Quantum Mechanical Restraints (QMR) usage

Contents

Authors

Nigel W. Moriarty

Theory and Background

In macromolecular crystallographic structure refinement, ligands present challenges for the generation of geometric restraints due to their large chemical variability, their possible novel nature and their specific interaction with the binding pocket of the protein. Quantum-mechanical approaches are useful for providing accurate ligand geometries, but can be plagued by the number of minima in flexible molecules. In an effort to avoid these issues, the Quantum Mechanical Restraints (QMR) procedure optimizes the ligand geometry in situ, thus accounting for the influence of the macromolecule on the local energy minima of the ligand. The optimized ligand geometry is used to generate target values for geometric restraints during the crystallographic refinement. As demonstrated using a sample of >2330 ligand instances in >1700 protein–ligand models, QMR restraints generally result in lower deviations from the target stereochemistry compared with conventionally generated restraints. In particular, the QMR approach provides accurate torsion restraints for ligands and other entities.

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

Running an example

There are two major ways to interact with the QMR modules in Phenix.

  1. Run directly in phenix.refine by supplying a PHIL scope to specify the ligand details. This will modify the restraints in memory.
  2. Run a command line program (mmtbx.quantum_interface) that creates the QMR PHIL scope (which also works for the phenix.refine option) and then using the same program run the QM step to write the restraints file for refinement.

Note: Using the python2 installer requires the setting of the PHENIX_MOPAC environmental variable to point to the MOPAC executable. The python3 installer is shipped with the MOPAC executables.

mmtbx.quantum_interface

For a number of reasons, we will cover the latter first. Using the example 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 format=qi write_qmr_phil=True

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 format=qi write_qmr_phil=True

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

   1 : "chain A and resid  200  and resname MBN"
   2 : "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_200_MBN.phil.

Alternatively, a selection can be supplied directly.:

mmtbx.quantum_interface 4w53.updated.pdb format=qi write_qmr_phil=True qi.selection="chain A and resid 200 and resname MBN"

A quick tour of the PHIL scope is helpful. The complete scope for the QMR module is shown at the end of this page. A reduced scope is shown here.

qi.qm_restraints {
  selection = "chain A and resid  200  and resname MBN"
  run_in_macro_cycles = *first_only first_and_last all last_only test
  buffer = 3.5
  calculate = *in_situ_opt starting_energy final_energy starting_strain final_strain starting_bound final_bound starting_higher_single_point final_higher_single_point
  write_files = *restraints pdb_core pdb_buffer pdb_final_core *pdb_final_buffer
  restraints_filename = Auto
  package {
    program = *mopac test
    charge = Auto
    multiplicity = Auto
    method = Auto
    basis_set = Auto
    solvent_model = None
    nproc = 1
    read_output_to_skip_opt_if_available = True
    ignore_input_differences = False
    view_output = None
  }
}

The key items are the selection, buffer and package items. The selection is the active part of the QM minimisation. The buffer is the radius from the selection to include in the QM environment. The package scope defines the 3rd party QM package details.

The program will also suggest the next command line for running the QM part of the restraints calculation. The skeleton restraints file may need to be included.

~> mmtbx.quantum_interface 4w53.updated.pdb run_qmr=True 4w53.updated_A_200_MBN.phil

The result is a set of QMR restraints:

4w53.updated_A_200_MBN_3.5_C_PM6-D3H4.cif

Provide this to the desired refinements. The final QM calculation upon which the restraints are based are in:

4w53.updated_cluster_final_A_200_MBN_3.5_C_PM6-D3H4.pdb

The input and output files for the MOPAC calculations are in the directory for inspection.

mopac_4w53.updated_A_200_MBN_3.5_C_PM6-D3H4.out
mopac_4w53.updated_A_200_MBN_3.5_C_PM6-D3H4.arc
mopac_4w53.updated_A_200_MBN_3.5_C_PM6-D3H4.mop

phenix.refine

The restraints file 4w53.updated_A_200_MBN_3.5_C_PM6-D3H4.cif can be used in a refinement or the restraints can be calculated on the fly in the refinement run.

To get a PHIL scope for phenix.refine, remove the format=qi parameter from the write_qmr command.:

~> mmtbx.quantum_interface 4w53.updated.pdb write_qmr_phil=True qi.selection="chain A and resid 200 and resname MBN"

The refinement command can then be run.:

~> phenix.refine 4w53.updated.pdb 4w53.mtz 4w53.updated_A_200_MBN.phil

The major output is below including the name of the restraints file.

========================== Update restraints from QM ==========================

QM restraints calculations for macro cycle 1

Time for calculation of "chain A and resid 200 and resname MBN" using PM6-D3H4 None: -

Updating QM restraints: "chain A and resid 200 and resname MBN"
Core atoms

" C MBN A 200 " ( 2721)

" C1 MBN A 200 " ( 2722)

" C2 MBN A 200 " ( 2723)

" C3 MBN A 200 " ( 2724)

" C4 MBN A 200 " ( 2725)

" C5 MBN A 200 " ( 2726)

" C6 MBN A 200 " ( 2727)

" H1 MBN A 200 " ( 2728)

" H2 MBN A 200 " ( 2729)

" H3 MBN A 200 " ( 2730)

" H2A MBN A 200 " ( 2731)

" H3A MBN A 200 " ( 2732)

" H4 MBN A 200 " ( 2733)

" H5 MBN A 200 " ( 2734)

" H6 MBN A 200 " ( 2735)

Buffer residues

ILE A 78

LEU A 84

VAL A 87

TYR A 88

LEU A 91

ALA A 99

MET A 102

VAL A 103

VAL A 111

LEU A 118

LEU A 121

PHE A 153

MBN A 200

Starting stats: bond: 0.011 angle: 1.42 dihedral: 0.00
RMS difference in entire QM model : 0.108
Interim stats : bond: 0.009 angle: 0.59 dihedral: 0.00
Writing PDB : qmr_cluster_final_01_A_200_MBN_3.5_C_PM6-D3H4.pdb

Checking

Transfer

29 " C1 MBN A 200 " - " C2 MBN A 200 " 1.394 ~> 1.405

30 " C1 MBN A 200 " - " C6 MBN A 200 " 1.394 ~> 1.405

33 " C4 MBN A 200 " - " C5 MBN A 200 " 1.388 ~> 1.398

45 " C3 MBN A 200 " - " C4 MBN A 200 " 1.389 ~> 1.398

47 " C MBN A 200 " - " C1 MBN A 200 " 1.502 ~> 1.493

51 " C2 MBN A 200 " - " C3 MBN A 200 " 1.388 ~> 1.396

52 " C5 MBN A 200 " - " C6 MBN A 200 " 1.389 ~> 1.397

1 " C1 MBN A 200 " - " C MBN A 200 " - " H1 MBN A 200 " 111.6 ~> 108.9

2 " H2A MBN A 200 " - " C MBN A 200 " - " H3A MBN A 200 " 107.3 ~> 108.4

3 " H1 MBN A 200 " - " C MBN A 200 " - " H2A MBN A 200 " 107.2 ~> 108.2

4 " C2 MBN A 200 " - " C1 MBN A 200 " - " C6 MBN A 200 " 118.3 ~> 119.2

5 " C1 MBN A 200 " - " C MBN A 200 " - " H2A MBN A 200 " 110.9 ~> 111.7

6 " C1 MBN A 200 " - " C6 MBN A 200 " - " C5 MBN A 200 " 121.0 ~> 120.2

7 " C1 MBN A 200 " - " C2 MBN A 200 " - " C3 MBN A 200 " 121.0 ~> 120.2

8 " C MBN A 200 " - " C1 MBN A 200 " - " C2 MBN A 200 " 120.8 ~> 120.1

9 " C1 MBN A 200 " - " C2 MBN A 200 " - " H2 MBN A 200 " 119.4 ~> 120.1

10 " C1 MBN A 200 " - " C6 MBN A 200 " - " H6 MBN A 200 " 119.4 ~> 120.0

11 " C2 MBN A 200 " - " C3 MBN A 200 " - " H3 MBN A 200 " 119.8 ~> 119.5

12 " C4 MBN A 200 " - " C5 MBN A 200 " - " H5 MBN A 200 " 120.1 ~> 119.8

13 " H1 MBN A 200 " - " C MBN A 200 " - " H3A MBN A 200 " 108.1 ~> 107.8

14 " C3 MBN A 200 " - " C4 MBN A 200 " - " C5 MBN A 200 " 119.4 ~> 119.6

15 " C MBN A 200 " - " C1 MBN A 200 " - " C6 MBN A 200 " 120.9 ~> 120.7

16 " C4 MBN A 200 " - " C3 MBN A 200 " - " H3 MBN A 200 " 120.0 ~> 120.2

17 " C5 MBN A 200 " - " C4 MBN A 200 " - " H4 MBN A 200 " 120.3 ~> 120.1

18 " C6 MBN A 200 " - " C5 MBN A 200 " - " H5 MBN A 200 " 119.8 ~> 119.9

19 " C5 MBN A 200 " - " C6 MBN A 200 " - " H6 MBN A 200 " 119.6 ~> 119.7

20 " C2 MBN A 200 " - " C3 MBN A 200 " - " C4 MBN A 200 " 120.2 ~> 120.3

21 " C4 MBN A 200 " - " C5 MBN A 200 " - " C6 MBN A 200 " 120.2 ~> 120.3

22 " C3 MBN A 200 " - " C2 MBN A 200 " - " H2 MBN A 200 " 119.6 ~> 119.6

23 " C1 MBN A 200 " - " C MBN A 200 " - " H3A MBN A 200 " 111.6 ~> 111.6

24 " C3 MBN A 200 " - " C4 MBN A 200 " - " H4 MBN A 200 " 120.3 ~> 120.2

1 " C2 MBN A 200 " - " C MBN A 200 " - " C1 MBN A 200 " - " H1 MBN A 200 " 31.7 ~> 87.0

Finished stats : bond: 0.000 angle: 0.00 dihedral: 0.00
planarity (n=1) mean: 0.034 min: 0.034 max: 0.034

Writing restraints : qmr_01_A_200_MBN_3.5_C_PM6-D3H4.cif

The PHIL scope can be used for all subsequent refinements to recalculate the QM restraints.

Parameters

Literature