FMO DATABASE

FMODB ID: Y98K2

Calculation Name: 1VKU-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VKU

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WY19

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-629257.00257
FMO2-HF: Nuclear repulsion	593912.676627
FMO2-HF: Total energy	-35344.325943
FMO2-MP2: Total energy	-35447.38039

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(A:-2:HIS)

Summations of interaction energy for fragment #1(A:-2: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.
-153.421	-149.734	0.614	-1.509	-2.792	-0.011

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.914

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	0	HIS	0	0.046	0.012	3.080	4.134	7.753	0.615	-1.502	-2.732	-0.011
4	A	1	MET	0	-0.047	-0.041	4.746	4.334	4.402	-0.001	-0.007	-0.060	0.000
5	A	2	GLU	-1	-0.848	-0.907	7.035	-31.101	-31.101	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.835	0.879	9.101	23.473	23.473	0.000	0.000	0.000	0.000
7	A	4	LYS	1	0.940	0.964	11.424	22.542	22.542	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.886	0.945	8.275	33.902	33.902	0.000	0.000	0.000	0.000
9	A	6	LEU	0	0.057	0.043	12.397	1.165	1.165	0.000	0.000	0.000	0.000
10	A	7	ILE	0	0.019	0.006	15.270	1.108	1.108	0.000	0.000	0.000	0.000
11	A	8	ALA	0	-0.028	-0.014	16.690	0.926	0.926	0.000	0.000	0.000	0.000
12	A	9	LYS	1	0.801	0.886	17.453	15.929	15.929	0.000	0.000	0.000	0.000
13	A	10	PHE	0	0.028	0.010	19.286	0.739	0.739	0.000	0.000	0.000	0.000
14	A	11	VAL	0	-0.002	-0.003	21.276	0.689	0.689	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.866	-0.912	21.073	-14.043	-14.043	0.000	0.000	0.000	0.000
16	A	13	ILE	0	0.012	0.005	21.623	0.647	0.647	0.000	0.000	0.000	0.000
17	A	14	ALA	0	0.015	-0.001	25.017	0.550	0.550	0.000	0.000	0.000	0.000
18	A	15	SER	0	-0.023	-0.001	26.785	0.663	0.663	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.975	-0.999	26.790	-11.426	-11.426	0.000	0.000	0.000	0.000
20	A	17	LYS	1	0.863	0.943	26.204	12.020	12.020	0.000	0.000	0.000	0.000
21	A	18	MET	0	-0.048	-0.011	28.627	0.136	0.136	0.000	0.000	0.000	0.000
22	A	19	GLY	0	-0.023	0.013	31.412	0.294	0.294	0.000	0.000	0.000	0.000
23	A	20	LYS	1	0.780	0.886	30.046	10.158	10.158	0.000	0.000	0.000	0.000
24	A	21	ASP	-1	-0.861	-0.945	29.069	-10.819	-10.819	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.080	-0.048	25.242	0.188	0.188	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.913	-0.929	25.251	-11.941	-11.941	0.000	0.000	0.000	0.000
27	A	24	THR	0	-0.095	-0.059	22.660	-0.589	-0.589	0.000	0.000	0.000	0.000
28	A	25	VAL	0	-0.014	0.000	21.333	0.339	0.339	0.000	0.000	0.000	0.000
29	A	26	ASP	-1	-0.875	-0.933	21.029	-14.342	-14.342	0.000	0.000	0.000	0.000
30	A	27	GLU	-1	-0.771	-0.879	15.262	-18.571	-18.571	0.000	0.000	0.000	0.000
31	A	28	GLU	-1	-0.866	-0.946	19.722	-13.461	-13.461	0.000	0.000	0.000	0.000
32	A	29	ASN	0	-0.046	-0.006	22.445	0.286	0.286	0.000	0.000	0.000	0.000
33	A	30	THR	0	-0.057	-0.069	24.781	-0.184	-0.184	0.000	0.000	0.000	0.000
34	A	31	PHE	0	0.074	0.023	22.998	0.153	0.153	0.000	0.000	0.000	0.000
35	A	32	LYS	1	0.960	0.982	28.236	8.999	8.999	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.886	-0.916	28.890	-10.264	-10.264	0.000	0.000	0.000	0.000
37	A	34	LEU	0	0.016	0.023	25.291	0.190	0.190	0.000	0.000	0.000	0.000
38	A	35	GLY	0	-0.018	0.000	29.968	0.054	0.054	0.000	0.000	0.000	0.000
39	A	36	PHE	0	-0.021	-0.017	27.754	0.026	0.026	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.892	-0.951	31.611	-8.850	-8.850	0.000	0.000	0.000	0.000
41	A	38	SER	0	-0.034	-0.035	31.805	-0.216	-0.216	0.000	0.000	0.000	0.000
42	A	39	ILE	0	-0.043	-0.018	32.234	-0.111	-0.111	0.000	0.000	0.000	0.000
43	A	40	ASP	-1	-0.770	-0.886	30.703	-9.716	-9.716	0.000	0.000	0.000	0.000
44	A	41	VAL	0	-0.034	-0.029	26.590	-0.388	-0.388	0.000	0.000	0.000	0.000
45	A	42	ILE	0	-0.020	-0.003	27.198	-0.385	-0.385	0.000	0.000	0.000	0.000
46	A	43	ASP	-1	-0.873	-0.939	28.179	-10.026	-10.026	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.049	-0.018	23.477	-0.393	-0.393	0.000	0.000	0.000	0.000
48	A	45	VAL	0	-0.020	-0.015	23.479	-0.628	-0.628	0.000	0.000	0.000	0.000
49	A	46	MET	0	0.010	0.006	23.788	-0.292	-0.292	0.000	0.000	0.000	0.000
50	A	47	PHE	0	0.006	-0.009	24.847	-0.138	-0.138	0.000	0.000	0.000	0.000
51	A	48	PHE	0	-0.014	-0.016	17.481	-0.565	-0.565	0.000	0.000	0.000	0.000
52	A	49	GLU	-1	-0.824	-0.900	20.258	-12.828	-12.828	0.000	0.000	0.000	0.000
53	A	50	ASP	-1	-0.952	-0.970	22.038	-12.425	-12.425	0.000	0.000	0.000	0.000
54	A	51	GLU	-1	-0.912	-0.958	20.053	-14.495	-14.495	0.000	0.000	0.000	0.000
55	A	52	PHE	0	-0.076	-0.043	14.395	-1.111	-1.111	0.000	0.000	0.000	0.000
56	A	53	ALA	0	-0.035	-0.003	17.660	-0.565	-0.565	0.000	0.000	0.000	0.000
57	A	54	LEU	0	-0.038	-0.008	16.104	-0.228	-0.228	0.000	0.000	0.000	0.000
58	A	55	ARG	1	0.787	0.872	20.223	12.225	12.225	0.000	0.000	0.000	0.000
59	A	56	ILE	0	-0.030	-0.029	19.827	-0.606	-0.606	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.879	-0.948	23.216	-11.621	-11.621	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.837	-0.916	26.310	-10.302	-10.302	0.000	0.000	0.000	0.000
62	A	59	GLU	-1	-0.867	-0.912	28.434	-10.061	-10.061	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.854	-0.915	21.830	-13.833	-13.833	0.000	0.000	0.000	0.000
64	A	61	ILE	0	0.049	0.027	24.995	-0.171	-0.171	0.000	0.000	0.000	0.000
65	A	62	SER	0	-0.058	-0.050	26.746	-0.034	-0.034	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.806	0.876	25.986	11.417	11.417	0.000	0.000	0.000	0.000
67	A	64	ILE	0	0.012	0.037	23.363	-0.088	-0.088	0.000	0.000	0.000	0.000
68	A	65	ARG	1	0.757	0.864	25.479	10.934	10.934	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.815	0.891	23.034	12.689	12.689	0.000	0.000	0.000	0.000
70	A	67	VAL	0	0.038	0.028	19.713	-0.266	-0.266	0.000	0.000	0.000	0.000
71	A	68	LYS	1	0.792	0.891	15.960	16.723	16.723	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.778	-0.879	18.305	-13.646	-13.646	0.000	0.000	0.000	0.000
73	A	70	LEU	0	0.024	0.018	19.571	-0.294	-0.294	0.000	0.000	0.000	0.000
74	A	71	ILE	0	-0.025	-0.011	14.327	-0.704	-0.704	0.000	0.000	0.000	0.000
75	A	72	ASP	-1	-0.772	-0.873	14.592	-19.919	-19.919	0.000	0.000	0.000	0.000
76	A	73	ILE	0	-0.044	-0.014	15.316	-0.557	-0.557	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.020	0.004	14.671	-0.287	-0.287	0.000	0.000	0.000	0.000
78	A	75	ILE	0	-0.018	-0.011	9.843	-0.724	-0.724	0.000	0.000	0.000	0.000
79	A	76	LYS	1	0.801	0.907	12.163	15.167	15.167	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.801	0.898	14.125	14.292	14.292	0.000	0.000	0.000	0.000
81	A	78	LEU	0	-0.028	-0.010	11.442	0.062	0.062	0.000	0.000	0.000	0.000
82	A	79	GLU	-1	-0.973	-0.992	8.953	-27.979	-27.979	0.000	0.000	0.000	0.000
83	A	80	GLU	-1	-0.902	-0.947	11.325	-16.272	-16.272	0.000	0.000	0.000	0.000
84	A	81	ILE	0	-0.131	-0.057	13.931	1.228	1.228	0.000	0.000	0.000	0.000
85	A	82	ASP	-2	-1.927	-1.943	8.507	-54.337	-54.337	0.000	0.000	0.000	0.000

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