Skip to main content

Table 1 The optimized maximum atomic occupancy (O max i ) and atomic solvation parameters (S i ) for all the atom types defined for FSD and SAMPL4 molecules

From: Accuracy enhancement in the estimation of molecular hydration free energies by implementing the intramolecular hydrogen bond effects

Atom type Description \(O_{i}^{max}\) (Å3) \(S_{i}\) (kcal/mol Å3)
FSD SAMPL4 FSD SAMPL4
C.3_1 sp3 carbon with 1 substituent 396.8 350.8 0.429 1.619
C.3_2 sp3 carbon with 2 substituents 372.4 368.3 0.524 0.143
C.3_3 sp3 carbon with 3 substituents 361.9 382.5 −0.429 0.095
C.3_4 sp3 carbon with 4 substituents 379.4 377.0 1.222 0.794
C.2_1 sp2 carbon with 1 substituent 360.3 339.5 2.048 0.905
C.2_2 sp2 carbon with 2 substituents 365.1 354.8 −0.905 0.873
C.2_3 sp2 carbon with 3 substituents 391.3 353.8 −1.222 −0.540
C.1_1 sp carbon with 1 substituent 377.0 NA −0.905 NA
C.1_2 sp carbon with 2 substituents 351.6 NA 0.143 NA
C.ar_2 Aromatic carbon with 2 substituents 392.9 381.1 −1.000 −0.889
C.ar_3 Aromatic carbon with 3 substituents 375.4 353.2 −0.048 0.524
C.CO_1 Carbonyl carbon with 1 substituent 337.1 354.0 −3.968 −2.619
C.CO_2 Carbonyl carbon with 2 substituents 393.3 369.0 −6.444 −1.746
N.1_1 sp nitrogen with 1 substituent 404.0 NA −10.079 NA
N.2_2 sp2 nitrogen with 2 substituents 424.4 NA −11.556 NA
N.3_1 sp3 nitrogen with 1 substituent 351.6 384.9 −9.333 −10.318
N.3_2 sp3 nitrogen with 2 substituents 437.6 364.4 −10.238 −10.333
N.3_3 sp3 nitrogen with 3 substituents 454.6 393.7 −14.921 −12.302
N.ar Aromatic nitrogen 357.8 352.4 −8.222 −11.349
N.pl_1 Planar nitrogen with 1 substituent 396.8 358.9 −10.159 −12.460
N.pl_2 Planar nitrogen with 2 substituents 330.0 367.5 −10.873 −11.667
N.pl_3 Planar nitrogen with 3 substituents 358.7 408.9 −8.444 −11.905
N.am_1 Amide nitrogen with 1 substituent 398.9 NA −8.429 NA
N.am_2 Amide nitrogen with 2 substituents 391.1 NA −9.603 NA
N.am_3 Amide nitrogen with 3 substituents 399.2 NA −3.635 NA
N.no2 Nitrogen in nitro group 357.9 372.2 −4.444 −4.921
O.3_1 sp3 oxygen with 1 substituent 330.8 366.2 −13.556 −11.619
O.3_2 sp3 oxygen with 2 substituents 304.4 311.4 −5.714 −5.873
O.pl_1 Planar oxygen with 1 substituent NA 316.2 NA −10.619
O.pl_2 Planar oxygen with 2 substituents NA 346.8 NA −6.825
O.es_1 sp3 oxygen in carboxylic acids 309.5 327.8 −6.508 −8.413
O.es_2 sp3 oxygen in esters 319.8 333.3 1.778 −2.603
O.2 sp2 oxygen 302.4 347.6 −7.619 −9.683
O.no2 Oxygen in nitro group 342.1 338.9 −0.476 0.825
O.intra Oxygen involved in intramolecular hydrogen bond 323.0 309.0 −1.270 −3.810
S.12 Sulfur with 12 valence electrons 410.3 NA −3.810 NA
S.3_1 sp3 sulfur with 1 substituent 429.4 NA −0.762 NA
S.3_2 sp3 sulfur with 2 substituents 402.4 NA −6.857 NA
S.2 sp2 sulfur 428.6 NA 1.556 NA
S.pl Planar sulfur 409.5 NA −0.190 NA
F Fluorine 284.1 NA −3.714 NA
F.intra Fluorine involved in intramolecular hydrogen bond 277.9 NA 1.365 NA
Cl Chlorine 452.4 408.7 −0.794 −3.016
Cl.intra Chlorine involved in intramolecular hydrogen bond 458.1 NA −0.317 NA
Br Bromine 500.8 NA −1.778 NA
I Iodine 549.2 NA −1.556 NA
P.10 Phosphorus with 10 valence electrons 404.4 NA −4.095 NA
H.C Hydrogen bonded to carbon 201.6 182.2 0.111 −0.444
H.N3 Hydrogen bonded to sp3 nitrogen 254.4 212.7 −5.556 −2.540
H.Np Hydrogen bonded to planar nitrogen 207.9 223.8 −1.746 −1.159
H.O3 Hydrogen bonded to sp3 oxygen 236.7 204.8 −7.159 −9.286
H.Op Hydrogen bonded to planar oxygen NA 237.3 NA −10.889
H.Oa Hydrogen bonded to carboxylic acid group 230.2 202.4 −3.444 −6.190
H.S Hydrogen bonded to sulfur 228.9 NA −5.397 NA
H.intra Hydrogen involved in intramolecular hydrogen bond 222.2 210.0 −3.190 −4.222
Back to article page

Journal of Cheminformatics

ISSN: 1758-2946

Contact us