FMO DATABASE

FMODB ID: 4JVQN

Calculation Name: 2COV-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2COV

Chain ID: D

ChEMBL ID:

UniProt ID: Q8RS40

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-687271.444172
FMO2-HF: Nuclear repulsion	649372.700373
FMO2-HF: Total energy	-37898.743799
FMO2-MP2: Total energy	-38007.98845

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(D:378:PRO)

Summations of interaction energy for fragment #1(D:378:PRO)

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.
-1.289	1.445	0.018	-0.89	-1.863	0.002

Interaction energy analysis for fragmet #1(D:378:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.011

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	D	380	GLU	-1	-0.884	-0.946	3.778	-2.504	-1.115	-0.021	-0.544	-0.825	0.003
4	D	381	ASN	0	-0.018	-0.027	6.417	-0.055	-0.055	0.000	0.000	0.000	0.000
5	D	382	CYS	0	-0.081	-0.024	3.936	0.651	0.950	0.001	-0.044	-0.256	0.000
6	D	383	GLN	0	-0.067	-0.034	3.253	0.401	1.381	0.039	-0.295	-0.724	-0.001
7	D	384	ASP	-1	-0.849	-0.887	4.695	-0.684	-0.618	-0.001	-0.007	-0.058	0.000
8	D	385	ASP	-1	-0.793	-0.901	8.278	-0.643	-0.643	0.000	0.000	0.000	0.000
9	D	386	PHE	0	-0.048	-0.004	10.142	0.118	0.118	0.000	0.000	0.000	0.000
10	D	387	ASN	0	0.005	-0.014	8.045	0.092	0.092	0.000	0.000	0.000	0.000
11	D	388	PHE	0	0.019	0.006	11.373	0.076	0.076	0.000	0.000	0.000	0.000
12	D	389	ASN	0	-0.008	0.003	10.068	-0.022	-0.022	0.000	0.000	0.000	0.000
13	D	390	TYR	0	-0.058	-0.058	12.539	-0.008	-0.008	0.000	0.000	0.000	0.000
14	D	391	VAL	0	-0.054	-0.008	14.218	0.045	0.045	0.000	0.000	0.000	0.000
15	D	392	SER	0	0.023	-0.010	16.971	0.028	0.028	0.000	0.000	0.000	0.000
16	D	393	ASP	-1	-0.825	-0.899	19.493	0.095	0.095	0.000	0.000	0.000	0.000
17	D	394	GLN	0	-0.079	-0.034	21.226	-0.007	-0.007	0.000	0.000	0.000	0.000
18	D	395	GLU	-1	-0.914	-0.954	20.794	0.030	0.030	0.000	0.000	0.000	0.000
19	D	396	ILE	0	-0.017	0.001	16.521	0.013	0.013	0.000	0.000	0.000	0.000
20	D	397	GLU	-1	-0.821	-0.902	14.044	-0.008	-0.008	0.000	0.000	0.000	0.000
21	D	398	VAL	0	-0.001	0.002	14.966	-0.030	-0.030	0.000	0.000	0.000	0.000
22	D	399	TYR	0	0.022	-0.019	7.909	0.076	0.076	0.000	0.000	0.000	0.000
23	D	400	HIS	0	0.013	-0.004	13.559	-0.060	-0.060	0.000	0.000	0.000	0.000
24	D	401	VAL	0	-0.037	-0.013	9.393	0.067	0.067	0.000	0.000	0.000	0.000
25	D	402	ASP	-1	-0.832	-0.913	12.835	-0.184	-0.184	0.000	0.000	0.000	0.000
26	D	403	LYS	1	0.786	0.879	11.941	0.524	0.524	0.000	0.000	0.000	0.000
27	D	404	GLY	0	-0.003	0.004	16.842	0.005	0.005	0.000	0.000	0.000	0.000
28	D	405	TRP	0	-0.045	-0.021	16.786	0.016	0.016	0.000	0.000	0.000	0.000
29	D	406	SER	0	-0.054	-0.052	22.687	0.004	0.004	0.000	0.000	0.000	0.000
30	D	407	ALA	0	-0.014	-0.003	22.788	0.007	0.007	0.000	0.000	0.000	0.000
31	D	408	GLY	0	-0.030	-0.021	24.897	0.009	0.009	0.000	0.000	0.000	0.000
32	D	409	TRP	0	-0.034	-0.017	26.450	0.008	0.008	0.000	0.000	0.000	0.000
33	D	410	ASN	0	-0.012	-0.028	21.884	-0.018	-0.018	0.000	0.000	0.000	0.000
34	D	411	TYR	0	-0.033	-0.023	23.827	0.017	0.017	0.000	0.000	0.000	0.000
35	D	412	VAL	0	0.035	0.029	18.991	-0.019	-0.019	0.000	0.000	0.000	0.000
36	D	413	CYS	0	-0.068	-0.051	21.463	0.010	0.010	0.000	0.000	0.000	0.000
37	D	414	LEU	0	0.068	0.049	20.176	-0.021	-0.021	0.000	0.000	0.000	0.000
38	D	415	ASN	0	0.042	0.010	22.931	0.002	0.002	0.000	0.000	0.000	0.000
39	D	416	ASP	-1	-0.896	-0.938	25.246	-0.114	-0.114	0.000	0.000	0.000	0.000
40	D	417	TYR	0	-0.019	0.016	26.329	0.009	0.009	0.000	0.000	0.000	0.000
41	D	419	LEU	0	0.029	0.012	24.651	0.011	0.011	0.000	0.000	0.000	0.000
42	D	420	PRO	0	0.040	0.022	24.635	-0.010	-0.010	0.000	0.000	0.000	0.000
43	D	421	GLY	0	0.024	0.021	21.386	0.009	0.009	0.000	0.000	0.000	0.000
44	D	422	ASN	0	-0.022	0.000	20.755	0.007	0.007	0.000	0.000	0.000	0.000
45	D	423	LYS	1	0.901	0.945	18.598	0.125	0.125	0.000	0.000	0.000	0.000
46	D	424	SER	0	-0.013	-0.005	17.163	0.024	0.024	0.000	0.000	0.000	0.000
47	D	425	ASN	0	-0.010	-0.038	13.046	-0.002	-0.002	0.000	0.000	0.000	0.000
48	D	426	GLY	0	0.042	0.030	12.615	-0.015	-0.015	0.000	0.000	0.000	0.000
49	D	427	ALA	0	0.016	0.028	12.309	-0.055	-0.055	0.000	0.000	0.000	0.000
50	D	428	PHE	0	-0.032	-0.011	14.449	0.054	0.054	0.000	0.000	0.000	0.000
51	D	429	ARG	1	0.829	0.897	11.624	0.015	0.015	0.000	0.000	0.000	0.000
52	D	430	LYS	1	0.812	0.895	17.457	0.057	0.057	0.000	0.000	0.000	0.000
53	D	431	THR	0	0.054	0.035	18.970	-0.019	-0.019	0.000	0.000	0.000	0.000
54	D	432	PHE	0	-0.053	-0.021	20.369	-0.002	-0.002	0.000	0.000	0.000	0.000
55	D	433	ASN	0	0.044	0.025	22.297	0.014	0.014	0.000	0.000	0.000	0.000
56	D	434	ALA	0	-0.045	-0.023	21.154	-0.016	-0.016	0.000	0.000	0.000	0.000
57	D	435	VAL	0	0.008	-0.001	23.247	0.016	0.016	0.000	0.000	0.000	0.000
58	D	436	LEU	0	0.019	0.010	17.700	-0.017	-0.017	0.000	0.000	0.000	0.000
59	D	437	GLY	0	-0.025	-0.011	19.995	0.005	0.005	0.000	0.000	0.000	0.000
60	D	438	GLN	0	-0.055	-0.017	21.526	-0.004	-0.004	0.000	0.000	0.000	0.000
61	D	439	ASP	-1	-0.843	-0.902	21.265	-0.153	-0.153	0.000	0.000	0.000	0.000
62	D	440	TYR	0	-0.052	-0.040	20.341	0.022	0.022	0.000	0.000	0.000	0.000
63	D	441	LYS	1	0.819	0.921	20.555	0.120	0.120	0.000	0.000	0.000	0.000
64	D	442	LEU	0	-0.012	-0.003	15.405	0.022	0.022	0.000	0.000	0.000	0.000
65	D	443	THR	0	-0.053	-0.065	19.715	-0.007	-0.007	0.000	0.000	0.000	0.000
66	D	444	PHE	0	-0.031	-0.007	18.440	0.011	0.011	0.000	0.000	0.000	0.000
67	D	445	LYS	1	0.915	0.956	20.551	0.113	0.113	0.000	0.000	0.000	0.000
68	D	446	VAL	0	0.003	0.009	21.178	0.011	0.011	0.000	0.000	0.000	0.000
69	D	447	GLU	-1	-0.763	-0.830	23.976	-0.110	-0.110	0.000	0.000	0.000	0.000
70	D	448	ASP	-1	-0.745	-0.886	25.047	-0.177	-0.177	0.000	0.000	0.000	0.000
71	D	449	ARG	1	0.850	0.917	25.497	0.169	0.169	0.000	0.000	0.000	0.000
72	D	450	TYR	0	0.006	-0.007	26.121	0.010	0.010	0.000	0.000	0.000	0.000
73	D	451	GLY	0	0.018	0.007	31.011	0.007	0.007	0.000	0.000	0.000	0.000
74	D	452	GLN	0	-0.085	-0.040	32.102	0.004	0.004	0.000	0.000	0.000	0.000
75	D	453	GLY	0	-0.006	-0.006	30.096	-0.002	-0.002	0.000	0.000	0.000	0.000
76	D	454	GLN	0	-0.031	-0.012	27.055	0.006	0.006	0.000	0.000	0.000	0.000
77	D	455	GLN	0	-0.049	-0.020	21.661	-0.023	-0.023	0.000	0.000	0.000	0.000
78	D	456	ILE	0	-0.010	-0.014	23.442	0.008	0.008	0.000	0.000	0.000	0.000
79	D	457	LEU	0	-0.003	0.012	17.523	-0.006	-0.006	0.000	0.000	0.000	0.000
80	D	458	ASP	-1	-0.761	-0.878	20.779	-0.166	-0.166	0.000	0.000	0.000	0.000
81	D	459	ARG	1	0.780	0.865	11.289	0.580	0.580	0.000	0.000	0.000	0.000
82	D	460	ASN	0	0.001	0.001	18.709	0.022	0.022	0.000	0.000	0.000	0.000
83	D	461	ILE	0	-0.061	-0.022	14.694	-0.042	-0.042	0.000	0.000	0.000	0.000
84	D	462	THR	0	0.057	0.013	16.928	0.022	0.022	0.000	0.000	0.000	0.000
85	D	463	PHE	0	-0.046	-0.016	16.270	-0.025	-0.025	0.000	0.000	0.000	0.000
86	D	464	THR	0	0.026	0.002	13.467	0.034	0.034	0.000	0.000	0.000	0.000
87	D	465	THR	0	0.055	0.007	14.067	-0.018	-0.018	0.000	0.000	0.000	0.000
88	D	466	GLN	0	-0.047	0.010	8.838	0.043	0.043	0.000	0.000	0.000	0.000
89	D	467	VAL	0	0.036	0.006	8.646	-0.059	-0.059	0.000	0.000	0.000	0.000
90	D	469	ASN	0	0.026	0.032	5.549	0.172	0.172	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:378:PRO)