CAV  CAK   180.00   0.0  0
 6MK  CONST_25  HAG  CAG  CAH  CAK   180.00   0.0  0
 6MK  CONST_26  HAK  CAK  CAH  CAG   180.00   0.0  0
 6MK  CONST_27  CAX  CAU  NAR  NAQ   180.00   0.0  0
 6MK  CONST_28  HAR  NAR  CAU  CAX     0.00   0.0  0
 6MK  CONST_29  NAR  NAQ  CAT  CAF   180.00   0.0  0
 6MK  CONST_30  NAR  NAQ  CAT  OAB     0.00   0.0  0
 6MK  CONST_31  OAC  CAU  NAR  NAQ     0.00   0.0  0
 6MK  CONST_32  HAQ  NAQ  CAT  CAF     0.00   0.0  0
 6MK  Var_01    CAV  CAO  CAW  CAX  -162.17  30.0  2
 6MK  Var_02    CAK  CAV  CAO  CAW    77.41  30.0  2
 6MK  Var_03    CAN  CAX  CAU  NAR   -55.72  30.0  2
 6MK  Var_04    CAT  CAF  CAE  CAS  -179.73   0.0  2
 6MK  Var_05    CAF  CAE  CAS  OAA    -1.37  30.0  2
 6MK  Var_06    OAB  CAT  CAF  CAE     0.55  30.0  2
 6MK  Var_07    CAU  NAR  NAQ  CAT   -75.02  30.0  2

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
 6MK  plan-1  CAU  0.020
 6MK  plan-1  CAX  0.020
 6MK  plan-1  CAN  0.020
 6MK  plan-1  NAP  0.020
 6MK  plan-1  CAJ  0.020
 6MK  plan-1  CAM  0.020
 6MK  plan-1  CAW  0.020
 6MK  plan-1  CAO  0.020
 6MK  plan-1  HAN  0.020
 6MK  plan-1  HAJ  0.020
 6MK  plan-1  HAM  0.020
 6MK  plan-2  CAO  0.020
 6MK  plan-2  CAV  0.020
 6MK  plan-2  CAK  0.020
 6MK  plan-2  CAH  0.020
 6MK  plan-2  CAG  0.020
 6MK  plan-2  CAI  0.020
 6MK  plan-2  CAL  0.020
 6MK  plan-2  HAK  0.020
 6MK  plan-2  HAL  0.020
 6MK  plan-2  HAH  0.020
 6MK  plan-2  HAG  0.020
 6MK  plan-2  HAI  0.020
 6MK  plan-3  CAF  0.020
 6MK  plan-3  CAT  0.020
 6MK  plan-3  OAB  0.020
 6MK  plan-3  NAQ  0.020
 6MK  plan-3  NAR  0.020
 6MK  plan-3  HAQ  0.020
 6MK  plan-4  NAQ  0.020
 6MK  plan-4  NAR  0.020
 6MK  plan-4  CAU  0.020
 6MK  plan-4  OAC  0.020
 6MK  plan-4  CAX  0.020
 6MK  plan-4  HAR  0.020
 6MK  plan-5  OAA  0.020
 6MK  plan-5  CAS  0.020
 6MK  plan-5  OAD  0.020
 6MK  plan-5  CAE  0.020
 6MK  plan-6  CAS  0.020
 6MK  plan-6  CAE  0.020
 6MK  plan-6  CAF  0.020
 6MK  plan-6  CAT  0.020
 6MK  plan-6  HAE  0.020
 6MK  plan-6  HAF  0.020

