FMO DATABASE

FMODB ID: JY9G9

Calculation Name: 5VSO-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5VSO

Chain ID: A

ChEMBL ID:

UniProt ID: P25491

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-458765.389177
FMO2-HF: Nuclear repulsion	428968.4653
FMO2-HF: Total energy	-29796.923877
FMO2-MP2: Total energy	-29884.083865

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:1:GLY)

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

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.
-67.796	-63.316	1.153	-3.286	-2.346	-0.04

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.898

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].
3	A	3	PHE	0	0.009	-0.017	2.361	-29.423	-24.998	1.154	-3.282	-2.297	-0.040
4	A	4	GLY	0	0.036	0.023	5.172	5.075	5.130	-0.001	-0.004	-0.049	0.000
5	A	5	SER	0	-0.048	-0.035	8.592	-0.082	-0.082	0.000	0.000	0.000	0.000
6	A	6	MET	0	0.004	-0.001	12.010	-0.631	-0.631	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.043	0.041	13.306	0.216	0.216	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.780	0.883	13.652	17.494	17.494	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.774	-0.882	15.298	-14.663	-14.663	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.013	-0.001	16.845	-0.800	-0.800	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.942	0.965	10.495	27.791	27.791	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.016	0.001	15.837	-0.223	-0.223	0.000	0.000	0.000	0.000
13	A	13	TYR	0	0.005	0.006	18.088	0.435	0.435	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.858	-0.937	16.809	-17.069	-17.069	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.081	-0.037	13.798	0.314	0.314	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.032	-0.018	17.707	0.516	0.516	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.023	-0.016	20.961	0.705	0.705	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.073	-0.039	22.540	0.867	0.867	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.049	0.024	23.458	-0.563	-0.563	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.102	0.038	22.424	0.110	0.110	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.032	-0.021	24.864	0.093	0.093	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.059	-0.004	27.042	0.435	0.435	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.036	-0.017	28.893	0.095	0.095	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.803	-0.920	30.527	-10.202	-10.202	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.039	-0.017	31.403	-0.123	-0.123	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.862	-0.917	29.111	-10.489	-10.489	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.065	0.036	26.008	-0.292	-0.292	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.842	0.912	27.474	9.855	9.855	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.937	0.965	29.335	9.675	9.675	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.022	0.000	25.057	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.095	0.055	24.193	-0.137	-0.137	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.884	0.940	25.868	10.028	10.028	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.828	0.924	24.565	12.459	12.459	0.000	0.000	0.000	0.000
34	A	34	CYS	0	-0.031	0.002	21.679	-0.257	-0.257	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.037	0.015	23.282	-0.283	-0.283	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.031	-0.034	25.041	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.887	0.950	24.394	12.905	12.905	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.003	-0.002	20.551	-0.046	-0.046	0.000	0.000	0.000	0.000
39	A	39	HIS	1	0.917	0.976	22.069	11.263	11.263	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.086	0.035	22.284	0.307	0.307	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.864	-0.913	24.019	-10.817	-10.817	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.770	0.855	26.798	10.855	10.855	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.044	0.001	22.861	0.345	0.345	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.052	0.016	22.689	-0.454	-0.454	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.002	0.004	18.355	0.008	0.008	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.883	-0.937	13.381	-21.750	-21.750	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.859	-0.927	13.052	-21.216	-21.216	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.122	-0.057	15.280	0.337	0.337	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.011	-0.005	18.126	0.501	0.501	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.856	-0.926	11.276	-25.435	-25.435	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.933	0.968	15.557	17.829	17.829	0.000	0.000	0.000	0.000
52	A	52	PHE	0	-0.073	-0.028	17.356	0.873	0.873	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.931	0.976	16.912	15.804	15.804	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.805	-0.903	13.650	-20.449	-20.449	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.020	-0.010	17.084	0.541	0.541	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.116	-0.082	20.447	0.795	0.795	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.064	0.030	18.153	0.545	0.545	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.026	0.010	19.366	0.293	0.293	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.028	-0.023	20.852	0.897	0.897	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.984	-0.998	22.722	-13.269	-13.269	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.010	0.007	20.304	0.342	0.342	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.011	-0.009	21.825	0.446	0.446	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.078	-0.053	25.547	0.552	0.552	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.868	-0.904	28.333	-9.895	-9.895	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.001	0.004	29.181	-0.325	-0.325	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.880	-0.935	30.131	-9.758	-9.758	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.899	0.949	26.218	11.311	11.311	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.728	0.857	25.636	11.047	11.047	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.795	-0.885	25.776	-11.101	-11.101	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.046	-0.021	25.036	-0.264	-0.264	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.060	-0.064	17.359	-0.476	-0.476	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.863	-0.926	22.230	-12.905	-12.905	0.000	0.000	0.000	0.000
73	A	73	GLN	0	-0.035	-0.009	24.154	0.077	0.077	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.096	-0.054	22.820	0.148	0.148	0.000	0.000	0.000	0.000
75	A	75	GLY	-1	-0.813	-0.882	17.876	-18.527	-18.527	0.000	0.000	0.000	0.000

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