Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'

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Markthaler, Daniel; Kraus, Hamzeh; Hansen, Niels, 2022, "Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'", https://doi.org/10.18419/darus-2109, DaRUS, V1

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Description	Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit[8]uril, CB8) were estimated from molecular dynamics (MD) simulations in the scope of the recent SAMPL8 CB8 "Drugs of Abuse" challenge using the GROMACS MD package. To compare with experimental data, a scheme for correcting the raw simulation estimates was proposed in the related publication on the basis of five training molecules (GT1-GT5) with experimentally known binding affinities towards CB8. The deposited dataset contains coordinates and molecular topologies in GROMACS format as well as free energy profiles accompanying the related publication. For each guest molecule, two protonation states were simulated (protonated, deprotonated) and for one of the drugs, G5, both of its enantiomeric forms (R, S) were considered.
Subject	Chemistry; Physics
Keyword	Molecular Dynamics Simulation, SAMPL8, Umbrella Sampling, Host-Guest Complex
Related Publication	D. Markthaler, H. Kraus, N. Hansen, Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange. In: Journal of Computer-Aided Molecular Design (2022). doi: 10.1007/s10822-021-00439-w
Data Generation	Simulation
License/Data Use Agreement	CC BY 4.0

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	FreeEnergyProfiles.tar.gz Results/Gzip Archive - 90.0 KB Published Jan 16, 2022 22 Downloads MD5: df6de9be7258c97195002494d939a4e0 Collection of free energy profiles from US simulations (SAMPL8 challenge and training set)	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	FreeEnergyProfiles_Chargescheme.pdf Results/Adobe PDF - 21.3 KB Published Jan 16, 2022 95 Downloads MD5: c2ee06a80c3f45654ca23c096a8bc632 Free energy profiles from US simulations for ligands G1 and GT1 based upon different charge schemes	Preview "Results/FreeEnergyProfiles_Chargescheme.pdf" Access File File Access Public Download Options Adobe PDF Download Metadata Data File Citation EndNote XML RIS BibTeX
	FreeEnergyProfiles_SAMPL8.pdf Results/Adobe PDF - 29.8 KB Published Jan 16, 2022 94 Downloads MD5: b3e3071f2ebe7bd1c2fc7c95ecf96778 Plot of free energy profiles from US simulations for ligand set of SAMPL8 challenge complexed with CB8	Preview "Results/FreeEnergyProfiles_SAMPL8.pdf" Access File File Access Public Download Options Adobe PDF Download Metadata Data File Citation EndNote XML RIS BibTeX
	FreeEnergyProfiles_TrainingSet.pdf Results/Adobe PDF - 22.6 KB Published Jan 16, 2022 94 Downloads MD5: 0d5718b3d3b125dbe809175bb9337b6a Plot of free energy profiles from US simulations for ligand training set complexed with CB8	Preview "Results/FreeEnergyProfiles_TrainingSet.pdf" Access File File Access Public Download Options Adobe PDF Download Metadata Data File Citation EndNote XML RIS BibTeX
	G1_deprotonated.gro Structure/G/Unknown - 1.2 KB Published Jan 16, 2022 26 Downloads MD5: 604e9c3171f6b3d0c6b125f60ec865d4 Cartesian coordinates of the guest molecule G1 in the deprotonated state in .gro format.	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	G1_protonated.gro Structure/G/Unknown - 1.3 KB Published Jan 16, 2022 22 Downloads MD5: f716959bee34257ead30a2ed4702f866 Cartesian coordinates of the guest molecule G1 in the protonated state in .gro format.	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	G2_deprotonated.gro Structure/G/Unknown - 2.4 KB Published Jan 16, 2022 21 Downloads MD5: 765fcbf16e313578f3df4dbfcfdf25ef Cartesian coordinates of the guest molecule G2 in the deprotonated state in .gro format.	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	G2_protonated.gro Structure/G/Unknown - 2.4 KB Published Jan 16, 2022 21 Downloads MD5: 95afb956768c2b05b061e67ce37234e3 Cartesian coordinates of the guest molecule G2 in the protonated state in .gro format.	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	G3_deprotonated.gro Structure/G/Unknown - 1.8 KB Published Jan 16, 2022 21 Downloads MD5: b508f78bb5842b8ce37b5616dd61ef87 Cartesian coordinates of the guest molecule G3 in the deprotonated state in .gro format.	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	G3_protonated.gro Structure/G/Unknown - 1.9 KB Published Jan 16, 2022 20 Downloads MD5: 2f992bdfbee105326f31db5b81dcc297 Cartesian coordinates of the guest molecule G3 in the protonated state in .gro format.	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.18419/darus-2109
Publication Date	2022-01-16
Title	Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Author	Markthaler, Daniel (Universität Stuttgart) - ORCID: 0000-0003-3281-436X Kraus, Hamzeh (Universität Stuttgart) - ORCID: 0000-0001-9643-4839 Hansen, Niels (Universität Stuttgart) - ORCID: 0000-0003-4366-6120
Point of Contact	Use email button above to contact. Hansen, Niels (Universität Stuttgart)
Description	Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit[8]uril, CB8) were estimated from molecular dynamics (MD) simulations in the scope of the recent SAMPL8 CB8 "Drugs of Abuse" challenge using the GROMACS MD package. To compare with experimental data, a scheme for correcting the raw simulation estimates was proposed in the related publication on the basis of five training molecules (GT1-GT5) with experimentally known binding affinities towards CB8. The deposited dataset contains coordinates and molecular topologies in GROMACS format as well as free energy profiles accompanying the related publication. For each guest molecule, two protonation states were simulated (protonated, deprotonated) and for one of the drugs, G5, both of its enantiomeric forms (R, S) were considered.
Subject	Chemistry; Physics
Keyword	Molecular Dynamics Simulation http://id.nlm.nih.gov/mesh/T729332 (MeSH) SAMPL8 Umbrella Sampling Host-Guest Complex
Related Publication	D. Markthaler, H. Kraus, N. Hansen, Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange. In: Journal of Computer-Aided Molecular Design (2022). doi: 10.1007/s10822-021-00439-w https://doi.org/10.1007/s10822-021-00439-w
Funding Information	Deutsche Forschungsgemeinschaft: EXC 2075 - 390740016
Depositor	Kraus, Hamzeh
Deposit Date	2021-08-04
Data Type	Input files for molecular dynamics simulations with GROMACS.

Process Metadata

Software

GROMACS Version: 2016.4 (https://www.gromacs.org/) LGPL 2.1 (H. J. C. Berendsen, D. van der Spoel, R. van Drunen, GROMACS: A message-passing parallel molecular dynamics implementation. In: Computer Physics Communications 91 (1995), 1-3, 43-56. doi: 10.1016/0010-4655(95)00042-E; B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. In: Journal of Chemical Theory and Computation 4 (2008), 3, 435-447. doi: 10.1021/ct700301q; M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl, GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. In: SoftwareX 1-2 (2015), 19-25. doi: 10.1016/j.softx.2015.06.001)
Ambertools Version: 2020 (https://ambermd.org/AmberTools.php) (D.A. Case, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz,R Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, A. Kovalenko, R. Krasny, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, L. Wilson, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York and P.A. Kollman (2020), AMBER 2020, University of California, San Francisco.)
PLUMED Version: 2.4.2 (https://www.plumed.org/) LGPL 3.0 (G. A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED 2: New feathers for an old bird. In: Computer Physics Communications 185 (2014), 2, 604-613. doi: 10.1016/j.cpc.2013.09.018)

Environments

bwForCluster BinAC

Engineering Metadata

Data Generation	Simulation
Controlled Variables	Number of atoms (N) Pressure (p) [bar] : 1 Temperature (T) [K] : 300
System or Phase Components	CB8 (Cucurbit[8]uril host molecule for host-guest interaction.) (SmilesCode: C1N2C3C4N(C2=O)CN5C6C7N(C5=O)CN8C9C2N(C8=O)CN5C8C%10N(C5=O)CN5C%11C%12N(C5=O)CN5C%13C%14N(C5=O)CN5C%15C%16N(C5=O)CN5C%17C(N1C5=O)N1CN3C(=O)N4CN6C(=O)N7CN9C(=O)N2CN8C(=O)N%10CN%11C(=O)N%12CN%13C(=O)N%14CN%15C(=O)N%16CN%17C1=O) (IUPAC Name: 3,5,8,10,13,15,18,20,23,25,28,30,33,35,38,40,41,43,45,47,51,53,55,57,59,61,63,65,67,69,71,73-dotriacontazapentacosacyclo[35.3.3.36,7.311,12.316,17.321,22.326,27.331,32.22,41.236,43.13,40.15,8.110,13.115,18.120,23.125,28.130,33.135,38.145,51.147,73.153,55.157,59.161,63.165,67.169,71]octacontane-44,46,48,49,50,52,54,56,58,60,62,64,66,68,70,72-hexadecone) , Force Field: GAFF CB7 (Cucurbit[7]uril host molecule for host-guest interaction.) (SmilesCode: C1N2C3C4N(C2=O)CN5C6C7N(C5=O)CN8C9C2N(C8=O)CN5C8C%10N(C5=O)CN5C%11C%12N(C5=O)CN5C%13C%14N(C5=O)CN5C%15C(N1C5=O)N1CN3C(=O)N4CN6C(=O)N7CN9C(=O)N2CN8C(=O)N%10CN%11C(=O)N%12CN%13C(=O)N%14CN%15C1=O) (IUPAC Name: 3,5,8,10,13,15,18,20,23,25,28,30,33,35,36,38,40,42,46,48,50,52,54,56,58,60,62,64-octacosazadocosacyclo[30.3.3.36,7.311,12.316,17.321,22.326,27.22,36.231,38.13,35.15,8.110,13.115,18.120,23.125,28.130,33.140,46.142,64.148,50.152,54.156,58.160,62]heptacontane-39,41,43,44,45,47,49,51,53,55,57,59,61,63-tetradecone) , Force Field: GAFF G1 (Methamphetamine guest molecule for host-guest interaction.) (SmilesCode: C[C@@H](CC1=CC=CC=C1)NC) (IUPAC Name: (2S)-N-methyl-1-phenylpropan-2-amine) , Force Field: GAFF G2 (Fentanyl guest molecule for host-guest interaction.) (SmilesCode: CCC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3) (IUPAC Name: N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide) , Force Field: GAFF G3 (Morphine guest molecule for host-guest interaction.) (SmilesCode: CN1CC[C@]23[C@@H]4[C@H]1CC5=C2C(=C(C=C5)O)O[C@H]3[C@H](C=C4)O) (IUPAC Name: (4R,4aR,7S,7aR,12bS)-3-methyl-2,4,4a,7,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol) , Force Field: GAFF G4 (Hydromorphone guest molecule for host-guest interaction.) (SmilesCode: CN1CC[C@]23[C@@H]4[C@H]1CC5=C2C(=C(C=C5)O)O[C@H]3C(=O)CC4) (IUPAC Name: (4R,4aR,7aR,12bS)-9-hydroxy-3-methyl-1,2,4,4a,5,6,7a,13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one) , Force Field: GAFF G5 (Ketamine guest molecule for host-guest interaction.) (SmilesCode: CNC1(CCCCC1=O)C2=CC=CC=C2Cl) (IUPAC Name: 2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one) , Force Field: GAFF G6 (Phencyclidine guest molecule for host-guest interaction.) (SmilesCode: C1CCC(CC1)(C2=CC=CC=C2)N3CCCCC3) (IUPAC Name: 1-(1-phenylcyclohexyl)piperidine) , Force Field: GAFF G7 (Cocaine guest molecule for host-guest interaction.) (SmilesCode: CN1[C@H]2CC[C@@H]1[C@H]([C@H](C2)OC(=O)C3=CC=CC=C3)C(=O)OC) (IUPAC Name: methyl (1R,2R,3S,5S)-3-benzoyloxy-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate) , Force Field: GAFF GT1 (Adamantane guest molecule for host-guest interaction.) (SmilesCode: CC12CC3CC(C1)CC(C3)(C2)C) (IUPAC Name: 3,5-dimethyl-1,1-adamantanamine) , Force Field: GAFF GT2 (Cyclododecanamine guest molecule for host-guest interaction.) (SmilesCode: C1CCCCCC(CCCCC1)N) (IUPAC Name: cyclododecanamine) , Force Field: GAFF GT3 (3-Amino-1-Adamantanol guest molecule for host-guest interaction.) (SmilesCode: C1C2CC3(CC1CC(C2)(C3)O)N) (IUPAC Name: 3-amino-1-adamantanol) , Force Field: GAFF GT4 (Cycloheptanamine guest molecule for host-guest interaction.) (SmilesCode: C1CCCC(CC1)N) (IUPAC Name: cycloheptanamine) , Force Field: GAFF GT5 (Cyclooctanamine guest molecule for host-guest interaction.) (SmilesCode: C1CCCC(CCC1)N) (IUPAC Name: cyclooctanamine) , Force Field: GAFF
Force Field	GAFF

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