Revision as of 18:27, 4 August 2017

Possible structure of the object including NMReDATA reflecting the format of NMReDATA tags of SDF files

Chemical structure

For the structure part originating from the .mol part of the SDF file:

object.structure (from the .mol part of the file)

object.structure.atom[n] (for each atom n) 
object.structure.atom[n].N integer atomic mumber of atom N) 
object.structure.atom[n].X float x coordinate in A 
object.structure.atom[n].Y float y coordinate in A 
object.structure.atom[n].Z float z coordinate in A 

object.structure.bond[m] (for each bond m)
object.structure.bond[m].a1 int first atom
object.structure.bond[m].a2 int second atom
object.structure.bond[m].type int 1:for single bond, 2: for double bond, 3: for triple bond

NMR isolated signals

For the <NMR_ASSIGNMENT> (previously named NMR_SIGNALS>) of the SDF file: The signals of all isotopes are listed together, they compile the information from the tag describing the spectra (see below)

object.assignment[n] (for each assignment n)
object.assignment[n].label string label give to the atom or set of atoms
object.assignment[n].cs float chemical shift of
object.assignment[n].atom[m] integer atom number(s) assigned to the signal (start numbering at 1)

J couplings

For the <NMR_J> of the SDF file: This includes all the coupling extracted from the spectra (see below)

object.J[n] (for each coupling n listed)
object.J[n].label1 string label of the first signal 
object.J[n].label2 string label of the second signal 
object.J[n].value float coupling constant between label1 and label2

Sample data

Information about the sample

object.version string verions (content of the NMREDATA_VERSION)
object.level int level (content of the NMREDATA_LEVEL)
object.ID[n] String ID n (line n of the NMREDATA_ID tag)

When using list of signals including interchangeable assignments (see .... for examples), set to 1.

When using ambiguously assigned signals in 1D or 2D spectra (see .... for examples), set to 2.

When using interchangeable and ambiguous assignment, set to 3.

<NMREDATA_ID> (for database)

This tag is optional but very much encouraged, in particular when data are originating from a stable database. When copied from database to database, multiple ID's may be included. These will be defined by database manager and software producers.

DB_ID= the code or number is assigned by the hosting database
Title= Full analysis of whatever from methanol extract of leafs  
Comment= Here more details could be given on the record.
Comment1= Here more details could be given on the record.
Comment2= Here more details could be given on the record.
Comment3= Here more details could be given on the record.
AUTHOR=Doe John, University of Tougalpa, Swinerland (optional)
ORIGIN_ONE=2345627486 (could be about the sample name)
ORIGIN_TWO=323212KKDKKS (could give a date or other reference)
Title_L1=after sep. hplc (this could be extracted from the first line of the title in the 1H spectrum)

One or more identifier can be given under "ID". The ID will be generated by the software generating data and/or the database storing the data, etc. There may be more than one ID (for example one from the software generating it, one from the university labelling the origin of the data, one from the database, one from the publisher of the associated data, etc.) it is to the “generator” of the file to decide if/how to make it unique if desired. InChIKey/SMILES could be given if the soft generating the data is able to specify it. CAS-number if it already exists.

<NMREDATA_SMILES>;optional be strongly encouraged

Here comes the smiles code mandatoryly with explicit H... The reason to includ the smiles in the NMReDATA is that when given with protons, it can be used to generate pure text MNR description of spectra (This is under elaboration ...)

<NMREDATA_SOLVENT>

The solvent is specified using this tag.

>  <NMREDATA_SOLVENT>
CDCl3

For mixture of solvents, the most abundant is first and they are separated by "/" followed by the raio in % separated by ":"

>  <NMREDATA_SOLVENT>
CDCl3/DMSO 80:20

>  <NMREDATA_SOLVENT>
CDCl3/DMSO/D2O 80:10:10

The proportions are given in % volumes.

In the case of RDC measurements, the medium used can be specified in the line following the name of the solvent.

>  <NMREDATA_SOLVENT>
CDCl3
PBLG

The quantity of the orientation medium should be given using usual units (this is vague, but we cannot do better). Agarose used at 1% mass ratio:

>  <NMREDATA_SOLVENT>
D2O
Agarose 1%

For solid-states samples:

>  <NMREDATA_SOLVENT >
solid

<NMREDATA_CONCENTRATION> (optional)

When known, the concentration should be given. Only “mM” are allowed, but the unit is specified.

<NMREDATA_CONCENTRATION>
12.3 mM

<NMREDATA_TEMPERATURE> (optional)

When available the temperature of the sample should be given (only K are allowed, but the unit is given)

>  <NMREDATA_TEMPERATURE>
298.0 K

1D spectra

object.spectrum1d[n] (for each 1D spectrum n)
object.spectrum1d[n].S Multiplicity (string)
object.spectrum1d[n].J Scalar coupling (string)
object.spectrum1d[n].N number of nuclei (int)
object.spectrum1d[n].L Label of the signal (string)
object.spectrum1d[n].E Integral (float)
object.spectrum1d[n].I Intensity (float)
object.spectrum1d[n].T1 T1 relaxation time (float)
object.spectrum1d[n].T2 T2 relaxation time (float)
object.spectrum1d[n].Diff diffusion rate (float)

2D spectra

object.spectrum2d[n] (for each 2D spectrum n)

object.spectrum2d[n].Ja Active scalar coupling (float)
object.spectrum2d[n].L1 Label of the signal (string)
object.spectrum2d[n].L2 Label of the signal (string)
object.spectrum2d[n].I Intensity (float)