FMO DATABASE

FMODB ID: VRRZ1

Calculation Name: 7PKU-B-Other89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7PKU

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: SolutionNMR

Registration Date: 2022-02-03

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 main protease and ligand complexes, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHLSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Waters within average of the temperature factors of receptor.
Procedure	Auto-FMO protocol ver. 1.20200406

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-281686.066803
FMO2-HF: Nuclear repulsion	254456.421985
FMO2-HF: Total energy	-27229.644818
FMO2-MP2: Total energy	-27307.976005

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:191:ARG)

Summations of interaction energy for fragment #1(B:191:ARG)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
76.186	79.914	0.005	-2.044	-1.689	0.002

Interaction energy analysis for fragmet #1(B:191:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.025 / q_NPA : 1.004

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	193	SER	0	0.023	0.006	3.603	2.749	5.879	-0.014	-1.702	-1.415	0.005
4	B	194	SER	0	-0.025	-0.013	3.336	-3.811	-3.213	0.019	-0.342	-0.274	-0.003
5	B	195	ARG	1	0.968	0.980	5.502	19.677	19.677	0.000	0.000	0.000	0.000
6	B	196	ASN	0	-0.007	-0.015	9.239	-0.613	-0.613	0.000	0.000	0.000	0.000
7	B	197	SER	0	0.039	0.025	9.941	-0.732	-0.732	0.000	0.000	0.000	0.000
8	B	198	THR	0	0.008	0.014	9.956	-1.239	-1.239	0.000	0.000	0.000	0.000
9	B	199	PRO	0	-0.002	-0.011	8.623	0.446	0.446	0.000	0.000	0.000	0.000
10	B	200	GLY	0	0.013	0.018	11.422	0.782	0.782	0.000	0.000	0.000	0.000
11	B	201	SER	0	-0.033	-0.016	14.922	0.102	0.102	0.000	0.000	0.000	0.000
12	B	202	SER	0	-0.032	-0.020	13.435	-0.161	-0.161	0.000	0.000	0.000	0.000
13	B	203	ARG	1	0.955	0.973	15.457	16.416	16.416	0.000	0.000	0.000	0.000
14	B	204	GLY	0	0.040	0.011	18.669	0.288	0.288	0.000	0.000	0.000	0.000
15	B	205	THR	0	-0.025	-0.007	22.124	-0.120	-0.120	0.000	0.000	0.000	0.000
16	B	206	SER	0	0.069	0.039	25.557	0.357	0.357	0.000	0.000	0.000	0.000
17	B	207	PRO	0	-0.040	-0.019	26.752	-0.092	-0.092	0.000	0.000	0.000	0.000
18	B	208	ALA	0	0.021	0.013	27.986	0.300	0.300	0.000	0.000	0.000	0.000
19	B	209	ARG	1	0.998	0.984	27.315	10.243	10.243	0.000	0.000	0.000	0.000
20	B	210	MET	0	-0.016	0.014	27.008	-0.010	-0.010	0.000	0.000	0.000	0.000
21	B	211	ALA	0	0.011	0.005	25.347	-0.379	-0.379	0.000	0.000	0.000	0.000
22	B	212	GLY	0	0.001	-0.007	22.823	0.238	0.238	0.000	0.000	0.000	0.000
23	B	213	ASN	0	-0.021	-0.010	18.240	0.210	0.210	0.000	0.000	0.000	0.000
24	B	214	GLY	0	0.057	0.002	16.590	-0.588	-0.588	0.000	0.000	0.000	0.000
25	B	215	GLY	0	-0.017	0.010	17.646	0.227	0.227	0.000	0.000	0.000	0.000
26	B	216	ASP	-1	-0.906	-0.939	18.667	-11.722	-11.722	0.000	0.000	0.000	0.000
27	B	217	ALA	0	-0.048	-0.028	18.433	-0.342	-0.342	0.000	0.000	0.000	0.000
28	B	218	ALA	0	0.026	0.016	13.614	-0.431	-0.431	0.000	0.000	0.000	0.000
29	B	219	LEU	0	0.025	-0.008	12.482	-0.827	-0.827	0.000	0.000	0.000	0.000
30	B	220	ALA	0	-0.009	-0.006	15.673	0.222	0.222	0.000	0.000	0.000	0.000
31	B	221	LEU	0	0.059	0.029	13.812	0.531	0.531	0.000	0.000	0.000	0.000
32	B	222	LEU	0	-0.002	0.008	13.310	0.285	0.285	0.000	0.000	0.000	0.000
33	B	223	LEU	0	-0.023	-0.023	17.531	0.455	0.455	0.000	0.000	0.000	0.000
34	B	224	LEU	0	0.008	0.014	21.008	0.547	0.547	0.000	0.000	0.000	0.000
35	B	225	ASP	-1	-0.840	-0.919	19.597	-12.402	-12.402	0.000	0.000	0.000	0.000
36	B	226	ARG	1	0.917	0.963	19.669	13.985	13.985	0.000	0.000	0.000	0.000
37	B	227	LEU	0	0.019	-0.004	22.133	0.360	0.360	0.000	0.000	0.000	0.000
38	B	228	ASN	0	0.018	0.011	25.196	0.310	0.310	0.000	0.000	0.000	0.000
39	B	229	GLN	0	-0.024	-0.018	22.930	0.654	0.654	0.000	0.000	0.000	0.000
40	B	230	LEU	0	-0.061	-0.004	25.648	0.193	0.193	0.000	0.000	0.000	0.000
41	B	231	GLU	-1	-0.914	-0.981	27.488	-8.790	-8.790	0.000	0.000	0.000	0.000
42	B	232	SER	0	-0.096	-0.031	29.762	0.431	0.431	0.000	0.000	0.000	0.000
43	B	233	LYS	1	0.912	0.953	31.379	8.995	8.995	0.000	0.000	0.000	0.000
44	B	234	MET	0	-0.032	-0.007	34.309	0.202	0.202	0.000	0.000	0.000	0.000
45	B	235	SER	0	-0.020	-0.007	34.225	-0.164	-0.164	0.000	0.000	0.000	0.000
46	B	236	GLY	0	0.061	0.011	33.950	0.161	0.161	0.000	0.000	0.000	0.000
47	B	237	LYS	1	0.910	0.980	29.902	8.604	8.604	0.000	0.000	0.000	0.000
48	B	238	GLY	0	0.039	0.016	28.950	-0.339	-0.339	0.000	0.000	0.000	0.000
49	B	239	GLN	0	-0.024	-0.012	29.280	0.452	0.452	0.000	0.000	0.000	0.000
50	B	240	GLN	0	0.012	0.006	29.424	-0.265	-0.265	0.000	0.000	0.000	0.000
51	B	241	GLN	0	0.018	0.012	30.842	-0.109	-0.109	0.000	0.000	0.000	0.000
52	B	242	GLN	0	0.023	0.009	28.281	0.259	0.259	0.000	0.000	0.000	0.000
53	B	243	GLY	0	0.014	0.013	32.441	0.059	0.059	0.000	0.000	0.000	0.000
54	B	244	GLN	0	-0.002	-0.011	35.389	0.015	0.015	0.000	0.000	0.000	0.000
55	B	245	THR	0	-0.037	-0.024	38.663	0.251	0.251	0.000	0.000	0.000	0.000
56	B	246	VAL	0	0.038	0.020	37.637	-0.151	-0.151	0.000	0.000	0.000	0.000
57	B	247	THR	0	0.003	-0.001	40.140	0.076	0.076	0.000	0.000	0.000	0.000
58	B	248	LYS	1	0.968	0.976	43.363	6.743	6.743	0.000	0.000	0.000	0.000
59	B	249	LYS	1	1.019	0.996	47.157	6.089	6.089	0.000	0.000	0.000	0.000
60	B	250	SER	0	0.016	0.013	45.688	0.059	0.059	0.000	0.000	0.000	0.000
61	B	251	ALA	0	0.041	0.024	46.417	0.053	0.053	0.000	0.000	0.000	0.000
62	B	252	ALA	0	0.012	0.008	48.420	0.097	0.097	0.000	0.000	0.000	0.000
63	B	253	GLU	-1	-0.910	-0.963	51.369	-5.698	-5.698	0.000	0.000	0.000	0.000
64	B	254	ALA	0	-0.027	-0.008	51.017	0.087	0.087	0.000	0.000	0.000	0.000
65	B	255	SER	0	0.022	0.013	51.910	0.055	0.055	0.000	0.000	0.000	0.000
66	B	256	LYS	1	0.930	0.982	54.592	5.337	5.337	0.000	0.000	0.000	0.000
67	B	257	LYS	1	0.957	0.974	56.506	5.230	5.230	0.000	0.000	0.000	0.000
68	B	258	PRO	0	0.042	0.026	56.680	-0.095	-0.095	0.000	0.000	0.000	0.000
69	B	259	ARG	1	0.851	0.916	54.467	5.721	5.721	0.000	0.000	0.000	0.000
70	B	260	GLN	0	0.007	0.013	56.382	-0.032	-0.032	0.000	0.000	0.000	0.000
71	B	261	LYS	1	0.947	0.958	50.034	6.085	6.085	0.000	0.000	0.000	0.000
72	B	262	ARG	1	0.910	0.963	52.893	5.815	5.815	0.000	0.000	0.000	0.000
73	B	263	THR	-1	-0.822	-0.895	56.323	-5.155	-5.155	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:191:ARG)