QM Flipping (QMF)

Contents

Authors

Nigel W. Moriarty

Introduction

Histidine can be protonated on either or both of the two nitrogen atoms of the imidazole moiety. Each of the three possible forms occur as a result of the stereochemical environment of the histidine sidechain. In an atomic model, comparing the possible protonation states in situ, looking at possible H-bonding and metal coordination, it is possible to predict which is most likely correct. We describe a more direct method that uses quantum mechanical methods to calculate – also in situ – the minimum geometry and energy for comparison, and therefore more accurate identification of the most likely protonation state.

QMF is part of the Quantum Interface (QI) module that covers the interaction of Phenix with QM packages.

Running an example

QMF can only be run stand-alone in the mmtbx.quantum_interface procedure as it's not reasonable to do this during refinement. Using the same example as QMR of PDB:4w53, download from the PDB website using:

~> phenix.fetch_pdb 4w53 --mtz

Command to produce PHIL scope for QM minimisation using mmtbx.quantum_interface is:

~> mmtbx.quantum_interface 4w53.pdb iterate_NQH=HIS

which will fail because of the bulk test for hydrogen atoms.

Sorry: Model must have Hydrogen atoms

Also note that the write_qmr_phil=True option writes a PHIL file. In this example, the format of the PHIL file works for QI interface but the default works for phenix.refine.Add Hydrogen atoms to the model using:

~> phenix.ready_set 4w53.pdb

which produces a file with hydrogens atoms – 4w53.updated.pdb. It also may produce a restraints file that needs to be used next but in this case because the restraints for BNZ (benzene) are shipped with Phenix it is not necessary to supply to the program unless you want a different list of restraints (not ideal values). This file can be created cheaply but is needed as the skeleton for the QMR values to be inserted in the bond, angle and torsion restraints. So, we can repeat the quantum interface command with the new files.:

~> mmtbx.quantum_interface 4w53.updated.pdb iterate_NQH=HIS

This will prompt for the selection of the ligand which in this case is “1”.

   1 : "chain A and resid   31  and resname HIS"
   2 : "chain A and resid  200  and resname MBN"
   3 : "chain A and resid  201  and resname EPE"

Enter selection by choosing number or typing a new one ~>

The result is a PHIL scope for MBN QMR restraints:

4w53.updated_A_31_HIS.phil.

There is also a command given to run the six configurations.

~> mmtbx.quantum_interface 4w53.updated.pdb iterate_NQH=HIS 4w53.updated_A_31_HIS.phil  run_qmr=True qi.nproc=6

Note that you can edit the number of nproc to run all six configurations at once.

Once the jobs are done the important metrics are listed in the table:

Energies in units of kcal/mol
  Proton energy used : 94.5100 kcal/mol

0. HD1                  : rotamer "t70"
1. HD1, HE2             :    -1272.239 kcal/mol ~>       3.19 kcal/mol. H-Bonds : 14 rmsd :    0.03 rotamer "t70"
2. HD1 only             :    -1275.425 kcal/mol ~>       0.00 kcal/mol. H-Bonds : 14 rmsd :    0.03 rotamer "t70"
3. HE2 only             :    -1249.172 kcal/mol ~>      26.25 kcal/mol. H-Bonds : 13 rmsd :    0.10 rotamer "t70"
4. HD1, HE2 flipped     :    -1258.856 kcal/mol ~>      16.57 kcal/mol. H-Bonds : 12 rmsd :    0.18 rotamer "t-90"
5. HD1 only flipped     :    -1265.615 kcal/mol ~>       9.81 kcal/mol. H-Bonds : 13 rmsd :    0.22 rotamer "t-90"
6. HE2 only flipped     :    -1254.390 kcal/mol ~>      21.03 kcal/mol. H-Bonds : 12 rmsd :    0.20 rotamer "t-90"

A Coot command is supplied:

phenix.start_coot qm_work_dir/iterate_HIS_01_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pdb qm_work_dir/iterate_HIS_02_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pdb qm_work_dir/iterate_HIS_03_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pdb qm_work_dir/iterate_HIS_04_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pdb qm_work_dir/iterate_HIS_05_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pdb qm_work_dir/iterate_HIS_06_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pdb

And a list of PyMOL commands:

phenix.pymol qm_work_dir/iterate_HIS_01_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pml &
phenix.pymol qm_work_dir/iterate_HIS_02_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pml &
phenix.pymol qm_work_dir/iterate_HIS_03_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pml &
phenix.pymol qm_work_dir/iterate_HIS_04_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pml &
phenix.pymol qm_work_dir/iterate_HIS_05_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pml &
phenix.pymol qm_work_dir/iterate_HIS_06_cluster_final_A_31_HIS_3.5_C_D_T_PM6-D3H4_EPS_equals_78.4.pml &

Finally the information about the lowest (and near) energy configuration:

!!!   2. HD1 only             :    -1275.425 kcal/mol ~>       0.00 kcal/mol. H-Bonds : 14 rmsd :    0.03 rotamer "t70" SAME

Close
  ><   1. HD1, HE2             :    -1272.239 kcal/mol ~>       3.19 kcal/mol. H-Bonds : 14 rmsd :    0.03 rotamer "t70"

Literature