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.
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.
2aminopyridine¶
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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
pyrazine¶
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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
phenol¶
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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
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
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
dcm¶
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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
pentane¶
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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
thymine-wc¶
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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
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
acetone¶
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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
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
dmso¶
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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
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
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
methylamine¶
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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
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
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
hydrogencyanide¶
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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
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
ch3oh¶
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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
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
cyclopentane¶
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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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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
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
adenine-stack¶
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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
water¶
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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
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
pyridine¶
translate: alt+click+drag
zoom: scroll
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
cl2¶
translate: alt+click+drag
zoom: scroll
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
benzene¶
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zoom: scroll
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
h2¶
translate: alt+click+drag
zoom: scroll
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
nmethylacetamide¶
translate: alt+click+drag
zoom: scroll
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¶
translate: alt+click+drag
zoom: scroll
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
nh3¶
translate: alt+click+drag
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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
methanol¶
translate: alt+click+drag
zoom: scroll
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
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
indole¶
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zoom: scroll
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
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
ethyne¶
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zoom: scroll
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-hb¶
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zoom: scroll
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
thymine-stack¶
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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
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
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