CLOGP Reference Manual

Daylight Version 4.9
Release Date 08/01/11

Copyright Notice

Copyright notice: This document is copyrighted © 1992-2011 by Daylight Chemical Information Systems, Inc. of Laguna Niguel, CA. Daylight explicitly grants permission to reproduce this document under the condition that it is reproduced in its entirety, including this notice. All other rights are reserved. The underlying program CLOGP is copyrighted (1988-2011) by Pomona College and BioByte, Inc. of Claremont, CA. All rights are reserved.


Table of Contents

1. Introduction 2. Fundamental Fragments
3. Correction Factors
4. Summary
5. Bibliography
6. Example CLOGP Calculations
7 Appendix - Example Calculations

1. Introduction

The CLOGP Reference Manual will help the user understand why the CLOGP program calculates logP(ow) the way it does. Although the procedure cannot be derived from first principles, we have tried to make the rules consistent with solvation theory, if for no other reason than they are more easily remembered. The method simply adds together values for structural parts of a solute molecule and correction factors dependent upon the particular way the parts are put together.

The CLOGP EXAMPLES section contains example CLOGP calculations for a variety of chemicals and is designed as a companion to the CLOGP Reference Manual. An asterisk (*) appears in the CLOGP Reference Manual when one or more examples are provided in CLOGP Example Calculations to illustrate aspects of the CLOGP computation. Examples also demonstrate DEPICT (chemical depiction).

Funding for the development of CLOGP was provided by the U.S. Environmental Protection Agency through Cooperative Agreement No. 809295, and we wish to acknowledge the encouragement and support of the project officer, Dr. Gilman Veith of ERL-Duluth.

1.1 Measurement and Past Uses of Partition Coefficients

The partition coefficient is the equilibrium concentration of solute in a non-polar solvent divided by the concentration of the same species in a polar solvent. In this and most other applications, the polar solvent is water. The logarithm of the partition coefficient, log P, has been successfully used as a hydrophobic parameter in 'extrathermo-dynamic' Hammett methodology. 1-octanol has much to recommend it as the choice for the non-polar phase (1) and logP(ow) has been used successfully in Quantitative Structure Activity Relationships (QSAR) in the following special fields: drug and pesticide design (2,3); pharmacokinetics (4); anaesthesiology (5); environmental transport and soil binding (6,7); toxicology (8); bioaccumulation (9); protein folding (10); enzyme binding (11,12); enzymic reactions in non-aqueous solvents (13); and host-guest complexation (14a,b).

In principle, the measurement of the equilibrium concentration of solute in the octanol and water phases, after shaking in a separatory funnel, is very simple, and since good measured values are always to be preferred over calculated ones, it would seem that there should be little need for a procedure to calculate them. As it turns out, reliable shake-flask measurements are time-consuming and often difficult to make. The criteria for high reliability are: measurements over a 10-fold concentration range (with upper concentration no more than 75% of solubility or CMC, or no more than 5% of the aqueous phase, whichever is lower) and standard deviation of 0.03 or less in log terms. This often requires working at sub-micromolar concentrations, and so, with either UV spectrophotometry or gas chromatography, it means that the standard curves must be established with utmost care. Radiotracer methods seem well-suited for analyses at these low concentrations, but impurities as well as adsorption at phase boundaries (including container walls) can introduce significant errors.

HPLC procedures provide a way around this bottleneck(15,16) and can save time if there is a limited variety of structural types, and the log P values fall in the range of 0.5 to 4.0. Most HPLC procedures which are used to develop log P(ow) values do no use octanol and thus have to be referred to that system by standard curves which can be different depending on whether the solutes do or do not contain certain basic fragments, such as pyridine nitrogen. If the solutes do not absorb well in the UV, difficulties in detecting the elution time eliminates any advantage HPLC may have over the shake-flask method.

Procedures which employ filter probes (17) or solubility columns(18) speed up partition coefficient measurements by eliminating centrifugation as the means of phase separation. However, each has its own set of disadvantages and limit its acceptance as a method for establishing the standard values for a calculation procedure.

More efficient methods of measurement of octanol/water partition coefficients are certain to be developed in the future, but no conceivable 'breakthrough' is likely to eliminate the need for logP calculation. To put the problem in proper prospective, one need only imagine some dedicated synthetic chemist making all possible tri-substituted benzoic acids with the methods commonly available today. When finished, there would be five million analogs for which partition coefficients could be determined. And of course only by calculation is one going to have an estimate of hydrophobicity before synthesis.

The Pomona MedChem Project saw these and other arguments as reason enough to develop a method to calculate log P(ow) from structure by an additive-constitutive procedure. As it turns out, the 'constitutive' portion of the procedure was, by the very nature of the two competing solvation equilibria, very complex, and the manual method required considerable effort before it could be applied with confidence. It is the aim of the second-generation program, CLOGP, to take most of the routine calculation burden from the user but still encourage him to study the interplay of hydrophobic and polar solvation forces which can be so crucial to the design of bioactive chemicals.

1.2 How to Understand CLOGP Calculations

The first published method for calculating log P(ow) from structure (19) was based on a 'substitution' procedure and was developed with substituent pi constants for aromatic rings in mind. Of course this method was limited to deriving a new log P from a 'parent' structure whose log P was already known. Rekker(20) was the first to publish a procedure which was more general in that it assigned 'fragmental constants' to a variety of structural pieces, and the calculated log P was the sum of the values appropriate for the molecule in question. The original pi system can be expressed as:

while the expression for Rekker's fragment system is:

The method developed by Pomona MedChem (21) follows Rekker's general formulation, but there are some important differences in the approach used to derive the actual working constants. Rekker used a 'reductionist' approach - deriving the constants for carbon and hydrogen as well as those for polar fragments from a statistical treatment of a large body of log P data which contained numerous interaction factors. Both the fragment values (f) and interaction factors (F) had to be identified and evaluated concurrently. Also, Rekker neglected to clearly define just what constitutes a fragment. Instead he provides a table in which the known constants can be found (see footnote). Rekker also treats all correction factors as some multiple of a 'Magic Number' (+0.28), but the selection of multiples was not made clear in his published work. Although his method gained some acceptance for manual calculation, we considered it too seriously flawed to serve as the basis for a computer method.

In order to construct a dependable, verifiable algorithm suitable for log P calculations used in developing QSAR at Pomona College, we first elected to clearly define what constitutes a fragment. Next we chose a 'constructionist' approach to evaluate them; that is, we accepted as axiomatic that the hydrophobic portions of solutes were those most 'hydrocarbon-like', and defined these carbons and hydrogen fragment values as being truly constant. We gave very heavy emphasis to the carefully-measured values for three solutes; molecular hydrogen, methane and ethane, because from these we could derive fragment constants for carbon and hydrogen, which would be free of obscuring interactions. For all hydrocarbon structures more complex than these, whose measured values were NOT the sum of fragment values, we attempted to define the difference in terms of universally-applicable correction factors. It appears that this approach has led not only to a workable algorithm, but has highlighted the importance of certain types of polar solvation forces which have received insufficient attention in the past.

The first attempt to reduce the 'Pomona Method' of log P calculation to computer algorithm was made in collaboration with Dr. Jack Chou and Dr. Peter Jurs of Pennsylvania State University (22). It was called CLOGP. A great deal was learned in the process of developing this first version, and it certainly established the real need for a 'stand-alone' program to make these calculations. Nevertheless, CLOGP was difficult to install and modify, and many well-known correction factors could not be implemented due to programming difficulties. In light of this experience, we deemed it essential to incorporate, in the second generation program, design features which would encourage its continuing evolution. To achieve that objective, the program had to be conceived as a 'modeling system' which could operate from one or more easily-revised 'value files'. As an example of the ease of updating, the largest fragment encountered to date is:

It took less than two minutes to enter it into the database and begin to use it in calculations.

A number of significant improvements have been made to CLOGP over the past few years. The most significant improvement is the ability to estimate a polar fragment value which has not appeared in a solute having a measure log P (oct). This type of estimation is designated as 'calculated'. If the fragment in question has appeared in a measured solute, but in a different bonding environment (e.g., aromatic attached when aliphatic attached is needed), the new 4.0 version allows for all extrapolations and designates the value as 'derived'. The methodology for the 'No Missing Fragments' algorithm is explained in more detail in ref. 23.

Earlier versions of CLOGP were able to assign corrections to polar fragments interacting over two Isolating Carbons (see Section 2. following). In the latest version, this distance has been extended to three I.C.s. A significant improvement in steroid calculations recognizes the unique contribution of polar groups at the 11 position as well as some long-range intramolecular hydrogen bonds. These and a few other minor improvements will be noted in the changed values in the CLOGP Example Calculations, 6.3 .

2. Fundamental Fragments

In view of the decision to make alkane carbons and hydrogens the most fundamental fragments in the system, it is necessary to define these very carefully before defining the polar, more hydrophilic fragments.

2.1. Isolating Carbons

An 'Isolating Carbon' (I.C.) atom is carbon which is NOT doubly- or triply- bonded to a hetero atom. An I.C. may be bonded to a hetero atom by a single or an aromatic bond. This definition can be made clearer from the following two examples:

In an earlier version of the manual calculation procedure (Ref. 21 p. 34) the Kekule structures for pyrimidine was considered; the earlier rule is now superceded. In coumarin, both rings are designated as aromatic, and the only carbon which is not isolating is the one in the carbonyl group, because it is doubly bonded to a hetero outside the ring.

Although the hydrophobic value of an I.C. is constant, several types must still be identified; the degree to which they delocalize electrons in any polar fragments attached to them has a great influence on overall log P. The types of I.C.s presently identified are listed below with appropriate symbols:

Symbol  Type
A  Aliphatic
Z  Benzyl
V  Vinyl
Y  Styryl
a  Aromatic

To be completely characterized, a polar fragment must have each of its 'valence bonds' designated with one of the above symbols (see section "Fragment Valence Types"). The numerical value of the fragment will increase roughly in the order 'A' to 'a', but must be experimentally determined for high reliability.

All hydrogens bonded to I.C.s are fragments. These two kinds of fundamental fragments are the most important members of the non-polar class. A comparison of their relative values (C = 0.2; H = 0.225) is a reminder that the measure of effective cavity size may not be as simple as using van der Waals radii or CPK models.

2.2. Polar Fragments

A fragment is any atom or group of atoms bounded by Isolating Carbon atoms, and all except hydrogen are considered polar. A fragment may have many internal bonds but those connecting it to I.C.s are called 'valence bonds'. Valence bonds are most often single, but can be aromatic, as in the case of the N fragments in pyrimidine shown above. Each hydrogen in methane is a fragment, but the hydrogens in formaldehyde are not because the carbon to which they are bonded is not isolating. This is very important to remember, for one frequently sees published calculations in which one fragment value is obtained from another by the replacement of a fragment hydrogen with another fragment of known value. At the present time a good rule to follow is: "Never break up a Fragment; estimations can be made from values measured for different bond environments (see below) but a Fragment cannot be constructed from parts." Examples of fragments which cannot be "broken down" further are:

Monovalent:  -Cl;-CN
Divalent  -OC(=O)NH-
Trivalent:  -OC(=O)N<
Tetravalent:  >NC(=O)N<

As will become evident in the following sections, polar fragments can interact in various ways. To quantitate this interaction it is necessary to define several types of polar fragments:

    (A) X = any halogen, but for one type of interaction fluorine must be assigned to a special subclass,'F'. (B) Y = all non-X fragments; these are further subdivided according to:
      sensitivity to halogen interaction as 'Y-1', 'Y-2', and 'Y-3' containing '-OH' or not.

2.3. Intrinsic Values

Here the term, 'intrinsic' fragment values, means those which would, if summed, yield the correct log P without any correction factors. It is worthwhile to examine some of the accepted hypotheses as to what solvation forces or other phenomena determine these intrinsic values.

It takes more energy to form a cavity in water than in octanol. One would predict, therefore, that increasing the size of a solute would increase its log P. Other factors being equal, this appears to be the case. However, other features of the solute can partly or completely override the effect of its size.

Water is much more capable than is octanol of accommodating localized dipoles, and it contains, on a molar basis, more hydrogen bond accepting and donating groups. So it is these three factors -size, localized dipole strength, and H-bonding ability - which largely determine the sign and magnitude of any fragment value.

2.3.1 Halogens

Halogens form an intense localized dipole when bonded to an aliphatic carbon atom.* This intensity is somewhat lessened if the I.C. is benzyl and greatly lessened if it is vinyl, styryl or aromatic.* Fluorine has a negative fragment value when attached to an aliphatic carbon, because the dipole effect outweighs the effect of size. Size is of greater importance with chlorine and bromine, but even bromine is less hydrophobic than a hydrogen in an aliphatic setting. As will become evident in the following section, much of this hydrophilic polar effect can be lost through 'shielding' by other halogens, or by electronic interaction with 'Y' type polar groups.

2.3.2 H-Polar Fragments

H-Polar Fragments ('Y') almost universally form some sort of hydrogen bonds with the donor (H) or acceptor (O) of the aqueous phase. This is thought to interrupt the peculiar 'ice-like' water shell which forms around the non-polar, hydrocarbon-like portions of each solute molecule, and thereby effectively reduces cavity size. As noted above, this should reduce log P.

2.3.3 Ions

Octanol can accept some larger solutes containing a full formal charge in sufficient concentration for measurement. However, one must be careful that the species measured is the same, because water easily supports complete ionization while ion-pairing is the usual condition in octanol except at the very lowest concentrations. Consistent values can be obtained if 'standard conditions' are adhered to: 0.1 M small counter-ion (Na+ or Cl-) and extrapolation to infinite dilution. Measured in this way a carboxylate ion is about 4.1 log units lower than the undissociated acid. No single value can be given to the positive charge on a protonatedamine or quaternary ammonium, because the charge is delocalized along the hydrocarbon chain and thus the effect is dependent on chain-length. It should be emphasized at this point that, except for zwitterions, CLOGP calculates values for the neutral solute only.*

2.3.4 Unsaturations

Double bonds in isolation have a slightly negative effect on log P.* This effect may arise from the polarity of the pi electrons or else it may be due to the shorter bond length reducing cavity size. At any rate, it disappears if the double bonds are conjugated.* Triple bonds are decidedly hydrophilic and require a large negative correction factor.

3. Correction Factors

3.1 Structural Factors

3.1.1 Bonds

To properly perform its calculations, CLOGP needs to know the number and types of certain bonds in the solute structure. There is some reason to believe that, for the bonds in question, factors other than bond length affect the size of the solvent cavity needed to contain the hydrophobic portions of the solute molecule.

The effect of all bonds within any fragment is taken care of by the fragment value, and so it is NOT necessary to keep track of them, NOR of any bonds to hydrogen. And, as explained below, it is convenient to allow for the bond effect in aromatic rings by including it in a special aromatic I.C. type, 'aromatic carbon'; therefore, aromatic bonds also are NOT given special attention.

Bonds which DO need to be identified are the following:

3.1.1.1 Chain bonds

Chain bonds are non-ring bonds between I.C.s plus any valence bonds to fragments*.
3.1.1.2 Ring Bonds
Ring bonds are non-aromatic ring bonds between I.C.s plus any valence bonds to fragments*.
3.1.1.3 Branch Bonds
Branch bonds are chain bonds emanating from 'Branched Fragments' (a fragment type presently limited to phosphate esters) and counted to the last I.C. preceding any polar fragment.*

A separate count of each of these bonds types must be made, and a negative correction applied. For chain bonds only, this correction applies to bonds AFTER the first in each chain. For example, there is no net bond correction for ethane but there is one for propane. This suggests that the correction accounts for flexing of the chain which is not possible in methane or ethane. 1,2-diethylbenzene gets only a net of two bond corrections, because each chain is counted separately. Also compatible with a 'flexing' hypothesis is the fact that the correction is greater for chains than for aliphatic rings.

As noted above, an isolated double bond is assigned a negative correction factor (-0.09). This factor actually becomes slightly positive if the double bonds are conjugated in a ring such as benzene. Since it is much more convenient to assign all bonds in large fused ring systems as aromatic type, rather than using the Kekule system of alternating doubles and singles, it is worthwhile to assign a special fragment value to an aromatic carbon and include all the necessary bonding effects therein. The value of aliphatic carbon is +0.20;the value for aromatic carbon which includes all bond effects associated with the aromatic ring system is +0.13.*

3.1.2 Branching at Isolating Carbons

3.1.2.1 Chain Branch
It is well-known that iso-alkanes are more water-soluble than their n-isomers.* This branching evidently does not produce a corresponding solubility increase in the octanol phase in the partitioning process, because the correction required in CLOGP is negative in sign.

In CLOGP, the concept of branching was expanded, and now replaces the earlier use of the 'ring' cluster' correction(21). Fusion carbons in non-aromatic rings are considered as branched and given the same correction factor as chains; i.e., -0.13.* They are designated cluster branches.

3.1.2.2 Group Branch
If an H-Polar group branches from an I.C. the increase in water solubility, compared to the n-isomer, is even greater than with chain branching. Again this carries over to partitioning equilibrium; H-Polar group branching requires a larger correction than does chain branching. For this reason isopropyl alcohol is given one group branch correction and no chain branch is considered.* Tertiary butyl alcohol gets one of each type.*

If a fragment has more than two external(valence) bonds, it could be considered a branching point. However, in all cases except the 'Branched Fragments' noted above (t-amines and phosphate esters), the entire negative branching effect is included in the fragment value itself. Only in the case of the 'Branched Fragments' is the effect chain-length dependent.

3.2 Interaction Factors

3.2.1 Aliphatic Proximity (Measured Topologically)

3.2.1.1 Halogen vs. Halogen (X vs. X)
The positive correction to log P for this interaction is thought to result from dipole shielding and is limited to halogens on the same (geminal) or adjacent (vicinal) I.C.s. The geminal interaction is designated 'X-C-X', and the corrections can be thought to arise as follows: adding a second halogen to an I.C. which already has one creates the first X-C-X pair, and the correction required is +0.60.* Adding the third halogen to the same I.C. creates two more such paintings, each of which requires a correction of +0.5.* If the fourth halogen is added, the dipole is almost completely shielded, and the three additional pairings require corrections of +0.40 each.* For carbon tetrachloride the total geminal halogen correction would be:

EQ on pg. 12

For the vicinal halogen correction, X-C-C-X, the bond between carbons must not be double.* The correction is evaluated by subtracting one from the number of halogens meeting the structural requirement and multiplying by the factor 0.28. (Again Rekker's Magic Constant pops up!)

3.2.1.2 H-Polar vs. H-Polar (Y vs. Y)
As noted in the section on 'Intrinsic Values', the negative sign on the 'Y' fragments is thought to result from their 'structure-breaking' (and thus cavity-reducing) ability in the water phase. 'Y' fragments appear to eliminate the cavity requirement for two or more I.C.s to which they are attached. Obviously if two 'Y' fragments are located on the same or adjacent I.C.s to which they are attached. Obviously if two 'Y' fragments are located on the same or adjacent I.C.s some of this cavity reduction is going to be counted twice. Thus a positive correction factor is called for when the topological separation is less than three I.C.s. The CLOGP algorithm is an improvement over the original Rekker procedure(20) in that, in place of the same correction for every Y-C-Y or Y-C-C-Y, it makes the correction proportional to how much hydrophilic character (negative fragment value) is involved. This proportionality appears to apply even if one of the fragments is charged and has a highly negative value, but as previously noted, the CLOGP algorithm currently does not treat ions.

If one of the 'Y' fragments in a Y-C-Y interaction contains an -OH moiety (e.g. -NHOH, -COOH, or -OH itself), a greater proportion of the hydrophilic character of the pair is lost. The coefficient by which the fragment sum is multiplied increases from 0.32 to 0.42.*

If both the 'Y' fragments and the carbons of Y-C-C-Y are in a ring, the hydrophilicity loss is not as great as if they are all in a chain (coefficient 0.26 vs. 0.20).* If one 'Y' is a substituent on the ring while the other is in the ring, the correction coefficients are averaged (0.23).* If one of the carbons has two 'Y' fragments, the geminal correction is applied first; then, for the (Y-C-C,Y'Y'') correction, both pairings are calculated and averaged.* If both I.C.s have geminal 'Y' fragments, then the vicinal correction is not applicable.* (See penicillin in EXAMPLES).

3.2.1.3 Halogen vs. H-Polar (X vs. Y)
The interaction being considered at this point is limited to that which takes place across single bonds. It is therefore, probably due to an inductive or field effect. (The electronic interaction between fragments on or in aromatic rings is discussed in the following section.) In evaluating the X-C-Y correction factor, all halogens can be treated alike. However, there are at least three levels of sensitivity shown by 'Y' type fragments. In CLOGP the most sensitive class, 'Y-3', is restricted to the structural type: -SO2-R.* 'Y-2' consists of the types: -CONH-R, -O-R, -S-R, and -NH-R; and 'Y-1' of all other, H-polar fragments.* The correction factor for the first alpha-halogen (i.e. X-C-Y) is the same for all three Y-types (+0.9). For 'Y-3' fragments, this correction factor is doubled when there are two alpha halogens (X{2}-C-Y3) and tripled when there are three (X{3}-C-Y3). For 'Y-2' fragments, the second and third alpha-halogens need much less correction, and for 'Y-1', virtually none. In the case of multiple halogenation, the X-C-X and the X-C-Y corrections are additive.

The CLOGP algorithm makes no separation of 'Y' types to make the X-C-C-Y correction, but needs to distinguish fluorine from the other 'X' halogens.*

3.2.2 Electronic (through Pi-bonds)

3.2.2.1 Fragment Valence Type
As previously noted, all fragments (X or Y type) are assigned the most negative values when bonded to aliphatic I.C.s (designated as 'A'). This can be considered as the 'base' or 'intrinsic' level. If the fragment value when attached to a vinyl I.C. (V) has not been measured it can be estimated as the average of the base and aromatic-bonded (a) values.* Likewise the value for the styryl-attached fragment can be estimated as two-thirds the way from the base to the aromatic value.* CLOGP will only make these estimations when measured values have not been entered in the database.
3.2.2.2 Extension of Aromaticity
The extension of the aromatic ring system through fusion (as in naphthalene or direct substitution (as in biphenyl)) appears to increase log P, especially if the heteroaromatic atom is next to the juncture.* If the ringjoining carbons are attached only to other aromatic carbons, electron delocalization is minimal and so is the correction: +0.10 for each I.C. If the I.C.s are also attached to a polar (fused-in) fragment, such as in quinoline or 2-phenylpyrimidine, the correction is greater, +0.31.*
3.2.2.3 Sigma/Rho Fragment Interaction
When two or more X and/or Y type fragments are attached to an aromatic ring system, the correction factors can be calculated by a method very similar to that used by Hammett(23) to calculate the electronic effects in other equilibria, such as acid ionization.* This requires the assignment of a measure of electronic 'strength' (sigma) and 'susceptibility' (rho). In dealing with electronic effects on partitioning equilibria, a few fragments appear to act 'bidirectionally' and require both sigma and rho values, although they cannot, of course, act upon themselves. Most of the details of sigma and rho assignment to X and Y type fragments can be found elsewhere (24), but it should be pointed out that the latest version of the program (CLOGP) follows a newer procedure for 'fused-in' fragments. Fragments fused in aromatic rings(e.g. -N= or >C=O) may also be assigned both rho and sigma constants and treated together with 'on-ring' fragments instead of requiring a separate treatment.*

Fragments on different rings in an aromatic ring system interact with one another but the effect is attenuated.* If the two rings in the system are fused, as in 5-acetyl-1-naphthylamine, the 'intrinsic' effect is only half the sigma rho product just as it is in the biphenyl system such as in 4-(m-chlorophenyl)aniline.

One frequently encounters aromatic ring systems containing several fragments with rho and sigma values assigned, and the potential correction from all cross products of sigma/rho could be very large. Since these multiple effects are NOT additive, some scaling down procedure was indicated. The one chosen for CLOGP takes the following steps:

a) The full potential sigma/rho product for each possible interaction is calculated and placed in descending value order, AFTER considering if the fragment pair are on the same or separate rings.

b) Except for the sigma for a pyridine type nitrogen, each use of sigma or rho causes it to 'age'. The first interaction at the top of the list is entered at full potential because the current age of its sigma and rho components is 'zero' for each. Each use reduces the effective sigma or rho value to 1/2 its previous value, and so if each were at 'age 1', the increment to the correction would only be 1/4 as much as a 'fresh' interaction. The mechanics of this computation are best understood by looking at the detailed output of some complex structures. Two such examples are provided in the example section.*

3.2.3 Special Ortho

As noted in the previous section, aromatic substituent (fragment) pairs, if they have sigma and rho values assigned to them, are given the same correction factor regardless of their relative position on the ring. It is important to keep in mind that if the fragment pair are on adjacent positions (i.e. ortho), an additional correction may be required.
3.2.3.1 Crowding
'Crowding' of certain fragment types can effectively lower their aromatic-attached values. This is most apparent in the case of fragments attached to the aromatic ring through a hetero atom which possesses an electron pair, such as -NHCOCH3.* A reasonable explanation of this observation is that the lone pair can no longer remain in the plane of the ring, making the fragment attachment resemble aliphatic (A) rather than true aromatic (a). The magnitude of the correction appears to depend on both steric and electronic (field) effects(25).

If this explanation is valid, one would expect the correction to vary continuously up to a maximum characteristic of each fragment type. It was surprising, therefore, to find that the rather large data set used in the original evaluation of the 'negative ortho' effect (24) seemed to fit multiples of Rekker's Magic Constant(20). This is handled in CLOGP by assigning integers to a matrix which has generalized fragment types for coordinates.

More recent data provides many examples which do not support this 'quantized' correction. Nevertheless, it is being retained for the present because of simplicity and because its maximum is only 0.14.

3.2.3.2 Intra-Molecular Hydrogen Bonding
Hydrogen bonding is known to occur intramolecularly between two ortho subsituents if one is a donor and the other an acceptor. A classical example of such an H-bond is that in o-nitrophenol. As might be expected, an intramolecular H-bond reduces water's ability to accommodate that solute, and the log P of o-nitrophenol is over two log units higher than the m- and p-isomers in the heptane and carbon tetrachloride solvent systems. One must always keep in mind, however, that the octanol phase possesses both H-donor and H-acceptor capability, not only because it is an alcohol, but because of the 2M water present at saturation. In actuality, the presence of the intramolecular H-bond in o-nitrophenol penalizes solvation in octanol slightly more than it does solvation in water, and its log P is 0.09 log units lower than the m- and p-isomers.

In terms of intramolecular H-bonding between aromatic ortho substituents, the octanol/water system appears to be sensitive to a very restricted class. The only clear-cut cases seem to result from a carbonyl group directly attached to the ring acting as acceptor, and a directly-attached -OH or -NH- acting as donor.* In all of the cases observed so far, the correction is very close to +0.63, and is stored in the same matrix used for the 'negative ortho' corrections. Thus the 'crowding' and H-bonding ortho effects never are applied simultaneously, but a sigma/rho correction cannot be added to either.

4. Summary

The fragment method of calculating log P(ow) has been proved valuable in many fields, including drug design and hazard assessment. However, manual calculations require a great deal of instructions and become very lengthy for complex structures and thus are error-prone. The computer program, CLOGP, enables the method to be applied by non-experts and includes an estimate of error, which is not possible in the future. Regular users can avail themselves of an annual update which will bring them current with all newly measured fragment values and improved correction factors. Versions with the Unified Driver compare the calculation from structure with a measured value from log P(ow) for neutral solutes. Starlist is also included in the annual updating service. We plan to make available in the near future a searching program, GENIE, which will extend the search of Starlist to close analogs.

The current literature contains many examples of QSAR accompanied by calculations of hydrophobicity which have not been made according to a consistent application of the rules they purport to follow. This has caused some confusion and cast doubt upon the entire approach. Perhaps, if the use of CLOGP becomes more widespread, published calculations will become more comparable, especially if reference is made to the program version.

Any prediction of the future is risky, but, judging from the recent past, we can expect an increasing demand for logP(ow) values. It is inconceivable that CLOGP will be perfected to such an extent that it supplants partition coefficient measurement. The two methods should remain as they are now: mutually complimentary.

With the STARLIST module in CLOGP, the user will be able to check the calculated value against an acceptable measured value if the solute structure entered is one of over 4,000 contained in that special file which is limited to non-tautomeric structures measured at a pH where the neutral form predominates.

5. Bibliography

1) Smith, R., Hansch, C. Ames, M., J. Pharm. Sci., 64, 599 (1975).
2) Martin, Y., Quantitative Drug Design, Medicinal Research Series No. 8, Marcel Dekker, New York, 1978.
3) Magee, P., Chemtech, 11, 378 (1981). 4) Smyth, R., Pfeffer, M., Van Harken, D., Cohen, A. and Hottendorf, G.,
     Antimicrob. Agents Chemother., 10, 1004, (1981).
5) Koblin, D., Eger II, E.,Johnson, B.,Collins, P., Terrell, R., and Spears, L., Anesth. Analg., 60, 464 (1981).
6) Brown, D. and Flagg, E., J. Environ. Qual., 10, 382 (1981).
7) Ellinghausen, H.,Guth, J. and Eser, H., Ecotox. Environ. Safety, 4, 26 (1980).
8) Levitan, H., Proc. Nat. Acad. Sci. USA, 74, 2914 (1977).
9) Neeley, W., Branson, D. and Blau, G., Environ. Sci. Technol., 8, 1113 (1974).
10) Tanford, C., The Hydrophobic Effect, Wiley, New York, 1980, 2nd Ed., Ch. 13.
11) Coats, E., Genther, G., Dietrich, S., Guo, Z., and Hansch, C., J. Med. Chem., 24, 1422 (1981).
12) Smith, R., Hansch, C. and Langridge, R., Arch. Giochem. Biophys., 215, 319 (1982).
13) Martinek, K., and Semenov, A.,J. Appl. Biochem., 3, 93 (1981).
14a) Newcomb, M., Moore, S. and Cram, D., J. Am. Chem. Soc.,99, 6405 (1977).
14b) Hansch, C., J. Org. Chem., 43, 4889 (1978).
15) Unger, S. and Feuerman, T.,J. Chromatog., 176, 426 (1979).
16) Mirrlees, R. and Taylor, P., J. Med. Chem., 19, 615 (1976).
17) Tomlinson, E., Proceedings of A.Ph.A., Symposium on Partition Coefficients, San Diego, CA, (1982).
18) Tewari, Y., Miller, M., Wasik, S. and Martire, D., J. Chem. Eng. Data, 27, 451 (1982).
19) Fujita, T., Iwasa, J. and Hansch, C.,J. Am. Chem. Soc., 86, 5157(1964).
20) Rekker, R., The Hydrophobic Fragmental Constant, Elsevier, Amsterdam (1977).
21) Hansch, C. and Leo, A., Substituent Constants for Correlation Analysis in Chemistry and Biology,
      Wiley Interscience New York (1979).
21) Leo., A. and Hoekman, D., Perspect. in Drug Discov. & Design, 18, 19 (2000).
22) Chou, J. and Jurs, P., J. Chem. Inf. Comput. Sci., 19, 172 (1979).
23) Hammett, L., Physical Organic Chemistry: Reaction Rates, Equilibria and Mechanism,
      McGrawHill, New York, 1970, 2nd Ed.
24) Leo, A., J. Chem. Soc., Perkin Trans. II, 825 (1983).
25) Ogino, A., Matsumura, S. and Fujita, T., J. Med. Chem., 23, 437 (1980).
26) Leo, A. and Hansch, C.,J. Org. Chem., 36, 1539, (1971).

6. Example CLOGP Calculations

The calculations shown in the following section illustrate how CLOGP treats the basic fragment types and correction factors discussed in the reference section. No attempt was made to illustrate every fragment in the database, of course. Additional output was generated to illustrate the unusually complex sigma/rho electronic correction factor for atrazine and adenine.

The examples are arranged according to the section number of the CLOGP Reference Manual text which deals with the main feature illustrated. Since some structures illustrate more than one feature, some of these "secondary features" are also indicated by section number in the output.

Please note that there is an upper limit of 255 characters on the input SMILES string.

6.1 Interpretation of Output

6.1.1 Maps

"Verbose" CLOGP output includes a section which shows the input SMILES and assignments of fragments, rings, hydrogen counts, and isolating carbon type. These "maps" are not shown in the example section, but are discussed here. The first line in the "Map Box" gives the SMILES as entered by the user. Fragment ordering, therefore, is NOT unique, and so to completely understand the tabular results, one should become familiar with the map. The second line in the map indicates Isolating Carbon type under their respective SMILES notations. The third line numbers the polar fragments (i.e., all those NOT I.C. or hydrogen) in the order entered. The fourth line shows the locations of hydrogen atoms, including those contained in fragments. The last lines indicate the location of atoms in rings. Even in simple structures these maps can be of help in interpreting the calculations. For example, in the four calculations in section 2.3.1, the value of the -Br fragment varies from 0.2000 to 1.090. The reason is apparent from the maps which show the variation in type of I.C. attachment.

6.1.2 Picture

Each example is accompanied by a picture of the chemical structure as generated by the DEPICT algorithm. DEPICT indicates aromaticity by drawing circles inside aromatic rings and suppressing all aromatic carbons symbols. More information about how aromaticity is defined and how the picture is generated may be found in the SMILES and DEPICT sections of the Daylight Software manual.

6.1.3 Tabular Results

Most of the nomenclature in the "calculation details" is understandable after reading the main body of the CLOGP Reference Manual, but a few terms could use further explanation:
    Under Class one may find "SCREEN". This is further documented under the Description section of the CLOGP Reference Manual. For instance, it may note "possibly anomalous steroid". Under Type one may find the ring number for an Ortho interaction, for example, because there may be more than one ring on which such a correction might potentially be applicable. Under Description one finds (ZW-) or (ZW+) after the name of each fragment which can participate in zwitterion formation. However, only when strong enough pairs are present is the correction actually entered (near the bottom of the table). A sulfonic acid is strong enough even if both it and the amine are aromatic; for a carboxylic acid, both it and the amine must be aliphatic. Under "Comment" column the "CLOGP=#" is the version number of the Biobyte algorithm that is being used in the calculation, e.g. CLOGP=3.05. The calculated CLOGP appears in the "Value" column.

6.2 Examples of Anomalies

The final set of calculations illustrate some of the present shortcomings of CLOGP. For the first five of these, some rational explanation can be given for the discrepancy, and even an estimation of the amount.
    Adenosine, like 84 other measured purine nucleosides, is underpredicted by CLOGP. There is good evidence that this is due to a long-range intramolecular hydrogen bond between the 5'OH and N3 of the purine. A paper documenting this effect has been submitted for publication, and it is planned to include this correcting in upcoming versions of CLOGP. Cortisone acetate is now well predicted with the special steroid correction factors. Chain overlap is a very difficult situation to identify. The earlier attempt to account for it as a 'Fragment Branch' correction has been abandoned.

7. Appendix - Example Calculations

SMILES: CCBr
ATOM #: 123.
ISOC-ID: AA..
FRAG-ID: ..1.
H-COUNT: 32..
ethylbromide 2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment Carbon ExFragment ExFragment
 # 1

Hydrog
Bonds
Bromide [A] 2 aliphatic isolating carbons 5 hydrogens on isolating carbons 1 chain and 0 alicyclic (net)
Measured
-
-
-
  0.200
  0.390
  1.135
 -0.120
RESULT DB=17 All fragments measured CLOGP=4.01 1.605
logPstar = 1.61

SMILES: BrCc1ccccc1
ATOM #: 1.23.45678.
ISOC-ID: ..Za.aaaaa.
FRAG-ID: 1..........
H-COUNT: ..2..11111.
RING  1: ...a.aaaaa.
benzylbromide 2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
 # 1


Hydrog
Bonds
 Bromide [Z]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 7 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
Measured
-
-
-
-
  0.480
  0.195
  0.780
  1.589
 -0.120
RESULT DB=17 All fragments measured CLOGP=4.01 2.924
logPstar = 2.92

SMILES: BrC=C
ATOM #: 1.2.3
ISOC-ID: ..V.V
FRAG-ID: 1....
H-COUNT: ..1.2
vinyl bromide 2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
 # 1

Hydrog
Bonds
Mbonds
 Bromide [V]
 2 aliphatic isolating carbons
 3 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
 1 double, 0 triple (isolated bond)
Measured
-
-
-
-
  0.690
  0.390
  0.681
 -0.120
 -0.030
RESULT DB=17 All fragments measured CLOGP=4.01 1.611
logPstar = 1.57

SMILES: Brc1ccccc1
ATOM #: 1.2.34567.
ISOC-ID: ..a.aaaaa.
FRAG-ID: 1.........
H-COUNT: ....11111.
RING  1: ..a.aaaaa.
bromobenzene 2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
 # 1

Hydrog
 Bromide [a]
 6 aromatic isolating carbons
 5 hydrogens on isolating carbons
Measured
-
-
  1.090
  0.780
  1.135
RESULT DB=17 All fragments measured CLOGP=4.01 3.005
logPstar = 2.99

SMILES: NC(Cc1ccccc1)C(O)=O
ATOM #: 12.34.56789..0.1..2
ISOC-ID: ...Za.aaaaa........
FRAG-ID: 11...........1.1..1
H-COUNT: 21.2..11111....1...
RING  1: ....a.aaaaa........
phenylalanine 2.3.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
 # 1


Hydrog
Bonds
 carboxy ZW(+), primary amine ZW(-) [Z]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 7 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
Measured
-
-
-
-
 -4.000
  0.195
  0.780
  1.589
 -0.120
RESULT DB=17 All fragments measured CLOGP=4.01 -1.556
logPstar = -1.52

SMILES: C=C
ATOM #: 1.2
ISOC-ID: V.V
FRAG-ID: ...
H-COUNT: 2.2
ethylene 2.3.4.
Class Type Log(P) Contribution Description Comment Value
Carbon    
ExFragment
ExFragment
Hydrog
Mbonds
 2 aliphatic isolating carbons
 4 hydrogens on isolating carbons
 1 double, 0 triple (isolated bond)
-
-
-
  0.390
  0.908
 -0.030
RESULT DB=17 All fragments measured CLOGP=4.01 1.268
logPstar = 1.13

SMILES: C=CC=C
ATOM #: 1.23.4
ISOC-ID: V.VV.V
FRAG-ID: ......
H-COUNT: 2.11.2
1,3-butadiene 2.3.4.
Class Type Log(P) Contribution Description Comment Value
Carbon    
ExFragment
ExFragment
Hydrog
Bonds
 4 aliphatic isolating carbons
 6 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
-
-
-
  0.780
  1.362
 -0.240
RESULT DB=17 All fragments measured CLOGP=4.01 1.902
logPstar = 1.99

SMILES: CCCC
ATOM #: 1234
ISOC-ID: AAAA
FRAG-ID: ....
H-COUNT: 3223
butane 3.1.1.1.
Class Type Log(P) Contribution Description Comment Value
Carbon    
ExFragment
ExFragment
Hydrog
Bonds
 4 aliphatic isolating carbons
 10 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
-
-
-
  0.780
  2.270
 -0.240
RESULT DB=17 All fragments measured CLOGP=4.01 2.810
logPstar = 2.89

SMILES: CCOCC
ATOM #: 12345
ISOC-ID: AA.AA
FRAG-ID: ..1..
H-COUNT: 32.23
ethyl ether 3.1.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
 # 1

Hydrog
Bonds
 Ether [AA]
 4 aliphatic isolating carbons
 10 hydrogens on isolating carbons
 3 chain and 0 alicyclic (net)
Measured
-
-
-
 -1.820
  0.780
  2.270
 -0.360
RESULT DB=17 All fragments measured CLOGP=4.01 0.870
logPstar = 0.89

SMILES: C1CCCCC1
ATOM #: 1.23456.
ISOC-ID: A.AAAAA.
FRAG-ID: ........
H-COUNT: 2.22222.
RING  1: A.AAAAA.
cyclohexane 3.1.1.2.
Class Type Log(P) Contribution Description Comment Value
Carbon    
ExFragment
ExFragment
Hydrog
Bonds
 6 aliphatic isolating carbons
 12 hydrogens on isolating carbons
 0 chain and 6 alicyclic (net)
-
-
-
  1.170
  2.724
 -0.540
RESULT DB=17 All fragments measured CLOGP=4.01 3.354
logPstar = 3.44

SMILES: C1CCOC1
ATOM #: 1.2345.
ISOC-ID: A.AR.R.
FRAG-ID: ....1..
H-COUNT: 2.22.2.
RING  1: A.AAAA.
tetrahydropyran 3.1.1.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
OrthoEther
Carbon    
ExFragment
ExFragment
 # 1


Hydrog
Bonds
 Ether [RR]
 Ether in a 5-member ring
 4 aliphatic isolating carbons
 8 hydrogens on isolating carbons
 0 chain and 5 alicyclic (net)
Measured
-
-
-
-
 -1.750
  0.130
  0.780
  1.816
 -0.450
RESULT DB=17 All fragments measured CLOGP=4.01 0.526
logPstar = 0.47

SMILES: CCN(CC)CC
ATOM #: 123.45.67
ISOC-ID: AA..AA.AA
FRAG-ID: ..1......
H-COUNT: 32..23.23
triethylamine 3.1.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
 # 1

Hydrog
Bonds
 Tertiary Amine [AAA]
 6 aliphatic isolating carbons
 15 hydrogens on isolating carbons
 5 chain and 0 alicyclic (net)
Measured
-
-
-
 -2.370
  1.170
  3.405
 -0.600
RESULT DB=17 All fragments measured CLOGP=4.01 1.605
logPstar = 1.45

SMILES: CCOP(=O)(OCC)OCC
ATOM #: 1234..5..678.901
ISOC-ID: AA........AA..AA
FRAG-ID: ..11..1..1...1..
H-COUNT: 32........23..23
triethylphosphate 3.1.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
Fragbranch
 # 1

Hydrog
Bonds
Frag 1
 Phosphate ester [AAA]
 6 aliphatic isolating carbons
 15 hydrogens on isolating carbons
 5 chain and 0 alicyclic (net)
 5 net bonds (out of  6) count
Measured
-
-
-
-
 -2.290
  1.170
  3.405
 -0.600
 -1.400
RESULT DB=17 All fragments measured CLOGP=4.01 0.285
logPstar = 0.80

SMILES: c1ccccc1
ATOM #: 1.23456.
ISOC-ID: a.aaaaa.
FRAG-ID: ........
H-COUNT: 1.11111.
RING  1: a.aaaaa.
benzene 3.1.1.
Class Type Log(P) Contribution Description Comment Value
Carbon    
ExFragment
Hydrog
 6 aromatic isolating carbons
 6 hydrogens on isolating carbons
-
-
  0.780
  1.362
RESULT DB=17 All fragments measured CLOGP=4.01 2.142
logPstar = 2.13

SMILES: CC(C)C
ATOM #: 12.3.4
ISOC-ID: AA.A.A
FRAG-ID: ......
H-COUNT: 31.3.3
isobutane 3.1.2.1.
Class Type Log(P) Contribution Description Comment Value
Carbon    
ExFragment
ExFragment
ExFragment
Branch
Hydrog
Bonds
 4 aliphatic isolating carbons
 1 chain and 0 cluster branch
 10 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
-
Chain
-
-
  0.780
 -0.130
  2.270
 -0.240
RESULT DB=17 All fragments measured CLOGP=4.01 2.680
logPstar = 2.76

SMILES: CC(=O)C3CCC4C2CCC1=CC(=O)CCC1(C)C2CCC34C
ATOM #: 12..3.4.567.8.901..23..4.567..8.9.012..3
ISOC-ID: A.....A.AAA.A.AAV..W.....RAA..A.A.AAA..A
FRAG-ID: .1..1...............2..2................
H-COUNT: 3.....1.221.1.22...1.....22...3.1.22...3
RING  1: ......A.AAA.........................A...
RING  2: ..........A.A...................A.AAA...
RING  3: ................A..AA....AAA............
RING  4: ............A.AAA..........A....A.......
progesterone 3.1.2.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
ExFragment
ExFragment
 # 1
 # 2

Branch
Branch
Hydrog
Bonds
Mbonds
 Carbonyl [AA]
 Carbonyl [AV]
 19 aliphatic isolating carbons
 2 chain and 6 cluster branches
 1 non-halogen, polar group branch
 30 hydrogens on isolating carbons
 1 chain and 20 alicyclic (net)
 1 double, 0 triple (isolated bond)
Measured
Measured
-
Combined
Group
-
(COMBINED)
-
 -1.840
 -1.690
  3.705
 -1.040
 -0.220
  6.810
 -1.920
 -0.030
RESULT DB=17 All fragments measured CLOGP=4.01 3.775
logPstar = 3.87

SMILES: CC(C)Cl
ATOM #: 12.3.4.
ISOC-ID: AA.A...
FRAG-ID: .....1.
H-COUNT: 31.3...
2-chloropropane 3.1.2.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
 # 1

Hydrog
Bonds
 Chloride [A]
 3 aliphatic isolating carbons
 7 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
Measured
-
-
-
  0.060
  0.585
  1.589
 -0.240
RESULT DB=17 All fragments measured CLOGP=4.01 1.994
logPstar = 1.90

SMILES: ClC1C(Cl)C(Cl)C(Cl)C(Cl)C1Cl
ATOM #: 1.2.3.4..5.6..7.8..9.0..1.2.
ISOC-ID: ..R.R....R....R....R....R...
FRAG-ID: 1.....2....3....4....5....6.
H-COUNT: ..1.1....1....1....1....1...
RING  1: ..A.A....A....A....A....A...
hexachlorocyclohexane 3.1.2.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5
 # 6

Hydrog
Bonds
XCCX
 Chloride [A]
 Chloride [A]
 Chloride [A]
 Chloride [A]
 Chloride [A]
 Chloride [A]
 6 aliphatic isolating carbons
 6 hydrogens on isolating carbons
 0 chain and 6 alicyclic (net)
 0 F and 6 non-F fragments; 5 used.
Measured
Measured
Measured
Measured
Measured
Measured
-
-
-
-
  0.060
  0.060
  0.060
  0.060
  0.060
  0.060
  1.170
  1.362
 -0.540
  1.400
RESULT DB=17 All fragments measured CLOGP=4.01 3.752
logPstar = 3.72

SMILES: CC(C)O
ATOM #: 12.3.4
ISOC-ID: AA.A..
FRAG-ID: .....1
H-COUNT: 31.3.1
isopropyl alcohol 3.1.2.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
 # 1

Branch
Hydrog
Bonds
 Alcohol or Hydroxy [A]
 3 aliphatic isolating carbons
 1 non-halogen, polar group branch
 7 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
Measured
-
Group
-
-
 -1.640
  0.585
 -0.220
  1.589
 -0.240
RESULT DB=17 All fragments measured CLOGP=4.01 0.074
logPstar = 0.05

SMILES: CC(C)(C)O
ATOM #: 12.3..4.5
ISOC-ID: AA.A..A..
FRAG-ID: ........1
H-COUNT: 3..3..3.1
tertiary butyl alcohol 3.1.2.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
ExFragment
 # 1

Branch
Branch
Hydrog
Bonds
 Alcohol or Hydroxy [A]
 4 aliphatic isolating carbons
 1 chain and 0 cluster branch
 1 non-halogen, polar group branch
 9 hydrogens on isolating carbons
 3 chain and 0 alicyclic (net)
Measured
-
Chain
Group
-
-
 -1.640
  0.780
 -0.130
 -0.220
  2.043
 -0.360
RESULT DB=17 All fragments measured CLOGP=4.01 0.473
logPstar = 0.35

SMILES: CCl
ATOM #: 12.
ISOC-ID: A..
FRAG-ID: .1.
H-COUNT: 3..
chloromethane 3.2.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
 # 1

Hydrog
 Chloride [A]
 1 aliphatic isolating carbon
 3 hydrogens on isolating carbons
Measured
-
-
  0.060
  0.195
  0.681
RESULT DB=17 All fragments measured CLOGP=4.01 0.936
logPstar = 0.91

SMILES: ClC(Cl)Cl
ATOM #: 1.2.3..4.
ISOC-ID: ..A......
FRAG-ID: 1...2..3.
H-COUNT: ..1......
chloroform 3.2.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2
 # 3

Hydrog
Bonds
XCX
 Chloride [A]
 Chloride [A]
 Chloride [A]
 1 aliphatic isolating carbon
 1 hydrogen on isolating carbon
 2 chain and 0 alicyclic (net)
 3 interacting fragments
Measured
Measured
Measured
-
-
-
-
  0.060
  0.060
  0.060
  0.195
  0.227
 -0.240
  1.590
RESULT DB=17 All fragments measured CLOGP=4.01 1.952
logPstar = 1.97

SMILES: ClCCl
ATOM #: 1.23.
ISOC-ID: ..A..
FRAG-ID: 1..2.
H-COUNT: ..2..
dichloromethane 3.2.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Hydrog
Bonds
XCX
 Chloride [A]
 Chloride [A]
 1 aliphatic isolating carbon
 2 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
 2 interacting fragments
Measured
Measured
-
-
-
-
  0.060
  0.060
  0.195
  0.454
 -0.120
  0.600
RESULT DB=17 All fragments measured CLOGP=4.01 1.249
logPstar = 1.25

SMILES: ClC(Cl)(Cl)Cl
ATOM #: 1.2.3...4..5.
ISOC-ID: ..A..........
FRAG-ID: 1...2...3..4.
H-COUNT: .............
carbontetrachloride 3.2.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
Proximity 
 # 1
 # 2
 # 3
 # 4

Bonds
XCX
 Chloride [A]
 Chloride [A]
 Chloride [A]
 Chloride [A]
 1 aliphatic isolating carbon
 3 chain and 0 alicyclic (net)
 4 interacting fragments
Measured
Measured
Measured
Measured
-
-
-
  0.060
  0.060
  0.060
  0.060
  0.195
 -0.360
  2.800
RESULT DB=17 All fragments measured CLOGP=4.01 2.875
logPstar = 2.83

SMILES: ClCCCl
ATOM #: 1.234.
ISOC-ID: ..AA..
FRAG-ID: 1...2.
H-COUNT: ..22..
1,2-dichloroethane 3.2.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Hydrog
Bonds
XCCX
 Chloride [A]
 Chloride [A]
 2 aliphatic isolating carbons
 4 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 0 F and 2 non-F fragments; 1 used.
Measured
Measured
-
-
-
-
  0.060
  0.060
  0.390
  0.908
 -0.240
  0.280
RESULT DB=17 All fragments measured CLOGP=4.01 1.458
logPstar = 1.47

SMILES: ClC=C(Cl)Cl
ATOM #: 1.2.3.4..5.
ISOC-ID: ..V.V......
FRAG-ID: 1.....2..3.
H-COUNT: ..1........
trichlorethylene 3.2.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
 # 1
 # 2
 # 3

Hydrog
Bonds
Mbonds
XCX
 Chloride [V]
 Chloride [V]
 Chloride [V]
 2 aliphatic isolating carbons
 1 hydrogen on isolating carbon
 3 chain and 0 alicyclic (net)
 1 double, 0 triple (isolated bond)
 2 interacting fragments
Measured
Measured
Measured
-
-
-
-
-
  0.600
  0.600
  0.600
  0.390
  0.227
 -0.360
 -0.030
  0.600
RESULT DB=17 All fragments measured CLOGP=4.01 2.627
logPstar = 2.61

SMILES: ClC(Cl)=C(Cl)Cl
ATOM #: 1.2.3...4.5..6.
ISOC-ID: ..V.....V......
FRAG-ID: 1...2.....3..4.
H-COUNT: ...............
tetrachloroethylene 3.2.1.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2
 # 3
 # 4

Bonds
Mbonds
XCX
 Chloride [V]
 Chloride [V]
 Chloride [V]
 Chloride [V]
 2 aliphatic isolating carbons
 4 chain and 0 alicyclic (net)
 1 double, 0 triple (isolated bond)
 4 interacting fragments
Measured
Measured
Measured
Measured
-
-
-
-
  0.600
  0.600
  0.600
  0.600
  0.390
 -0.480
 -0.030
  1.200
RESULT DB=17 All fragments measured CLOGP=4.01 3.480
logPstar = 3.40

SMILES: CCOC(C)OCC
ATOM #: 1234.5.678
ISOC-ID: AA.A.A..AA
FRAG-ID: ..1....2..
H-COUNT: 32.1.3..23
diethylacetal 3.2.1.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Branch
Hydrog
Bonds
YCY
 Ether [AA]
 Ether [AA]
 6 aliphatic isolating carbons
 1 non-halogen, polar group branch
 14 hydrogens on isolating carbons
 6 chain and 0 alicyclic (net)
 Fragments 1 & 2: -.32 (-1.82+-1.82)
Measured
Measured
-
Group
-
-
-
 -1.820
 -1.820
  1.170
 -0.220
  3.178
 -0.720
  1.165
RESULT DB=17 All fragments measured CLOGP=4.01 0.933
logPstar = 0.84

SMILES: OC(=O)COc1ccccc1
ATOM #: 12..3.456.78901.
ISOC-ID: ......A.a.aaaaa.
FRAG-ID: 11..1..2........
H-COUNT: 1.....2...11111.
RING  1: ........a.aaaaa.
phenoxyacetic acid 3.2.1.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2


Hydrog
Bonds
YCY
 Carboxy (ZW-) [A]
 Ether [Aa]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 7 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 Fragments 1 & 2: -.42 (-1.07+-0.61)
Measured
Measured
-
-
-
-
-
 -1.070
 -0.610
  0.195
  0.780
  1.589
 -0.240
  0.706
RESULT DB=17 All fragments measured CLOGP=4.01 1.350
logPstar = 1.34

SMILES: OCCO
ATOM #: 1234
ISOC-ID: .AA.
FRAG-ID: 1..2
H-COUNT: 1221
ethylene glycol 3.2.1.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Hydrog
Bonds
YCCY
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 2 aliphatic isolating carbons
 4 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 1 pair over bond  3- 2 (AvWt=-.260)
Measured
Measured
-
-
-
-
 -1.640
 -1.640
  0.390
  0.908
 -0.240
  0.853
RESULT DB=17 All fragments measured CLOGP=4.01 -1.369
logPstar = -1.36

SMILES: O=NN1CCOCC1
ATOM #: 1.23.45678.
ISOC-ID: .....RR.RR.
FRAG-ID: 1.11...2...
H-COUNT: .....22.22.
RING  1: ...A.AAAAA.
N-nitrosomorpholine 3.2.1.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2

Hydrog
Bonds
YCCY
YCCY
 Nitrosamine [AA]
 Ether [RR]
 4 aliphatic isolating carbons
 8 hydrogens on isolating carbons
 0 chain and 6 alicyclic (net)
 1 pair over bond  5- 4 (AvWt=-.150)
 1 pair over bond  8- 7 (AvWt=-.150)
Measured
Measured
-
-
-
-
-
 -2.250
 -1.750
  0.780
  1.816
 -0.540
  0.600
  0.600
RESULT DB=17 All fragments measured CLOGP=4.01 -0.744
logPstar = -0.44

SMILES: OC1COC(O)C(O)C1O
ATOM #: 12.345.6.7.8.9.0
ISOC-ID: .R.R.R...R...R..
FRAG-ID: 1...2..3...4...5
H-COUNT: 11.2.1.1.1.1.1.1
RING  1: .A.AAA...A...A..
arabinose 3.2.1.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5

Branch
Hydrog
Bonds
YCY
YCCY
YCCY
YCCY
YCCY
YCCCY
 Alcohol or Hydroxy [A]
 Ether [RR]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 5 aliphatic isolating carbons
 4 non-halogen, polar group branches
 6 hydrogens on isolating carbons
 0 chain and 6 alicyclic (net)
 Fragments 2 & 3: -.37 (-1.75+-1.64)
 1 pair over bond  3- 2 (AvWt=-.230)
 2 pairs over bond  7- 5 (AvWt=-.245)
 1 pair over bond  9- 7 (AvWt=-.260)
 1 pair over bond  9- 2 (AvWt=-.260)
 1 pair over bond  7- 2 (AvWt=-.200)
Measured
Measured
Measured
Measured
Measured
-
Group
-
-
-
-
-
-
-
Branch
 -1.640
 -1.750
 -1.640
 -1.640
 -1.640
  0.975
 -0.880
  1.362
 -0.540
  1.254
  0.780
  0.816
  0.853
  0.853
  0.656
RESULT DB=17 All fragments measured CLOGP=4.01 -2.181
logPstar = -2.32

SMILES: CC3(C)SC2C(NC(=O)Cc1ccccc1)C(=O)N2C3C(O)=O
ATOM #: 12..3.45.6.78..9.01.23456..7..8.9.0.1.2..3
ISOC-ID: AR..A..R.R.......Za.aaaaa.........R.......
FRAG-ID: ......1....22..2...........3..3.3...4.4..4
H-COUNT: 3...3..1.1.1.....2..11111.........1...1...
RING  1: .......A.A.................A....A.........
RING  2: .A....AA........................A.A.......
RING  3: ..................a.aaaaa.................
benzylpenicillin 3.2.1.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4


Branch
Branch
Hydrog
Bonds
YCY
YCY
YCY
YCCY
 Sulfide [RR]
 NH-Amide [AZ/AA]
 Amide [AAA]
 Carboxy (ZW-) [A]
 7 aliphatic isolating carbons
 6 aromatic isolating carbons
 2 chain and 1 cluster branches
 2 non-halogen, polar group branches
 16 hydrogens on isolating carbons
 2 chain and 7 alicyclic (net)
 Fragments 1 & 3: -.32 (-0.70+-3.19)
 Fragments 2 & 3: -.32 (-2.51+-3.19)
 Fragments 3 & 4: -.37 (-3.19+-1.07)
 2 pairs over bond 20- 2 (AvWt=-.190)
Derived
Adjusted
Measured
Measured
-
-
Combined
Group
-
(COMBINED)
-
-
-
-
 -0.700
 -2.510
 -3.190
 -1.070
  1.365
  0.780
 -0.390
 -0.440
  3.632
 -0.870
  1.245
  1.824
  1.576
  0.495
RESULT DB=17 Adjusted (1) from measured value CLOGP=4.01 1.747
logPstar = 1.83

SMILES: FC(F)(F)S(=O)(=O)Nc1ccccc1
ATOM #: 12.3..4.5..6...7.89.01234.
ISOC-ID: .A................a.aaaaa.
FRAG-ID: 1..2..3.4..4...4.4........
H-COUNT: .................1..11111.
RING  1: ..................a.aaaaa.
CF3-sulfonanilide 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4


Hydrog
Bonds
XCX
Y3-X3
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 NH-Sulfonamide [aA]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 5 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 3 interacting fragments
 Effect for Y-fragment # 4
Measured
Measured
Measured
Measured
-
-
-
-
-
-
 -0.380
 -0.380
 -0.380
 -1.720
  0.195
  0.780
  1.135
 -0.480
  1.590
  2.700
RESULT DB=17 All fragments measured CLOGP=4.01 3.060
logPstar = 3.05

SMILES: FC(F)(F)S(=O)(=O)c1ccccc1
ATOM #: 12.3..4.5..6...7.8.90123.
ISOC-ID: .A...............a.aaaaa.
FRAG-ID: 1..2..3.4..4...4.........
H-COUNT: ...................11111.
RING  1: .................a.aaaaa.
CF3-phenyl-sulfone 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4


Hydrog
Bonds
XCX
Y3-X3
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 Sulfonyl [Aa]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 5 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 3 interacting fragments
 Effect for Y-fragment # 4
Measured
Measured
Measured
Measured
-
-
-
-
-
-
 -0.380
 -0.380
 -0.380
 -2.170
  0.195
  0.780
  1.135
 -0.480
  1.590
  2.700
RESULT DB=17 All fragments measured CLOGP=4.01 2.610
logPstar = 2.68

SMILES: NC(=O)C(F)(F)F
ATOM #: 12..3.4.5..6.7
ISOC-ID: ......A.......
FRAG-ID: 11..1...2..3.4
H-COUNT: 2.............
trifluoroacetamide 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4

Bonds
XCX
Y2-X3
 NH2-Amide [A]
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 1 aliphatic isolating carbon
 3 chain and 0 alicyclic (net)
 3 interacting fragments
 Effect for Y-fragment # 1
Measured
Measured
Measured
Measured
-
-
-
-
 -1.990
 -0.380
 -0.380
 -0.380
  0.195
 -0.360
  1.590
  1.700
RESULT DB=17 All fragments measured CLOGP=4.01 -0.005
logPstar = 0.12

SMILES: FC(F)(F)C(=O)Nc1ccccc1
ATOM #: 12.3..4.5..6.78.90123.
ISOC-ID: .A............a.aaaaa.
FRAG-ID: 1..2..3.4..4.4........
H-COUNT: .............1..11111.
RING  1: ..............a.aaaaa.
trifluoroacetanilide 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4


Hydrog
Bonds
XCX
Y2-X3
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 NH-Amide [aA]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 5 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 3 interacting fragments
 Effect for Y-fragment # 4
Measured
Measured
Measured
Measured
-
-
-
-
-
-
 -0.380
 -0.380
 -0.380
 -1.510
  0.195
  0.780
  1.135
 -0.480
  1.590
  1.700
RESULT DB=17 All fragments measured CLOGP=4.01 2.270
logPstar = 2.21

SMILES: FC(F)(F)Oc1ccccc1
ATOM #: 12.3..4.56.78901.
ISOC-ID: .A.......a.aaaaa.
FRAG-ID: 1..2..3.4........
H-COUNT: ...........11111.
RING  1: .........a.aaaaa.
trifluoroanisole 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4


Hydrog
Bonds
XCX
Y2-X3
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 Ether [Aa]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 5 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 3 interacting fragments
 Effect for Y-fragment # 4
Measured
Measured
Measured
Measured
-
-
-
-
-
-
 -0.380
 -0.380
 -0.380
 -0.610
  0.195
  0.780
  1.135
 -0.480
  1.590
  1.700
RESULT DB=17 All fragments measured CLOGP=4.01 3.170
logPstar = 3.17

SMILES: CCOC(=O)C(F)(F)F
ATOM #: 1234..5.6.7..8.9
ISOC-ID: AA......A.......
FRAG-ID: ..11..1...2..3.4
H-COUNT: 32..............
trifluoroacetic acid, et.ester 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4

Hydrog
Bonds
XCX
Y1-X3
 Ester [AA]
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 3 aliphatic isolating carbons
 5 hydrogens on isolating carbons
 5 chain and 0 alicyclic (net)
 3 interacting fragments
 Effect for Y-fragment # 1
Measured
Measured
Measured
Measured
-
-
-
-
-
 -1.450
 -0.380
 -0.380
 -0.380
  0.585
  1.135
 -0.600
  1.590
  1.150
RESULT DB=17 All fragments measured CLOGP=4.01 1.270
logPstar = 1.18

SMILES: NC(=O)CCl
ATOM #: 12..3.45.
ISOC-ID: ......A..
FRAG-ID: 11..1..2.
H-COUNT: 2.....2..
chloroacetamide 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Hydrog
Bonds
Y2-X1
 NH2-Amide [A]
 Chloride [A]
 1 aliphatic isolating carbon
 2 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
 Effect for Y-fragment # 1
Measured
Measured
-
-
-
-
 -1.990
  0.060
  0.195
  0.454
 -0.120
  0.900
RESULT DB=17 All fragments measured CLOGP=4.01 -0.501
logPstar = -0.53

SMILES: CC(=O)NC(CO)C(O)c1ccc(cc1)N(=O)=O
ATOM #: 12..3.45.67.8.9.0.123.45..6..7..8
ISOC-ID: A......A.A..Z...a.aaa.aa.........
FRAG-ID: .1..1.1...2...3...........4..4..4
H-COUNT: 3.....11.21.1.1...11..11.........
RING  1: ................a.aaa.aa.........
parent amphenicol 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4


Branch
Hydrog
Bonds
YCCY
YCCY
YCCCY
 NH-Amide [AA]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [Z]
 Nitro [a]
 4 aliphatic isolating carbons
 6 aromatic isolating carbons
 2 non-halogen, polar group branches
 11 hydrogens on isolating carbons
 6 chain and 0 alicyclic (net)
 1 pair over bond  6- 5 (AvWt=-.260)
 1 pair over bond  8- 5 (AvWt=-.260)
 1 pair over bond  8- 6 (AvWt=-.200)
Measured
Measured
Measured
Measured
-
-
Group
-
-
-
-
Branch
 -2.710
 -1.640
 -1.340
 -0.030
  0.780
  0.780
 -0.440
  2.497
 -0.720
  1.131
  1.053
  0.596
RESULT DB=17 All fragments measured CLOGP=4.01 -0.043
logPstar = -0.03

SMILES: OCC(NC(=O)CCl)C(O)c1ccc(cc1)N(=O)=O
ATOM #: 123.45..6.78..9.0.1.234.56..7..8..9
ISOC-ID: .AA.......A...Z...a.aaa.aa.........
FRAG-ID: 1...22..2..3....4...........5..5..5
H-COUNT: 121.1.....2...1.1...11..11.........
RING  1: ..................a.aaa.aa.........
monochloramphenicol 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5


Branch
Hydrog
Bonds
Y2-X1
YCCY
YCCY
YCCCY
 Alcohol or Hydroxy [A]
 NH-Amide [AA]
 Chloride [A]
 Alcohol or Hydroxy [Z]
 Nitro [a]
 4 aliphatic isolating carbons
 6 aromatic isolating carbons
 2 non-halogen, polar group branches
 10 hydrogens on isolating carbons
 7 chain and 0 alicyclic (net)
 Effect for Y-fragment # 2
 1 pair over bond  3- 2 (AvWt=-.260)
 1 pair over bond  9- 3 (AvWt=-.260)
 1 pair over bond  9- 2 (AvWt=-.200)
Measured
Measured
Measured
Measured
Measured
-
-
Group
-
-
-
-
-
Branch
 -1.640
 -2.710
  0.060
 -1.340
 -0.030
  0.780
  0.780
 -0.440
  2.270
 -0.840
  0.900
  1.131
  1.053
  0.596
RESULT DB=17 All fragments measured CLOGP=4.01 0.570
logPstar = 0.59

SMILES: OCC(NC(=O)C(Cl)Cl)C(O)c1ccc(cc1)N(=O)=O
ATOM #: 123.45..6.7.8..9..0.1.2.345.67..8..9..0
ISOC-ID: .AA.......A.......Z...a.aaa.aa.........
FRAG-ID: 1...22..2...3..4....5...........6..6..6
H-COUNT: 121.1.....1.......1.1...11..11.........
RING  1: ......................a.aaa.aa.........
chloramphenicol 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5
 # 6


Branch
Hydrog
Bonds
XCX
Y2-X2
YCCY
YCCY
YCCCY
 Alcohol or Hydroxy [A]
 NH-Amide [AA]
 Chloride [A]
 Chloride [A]
 Alcohol or Hydroxy [Z]
 Nitro [a]
 4 aliphatic isolating carbons
 6 aromatic isolating carbons
 2 non-halogen, polar group branches
 9 hydrogens on isolating carbons
 8 chain and 0 alicyclic (net)
 2 interacting fragments
 Effect for Y-fragment # 2
 1 pair over bond  3- 2 (AvWt=-.260)
 1 pair over bond 10- 3 (AvWt=-.260)
 1 pair over bond 10- 2 (AvWt=-.200)
Measured
Measured
Measured
Measured
Measured
Measured
-
-
Group
-
-
-
-
-
-
Branch
 -1.640
 -2.710
  0.060
  0.060
 -1.340
 -0.030
  0.780
  0.780
 -0.440
  2.043
 -0.960
  0.600
  1.300
  1.131
  1.053
  0.596
RESULT DB=17 All fragments measured CLOGP=4.01 1.283
logPstar = 1.14

SMILES: OCC(NC(=O)C(Cl)(Cl)Cl)C(O)c1ccc(cc1)N(=O)=O
ATOM #: 123.45..6.7.8...9..0..1.2.3.456.78..9..0..1
ISOC-ID: .AA.......A...........Z...a.aaa.aa.........
FRAG-ID: 1...22..2...3...4..5....6...........7..7..7
H-COUNT: 121.1.................1.1...11..11.........
RING  1: ..........................a.aaa.aa.........
trichloramphenicol 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5
 # 6
 # 7


Branch
Hydrog
Bonds
XCX
Y2-X3
YCCY
YCCY
YCCCY
 Alcohol or Hydroxy [A]
 NH-Amide [AA]
 Chloride [A]
 Chloride [A]
 Chloride [A]
 Alcohol or Hydroxy [Z]
 Nitro [a]
 4 aliphatic isolating carbons
 6 aromatic isolating carbons
 2 non-halogen, polar group branches
 8 hydrogens on isolating carbons
 9 chain and 0 alicyclic (net)
 3 interacting fragments
 Effect for Y-fragment # 2
 1 pair over bond  3- 2 (AvWt=-.260)
 1 pair over bond 11- 3 (AvWt=-.260)
 1 pair over bond 11- 2 (AvWt=-.200)
Measured
Measured
Measured
Measured
Measured
Measured
Measured
-
-
Group
-
-
-
-
-
-
Branch
 -1.640
 -2.710
  0.060
  0.060
  0.060
 -1.340
 -0.030
  0.780
  0.780
 -0.440
  1.816
 -1.080
  1.590
  1.700
  1.131
  1.053
  0.596
RESULT DB=17 All fragments measured CLOGP=4.01 2.386
logPstar = 1.97

SMILES: OCC(Cl)Cl
ATOM #: 123.4..5.
ISOC-ID: .AA......
FRAG-ID: 1...2..3.
H-COUNT: 121......
2,2-dichloroethanol 3.2.1.3
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3

Hydrog
Bonds
XCX
XCCY
 Alcohol or Hydroxy [A]
 Chloride [A]
 Chloride [A]
 2 aliphatic isolating carbons
 3 hydrogens on isolating carbons
 3 chain and 0 alicyclic (net)
 2 interacting fragments
 0 F and 2 non-F interactions
Measured
Measured
Measured
-
-
-
-
-
 -1.640
  0.060
  0.060
  0.390
  0.681
 -0.360
  0.600
  0.700
RESULT DB=17 All fragments measured CLOGP=4.01 0.491
logPstar = 0.37

SMILES: OCC(Cl)(Cl)Cl
ATOM #: 123.4...5..6.
ISOC-ID: .AA..........
FRAG-ID: 1...2...3..4.
H-COUNT: 12...........
2,2,2-trichloroethanol 3.2.1.3
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4

Hydrog
Bonds
XCX
XCCY
 Alcohol or Hydroxy [A]
 Chloride [A]
 Chloride [A]
 Chloride [A]
 2 aliphatic isolating carbons
 2 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 3 interacting fragments
 0 F and 3 non-F interactions
Measured
Measured
Measured
Measured
-
-
-
-
-
 -1.640
  0.060
  0.060
  0.060
  0.390
  0.454
 -0.480
  1.590
  1.050
RESULT DB=17 All fragments measured CLOGP=4.01 1.544
logPstar = 1.42

SMILES: OCC(F)(F)F
ATOM #: 123.4..5.6
ISOC-ID: .AA.......
FRAG-ID: 1...2..3.4
H-COUNT: 12........
2,2,2-trifluoroethanol 3.2.1.3
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4

Hydrog
Bonds
XCX
XCCY
 Alcohol or Hydroxy [A]
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 2 aliphatic isolating carbons
 2 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 3 interacting fragments
 3 F and 0 non-F interactions
Measured
Measured
Measured
Measured
-
-
-
-
-
 -1.640
 -0.380
 -0.380
 -0.380
  0.390
  0.454
 -0.480
  1.590
  1.350
RESULT DB=17 All fragments measured CLOGP=4.01 0.524
logPstar = 0.41

SMILES: OCCCl
ATOM #: 1234.
ISOC-ID: .AA..
FRAG-ID: 1..2.
H-COUNT: 122..
2-chloroethanol 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Hydrog
Bonds
XCCY
 Alcohol or Hydroxy [A]
 Chloride [A]
 2 aliphatic isolating carbons
 4 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 0 F and 1 non-F interactions
Measured
Measured
-
-
-
-
 -1.640
  0.060
  0.390
  0.908
 -0.240
  0.350
RESULT DB=17 All fragments measured CLOGP=4.01 -0.172
logPstar = -0.06

SMILES: OCCF
ATOM #: 1234
ISOC-ID: .AA.
FRAG-ID: 1..2
H-COUNT: 122.
2-fluoroethanol 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Hydrog
Bonds
XCCY
 Alcohol or Hydroxy [A]
 Fluoride [A]
 2 aliphatic isolating carbons
 4 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 1 F and 0 non-F interactions
Measured
Measured
-
-
-
-
 -1.640
 -0.380
  0.390
  0.908
 -0.240
  0.450
RESULT DB=17 All fragments measured CLOGP=4.01 -0.512
logPstar = -0.76

SMILES: OC(CF)CF
ATOM #: 12.34.56
ISOC-ID: .A.A..A.
FRAG-ID: 1...2..3
H-COUNT: 11.2..2.
1,3-difluoro-2-propanol 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
 # 1
 # 2
 # 3

Branch
Hydrog
Bonds
XCCY
 Alcohol or Hydroxy [A]
 Fluoride [A]
 Fluoride [A]
 3 aliphatic isolating carbons
 1 non-halogen, polar group branch
 5 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 2 F and 0 non-F interactions
Measured
Measured
Measured
-
Group
-
-
-
 -1.640
 -0.380
 -0.380
  0.585
 -0.220
  1.135
 -0.480
  0.900
RESULT DB=17 All fragments measured CLOGP=4.01 -0.480
logPstar = -0.36

SMILES: FC(F)(F)CN(CC(F)(F)F)N=O
ATOM #: 12.3..4.56.78.9..0.1.2.3
ISOC-ID: .A......A..AA...........
FRAG-ID: 1..2..3..4....5..6.7.4.4
H-COUNT: ........2..2............
n-NO-bis(2,2,2-triflet)amine 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5
 # 6
 # 7

Hydrog
Bonds
XCX
XCCY
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 Nitrosamine [AA]
 Fluoride [A]
 Fluoride [A]
 Fluoride [A]
 4 aliphatic isolating carbons
 4 hydrogens on isolating carbons
 9 chain and 0 alicyclic (net)
 6 interacting fragments
 6 F and 0 non-F interactions
Measured
Measured
Measured
Measured
Measured
Measured
Measured
-
-
-
-
-
 -0.380
 -0.380
 -0.380
 -2.250
 -0.380
 -0.380
 -0.380
  0.780
  0.908
 -1.080
  3.180
  2.700
RESULT DB=17 All fragments measured CLOGP=4.01 1.958
logPstar = 2.15

SMILES: CCOCCCl
ATOM #: 123456.
ISOC-ID: AA.AA..
FRAG-ID: ..1..2.
H-COUNT: 32.22..
2-chloroethylether 3.2.1.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
Proximity 
 # 1
 # 2

Hydrog
Bonds
XCCY
 Ether [AA]
 Chloride [A]
 4 aliphatic isolating carbons
 9 hydrogens on isolating carbons
 4 chain and 0 alicyclic (net)
 0 F and 1 non-F interactions
Measured
Measured
-
-
-
-
 -1.820
  0.060
  0.780
  2.043
 -0.480
  0.350
RESULT DB=17 All fragments measured CLOGP=4.01 0.933
logPstar = 0.98

SMILES: CCCC(O)=O
ATOM #: 1234.5..6
ISOC-ID: AAA......
FRAG-ID: ...1.1..1
H-COUNT: 322..1...
butyric acid 3.2.2.1
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
 # 1

Hydrog
Bonds
 Carboxy (ZW-) [A]
 3 aliphatic isolating carbons
 7 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
Measured
-
-
-
 -1.070
  0.585
  1.589
 -0.240
RESULT DB=17 All fragments measured CLOGP=4.01 0.864
logPstar = 0.79

SMILES: OC(=O)Cc1ccccc1
ATOM #: 12..3.45.67890.
ISOC-ID: ......Za.aaaaa.
FRAG-ID: 11..1..........
H-COUNT: 1.....2..11111.
RING  1: .......a.aaaaa.
phenylacetic acid 3.2.2.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
 # 1


Hydrog
Bonds
 Carboxy (ZW-) [Z]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 7 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
Measured
-
-
-
-
 -1.030
  0.195
  0.780
  1.589
 -0.120
RESULT DB=17 All fragments measured CLOGP=4.01 1.414
logPstar = 1.41

SMILES: CC=CC(O)=O
ATOM #: 12.34.5..6
ISOC-ID: AV.V......
FRAG-ID: ....1.1..1
H-COUNT: 31.1..1...
crotonic acid 3.2.2.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
 # 1

Hydrog
Bonds
Mbonds
 Carboxy (ZW-) [V]
 3 aliphatic isolating carbons
 5 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 1 double, 0 triple (isolated bond)
Measured
-
-
-
-
 -0.570
  0.585
  1.135
 -0.240
 -0.030
RESULT DB=17 All fragments measured CLOGP=4.01 0.880
logPstar = 0.72

SMILES: OC(=O)C=Cc1ccccc1
ATOM #: 12..3.4.56.78901.
ISOC-ID: ......Y.Ya.aaaaa.
FRAG-ID: 11..1............
H-COUNT: 1.....1.1..11111.
RING  1: .........a.aaaaa.
cinnamic acid 3.2.2.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Proximity 
 # 1


Hydrog
Bonds
PCCY
 Carboxy (ZW-) [Y]
 2 aliphatic isolating carbons
 6 aromatic isolating carbons
 7 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 1 phenyl-fragment pair
Measured
-
-
-
-
-
 -0.430
  0.390
  0.780
  1.589
 -0.240
  0.150
RESULT DB=17 All fragments measured CLOGP=4.01 2.239
logPstar = 2.13

SMILES: OC(=O)c1ccccc1
ATOM #: 12..3.4.56789.
ISOC-ID: ......a.aaaaa.
FRAG-ID: 11..1.........
H-COUNT: 1.......11111.
RING  1: ......a.aaaaa.
benzoic acid 3.2.2.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
ExFragment
 # 1

Hydrog
 Carboxy (ZW-) [a]
 6 aromatic isolating carbons
 5 hydrogens on isolating carbons
Measured
-
-
 -0.030
  0.780
  1.135
RESULT DB=17 All fragments measured CLOGP=4.01 1.885
logPstar = 1.87

SMILES: c2ccc1ccccc1c2
ATOM #: 1.234.56789.0.
ISOC-ID: a.aaa.aaaaa.a.
FRAG-ID: ..............
H-COUNT: 1.11..1111..1.
RING  1: ....a.aaaaa...
RING  2: a.aaa.....a.a.
naphthalene 3.2.2.2.
Class Type Log(P) Contribution Description Comment Value
Carbon    
Fusion    
ExFragment
Carbon
Hydrog
 10 aromatic isolating carbons
 2 extended aromatic iso-C's
 8 hydrogens on isolating carbons
-
-
-
  1.300
  0.200
  1.816
RESULT DB=17 All fragments measured CLOGP=4.01 3.316
logPstar = 3.30

SMILES: c1ccc(cc1)c2ccccc2
ATOM #: 1.234.56..7.89012.
ISOC-ID: a.aaa.aa..a.aaaaa.
FRAG-ID: ..................
H-COUNT: 1.11..11....11111.
RING  1: ..........a.aaaaa.
RING  2: a.aaa.aa..........
biphenyl 3.2.2.2.
Class Type Log(P) Contribution Description Comment Value
Carbon    
Fusion    
ExFragment
Carbon
Hydrog
 12 aromatic isolating carbons
 2 extended aromatic iso-C's
 10 hydrogens on isolating carbons
-
-
-
  1.560
  0.200
  2.270
RESULT DB=17 All fragments measured CLOGP=4.01 4.030
logPstar = 4.01

SMILES: c2ccc1ncccc1c2
ATOM #: 1.234.56789.0.
ISOC-ID: a.aaa..aaaa.a.
FRAG-ID: ......1.......
H-COUNT: 1.11...111..1.
RING  1: ....a.aaaaa...
RING  2: a.aaa.....a.a.
quinoline 3.2.2.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
Fusion    
Fusion    
ExFragment
 # 1

Carbon
Carbon
Hydrog
 Aromatic nitrogen (TYPE 2) [aa]
 9 aromatic isolating carbons
 1 extended aromatic iso-C
 1 extended hetero-aromatic iso-C
 7 hydrogens on isolating carbons
Measured
-
-
-
-
 -1.140
  1.170
  0.100
  0.310
  1.589
RESULT DB=17 All fragments measured CLOGP=4.01 2.029
logPstar = 2.03

SMILES: c3ccc2nc1ccccc1nc2c3
ATOM #: 1.234.56.78901.23.4.
ISOC-ID: a.aaa..a.aaaaa..a.a.
FRAG-ID: ......1........2....
H-COUNT: 1.11.....1111.....1.
RING  1: .......a.aaaaa......
RING  2: ....a.aa.....a.aa...
RING  3: a.aaa...........a.a.
phenazine 3.2.2.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
Fusion    
ExFragment
Electronic
 # 1
 # 2

Carbon
Hydrog
SigRho
 Aromatic nitrogen (TYPE 2) [aa]
 Aromatic nitrogen (TYPE 2) [aa]
 12 aromatic isolating carbons
 4 extended hetero-aromatic iso-C's
 8 hydrogens on isolating carbons
 2 potential interactions; 2.00 used
Measured
Measured
-
-
-
WithinRing
 -1.140
 -1.140
  1.560
  1.240
  1.816
  0.540
RESULT DB=17 All fragments measured CLOGP=4.01 2.876
logPstar = 2.84

SMILES: Nc1cccc(c1)N(=O)=O
ATOM #: 12.3456.7..8..9..0
ISOC-ID: .a.aaaa.a.........
FRAG-ID: 1..........2..2..2
H-COUNT: 2..111..1.........
RING  1: .a.aaaa.a.........
m-nitroaniline 3.2.2.3
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
Electronic
 # 1
 # 2

Hydrog
SigRho
 Primary Amine [a]
 Nitro [a]
 6 aromatic isolating carbons
 4 hydrogens on isolating carbons
 1 potential interaction; 1.00 used
Measured
Measured
-
-
WithinRing
 -1.000
 -0.030
  0.780
  0.908
  0.600
RESULT DB=17 All fragments measured CLOGP=4.01 1.258
logPstar = 1.37

SMILES: Nc1nc(N)nc(n1)c2ccccc2
ATOM #: 12.34.5.67.8..9.01234.
ISOC-ID: .a..a....a....a.aaaaa.
FRAG-ID: 1..2..3.4..5..........
H-COUNT: 2.....2.........11111.
RING  1: ..............a.aaaaa.
RING  2: .a.aa...aa.a..........
benzoguanamine 3.2.2.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Fusion    
Fusion    
ExFragment
Electronic
 # 1
 # 2
 # 3
 # 4
 # 5

Carbon
Carbon
Hydrog
SigRho
 Primary Amine [a]
 Aromatic nitrogen (TYPE 2) [aa]
 Primary Amine [a]
 Aromatic nitrogen (TYPE 2) [aa]
 Aromatic nitrogen (TYPE 2) [aa]
 9 aromatic isolating carbons
 1 extended aromatic iso-C
 1 extended hetero-aromatic iso-C
 5 hydrogens on isolating carbons
 12 potential interactions; 6.99 used
Measured
Measured
Measured
Measured
Measured
-
-
-
-
WithinRing
 -1.000
 -1.140
 -1.000
 -1.140
 -1.140
  1.170
  0.100
  0.310
  1.135
  3.744
RESULT DB=17 All fragments measured CLOGP=4.01 1.039
logPstar = 1.36

SMILES: CCNc1nc(Cl)nc(NC(C)C)n1
ATOM #: 1234.56.7..89.01.2.3.4.
ISOC-ID: AA.a..a.....a..A.A.A...
FRAG-ID: ..1..2..3..4..5......6.
H-COUNT: 321...........11.3.3...
RING  1: ...a.aa....aa........a.
atrazine 3.2.2.3.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
Electronic
 # 1
 # 2
 # 3
 # 4
 # 5
 # 6


Branch
Hydrog
Bonds
SigRho
 Secondary amine [Aa]
 Aromatic nitrogen (TYPE 2) [aa]
 Chloride [a]
 Aromatic nitrogen (TYPE 2) [aa]
 Secondary amine [Aa]
 Aromatic nitrogen (TYPE 2) [aa]
 5 aliphatic isolating carbons
 3 aromatic isolating carbons
 1 non-halogen, polar group branch
 12 hydrogens on isolating carbons
 5 chain and 0 alicyclic (net)
 17 potential interactions; 7.07 used
Measured
Measured
Measured
Measured
Measured
Measured
-
-
Group
-
-
WithinRing
 -1.030
 -1.140
  0.940
 -1.140
 -1.030
 -1.140
  0.975
  0.390
 -0.220
  2.724
 -0.600
  3.974
RESULT DB=17 All fragments measured CLOGP=4.01 2.703
logPstar = 2.61

SMILES: CN(C)c1cccc2c(cccc12)S(N)(=O)=O
ATOM #: 12.3.4.5678.9.0123...4.5...6..7
ISOC-ID: A..A.a.aaaa.a.aaaa.............
FRAG-ID: .1...................2.2...2..2
H-COUNT: 3..3...111....111......2.......
RING  1: ..........a.a.aaaa.............
RING  2: .....a.aaaa......a.............
1-dimeam-5-SO2NH2-naphth 3.2.2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
Carbon    
Fusion    
ExFragment
ExFragment
Electronic
 # 1
 # 2


Carbon
Hydrog
Bonds
SigRho
 Tertiary Amine [AAa]
 NH2-Sulfonamide [a]
 2 aliphatic isolating carbons
 10 aromatic isolating carbons
 2 extended aromatic iso-C's
 12 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 1 potential interaction; 1.00 used
Measured
Measured
-
-
-
-
-
FusedRings
 -1.120
 -1.610
  0.390
  1.300
  0.200
  2.724
 -0.240
  0.160
RESULT DB=17 All fragments measured CLOGP=4.01 1.804
logPstar = 2.01

SMILES: CCOc2ccc1sc(nc1c2)S(N)(=O)=O
ATOM #: 1234.567.89.01.2..3.4...5..6
ISOC-ID: AA.a.aaa..a..a.a............
FRAG-ID: ..1......2..3.....4.4...4..4
H-COUNT: 32...11........1....2.......
RING  1: .......a.aa.aa..............
RING  2: ...a.aaa.....a.a............
ethoxyzolamide 3.2.2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
Fusion    
ExFragment
ExFragment
Electronic
Electronic
H-bonding 
 # 1
 # 2
 # 3
 # 4


Carbon
Hydrog
Bonds
SigRho
SigRho
Ring 1
 Ether [Aa]
 Thiophenyl [aa]
 Aromatic nitrogen (TYPE 2) [aa]
 NH2-Sulfonamide [a]
 2 aliphatic isolating carbons
 7 aromatic isolating carbons
 2 extended hetero-aromatic iso-C's
 8 hydrogens on isolating carbons
 2 chain and 0 alicyclic (net)
 6 potential interactions; 3.03 used
 6 potential interactions; 1.64 used
 Frag-pair: 4 & 3
Measured
Measured
Measured
Measured
-
-
-
-
-
WithinRing
FusedRings
-
 -0.610
  0.360
 -1.140
 -1.610
  0.390
  0.910
  0.620
  1.816
 -0.240
  1.043
  0.408
  0.100
RESULT DB=17 All fragments measured CLOGP=4.01 2.047

SMILES: Nc1ncnc2nc[nH]c12
ATOM #: 12.3456.78.9..0..
ISOC-ID: .a..a.a..a....a..
FRAG-ID: 1..2.3..4..5.....
H-COUNT: 2...1....1.1.....
RING  1: ......a.aa.a..a..
RING  2: .a.aaaa.......a..
adenine 3.2.2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Fusion    
ExFragment
Electronic
Electronic
 # 1
 # 2
 # 3
 # 4
 # 5

Carbon
Hydrog
SigRho
SigRho
 Primary Amine [a]
 Aromatic nitrogen (TYPE 2) [aa]
 Aromatic nitrogen (TYPE 2) [aa]
 Aromatic nitrogen (TYPE 2) [aa]
 Aromatic NH [aa]
 5 aromatic isolating carbons
 2 extended hetero-aromatic iso-C's
 2 hydrogens on isolating carbons
 5 potential interactions; 4.35 used
 7 potential interactions; 2.64 used
Measured
Measured
Measured
Measured
Measured
-
-
-
WithinRing
FusedRings
 -1.000
 -1.140
 -1.140
 -1.140
 -0.680
  0.650
  0.620
  0.454
  2.475
  0.753
RESULT DB=17 All fragments measured CLOGP=4.01 -0.148

SMILES: CC(=O)Nc1ccccc1C
ATOM #: 12..3.45.67890.1
ISOC-ID: A......a.aaaaa.Z
FRAG-ID: .1..1.1.........
H-COUNT: 3.....1..1111..3
RING  1: .......a.aaaaa..
ortho-methylacetanilide 3.2.3.1. (m=0.85)
Class Type Log(P) Contribution Description Comment Value
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Benzylbond
Ortho     
 # 1


Hydrog
Bonds
Simple
Ring 1
 NH-Amide [aA]
 2 aliphatic isolating carbons
 6 aromatic isolating carbons
 10 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
 1 benzyl bond to simple aromatic
 1 normal ortho interaction
Measured
-
-
-
-
-
-
 -1.510
  0.390
  0.780
  2.270
 -0.120
 -0.150
 -0.650
RESULT DB=17 All fragments measured CLOGP=4.01 1.010
logPstar = 0.86

SMILES: NC(=O)c1ccccc1C(N)=O
ATOM #: 12..3.4.56789.0.1..2
ISOC-ID: ......a.aaaaa.......
FRAG-ID: 11..1.........2.2..2
H-COUNT: 2.......1111....2...
RING  1: ......a.aaaaa.......
o-phthalamide 3.2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
Electronic
Ortho     
 # 1
 # 2

Hydrog
SigRho
Ring 1
 NH2-Amide [a]
 NH2-Amide [a]
 6 aromatic isolating carbons
 4 hydrogens on isolating carbons
 2 potential interactions; 2.00 used
 1 normal ortho interaction
Measured
Measured
-
-
WithinRing
-
 -1.260
 -1.260
  0.780
  0.908
  0.384
 -1.360
RESULT DB=17 All fragments measured CLOGP=4.01 -1.808
logPstar = -1.73

SMILES: CC(=O)Nc1ccccc1Cl
ATOM #: 12..3.45.67890.1.
ISOC-ID: A......a.aaaaa...
FRAG-ID: .1..1.1........2.
H-COUNT: 3.....1..1111....
RING  1: .......a.aaaaa...
o-chloroacetanilide 3.2.3.1.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
Electronic
Ortho     
 # 1
 # 2


Hydrog
Bonds
SigRho
Ring 1
 NH-Amide [aA]
 Chloride [a]
 1 aliphatic isolating carbon
 6 aromatic isolating carbons
 7 hydrogens on isolating carbons
 1 chain and 0 alicyclic (net)
 1 potential interaction; 1.00 used
 1 normal ortho interaction
Measured
Measured
-
-
-
-
WithinRing
-
 -1.510
  0.940
  0.195
  0.780
  1.589
 -0.120
  0.258
 -0.850
RESULT DB=17 All fragments measured CLOGP=4.01 1.282
logPstar = 1.28

SMILES: OC(=O)c1ccccc1O
ATOM #: 12..3.4.56789.0
ISOC-ID: ......a.aaaaa..
FRAG-ID: 11..1.........2
H-COUNT: 1.......1111..1
RING  1: ......a.aaaaa..
salicylic acid 3.2.3.2.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
ExFragment
Electronic
H-bonding 
 # 1
 # 2

Hydrog
SigRho
Ring 1
 Carboxy (ZW-) [a]
 Alcohol or Hydroxy [a]
 6 aromatic isolating carbons
 4 hydrogens on isolating carbons
 1 potential interaction; 1.00 used
 Frag-pair: 1 & 2
Measured
Measured
-
-
WithinRing
-
 -0.030
 -0.440
  0.780
  0.908
  0.339
  0.630
RESULT DB=17 All fragments measured CLOGP=4.01 2.187
logPstar = 2.26

SMILES: Nc1ncnc2n(cnc12)C3OC(CO)C(O)C3O
ATOM #: 12.3456.7.890...1.23.45.6.7.8.9
ISOC-ID: .a..a.a...a.a...R..R.A..R...R..
FRAG-ID: 1..2.3..4..5......6...7...8...9
H-COUNT: 2...1.....1.....1..1.21.1.1.1.1
RING  1: ................A.AA....A...A..
RING  2: ......a.a.aaa..................
RING  3: .a.aaaa.....a..................
adenosine
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
OrthoEther
Carbon    
Carbon    
Fusion    
ExFragment
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
Electronic
Electronic
 # 1
 # 2
 # 3
 # 4
 # 5
 # 6
 # 7
 # 8
 # 9



Carbon
Branch
Branch
Hydrog
Bonds
YCY
YCCY
YCCY
YCCY
YCCY
YCCCY
SigRho
SigRho
 Primary Amine [a]
 Aromatic nitrogen (TYPE 2) [aa]
 Aromatic nitrogen (TYPE 2) [aa]
 1-Pyrrole [Aaa]
 Aromatic nitrogen (TYPE 2) [aa]
 Ether [RR]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Ether in a 5-member ring
 5 aliphatic isolating carbons
 5 aromatic isolating carbons
 2 extended hetero-aromatic iso-C's
 1 chain and 0 cluster branch
 3 non-halogen, polar group branches
 8 hydrogens on isolating carbons
 1 chain and 5 alicyclic (net)
 Fragments 4 & 6: -.32 (-1.09+-1.75)
 1 pair over bond 14-13 (AvWt=-.230)
 1 pair over bond 16-13 (AvWt=-.230)
 1 pair over bond 18-16 (AvWt=-.260)
 2 pairs over bond 18-11 (AvWt=-.230)
 1 pair over bond 16-14 (AvWt=-.200)
 6 potential interactions; 4.39 used
 10 potential interactions; 2.70 used
Measured
Measured
Measured
Measured
Measured
Measured
Measured
Measured
Measured
-
-
-
-
Chain
Group
-
(COMBINED)
-
-
-
-
-
Branch
WithinRing
FusedRings
 -1.000
 -1.140
 -1.140
 -1.090
 -1.140
 -1.750
 -1.640
 -1.640
 -1.640
  0.130
  0.975
  0.650
  0.620
 -0.130
 -0.660
  1.816
 -0.570
  0.909
  0.780
  0.780
  0.853
  0.704
  0.656
  1.938
  0.572
RESULT DB=17 All fragments measured CLOGP=4.01 -2.158
logPstar = -1.05

SMILES: CC(=O)OCC(=O)C3(O)CCC4C2CCC1=CC(=O)CCC1(C)C2C(=O)CC34C
ATOM #: 12..3.456..7.8..9.012.3.456..78..9.012..3.4.5..6.78..9
ISOC-ID: A......A.....R....AAA.A.AAV..W.....RAA..A.R......RA..A
FRAG-ID: .1..1.1.2..2....3.............4..4..........5..5......
H-COUNT: 3......2........1.221.1.22...1.....22...3.1......2...3
RING  1: .............A....AAA.............................A...
RING  2: ....................A.A...................A.A....AA...
RING  3: ..........................A..AA....AAA................
RING  4: ......................A.AAA..........A....A...........
cortisone ac.
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
STEROID   
 # 1
 # 2
 # 3
 # 4
 # 5

Branch
Branch
Hydrog
Bonds
Mbonds
YCY
YCY
STRONG
 Ester [AA]
 Carbonyl [AA]
 Alcohol or Hydroxy [A]
 Carbonyl [AV]
 Carbonyl [AA]
 19 aliphatic isolating carbons
 2 chain and 6 cluster branches
 2 non-halogen, polar group branches
 29 hydrogens on isolating carbons
 3 chain and 20 alicyclic (net)
 1 double, 0 triple (isolated bond)
 Fragments 1 & 2: -.32 (-1.45+-1.84)
 Fragments 2 & 3: -.42 (-1.84+-1.64)
   11-keto steroid
Measured
Measured
Measured
Measured
Measured
-
Combined
Group
-
(COMBINED)
-
-
-
-
 -1.450
 -1.840
 -1.640
 -1.690
 -1.840
  3.705
 -1.040
 -0.440
  6.583
 -2.160
 -0.030
  1.053
  1.462
  1.160
RESULT DB=17 All fragments measured CLOGP=4.01 1.832
logPstar = 2.10

SMILES: CCCCCN(CCCCC)CC(O)c1ccccc1
ATOM #: 123456.78901.23.4.5.67890.
ISOC-ID: AAAAA..AAAAA.AZ...a.aaaaa.
FRAG-ID: .....1..........2.........
H-COUNT: 32222..22223.21.1...11111.
RING  1: ..................a.aaaaa.
2(N,N-dipentam)1-phenylethanol
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
 # 1
 # 2


Branch
Hydrog
Bonds
YCCY
 Tertiary Amine [AAA]
 Alcohol or Hydroxy [Z]
 12 aliphatic isolating carbons
 6 aromatic isolating carbons
 1 non-halogen, polar group branch
 30 hydrogens on isolating carbons
 13 chain and 0 alicyclic (net)
 1 pair over bond 13-12 (AvWt=-.260)
Measured
Measured
-
-
Group
-
-
-
 -2.370
 -1.340
  2.340
  0.780
 -0.220
  6.810
 -1.560
  0.965
RESULT DB=17 All fragments measured CLOGP=4.01 5.405
logPstar = 2.86

SMILES: CCN(CC)CC(O)c1ccccc1
ATOM #: 123.45.67.8.9.01234.
ISOC-ID: AA..AA.AZ...a.aaaaa.
FRAG-ID: ..1.......2.........
H-COUNT: 32..23.21.1...11111.
RING  1: ............a.aaaaa.
2(N,N-dietam)1-phenylethanol
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
 # 1
 # 2


Branch
Hydrog
Bonds
YCCY
 Tertiary Amine [AAA]
 Alcohol or Hydroxy [Z]
 6 aliphatic isolating carbons
 6 aromatic isolating carbons
 1 non-halogen, polar group branch
 18 hydrogens on isolating carbons
 7 chain and 0 alicyclic (net)
 1 pair over bond  7- 6 (AvWt=-.260)
Measured
Measured
-
-
Group
-
-
-
 -2.370
 -1.340
  1.170
  0.780
 -0.220
  4.086
 -0.840
  0.965
RESULT DB=17 All fragments measured CLOGP=4.01 2.231
logPstar = 2.02

SMILES: CN1CCC24C3Oc5c(O)ccc(CC1C2C=CC3O)c45
ATOM #: 12.345..6.78.9.0.123.45.6.7.89.0.1..
ISOC-ID: A..RAZ..A..a.a...aaa.ZR.A.V.VR...a..
FRAG-ID: .1........2....3...............4....
H-COUNT: 3..22...1......1.11..21.1.1.11.1....
RING  1: .....A..A.AA.....................A..
RING  2: .....A..A...............A.A.AA......
RING  3: .A.AAA................A.A...........
RING  4: .....A.............A.AA.A........A..
RING  5: ...........a.a...aaa.............a..
morphine
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
Carbon    
ExFragment
ExFragment
ExFragment
ExFragment
ExFragment
Benzylbond
Proximity 
Proximity 
Proximity 
Electronic
 # 1
 # 2
 # 3
 # 4


Branch
Branch
Hydrog
Bonds
Mbonds
Simple
YCC=C
PCCY
YCCY
SigRho
 Tertiary Amine [ARR]
 Ether [Aa]
 Alcohol or Hydroxy [a]
 Alcohol or Hydroxy [A]
 11 aliphatic isolating carbons
 6 aromatic isolating carbons
 0 chain and 5 cluster branches
 1 non-halogen, polar group branch
 17 hydrogens on isolating carbons
 0 chain and 13 alicyclic (net)
 1 double, 0 triple (isolated bond)
 2 benzyl bonds to simple aromatics
 1 allylic structure
 1 phenyl-fragment pair
 1 pair over bond 19- 6 (AvWt=-.230)
 1 potential interaction; 1.00 used
Measured
Measured
Measured
Measured
-
-
Cluster
Group
-
-
-
-
-
-
-
WithinRing
 -2.200
 -0.610
 -0.440
 -1.640
  2.145
  0.780
 -0.650
 -0.220
  3.859
 -1.170
 -0.030
 -0.300
  0.200
  0.150
  0.517
  0.180
RESULT DB=17 All fragments measured CLOGP=4.01 0.572
logPstar = 0.76

SMILES: OC(CBr)C(O)C(O)C(O)CBr
ATOM #: 12.34..5.6.7.8.9.0.12.
ISOC-ID: .A.A...A...A...A...A..
FRAG-ID: 1...2....3...4...5..6.
H-COUNT: 11.2...1.1.1.1.1.1.2..
dibromodeoxymannitol
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5
 # 6

Branch
Hydrog
Bonds
XCCY
YCCY
YCCY
YCCY
XCCCY
YCCCY
YCCCY
 Alcohol or Hydroxy [A]
 Bromide [A]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Bromide [A]
 6 aliphatic isolating carbons
 4 non-halogen, polar group branches
 8 hydrogens on isolating carbons
 10 chain and 0 alicyclic (net)
 0 F and 2 non-F interactions
 1 pair over bond  5- 2 (AvWt=-.260)
 1 pair over bond  7- 5 (AvWt=-.260)
 1 pair over bond  9- 7 (AvWt=-.260)
 2 unbranched XCCCY adjustments (0.15)
 1 pair over bond  7- 2 (AvWt=-.200)
 1 pair over bond  9- 5 (AvWt=-.200)
Measured
Measured
Measured
Measured
Measured
Measured
-
Group
-
-
-
-
-
-
-
Branch
Branch
 -1.640
  0.200
 -1.640
 -1.640
 -1.640
  0.200
  1.170
 -0.880
  1.816
 -1.200
  0.700
  0.853
  0.853
  0.853
  0.300
  0.656
  0.656
RESULT DB=17 All fragments measured CLOGP=4.01 -0.384
logPstar = -0.29

SMILES: CC2C1CCC4C(O)C1(CC(O)C3(O)C2CC(O)C3(C)C)CC4(C)O
ATOM #: 12.3.456.7.8.9..01.2.3..4.5.67.8.9..0.1.23..4.5
ISOC-ID: AA.A.AAA.R...A..AR...R....A.AR...A..A.A.AR..A..
FRAG-ID: ...........1.......2....3......4..............5
H-COUNT: 31.1.221.1.1....21.1....1.1.21.1....3.3.2...3.1
RING  1: .......A.A...A..........................AA.....
RING  2: .....................A....A.AA...A.............
RING  3: ...A.AAA.A...A.................................
RING  4: .A.A.........A..AA...A....A....................
dihydrograyanotoxin
Class Type Log(P) Contribution Description Comment Value
Fragment  
Fragment  
Fragment  
Fragment  
Fragment  
Carbon    
ExFragment
ExFragment
ExFragment
ExFragment
Proximity 
Proximity 
Proximity 
 # 1
 # 2
 # 3
 # 4
 # 5

Branch
Branch
Hydrog
Bonds
YCCY
YCCCY
YCCCY
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 Alcohol or Hydroxy [A]
 20 aliphatic isolating carbons
 4 chain and 6 cluster branches
 5 non-halogen, polar group branches
 29 hydrogens on isolating carbons
 0 chain and 19 alicyclic (net)
 1 pair over bond 13-11 (AvWt=-.260)
 1 pair over bond 17-13 (AvWt=-.200)
 1 pair over bond 23- 7 (AvWt=-.200)
Measured
Measured
Measured
Measured
Measured
-
Combined
Group
-
-
-
-
-
 -1.640
 -1.640
 -1.640
 -1.640
 -1.640
  3.900
 -1.300
 -1.100
  6.583
 -1.710
  0.853
  0.656
  0.656
RESULT DB=17 All fragments measured CLOGP=4.01 0.338
logPstar = 1.51