FMO DATABASE

FMODB ID: JYR59

Calculation Name: 4XUW-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XUW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ATH2

Base Structure: X-ray

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-579579.883449
FMO2-HF: Nuclear repulsion	544762.706989
FMO2-HF: Total energy	-34817.17646
FMO2-MP2: Total energy	-34912.957273

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:24:SER)

Summations of interaction energy for fragment #1(A:24:SER)

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.
55.595	54.453	20.503	-11.092	-8.269	-0.098

Interaction energy analysis for fragmet #1(A:24:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.895

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	26	THR	0	0.042	0.005	2.966	-1.247	1.100	0.228	-1.157	-1.419	-0.005
4	A	27	CYS	0	0.008	0.016	5.084	4.737	4.758	-0.002	-0.001	-0.018	0.000
37	A	61	ALA	0	-0.024	0.003	3.189	-2.885	-2.596	0.051	-0.117	-0.222	-0.001
38	A	62	SER	0	-0.096	-0.075	2.498	-26.043	-23.112	1.228	-2.107	-2.052	-0.024
39	A	63	ARG	1	0.987	0.997	4.397	52.714	52.783	-0.001	-0.013	-0.055	0.000
40	A	64	THR	0	-0.036	-0.044	4.468	8.869	8.908	-0.001	-0.005	-0.033	0.000
43	A	67	ASP	-1	-0.807	-0.837	1.615	-102.522	-109.517	19.002	-7.664	-4.344	-0.068
44	A	68	ARG	1	0.823	0.871	3.960	32.855	32.981	-0.001	-0.022	-0.102	0.000
46	A	70	SER	0	-0.016	-0.017	4.419	3.324	3.355	-0.001	-0.006	-0.024	0.000
5	A	28	PRO	0	0.075	0.020	7.912	1.446	1.446	0.000	0.000	0.000	0.000
6	A	29	GLN	0	0.085	0.065	6.474	-2.171	-2.171	0.000	0.000	0.000	0.000
7	A	30	ILE	0	0.004	0.012	5.387	1.699	1.699	0.000	0.000	0.000	0.000
8	A	31	LYS	1	0.974	0.977	9.322	22.883	22.883	0.000	0.000	0.000	0.000
9	A	32	GLY	0	0.019	0.027	12.295	1.640	1.640	0.000	0.000	0.000	0.000
10	A	33	ASN	0	-0.053	-0.046	9.874	2.496	2.496	0.000	0.000	0.000	0.000
11	A	34	LEU	0	0.032	0.003	11.956	1.072	1.072	0.000	0.000	0.000	0.000
12	A	35	THR	0	-0.004	0.007	14.960	1.520	1.520	0.000	0.000	0.000	0.000
13	A	36	PRO	0	-0.032	-0.024	16.673	1.020	1.020	0.000	0.000	0.000	0.000
14	A	37	CYS	0	-0.046	0.008	16.827	-0.804	-0.804	0.000	0.000	0.000	0.000
15	A	38	VAL	0	0.017	0.014	19.627	0.617	0.617	0.000	0.000	0.000	0.000
16	A	39	LEU	0	0.012	0.009	21.694	0.414	0.414	0.000	0.000	0.000	0.000
17	A	40	TYR	0	0.069	0.029	21.874	0.383	0.383	0.000	0.000	0.000	0.000
18	A	41	LEU	0	-0.007	-0.018	18.119	0.192	0.192	0.000	0.000	0.000	0.000
19	A	42	LYS	1	0.892	0.976	22.811	11.768	11.768	0.000	0.000	0.000	0.000
20	A	43	ASN	0	0.029	0.001	26.262	0.228	0.228	0.000	0.000	0.000	0.000
21	A	44	GLY	0	-0.002	0.012	26.698	0.343	0.343	0.000	0.000	0.000	0.000
22	A	45	GLY	0	0.002	-0.003	27.706	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	46	VAL	0	0.003	-0.005	26.775	-0.206	-0.206	0.000	0.000	0.000	0.000
24	A	47	LEU	0	0.023	0.010	20.317	-0.257	-0.257	0.000	0.000	0.000	0.000
25	A	48	PRO	0	-0.004	-0.003	21.535	0.031	0.031	0.000	0.000	0.000	0.000
26	A	49	PRO	0	0.079	0.025	20.758	-0.793	-0.793	0.000	0.000	0.000	0.000
27	A	50	SER	0	0.003	0.005	18.531	-0.794	-0.794	0.000	0.000	0.000	0.000
28	A	52	CYS	0	-0.006	0.007	15.858	-0.617	-0.617	0.000	0.000	0.000	0.000
29	A	53	LYS	1	0.951	0.976	14.679	17.503	17.503	0.000	0.000	0.000	0.000
30	A	54	GLY	0	0.034	0.025	12.501	-1.685	-1.685	0.000	0.000	0.000	0.000
31	A	55	VAL	0	0.007	-0.024	11.066	-2.471	-2.471	0.000	0.000	0.000	0.000
32	A	56	ARG	1	0.885	0.930	10.946	20.108	20.108	0.000	0.000	0.000	0.000
33	A	57	ALA	0	-0.015	0.004	9.268	-2.131	-2.131	0.000	0.000	0.000	0.000
34	A	58	VAL	0	-0.022	-0.020	6.479	-5.319	-5.319	0.000	0.000	0.000	0.000
35	A	59	ASN	0	-0.031	-0.008	6.069	-4.448	-4.448	0.000	0.000	0.000	0.000
36	A	60	ASP	-1	-0.788	-0.879	7.270	-28.989	-28.989	0.000	0.000	0.000	0.000
41	A	65	THR	0	0.052	-0.003	6.899	-2.227	-2.227	0.000	0.000	0.000	0.000
42	A	66	SER	0	0.047	0.020	5.703	1.178	1.178	0.000	0.000	0.000	0.000
45	A	69	GLN	0	-0.039	-0.019	7.168	2.252	2.252	0.000	0.000	0.000	0.000
47	A	71	ALA	0	0.003	-0.003	5.244	2.558	2.558	0.000	0.000	0.000	0.000
48	A	72	CYS	0	-0.042	-0.021	6.689	4.095	4.095	0.000	0.000	0.000	0.000
49	A	73	ASN	0	0.035	-0.010	9.753	3.658	3.658	0.000	0.000	0.000	0.000
50	A	75	LEU	0	0.006	0.006	10.077	1.920	1.920	0.000	0.000	0.000	0.000
51	A	76	LYS	1	0.850	0.945	12.247	19.708	19.708	0.000	0.000	0.000	0.000
52	A	77	ASP	-1	-0.806	-0.913	13.629	-17.004	-17.004	0.000	0.000	0.000	0.000
53	A	78	THR	0	-0.090	-0.064	13.027	0.518	0.518	0.000	0.000	0.000	0.000
54	A	79	ALA	0	-0.044	-0.028	15.656	0.996	0.996	0.000	0.000	0.000	0.000
55	A	80	LYS	1	0.826	0.906	17.403	16.822	16.822	0.000	0.000	0.000	0.000
56	A	81	GLY	0	0.017	0.028	18.959	0.612	0.612	0.000	0.000	0.000	0.000
57	A	82	ILE	0	-0.067	-0.024	18.502	0.505	0.505	0.000	0.000	0.000	0.000
58	A	83	ALA	0	0.038	0.014	21.972	0.237	0.237	0.000	0.000	0.000	0.000
59	A	84	GLY	0	0.025	0.005	25.494	0.211	0.211	0.000	0.000	0.000	0.000
60	A	85	LEU	0	-0.046	-0.014	19.836	0.003	0.003	0.000	0.000	0.000	0.000
61	A	86	ASN	0	0.061	0.031	24.232	0.009	0.009	0.000	0.000	0.000	0.000
62	A	87	PRO	0	0.037	0.007	22.826	-0.541	-0.541	0.000	0.000	0.000	0.000
63	A	88	ASN	0	0.003	-0.003	23.042	-0.390	-0.390	0.000	0.000	0.000	0.000
64	A	89	LEU	0	0.001	0.009	24.020	-0.324	-0.324	0.000	0.000	0.000	0.000
65	A	90	ALA	0	0.012	0.000	19.372	-0.561	-0.561	0.000	0.000	0.000	0.000
66	A	91	ALA	0	-0.029	-0.017	19.012	-0.907	-0.907	0.000	0.000	0.000	0.000
67	A	92	GLY	0	0.021	0.012	20.323	-0.368	-0.368	0.000	0.000	0.000	0.000
68	A	93	LEU	0	-0.030	-0.007	17.432	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	94	PRO	0	0.010	-0.010	15.061	0.008	0.008	0.000	0.000	0.000	0.000
70	A	95	GLY	0	0.059	0.042	16.963	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	96	LYS	1	0.932	0.962	19.960	12.507	12.507	0.000	0.000	0.000	0.000
72	A	98	GLY	0	0.023	0.024	18.165	-0.422	-0.422	0.000	0.000	0.000	0.000
73	A	99	VAL	0	-0.055	-0.023	12.782	-0.754	-0.754	0.000	0.000	0.000	0.000
74	A	100	ASN	0	-0.016	-0.018	15.058	1.483	1.483	0.000	0.000	0.000	0.000
75	A	101	ILE	0	0.037	0.030	10.741	-0.868	-0.868	0.000	0.000	0.000	0.000
76	A	102	PRO	0	-0.018	0.002	11.694	1.345	1.345	0.000	0.000	0.000	0.000
77	A	103	TYR	0	0.014	-0.012	9.739	-0.196	-0.196	0.000	0.000	0.000	0.000
78	A	104	LYS	1	0.890	0.943	15.397	15.988	15.988	0.000	0.000	0.000	0.000
79	A	105	ILE	0	0.021	0.022	14.246	-0.626	-0.626	0.000	0.000	0.000	0.000
80	A	106	SER	0	0.035	-0.012	16.488	1.243	1.243	0.000	0.000	0.000	0.000
81	A	107	PRO	0	0.046	0.017	17.526	-0.865	-0.865	0.000	0.000	0.000	0.000
82	A	108	SER	0	0.024	0.003	19.493	0.011	0.011	0.000	0.000	0.000	0.000
83	A	109	THR	0	-0.030	0.002	15.594	0.577	0.577	0.000	0.000	0.000	0.000
84	A	110	ASN	0	0.042	0.019	16.596	-1.275	-1.275	0.000	0.000	0.000	0.000
85	A	112	ASN	0	0.057	0.036	12.941	-1.993	-1.993	0.000	0.000	0.000	0.000
86	A	113	ASN	0	0.007	0.010	14.514	0.319	0.319	0.000	0.000	0.000	0.000
87	A	114	VAL	0	-0.010	0.008	11.533	0.550	0.550	0.000	0.000	0.000	0.000
88	A	115	LYS	0	0.165	0.148	12.358	-8.838	-8.838	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:SER)