FMO DATABASE

FMODB ID: L6ZG9

Calculation Name: 3F3B-A-Xray549

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3F3B

Chain ID: A

ChEMBL ID:

UniProt ID: P54328

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-937558.719374
FMO2-HF: Nuclear repulsion	890215.225826
FMO2-HF: Total energy	-47343.493549
FMO2-MP2: Total energy	-47482.842315

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:4:ARG)

Summations of interaction energy for fragment #1(A:4:ARG)

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.
-56.203	-52.389	0.666	-1.905	-2.575	-0.019

Interaction energy analysis for fragmet #1(A:4:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.832 / q_NPA : 1.907

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	6	MET	0	-0.018	-0.015	2.677	-16.793	-13.068	0.667	-1.894	-2.498	-0.019
50	A	53	THR	0	-0.056	-0.023	4.430	-9.796	-9.707	-0.001	-0.011	-0.077	0.000
4	A	7	LEU	0	0.010	0.014	5.499	6.260	6.260	0.000	0.000	0.000	0.000
5	A	8	ILE	0	-0.035	-0.017	8.298	-0.478	-0.478	0.000	0.000	0.000	0.000
6	A	9	HIS	0	0.013	0.014	9.071	3.645	3.645	0.000	0.000	0.000	0.000
7	A	10	ARG	1	0.863	0.929	13.594	32.064	32.064	0.000	0.000	0.000	0.000
8	A	11	CYS	0	-0.068	-0.028	17.362	-0.299	-0.299	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.797	-0.890	19.265	-24.666	-24.666	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.032	-0.028	20.155	-0.521	-0.521	0.000	0.000	0.000	0.000
11	A	14	TYR	0	-0.002	0.005	23.630	1.010	1.010	0.000	0.000	0.000	0.000
12	A	15	HIS	1	0.746	0.835	24.697	22.859	22.859	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.864	-0.939	28.185	-19.540	-19.540	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.026	-0.018	30.445	0.089	0.089	0.000	0.000	0.000	0.000
15	A	18	ALA	0	-0.019	-0.015	34.018	0.174	0.174	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.016	-0.001	35.812	0.523	0.523	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.011	-0.008	39.719	0.250	0.250	0.000	0.000	0.000	0.000
18	A	21	PRO	0	-0.032	-0.025	43.409	0.065	0.065	0.000	0.000	0.000	0.000
19	A	22	SER	0	0.012	0.010	45.514	0.395	0.395	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.020	-0.001	46.852	-0.156	-0.156	0.000	0.000	0.000	0.000
21	A	24	GLY	0	0.058	0.033	47.321	0.051	0.051	0.000	0.000	0.000	0.000
22	A	25	ARG	1	0.933	0.947	46.918	13.113	13.113	0.000	0.000	0.000	0.000
23	A	26	PHE	0	-0.010	-0.016	50.668	0.065	0.065	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.046	0.038	52.401	0.188	0.188	0.000	0.000	0.000	0.000
25	A	28	ILE	0	-0.014	-0.001	50.529	0.161	0.161	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.024	-0.024	50.635	-0.241	-0.241	0.000	0.000	0.000	0.000
27	A	30	ALA	0	-0.005	0.007	45.815	-0.083	-0.083	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.835	-0.915	45.089	-13.451	-13.451	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.910	0.942	44.638	12.547	12.547	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.035	-0.014	41.821	-0.312	-0.312	0.000	0.000	0.000	0.000
31	A	34	GLN	0	-0.045	-0.017	38.227	-0.409	-0.409	0.000	0.000	0.000	0.000
32	A	35	PRO	0	0.010	0.008	39.515	0.196	0.196	0.000	0.000	0.000	0.000
33	A	36	VAL	0	0.012	0.007	38.757	-0.222	-0.222	0.000	0.000	0.000	0.000
34	A	37	ILE	0	-0.031	-0.011	33.107	0.045	0.045	0.000	0.000	0.000	0.000
35	A	38	SER	0	0.011	0.006	33.192	0.222	0.222	0.000	0.000	0.000	0.000
36	A	39	TYR	0	-0.007	-0.027	26.732	0.132	0.132	0.000	0.000	0.000	0.000
37	A	40	PRO	0	0.001	0.018	30.573	0.586	0.586	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.895	-0.956	31.769	-17.679	-17.679	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.061	-0.029	31.206	-0.168	-0.168	0.000	0.000	0.000	0.000
40	A	43	PRO	0	-0.049	-0.028	26.450	0.023	0.023	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.848	-0.915	27.796	-19.955	-19.955	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.859	-0.924	24.098	-25.036	-25.036	0.000	0.000	0.000	0.000
43	A	46	GLN	0	-0.020	-0.015	24.606	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.856	-0.932	21.362	-28.997	-28.997	0.000	0.000	0.000	0.000
45	A	48	VAL	0	0.018	0.012	18.707	-1.003	-1.003	0.000	0.000	0.000	0.000
46	A	49	PRO	0	-0.039	-0.014	15.820	-1.621	-1.621	0.000	0.000	0.000	0.000
47	A	50	CYS	0	-0.029	-0.013	13.697	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	51	TYR	0	-0.008	-0.019	6.759	-4.562	-4.562	0.000	0.000	0.000	0.000
49	A	52	PHE	0	0.039	0.016	8.189	1.183	1.183	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.920	-0.976	6.422	-46.629	-46.629	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.869	0.943	5.618	67.573	67.573	0.000	0.000	0.000	0.000
53	A	56	THR	0	0.027	0.032	8.677	-2.275	-2.275	0.000	0.000	0.000	0.000
54	A	57	GLN	0	-0.049	-0.032	9.963	1.429	1.429	0.000	0.000	0.000	0.000
55	A	58	GLN	0	0.024	0.012	12.880	0.077	0.077	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.031	0.023	16.555	-0.695	-0.695	0.000	0.000	0.000	0.000
57	A	60	ILE	0	-0.052	-0.039	19.118	0.355	0.355	0.000	0.000	0.000	0.000
58	A	61	GLN	0	-0.050	-0.025	21.941	1.214	1.214	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.896	-0.947	22.815	-23.136	-23.136	0.000	0.000	0.000	0.000
60	A	63	GLU	-1	-0.980	-0.967	25.244	-18.273	-18.273	0.000	0.000	0.000	0.000
61	A	64	PRO	0	-0.053	-0.029	24.707	0.572	0.572	0.000	0.000	0.000	0.000
62	A	65	ASP	-1	-0.830	-0.933	20.557	-24.533	-24.533	0.000	0.000	0.000	0.000
63	A	66	GLN	0	-0.066	-0.025	19.836	-0.670	-0.670	0.000	0.000	0.000	0.000
64	A	67	THR	0	-0.013	-0.004	13.898	-0.223	-0.223	0.000	0.000	0.000	0.000
65	A	68	VAL	0	0.020	0.016	15.341	-0.428	-0.428	0.000	0.000	0.000	0.000
66	A	69	TYR	0	0.015	-0.009	8.702	-4.595	-4.595	0.000	0.000	0.000	0.000
67	A	70	HIS	0	0.000	0.010	13.866	1.421	1.421	0.000	0.000	0.000	0.000
68	A	71	SER	0	0.038	0.010	14.032	0.891	0.891	0.000	0.000	0.000	0.000
69	A	72	PHE	0	0.001	-0.005	10.569	-3.932	-3.932	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.027	0.016	9.792	3.037	3.037	0.000	0.000	0.000	0.000
71	A	74	VAL	0	0.010	-0.003	10.007	-5.146	-5.146	0.000	0.000	0.000	0.000
72	A	75	HIS	1	0.801	0.904	8.344	56.600	56.600	0.000	0.000	0.000	0.000
73	A	76	PHE	0	0.097	0.032	12.256	-1.022	-1.022	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.036	0.008	15.394	-0.455	-0.455	0.000	0.000	0.000	0.000
75	A	78	LEU	0	0.000	-0.005	17.081	1.098	1.098	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.043	-0.022	19.366	0.646	0.646	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.018	0.026	20.052	0.908	0.908	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.830	-0.875	22.007	-22.552	-22.552	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.017	-0.006	18.989	-0.129	-0.129	0.000	0.000	0.000	0.000
80	A	83	ARG	1	0.822	0.870	22.192	21.929	21.929	0.000	0.000	0.000	0.000
81	A	84	VAL	0	-0.015	-0.014	22.442	-0.751	-0.751	0.000	0.000	0.000	0.000
82	A	85	ASN	0	-0.005	-0.009	23.783	0.629	0.629	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.729	-0.826	22.696	-23.788	-23.788	0.000	0.000	0.000	0.000
84	A	87	LYS	1	0.916	0.984	22.870	20.653	20.653	0.000	0.000	0.000	0.000
85	A	88	ILE	0	-0.018	-0.020	16.834	0.044	0.044	0.000	0.000	0.000	0.000
86	A	89	ILE	0	-0.012	-0.005	20.991	-0.056	-0.056	0.000	0.000	0.000	0.000
87	A	90	TRP	0	-0.014	-0.011	12.205	-1.121	-1.121	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.875	-0.950	14.904	-36.721	-36.721	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.028	-0.015	18.848	0.646	0.646	0.000	0.000	0.000	0.000
90	A	93	HIS	0	-0.050	-0.009	18.587	1.419	1.419	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.974	0.988	20.562	21.271	21.271	0.000	0.000	0.000	0.000
92	A	95	TYR	0	-0.007	-0.007	16.116	-0.963	-0.963	0.000	0.000	0.000	0.000
93	A	96	ILE	0	0.025	0.025	20.211	0.379	0.379	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.044	-0.020	17.918	-1.611	-1.611	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.916	0.969	19.710	25.801	25.801	0.000	0.000	0.000	0.000
96	A	99	LEU	0	0.025	0.007	18.448	0.985	0.985	0.000	0.000	0.000	0.000
97	A	100	PRO	0	0.010	-0.008	20.312	-0.311	-0.311	0.000	0.000	0.000	0.000
98	A	101	LYS	1	0.848	0.949	18.741	25.075	25.075	0.000	0.000	0.000	0.000
99	A	102	ARG	1	0.885	0.940	13.654	39.191	39.191	0.000	0.000	0.000	0.000
100	A	103	ILE	0	0.034	0.023	17.604	-1.228	-1.228	0.000	0.000	0.000	0.000
101	A	104	ARG	1	0.816	0.886	8.963	51.321	51.321	0.000	0.000	0.000	0.000
102	A	105	HIS	0	0.003	-0.002	8.470	2.033	2.033	0.000	0.000	0.000	0.000
103	A	106	HIS	0	0.028	0.022	12.541	-0.867	-0.867	0.000	0.000	0.000	0.000
104	A	107	HIS	0	0.013	0.017	9.811	-1.790	-1.790	0.000	0.000	0.000	0.000
105	A	108	TRP	0	0.049	0.016	14.917	1.009	1.009	0.000	0.000	0.000	0.000
106	A	109	GLU	-1	-0.838	-0.911	11.203	-50.713	-50.713	0.000	0.000	0.000	0.000
107	A	110	VAL	0	0.056	0.010	14.366	2.433	2.433	0.000	0.000	0.000	0.000
108	A	111	VAL	0	0.001	0.012	14.376	-2.109	-2.109	0.000	0.000	0.000	0.000
109	A	112	ALA	0	0.011	0.017	15.061	2.341	2.341	0.000	0.000	0.000	0.000
110	A	113	VAL	0	0.004	-0.017	16.093	-2.046	-2.046	0.000	0.000	0.000	0.000
111	A	114	ARG	1	0.907	0.970	18.413	26.660	26.660	0.000	0.000	0.000	0.000
112	A	115	ASP	-1	-0.876	-0.952	19.847	-22.479	-22.479	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.895	-0.953	23.526	-21.978	-21.978	0.000	0.000	0.000	0.000
114	A	117	SER	0	-0.147	-0.094	21.427	-0.483	-0.483	0.000	0.000	0.000	0.000
115	A	118	LEU	-1	-0.926	-0.942	22.988	-21.964	-21.964	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ARG)