FMO DATABASE

FMODB ID: 5JVRZ

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	OptAll
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	-687227.907939
FMO2-HF: Nuclear repulsion	649329.06985
FMO2-HF: Total energy	-37898.838089
FMO2-MP2: Total energy	-38008.1477

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.
-2.178	0.798	0.32	-1.024	-2.272	0

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 : 0.028 / q_NPA : -0.010

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	-0.874	-0.946	3.893	-2.416	-1.248	-0.007	-0.472	-0.689	0.002
4	D	381	ASN	0	-0.013	-0.018	6.132	-0.108	-0.108	0.000	0.000	0.000	0.000
5	D	382	CYS	0	-0.080	-0.023	3.914	0.451	0.794	0.004	-0.056	-0.291	0.000
6	D	383	GLN	0	-0.077	-0.042	2.666	-0.017	1.283	0.325	-0.476	-1.149	-0.002
7	D	384	ASP	-1	-0.831	-0.876	4.341	-0.606	-0.530	-0.001	-0.018	-0.057	0.000
8	D	385	ASP	-1	-0.804	-0.907	8.101	-0.628	-0.628	0.000	0.000	0.000	0.000
9	D	386	PHE	0	-0.055	-0.013	9.978	0.098	0.098	0.000	0.000	0.000	0.000
10	D	387	ASN	0	0.020	0.001	7.876	0.113	0.113	0.000	0.000	0.000	0.000
11	D	388	PHE	0	0.018	0.003	11.042	0.068	0.068	0.000	0.000	0.000	0.000
12	D	389	ASN	0	0.002	0.008	9.603	-0.048	-0.048	0.000	0.000	0.000	0.000
13	D	390	TYR	0	-0.032	-0.043	11.970	0.001	0.001	0.000	0.000	0.000	0.000
14	D	391	VAL	0	-0.059	-0.019	14.293	0.024	0.024	0.000	0.000	0.000	0.000
15	D	392	SER	0	0.027	-0.012	17.118	0.020	0.020	0.000	0.000	0.000	0.000
16	D	393	ASP	-1	-0.834	-0.906	19.685	0.060	0.060	0.000	0.000	0.000	0.000
17	D	394	GLN	0	-0.060	-0.016	21.339	-0.005	-0.005	0.000	0.000	0.000	0.000
18	D	395	GLU	-1	-0.924	-0.956	20.348	-0.013	-0.013	0.000	0.000	0.000	0.000
19	D	396	ILE	0	0.011	0.010	15.906	0.009	0.009	0.000	0.000	0.000	0.000
20	D	397	GLU	-1	-0.829	-0.912	13.626	-0.096	-0.096	0.000	0.000	0.000	0.000
21	D	398	VAL	0	0.001	0.009	14.279	-0.033	-0.033	0.000	0.000	0.000	0.000
22	D	399	TYR	0	0.001	-0.020	7.467	0.064	0.064	0.000	0.000	0.000	0.000
23	D	400	HIS	0	-0.002	-0.016	13.425	-0.042	-0.042	0.000	0.000	0.000	0.000
24	D	401	VAL	0	-0.022	-0.008	9.042	0.060	0.060	0.000	0.000	0.000	0.000
25	D	402	ASP	-1	-0.815	-0.907	12.488	-0.208	-0.208	0.000	0.000	0.000	0.000
26	D	403	LYS	1	0.770	0.875	11.759	0.507	0.507	0.000	0.000	0.000	0.000
27	D	404	GLY	0	-0.006	0.007	16.524	0.009	0.009	0.000	0.000	0.000	0.000
28	D	405	TRP	0	-0.039	-0.025	16.770	0.016	0.016	0.000	0.000	0.000	0.000
29	D	406	SER	0	-0.051	-0.050	22.442	0.002	0.002	0.000	0.000	0.000	0.000
30	D	407	ALA	0	-0.027	-0.014	22.618	0.007	0.007	0.000	0.000	0.000	0.000
31	D	408	GLY	0	-0.013	-0.006	24.732	0.006	0.006	0.000	0.000	0.000	0.000
32	D	409	TRP	0	-0.046	-0.020	26.668	0.008	0.008	0.000	0.000	0.000	0.000
33	D	410	ASN	0	-0.015	-0.030	21.686	-0.019	-0.019	0.000	0.000	0.000	0.000
34	D	411	TYR	0	-0.020	-0.010	23.663	0.017	0.017	0.000	0.000	0.000	0.000
35	D	412	VAL	0	0.034	0.029	18.339	-0.016	-0.016	0.000	0.000	0.000	0.000
36	D	413	CYS	0	-0.088	-0.049	21.079	0.010	0.010	0.000	0.000	0.000	0.000
37	D	414	LEU	0	0.072	0.050	19.738	-0.021	-0.021	0.000	0.000	0.000	0.000
38	D	415	ASN	0	0.018	-0.003	22.585	0.003	0.003	0.000	0.000	0.000	0.000
39	D	416	ASP	-1	-0.811	-0.891	24.992	-0.120	-0.120	0.000	0.000	0.000	0.000
40	D	417	TYR	0	0.000	0.024	25.736	0.007	0.007	0.000	0.000	0.000	0.000
41	D	419	LEU	0	0.035	0.013	24.186	0.012	0.012	0.000	0.000	0.000	0.000
42	D	420	PRO	0	0.004	0.000	24.093	-0.012	-0.012	0.000	0.000	0.000	0.000
43	D	421	GLY	0	0.042	0.042	21.123	0.008	0.008	0.000	0.000	0.000	0.000
44	D	422	ASN	0	-0.010	-0.002	20.321	0.005	0.005	0.000	0.000	0.000	0.000
45	D	423	LYS	1	0.877	0.940	18.407	0.154	0.154	0.000	0.000	0.000	0.000
46	D	424	SER	0	0.001	-0.003	17.147	0.023	0.023	0.000	0.000	0.000	0.000
47	D	425	ASN	0	-0.006	-0.016	12.978	-0.008	-0.008	0.000	0.000	0.000	0.000
48	D	426	GLY	0	0.050	0.030	12.357	-0.026	-0.026	0.000	0.000	0.000	0.000
49	D	427	ALA	0	0.015	0.020	12.081	-0.054	-0.054	0.000	0.000	0.000	0.000
50	D	428	PHE	0	-0.027	-0.006	14.200	0.051	0.051	0.000	0.000	0.000	0.000
51	D	429	ARG	1	0.800	0.876	11.474	0.118	0.118	0.000	0.000	0.000	0.000
52	D	430	LYS	1	0.822	0.891	16.845	0.090	0.090	0.000	0.000	0.000	0.000
53	D	431	THR	0	0.038	0.030	18.511	-0.019	-0.019	0.000	0.000	0.000	0.000
54	D	432	PHE	0	-0.043	-0.014	19.819	0.000	0.000	0.000	0.000	0.000	0.000
55	D	433	ASN	0	0.033	0.016	21.595	0.011	0.011	0.000	0.000	0.000	0.000
56	D	434	ALA	0	-0.041	-0.019	20.956	-0.013	-0.013	0.000	0.000	0.000	0.000
57	D	435	VAL	0	0.012	-0.002	22.985	0.014	0.014	0.000	0.000	0.000	0.000
58	D	436	LEU	0	-0.001	0.011	17.698	-0.014	-0.014	0.000	0.000	0.000	0.000
59	D	437	GLY	0	-0.022	-0.011	20.014	0.008	0.008	0.000	0.000	0.000	0.000
60	D	438	GLN	0	-0.041	-0.010	21.572	-0.002	-0.002	0.000	0.000	0.000	0.000
61	D	439	ASP	-1	-0.856	-0.912	20.968	-0.154	-0.154	0.000	0.000	0.000	0.000
62	D	440	TYR	0	-0.040	-0.036	19.975	0.021	0.021	0.000	0.000	0.000	0.000
63	D	441	LYS	1	0.782	0.888	19.994	0.133	0.133	0.000	0.000	0.000	0.000
64	D	442	LEU	0	-0.001	0.006	14.957	0.018	0.018	0.000	0.000	0.000	0.000
65	D	443	THR	0	-0.051	-0.061	19.231	-0.003	-0.003	0.000	0.000	0.000	0.000
66	D	444	PHE	0	-0.019	-0.009	18.449	0.006	0.006	0.000	0.000	0.000	0.000
67	D	445	LYS	1	0.870	0.919	20.591	0.129	0.129	0.000	0.000	0.000	0.000
68	D	446	VAL	0	-0.015	0.001	21.382	0.010	0.010	0.000	0.000	0.000	0.000
69	D	447	GLU	-1	-0.746	-0.829	24.235	-0.116	-0.116	0.000	0.000	0.000	0.000
70	D	448	ASP	-1	-0.746	-0.875	25.310	-0.181	-0.181	0.000	0.000	0.000	0.000
71	D	449	ARG	1	0.832	0.898	25.383	0.169	0.169	0.000	0.000	0.000	0.000
72	D	450	TYR	0	0.015	0.005	26.249	0.009	0.009	0.000	0.000	0.000	0.000
73	D	451	GLY	0	-0.008	-0.004	30.867	0.007	0.007	0.000	0.000	0.000	0.000
74	D	452	GLN	0	-0.084	-0.040	32.457	0.004	0.004	0.000	0.000	0.000	0.000
75	D	453	GLY	0	0.003	-0.004	30.163	-0.002	-0.002	0.000	0.000	0.000	0.000
76	D	454	GLN	0	-0.026	-0.009	27.279	0.002	0.002	0.000	0.000	0.000	0.000
77	D	455	GLN	0	-0.048	-0.026	21.516	-0.021	-0.021	0.000	0.000	0.000	0.000
78	D	456	ILE	0	-0.004	-0.008	23.320	0.007	0.007	0.000	0.000	0.000	0.000
79	D	457	LEU	0	-0.025	0.004	17.396	-0.006	-0.006	0.000	0.000	0.000	0.000
80	D	458	ASP	-1	-0.736	-0.869	20.243	-0.169	-0.169	0.000	0.000	0.000	0.000
81	D	459	ARG	1	0.767	0.865	10.957	0.550	0.550	0.000	0.000	0.000	0.000
82	D	460	ASN	0	0.004	0.003	18.473	0.021	0.021	0.000	0.000	0.000	0.000
83	D	461	ILE	0	-0.043	-0.011	14.127	-0.043	-0.043	0.000	0.000	0.000	0.000
84	D	462	THR	0	0.053	0.013	16.877	0.023	0.023	0.000	0.000	0.000	0.000
85	D	463	PHE	0	-0.054	-0.024	16.151	-0.024	-0.024	0.000	0.000	0.000	0.000
86	D	464	THR	0	0.018	0.001	13.211	0.031	0.031	0.000	0.000	0.000	0.000
87	D	465	THR	0	0.039	-0.004	14.163	-0.020	-0.020	0.000	0.000	0.000	0.000
88	D	466	GLN	0	-0.030	0.016	8.930	0.048	0.048	0.000	0.000	0.000	0.000
89	D	467	VAL	0	0.008	-0.011	8.580	-0.039	-0.039	0.000	0.000	0.000	0.000
90	D	469	ASN	0	0.023	0.037	5.139	-0.098	-0.009	-0.001	-0.002	-0.086	0.000

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