FMO DATABASE

FMODB ID: VRM41

Calculation Name: 3ENC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ENC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZI1

Base Structure: X-ray

Registration Date: 2023-06-20

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-509983.031951
FMO2-HF: Nuclear repulsion	478878.860946
FMO2-HF: Total energy	-31104.171005
FMO2-MP2: Total energy	-31196.854521

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(A:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
73.161	74.711	0.005	-0.689	-0.866	0.002

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.984 / q_NPA : 0.977

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	A	4	LYS	1	0.921	0.934	3.802	43.922	45.472	0.005	-0.689	-0.866	0.002
4	A	5	ARG	1	0.960	0.981	6.594	23.531	23.531	0.000	0.000	0.000	0.000
5	A	6	VAL	0	-0.024	0.004	9.403	-1.000	-1.000	0.000	0.000	0.000	0.000
6	A	7	GLN	0	0.048	0.020	11.997	0.900	0.900	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.026	-0.009	15.719	-0.729	-0.729	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.841	0.908	18.006	12.565	12.565	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.028	-0.005	20.198	-0.248	-0.248	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.829	-0.908	24.042	-10.684	-10.684	0.000	0.000	0.000	0.000
11	A	12	MET	0	-0.047	-0.017	27.837	-0.206	-0.206	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.819	-0.911	30.443	-8.764	-8.764	0.000	0.000	0.000	0.000
13	A	14	PHE	0	0.008	-0.004	32.290	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	15	PRO	0	-0.020	-0.015	37.162	0.095	0.095	0.000	0.000	0.000	0.000
15	A	16	SER	0	0.017	-0.002	40.738	0.161	0.161	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.778	-0.885	40.422	-7.996	-7.996	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.858	-0.923	40.497	-7.095	-7.095	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.049	-0.019	38.465	0.028	0.028	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.005	0.006	36.182	-0.170	-0.170	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.870	0.934	36.194	7.650	7.650	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.055	0.037	37.402	-0.136	-0.136	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.000	0.000	32.845	-0.131	-0.131	0.000	0.000	0.000	0.000
23	A	24	TYR	0	-0.021	-0.011	31.211	-0.372	-0.372	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.891	-0.968	33.232	-8.055	-8.055	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.004	0.010	35.209	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.007	-0.010	28.664	-0.152	-0.152	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.052	-0.019	30.285	-0.318	-0.318	0.000	0.000	0.000	0.000
28	A	29	TYR	0	0.045	0.025	31.660	-0.055	-0.055	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.843	-0.916	29.484	-9.460	-9.460	0.000	0.000	0.000	0.000
30	A	31	HIS	0	-0.006	-0.006	25.746	-0.625	-0.625	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.027	-0.016	27.856	-0.239	-0.239	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.049	-0.021	30.570	0.137	0.137	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.059	-0.017	25.261	-0.079	-0.079	0.000	0.000	0.000	0.000
34	A	35	PRO	0	0.022	0.002	25.369	-0.485	-0.485	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.046	-0.026	21.995	-0.246	-0.246	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.891	0.949	20.972	11.582	11.582	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.948	0.982	15.988	13.926	13.926	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.016	0.000	14.792	-0.506	-0.506	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.839	-0.903	17.208	-15.468	-15.468	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.003	-0.009	19.497	-0.490	-0.490	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.846	-0.897	22.351	-10.762	-10.762	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.009	-0.013	25.369	-0.066	-0.066	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.843	0.908	27.276	10.749	10.749	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.029	0.006	30.775	-0.155	-0.155	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.926	-0.941	33.630	-8.989	-8.989	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.008	-0.005	36.645	0.277	0.277	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.867	0.911	37.321	8.105	8.105	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.841	0.907	31.144	9.828	9.828	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.020	0.013	29.309	0.019	0.019	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.036	-0.017	27.477	-0.281	-0.281	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.015	0.009	22.919	0.050	0.050	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.768	-0.861	22.196	-13.160	-13.160	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.013	-0.017	17.085	0.132	0.132	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.836	0.884	15.398	16.027	16.027	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.027	-0.011	12.369	0.741	0.741	0.000	0.000	0.000	0.000
56	A	57	THR	0	0.030	-0.009	9.180	-0.561	-0.561	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.841	-0.898	6.180	-26.641	-26.641	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.026	-0.010	6.193	2.036	2.036	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.046	-0.024	8.414	1.926	1.926	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.016	0.011	10.135	1.451	1.451	0.000	0.000	0.000	0.000
61	A	62	LEU	0	0.024	0.022	11.722	0.941	0.941	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.943	0.968	10.773	20.398	20.398	0.000	0.000	0.000	0.000
63	A	64	GLY	0	-0.001	0.006	14.266	0.890	0.890	0.000	0.000	0.000	0.000
64	A	65	THR	0	0.027	-0.008	16.293	0.973	0.973	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.010	0.005	17.411	0.685	0.685	0.000	0.000	0.000	0.000
66	A	67	ASN	0	-0.052	-0.037	17.431	1.066	1.066	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.018	0.015	20.394	0.568	0.568	0.000	0.000	0.000	0.000
68	A	69	TYR	0	0.064	0.027	21.664	0.480	0.480	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.003	0.004	21.702	0.397	0.397	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.825	0.908	22.456	11.989	11.989	0.000	0.000	0.000	0.000
71	A	72	TRP	0	0.029	0.010	23.903	-0.093	-0.093	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.035	0.003	26.470	0.262	0.262	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.857	0.936	26.968	10.527	10.527	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.056	0.029	30.601	0.258	0.258	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.004	0.006	32.435	0.264	0.264	0.000	0.000	0.000	0.000
76	A	77	ILE	0	-0.034	-0.024	32.950	0.186	0.186	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.919	-0.970	33.375	-8.550	-8.550	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.065	-0.022	36.613	0.202	0.202	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.054	-0.010	38.067	0.225	0.225	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)