# Interface to LIBEFP by I. Kaliman

Code author: Andrew C. Simmonett, A. Eugene DePrince III, Rollin A. King, and Lori A. Burns

Section author: Lori A. Burns

Module: Keywords, PSI Variables, LIBEFP

Psi4 contains code to interface to the LIBEFP library developed in L. Slipchenko’s group by I. Kaliman. LIBEFP at version 1.2.1 is distributed with Psi4 and requires no additional licence, downloads, or configuration. Conversely, Psi4 cannot build without LIBEFP. More information about the LIBEFP project is available at http://www.libefp.org/ and source is hosted at https://github.com/libefp/libefp.

## EFP Fragments

LIBEFP comes with a couple dozen ready-to-use fragments (water, benzene, common solvents, etc.) listed here with source psi4/lib/efpfrag. Any of these may be used directly in a Psi4 input file as described here.

Note

The built-in fragment library distributed with Q-Chem (as of version 4.0.1) is not equivalent to that distributed with LIBEFP. Although many of the same molecules are present and should perform similarly in computations, exact matches of fragment geometries or efp energies should not be expected. See files in test case directories qchem-efp-sp and qchem-qmefp-sp for equivalent Q-Chem and Psi4 EFP input files.

Creating new efp fragments requires the GAMESS quantum chemistry package. Instructions on building new fragments are here. Once your new fragment is ready, make it assessible to Psi4 by including the directory in which the `.efp` file is located to the colon separated environment variable `PSIPATH`. Fragments are searched for first in the current directory, next in the paths of `PSIPATH`, and finally in built-in library. If Psi4 is unable to find the fragment, an error will be reported.

Note

When constructing new fragment files, the name of the name of the file should be lowercase and have extension `.efp`. The molecule name within the file, e.g., `$NH3` must correspond to the name of the fragment file.

## Molecule Specification

EFP fragment geometries are specified alongside the quantum mechanical (QM) molecule and make use of the `--` fragment separation scheme described here. Each EFP fragment has its own fragment section that includes the label `efp`, the name of the file fragname from which EFP parameters are to be read, and the position specification for the fragment in one of two ways, XYZABC or POINTS. For XYZABC, the fragment specification is all on one line: `efp` and fragname are followed by two sets of three numbers: the coordinates of the center of mass of the fragment and the three Euler angles that specify orientation about the center of mass. This format is compact but not readily generated from molecule viewing software.

    efp  nh3  0.0 0.0 5.0  5 2 8

More convenient is the POINTS fragment specification. This consists of four lines, the first of which is `efp` and fragname. The next lines are the coordinates (without element labels) of the first three atoms in the fragment. Note that EFP fragment geometries are rigid, so the first atom will be placed exactly where specified by the first point, the second atom will be placed along the vector between the first and second points, and the third atom will be placed in the plane formed by the three points.

    efp ch3oh
    1.275    -2.447    -4.673
    0.709    -3.191    -3.592
    2.213    -1.978    -4.343

Note

At present, Psi4 has limited support for diatomic and monoatomic EFP fragments. Single points are allowed when the di-/mono-atomic fragments are specified in XYZABC format. Optimizations are not allowed.

Just as for QM, the center of mass coordinates in the XYZABC format and all coordinates in the POINTS format are taken to be in Angstroms by default or in Bohr if `units au` is present. Charge and multiplicity specifications are encoded in the fragment file and so are not read from input.

Any combination of EFP and QM fragments can be placed in a molecule; even the oddity below is legitimate. Note that symmetry and reorientation are automatically turned off when EFP fragments are present (`symmetry c1` and `no_com` and `no_reorient` are implied).

    molecule qmefp {
      efp nh3 0.0 0.0 5.0 5 2 8
      --
      C  0.0 0.0 0.0
      O  0.0 1.5 0.0
      O  0.0 -1.5 0.0
      --
      efp h2o 5.0 0.0 0.0 5 2 8
      --
      He  -3.0 4.0 4.0
      He  -4.0 5.0 4.0
      --
      efp ch3oh
      1.275    -2.447    -4.673
      0.709    -3.191    -3.592
      2.213    -1.978    -4.343
    }

## Running EFP

EFP can be invoked in similar fashion as other theories provided in Psi4. For example, if you want to obtain the EFP interaction energy for benzene and two waters, simply provide the following:

    molecule {
      efp c6h6  0.0 0.0 0.0   0.0 0.0 0.0
      --
      efp h2o   4.0 0.0 0.0   0.0 0.0 0.0
      --
      efp h2o  -4.0 0.0 0.0   0.0 0.0 0.0
    }

    energy('efp')

This computation involves purely EFP/EFP fragment interactions and is performed entirely by the LIBEFP library. Psi4 can also handle mixed systems of quantum mechanical (QM) and EFP fragments through the native SCF code augmented by calls to the LIBEFP library. For example, turning one of the waters in the example above into a QM fragment is shown below.

    molecule {
      efp c6h6  0.0 0.0 0.0   0.0 0.0 0.0
      --
      O  4.0   0.0   0.0
      H  4.7   0.7   0.0
      H  3.3  -0.7   0.0
      --
      efp h2o  -4.0 0.0 0.0   0.0 0.0 0.0
    }

    set basis 6-31g
    energy('scf')

Whenever an EFP fragment is present in the active molecule, the SCF energy will include EFP contributions.

Warning

Although the EFP geometry is specified alongside the QM geometry in a `molecule name {...}` block, internally the handling of EFP is not so clean. In straightforward input files that involve any number of [molecule block, energy/opt/etc, clean()] portions, there should be no problem; the energy/opt computation will always be run on the molecule defined in the preceding block. For advanced users, unexpected difficulties may arise due to: (1) the EFP fragment from the last molecule block executed will always be active (and potentially interfering with SCF) and (2) recalling a molecule through `activate(name)` (where `name` was the python handle in the molecule block) will not load up any EFP portion of that molecule. This divergent treatment is a stopgap while we determine how best to handle molecules with different domains.

At this time, Psi4 is only able to perform pure-efp single-points and geometry optimizations and mixed qm/efp SCF single-points.

> name | molecule composition | calls method
> --- | --- | ---
> efp efp efp | pure EFP | EFP interaction energy (IE) on all frags
> mixed QM/EFP | EFP IE on EFP frags only
> pure QM | error
> scf scf scf | pure EFP | error
> mixed QM/EFP | SCF energy on QM frags w/coupling to EFP frags, plus EFP IE on EFP frags
> pure QM | SCF energy on all frags (normal Psi4 operation)

## Fragment Library

Below are documented the EFP fragments available from the LIBEFP library. These systems are accessible in `molecule {...}` blocks without additional configuration.

### aceticacid-gp

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Comment

    Acetic acid, gas phase monomer, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.039926    -0.101371     0.000000
    O          0.671568    -1.131236     0.000000
    O          0.631656     1.119162     0.000000
    H          1.583763     0.941625     0.000000
    C         -1.452898     0.022190     0.000000
    H         -1.897231    -0.965551     0.000000
    H         -1.772814     0.579167     0.877400
    H         -1.772814     0.579167    -0.877400

### ethene

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Comment

    Ethylene (ethene)  Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C         -0.667396     0.000087     0.000000
    C          0.667396     0.000087     0.000000
    H         -1.233788     0.923077     0.000000
    H          1.233788     0.923077     0.000000
    H         -1.231016    -0.924113     0.000000
    H          1.231016    -0.924113     0.000000

### h2o

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Comment

              FRAGNAMEEFP GENERATED AT Tue Mar 27 16:14:27 2012
     $H2O
    EFP DATA FOR FRAGNAME SCFTYP=RHF   ... GENERATED WITH BASIS SET=6-311++G(3df,2p)

Full Geometry in Angstroms

    O          0.000000     0.063030     0.000000
    H         -0.752652    -0.500166     0.000000
    H          0.752652    -0.500166     0.000000

### benzene

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Comment

    Benzene Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.696821    -1.206894     0.000000
    C          1.393641     0.000000     0.000000
    C          0.696821     1.206894     0.000000
    C         -0.696821     1.206894     0.000000
    C         -1.393641     0.000000     0.000000
    C         -0.696821    -1.206894     0.000000
    H          1.237534    -2.143485     0.000000
    H          2.475068     0.000000     0.000000
    H          1.237534     2.143485     0.000000
    H         -1.237534     2.143485     0.000000
    H         -2.475068     0.000000     0.000000
    H         -1.237534    -2.143485     0.000000

### ethyne

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Comment

    Acetylene (ethyne) Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.000000     0.000000     0.603725
    C          0.000000     0.000000    -0.603535
    H          0.000000     0.000000    -1.669425
    H          0.000000     0.000000     1.667155
    D          2.000000     0.000000     0.603725

### acetamide-gp

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Comment

    Acetamide, S66 gas phase monomer, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.043961     0.085203    -0.005602
    O          0.471547     1.227060     0.003308
    N          0.868937    -1.004398    -0.020023
    H          1.850976    -0.843990     0.117452
    H          0.508877    -1.928314     0.122079
    C         -1.431795    -0.238820     0.000340
    H         -1.769813    -0.327018     1.031932
    H         -1.652592    -1.169599    -0.517030
    H         -1.969844     0.579150    -0.466069

### neopentane

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Comment

    Neopentane, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.000000     0.000000     0.000000
    C          0.881340     0.881340     0.881340
    H          1.521730     1.521730     0.273200
    H          0.273200     1.521730     1.521730
    H          1.521730     0.273200     1.521730
    C         -0.881340     0.881340    -0.881340
    H         -1.521730     0.273200    -1.521730
    H         -1.521730     1.521730    -0.273200
    H         -0.273200     1.521730    -1.521730
    C         -0.881340    -0.881340     0.881340
    H         -1.521730    -1.521730     0.273200
    H         -1.521730    -0.273200     1.521730
    H         -0.273200    -1.521730     1.521730
    C          0.881340    -0.881340    -0.881340
    H          1.521730    -1.521730    -0.273200
    H          0.273200    -1.521730    -1.521730
    H          1.521730    -0.273200    -1.521730

### ch4

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Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 11:27:40 2012
     $CH4
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -0.000007    -0.000002     0.000023
    H          0.559197    -0.843228     0.384108
    H         -1.038888    -0.094506     0.288197
    H          0.074416     0.020487    -1.079492
    H          0.405361     0.917269     0.406907

### aceticacid-hb

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Comment

    Acetic acid, H-bond monomer, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C         -0.044538     0.078342     0.000537
    O         -0.602629     1.168456    -0.000109
    O         -0.683477    -1.080692     0.000022
    H         -1.662790    -0.908206    -0.001780
    C          1.444042    -0.084071     0.000078
    H          1.920832     0.888253     0.019147
    H          1.744328    -0.670527     0.864997
    H          1.745414    -0.634190    -0.888299

### nh3

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Comment

              FRAGNAMEEFP GENERATED AT Tue Mar 27 16:16:45 2012
     $NH3
    EFP DATA FOR FRAGNAME SCFTYP=RHF   ... GENERATED WITH BASIS SET=6-311++G(3df,2p)

Full Geometry in Angstroms

    N          0.000000     0.000000    -0.063177
    H         -0.466791    -0.808506     0.292603
    H         -0.466791     0.808506     0.292603
    H          0.933582     0.000000     0.292603

### uracil

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Comment

    Uracil, S22 H-Bond, Stack Dimer Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N         -1.176150    -1.013895     0.009636
    C         -0.014859    -1.735764    -0.010189
    H         -0.135102    -2.807995    -0.049711
    C          1.195422    -1.139958     0.012847
    H          2.105169    -1.714739    -0.003735
    C          1.284759     0.308466     0.015077
    O          2.313695     0.963702    -0.052809
    N          0.038116     0.943313     0.083774
    H          0.044958     1.955145     0.033206
    C         -1.216003     0.367805     0.015837
    O         -2.251460     1.002337    -0.044844
    H         -2.065926    -1.465704    -0.127550

### ethane

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Comment

              FRAGNAMEEFP GENERATED AT Tue Apr 30 16:36:03 2013
     $ETHANE
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -0.762615     0.000001     0.000000
    C          0.762622     0.000002     0.000000
    H         -1.154948    -1.010792    -0.000154
    H         -1.154973     0.505513    -0.875291
    H         -1.154973     0.505245     0.875445
    H          1.154917     1.010805     0.000154
    H          1.154946    -0.505267    -0.875444
    H          1.154946    -0.505535     0.875290

### adenine-wc

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Comment

    Adenine, S22 WC Dimer Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N          1.946697    -0.459208     0.002694
    C          1.211505     0.664598     0.000648
    C         -0.190020     0.525984     0.000085
    C         -0.684328    -0.778091    -0.001247
    N          0.023373    -1.915426    -0.001448
    C          1.328477    -1.659339     0.001164
    N         -1.200813     1.458758     0.001843
    C         -2.297901     0.720321     0.001175
    N         -2.048907    -0.624562    -0.000942
    N          1.818193     1.859760    -0.009631
    H          1.995293    -2.512331     0.002475
    H         -3.302020     1.110149     0.002177
    H         -2.725592    -1.369501    -0.001541
    H          2.830565     1.920513     0.043317
    H          1.247354     2.683679     0.035843

### nmethylacetamide

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Comment

    Peptide bond model, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          1.769122     0.676337    -0.000351
    H          1.631806     1.755107     0.004384
    H          2.340337     0.391745    -0.880485
    H          2.345268     0.384570     0.874148
    C          0.472184    -0.099167     0.000208
    O          0.451228    -1.322406     0.000079
    N         -0.656393     0.664064     0.000788
    H         -0.556234     1.662010    -0.000907
    C         -1.978861     0.079841    -0.000490
    H         -1.848969    -0.997750     0.008358
    H         -2.542617     0.378205     0.881590
    H         -2.535629     0.363993    -0.891762

### c6h6

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Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 19:03:10 2012
     $C6H6
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -0.515357     1.283171     0.001941
    C          0.853604     1.087880    -0.004609
    C          1.369001    -0.195289     0.002620
    C         -1.369006     0.195278     0.002888
    C         -0.853584    -1.087872    -0.004803
    C          0.515338    -1.283143     0.002177
    H         -0.915324     2.279459     0.005656
    H          1.516245     1.932490    -0.015766
    H          2.431801    -0.346996     0.008184
    H         -2.431828     0.346799     0.009774
    H         -1.516042    -1.932593    -0.017856
    H          0.915184    -2.279454     0.007457

### cl2

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Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 15:34:43 2012
     $CL2
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    CL        -0.987026     0.000000     0.000000
    CL         0.987026     0.000000     0.000000

### formamide

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Comment

    Formamide, S22 Dimer Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C         -0.085066    -0.404452     0.000000
    O         -1.129812     0.205930     0.000000
    N          1.138474     0.166062     0.000000
    H         -0.043279    -1.493705     0.000000
    H          1.225622     1.163209     0.000000
    H          1.943097    -0.429351     0.000000

### h2

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Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 15:25:29 2012
     $H2
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    H         -0.367112     0.000000     0.000000
    H          0.367112     0.000000     0.000000

### pyridine

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Comment

    Pyridine, S66, Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N          0.000000     0.000000     1.393973
    C          0.000000    -1.140880     0.691923
    H          0.000000    -2.054940     1.273233
    C          0.000000    -1.194050    -0.699677
    H          0.000000    -2.148990    -1.206027
    C          0.000000     0.000000    -1.412947
    H          0.000000     0.000000    -2.494377
    C          0.000000     1.194050    -0.699677
    H          0.000000     2.148990    -1.206027
    C          0.000000     1.140880     0.691923
    H          0.000000     2.054940     1.273233

### ccl4

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Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 13:15:17 2012
     $CCL4
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -0.000049     0.000028    -0.000070
    CL         0.259957    -0.246051     1.724202
    CL        -1.717643     0.239125    -0.306444
    CL         0.563161    -1.413802    -0.886119
    CL         0.894541     1.420719    -0.531616

### methanol

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Comment

    Methanol, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    O          0.689845    -0.063814     0.000000
    H          1.026676     0.834594     0.000000
    C         -0.726417     0.012939     0.000000
    H         -1.095741    -1.008091     0.000000
    H         -1.114977     0.516104     0.887270
    H         -1.114977     0.516104    -0.887270

### pyridone

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Comment

    2-pyridoxine, S22 Complex Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    O         -2.242413    -0.023741    -0.004502
    N         -0.264207     1.117772     0.005036
    C          1.171258    -1.194422     0.000846
    C          1.847365     0.047728    -0.003389
    C          1.088474     1.183810    -0.001402
    C         -1.002652    -0.057887     0.000815
    C         -0.196628    -1.250542     0.003061
    H          1.740815    -2.114468     0.000629
    H          2.923048     0.113247    -0.008063
    H          1.510672     2.178411    -0.005974
    H         -0.724612    -2.192307     0.003870
    H         -0.813109     1.998495     0.011847

### formicacid

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Comment

    Formic Acid, S22 H-bond Dimer Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.077691    -0.404110     0.000000
    O         -1.128002     0.119130     0.000000
    O          1.133662     0.208328     0.000000
    H          0.043506    -1.497035     0.000000
    H         -1.058384     1.111703     0.000000

### ammonia

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Comment

    Ammonia Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N          0.000000     0.000000     0.069609
    H          0.000000     0.932400    -0.322391
    H          0.807400    -0.466200    -0.322391
    H         -0.807400    -0.466200    -0.322391

### methane

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Comment

    Methane Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.000000     0.000000     0.000000
    H          0.626700     0.626700     0.626700
    H         -0.626700    -0.626700     0.626700
    H         -0.626700     0.626700    -0.626700
    H          0.626700    -0.626700    -0.626700

### phenol

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Visualization by ChemDoodle Web

Comment

    Phenol Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C         -0.916997    -0.003850     0.000000
    C         -0.216641    -1.208924     0.000000
    C          1.176611    -1.202006     0.000000
    C          1.874269     0.002563     0.000000
    C          1.166193     1.203675     0.000000
    C         -0.224514     1.205644     0.000000
    O         -2.283318     0.056000     0.000000
    H         -2.621973    -0.845239     0.000000
    H         -0.757484    -2.147764     0.000000
    H          1.711976    -2.141562     0.000000
    H          2.954799     0.006025     0.000000
    H          1.696953     2.145764     0.000000
    H         -0.787062     2.128534     0.000000

### 2aminopyridine

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Visualization by ChemDoodle Web

Comment

    2-aminopyridine, S22 Complex Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N         -0.297712    -1.170382     0.001714
    C         -0.912531     0.026013     0.004723
    C         -0.175714     1.226496     0.003700
    C          1.204216     1.176210     0.000547
    C          1.842683    -0.065832    -0.001280
    C          1.045154    -1.196712     0.000533
    H         -0.697132     2.173907     0.003778
    H          1.778223     2.092763     0.001427
    H          2.918377    -0.152929    -0.000909
    H          1.493951    -2.183173     0.004591
    N         -2.277071     0.027597    -0.043650
    H         -2.727502     0.885639     0.221497
    H         -2.756811    -0.823399     0.254372

### thymine-stack

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Visualization by ChemDoodle Web

Comment

    Thymine, S22 Stack Dimer Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N         -0.631068     1.008373     0.000000
    H         -0.956616     1.965303     0.000000
    C         -1.621963     0.046276     0.000000
    O         -2.811896     0.294542     0.000000
    N         -1.111269    -1.236531     0.000000
    H         -1.799085    -1.970904     0.000000
    C          0.232329    -1.524996     0.000000
    H          0.479851    -2.577001     0.000000
    C          1.183246    -0.566233     0.000000
    C          0.755835     0.828589     0.000000
    O          1.508925     1.789508     0.000000
    C          2.648712    -0.848917     0.000000
    H          2.838441    -1.920120     0.000000
    H          3.122602    -0.405796    -0.874359
    H          3.122602    -0.405796     0.874359

### water

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Visualization by ChemDoodle Web

Comment

    Water Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    O          0.000000     0.000000     0.066433
    H          0.000000     0.753200    -0.527167
    H          0.000000    -0.753200    -0.527167

### adenine-stack

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Visualization by ChemDoodle Web

Comment

    Adenine, S22 Stack Dimer Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C         -0.190801    -0.524795     0.001097
    N         -1.202629    -1.457753    -0.007931
    C         -2.298700    -0.718488    -0.005752
    H         -3.302884    -1.108459    -0.010975
    N         -2.051553     0.626758     0.004323
    H         -2.729780     1.370239     0.006955
    C         -0.686448     0.780599     0.005930
    N          0.025517     1.911707     0.005800
    C          1.333038     1.649644    -0.005645
    H          1.989156     2.509848    -0.011294
    N          1.955190     0.454345    -0.012177
    C          1.208229    -0.651995    -0.002132
    N          1.816774    -1.865535     0.044799
    H          1.259232    -2.666552    -0.195276
    H          2.792551    -1.883031    -0.195708

### pyrazine

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Visualization by ChemDoodle Web

Comment

    Pyrazine Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.696140    -1.130872    -0.001974
    C         -0.696140    -1.130872    -0.001974
    N         -1.414480     0.000953     0.003286
    C         -0.696730     1.129848    -0.001397
    C          0.696730     1.129848    -0.001397
    N          1.414480     0.000953     0.003286
    H          1.247280    -2.062705    -0.000861
    H         -1.247280    -2.062705    -0.000861
    H         -1.247560     2.061660    -0.004657
    H          1.247560     2.061660    -0.004657

### hydrogencyanide

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Visualization by ChemDoodle Web

Comment

    Hydrogen cyanide Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N         -0.602008     0.000025     0.000000
    C          0.565331    -0.000061     0.000000
    H          1.633210     0.000379     0.000000
    D          3.633210     0.000379     0.000000

### dmso

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Visualization by ChemDoodle Web

Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 14:07:02 2012
     $DMSO
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -1.351465    -0.848122     0.222043
    S         -0.000001     0.139397    -0.408502
    C          1.351490    -0.848085     0.222043
    O         -0.000022     1.383228     0.354940
    H         -2.266866    -0.340402    -0.045273
    H         -1.275457    -0.919582     1.298559
    H         -1.332873    -1.829381    -0.234075
    H          2.266876    -0.340333    -0.045265
    H          1.332930    -1.829340    -0.234080
    H          1.275483    -0.919549     1.298560

### ch3oh

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Visualization by ChemDoodle Web

Comment

              FRAGNAMEEFP GENERATED AT Fri Jun  8 14:12:58 2012
     $CH3OH
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -0.717119     0.013446    -0.000001
    O          0.678634    -0.063043    -0.000001
    H         -1.094134     0.520396     0.883227
    H         -1.094993    -0.998593    -0.000048
    H         -1.094156     0.520490    -0.883163
    H          1.051482     0.798141     0.000002

### methylamine

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Visualization by ChemDoodle Web

Comment

    Methylamine, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N         -0.721090     0.000000     0.073284
    H         -1.089325     0.805920    -0.414424
    H         -1.089325    -0.805920    -0.414424
    C          0.738880     0.000000    -0.013895
    H          1.127039    -0.875000     0.502646
    H          1.145923     0.000000    -1.029223
    H          1.127039     0.875000     0.502646

### dcm

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Visualization by ChemDoodle Web

Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 14:30:26 2012
     $DCM
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C          0.000001    -0.801518    -0.000010
    H          0.000001    -1.404844     0.886898
    H         -0.000001    -1.405115    -0.886674
    CL         1.467770     0.178018    -0.000002
    CL        -1.467770     0.178018    -0.000002

### cyclopentane

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Visualization by ChemDoodle Web

Comment

    Cyclopentane, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          1.274536    -0.248276     0.015408
    H          1.896288    -0.262311     0.908883
    H          1.925746    -0.475194    -0.826626
    C          0.122240    -1.275242     0.135374
    H          0.030375    -1.612348     1.168149
    H          0.283877    -2.158931    -0.478951
    C         -1.141588    -0.502663    -0.256509
    H         -2.051894    -0.944460     0.145791
    H         -1.238924    -0.466814    -1.343857
    C         -0.855666     0.901314     0.270158
    H         -0.925362     0.902335     1.360459
    H         -1.539386     1.658704    -0.110278
    C          0.593814     1.127109    -0.164593
    H          1.090504     1.917557     0.395015
    H          0.608118     1.414764    -1.216652

### uracil-gp

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Visualization by ChemDoodle Web

Comment

    Uracil, S66, gas-phase monomer, Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N          0.035189     0.942883     0.000000
    H          0.048212     1.953603     0.000000
    C          1.288023     0.310598     0.000000
    O          2.313485     0.968410     0.000000
    C          1.199593    -1.140061     0.000000
    H          2.110130    -1.713656     0.000000
    C         -0.009221    -1.736613     0.000000
    H         -0.126582    -2.810017     0.000000
    N         -1.174184    -1.015535     0.000000
    H         -2.070599    -1.472561     0.000000
    C         -1.219411     0.368896     0.000000
    O         -2.258420     0.998327     0.000000

### thymine-wc

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Visualization by ChemDoodle Web

Comment

    Thymine, S22 WC Dimer Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    N         -1.107052    -1.237551    -0.000444
    C          0.232428    -1.528255    -0.000172
    C          1.179726    -0.564194     0.000001
    C          0.737089     0.822586    -0.000260
    N         -0.631886     1.017361    -0.001470
    C         -1.612422     0.050836    -0.000138
    C          2.646037    -0.841169     0.000415
    O          1.513440     1.779919     0.000594
    O         -2.806912     0.289393     0.001180
    H         -1.798058    -1.969059     0.000258
    H         -0.969551     2.003107    -0.001666
    H          0.482619    -2.579865     0.000083
    H          3.119129    -0.396887    -0.873926
    H          3.118566    -0.397012     0.875117
    H          2.839304    -1.911955     0.000403

### acetone

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Visualization by ChemDoodle Web

Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 13:43:09 2012
     $ACETONE
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -1.285598    -0.688680     0.000011
    C          0.000000     0.106222     0.000002
    C          1.285605    -0.688669    -0.000016
    O         -0.000007     1.291739     0.000000
    H         -2.133453    -0.021018    -0.000541
    H         -1.325618    -1.330608     0.873525
    H         -1.325183    -1.331262    -0.873061
    H          2.133453    -0.020997    -0.000449
    H          1.325147    -1.331335    -0.873014
    H          1.325680    -1.330511     0.873573

### acetamide-hb

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Visualization by ChemDoodle Web

Comment

    Acetamide, S66 H-bond monomer, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C         -0.046141     0.068233     0.000369
    O         -0.356977     1.261505    -0.000067
    N         -0.952698    -0.925993     0.000094
    H         -1.951019    -0.708901    -0.001835
    H         -0.652211    -1.881153    -0.000309
    C          1.405590    -0.345673    -0.000025
    H          1.882100     0.069306    -0.884682
    H          1.547735    -1.423089     0.013128
    H          1.889264     0.092320     0.869357

### c2h5oh

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Comment

              FRAGNAMEEFP GENERATED AT Wed Jul 18 11:34:09 2012
     $C2H5OH
    EFP DATA FOR FRAGNAME SCFTYP=RHF     ... GENERATED WITH BASIS SET=XXX

Full Geometry in Angstroms

    C         -1.270523     0.250209     0.013482
    C          0.014745    -0.557291    -0.030369
    O          1.161120     0.243635     0.058487
    H         -2.133098    -0.406516    -0.022769
    H         -1.334218     0.928151    -0.832514
    H         -1.321263     0.837360     0.922331
    H          0.060238    -1.232834     0.813290
    H          0.046243    -1.164406    -0.931998
    H          1.206620     0.827957    -0.675504

### indole

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Visualization by ChemDoodle Web

Comment

    Indole, S22 Complex Elec.: 6-31G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    H          3.112818     1.194452     0.003879
    C          2.157723     0.686391     0.004452
    C          0.988223     1.429181    -0.000611
    H          1.022763     2.511112    -0.004525
    C         -0.243711     0.754051    -0.002940
    C         -1.607660     1.168976     0.000133
    H         -1.985680     2.177226    -0.009178
    C         -2.374160     0.025843     0.005666
    N         -1.552555    -1.074140    -0.009326
    C         -0.243529    -0.668572    -0.000083
    C          0.933683    -1.419112    -0.002547
    H          0.913892    -2.501057     0.001284
    C          2.132045    -0.722899     0.000520
    H          3.064732    -1.270666     0.000627
    H         -1.860733    -2.026513     0.074060
    H         -3.445035    -0.089573     0.008789

### pentane

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Visualization by ChemDoodle Web

Comment

    Pentane, S66, Elec.: 6-31+G* Rest: 6-311++G(3df,2p)

Full Geometry in Angstroms

    C          0.000000     2.533200     0.334434
    H         -0.879710     2.565090     0.977044
    H          0.879710     2.565090     0.977044
    H          0.000000     3.433960    -0.277306
    C          0.000000     1.271780    -0.519136
    H          0.874580     1.269170    -1.173596
    H         -0.874580     1.269170    -1.173596
    C          0.000000     0.000000     0.318304
    H          0.875270     0.000000     0.974624
    H         -0.875270     0.000000     0.974624
    C          0.000000    -1.271780    -0.519136
    H          0.874580    -1.269170    -1.173596
    H         -0.874580    -1.269170    -1.173596
    C          0.000000    -2.533200     0.334434
    H         -0.879710    -2.565090     0.977044
    H          0.000000    -3.433960    -0.277306
    H          0.879710    -2.565090     0.977044