FMO DATABASE

FMODB ID: 5RYVZ

Calculation Name: 2H5F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | potassium ion

Ligand 3-letter code: PO4 | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2H5F

Chain ID: A

ChEMBL ID:

UniProt ID: Q06ZW0

Base Structure: X-ray

Registration Date: 2025-09-02

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	70
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-442411.519011
FMO2-HF: Nuclear repulsion	410077.856535
FMO2-HF: Total energy	-32333.662476
FMO2-MP2: Total energy	-32416.807429

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:3:VAL)

Summations of interaction energy for fragment #1(A:3: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.
79.064	80.597	4.727	-2.262	-3.998	-0.003

Interaction energy analysis for fragmet #1(A:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.890 / q_NPA : 0.921

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	5	LEU	0	-0.011	0.014	2.115	2.158	3.557	4.728	-2.248	-3.880	-0.003
4	A	6	PRO	0	0.050	0.042	4.463	2.596	2.730	-0.001	-0.014	-0.118	0.000
5	A	7	HIS	0	-0.022	-0.042	6.094	1.734	1.734	0.000	0.000	0.000	0.000
6	A	8	GLY	0	0.070	0.041	9.231	0.567	0.567	0.000	0.000	0.000	0.000
7	A	9	PHE	0	-0.015	-0.015	11.824	-1.165	-1.165	0.000	0.000	0.000	0.000
8	A	10	CYS	0	0.042	0.023	14.354	0.196	0.196	0.000	0.000	0.000	0.000
9	A	11	ILE	0	0.021	0.025	17.662	-0.344	-0.344	0.000	0.000	0.000	0.000
10	A	12	GLN	0	-0.071	-0.047	14.118	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	13	CYS	0	-0.067	-0.032	19.805	-0.175	-0.175	0.000	0.000	0.000	0.000
12	A	14	ASN	0	0.058	0.026	23.231	0.297	0.297	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.881	0.950	26.492	9.028	9.028	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.946	0.966	29.413	8.519	8.519	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.005	0.015	26.975	0.041	0.041	0.000	0.000	0.000	0.000
16	A	18	TRP	0	0.017	0.002	29.413	0.013	0.013	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.003	-0.002	23.768	-0.249	-0.249	0.000	0.000	0.000	0.000
18	A	20	ASN	0	0.056	0.012	24.511	0.338	0.338	0.000	0.000	0.000	0.000
19	A	22	SER	0	0.045	0.031	25.283	0.083	0.083	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.040	-0.007	20.719	-0.067	-0.067	0.000	0.000	0.000	0.000
21	A	24	GLY	0	0.010	0.007	18.623	0.001	0.001	0.000	0.000	0.000	0.000
22	A	25	HIS	0	-0.005	-0.011	14.998	-0.887	-0.887	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.965	0.980	7.547	25.505	25.505	0.000	0.000	0.000	0.000
24	A	27	CYS	0	-0.055	0.014	11.576	0.773	0.773	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.066	0.027	9.563	-1.987	-1.987	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.010	-0.012	5.542	0.310	0.310	0.000	0.000	0.000	0.000
27	A	30	TYR	0	0.010	-0.027	6.828	1.846	1.846	0.000	0.000	0.000	0.000
28	A	31	HIS	0	-0.047	-0.019	10.622	2.276	2.276	0.000	0.000	0.000	0.000
29	A	32	MET	0	0.007	0.012	11.329	-0.729	-0.729	0.000	0.000	0.000	0.000
30	A	33	THR	0	-0.017	0.009	14.406	0.917	0.917	0.000	0.000	0.000	0.000
31	A	35	TYR	0	-0.006	-0.012	19.329	0.408	0.408	0.000	0.000	0.000	0.000
32	A	36	THR	0	0.024	0.010	22.593	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	37	LEU	0	-0.032	-0.009	25.758	0.125	0.125	0.000	0.000	0.000	0.000
34	A	38	TYR	0	-0.039	-0.041	27.931	0.205	0.205	0.000	0.000	0.000	0.000
35	A	39	LYS	1	0.855	0.905	30.527	9.344	9.344	0.000	0.000	0.000	0.000
36	A	40	PRO	0	0.054	0.029	34.363	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	41	ASP	-1	-0.868	-0.907	36.992	-7.851	-7.851	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.920	-0.956	39.302	-7.078	-7.078	0.000	0.000	0.000	0.000
39	A	43	ASN	0	-0.053	-0.036	43.066	0.079	0.079	0.000	0.000	0.000	0.000
40	A	44	GLY	0	0.026	0.023	42.317	0.107	0.107	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.870	-0.913	40.883	-7.460	-7.460	0.000	0.000	0.000	0.000
42	A	46	MET	0	-0.095	-0.042	35.383	-0.286	-0.286	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.854	0.901	34.922	8.161	8.161	0.000	0.000	0.000	0.000
44	A	48	TRP	0	0.013	-0.004	27.227	-0.204	-0.204	0.000	0.000	0.000	0.000
45	A	49	ALA	0	0.003	-0.012	30.090	0.167	0.167	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.010	-0.001	23.928	-0.097	-0.097	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.848	0.928	23.018	11.023	11.023	0.000	0.000	0.000	0.000
48	A	52	GLY	0	0.060	0.033	19.513	-0.152	-0.152	0.000	0.000	0.000	0.000
49	A	54	ALA	0	0.035	0.015	16.741	0.230	0.230	0.000	0.000	0.000	0.000
50	A	55	ARG	1	0.905	0.963	10.852	21.357	21.357	0.000	0.000	0.000	0.000
51	A	56	MET	0	0.016	0.008	15.913	-0.197	-0.197	0.000	0.000	0.000	0.000
52	A	57	CYS	0	-0.005	-0.010	19.691	-0.183	-0.183	0.000	0.000	0.000	0.000
53	A	58	PRO	0	0.015	0.004	21.520	0.279	0.279	0.000	0.000	0.000	0.000
54	A	59	THR	0	0.000	0.003	23.938	0.338	0.338	0.000	0.000	0.000	0.000
55	A	60	ALA	0	-0.022	-0.003	27.332	0.008	0.008	0.000	0.000	0.000	0.000
56	A	61	LYS	1	0.991	1.006	30.136	9.063	9.063	0.000	0.000	0.000	0.000
57	A	62	SER	0	0.055	0.004	32.719	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	63	GLY	0	0.015	0.018	36.443	0.021	0.021	0.000	0.000	0.000	0.000
59	A	64	GLU	-1	-0.847	-0.925	31.229	-9.382	-9.382	0.000	0.000	0.000	0.000
60	A	65	ARG	1	0.965	0.977	31.954	8.828	8.828	0.000	0.000	0.000	0.000
61	A	66	VAL	0	0.018	0.006	25.487	-0.138	-0.138	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.948	0.982	27.348	9.846	9.846	0.000	0.000	0.000	0.000
63	A	69	CYS	0	-0.027	0.020	20.071	0.794	0.794	0.000	0.000	0.000	0.000
64	A	70	THR	0	0.045	0.017	17.420	-0.415	-0.415	0.000	0.000	0.000	0.000
65	A	71	GLY	0	0.051	0.017	18.252	0.457	0.457	0.000	0.000	0.000	0.000
66	A	72	ALA	0	-0.030	-0.013	16.766	-0.056	-0.056	0.000	0.000	0.000	0.000
67	A	73	SER	0	-0.001	-0.022	17.916	0.505	0.505	0.000	0.000	0.000	0.000
68	A	75	ASN	0	0.026	0.012	20.836	0.122	0.122	0.000	0.000	0.000	0.000
69	A	76	SER	0	0.012	-0.029	23.605	0.003	0.003	0.000	0.000	0.000	0.000
70	A	77	ASP	-2	-1.880	-1.899	25.150	-20.427	-20.427	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:VAL)