FMO DATABASE

FMODB ID: ZV2ZN

Calculation Name: 3M8F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M8F

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KNP2

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-685962.040917
FMO2-HF: Nuclear repulsion	646637.193989
FMO2-HF: Total energy	-39324.846929
FMO2-MP2: Total energy	-39435.519487

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:5:HIS)

Summations of interaction energy for fragment #1(A:5:HIS)

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.
-0.806	2.166	0.038	-1.374	-1.636	0.006

Interaction energy analysis for fragmet #1(A:5:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.003

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	7	TYR	0	0.008	-0.007	3.764	0.850	3.822	0.038	-1.374	-1.636	0.006
4	A	8	THR	0	-0.013	-0.004	5.561	-0.456	-0.456	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.017	0.011	9.135	-0.052	-0.052	0.000	0.000	0.000	0.000
6	A	10	ASN	0	0.029	0.007	11.190	0.078	0.078	0.000	0.000	0.000	0.000
7	A	11	ILE	0	0.071	0.025	14.866	-0.061	-0.061	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.045	0.023	16.346	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.845	-0.909	17.121	-0.487	-0.487	0.000	0.000	0.000	0.000
10	A	14	ILE	0	-0.011	-0.005	13.474	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	15	ALA	0	0.036	0.014	18.003	0.007	0.007	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.883	-0.922	21.029	-0.224	-0.224	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.791	0.888	17.296	0.585	0.585	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.018	0.004	19.000	0.013	0.013	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.011	0.007	22.790	0.018	0.018	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.119	-0.067	25.166	0.035	0.035	0.000	0.000	0.000	0.000
17	A	21	ASP	-1	-0.916	-0.945	24.653	-0.350	-0.350	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.887	-0.951	26.612	-0.217	-0.217	0.000	0.000	0.000	0.000
19	A	23	CYS	0	-0.006	-0.001	27.239	0.011	0.011	0.000	0.000	0.000	0.000
20	A	24	ALA	0	-0.035	-0.033	23.403	0.002	0.002	0.000	0.000	0.000	0.000
21	A	25	TYR	0	0.005	0.007	25.510	0.006	0.006	0.000	0.000	0.000	0.000
22	A	26	GLN	0	0.005	-0.015	27.151	0.022	0.022	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.023	-0.016	25.281	0.012	0.012	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.039	-0.013	22.246	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	29	MET	0	0.000	-0.006	25.499	0.009	0.009	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.033	0.034	28.709	0.016	0.016	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.086	-0.048	25.037	0.010	0.010	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.021	0.000	26.410	0.006	0.006	0.000	0.000	0.000	0.000
29	A	33	ASN	0	-0.019	0.000	29.932	0.003	0.003	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.887	-0.963	33.255	-0.101	-0.101	0.000	0.000	0.000	0.000
31	A	35	ASN	0	-0.143	-0.061	34.521	0.005	0.005	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.022	-0.007	32.319	0.006	0.006	0.000	0.000	0.000	0.000
33	A	37	GLU	-1	-0.891	-0.930	29.544	-0.089	-0.089	0.000	0.000	0.000	0.000
34	A	38	ALA	0	0.015	-0.005	25.535	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.073	-0.033	27.562	0.024	0.024	0.000	0.000	0.000	0.000
36	A	40	MET	0	-0.032	-0.021	26.637	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.020	0.011	27.076	0.011	0.011	0.000	0.000	0.000	0.000
38	A	42	ASN	0	0.006	0.015	27.120	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.895	0.933	23.914	0.318	0.318	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.074	-0.046	28.804	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	45	ALA	0	0.089	0.049	31.957	0.002	0.002	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.051	0.031	27.639	0.004	0.004	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.081	-0.067	31.118	0.003	0.003	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.883	-0.928	32.917	-0.152	-0.152	0.000	0.000	0.000	0.000
45	A	49	MET	0	-0.032	-0.011	33.280	0.005	0.005	0.000	0.000	0.000	0.000
46	A	50	ILE	0	0.000	0.032	30.445	0.003	0.003	0.000	0.000	0.000	0.000
47	A	51	GLN	0	-0.007	0.004	34.831	0.003	0.003	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.054	0.006	31.464	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	53	SER	0	-0.058	-0.037	32.626	0.003	0.003	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.946	0.967	32.524	0.162	0.162	0.000	0.000	0.000	0.000
51	A	55	PRO	0	-0.006	-0.007	31.052	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.048	0.047	28.673	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	57	VAL	0	0.064	0.049	27.573	-0.026	-0.026	0.000	0.000	0.000	0.000
54	A	58	PHE	0	-0.032	-0.025	27.274	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	59	ALA	0	-0.041	-0.022	24.776	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	60	THR	0	0.009	-0.004	23.142	-0.041	-0.041	0.000	0.000	0.000	0.000
57	A	61	VAL	0	0.013	0.011	22.425	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	62	ASN	0	-0.016	-0.025	21.277	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	63	TRP	0	0.056	0.028	17.471	-0.032	-0.032	0.000	0.000	0.000	0.000
60	A	64	PHE	0	0.035	0.019	17.337	-0.075	-0.075	0.000	0.000	0.000	0.000
61	A	65	TYR	0	-0.022	0.004	16.866	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	66	CYS	0	-0.058	-0.034	14.419	-0.037	-0.037	0.000	0.000	0.000	0.000
63	A	67	ALA	0	-0.054	-0.024	13.093	-0.103	-0.103	0.000	0.000	0.000	0.000
64	A	68	GLY	0	0.025	0.030	13.084	-0.071	-0.071	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.049	-0.010	14.042	0.073	0.073	0.000	0.000	0.000	0.000
66	A	70	ILE	0	-0.008	0.002	17.459	0.060	0.060	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.841	-0.909	16.126	-0.420	-0.420	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.839	-0.896	18.548	-0.272	-0.272	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.005	-0.001	19.970	0.014	0.014	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.867	0.906	22.369	0.245	0.245	0.000	0.000	0.000	0.000
71	A	75	VAL	0	0.039	0.026	25.113	0.018	0.018	0.000	0.000	0.000	0.000
72	A	76	GLY	0	-0.004	-0.010	28.546	0.001	0.001	0.000	0.000	0.000	0.000
73	A	77	ARG	1	0.913	0.958	30.529	0.099	0.099	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.032	-0.004	29.781	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	79	LYN	0	0.017	0.017	24.286	0.001	0.001	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.036	-0.025	25.598	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	81	TYR	0	0.005	-0.041	21.038	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	82	THR	0	0.061	0.033	21.123	0.030	0.030	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.026	-0.003	20.980	-0.034	-0.034	0.000	0.000	0.000	0.000
80	A	84	SER	0	0.015	-0.007	15.585	0.037	0.037	0.000	0.000	0.000	0.000
81	A	85	ASP	-1	-0.879	-0.956	15.244	-0.204	-0.204	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.022	-0.010	13.093	0.018	0.018	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.010	-0.007	16.634	0.012	0.012	0.000	0.000	0.000	0.000
84	A	88	VAL	0	-0.004	-0.009	19.670	0.019	0.019	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.911	-0.955	17.646	-0.148	-0.148	0.000	0.000	0.000	0.000
86	A	90	ILE	0	-0.039	-0.021	17.494	0.010	0.010	0.000	0.000	0.000	0.000
87	A	91	VAL	0	0.010	-0.005	21.167	0.014	0.014	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.800	-0.890	23.150	-0.094	-0.094	0.000	0.000	0.000	0.000
89	A	93	CYS	0	-0.056	-0.006	21.764	0.011	0.011	0.000	0.000	0.000	0.000
90	A	94	PHE	0	0.007	-0.005	23.859	0.013	0.013	0.000	0.000	0.000	0.000
91	A	95	LYS	1	0.838	0.912	27.213	0.112	0.112	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.039	-0.033	25.349	0.014	0.014	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.873	0.926	23.696	0.237	0.237	0.000	0.000	0.000	0.000
94	A	98	ALA	0	-0.045	-0.012	29.589	0.004	0.004	0.000	0.000	0.000	0.000
95	A	99	MET	0	-0.094	-0.036	32.211	0.009	0.009	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.995	-0.980	30.263	-0.083	-0.083	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:HIS)