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Differences between Parameters for AutoDock 3.0 and those for Earlier Versions. More Non-Bond Parameters for AutoDock, including:
* Halogens
* IronNon-Bond Parameters formatted for AutoGrid and AutoDock Parameter Files.
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Atomic radii: van der Waals, ionic and covalent radii. A link to WebElements:
The AutoDock 3.0 scoring function is based on an empirically-derived
linear free energy model that is designed to reproduce observed binding
constants for small organic molecules bound to proteins. AutoDock 2.4 had
terms for van der Waals energy, hydrogen bond energy and Coulombic energy.
The new scoring function has additional terms compared with AutoDock 2.4's
and earlier versions, to model (1) the change in desolvation free energy
and (2) the loss of torsional degrees of freedom upon binding. The 3.0
linear free energy function that we use was the best model out of 900 contenders.
The coefficients of this linear model for the van der Waals term and the
hydrogen bonding term multiply the corresponding well depths, or epsilon-ij
values
from AutoDock 2.4's parameters, to give the epsilon-ij
values
for AutoDock 3.0.
In AutoDock 3.0, we also found that in the best model for binding free energy, it was sufficient that desolvation be modelled only for carbon atom types in the ligand. It was necessary, however, to distinguish between aliphatic and aromatic carbons.
Thus, in the PDBQ file of the ligand, the first letter of the atom names of aliphatic carbons should be changed to 'C', and likewise for aromatic carbons, to 'A'. AutoTors has been updated to perform this atom name changing operation automatically.
To summarize, the coefficients for the terms in the AutoDock 3.0 linear
free energy model (actually number 140n out of 900, where the n signifies
that there is no constant term to be added) are given in this table:
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| van der Waals | 0.1485 |
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You could, of course, derive your own linear free energy model and use your own coefficients instead of these.
We have received several requests for parameters for Cl and other
halogens. There are several force fields which possess these, including,
for examplel, CHARMM, MM3 and the Merck MMFF.
The AutoDock force field is based on the AMBER force field reported in Weiner, Kollman, Nguyen and Case, (1986), J.Comput.Chem., 7, 230-252. This lacks parameters for halogen atoms. The more recent report of the AMBER force field [Cornell et al., (1995), J.Am.Chem.Soc, 117, 5179-5197] has a parameter for F, fluorine, but not for Cl, Br or I.
The following parameters are derived from two different force fields, AMBER (1986) and the Merck FF, MMFF [T. A. Halgren, (1992), "Representation of van der Waals (vdW) Interactions in Molecular Mechanics Force Fields: Potential Form, Combination Rules, and vdW Parameters", JACS, 114, 7827-7843]. The combined AMBER (1986)/MMFF parameters represent a new and untested set of parameters, so they should be used with caution.
The AutoDock single-letter codes are as follows:
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| A | carbon (aromatic) |
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Remember that if you want to use the iron, chlorine or bromine parameters in AutoDock, you must edit the atom names of the appropriate ATOM or HETATM records in your PDBQ file, so that the first letter corresponds to the single-letter code. (Sorry, at the moment we do not provide a mechanism to recognise these automatically, so you must do this by hand or figure out a way to automate it).
Here are the equilibrium separations, Rij, and the well depths,
epsilon-ij,
along with the van der Waals coefficients for the 12 and 6 terms in the
potential expression:
| Note: if you wish to use these 2.4 values in AutoDock 3.0's free energy function, you should multiply the well depths (epsij) and C12 and C6 values by the coefficient for van der Waals energy (or the coefficients for hydrogen bonding if you derive 12,10 interactions). |
i = ligand atom type;
j = macromolecule atom type.
AutoDock 2.4 AutoDock 2.4 AutoDock 2.4
i-j Rij epsij C12 C6 ___ ____ _____ ___________ ___________ -1 -1 12 -1 6 /A /kcal mol /kcal mol A /kcal mol A ___ ____ _____ ___________ ___________ C-C 4.00 0.150 2516582.400 1228.800000 C-N 3.75 0.155 1198066.249 861.634784 C-O 3.60 0.173 820711.722 754.059521 C-P 4.10 0.173 3908111.160 1645.484377 C-S 4.00 0.173 2905899.052 1418.896022 C-H 3.00 0.055 29108.222 79.857949 C-f 2.65 0.039 4645.111 26.825688 C-F 3.54 0.110 431504.667 434.828555 C-c 4.04 0.203 3904113.922 1782.548364 C-b 4.17 0.242 6582645.981 2521.973160 C-I 4.36 0.288 13578538.863 3953.339390 N-C 3.75 0.155 1198066.249 861.634784 N-N 3.50 0.160 540675.281 588.245000 N-O 3.35 0.179 357365.541 505.677729 N-P 3.85 0.179 1897159.056 1165.116525 N-S 3.75 0.179 1383407.742 994.930149 N-H 2.75 0.057 10581.989 48.932922 N-f 2.40 0.040 1460.814 15.288238 N-F 3.29 0.113 185297.693 289.579287 N-c 3.79 0.210 1875235.842 1255.495642 N-b 3.92 0.249 3234565.788 1796.616509 N-I 4.11 0.297 6904486.626 2864.906529 O-C 3.60 0.173 820711.722 754.059521 O-N 3.35 0.179 357365.541 505.677729 O-O 3.20 0.200 230584.301 429.496730 O-P 3.70 0.200 1316590.401 1026.290564 O-S 3.60 0.200 947676.268 870.712934 O-H 2.60 0.063 6035.457 39.075098 O-f 2.25 0.045 752.844 11.604865 O-F 3.15 0.126 118442.561 244.801394 O-c 3.65 0.235 1292230.332 1102.007957 O-b 3.77 0.279 2262921.897 1588.947973 O-I 3.96 0.332 4941135.547 2562.628477 P-C 4.10 0.173 3908111.160 1645.484377 P-N 3.85 0.179 1897159.056 1165.116525 P-O 3.70 0.200 1316590.401 1026.290564 P-P 4.20 0.200 6025893.897 2195.612698 P-S 4.10 0.200 4512698.060 1900.041696 P-H 3.10 0.063 49816.168 112.261323 P-f 2.75 0.045 8365.797 38.684871 P-F 3.65 0.126 695713.424 593.301140 P-c 4.14 0.235 6043158.116 2383.124568 P-b 4.27 0.279 10104579.020 3357.639050 P-I 4.46 0.332 20582723.561 5230.264891 S-C 4.00 0.173 2905899.052 1418.896022 S-N 3.75 0.179 1383407.742 994.930149 S-O 3.60 0.200 947676.268 870.712934 S-P 4.10 0.200 4512698.060 1900.041696 S-S 4.00 0.200 3355443.200 1638.400000 S-H 3.00 0.063 33611.280 92.212017 S-f 2.65 0.045 5363.712 30.975636 S-F 3.54 0.126 498258.671 502.096766 S-c 4.04 0.235 4508082.448 2058.309555 S-b 4.17 0.279 7600984.859 2912.123766 S-I 4.36 0.332 15679146.136 4564.923122 H-C 3.00 0.055 29108.222 79.857949 H-N 2.75 0.057 10581.989 48.932922 H-O 2.60 0.063 6035.457 39.075098 H-P 3.10 0.063 49816.168 112.261323 H-S 3.00 0.063 33611.280 92.212017 H-H 2.00 0.020 81.920 2.560000 H-f 1.65 0.014 5.759 0.570754 H-F 2.54 0.040 2953.340 21.737856 H-c 3.04 0.074 47208.163 118.446796 H-b 3.17 0.088 89119.834 177.321779 H-I 3.36 0.105 217548.386 302.378005 f-C 2.65 0.039 4645.111 26.825688 f-N 2.40 0.040 1460.814 15.288238 f-O 2.25 0.045 752.844 11.604865 f-P 2.75 0.045 8365.797 38.684871 f-S 2.65 0.045 5363.712 30.975636 f-H 1.65 0.014 5.759 0.570754 f-f 1.30 0.010 0.233 0.096536 f-F 2.19 0.028 353.801 6.326771 f-c 2.69 0.053 7711.871 40.256606 f-b 2.81 0.062 15442.428 62.069063 f-I 3.01 0.074 41092.966 110.509219 F-C 3.54 0.110 431504.667 434.828555 F-N 3.29 0.113 185297.693 289.579287 F-O 3.15 0.126 118442.561 244.801394 F-P 3.65 0.126 695713.424 593.301140 F-S 3.54 0.126 498258.671 502.096766 F-H 2.54 0.040 2953.340 21.737856 F-f 2.19 0.028 353.801 6.326771 F-F 3.09 0.080 60616.623 139.274260 F-c 3.59 0.149 680977.743 636.203746 F-b 3.71 0.176 1199517.835 920.011482 F-I 3.90 0.210 2642207.925 1490.289897 c-C 4.04 0.203 3904113.922 1782.548364 c-N 3.79 0.210 1875235.842 1255.495642 c-O 3.65 0.235 1292230.332 1102.007957 c-P 4.14 0.235 6043158.116 2383.124568 c-S 4.04 0.235 4508082.448 2058.309555 c-H 3.04 0.074 47208.163 118.446796 c-f 2.69 0.053 7711.871 40.256606 c-F 3.59 0.149 680977.743 636.203746 c-c 4.09 0.276 6047679.649 2583.919181 c-b 4.21 0.328 10158146.964 3648.815570 c-I 4.40 0.390 20834113.840 5703.343803 b-C 4.17 0.242 6582645.981 2521.973160 b-N 3.92 0.249 3234565.788 1796.616509 b-O 3.77 0.279 2262921.897 1588.947973 b-P 4.27 0.279 10104579.020 3357.639050 b-S 4.17 0.279 7600984.859 2912.123766 b-H 3.17 0.088 89119.834 177.321779 b-f 2.81 0.062 15442.428 62.069063 b-F 3.71 0.176 1199517.835 920.011482 b-c 4.21 0.328 10158146.964 3648.815570 b-b 4.33 0.389 16896795.876 5127.515420 b-I 4.53 0.463 34148162.705 7955.836263 I-C 4.36 0.288 13578538.863 3953.339390 I-N 4.11 0.297 6904486.626 2864.906529 I-O 3.96 0.332 4941135.547 2562.628477 I-P 4.46 0.332 20582723.561 5230.264891 I-S 4.36 0.332 15679146.136 4564.923122 I-H 3.36 0.105 217548.386 302.378005 I-f 3.01 0.074 41092.966 110.509219 I-F 3.90 0.210 2642207.925 1490.289897 I-c 4.40 0.390 20834113.840 5703.343803 I-b 4.53 0.463 34148162.705 7955.836263 I-I 4.72 0.552 67490564.606 12207.340687 ___ ____ _____ ___________ ___________
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This section gives lines that are formatted in a way that can be used with AutoGrid and AutoDock parameter files. You can copy and paste the relevant lines right into your favorite text editor.
However, make sure you use these lines in the correct order.
?-C
?-N
?-O
?-S
?-H
?-X
?-M
where the '?' is replaced by C, then N, then O, then H and finally c, depending on the parameter block. There are always 7 lines in these blocks. The seven lines correspond to the interaction of the current ligand atom type with up to 7 different protein atom types. The order is always C, N, O,S, H, X and M (the last two are often repetitions of the H values, when X and M are not present in the protein. If there are no X or M in the protein, these lines are ignored by AutoGrid).
A parameter "block" in an AutoGrid 3 GPF looks like this (this block
is for aliphatic carbon atom types in the ligand interacting with the various
atom types in the protein):
| map 1hvr.C.map
#filename of grid map
nbp_r_eps 4.00 0.0222750 12 6 #C-C lj nbp_r_eps 3.75 0.0230026 12 6 #C-N lj nbp_r_eps 3.60 0.0257202 12 6 #C-O lj nbp_r_eps 4.00 0.0257202 12 6 #C-S lj nbp_r_eps 3.00 0.0081378 12 6 #C-H lj nbp_r_eps 3.00 0.0081378 12 6 #C-H lj nbp_r_eps 3.00 0.0081378 12 6 #C-H lj sol_par 12.77 0.6844 #C atomic fragmental volume, solvation param. constant 0.000 #C grid map constant energy |
| types CNOHc # atom type names |
Further down in the DPF, the internal energy parameters would be given in the following order:
C-C, C-N, C-O, C-H, C-c, N-N, N-O, N-H, N-c, O-O, O-H, O-c, H-H, H-c, and finally, c-c.
A real-world example, from an HIV-1 protease inhibitor with ligand atoms
types C [aliphatic carbon], A [aromatic carbon],
N, O and H, would be:
| intnbp_r_eps 4.00 0.0222750 12
6 #C-C lj
intnbp_r_eps 4.00 0.0222750 12 6 #C-A lj intnbp_r_eps 3.75 0.0230026 12 6 #C-N lj intnbp_r_eps 3.60 0.0257202 12 6 #C-O lj intnbp_r_eps 3.00 0.0081378 12 6 #C-H lj intnbp_r_eps 4.00 0.0222750 12 6 #N-A lj intnbp_r_eps 3.75 0.0230026 12 6 #N-N lj intnbp_r_eps 3.60 0.0257202 12 6 #A-O lj intnbp_r_eps 3.00 0.0081378 12 6 #A-H lj intnbp_r_eps 3.50 0.0237600 12 6 #N-N lj intnbp_r_eps 3.35 0.0265667 12 6 #N-O lj intnbp_r_eps 2.75 0.0084051 12 6 #N-H lj intnbp_r_eps 3.20 0.0297000 12 6 #O-O lj intnbp_r_eps 1.90 0.3280000 12 10 #O-H hb intnbp_r_eps 2.00 0.0029700 12 6 #H-H lj |
Just to clarify...
| types | intnbps_r_eps |
| 12 | 11
12 22 |
| 123 | 11
12 13 22 23 33 |
| 1234 | 11
12 13 14 22 23 24 33 34 44 |
| 12345 | 11
12 13 14 15 22 23 24 25 33 34 35 44 45 55 |
C.map nbp_coeffs 2516582.400 1228.800000 12 6 # C-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1198066.249 861.634784 12 6 # C-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 820711.722 754.059521 12 6 # C-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 3908111.160 1645.484377 12 6 # C-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 2905899.052 1418.896022 12 6 # C-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 29108.222 79.857949 12 6 # C-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4645.111 26.825688 12 6 # C-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 431504.667 434.828555 12 6 # C-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 3904113.922 1782.548364 12 6 # C-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6582645.981 2521.973160 12 6 # C-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 13578538.863 3953.339390 12 6 # C-I_non-bond-parameters/Cn,Cm,n,m N.map nbp_coeffs 1198066.249 861.634784 12 6 # N-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 540675.281 588.245000 12 6 # N-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 357365.541 505.677729 12 6 # N-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1897159.056 1165.116525 12 6 # N-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1383407.742 994.930149 12 6 # N-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 10581.989 48.932922 12 6 # N-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1460.814 15.288238 12 6 # N-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 185297.693 289.579287 12 6 # N-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1875235.842 1255.495642 12 6 # N-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 3234565.788 1796.616509 12 6 # N-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6904486.626 2864.906529 12 6 # N-I_non-bond-parameters/Cn,Cm,n,m O.map nbp_coeffs 820711.722 754.059521 12 6 # O-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 357365.541 505.677729 12 6 # O-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 230584.301 429.496730 12 6 # O-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1316590.401 1026.290564 12 6 # O-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 947676.268 870.712934 12 6 # O-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6035.457 39.075098 12 6 # O-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 752.844 11.604865 12 6 # O-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 118442.561 244.801394 12 6 # O-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1292230.332 1102.007957 12 6 # O-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 2262921.897 1588.947973 12 6 # O-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4941135.547 2562.628477 12 6 # O-I_non-bond-parameters/Cn,Cm,n,m P.map nbp_coeffs 3908111.160 1645.484377 12 6 # P-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1897159.056 1165.116525 12 6 # P-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1316590.401 1026.290564 12 6 # P-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6025893.897 2195.612698 12 6 # P-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4512698.060 1900.041696 12 6 # P-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 49816.168 112.261323 12 6 # P-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 8365.797 38.684871 12 6 # P-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 695713.424 593.301140 12 6 # P-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6043158.116 2383.124568 12 6 # P-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 10104579.020 3357.639050 12 6 # P-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 20582723.561 5230.264891 12 6 # P-I_non-bond-parameters/Cn,Cm,n,m S.map nbp_coeffs 2905899.052 1418.896022 12 6 # S-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1383407.742 994.930149 12 6 # S-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 947676.268 870.712934 12 6 # S-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4512698.060 1900.041696 12 6 # S-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 3355443.200 1638.400000 12 6 # S-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 33611.280 92.212017 12 6 # S-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 5363.712 30.975636 12 6 # S-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 498258.671 502.096766 12 6 # S-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4508082.448 2058.309555 12 6 # S-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 7600984.859 2912.123766 12 6 # S-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 15679146.136 4564.923122 12 6 # S-I_non-bond-parameters/Cn,Cm,n,m H.map nbp_coeffs 29108.222 79.857949 12 6 # H-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 10581.989 48.932922 12 6 # H-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6035.457 39.075098 12 6 # H-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 49816.168 112.261323 12 6 # H-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 33611.280 92.212017 12 6 # H-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 81.920 2.560000 12 6 # H-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 5.759 0.570754 12 6 # H-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 2953.340 21.737856 12 6 # H-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 47208.163 118.446796 12 6 # H-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 89119.834 177.321779 12 6 # H-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 217548.386 302.378005 12 6 # H-I_non-bond-parameters/Cn,Cm,n,m f.map nbp_coeffs 4645.111 26.825688 12 6 # f-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1460.814 15.288238 12 6 # f-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 752.844 11.604865 12 6 # f-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 8365.797 38.684871 12 6 # f-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 5363.712 30.975636 12 6 # f-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 5.759 0.570754 12 6 # f-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 0.233 0.096536 12 6 # f-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 353.801 6.326771 12 6 # f-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 7711.871 40.256606 12 6 # f-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 15442.428 62.069063 12 6 # f-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 41092.966 110.509219 12 6 # f-I_non-bond-parameters/Cn,Cm,n,m F.map nbp_coeffs 431504.667 434.828555 12 6 # F-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 185297.693 289.579287 12 6 # F-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 118442.561 244.801394 12 6 # F-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 695713.424 593.301140 12 6 # F-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 498258.671 502.096766 12 6 # F-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 2953.340 21.737856 12 6 # F-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 353.801 6.326771 12 6 # F-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 60616.623 139.274260 12 6 # F-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 680977.743 636.203746 12 6 # F-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1199517.835 920.011482 12 6 # F-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 2642207.925 1490.289897 12 6 # F-I_non-bond-parameters/Cn,Cm,n,m c.map nbp_coeffs 3904113.922 1782.548364 12 6 # c-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1875235.842 1255.495642 12 6 # c-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1292230.332 1102.007957 12 6 # c-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6043158.116 2383.124568 12 6 # c-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4508082.448 2058.309555 12 6 # c-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 47208.163 118.446796 12 6 # c-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 7711.871 40.256606 12 6 # c-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 680977.743 636.203746 12 6 # c-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6047679.649 2583.919181 12 6 # c-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 10158146.964 3648.815570 12 6 # c-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 20834113.840 5703.343803 12 6 # c-I_non-bond-parameters/Cn,Cm,n,m b.map nbp_coeffs 6582645.981 2521.973160 12 6 # b-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 3234565.788 1796.616509 12 6 # b-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 2262921.897 1588.947973 12 6 # b-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 10104579.020 3357.639050 12 6 # b-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 7600984.859 2912.123766 12 6 # b-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 89119.834 177.321779 12 6 # b-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 15442.428 62.069063 12 6 # b-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1199517.835 920.011482 12 6 # b-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 10158146.964 3648.815570 12 6 # b-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 16896795.876 5127.515420 12 6 # b-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 34148162.705 7955.836263 12 6 # b-I_non-bond-parameters/Cn,Cm,n,m I.map nbp_coeffs 13578538.863 3953.339390 12 6 # I-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6904486.626 2864.906529 12 6 # I-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4941135.547 2562.628477 12 6 # I-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 20582723.561 5230.264891 12 6 # I-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 15679146.136 4564.923122 12 6 # I-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 217548.386 302.378005 12 6 # I-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 41092.966 110.509219 12 6 # I-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 2642207.925 1490.289897 12 6 # I-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 20834113.840 5703.343803 12 6 # I-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 34148162.705 7955.836263 12 6 # I-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 67490564.606 12207.340687 12 6 # I-I_non-bond-parameters/Cn,Cm,n,m
C.map nbp_r_eps 4.00 0.1500 12 6 #C-C equilibrium separation and well-depth nbp_r_eps 3.75 0.1549 12 6 #C-N equilibrium separation and well-depth nbp_r_eps 3.60 0.1732 12 6 #C-O equilibrium separation and well-depth nbp_r_eps 4.10 0.1732 12 6 #C-P equilibrium separation and well-depth nbp_r_eps 4.00 0.1732 12 6 #C-S equilibrium separation and well-depth nbp_r_eps 3.00 0.0548 12 6 #C-H equilibrium separation and well-depth nbp_r_eps 2.65 0.0387 12 6 #C-f equilibrium separation and well-depth nbp_r_eps 3.54 0.1095 12 6 #C-F equilibrium separation and well-depth nbp_r_eps 4.04 0.2035 12 6 #C-c equilibrium separation and well-depth nbp_r_eps 4.17 0.2416 12 6 #C-b equilibrium separation and well-depth nbp_r_eps 4.36 0.2877 12 6 #C-I equilibrium separation and well-depth N.map nbp_r_eps 3.75 0.1549 12 6 #N-C equilibrium separation and well-depth nbp_r_eps 3.50 0.1600 12 6 #N-N equilibrium separation and well-depth nbp_r_eps 3.35 0.1789 12 6 #N-O equilibrium separation and well-depth nbp_r_eps 3.85 0.1789 12 6 #N-P equilibrium separation and well-depth nbp_r_eps 3.75 0.1789 12 6 #N-S equilibrium separation and well-depth nbp_r_eps 2.75 0.0566 12 6 #N-H equilibrium separation and well-depth nbp_r_eps 2.40 0.0400 12 6 #N-f equilibrium separation and well-depth nbp_r_eps 3.29 0.1131 12 6 #N-F equilibrium separation and well-depth nbp_r_eps 3.79 0.2101 12 6 #N-c equilibrium separation and well-depth nbp_r_eps 3.92 0.2495 12 6 #N-b equilibrium separation and well-depth nbp_r_eps 4.11 0.2972 12 6 #N-I equilibrium separation and well-depth O.map nbp_r_eps 3.60 0.1732 12 6 #O-C equilibrium separation and well-depth nbp_r_eps 3.35 0.1789 12 6 #O-N equilibrium separation and well-depth nbp_r_eps 3.20 0.2000 12 6 #O-O equilibrium separation and well-depth nbp_r_eps 3.70 0.2000 12 6 #O-P equilibrium separation and well-depth nbp_r_eps 3.60 0.2000 12 6 #O-S equilibrium separation and well-depth nbp_r_eps 2.60 0.0632 12 6 #O-H equilibrium separation and well-depth nbp_r_eps 2.25 0.0447 12 6 #O-f equilibrium separation and well-depth nbp_r_eps 3.15 0.1265 12 6 #O-F equilibrium separation and well-depth nbp_r_eps 3.65 0.2349 12 6 #O-c equilibrium separation and well-depth nbp_r_eps 3.77 0.2789 12 6 #O-b equilibrium separation and well-depth nbp_r_eps 3.96 0.3323 12 6 #O-I equilibrium separation and well-depth P.map nbp_r_eps 4.10 0.1732 12 6 #P-C equilibrium separation and well-depth nbp_r_eps 3.85 0.1789 12 6 #P-N equilibrium separation and well-depth nbp_r_eps 3.70 0.2000 12 6 #P-O equilibrium separation and well-depth nbp_r_eps 4.20 0.2000 12 6 #P-P equilibrium separation and well-depth nbp_r_eps 4.10 0.2000 12 6 #P-S equilibrium separation and well-depth nbp_r_eps 3.10 0.0632 12 6 #P-H equilibrium separation and well-depth nbp_r_eps 2.75 0.0447 12 6 #P-f equilibrium separation and well-depth nbp_r_eps 3.65 0.1265 12 6 #P-F equilibrium separation and well-depth nbp_r_eps 4.14 0.2349 12 6 #P-c equilibrium separation and well-depth nbp_r_eps 4.27 0.2789 12 6 #P-b equilibrium separation and well-depth nbp_r_eps 4.46 0.3323 12 6 #P-I equilibrium separation and well-depth S.map nbp_r_eps 4.00 0.1732 12 6 #S-C equilibrium separation and well-depth nbp_r_eps 3.75 0.1789 12 6 #S-N equilibrium separation and well-depth nbp_r_eps 3.60 0.2000 12 6 #S-O equilibrium separation and well-depth nbp_r_eps 4.10 0.2000 12 6 #S-P equilibrium separation and well-depth nbp_r_eps 4.00 0.2000 12 6 #S-S equilibrium separation and well-depth nbp_r_eps 3.00 0.0632 12 6 #S-H equilibrium separation and well-depth nbp_r_eps 2.65 0.0447 12 6 #S-f equilibrium separation and well-depth nbp_r_eps 3.54 0.1265 12 6 #S-F equilibrium separation and well-depth nbp_r_eps 4.04 0.2349 12 6 #S-c equilibrium separation and well-depth nbp_r_eps 4.17 0.2789 12 6 #S-b equilibrium separation and well-depth nbp_r_eps 4.36 0.3323 12 6 #S-I equilibrium separation and well-depth H.map nbp_r_eps 3.00 0.0548 12 6 #H-C equilibrium separation and well-depth nbp_r_eps 2.75 0.0566 12 6 #H-N equilibrium separation and well-depth nbp_r_eps 2.60 0.0632 12 6 #H-O equilibrium separation and well-depth nbp_r_eps 3.10 0.0632 12 6 #H-P equilibrium separation and well-depth nbp_r_eps 3.00 0.0632 12 6 #H-S equilibrium separation and well-depth nbp_r_eps 2.00 0.0200 12 6 #H-H equilibrium separation and well-depth nbp_r_eps 1.65 0.0141 12 6 #H-f equilibrium separation and well-depth nbp_r_eps 2.54 0.0400 12 6 #H-F equilibrium separation and well-depth nbp_r_eps 3.04 0.0743 12 6 #H-c equilibrium separation and well-depth nbp_r_eps 3.17 0.0882 12 6 #H-b equilibrium separation and well-depth nbp_r_eps 3.36 0.1051 12 6 #H-I equilibrium separation and well-depth f.map nbp_r_eps 2.65 0.0387 12 6 #f-C equilibrium separation and well-depth nbp_r_eps 2.40 0.0400 12 6 #f-N equilibrium separation and well-depth nbp_r_eps 2.25 0.0447 12 6 #f-O equilibrium separation and well-depth nbp_r_eps 2.75 0.0447 12 6 #f-P equilibrium separation and well-depth nbp_r_eps 2.65 0.0447 12 6 #f-S equilibrium separation and well-depth nbp_r_eps 1.65 0.0141 12 6 #f-H equilibrium separation and well-depth nbp_r_eps 1.30 0.0100 12 6 #f-f equilibrium separation and well-depth nbp_r_eps 2.19 0.0283 12 6 #f-F equilibrium separation and well-depth nbp_r_eps 2.69 0.0525 12 6 #f-c equilibrium separation and well-depth nbp_r_eps 2.81 0.0624 12 6 #f-b equilibrium separation and well-depth nbp_r_eps 3.01 0.0743 12 6 #f-I equilibrium separation and well-depth F.map nbp_r_eps 3.54 0.1095 12 6 #F-C equilibrium separation and well-depth nbp_r_eps 3.29 0.1131 12 6 #F-N equilibrium separation and well-depth nbp_r_eps 3.15 0.1265 12 6 #F-O equilibrium separation and well-depth nbp_r_eps 3.65 0.1265 12 6 #F-P equilibrium separation and well-depth nbp_r_eps 3.54 0.1265 12 6 #F-S equilibrium separation and well-depth nbp_r_eps 2.54 0.0400 12 6 #F-H equilibrium separation and well-depth nbp_r_eps 2.19 0.0283 12 6 #F-f equilibrium separation and well-depth nbp_r_eps 3.09 0.0800 12 6 #F-F equilibrium separation and well-depth nbp_r_eps 3.59 0.1486 12 6 #F-c equilibrium separation and well-depth nbp_r_eps 3.71 0.1764 12 6 #F-b equilibrium separation and well-depth nbp_r_eps 3.90 0.2101 12 6 #F-I equilibrium separation and well-depth c.map nbp_r_eps 4.04 0.2035 12 6 #c-C equilibrium separation and well-depth nbp_r_eps 3.79 0.2101 12 6 #c-N equilibrium separation and well-depth nbp_r_eps 3.65 0.2349 12 6 #c-O equilibrium separation and well-depth nbp_r_eps 4.14 0.2349 12 6 #c-P equilibrium separation and well-depth nbp_r_eps 4.04 0.2349 12 6 #c-S equilibrium separation and well-depth nbp_r_eps 3.04 0.0743 12 6 #c-H equilibrium separation and well-depth nbp_r_eps 2.69 0.0525 12 6 #c-f equilibrium separation and well-depth nbp_r_eps 3.59 0.1486 12 6 #c-F equilibrium separation and well-depth nbp_r_eps 4.09 0.2760 12 6 #c-c equilibrium separation and well-depth nbp_r_eps 4.21 0.3277 12 6 #c-b equilibrium separation and well-depth nbp_r_eps 4.40 0.3903 12 6 #c-I equilibrium separation and well-depth b.map nbp_r_eps 4.17 0.2416 12 6 #b-C equilibrium separation and well-depth nbp_r_eps 3.92 0.2495 12 6 #b-N equilibrium separation and well-depth nbp_r_eps 3.77 0.2789 12 6 #b-O equilibrium separation and well-depth nbp_r_eps 4.27 0.2789 12 6 #b-P equilibrium separation and well-depth nbp_r_eps 4.17 0.2789 12 6 #b-S equilibrium separation and well-depth nbp_r_eps 3.17 0.0882 12 6 #b-H equilibrium separation and well-depth nbp_r_eps 2.81 0.0624 12 6 #b-f equilibrium separation and well-depth nbp_r_eps 3.71 0.1764 12 6 #b-F equilibrium separation and well-depth nbp_r_eps 4.21 0.3277 12 6 #b-c equilibrium separation and well-depth nbp_r_eps 4.33 0.3890 12 6 #b-b equilibrium separation and well-depth nbp_r_eps 4.53 0.4634 12 6 #b-I equilibrium separation and well-depth I.map nbp_r_eps 4.36 0.2877 12 6 #I-C equilibrium separation and well-depth nbp_r_eps 4.11 0.2972 12 6 #I-N equilibrium separation and well-depth nbp_r_eps 3.96 0.3323 12 6 #I-O equilibrium separation and well-depth nbp_r_eps 4.46 0.3323 12 6 #I-P equilibrium separation and well-depth nbp_r_eps 4.36 0.3323 12 6 #I-S equilibrium separation and well-depth nbp_r_eps 3.36 0.1051 12 6 #I-H equilibrium separation and well-depth nbp_r_eps 3.01 0.0743 12 6 #I-f equilibrium separation and well-depth nbp_r_eps 3.90 0.2101 12 6 #I-F equilibrium separation and well-depth nbp_r_eps 4.40 0.3903 12 6 #I-c equilibrium separation and well-depth nbp_r_eps 4.53 0.4634 12 6 #I-b equilibrium separation and well-depth nbp_r_eps 4.72 0.5520 12 6 #I-I equilibrium separation and well-depth
The following table lists the van der Waals, ionic and covalent
radii for a selection of biochemically important elements. Not all have
been listed here; if you spot a glaring omission, please e-mail
Garrett M. Morris.
Van der Waals radii are from:
A. Bondi, J. Phys. Chem., (1964), 68, 441.
Ionic (sometimes called ''crystal'') radii are from:
R. D. Shannon, Acta Crystallogr., (1976), A32, 751.
Covalent radii are estimated from homonuclear bond lengths; where available and from selected heteronuclear bond lengths otherwise. Bond lengths are taken from:
L. Sutton, ed., "Tables of interatomic Distances and Configuration in Molecules and Ions," Spec. Publ. No. 11 and 18, The Chemical Society, London, 1958, 1965.
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See also:
WebElements.
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