Mol文件和SDF文件介绍
SDF 或 MOL 文件中化合物是什么？
Mol 文件是文本文件，其中包含单个分子化合物的结构信息。
SDF（结构数据文件）由一系列连接在一起的 mol 文件以及有关化合物的一些附加信息组成。它们经常用于共享化合物结构数据库。
MDL Molfile是一种文件格式，用于保存有关分子的原子、键、连接性和坐标的信息。
molfile 包含一些头信息（header information），包含原子信息的连接表 （the Connection Table (CT)），然后是键连接和类型，然后是更复杂信息的部分。
当前事实上的标准版本是 molfile V2000，尽最近，V3000 格式已经广泛传播，足以为那些尚不支持 V3000 的应用程序带来潜在的兼容性问题。
The contents of a Molfile of L-Alanine
Alanine
L-Alanine
Title line (can be blank but line must exist) Header Block
(3 lines)
ABCDEFGH09071717443D
Program / file timestamp line
(Name of source program and a file timestamp)
Exported
Comment line (can be blank but line must exist)
6 5 0 0 1 0 3 V2000
Counts line Connection table
-0.6622 0.5342 0.0000 C 0 0 2 0 0 00.6622 -0.3000 0.0000 C 0 0 0 0 0 0-0.7207 2.0817 0.0000 C 1 0 0 0 0 0-1.8622 -0.3695 0.0000 N 0 3 0 0 0 00.6220 -1.8037 0.0000 O 0 0 0 0 0 01.9464 0.4244 0.0000 O 0 5 0 0 0 0
Atom block
(1 line for each atom): x, y, z (in angstroms), element, etc.
1 2 1 0 0 0 1 3 1 1 0 01 4 1 0 0 02 5 2 0 0 02 6 1 0 0 0
Bond block
(1 line for each bond): 1st atom, 2nd atom, type, etc.
M CHG 2 4 1 6 -1 M ISO 1 3 13
Properties block
M END
END line
(NOTE: some programs don't like a blank line before M END)
END
Counts line block specification[edit]
Counts line block specification[edit]
| Value | 6 | 5 | 0 | 0 | 0 | 1 | V2000 |
|---|---|---|---|---|---|---|---|
| Description | number of atoms | number of bonds | number of atom list | Chiral flag, 1 = chiral; 0 = not chiral | number of stext entries | number of lines of additional properties | mol version |
| Type | [Generic] | [Generic] | [Query] | [Generic] | [ISIS/Desktop] | [Generic] |
Bond block specification[edit]
The Bond Block is made up of bond lines, one line per bond, with the following format:
111 222 ttt sss xxx rrr ccc
where the values are described in the following table:
| Field | Meaning | Values |
|---|---|---|
| 111 | first atom number | |
| 222 | second atom number | |
| ttt | bond type | 1= Single, 2 = Double, 3 = Triple, 4 = Aromatic,5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = Any |
| sss | bond stereo | For single bonds: 0 = not stereo; 1= up; 4=either, 6= down For double bonds: 0= Use x-, y-, z-coords from atom block to determine cis or trans; 3=Cis or trans (either) double bond |
| xxx | not used | |
| rrr | bond topology | 0 = Either, 1 = Ring, 2 = Chain |
| ccc | reacting center status | 0 = unmarked, 1 = a center, -1 = not a center, Additional: 2 = no change, 4 = bond made/broken, 8 = bond order changes 12 = 4+8 (both made/broken and changes); 5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1) are also possible |
Extended Connection Table (V3000)[edit]
The extended (V3000) molfile consists of a regular molfile “no structure” followed by a single molfile appendix that contains the body of the connection table (Ctab). The following figure shows both an alanine structure and the extended molfile corresponding to it.
Note that the “no structure” is flagged with the “V3000” instead of the “V2000” version stamp. There are two other changes to the header in addition to the version:
- The number of appendix lines is always written as 999, regardless of how many there actually are. (All current readers will disregard the count and stop at M END.)
- The “dimensional code” is maintained more explicitly. Thus “3D” really means 3D, although “2D” will be interpreted as 3D if any non-zero Z-coordinates are found.
Unlike the V2000 molfile, the V3000 extended Rgroup molfile has the same header format as a non-Rgroup molfile.
L-Alanine
Description Header block
GSMACCS-II07189510252D 1 0.00366 0.00000 0
Header with timestamp
Figure 1, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992
Comment line
0 0 0 0 0 999 V3000
V2000-compatibility line
M V30 BEGIN CTAB
Connection table
M V30 COUNTS 6 5 0 0 1
Counts line
M V30 BEGIN ATOM M V30 1 C -0.6622 0.5342 0 0 CFG=2M V30 2 C 0.6622 -0.3 0 0M V30 3 C -0.7207 2.0817 0 0 MASS=13M V30 4 N -1.8622 -0.3695 0 0 CHG=1M V30 5 O 0.622 -1.8037 0 0M V30 6 O 1.9464 0.4244 0 0 CHG=-1M V30 END ATOM
Atom block
M V30 BEGIN BOND M V30 1 1 1 2M V30 2 1 1 3 CFG=1M V30 3 1 1 4M V30 4 2 2 5M V30 5 1 2 6M V30 END BOND
Bond block
M V30 END CTAB M END
Counts line[edit]
A counts line is required, and must be first. It specifies the number of atoms, bonds, 3D objects, and Sgroups. It also specifies whether or not the CHIRAL flag is set. Optionally, the counts line can specify molregno. This is only used when the regno exceeds 999999 (the limit of the format in the molfile header line). The format of the counts line is:
M V30 COUNTS na nb nsg n3d chiral
M V30 COUNTS na nb nsg n3d chiral [REGNO=regno] M V30 COUNTS 6 5 0 0 1
number of atoms
number of bonds
number of Sgroups
number of 3D constrains
if 1 = molecule is chiral
molecule or model regno
https://en.wikipedia.org/wiki/Chemical_table_file
2.2.2: Anatomy of a MOL file - Chemistry LibreTexts