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Chapter 18. Flexible target atoms
Atom Type numbers from 200 to 399 are reserved for Target atoms whose conformation may change in response to the Probe (see Directive MOVE for more informtion about conformationally flexible Target atoms). Each type number between 200 and 399 corresponds to a smaller Type number in the range 0 to 99. For example, Type 228 here corresponds to Type 28 above.
18.1. Types of flexible target atoms
18.1.1. Type 228 (N1IN = 228)
This is an ether oxygen atom which connects the Core of the Target to a flexible side chain. It is actually an atom (or HETATM) in the Core, and its position does not alter. However, it can rotate with any attached side chain atoms, as their position or conformation changes. A simple example is provided by:
C==C CH2--CH3 / \ / C C---O \\ // C--C |
in which the benzene ring and oxygen are the Core of the Target, and the ethyl group is the "flexible side-chain". In this case the position of the oxygen would not alter relative to the Core when the methylene group rotated about the C---O axis, but the direction in which the oxygen's lone pair electrons pointed would change. With a Type 228 oxygen as shown above, they would point down (and to the right) because the methylene is oriented upwards. On the other hand the lone pair electrons would point up (and to the right) after rotation when the methylene was down:
C==C / \ C C---O \\ // \ C--C CH2--CH3 |
The Type 228 ether oxygen accepts two weak and poorly oriented hydrogen bonds exactly like a conventional Type 28 ether oxygen, but the direction from which Type 228 receives those hydrogen bonds changes when the attached side chain rotates.
A Type 228 oxygen cannot donate hydrogen bonds. It becomes a Type 28 ether oxygen when Directive MOVE=0 in Grid.
The energy variable JTYPE for the Probe may not take the value 228. If you want an ether oxygen Probe use Type 28 instead.
Effects of directive MOVE on ethers: Ether oxygens are always assigned Type 28 when MOVE=0 in Programme GRIN. They are assigned Type 228 as described above, when MOVE=1 in Programme GRIN, and when the C---O distance corresponds to a single bond. However, they are assigned Type 28 when MOVE=1 if the Carbon-Oxygen bond to the Core is short:
In this case C==O is treated as a partial double bond, and full rotation of the methylene group as described above is not permitted. The methylene CH2 can only move a small distance from its specified position in the PDB file, and the methyl CH3 is the first side-chain group which shows full conformational flexibility.
18.1.2. Type 282 (N1IN = 282)
This is an aliphatic NH2: group with two hydrogens and a lone pair. It is connected to the Core of the Target by a methylene group like this:
L---CH2
\
NH2: |
in which L represents an atom of the Core to which the side-chain is linked. The methylene connects the Core of the Target to the nitrogen atom, and the methylene is also an atom (or HETATM) in the Core. When Directive MOVE>0 the NH2: group can rotate round the L--CH2 axis, and can both accept or donate a hydrogen bond throughout the circular arc of rotation. The direction in which it makes the hydrogen bond will change when it rotates.
The position of the nitrogen is fixed and it becomes a Type 82 NH2: group when Directive MOVE=0 in Grid.
The energy variable JTYPE for the Probe may not take the value 282. If you want an NH2: Probe use Type 82 instead.
18.1.3. Type 283 (N1IN = 283)
This is an aliphatic NH3+ cation group which is connected to the Core of the Target by a methylene group like this:
L---CH2
\
NH3+ |
in which L represents an atom of the Core to which the side-chain is linked. The methylene connects the Core of the Target to the nitrogen, and the methylene is also an atom (or HETATM) in the Core. When Directive MOVE>0 the NH3+ Group can rotate round the L--CH2 axis, and can donate a hydrogen bond throughout the circular arc of rotation. The direction in which it makes the hydrogen bond will change when it rotates.
The position of the nitrogen is fixed and it becomes a fixed Type 83 amino Group, when Directive MOVE=0 in Grid.
The energy variable JTYPE for the Probe may not take the value 283. If you want an NH3+ Probe use Type 83 instead.
18.1.4. Type 284 (N1IN = 284)
This is an aliphatic hydroxyl group which is connected to the Core of the Target by a methylene group like this:
L---CH2
\
OH |
in which L represents an atom of the Core to which the side-chain is linked. The methylene connects the Core of the Target to the hydroxyl oxygen, and the methylene is also an atom (or HETATM) in the Core. When Directive MOVE>0 the hydroxyl group can rotate round the L--CH2 axis, and can both accept or donate a hydrogen bond throughout the circular arc of rotation. The direction in which it makes the hydrogen bond will change when it rotates.
The position of the oxygen is fixed and it becomes a Type 84 hydroxy group, when Directive MOVE=0 in Grid.
The energy variable JTYPE for the Probe may not take the value 284. If you want an aliphatic hydroxyl Probe use Type 84 instead.
18.1.5. Type 297 (N1IN = 297)
This could be, for example, the nitrogen of a cyanide group which was connected to the Core of the Target by a methylene CH2 group like this:
L---CH2
\
C
\\
N |
in which L represents an atom of the Core to which the side-chain is linked. The methylene connects the Core of the Target to the cyanide carbon, and the methylene is also an atom (or HETATM) in the Core. When Directive MOVE>0 the cyanide group can rotate round the L--CH2 axis, and the cyanide carbon can accept a hydrogen bond throughout the circular arc of rotation. The direction from which it receives the hydrogen bond will change when it rotates. It cannot donate hydrogen bonds.
The positions of the cyanide carbon and nitrogen are fixed, and it becomes a Type 97 nitrogen, when Directive MOVE=0 in Grid.
The energy variable JTYPE for the Probe may not take the value 297. Use Type 97 instead.
18.1.6. Type 397 (N1IN = 397)
This might also be the nitrogen of a cyanide group, but this cyanide is connected to the Core of the Target by a pair of methylene CH2 groups like this:
x L---CH2 - - - a
\
CH2---C===N y
z |
in which L represents an atom of the Core to which the side-chain is linked. The first methylene (marked with an 'x') connects the Core of the Target to the second methylene ('z'), and this second methylene is bonded to the cyanide carbon. Note that methylene 'x' is treated as an atom (or HETATM) in the Core.
This whole side chain can rotate round the L---CH2 - - - a axis. Furthermore the CH2---C===N moiety can rotate round the axis x---z between the methylene groups. In any one conformation such as that shown above, the cyanide group would tend to accept hydrogen bonds in the direction from y towards z, and this direction would be predefined for Programme GRID by a pointer from the cyanide nitrogen to the cyanide carbon. (Programme GRIN would precompute this pointer if MOVE=0 in GRIN, and would then assign Type 97 to the cyanide nitrogen).
In the present case Directive MOVE was set as MOVE=1 in GRIN and the cyanide nitrogen was therefore assigned as Type 397. Rotational motion is permitted about both axes, and a better approximation for the hydrogen-bond vector is obtained by choosing a pointer from the cyanide nitrogen (at its instantaneous position) towards the carbon of methylene group 'x' which is the centre of rotation. The cyanide group can rotate round both axes, and the cyanide carbon can accept a hydrogen bond throughout a spherical arc of rotation. The direction from which it receives the hydrogen bond will change when it rotates. It cannot donate hydrogen bonds.
The positions of the cyanide carbon and nitrogen are fixed, and it becomes a Type 97 nitrogen, when Directive MOVE=0 in Grid.
The energy variable JTYPE for the Probe may not take the value 297. Use Type 97 instead.
18.2. Type specifications
The specifications of H-bonding Types are described above:
The number of nearby atoms to which pointers are needed.
The number of hydrogen bonds IAIN and IDIN which the group can accept and donate. Note, however, that IAIN and IDIN may also be defined by the User in datafile GRUB, and if this has been done the GRUB values will have priority over the default values .
The geometry of hydrogen bonding. This is known as the "Case", as opposed to the "Type" of hydrogen bond, since Type is a wider concept which also embraces the number of hydrogen bonds.
Alternative arrangements of the hydrogen bonds which are made by the atom. For example the alternative hydrogen positions of the hydrogen on a phenolic hydroxyl group, or the fact that a Type 83 group can rotate while a Type 3 cannot.
Note on hydrogen bond strength and length: the 'Type' of a hydrogen bond does not determine its strength or length, which depend on the values of EMIN and RMIN (or EMINH and RMINH) in datafile GRUB. The adventurous User can therefore devise a wide range of different hydrogen bonding atoms or hetatms with varied geometry, length, strength, and number of donated and accepted hydrogen bonds.
The User needs to understand the concept of hydrogen bond Type which is determined for each atom and hetatm by variable N1IN. He or she also needs to know the different Types of hydrogen bond which are available in the current version of the MD Programmes. They are listed above.
The User may eventually need to study the use of directive IHVA in Programme GRIN. It is described below under the heading "control directives". However it is NOT normally necessary for Users to study the variables N3IN, N4IN and N5IN because they are used automatically by the Programme.
18.3. Hydrogen case
The "Type" of a hydrogen is a broad concept as explained above. It embraces both the number of hydrogen bonds formed by an atom (if any); and their geometry; and their alternative positions; and rotation of the atom around its bond.
The geometry itself is defined as the "Case" of the hydrogen. Case is therefore a subproperty of Type, and the Type calls the Case as each ATOM or HETATM is input from the PDB file.
18.4. Hydrogen bonds of multi-atom probes
A slightly different treatment is required for Multi-Atom Probes such as the multi-atom ionised carboxy group, because the concept of hydrogen bonding Type is not sufficient to define the hydrogen bonds in such a case. For example, each of the oxygens in:
is Type 8 as described above, but this information alone does not characterise the hydrogen bond orientations of one oxygen relative to the other.
Note on alternative probes: several alternative carboxy Probes are supplied. The single-atom O:: Probe should be used to find sites on the Target where only one oxygen may interact. The multi-atom Probes COO- and AR.COO- should only be used in order to find the smaller number of sites at which the interactions may involve the full hydrogen bonding potential of both carboxy oxygens. Similar considerations apply for the other multi-atom Probes.
18.5. Hydrogen bonds in unknown molecules
An Unknown Molecule has records in the PDB file which begin with the six characters 'ATOM ', but the molecule name ACID(I) in these records does not correspond to any of the molecule names in datafile GRUB. Unknown Molecules are "unknown" to GRUB, and and are provided as a default fall-back feature which should never be used intentionally.
The Energy Variables for the atoms in an Unknown Molecule are selected as described above, from ATOMS which have the same ATOM name in datafile GRUB. These Energy Variables include the hydrogen bond Type. Programme GRIN searches from the top of GRUB until it finds an ATOM with a name which is identical to the name of the Target atom. The Energy Variables of this atom in GRUB are accepted, irrespective of the name of the molecule in GRUB, and a message is normally printed to the lineprinter output file GRINLOUT to remind the user that the Energy Variables have been chosen in this way.
If a matching ATOM name is not found in GRUB, Energy Variables will be guessed for that ATOM in the Unknown Molecule, and a warning will be printed to output file GRINLOUT. In this case no attempt will be made to guess hydrogen-bonding variables, and the atom will be Type 0; i.e. it will not make hydrogen bonds.
The Energy Variables for the ATOMS in an Unknown Molecule never come from the HET list at the end of GRUB (See the following Section). Those HET variables are reserved for HETATMS which have records starting with the characters 'HETATM' in the original PDB file.
18.6. HETATM hydrogen bonds
The hydrogen bonding characteristics of HETATMs are determined by the hydrogen bond Type, just as they are for ATOMs, but the Type of a HETATM is selected from the HET list at the end of datafile GRUB.
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