FMO DATABASE

FMODB ID: KGLK3

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	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-686513.477332
FMO2-HF: Nuclear repulsion	648615.322137
FMO2-HF: Total energy	-37898.155195
FMO2-MP2: Total energy	-38007.379018

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.
-1.43	1.513	-0.009	-1.031	-1.903	0.004

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 : 0.034 / q_NPA : 0.006

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	-0.873	-0.940	3.778	-2.760	-0.991	-0.023	-0.770	-0.976	0.004
4	D	381	ASN	0	-0.031	-0.027	6.515	-0.100	-0.100	0.000	0.000	0.000	0.000
5	D	382	CYS	0	-0.076	-0.028	3.939	0.686	0.967	0.000	-0.041	-0.240	0.000
6	D	383	GLN	0	-0.072	-0.029	3.512	0.456	1.286	0.015	-0.214	-0.631	0.000
7	D	384	ASP	-1	-0.928	-0.947	4.742	-0.659	-0.596	-0.001	-0.006	-0.056	0.000
8	D	385	ASP	-1	-0.813	-0.923	8.263	-0.491	-0.491	0.000	0.000	0.000	0.000
9	D	386	PHE	0	-0.055	-0.007	10.127	0.128	0.128	0.000	0.000	0.000	0.000
10	D	387	ASN	0	-0.013	-0.025	7.994	0.074	0.074	0.000	0.000	0.000	0.000
11	D	388	PHE	0	0.011	0.004	11.317	0.085	0.085	0.000	0.000	0.000	0.000
12	D	389	ASN	0	-0.010	-0.005	10.275	-0.027	-0.027	0.000	0.000	0.000	0.000
13	D	390	TYR	0	-0.068	-0.062	12.512	-0.010	-0.010	0.000	0.000	0.000	0.000
14	D	391	VAL	0	-0.039	-0.002	14.191	0.059	0.059	0.000	0.000	0.000	0.000
15	D	392	SER	0	0.025	-0.004	16.943	0.027	0.027	0.000	0.000	0.000	0.000
16	D	393	ASP	-1	-0.822	-0.894	19.471	0.053	0.053	0.000	0.000	0.000	0.000
17	D	394	GLN	0	-0.092	-0.049	21.205	-0.008	-0.008	0.000	0.000	0.000	0.000
18	D	395	GLU	-1	-0.914	-0.954	20.717	0.057	0.057	0.000	0.000	0.000	0.000
19	D	396	ILE	0	-0.016	0.001	16.474	0.011	0.011	0.000	0.000	0.000	0.000
20	D	397	GLU	-1	-0.836	-0.916	14.347	0.110	0.110	0.000	0.000	0.000	0.000
21	D	398	VAL	0	0.008	0.001	15.027	-0.029	-0.029	0.000	0.000	0.000	0.000
22	D	399	TYR	0	0.019	-0.024	7.849	0.083	0.083	0.000	0.000	0.000	0.000
23	D	400	HIS	0	0.010	-0.007	13.526	-0.082	-0.082	0.000	0.000	0.000	0.000
24	D	401	VAL	0	-0.035	-0.012	9.374	0.074	0.074	0.000	0.000	0.000	0.000
25	D	402	ASP	-1	-0.848	-0.924	12.775	-0.094	-0.094	0.000	0.000	0.000	0.000
26	D	403	LYS	1	0.818	0.903	12.486	0.362	0.362	0.000	0.000	0.000	0.000
27	D	404	GLY	0	-0.003	0.003	16.816	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	405	TRP	0	-0.038	-0.008	16.820	0.013	0.013	0.000	0.000	0.000	0.000
29	D	406	SER	0	-0.057	-0.043	22.653	0.007	0.007	0.000	0.000	0.000	0.000
30	D	407	ALA	0	-0.016	-0.005	22.764	0.009	0.009	0.000	0.000	0.000	0.000
31	D	408	GLY	0	-0.027	-0.015	24.842	0.010	0.010	0.000	0.000	0.000	0.000
32	D	409	TRP	0	-0.033	-0.014	26.501	0.007	0.007	0.000	0.000	0.000	0.000
33	D	410	ASN	0	-0.004	-0.023	21.992	-0.014	-0.014	0.000	0.000	0.000	0.000
34	D	411	TYR	0	-0.037	-0.026	23.751	0.015	0.015	0.000	0.000	0.000	0.000
35	D	412	VAL	0	0.036	0.030	19.034	-0.017	-0.017	0.000	0.000	0.000	0.000
36	D	413	CYS	0	-0.079	-0.057	21.428	0.010	0.010	0.000	0.000	0.000	0.000
37	D	414	LEU	0	0.062	0.045	20.235	-0.021	-0.021	0.000	0.000	0.000	0.000
38	D	415	ASN	0	0.037	0.004	22.888	0.000	0.000	0.000	0.000	0.000	0.000
39	D	416	ASP	-1	-0.884	-0.925	25.228	-0.102	-0.102	0.000	0.000	0.000	0.000
40	D	417	TYR	0	-0.021	0.009	26.304	0.010	0.010	0.000	0.000	0.000	0.000
41	D	419	LEU	0	0.012	-0.001	24.604	0.010	0.010	0.000	0.000	0.000	0.000
42	D	420	PRO	0	0.031	0.019	24.604	-0.008	-0.008	0.000	0.000	0.000	0.000
43	D	421	GLY	0	0.010	0.009	21.480	0.008	0.008	0.000	0.000	0.000	0.000
44	D	422	ASN	0	-0.063	-0.030	20.862	0.011	0.011	0.000	0.000	0.000	0.000
45	D	423	LYS	1	0.923	0.961	18.315	0.020	0.020	0.000	0.000	0.000	0.000
46	D	424	SER	0	-0.020	-0.011	17.349	0.025	0.025	0.000	0.000	0.000	0.000
47	D	425	ASN	0	0.015	-0.017	13.102	0.004	0.004	0.000	0.000	0.000	0.000
48	D	426	GLY	0	0.038	0.026	12.731	0.013	0.013	0.000	0.000	0.000	0.000
49	D	427	ALA	0	0.020	0.032	12.523	-0.053	-0.053	0.000	0.000	0.000	0.000
50	D	428	PHE	0	-0.026	-0.009	14.641	0.046	0.046	0.000	0.000	0.000	0.000
51	D	429	ARG	1	0.841	0.915	11.741	-0.162	-0.162	0.000	0.000	0.000	0.000
52	D	430	LYS	1	0.892	0.948	17.696	-0.004	-0.004	0.000	0.000	0.000	0.000
53	D	431	THR	0	0.042	0.031	19.138	-0.010	-0.010	0.000	0.000	0.000	0.000
54	D	432	PHE	0	-0.081	-0.026	20.457	-0.004	-0.004	0.000	0.000	0.000	0.000
55	D	433	ASN	0	0.051	0.026	22.307	0.013	0.013	0.000	0.000	0.000	0.000
56	D	434	ALA	0	-0.047	-0.027	21.114	-0.015	-0.015	0.000	0.000	0.000	0.000
57	D	435	VAL	0	0.005	-0.001	23.187	0.016	0.016	0.000	0.000	0.000	0.000
58	D	436	LEU	0	0.014	0.004	17.700	-0.019	-0.019	0.000	0.000	0.000	0.000
59	D	437	GLY	0	-0.027	-0.012	19.966	0.006	0.006	0.000	0.000	0.000	0.000
60	D	438	GLN	0	-0.053	-0.015	21.500	-0.007	-0.007	0.000	0.000	0.000	0.000
61	D	439	ASP	-1	-0.842	-0.906	21.229	-0.189	-0.189	0.000	0.000	0.000	0.000
62	D	440	TYR	0	-0.046	-0.030	20.257	0.026	0.026	0.000	0.000	0.000	0.000
63	D	441	LYS	1	0.869	0.932	20.550	0.109	0.109	0.000	0.000	0.000	0.000
64	D	442	LEU	0	-0.024	-0.006	15.429	0.025	0.025	0.000	0.000	0.000	0.000
65	D	443	THR	0	-0.032	-0.039	19.693	-0.011	-0.011	0.000	0.000	0.000	0.000
66	D	444	PHE	0	-0.019	-0.001	18.402	0.017	0.017	0.000	0.000	0.000	0.000
67	D	445	LYS	1	0.931	0.963	20.518	0.084	0.084	0.000	0.000	0.000	0.000
68	D	446	VAL	0	-0.001	0.007	21.176	0.014	0.014	0.000	0.000	0.000	0.000
69	D	447	GLU	-1	-0.777	-0.851	23.937	-0.066	-0.066	0.000	0.000	0.000	0.000
70	D	448	ASP	-1	-0.754	-0.908	24.735	-0.118	-0.118	0.000	0.000	0.000	0.000
71	D	449	ARG	1	0.891	0.945	26.583	0.117	0.117	0.000	0.000	0.000	0.000
72	D	450	TYR	0	0.000	-0.010	26.656	0.007	0.007	0.000	0.000	0.000	0.000
73	D	451	GLY	0	0.012	0.008	30.979	0.005	0.005	0.000	0.000	0.000	0.000
74	D	452	GLN	0	-0.078	-0.042	32.097	-0.001	-0.001	0.000	0.000	0.000	0.000
75	D	453	GLY	0	-0.017	-0.011	30.088	-0.004	-0.004	0.000	0.000	0.000	0.000
76	D	454	GLN	0	-0.022	-0.003	27.042	0.010	0.010	0.000	0.000	0.000	0.000
77	D	455	GLN	0	-0.061	-0.025	21.701	-0.020	-0.020	0.000	0.000	0.000	0.000
78	D	456	ILE	0	-0.010	-0.015	23.424	0.010	0.010	0.000	0.000	0.000	0.000
79	D	457	LEU	0	0.006	0.018	17.337	-0.008	-0.008	0.000	0.000	0.000	0.000
80	D	458	ASP	-1	-0.837	-0.925	20.768	-0.154	-0.154	0.000	0.000	0.000	0.000
81	D	459	ARG	1	0.890	0.937	11.362	0.550	0.550	0.000	0.000	0.000	0.000
82	D	460	ASN	0	0.002	0.009	18.726	0.031	0.031	0.000	0.000	0.000	0.000
83	D	461	ILE	0	-0.067	-0.024	14.686	-0.047	-0.047	0.000	0.000	0.000	0.000
84	D	462	THR	0	0.050	0.010	16.912	0.025	0.025	0.000	0.000	0.000	0.000
85	D	463	PHE	0	-0.033	-0.009	16.220	-0.033	-0.033	0.000	0.000	0.000	0.000
86	D	464	THR	0	0.029	0.008	13.105	0.032	0.032	0.000	0.000	0.000	0.000
87	D	465	THR	0	0.052	0.002	14.049	-0.013	-0.013	0.000	0.000	0.000	0.000
88	D	466	GLN	0	-0.045	0.005	8.786	-0.006	-0.006	0.000	0.000	0.000	0.000
89	D	467	VAL	0	0.032	0.006	8.621	-0.020	-0.020	0.000	0.000	0.000	0.000
90	D	469	ASN	0	0.023	0.027	5.824	0.378	0.378	0.000	0.000	0.000	0.000

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