FMO DATABASE

FMODB ID: Y7RG2

Calculation Name: 5VYC-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5VYC

Chain ID: A

ChEMBL ID:

UniProt ID: O43583

Base Structure: X-ray

Registration Date: 2025-10-06

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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-219228.350261
FMO2-HF: Nuclear repulsion	196803.547871
FMO2-HF: Total energy	-22424.80239
FMO2-MP2: Total energy	-22490.998399

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:VAL)

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

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.
155.513	157.818	0.015	-1.112	-1.208	-0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.873 / q_NPA : 0.923

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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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	GLY	0	0.087	0.064	3.337	0.671	2.976	0.015	-1.112	-1.208	-0.005
4	A	5	SER	0	-0.037	-0.013	5.063	6.433	6.433	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.009	0.001	5.961	-0.679	-0.679	0.000	0.000	0.000	0.000
6	A	7	ALA	0	0.020	0.012	7.677	2.262	2.262	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.935	0.976	9.969	26.262	26.262	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.069	0.029	12.110	-1.119	-1.119	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.023	0.006	14.328	0.915	0.915	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.973	0.984	16.923	15.912	15.912	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.021	0.008	18.857	0.427	0.427	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.902	0.947	21.733	13.121	13.121	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.030	0.004	23.162	-0.184	-0.184	0.000	0.000	0.000	0.000
14	A	15	GLN	0	0.040	0.026	23.908	0.297	0.297	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.037	0.003	25.992	0.270	0.270	0.000	0.000	0.000	0.000
16	A	17	PRO	0	0.053	0.022	27.911	0.088	0.088	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.951	0.989	30.240	9.727	9.727	0.000	0.000	0.000	0.000
18	A	19	VAL	0	0.011	0.007	32.008	0.272	0.272	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.013	0.006	34.500	-0.178	-0.178	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.915	0.938	36.346	8.240	8.240	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.077	0.056	39.614	-0.072	-0.072	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.928	-0.962	43.427	-6.866	-6.866	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.964	0.975	45.232	6.185	6.185	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.952	0.971	48.701	6.011	6.011	0.000	0.000	0.000	0.000
25	A	26	LYS	1	1.093	1.046	47.710	6.249	6.249	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.912	0.955	46.446	6.911	6.911	0.000	0.000	0.000	0.000
27	A	28	LYS	1	1.009	0.997	48.799	6.018	6.018	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.071	0.027	46.500	0.126	0.126	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.057	0.032	49.965	0.119	0.119	0.000	0.000	0.000	0.000
30	A	31	ARG	1	1.060	1.019	52.199	5.299	5.299	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.006	0.012	54.191	0.043	0.043	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.857	0.916	49.268	6.296	6.296	0.000	0.000	0.000	0.000
33	A	34	ARG	1	1.018	1.015	47.432	6.517	6.517	0.000	0.000	0.000	0.000
34	A	35	ARG	1	1.028	1.020	53.070	5.267	5.267	0.000	0.000	0.000	0.000
35	A	36	MET	0	-0.035	-0.017	52.798	0.006	0.006	0.000	0.000	0.000	0.000
36	A	37	GLN	0	-0.001	-0.004	48.183	0.037	0.037	0.000	0.000	0.000	0.000
37	A	38	TYR	0	0.028	0.021	52.692	-0.057	-0.057	0.000	0.000	0.000	0.000
38	A	39	ASN	0	0.023	-0.011	55.966	0.078	0.078	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.904	0.962	50.715	6.175	6.175	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.885	0.952	52.399	5.842	5.842	0.000	0.000	0.000	0.000
41	A	42	PHE	0	0.026	0.002	56.356	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.033	0.019	59.883	0.078	0.078	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.050	-0.008	56.509	0.090	0.090	0.000	0.000	0.000	0.000
44	A	45	VAL	0	0.077	0.039	60.839	0.026	0.026	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.030	-0.023	60.223	-0.094	-0.094	0.000	0.000	0.000	0.000
46	A	47	PRO	0	0.029	0.033	60.282	0.046	0.046	0.000	0.000	0.000	0.000
47	A	48	THR	0	0.037	0.026	58.869	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	49	PHE	0	0.003	-0.015	55.798	-0.067	-0.067	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.017	0.002	54.543	0.056	0.056	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.973	0.968	52.849	5.800	5.800	0.000	0.000	0.000	0.000
51	A	52	LYS	1	1.010	0.994	48.196	6.505	6.505	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.933	1.007	48.312	6.348	6.348	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.020	0.008	46.064	0.065	0.065	0.000	0.000	0.000	0.000
54	A	55	PRO	0	-0.028	-0.032	45.970	0.020	0.020	0.000	0.000	0.000	0.000
55	A	56	ASN	0	-0.033	-0.024	40.583	0.115	0.115	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.009	0.011	43.712	-0.131	-0.131	0.000	0.000	0.000	0.000
57	A	58	ASN	0	0.002	-0.012	42.348	0.082	0.082	0.000	0.000	0.000	0.000
58	A	59	SER	-1	-0.904	-0.937	46.045	-6.337	-6.337	0.000	0.000	0.000	0.000

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