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Users can search and browse the Chemical Component Dictionary using resources such as MSDchem and Ligand Expo.
Users can search and browse the Chemical Component Dictionary using resources such as MSDchem and Ligand Expo.
Recently, redundant definitions were removed, small modifying functional groups were absorbed into complete components, and definitions with ambiguous chemical descriptions were removed. Beyond ensuring that atom names begin with their type symbol, no attempt was made to extend systematic nomenclature to non-polymer chemical components. Where possible, single atoms and small groups have been replaced by complex single compound entries. For example, the ethyl group (ETH) has been obsoleted and new definitions have been created that combine ethyl groups with neighboring residues. Any obsoleted components remain in the dictionary marked with status OBS.
The entire Chemical Component Dictionary and the companion dictionary of amino acid protonation variants can be downloaded from the wwPDB ftp site:
Chemical Component Dictionary: mmCIF (plain text) | mmCIF (gz)
Protonation Variants Companion Dictionary: mmCIF (plain text) | mmCIF (gz)
Please note that these files are large, and may take awhile to download.
The dictionary of protonation variants provides additional nomenclature information for the protonation states of standard amino acids in N-terminal, C-terminal, and free forms, and includes common side chain protonation states. The identifiers used in this extension dictionary longer identifier codes to distinguish the various protonation forms of the standard amino acids. For instance, an identifier code ARG_LFOH_DHH12 is used to identify the arginine variant with a neutral peptide unit and side chain protonated at NH1. The extended identifier codes are not compatible with the 3-character format restrictions for the residue identifier in the PDB format, so these codes do not currently appear in PDB files. In PDB entries, protonated residues are identified by the 3-character code of their parent amino acid; however, the atom nomenclature for protonated forms will be taken from the variant dictionary definitions.
Prior to development of the Chemical Component Dictionary, PDB chemical information was solely in the form of connection tables. This older representation, called the PDB HET dictionary, is still made available on the wwPDB ftp site (download). PDB HET format dictionary entries for individual components are available at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/.
Descriptions of chemical components in mmCIF and PDB formats are provided below.
MSDchem1 offers a wide range of possibilities for searching and exploring the dictionary:
- Search for a particular 3-letter code
- Search using part of the name
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Users can also search by references in macromolecules, molecule classification, and atom energy type.
A generic browsing interface lets users follow links that are available from every record in order to navigate through the relationships of the dictionary. For example, a relationship link can be followed to view the atoms of a ligand and then for a particular atom, its bonds and energy types and so on.
For more information, please see
http://www.ebi.ac.uk/msd-srv/msdchem/ligand/help.htm
Ligand Expo, formerly the Ligand Depot2, can be used to navigate the Chemical Component Dictionary. It integrates databases, services, tools and methods related to small molecules, and allows users to:
- Search for a chemical component
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- Download model and ideal chemical component coordinates
- View all instances of a component in released PDB entries
Ligand Expo provides information in Chemical Component Dictionary and individual chemical components within PDB entries for download in a variety of formats and packaging at http://ligand-expo.rcsb.org/ld-download.html.
Chemical Components in mmCIF Format
The mmCIF format combines collections of related data items (tokens) into categories. A category is essentially a table in which each token represents a row in the table. The question mark (?) is used to mark an item value as missing. A period (.) may be used to identify that there is no appropriate value for the item or that a value has been intentionally omitted.
Vectors and tables of data may be encoded in mmCIF using a loop_ directive. To build a table, the data item names corresponding to the table columns are preceded by the loop_ directive, and followed by the corresponding rows of data.
A detailed description of the mmCIF syntax and logic structure is available.
In the Chemical Component Dictionary, each chemical component is defined by sets of tokens in the five categories:
| Category (click on link for dictionary definition) | Summary of Category Contents (with examples) |
| chem_comp | Table 1 |
| chem_comp_atom | Table 2 |
| chem_comp_bond | Table 3 |
| pdbx_chem_comp_descriptor | Table 4 |
| pdbx_chem_comp_identifier | Table 5 |
In a PDB entry, the mmCIF category chem_comp is used to describe the chemical components in the file. The chemical name is described in chem_comp.name, chemical formula in chem_comp.formula, and molecular weight in chem_comp.formula_weight.
For example, the mmCIF file for PDB entry 1t5d contains the ligand 4-Chloro-benzoic Acid (ID code: 174):
Further information describing this residue (174) is then provided in the Chemical Component Dictionary (See the Example).
Chemical Components in PDB Format
The heterogen section of a PDB coordinate file describes ligands in the entry. The chemical name of the ligand is given in the HETNAM record and the chemical formula is given in the FORMUL record. Any synonyms for the chemical name are given in the HETSYN records.
For example, the PDB format file for PDB entry 1t5d contains the ligand 4-Chloro-benzoic Acid (ID code: 174):
Further information describing this residue (174) is then provided in the Chemical Component Dictionary (See the Example).
Please refer to the PDB File Format Guide for further description.
Note: Diagrams are not included in the Chemical Component Dictionary.
2 Z. Feng, L. Chen, H. Maddula, O. Akcan, R. Oughtred, H.M. Berman, J. Westbrook. (2004) Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformati
Chemical Component Dictionary
The Chemical Component Dictionary (formerly the HET Group Dictionary) is as an external reference file describing all residue and small molecule components found in PDB entries. This dictionary contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.
The chemical component dictionary is organized by the 3-character alphanumeric code that PDB assigns to each chemical component. New chemical component definitions appear in the dictionary as the entries in which they are observed are released in the PDB archive; consequently, the dictionary is updated with each weekly PDB release.
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The Concept of Musharakah ( Top )
But there are cases where this kind of "Shirkah" comes to operate automatically without any action taken by the parties. For example, after the death of a person, all his heirs inherit his property which comes into their joint ownership as an automatic consequence of the death of that person.
(2) Shirkat-ul-‘aqd: This is the second type of Shirkah which means "a partnership effected by a mutual contract". For the purpose of brevity it may also be translated as "joint commercial enterprise."
Shirkat-ul-‘aqd is further divided into three kinds:
(i) Shirkat-ul-amwal where all the partners invest some capital into a commercial enterprise.
(ii) Shirkat-ul-A‘mal where all the partners jointly undertake to render some services for their customers, and the fee charged from them is distributed among them according to an agreed ratio. For example, if two persons agree to undertake tailoring services for their customers on the condition that the wages so earned will go to a joint pool which shall be distributed between them irrespective of the size of work each partner has actually done, this partnership will be a shirkat-ul-a‘mal which is also called Shirkat-ut-taqabbul or Shirkat-us-sana’i‘ or Shirkat-ul-abdan.
(iii)The third kind of Shirkat-ul-‘aqd is Shirkat-ul-wujooh. Here the partners have no investment at all. All they do is that they purchase the commodities on a deferred price and sell them at spot. The profit so earned is distributed between them at an agreed ratio.
All these modes of "Sharing" or partnership are termed as "Shirkah" in the terminology of Islamic Fiqh, while the term "musharakah" is not found in the books of Fiqh. This term (i.e. musharakah) has been introduced recently by those who have written on the subject of Islamic modes of financing and it is normally restricted to a particular type of "Shirkah", that is, the Shirkat-ul-amwal, where two or more persons invest some of their capital in a joint commercial venture. However, sometimes it includes Shirkat-ul-a‘mal also where partnership takes place in the business of services.
It is evident from this discussion that the term "Shirkah" has a much wider sense than the term "musharakah" as is being used today. The latter is limited to the "Shirkat-ul-amwal " only, while the the former includes all types of joint ownership and those of partnership. Table 1 will show the different kinds of "Shirkah" and the two kinds which are called Musharakah" in the modern terminology.
Since "musharakah" is more relevant for the purpose of our discussion, and it is almost analogous to "Shirkat-ul-amwal", we shall now dwell upon it, explaining at the first instance, the traditional concept of this type of Shirkah, then giving a brief account of its application to the concept of financing in the modern context.
The basic rules of Musharakah ( Top )
1. Musharakah or Shirkat-ul-amwal is a relationship established by the parties through a mutual contract. Therefore, it goes without saying that all the necessary ingredients of a valid contract must be present here also. For example, the parties should be capable of entering into a contract; the contract must take place with free consent of the parties without any duress, fraud or misrepresentation, etc., etc.
But there are certain ingredients which are peculiar to the contract of "musharakah". They are summarized here:
Distribution of Profit ( Top )
The proportion of profit to be distributed between the partners must be agreed upon at the time of effecting the contract. If no such proportion has been determined, the contract is not valid in Shari‘ah.
The ratio of profit for each partner must be determined in proportion to the actual profit accrued to the business, and not in proportion to the capital invested by him. It is not allowed to fix a lump sum amount for any one of the partners, or any rate of profit tied up with his investment.
Therefore, if A and B enter into a partnership and it is agreed between them that A shall be given Rs 10,000/- per month as his share in the profit, and the rest will go to B, the partnership is invalid. Similarly, if it is agreed between them that A will get 15% of his investment, the contract is not valid. The correct basis for distribution would be an agreed percentage of the actual profit accrued to the business.
If a lump sum amount or a certain percentage of the investment has been agreed for any one of the partners, it must be expressly mentioned in the agreement that it will be subject to the final settlement at the end of the term, meaning thereby that any amount so drawn by any partner shall be treated as 'on account payment' and will be adjusted to the actual profit he may deserve at the end of the term. But if no profit is actually earned or is less than anticipated, the amount drawn by the partner shall have to be returned.
Is it necessary that the ratio of profit of each partner conforms to the ratio of capital invested by him? There is a difference of opinion among the Muslim jurists about this question.
In the view of Imam Malik and Imam Shafi‘i, it is necessary for the validity of musharakah that each partner gets the profit exactly in the proportion of his investment. Therefore, if A has invested 40% of the total capital, he must get 40% of the profit. Any agreement to the contrary which makes him entitled to get more or less than 40% will render the musharakah invalid in Shari‘ah.
On the contrary, the view of Imam Ahmad is that the ratio of profit may differ from the ratio of investment if it is agreed between the partners with their free consent. Therefore, it is permissible that a partner with 40% of investment gets 60% or 70% of the profit, while the other partner with 60% of investment gets only 40% or 30%.
The third view is presented by Imam Abu Hanifah which can be taken as a via media between the two opinions mentioned above. He says that the ratio of profit may differ from the ratio of investment in normal conditions. However, if a partner has put an express condition in the agreement that he will never work for the musharakah and will remain a sleeping partner throughout the term of musharakah, then his share of profit cannot be more than the ratio of his investment.
Sharing of Loss ( Top )
But in the case of loss, all the Muslim jurists are unanimous on the point that each partner shall suffer the loss exactly according to the ratio of his investment. Therefore, if a partner has invested 40% of the capital, he must suffer 40% of the loss, not more, not less, and any condition to the contrary shall render the contract invalid. There is a complete consensus of jurists on this principle. 3
Therefore, according to Imam Shafi‘i, the ratio of the share of a partner in profit and loss both must conform to the ratio of his investment. But according to Imam Abu Hanifah and Imam Ahmad, the ratio of the profit may differ from the ratio of investment according to the agreement of the partners, but the loss must be divided between them exactly in accordance with the ratio of capital invested by each one of them. It is this principle that has been mentioned in the famous maxim:
 Profit is based on the agreement of the parties, but loss is always subject to the ratio of investment. |
The Nature of the Capital ( Top )
Most of the Muslim jurists are of the opinion that the capital invested by each partner must be in liquid form. It means that the contract of musharakah can be based only on money, and not on commodities. In other words, the share capital of a joint venture must be in monetary form. No part of it can be contributed in kind. However, there are different views in this respect.
1. Imam Malik is of the view that the liquidity of capital is not a condition for the validity of musharakah, therefore, it is permissible that a partner contributes to the musharakah in kind, but his share shall be determined on the basis of evaluation according to the market price prevalent at the date of the contract. This view is also adopted by some Hanbali jurists.
2. Imam Abu Hanifah and Imam Ahmad are of the view that no contribution in kind is acceptable in a musharakah. Their standpoint is based on two reasons:
Firstly, they say that the commodities of each partner are always distinguishable from the commodities of the other. For example, if A has contributed one motor car to the business, and B has come with another motor car, each one of the two cars is the exclusive property of its original owner. Now, if the car of A is sold, its sale-proceeds should go to A. B has no right to claim a share in its price. Therefore, so far as the property of each partner is distinguished from the property of the other, no partnership can take place. On the contrary, if the capital invested by every partner is in the form of money, the share capital of each partner cannot be distinguished from that of the other, because the units of money are not distinguishable, therefore, they will be deemed to form a common pool, and thus the partnership comes into existence.
Secondly, they say, there are a number of situations in a contract of musharakah where the partners have to resort to redistribution of the share-capital to each partner. If the share-capital was in the form of commodities, such redistribution cannot take place, because the commodities may have been sold at that time. If the capital is repaid on the basis of its value, the value may have increased, and there is a possibility that a partner gets all the profit of the business, because of the appreciation in the value of the commodities he has invested, leaving nothing for the other partner. Conversely, if the value of those commodities decreases, there is a possibility that one partner secures some part of the original price of the commodity of the other partner in addition to his own investment.
3. Imam al-Shafi‘i has come with a via media between the two points of view explained above. He says that the commodities are of two kinds:
(i) Dhawat-ul-amthal 
(ii) Dhawat-ul-qeemah 
Now, Imam al-Shafi‘i says that the commodities of the first kind (i.e. Dhawat-ul-amthal) may be contributed to the musharakah as the share of a partner in the capital, while the commodities of the second kind (i.e. the Dhawat-ul-qeemah) cannot form part of the share capital.
By this distinction between Dhawat-ul-amthal and Dhawat-ul-qeemah, Imam al-Shafi‘i has met the second objection on 'participation by commodities' as was raised by Imam Ahmad. For in the case of Dhawat-ul-amthal, redistribution of capital may take place by giving to each partner the similar commodities he had invested. However, the first objection remains still unanswered by Imam al-Shafi‘i.
In order to meet this objection also, Imam Abu Hanifah says that the commodities falling under the category of Dhawat-ul-amthal can form part of the share capital only if the commodities contributed by each partner have been mixed together, in such a way that the commodity of one partner cannot be distinguished from that of the other.
In short, if a partner wants to participate in a musharakah by contributing some commodities to it, he can do so according to Imam Malik without any restriction, and his share in the musharakah shall be determined on the basis of the current market value of the commodities, prevalent at the date of the commencement of musharakah. According to Imam al-Shafi‘i, however, this can be done only if the commodity is from the category of Dhawat-ul-amthal.
According to Imam Abu Hanifah, if the commodities are Dhawat-ul-amthal, this can be done by mixing the commodities of each partner together. And if the commodities are Dhawat-ul-qeemah, then, they cannot form part of the share capital.
It seems that the view of Imam Malik is more simple and reasonable and meets the needs of the modern business. Therefore, this view can be acted upon.
We may, therefore, conclude from the above discussion that the share capital in a musharakah can be contributed either in cash or in the form of commodities. In the latter case, the market value of the commodities shall determine the share of the partner in the capital.
Management of Musharakah ( Top )
The normal principle of musharakah is that every partner has a right to take part in its management and to work for it. However, the partners may agree upon a condition that the management shall be carried out by one of them, and no other partner shall work for the musharakah. But in this case the sleeping partner shall be entitled to the profit only to the extent of his investment, and the ratio of profit allocated to him should not exceed the ratio of his investment, as discussed earlier.
However, if all the partners agree to work for the joint venture, each one of them shall be treated as the agent of the other in all the matters of the business and any work done by one of them in the normal course of business shall be deemed to be authorized by all the partners.
Termination of Musharakah ( Top )
Musharakah is deemed to be terminated in any one of the following events:
(1) Every partner has a right to terminate the musharakah at any time after giving his partner a notice to this effect, whereby the musharakah will come to an end.
In this case, if the assets of the musharakah are in cash form, all of them will be distributed pro rata between the partners. But if the assets are not liquidated, the partners may agree either on the liquidation of the assets, or on their distribution or partition between the partners as they are. If there is a dispute between the partners in this matter i.e. one partner seeks liquidation while the other wants partition or distribution of the non-liquid assets themselves, the latter shall be preferred, because after the termination of musharakah, all the assets are in the joint ownership of the partners, and a co-owner has a right to seek partition or separation, and no one can compel him on liquidation. However, if the assets are such that they cannot be separated or partitioned, such as machinery, then they shall be sold and the sale-proceeds shall be distributed.
(2) If any one of the partners dies during the currency of musharakah, the contract of musharakah with him stands terminated. His heirs in this case, will have the option either to draw the share of the deceased from the business, or to continue with the contract of musharakah.
(3) If any one of the partners becomes insane or otherwise becomes incapable of effecting commercial transactions, the musharakah stands terminated. Termination of Musharakah without closing the business If one of the partners wants termination of the musharakah, while the other partner or partners like to continue with the business, this purpose can be achieved by mutual agreement. The partners who want to run the business may purchase the share of the partner who wants to terminate his partnership, because the termination of musharakah with one partner does not imply its termination between the other partners.
However, in this case, the price of the share of the leaving partner must be determined by mutual consent, and if there is a dispute about the valuation of the share and the partners do not arrive at an agreed price, the leaving partner may compel other partners on the liquidation or on the distribution of the assets themselves.
The question arises whether the partners can agree, while entering into the contract of the musharakah, on a condition that the liquidation or separation of the business shall not be effected unless all the partners, or the majority of them wants to do so, and that a single partner who wants to come out of the partnership shall have to sell his share to the other partners and shall not force them on liquidation or separation.
Most of the traditional books of Islamic Fiqh seem to be silent on this question. However, it appears that there is no bar from the Shari‘ah point of view if the partners agree to such a condition right at the beginning of the musharakah. This is expressly permitted by some Hanbali jurists. This condition may be justified, especially in the modern situations, on the ground that the nature of business, in most cases today, requires continuity for its success, and the liquidation or separation at the instance of a single partner only may cause irreparable damage to the other partners.
If a particular business has been started with huge amounts of money which has been invested in a long term project, and one of the partners seeks liquidation in the infancy of the project, it may be fatal to the interests of the partners, as well as to the economic growth of the society, to give him such an arbitrary power of liquidation or separation. Therefore, such a condition seems to be justified, and it can be supported by the general principle laid down by the Holy Prophet ’
 All the conditions agreed upon by the muslims are upheld, except a condition which allows what is prohibited or prohibits what is lawful. |
So far the basic concept of shirkat-ul-amwal or musharakah in its original and traditional sense have been summarized.
Now we are in a position to discuss some basic issues involved in its application to the modern conditions as an approved mode of financing. But it seems more pertinent to discuss these issues after giving an introductory account of mudarabah which is another type of profit-sharing and a typical mode of financing. Since the rules of financing in both musharakah and mudarabah are similar and the issues involved in their application are inter related, it will be more useful to discuss the concept of mudarabah before embarking on these issues.
The Concept of Musharakah ( Top )
"Shirkah" means "Sharing" and in the terminology of Islamic Fiqh, it has been divided into two kinds:
