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. Author manuscript; available in PMC: 2020 Jan 28.
Published in final edited form as: J Chem Inf Model. 2018 Nov 27;59(1):215–228. doi: 10.1021/acs.jcim.8b00616

Table 2.

Analysis of the angle (ϕ, deg) and distance (r, Å) deviations of the protein-ligand intermolecular simulated geometries compared to the crystal structures for all eight protein systems. Average differences (AVG) and standard error (SE), absolute unsigned error (AUD), root-mean-square differences (RMSD), and the number of each type of interaction (Count) were obtained from three independent simulations.

All systems All systems excluding PDB:4NIT
ALLa Init-Drude Opt-Drude Init-CGenFF Opt-CGenFF Init-Drude Opt-Drude Init-CGenFF Opt-CGenFF
AVG ϕ −9.59 −3.53 −9.13 −5.13 −2.19 −2.19 −4.43 −4.44
r 0.57 0.21 0.63 0.17 0.33 0.18 0.20 0.16
SE ϕ 3.77 1.49 2.71 1.45 1.24 1.51 1.23 1.60
r 0.14 0.07 0.23 0.06 0.08 0.07 0.09 0.07
AUD ϕ 12.34 7.09 8.74 7.09 5.15 6.05 6.14 6.88
r 0.63 0.33 0.58 0.29 0.40 0.30 0.32 0.30
RMSD ϕ 23.06 9.02 14.62 9.47 6.80 8.17 7.78 9.43
r 0.95 0.44 1.21 0.37 0.52 0.42 0.51 0.38
Count 32 28
X-HBDb,c Init-Drude Opt-Drude Init-CGenFF Opt-CGenFF Init-Drude Opt-Drude Init-CGenFF Opt-CGenFF
AVG ϕ 1.66 4.30 −4.82 −3.41
r 0.40 0.18 0.23 0.12
SE ϕ 0.97 1.76 3.22 3.20
r 0.15 0.10 0.07 0.09
AUD ϕ 2.64 5.37 8.56 7.00
r 0.44 0.26 0.24 0.23
RMSD ϕ 2.90 6.08 9.25 8.54
r 0.55 0.31 0.29 0.26
Count 7
XBd Init-Drude Opt-Drude Init-CGenFF Opt-CGenFF Init-Drude Opt-Drude Init-CgenFF Opt-CGenFF
AVG ϕ −23.82 −10.54 −13.71 −4.14 −9.82 −9.93 −0.55 −2.55
r 0.79 0.30 0.91 −0.08 0.23 0.17 −0.14 −0.16
SE ϕ 14.21 2.36 13.21 2.43 3.20 2.95 1.42 2.37
r 0.57 0.17 1.06 0.17 0.16 0.14 0.20 0.19
AUE ϕ 23.82 10.54 14.70 5.27 9.82 9.93 1.79 3.97
r 0.87 0.40 1.27 0.33 0.34 0.29 0.32 0.35
RMSD ϕ 37.09 11.55 29.76 6.38 11.28 11.17 2.53 4.83
r 1.39 0.46 2.30 0.35 0.36 0.29 0.37 0.37
Count 5 4
a

All indicates all interactions based on all protein nitrogen and oxygen atoms within 4.5 Å of the ligand halogen atoms in the crystal structures.

b

X-HBD results limited to interaction geometries in Table S5–S12 where C-X..O/NHBD angles from crystals are less than 120° and belong to HBD groups (i.e. Cl…NSER in PDB id 2ZC9, Cl…NTYR and Cl…OSER in PDB id 4DT6, Br…NHIS in PDB id 3JUM, Br…OSER in PDB id 4NMV, BR…NHIS and Br…OTYR in PDB id 2AG6 of Table S5–S12).

c

As there are no X-HBD interaction with PDB id: 4N1T, only one set of X-HBD interactions are presented.

d

XB results are limited to interaction geometries in Table S5–S12 where C-X..O/NHBA angles from crystals are between 150–180° and belong to HBA groups (i.e. Cl…NGLY in PDB id 2UW8, Cl…OTRP and Cl…NPHE in PDB id 4DT6, Br…OTYR in PDB id 3IX8, Cl…OTHR in PDB id 4N1T of Table S5–S12).