Donor Atom

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Tripos Bookshelf > SLN > Specify 3D Queries > Define Ligand/Receptor Interaction Features

6.3.3 Donor Atom

Finds an atom that can act as a hydrogen-bond donor. It includes both explicit donors (with an H attached), and implicit donors (basic atoms that can be a donor when protonated or in a different tautomeric form). When defining the donor atom, you can associate it to a particular acceptor site feature, and thereby specify the directionality of the hydrogen bond. If an acceptor site is associated to the atom, a line connecting the two is displayed. This feature type is represented by a single point at the designated location.

Limitation:

UNITY attempts to model what would happen to a molecule at physiological pH. As a result, some structures might yield slightly different site points than expected.

SLN Format

donor_atom[name=feature_name;target=target_spec;\ 
	 connection=acceptor_site;rules=rule_names;\
	 color=name_of_color]

name--Name for the heteroatom forming the hydrogen bond.
target--Target value for the feature.
connection--Specify an existing acceptor site that forms the acceptor-donor pair with this donor atom.
rules--List of rules, from the file $TA_ROOT/tables/sln3d_macros.def, to apply. Only the rules listed are applied, and they are applied in the order given.
color--Optional. Color to use for the feature.

SLN Example

 
        donor_atom[name=donor_atom1;target=(-3.511,4.010,\
	 -1.841);connection=acceptor_site1;color=magenta]

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Define Donor Atom Feature in SYBYL

Define donor atom:

UNITY > Define Query > Manage

Select MACRO and DONOR_ATOM as class and type, respectively.
Press Add.
Click atom/feature defining new feature.
Enter a name for new feature.
Select an existing acceptor site to associate with the donor atom, if desired; otherwise, press End Select.
Specify if a spatial constraint should be created. If Yes, enter a tolerance and a color.

or UNITY > Features > Donor Atom

Specify molecular area containing the query.
Select method of defining the feature:
ENTER_TARGET--Enter coordinates for new feature.
PICK_FEATURE_OR_ATOM--Click feature/atom defining new feature.
POSITION_WITH_MOUSE--Click and drag displayed feature point to desired location.
Enter a name for new feature.
Select an existing acceptor site to associate with the donor atom, if desired; otherwise, press End Select.
Specify if a spatial constraint should be created. If Yes, enter a tolerance and a color.

Command:

DEFINE UNITY_FEATURE DONOR_ATOM \ mol_area ENTER_TARGET|\ PICK_FEATURE_OR_ATOM [xyz] name \ assoc_feature constraint [tolerance]

mol_area--Area containing the query.
ENTER_TARGET--Enter coordinates identifying feature's target location.
PICK_FEATURE_OR_ATOM--Click atom/feature defining new feature.
name--Name for new feature.
assoc_feature--Identify an existing acceptor site to associate with the donor atom, if desired; otherwise enter the end loop character (in picking mode press End Select).
constraint--Specify if a spatial constraint should be created. If YES, enter a tolerance and a color.

Define donor atom:	UNITY > Define Query > Manage Select MACRO and DONOR_ATOM as class and type, respectively. Press Add. Click atom/feature defining new feature. Enter a name for new feature. Select an existing acceptor site to associate with the donor atom, if desired; otherwise, press End Select. Specify if a spatial constraint should be created. If Yes, enter a tolerance and a color.
	or UNITY > Features > Donor Atom Specify molecular area containing the query. Select method of defining the feature: ENTER_TARGET--Enter coordinates for new feature. PICK_FEATURE_OR_ATOM--Click feature/atom defining new feature. POSITION_WITH_MOUSE--Click and drag displayed feature point to desired location. Enter a name for new feature. Select an existing acceptor site to associate with the donor atom, if desired; otherwise, press End Select. Specify if a spatial constraint should be created. If Yes, enter a tolerance and a color.
Command:	`DEFINE UNITY_FEATURE DONOR_ATOM \` `mol_area ENTER_TARGET\|\` `PICK_FEATURE_OR_ATOM [xyz] name \` `assoc_feature constraint [tolerance]` mol_area--Area containing the query. `ENTER_TARGET`--Enter coordinates identifying feature's target location. `PICK_FEATURE_OR_ATOM`--Click atom/feature defining new feature. name--Name for new feature. assoc_feature--Identify an existing acceptor site to associate with the donor atom, if desired; otherwise enter the end loop character (in picking mode press End Select). constraint--Specify if a spatial constraint should be created. If `YES`, enter a tolerance and a color.

UNITY > Define Query > Feature Sets

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