FMO DATABASE

FMODB ID: 2LYVR

Calculation Name: 1FI8-D-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FI8

Chain ID: D

ChEMBL ID:

UniProt ID: P23827

Base Structure: X-ray

Registration Date: 2025-07-10

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

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-184304.738301
FMO2-HF: Nuclear repulsion	165154.927759
FMO2-HF: Total energy	-19149.810542
FMO2-MP2: Total energy	-19205.886954

3D Structure Molmil

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:95:LYS)

Summations of interaction energy for fragment #1(D:95: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.
-1.742	0.472	-0.008	-1.204	-1.001	0.005

Interaction energy analysis for fragmet #1(D:95:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.174 / q_NPA : 0.037

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

Sort

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].
4	D	96	PHE	0	-0.046	0.107	4.608	0.012	0.352	0.000	-0.156	-0.184	0.000
5	D	97	VAL	0	-0.013	-0.134	3.849	-1.821	-0.032	-0.007	-1.033	-0.749	0.005
6	D	97	VAL	0	-0.077	0.110	4.150	-0.053	0.032	-0.001	-0.015	-0.068	0.000
7	D	98	THR	0	0.074	-0.090	6.357	0.368	0.368	0.000	0.000	0.000	0.000
8	D	98	THR	0	-0.030	0.077	8.588	0.037	0.037	0.000	0.000	0.000	0.000
9	D	99	ALA	0	0.105	-0.080	9.712	-0.089	-0.089	0.000	0.000	0.000	0.000
10	D	99	ALA	0	-0.046	0.124	13.332	0.021	0.021	0.000	0.000	0.000	0.000
11	D	100	TYR	0	0.073	-0.116	12.761	0.045	0.045	0.000	0.000	0.000	0.000
12	D	100	TYR	0	-0.090	0.109	14.785	-0.002	-0.002	0.000	0.000	0.000	0.000
13	D	101	LEU	0	0.007	-0.131	15.231	0.022	0.022	0.000	0.000	0.000	0.000
14	D	101	LEU	0	-0.023	0.125	15.948	0.005	0.005	0.000	0.000	0.000	0.000
15	D	102	GLY	0	0.018	-0.094	18.092	0.044	0.044	0.000	0.000	0.000	0.000
16	D	103	ASP	0	0.059	-0.019	20.161	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	103	ASP	-1	-0.912	-0.821	24.297	-0.226	-0.226	0.000	0.000	0.000	0.000
18	D	104	ALA	0	0.051	-0.109	22.694	0.024	0.024	0.000	0.000	0.000	0.000
19	D	104	ALA	0	-0.064	0.116	22.053	-0.002	-0.002	0.000	0.000	0.000	0.000
20	D	105	GLY	0	-0.039	-0.132	18.707	-0.004	-0.004	0.000	0.000	0.000	0.000
21	D	106	MET	0	0.021	-0.018	19.630	0.005	0.005	0.000	0.000	0.000	0.000
22	D	106	MET	0	-0.113	0.109	20.163	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	107	LEU	0	0.073	-0.127	21.744	0.019	0.019	0.000	0.000	0.000	0.000
24	D	107	LEU	0	-0.058	0.116	21.730	0.004	0.004	0.000	0.000	0.000	0.000
25	D	108	ARG	0	0.135	-0.078	23.780	0.010	0.010	0.000	0.000	0.000	0.000
26	D	108	ARG	1	0.839	1.061	28.217	0.082	0.082	0.000	0.000	0.000	0.000
27	D	109	TYR	0	0.141	-0.089	25.750	-0.005	-0.005	0.000	0.000	0.000	0.000
28	D	109	TYR	0	-0.082	0.117	23.948	0.001	0.001	0.000	0.000	0.000	0.000
29	D	110	ASN	0	0.036	-0.091	26.503	0.008	0.008	0.000	0.000	0.000	0.000
30	D	110	ASN	0	-0.132	0.043	29.392	0.006	0.006	0.000	0.000	0.000	0.000
31	D	111	SER	0	0.109	-0.065	27.987	-0.008	-0.008	0.000	0.000	0.000	0.000
32	D	111	SER	0	-0.037	0.073	28.196	0.000	0.000	0.000	0.000	0.000	0.000
33	D	112	LYS	0	0.071	-0.050	28.941	0.003	0.003	0.000	0.000	0.000	0.000
34	D	112	LYS	1	0.852	1.041	33.102	0.047	0.047	0.000	0.000	0.000	0.000
35	D	113	LEU	0	0.033	-0.115	30.050	0.005	0.005	0.000	0.000	0.000	0.000
36	D	113	LEU	0	-0.047	0.101	30.201	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	114	PRO	0	0.006	-0.079	26.705	0.000	0.000	0.000	0.000	0.000	0.000
38	D	115	ILE	0	0.133	0.017	23.468	-0.001	-0.001	0.000	0.000	0.000	0.000
39	D	115	ILE	0	-0.076	0.099	21.835	-0.001	-0.001	0.000	0.000	0.000	0.000
40	D	116	VAL	0	0.016	-0.128	23.449	0.001	0.001	0.000	0.000	0.000	0.000
41	D	116	VAL	0	-0.079	0.109	24.680	0.002	0.002	0.000	0.000	0.000	0.000
42	D	117	VAL	0	0.019	-0.116	20.289	0.005	0.005	0.000	0.000	0.000	0.000
43	D	117	VAL	0	-0.044	0.099	18.637	-0.004	-0.004	0.000	0.000	0.000	0.000
44	D	118	TYR	0	0.074	-0.105	21.296	0.009	0.009	0.000	0.000	0.000	0.000
45	D	118	TYR	0	-0.066	0.107	22.870	0.008	0.008	0.000	0.000	0.000	0.000
46	D	119	THR	0	-0.063	-0.101	17.211	-0.003	-0.003	0.000	0.000	0.000	0.000
47	D	119	THR	0	-0.014	0.057	16.002	0.015	0.015	0.000	0.000	0.000	0.000
48	D	120	PRO	0	0.036	-0.092	16.579	0.028	0.028	0.000	0.000	0.000	0.000
49	D	121	ASP	0	0.076	-0.004	16.480	-0.057	-0.057	0.000	0.000	0.000	0.000
50	D	121	ASP	-1	-0.916	-0.828	18.183	-0.267	-0.267	0.000	0.000	0.000	0.000
51	D	122	ASN	0	-0.002	-0.053	13.473	0.037	0.037	0.000	0.000	0.000	0.000
52	D	122	ASN	0	-0.094	0.041	12.854	0.024	0.024	0.000	0.000	0.000	0.000
53	D	123	VAL	0	0.065	-0.117	11.935	-0.183	-0.183	0.000	0.000	0.000	0.000
54	D	123	VAL	0	-0.108	0.091	12.498	-0.008	-0.008	0.000	0.000	0.000	0.000
55	D	124	ASP	0	0.171	-0.070	11.331	0.120	0.120	0.000	0.000	0.000	0.000
56	D	124	ASP	-1	-0.934	-0.834	9.382	-0.690	-0.690	0.000	0.000	0.000	0.000
57	D	125	VAL	0	0.043	-0.097	12.539	-0.102	-0.102	0.000	0.000	0.000	0.000
58	D	125	VAL	0	-0.039	0.127	15.955	0.008	0.008	0.000	0.000	0.000	0.000
59	D	126	LYS	0	0.024	-0.103	11.951	0.070	0.070	0.000	0.000	0.000	0.000
60	D	126	LYS	1	0.778	0.988	7.776	0.635	0.635	0.000	0.000	0.000	0.000
61	D	127	TYR	0	0.028	-0.094	13.439	-0.061	-0.061	0.000	0.000	0.000	0.000
62	D	127	TYR	0	-0.040	0.101	16.864	0.011	0.011	0.000	0.000	0.000	0.000
63	D	128	ARG	0	0.070	-0.087	14.914	0.040	0.040	0.000	0.000	0.000	0.000
64	D	128	ARG	1	0.910	1.070	13.083	0.064	0.064	0.000	0.000	0.000	0.000
65	D	129	VAL	0	0.059	-0.102	16.592	-0.031	-0.031	0.000	0.000	0.000	0.000
66	D	129	VAL	0	-0.042	0.115	20.351	0.002	0.002	0.000	0.000	0.000	0.000
67	D	130	TRP	0	0.009	-0.134	19.526	0.012	0.012	0.000	0.000	0.000	0.000
68	D	130	TRP	0	-0.042	0.119	16.885	0.009	0.009	0.000	0.000	0.000	0.000
69	D	131	LYS	0	0.119	-0.094	21.801	-0.006	-0.006	0.000	0.000	0.000	0.000
70	D	131	LYS	1	0.714	0.973	24.470	0.005	0.005	0.000	0.000	0.000	0.000
71	D	132	ALA	0	0.093	-0.088	25.159	0.002	0.002	0.000	0.000	0.000	0.000
72	D	132	ALA	0	-0.046	0.112	28.680	-0.001	-0.001	0.000	0.000	0.000	0.000
73	D	133	GLU	0	0.049	-0.127	27.814	0.009	0.009	0.000	0.000	0.000	0.000
74	D	133	GLU	-1	-0.961	-0.846	27.474	-0.017	-0.017	0.000	0.000	0.000	0.000
75	D	134	GLU	0	0.035	-0.122	29.523	-0.007	-0.007	0.000	0.000	0.000	0.000
76	D	134	GLU	-1	-0.901	-0.785	30.964	0.002	0.002	0.000	0.000	0.000	0.000
77	D	135	LYS	0	0.034	-0.068	32.783	-0.001	-0.001	0.000	0.000	0.000	0.000
78	D	135	LYS	1	0.811	1.022	30.681	0.026	0.026	0.000	0.000	0.000	0.000
79	D	136	ILE	0	0.060	-0.119	33.295	-0.003	-0.003	0.000	0.000	0.000	0.000
80	D	136	ILE	0	-0.078	0.104	34.404	-0.001	-0.001	0.000	0.000	0.000	0.000
81	D	137	ASP	0	0.084	-0.085	34.961	0.003	0.003	0.000	0.000	0.000	0.000
82	D	137	ASP	-1	-0.945	-0.840	33.690	-0.027	-0.027	0.000	0.000	0.000	0.000
83	D	138	ASN	0	0.061	-0.098	36.733	-0.004	-0.004	0.000	0.000	0.000	0.000
84	D	138	ASN	0	-0.090	0.080	40.272	-0.001	-0.001	0.000	0.000	0.000	0.000
85	D	139	ALA	0	0.151	-0.077	38.365	0.002	0.002	0.000	0.000	0.000	0.000
86	D	139	ALA	0	-0.077	0.102	38.246	-0.001	-0.001	0.000	0.000	0.000	0.000
87	D	140	VAL	0	0.021	-0.118	39.212	0.003	0.003	0.000	0.000	0.000	0.000
88	D	140	VAL	0	-0.078	0.098	40.057	0.000	0.000	0.000	0.000	0.000	0.000
89	D	141	VAL	0	0.080	-0.123	41.479	-0.004	-0.004	0.000	0.000	0.000	0.000
90	D	141	VAL	0	-0.061	0.132	44.649	0.000	0.000	0.000	0.000	0.000	0.000
91	D	142	ARG	0	-0.038	-0.103	42.686	0.001	0.001	0.000	0.000	0.000	0.000
92	D	142	ARG	1	1.000	0.999	37.207	0.046	0.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:95:LYS)