CHARMM-GUI

CHARMM-GUI Archive - COVID-19 Proteins Library

This archive currently contains simulation systems related to COVID-19 proteins.

Please note that

it is your responsibility to use these systems for your study
these systems were generated mostly using Solution Builder or Membrane Builder
the standard protonation state corresponding to pH 7 was used for all titratable residues
150 mM KCl solution was used for bulk
unless specified explicitly, temperature was set to 303.15K
equilibration was not performed
detailed information on each system can be obtained from sysinfo
you can download the initial simulation structure (PDB File)
you can also download the entire files including inputs, outputs, and coordinates (Tarball)
equilibration and production inputs are provided for simulation with CHARMM, NAMD, Gromacs, Amber, GENESIS, OpenMM using the CHARMM force field
hydrogen mass repartitioning (HMR) was used for 4-fs time-step

References:

S. Jo, T. Kim, V.G. Iyer, and W. Im (2008)
CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865

H. Woo, S-J. Park, Y.K. Choi, T. Park, M. Tanveer, Y. Cao, N.R. Kern, J. Lee, M.S. Yeom, T.I. Croll, C. Seok, and W. Im (2020)
Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane. J. Phys. Chem. B. 124:7128–7137

Y.K. Choi, Y. Cao, M. Frank, H. Woo, S-J. Park, M.S. Yeom, T.I. Croll, C. Seok, W. Im (2021)
Structure, Dynamics, Receptor Binding, and Antibody Binding of Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane. J. Chem. Theory Comput. 17:2479-2487

Y. Cao, Y.K. Choi, M. Frank, H. Woo, S.-J. Park, M.S. Yeom, C. Seok, and W. Im (2021)
Dynamic Interactions of Fully-glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. J. Chem. Theory Comput. 17:6559-6569

Spike protein

• Fully-glycosylated full-length S protein models (read the above reference and watch this video demo first!)

	6VSB					6VXX
1_1_1	Dimension: 252.4 X 252.4 X 383.5 Number of total atoms: 2343394 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 668899 Number of K+/CL- ions: 2128 / 1857 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 252.4 X 252.4 X 370.0 Number of total atoms: 2260694 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 641385 Number of K+/CL- ions: 2049 / 1778 sysinfo	PDB File	Tarball	dcd	xtc
1_1_2	Dimension: 254.5 X 254.5 X 385.0 Number of total atoms: 2390971 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 682889 Number of K+/CL- ions: 2174 / 1898 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 254.5 X 254.5 X 371.0 Number of total atoms: 2307119 Number of lipidtop: 1200 Number of lipidbot: 1200 Number of water molecules: 654993 Number of K+/CL- ions: 2092 / 1816 sysinfo	PDB File	Tarball	dcd	xtc
1_2_1	Dimension: 252.4 X 252.4 X 386.4 Number of total atoms: 2363711 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 675660 Number of K+/CL- ions: 2145 / 1874 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 252.5 X 252.5 X 372.4 Number of total atoms: 2281713 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 648380 Number of K+/CL- ions: 2066 / 1795 sysinfo	PDB File	Tarball	dcd	xtc
1_2_2	Dimension: 254.6 X 254.6 X 387.6 Number of total atoms: 2411041 Number of lipidtop: 1200 Number of lipidbot: 1200 Number of water molecules: 689569 Number of K+/CL- ions: 2189 / 1913 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 254.6 X 254.6 X 373.7 Number of total atoms: 2326964 Number of lipidtop: 1200 Number of lipidbot: 1200 Number of water molecules: 661596 Number of K+/CL- ions: 2110 / 1834 sysinfo	PDB File	Tarball	dcd	xtc
2_1_1	Dimension: 252.4 X 252.4 X 394.0 Number of total atoms: 2417135 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 693440 Number of K+/CL- ions: 2187 / 1916 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 252.3 X 252.3 X 379.8 Number of total atoms: 2324002 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 662449 Number of K+/CL- ions: 2107 / 1836 sysinfo	PDB File	Tarball	dcd	xtc
2_1_2	Dimension: 254.5 X 254.5 X 396.2 Number of total atoms: 2470941 Number of lipidtop: 1200 Number of lipidbot: 1200 Number of water molecules: 709503 Number of K+/CL- ions: 2238 / 1962 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 254.4 X 254.4 X 381.6 Number of total atoms: 2371405 Number of lipidtop: 1200 Number of lipidbot: 1200 Number of water molecules: 676381 Number of K+/CL- ions: 2153 / 1877 sysinfo	PDB File	Tarball	dcd	xtc
2_2_1	Dimension: 252.3 X 252.3 X 392.6 Number of total atoms: 2408296 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 690499 Number of K+/CL- ions: 2179 / 1908 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 252.4 X 252.4 X 378.0 Number of total atoms: 2316149 Number of lipidtop: 1200 Number of lipidbot: 1150 Number of water molecules: 659838 Number of K+/CL- ions: 2097 / 1826 sysinfo	PDB File	Tarball	dcd	xtc
2_2_2	Dimension: 254.5 X 254.5 X 394.0 Number of total atoms: 2454598 Number of lipidtop: 1200 Number of lipidbot: 1200 Number of water molecules: 704064 Number of K+/CL- ions: 2225 / 1949 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 254.4 X 254.4 X 379.8 Number of total atoms: 2363342 Number of lipidtop: 1200 Number of lipidbot: 1200 Number of water molecules: 673700 Number of K+/CL- ions: 2143 / 1867 sysinfo	PDB File	Tarball	dcd	xtc

• Fully-glycosylated full-length S protein complex models


S309 (6WPT, 6WPS)	PDB File	PDB File
H11-D4 (6Z43)	PDB File	PDB File
ACE2 (6VW1)	PDB File

• Fully-glycosylated S protein head-only models (residue 1-1146)

	6VSB			6VXX			6X2B
S only	Dimension: 202 X 202 X 202 Number of total atoms: 773227 Number of water molecules: 235708 Number of K+/CL- ions: 680 / 665 sysinfo	PDB File	Tarball	Dimension: 201 X 201 X 201 Number of total atoms: 762293 Number of water molecules: 232070 Number of K+/CL- ions: 670 / 655 sysinfo	PDB File	Tarball	Dimension: 203 X 203 X 203 Number of total atoms: 784751 Number of water molecules: 239531 Number of K+/CL- ions: 691 / 676 sysinfo	PDB File	Tarball
S309 (6WPT, 6WPS)	Dimension: 202 X 202 X 202 Number of total atoms: 772597 Number of water molecules: 233250 Number of K+/CL- ions: 667 / 658 sysinfo	PDB File	Tarball	Dimension: 212 X 212 X 212 Number of total atoms: 898420 Number of water molecules: 273854 Number of K+/CL- ions: 776 / 770 sysinfo	PDB File	Tarball
H11-D4 (6Z43)	Dimension: 232 X 232 X 232 Number of total atoms: 1176465 Number of water molecules: 367585 Number of K+/CL- ions: 1053 / 1041 sysinfo	PDB File	Tarball	Dimension: 210 X 210 X 210 Number of total atoms: 870609 Number of water molecules: 265827 Number of K+/CL- ions: 762 / 750 sysinfo	PDB File	Tarball
ACE2 (6VW1)	Dimension: 255 X 255 X 255 Number of total atoms: 1564467 Number of water molecules: 495442 Number of K+/CL- ions: 1448 / 1406 sysinfo	PDB File	Tarball

• Fully-glycosylated S protein (head-only) in complex with antibodies

	CCC					OCC					OOC					OOO
C105						Dimension: 245 X 245 X 245 Number of total atoms: 1387259 Number of water molecules: 438890 Number of K+/CL- ions: 1259 / 1244 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 241 X 241 X 241 Number of total atoms: 1317296 Number of water molecules: 414505 Number of K+/CL- ions: 1191 / 1176 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 239 X 239 X 239 Number of total atoms: 1284056 Number of water molecules: 402339 Number of K+/CL- ions: 1156 / 1141 sysinfo	PDB File	Tarball	dcd	xtc
C002						Dimension: 250 X 250 X 250 Number of total atoms: 1476141 Number of water molecules: 466059 Number of K+/CL- ions: 1323 / 1320 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 254 X 254 X 254 Number of total atoms: 1543972 Number of water molecules: 488707 Number of K+/CL- ions: 1394 / 1388 sysinfo	PDB File	Tarball	dcd	xtc
C119	Dimension: 224 X 224 X 224 Number of total atoms: 1057437 Number of water molecules: 326759 Number of K+/CL- ions: 930 / 924 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 237 X 237 X 237 Number of total atoms: 1253435 Number of water molecules: 391967 Number of K+/CL- ions: 1117 / 1111 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 233 X 233 X 233 Number of total atoms: 1193979 Number of water molecules: 372189 Number of K+/CL- ions: 1056 / 1050 sysinfo	PDB File	Tarball	dcd	xtc
C121						Dimension: 263 X 263 X 263 Number of total atoms: 1720188 Number of water molecules: 547270 Number of K+/CL- ions: 1554 / 1551 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 254 X 254 X 254 Number of total atoms: 1544404 Number of water molecules: 488784 Number of K+/CL- ions: 1391 / 1388 sysinfo	PDB File	Tarball	dcd	xtc
S309	Dimension: 210 X 210 X 210 Number of total atoms: 870106 Number of water molecules: 264568 Number of K+/CL- ions: 752 / 746 sysinfo	PDB File	Tarball	dcd	xtc	Dimension: 213 X 213 X 213 Number of total atoms: 908307 Number of water molecules: 277324 Number of K+/CL- ions: 785 / 781 sysinfo	PDB File	Tarball	dcd	xtc
EY6A																Dimension: 231 X 231 X 231 Number of total atoms: 1161006 Number of water molecules: 358225 Number of K+/CL- ions: 1011 / 1011 sysinfo	PDB File	Tarball	dcd	xtc

S1-ACE2 complex

• PDB ID: 7DMU (Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39)

Dimension: 131 X 131 X 131
Number of total atoms: 211815
Number of water molecules: 66140
Number of K+/CL- ions: 214 / 187

sysinfo

Archive

Spike protein

• Fully-glycosylated full-length S protein models (read the above reference and watch this video demo first!)

• Fully-glycosylated full-length S protein complex models

• Fully-glycosylated S protein head-only models (residue 1-1146)

• Fully-glycosylated S protein (head-only) in complex with antibodies

S1-ACE2 complex

• PDB ID: 7DMU (Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39)

• PDB ID: 7KMB (ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4)

• PDB ID: 7A92 (Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Unmasked Refinement))

• PDB ID: 7C8D (cat ACE2 and SARS-CoV-2 RBD)

• PDB ID: 6M17 (S1 RBD + ACE2 + B0AT1 Complex in a POPC Bilayer)

• PDB ID: 6VW1 (S1 RBD + ACE2 Complex)

• PDB ID: 6VW1 (S1 RBD + ACE2 Complex with Zn/Cl ions + N-glycan Pentasaccharide)

S1 RBD with antibody

• PDB ID: 6ZLR (Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex)

• PDB ID: 7B3O (Crystal structure of the SARS-CoV-2 RBD in complex with STE90-C11 Fab)

• PDB ID: 7JVB (RBD with nanobody Nb20)

• PDB ID: 7KFV (Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab))

• PDB ID: 7KFW (Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab))

• PDB ID: 7KFX (Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab))

• PDB ID: 7KFY (Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-F10 Fab))

• PDB ID: 7CDI (Crystal structure of SARS-CoV-2 antibody P2C-1F11 with RBD)

• PDB ID: 7CDJ (Crystal structure of SARS-CoV-2 antibody P2C-1A3 with RBD)

• PDB ID: 7CJF (Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody Fab)

• PDB ID: 6XKP (receptor binding domain + neutralizing antibody CV07-270)

• PDB ID: 6XKQ (receptor binding domain + neutralizing antibody CV07-250)

• PDB ID: 7JMW (spike protein receptor-binding domain + cross-neutralizing antibody COVA1-16 Fab)

• PDB ID: 7JV2 (spike + S2H13 neutralizing antibody Fab fragment)

• PDB ID: 7JVA (spike + S2A4 neutralizing antibody Fab fragment)

• PDB ID: 7JX3 (Mapping neutralizing and immunodominant sites on spike receptor-binding domain by structure-guided high-resolution serology)

• PDB ID: 7K8M (anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C110)

• PDB ID: 7K9Z (RBD + Fab fragments of neutralizing antibodies 298 and 52)

• PDB ID: 7A5S (spike and CR3022 Fab (Homogeneous Refinement))

• PDB ID: 7CH4 (S RBD + BD-604 Fab)

• PDB ID: 7CH5 (S RBD + BD-629 Fab)

• PDB ID: 7CHB (RBD + BD-236 Fab)

• PDB ID: 7CHC (S RBD + BD-629 Fab and BD-368-2 Fab)

• PDB ID: 7CHE (RBD + BD-236 Fab and BD-368-2 Fab)

• PDB ID: 7CHF (RBD + BD-604 Fab and BD-368-2 Fab)

• PDB ID: 7K45 (spike + S2E12 neutralizing antibody Fab fragment (local refinement of the RBD and Fab variable domains))

• PDB ID: 6ZH9 (Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2))

• PDB ID: 7JMO (RBD in complex with neutralizing antibody COVA2-04)

• PDB ID: 7JMP (RBD in complex with neutralizing antibody COVA2-39)

• PDB ID: 7CAH (interface of H014 Fab binds to SARS-CoV-2 S)

• PDB ID: 6ZBP (H11-H4 complex with SARS-CoV-2)

• PDB ID: 6XC2 (RBD + antibody CC12.1)

• PDB ID: 6XC3 (RBD + antibodies CC12.1 and CR3022)

• PDB ID: 6XC4 (RBD + antibody CC12.3)

• PDB ID: 6XC7 (RBD + Antibodies CC12.3 and CR3022)

• PDB ID: 6ZFO (Association of two complexes of largely structurally disordered Spike ectodomain + EY6A Fab)

• PDB ID: 6XDG (RBD + Fab fragments of REGN10933 & REGN10987)

• PDB ID: 6ZCZ (glycoprotein + EY6A Fab + nanobody)

• PDB ID: 6ZER (S1 RBD + EY6A Fab)

• PDB ID: 7C8V (sybody SR4 + S RBD)

• PDB ID: 7C8W (sybody MR17 + S RBD)

• PDB ID: 7CAN (sybody MR17-K99Y + S RBD)

• PDB ID: 6YZ5 (SARS-CoV-2 RBD + H11-D4 Nanobody)

• PDB ID: 6YZ7 (SARS-CoV-2 RBD + H11-D4 Nanobody + CR3022 Antibody ternary complex)

• PDB ID: 6Z2M (SARS-CoV-2 RBD + H11-D4 Nanobody +CR3022 Antibody ternary complex)

• PDB ID: 7BWJ (crystal structure of SARS-CoV-2 antibody with RBD)

• PDB ID: 7C01 (S1 + antibody CB6)

• PDB ID: 7BZ5 (S RBD + B38 (neutralizing antibody))

• PDB ID: 6YM0 (RBD + CR3022 Fab (crystal form 1))

• PDB ID: 6YOR (S1 + CR3022 Fab)

• PDB ID: 6W41 (receptor binding domain in complex with human antibody CR3022)

• PDB ID: 6YLA (receptor binding domain in complex with CR3022 Fab)

Main protease

• PDB ID: 7KVG (SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues)

• PDB ID: 7L5D (The crystal structure of SARS-CoV-2 Main Protease in complex with demethylated analog of masitinib)

• PDB ID: 7A1U (Structure of SARS-CoV-2 Main Protease bound to Fusidic Acid)

• PDB ID: 7ABU (Structure of SARS-CoV-2 Main Protease bound to RS102895)

• PDB ID: 7AF0 (Structure of SARS-CoV-2 Main Protease bound to Ipidacrine)

• PDB ID: 7AGA (Structure of SARS-CoV-2 Main Protease bound to AT7519)

• PDB ID: 7AHA (Structure of SARS-CoV-2 Main Protease bound to Maleate)

• PDB ID: 7AK4 (Structure of SARS-CoV-2 Main Protease bound to Tretazicar)

• PDB ID: 7ALH (Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 at 1.65A resolution (spacegroup C2))

• PDB ID: 7ALI (Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 at 1.65A resolution (spacegroup P2(1)))

• PDB ID: 7AMJ (Structure of SARS-CoV-2 Main Protease bound to PD 168568)

• PDB ID: 7ANS (Structure of SARS-CoV-2 Main Protease bound to Adrafinil)