# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:34:42 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 1-methyl-2-[(E)-{[(pentafluorobenzyl)oxy]imino}methyl]pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccccc1/C=N/OCc2c(F)c(F)c(F)c(F)c2F
#
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
 MF5  MF5  1-methyl-2-[(E)-{[(pentafluorobenzyl)oxy]imino}methyl]pyridinium  ligand  32  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MF5
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
 MF5  FAE   F  F     0  -0.284   1.8893  -2.4166  -0.1647
 MF5  CAS   C  CR6   0   0.458   2.4294  -1.2031  -0.1264
 MF5  CAQ   C  CR6   0   0.281   3.6990  -1.0713   0.4026
 MF5  FAC   F  F     0  -0.287   4.3553  -2.1310   0.8593
 MF5  CAP   C  CR6   0   0.293   4.2835   0.1798   0.4629
 MF5  FAB   F  F     0  -0.281   5.4985   0.3171   0.9697
 MF5  CAR   C  CR6   0   0.281   3.6008   1.2863  -0.0069
 MF5  FAD   F  F     0  -0.287   4.1624   2.4874   0.0545
 MF5  CAT   C  CR6   0   0.458   2.3327   1.1277  -0.5311
 MF5  FAF   F  F     0  -0.284   1.6946   2.2079  -0.9694
 MF5  CAU   C  CR6   0  -0.403   1.7246  -0.1154  -0.6179
 MF5  CAL   C  CH2   0  -0.183   0.3417  -0.2636  -1.1684
 MF5  OAN   O  O2    0  -0.365  -0.5530  -0.0640  -0.0704
 MF5  NAM   N  N     0  -0.046  -1.8215  -0.0830  -0.4967
 MF5  CAG   C  C1    0  -0.071  -2.6655   0.0460   0.4442
 MF5  CAO   C  CR6   0   0.394  -4.0777   0.0826   0.0711
 MF5  CAJ   C  CR16  0  -0.327  -4.4873   0.2844  -1.2385
 MF5  CAH   C  CR16  0  -0.084  -5.8315   0.3173  -1.5514
 MF5  CAI   C  CR16  0  -0.329  -6.7674   0.1563  -0.5405
 MF5  CAK   C  CR16  0   0.060  -6.3230  -0.0395   0.7429
 MF5  NAV   N  NR6   1  -0.478  -5.0131  -0.0775   1.0342
 MF5  CAA   C  CH3   0  -0.566  -4.6182  -0.3132   2.4300
 MF5  HAL1  H  HCH2  0   0.272   0.1503   0.4737  -1.9485
 MF5  HAL2  H  HCH2  0   0.271   0.1940  -1.2543  -1.5993
 MF5  HAG1  H  H     0   0.307  -2.3633   0.1468   1.4819
 MF5  HAJ   H  HCR6  0   0.315  -3.7379   0.4230  -2.0027
 MF5  HAH   H  HCR6  0   0.315  -6.1453   0.4765  -2.5733
 MF5  HAI   H  HCR6  0   0.317  -7.8292   0.1818  -0.7325
 MF5  HAK   H  HCR6  0   0.351  -7.0033  -0.1718   1.5697
 MF5  HAA1  H  HCH3  0   0.301  -4.0858   0.5514   2.8169
 MF5  HAA2  H  HCH3  0   0.301  -5.5118  -0.4711   3.0216
 MF5  HAA3  H  HCH3  0   0.302  -3.9928  -1.1992   2.4905

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
 MF5  FAE  CAS   single    1.329  0.020  1.329
 MF5  CAS  CAQ   aromatic  1.382  0.020  1.382
 MF5  CAS  CAU   aromatic  1.386  0.020  1.386
 MF5  CAQ  FAC   single    1.327  0.020  1.327
 MF5  CAQ  CAP   aromatic  1.382  0.020  1.382
 MF5  CAP  FAB   single    1.324  0.020  1.324
 MF5  CAP  CAR   aromatic  1.382  0.020  1.382
 MF5  CAR  FAD   single    1.327  0.020  1.327
 MF5  CAR  CAT   aromatic  1.381  0.020  1.381
 MF5  CAT  FAF   single    1.329  0.020  1.329
 MF5  CAT  CAU   aromatic  1.387  0.020  1.387
 MF5  CAU  CAL   single    1.496  0.020  1.496
 MF5  CAL  OAN   single    1.430  0.020  1.430
 MF5  OAN  NAM   single    1.338  0.020  1.338
 MF5  NAM  CAG   double    1.271  0.020  1.271
 MF5  CAG  CAO   single    1.461  0.020  1.461
 MF5  CAO  CAJ   aromatic  1.387  0.020  1.387
 MF5  CAO  NAV   aromatic  1.352  0.020  1.352
 MF5  CAJ  CAH   aromatic  1.381  0.020  1.381
 MF5  CAH  CAI   aromatic  1.387  0.020  1.387
 MF5  CAI  CAK   aromatic  1.372  0.020  1.372
 MF5  CAK  NAV   aromatic  1.342  0.020  1.342
 MF5  NAV  CAA   single    1.470  0.020  1.470
 MF5  CAL  HAL1  single    0.970  0.020  1.090
 MF5  CAL  HAL2  single    0.970  0.020  1.090
 MF5  CAG  HAG1  single    0.930  0.020  1.080
 MF5  CAJ  HAJ   single    0.930  0.020  1.080
 MF5  CAH  HAH   single    0.930  0.020  1.080
 MF5  CAI  HAI   single    0.930  0.020  1.080
 MF5  CAK  HAK   single    0.930  0.020  1.080
 MF5  CAA  HAA1  single    0.970  0.020  1.090
 MF5  CAA  HAA2  single    0.970  0.020  1.090
 MF5  CAA  HAA3  single    0.970  0.020  1.090

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
 MF5  CAU   CAS  CAQ   121.87  3.000
 MF5  CAU   CAS  FAE   119.98  3.000
 MF5  CAQ   CAS  FAE   118.14  3.000
 MF5  CAP   CAQ  FAC   119.90  3.000
 MF5  CAP   CAQ  CAS   119.45  3.000
 MF5  FAC   CAQ  CAS   120.65  3.000
 MF5  CAR   CAP  FAB   120.02  3.000
 MF5  CAR   CAP  CAQ   120.06  3.000
 MF5  FAB   CAP  CAQ   119.92  3.000
 MF5  CAT   CAR  FAD   120.65  3.000
 MF5  CAT   CAR  CAP   119.37  3.000
 MF5  FAD   CAR  CAP   119.98  3.000
 MF5  CAU   CAT  FAF   119.84  3.000
 MF5  CAU   CAT  CAR   121.95  3.000
 MF5  FAF   CAT  CAR   118.21  3.000
 MF5  CAL   CAU  CAT   121.15  3.000
 MF5  CAL   CAU  CAS   121.52  3.000
 MF5  CAT   CAU  CAS   117.28  3.000
 MF5  HAL2  CAL  HAL1  107.94  3.000
 MF5  HAL2  CAL  OAN   110.21  3.000
 MF5  HAL1  CAL  OAN   110.18  3.000
 MF5  HAL2  CAL  CAU   111.14  3.000
 MF5  HAL1  CAL  CAU   111.01  3.000
 MF5  OAN   CAL  CAU   106.37  3.000
 MF5  NAM   OAN  CAL   110.26  3.000
 MF5  CAG   NAM  OAN   113.09  3.000
 MF5  HAG1  CAG  CAO   120.72  3.000
 MF5  HAG1  CAG  NAM   122.17  3.000
 MF5  CAO   CAG  NAM   117.10  3.000
 MF5  NAV   CAO  CAJ   119.04  3.000
 MF5  NAV   CAO  CAG   118.94  3.000
 MF5  CAJ   CAO  CAG   122.02  3.000
 MF5  HAJ   CAJ  CAH   120.83  3.000
 MF5  HAJ   CAJ  CAO   118.83  3.000
 MF5  CAH   CAJ  CAO   120.34  3.000
 MF5  HAH   CAH  CAI   120.68  3.000
 MF5  HAH   CAH  CAJ   120.03  3.000
 MF5  CAI   CAH  CAJ   119.28  3.000
 MF5  HAI   CAI  CAK   119.23  3.000
 MF5  HAI   CAI  CAH   122.10  3.000
 MF5  CAK   CAI  CAH   118.66  3.000
 MF5  HAK   CAK  NAV   116.46  3.000
 MF5  HAK   CAK  CAI   122.01  3.000
 MF5  NAV   CAK  CAI   121.53  3.000
 MF5  CAA   NAV  CAK   118.22  3.000
 MF5  CAA   NAV  CAO   120.63  3.000
 MF5  CAK   NAV  CAO   121.14  3.000
 MF5  HAA3  CAA  HAA2  109.01  3.000
 MF5  HAA3  CAA  HAA1  110.31  3.000
 MF5  HAA2  CAA  HAA1  109.00  3.000
 MF5  HAA3  CAA  NAV   109.79  3.000
 MF5  HAA2  CAA  NAV   108.69  3.000
 MF5  HAA1  CAA  NAV   110.02  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
 MF5  CONST_01  CAR   CAP  CAQ  CAS    0.00   0.0  0
 MF5  CONST_02  CAR   CAT  CAU  CAS    0.00   0.0  0
 MF5  CONST_03  CAT   CAU  CAS  CAQ    0.00   0.0  0
 MF5  CONST_04  CAT   CAR  CAP  CAQ    0.00   0.0  0
 MF5  CONST_05  CAU   CAS  CAQ  CAP    0.00   0.0  0
 MF5  CONST_06  CAU   CAT  CAR  CAP    0.00   0.0  0
 MF5  CONST_07  CAI   CAH  CAJ  CAO    0.00   0.0  0
 MF5  CONST_08  CAI   CAK  NAV  CAO    0.00   0.0  0
 MF5  CONST_09  CAK   NAV  CAO  CAJ    0.00   0.0  0
 MF5  CONST_10  CAK   CAI  CAH  CAJ    0.00   0.0  0
 MF5  CONST_11  NAV   CAO  CAJ  CAH    0.00   0.0  0
 MF5  CONST_12  NAV   CAK  CAI  CAH    0.00   0.0  0
 MF5  CONST_13  CAP   CAQ  CAS  FAE  180.00   0.0  0
 MF5  CONST_14  CAT   CAU  CAS  FAE  180.00   0.0  0
 MF5  CONST_15  FAB   CAP  CAQ  CAS  180.00   0.0  0
 MF5  CONST_16  FAF   CAT  CAU  CAS  180.00   0.0  0
 MF5  CONST_17  CAL   CAU  CAS  CAQ  180.00   0.0  0
 MF5  CONST_18  FAD   CAR  CAP  CAQ  180.00   0.0  0
 MF5  CONST_19  CAU   CAS  CAQ  FAC  180.00   0.0  0
 MF5  CONST_20  CAR   CAP  CAQ  FAC  180.00   0.0  0
 MF5  CONST_21  FAF   CAT  CAR  CAP  180.00   0.0  0
 MF5  CONST_22  CAT   CAR  CAP  FAB  180.00   0.0  0
 MF5  CONST_23  CAL   CAU  CAT  CAR  180.00   0.0  0
 MF5  CONST_24  CAU   CAT  CAR  FAD  180.00   0.0  0
 MF5  CONST_25  CAH   CAJ  CAO  CAG  180.00   0.0  0
 MF5  CONST_26  CAK   NAV  CAO  CAG  180.00   0.0  0
 MF5  CONST_27  CAA   NAV  CAO  CAJ  180.00   0.0  0
 MF5  CONST_28  CAA   NAV  CAK  CAI  180.00   0.0  0
 MF5  CONST_29  HAH   CAH  CAJ  CAO  180.00   0.0  0
 MF5  CONST_30  HAK   CAK  NAV  CAO  180.00   0.0  0
 MF5  CONST_31  HAI   CAI  CAH  CAJ  180.00   0.0  0
 MF5  CONST_32  HAJ   CAJ  CAH  CAI  180.00   0.0  0
 MF5  Var_01    OAN   CAL  CAU  CAS   90.56  30.0  2
 MF5  Var_02    CAJ   CAO  CAG  NAM  -14.79  30.0  2
 MF5  Var_03    HAA1  CAA  NAV  CAO   64.04  30.0  2
 MF5  Var_04    CAO   CAG  NAM  OAN  177.98   0.0  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
 MF5  plan-1  FAE   0.020
 MF5  plan-1  CAS   0.020
 MF5  plan-1  CAQ   0.020
 MF5  plan-1  FAC   0.020
 MF5  plan-1  CAP   0.020
 MF5  plan-1  FAB   0.020
 MF5  plan-1  CAR   0.020
 MF5  plan-1  FAD   0.020
 MF5  plan-1  CAT   0.020
 MF5  plan-1  FAF   0.020
 MF5  plan-1  CAU   0.020
 MF5  plan-1  CAL   0.020
 MF5  plan-2  CAG   0.020
 MF5  plan-2  CAO   0.020
 MF5  plan-2  CAJ   0.020
 MF5  plan-2  CAH   0.020
 MF5  plan-2  CAI   0.020
 MF5  plan-2  CAK   0.020
 MF5  plan-2  NAV   0.020
 MF5  plan-2  CAA   0.020
 MF5  plan-2  HAJ   0.020
 MF5  plan-2  HAH   0.020
 MF5  plan-2  HAI   0.020
 MF5  plan-2  HAK   0.020
 MF5  plan-3  OAN   0.020
 MF5  plan-3  NAM   0.020
 MF5  plan-3  CAG   0.020
 MF5  plan-3  CAO   0.020
 MF5  plan-3  HAG1  0.020

