FMO DATABASE

FMODB ID: J4789

Calculation Name: 1MZ8-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MZ8

Chain ID: B

ChEMBL ID:

UniProt ID: Q47112

Base Structure: X-ray

Registration Date: 2025-10-03

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1207641.067935
FMO2-HF: Nuclear repulsion	1155529.988894
FMO2-HF: Total energy	-52111.079041
FMO2-MP2: Total energy	-52265.563234

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:446:LYS)

Summations of interaction energy for fragment #1(A:446:LYS)

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.
147.777	147.939	22.875	-9.992	-13.046	0.032

Interaction energy analysis for fragmet #1(A:446:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.946 / q_NPA : 0.979

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	448	ASN	0	0.011	0.007	2.207	0.233	4.429	2.571	-2.517	-4.250	-0.010
4	A	449	LYS	1	0.916	0.958	1.903	35.713	30.763	17.332	-5.613	-6.770	0.055
5	A	450	PRO	0	0.066	0.049	4.631	-1.608	-1.516	-0.001	-0.017	-0.074	0.000
104	A	549	ILE	0	-0.033	-0.030	2.040	-5.758	-5.236	2.953	-1.749	-1.727	-0.012
110	A	555	VAL	0	-0.022	-0.022	3.378	0.009	0.311	0.020	-0.096	-0.225	-0.001
6	A	451	GLY	0	-0.008	-0.008	6.592	-3.988	-3.988	0.000	0.000	0.000	0.000
7	A	452	LYS	1	0.866	0.930	8.609	21.244	21.244	0.000	0.000	0.000	0.000
8	A	453	ALA	0	-0.029	-0.003	11.359	-1.483	-1.483	0.000	0.000	0.000	0.000
9	A	454	THR	0	0.002	-0.003	12.637	1.406	1.406	0.000	0.000	0.000	0.000
10	A	455	GLY	0	0.094	0.055	15.171	-0.269	-0.269	0.000	0.000	0.000	0.000
11	A	456	LYS	1	0.907	0.931	17.399	13.498	13.498	0.000	0.000	0.000	0.000
12	A	457	GLY	0	0.028	0.017	19.800	0.373	0.373	0.000	0.000	0.000	0.000
13	A	458	LYS	1	0.932	0.952	20.883	14.008	14.008	0.000	0.000	0.000	0.000
14	A	459	PRO	0	0.063	0.054	24.210	-0.142	-0.142	0.000	0.000	0.000	0.000
15	A	460	VAL	0	-0.057	-0.031	25.072	-0.077	-0.077	0.000	0.000	0.000	0.000
16	A	461	ASN	0	0.073	0.034	28.325	0.018	0.018	0.000	0.000	0.000	0.000
17	A	462	ASN	0	0.028	0.007	30.603	-0.365	-0.365	0.000	0.000	0.000	0.000
18	A	463	LYS	1	0.908	0.950	31.429	9.214	9.214	0.000	0.000	0.000	0.000
19	A	464	TRP	0	0.042	0.033	21.453	-0.083	-0.083	0.000	0.000	0.000	0.000
20	A	465	LEU	0	0.010	0.015	22.963	-0.358	-0.358	0.000	0.000	0.000	0.000
21	A	466	ASN	0	-0.034	-0.021	26.241	-0.174	-0.174	0.000	0.000	0.000	0.000
22	A	467	ASN	0	0.021	0.005	26.787	0.354	0.354	0.000	0.000	0.000	0.000
23	A	468	ALA	0	0.029	0.029	22.500	-0.304	-0.304	0.000	0.000	0.000	0.000
24	A	469	GLY	0	0.015	-0.001	22.539	-0.512	-0.512	0.000	0.000	0.000	0.000
25	A	470	LYS	1	0.844	0.912	24.663	11.181	11.181	0.000	0.000	0.000	0.000
26	A	471	ASP	-1	-0.796	-0.887	23.633	-12.035	-12.035	0.000	0.000	0.000	0.000
27	A	472	LEU	0	0.086	0.044	17.623	-0.399	-0.399	0.000	0.000	0.000	0.000
28	A	473	GLY	0	-0.017	0.015	19.230	-0.840	-0.840	0.000	0.000	0.000	0.000
29	A	474	SER	0	-0.064	-0.056	21.614	0.297	0.297	0.000	0.000	0.000	0.000
30	A	475	PRO	0	0.037	0.018	19.912	-0.787	-0.787	0.000	0.000	0.000	0.000
31	A	476	VAL	0	0.040	0.021	16.466	0.393	0.393	0.000	0.000	0.000	0.000
32	A	477	PRO	0	-0.017	-0.007	19.752	0.321	0.321	0.000	0.000	0.000	0.000
33	A	478	ASP	-1	-0.764	-0.874	22.334	-12.088	-12.088	0.000	0.000	0.000	0.000
34	A	479	ARG	1	0.803	0.868	23.848	10.565	10.565	0.000	0.000	0.000	0.000
35	A	480	ILE	0	-0.031	-0.017	20.060	0.084	0.084	0.000	0.000	0.000	0.000
36	A	481	ALA	0	0.069	0.017	19.308	-0.456	-0.456	0.000	0.000	0.000	0.000
37	A	482	ASN	0	0.001	-0.008	20.300	-0.725	-0.725	0.000	0.000	0.000	0.000
38	A	483	LYS	1	0.869	0.955	22.328	12.297	12.297	0.000	0.000	0.000	0.000
39	A	484	LEU	0	-0.046	-0.030	16.889	-0.158	-0.158	0.000	0.000	0.000	0.000
40	A	485	ARG	1	0.848	0.917	17.204	13.856	13.856	0.000	0.000	0.000	0.000
41	A	486	ASP	-1	-0.874	-0.936	16.399	-15.812	-15.812	0.000	0.000	0.000	0.000
42	A	487	LYS	1	0.891	0.967	16.491	14.838	14.838	0.000	0.000	0.000	0.000
43	A	488	GLU	-1	-0.842	-0.925	12.779	-20.118	-20.118	0.000	0.000	0.000	0.000
44	A	489	PHE	0	-0.009	0.002	10.992	1.464	1.464	0.000	0.000	0.000	0.000
45	A	490	LYS	1	0.968	0.959	10.068	17.744	17.744	0.000	0.000	0.000	0.000
46	A	491	SER	0	-0.009	-0.010	7.144	-2.876	-2.876	0.000	0.000	0.000	0.000
47	A	492	PHE	0	0.081	0.019	6.896	2.366	2.366	0.000	0.000	0.000	0.000
48	A	493	ASP	-1	-0.803	-0.883	8.640	-19.032	-19.032	0.000	0.000	0.000	0.000
49	A	494	ASP	-1	-0.891	-0.933	10.707	-20.061	-20.061	0.000	0.000	0.000	0.000
50	A	495	PHE	0	0.034	0.014	11.447	1.378	1.378	0.000	0.000	0.000	0.000
51	A	496	ARG	1	0.783	0.879	12.521	21.616	21.616	0.000	0.000	0.000	0.000
52	A	497	LYS	1	0.833	0.917	13.904	20.713	20.713	0.000	0.000	0.000	0.000
53	A	498	LYS	1	0.960	0.971	16.446	16.294	16.294	0.000	0.000	0.000	0.000
54	A	499	PHE	0	0.003	-0.004	16.544	1.027	1.027	0.000	0.000	0.000	0.000
55	A	500	TRP	0	0.028	-0.004	17.618	1.189	1.189	0.000	0.000	0.000	0.000
56	A	501	GLU	-1	-0.841	-0.925	20.095	-14.485	-14.485	0.000	0.000	0.000	0.000
57	A	502	GLU	-1	-0.825	-0.895	21.428	-12.706	-12.706	0.000	0.000	0.000	0.000
58	A	503	VAL	0	0.009	0.004	22.311	0.643	0.643	0.000	0.000	0.000	0.000
59	A	504	SER	0	-0.090	-0.061	24.765	0.638	0.638	0.000	0.000	0.000	0.000
60	A	505	LYS	1	0.814	0.898	24.402	13.120	13.120	0.000	0.000	0.000	0.000
61	A	506	ASP	-1	-0.761	-0.850	27.063	-10.720	-10.720	0.000	0.000	0.000	0.000
62	A	507	PRO	0	0.037	0.017	29.001	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	508	GLU	-1	-0.909	-0.949	31.383	-9.007	-9.007	0.000	0.000	0.000	0.000
64	A	509	LEU	0	-0.083	-0.029	25.156	-0.099	-0.099	0.000	0.000	0.000	0.000
65	A	510	SER	0	0.034	0.012	29.089	0.166	0.166	0.000	0.000	0.000	0.000
66	A	511	LYS	1	0.968	0.991	30.189	8.521	8.521	0.000	0.000	0.000	0.000
67	A	512	GLN	0	-0.081	-0.045	29.854	0.170	0.170	0.000	0.000	0.000	0.000
68	A	513	PHE	0	-0.029	-0.013	25.642	-0.178	-0.178	0.000	0.000	0.000	0.000
69	A	514	SER	0	0.037	0.015	30.801	0.159	0.159	0.000	0.000	0.000	0.000
70	A	515	ARG	1	1.024	1.001	31.205	7.868	7.868	0.000	0.000	0.000	0.000
71	A	516	ASN	0	0.092	0.043	30.599	-0.108	-0.108	0.000	0.000	0.000	0.000
72	A	517	ASN	0	0.002	0.004	27.068	-0.541	-0.541	0.000	0.000	0.000	0.000
73	A	518	ASN	0	-0.021	-0.023	26.522	-0.726	-0.726	0.000	0.000	0.000	0.000
74	A	519	ASP	-1	-0.866	-0.929	27.303	-10.246	-10.246	0.000	0.000	0.000	0.000
75	A	520	ARG	1	0.755	0.873	21.830	12.526	12.526	0.000	0.000	0.000	0.000
76	A	521	MET	0	-0.035	0.000	22.712	-0.634	-0.634	0.000	0.000	0.000	0.000
77	A	522	LYS	1	0.981	0.993	23.034	10.683	10.683	0.000	0.000	0.000	0.000
78	A	523	VAL	0	-0.026	-0.008	22.849	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	524	GLY	0	0.070	0.056	19.252	-0.481	-0.481	0.000	0.000	0.000	0.000
80	A	525	LYS	1	0.868	0.931	18.157	11.852	11.852	0.000	0.000	0.000	0.000
81	A	526	ALA	0	0.054	0.043	18.482	0.429	0.429	0.000	0.000	0.000	0.000
82	A	527	PRO	0	0.039	0.035	20.380	0.474	0.474	0.000	0.000	0.000	0.000
83	A	528	LYS	1	0.877	0.940	22.964	11.450	11.450	0.000	0.000	0.000	0.000
84	A	529	THR	0	-0.004	0.003	23.267	0.040	0.040	0.000	0.000	0.000	0.000
85	A	530	ARG	1	0.965	0.988	26.046	9.847	9.847	0.000	0.000	0.000	0.000
86	A	531	THR	0	0.052	0.003	28.157	-0.397	-0.397	0.000	0.000	0.000	0.000
87	A	532	GLN	0	0.000	0.005	29.391	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	533	ASP	-1	-0.868	-0.941	25.300	-11.215	-11.215	0.000	0.000	0.000	0.000
89	A	534	VAL	0	-0.055	-0.024	24.242	-0.643	-0.643	0.000	0.000	0.000	0.000
90	A	535	SER	0	0.004	0.008	21.306	0.315	0.315	0.000	0.000	0.000	0.000
91	A	536	GLY	0	0.061	0.026	22.217	-0.490	-0.490	0.000	0.000	0.000	0.000
92	A	537	LYS	1	0.993	0.983	19.685	13.939	13.939	0.000	0.000	0.000	0.000
93	A	538	ARG	1	0.810	0.884	15.469	17.375	17.375	0.000	0.000	0.000	0.000
94	A	539	THR	0	0.037	0.011	20.494	0.412	0.412	0.000	0.000	0.000	0.000
95	A	540	SER	0	-0.026	-0.042	19.767	0.577	0.577	0.000	0.000	0.000	0.000
96	A	541	PHE	0	0.019	0.007	20.247	-0.286	-0.286	0.000	0.000	0.000	0.000
97	A	542	GLU	-1	-0.786	-0.851	15.300	-18.052	-18.052	0.000	0.000	0.000	0.000
98	A	543	LEU	0	-0.036	-0.015	13.092	0.409	0.409	0.000	0.000	0.000	0.000
99	A	544	HIS	0	0.036	0.021	12.591	-2.041	-2.041	0.000	0.000	0.000	0.000
100	A	545	HIS	0	-0.072	-0.047	7.800	-1.614	-1.614	0.000	0.000	0.000	0.000
101	A	546	GLU	-1	-0.936	-0.957	11.315	-17.011	-17.011	0.000	0.000	0.000	0.000
102	A	547	LYS	1	0.913	0.954	11.050	24.589	24.589	0.000	0.000	0.000	0.000
103	A	548	PRO	0	0.067	0.026	8.588	-2.649	-2.649	0.000	0.000	0.000	0.000
105	A	550	SER	0	-0.035	-0.024	5.427	-2.955	-2.955	0.000	0.000	0.000	0.000
106	A	551	GLN	0	0.056	0.037	6.550	2.408	2.408	0.000	0.000	0.000	0.000
107	A	552	ASN	0	0.029	0.011	7.945	3.972	3.972	0.000	0.000	0.000	0.000
108	A	553	GLY	0	0.010	0.034	7.619	2.772	2.772	0.000	0.000	0.000	0.000
109	A	554	GLY	0	0.038	0.005	6.430	-5.257	-5.257	0.000	0.000	0.000	0.000
111	A	556	TYR	0	-0.002	-0.023	6.170	3.110	3.110	0.000	0.000	0.000	0.000
112	A	557	ASP	-1	-0.833	-0.904	9.941	-19.706	-19.706	0.000	0.000	0.000	0.000
113	A	558	MET	0	-0.079	-0.044	12.122	0.170	0.170	0.000	0.000	0.000	0.000
114	A	559	ASP	-1	-0.808	-0.883	15.169	-15.048	-15.048	0.000	0.000	0.000	0.000
115	A	560	ASN	0	-0.034	0.000	9.910	1.623	1.623	0.000	0.000	0.000	0.000
116	A	561	ILE	0	-0.052	-0.016	10.851	-1.010	-1.010	0.000	0.000	0.000	0.000
117	A	562	SER	0	-0.015	-0.017	14.139	0.882	0.882	0.000	0.000	0.000	0.000
118	A	563	VAL	0	-0.038	-0.024	16.268	-0.880	-0.880	0.000	0.000	0.000	0.000
119	A	564	VAL	0	0.040	0.021	16.847	0.917	0.917	0.000	0.000	0.000	0.000
120	A	565	THR	0	0.007	-0.002	19.685	-0.216	-0.216	0.000	0.000	0.000	0.000
121	A	566	PRO	0	-0.033	-0.014	18.894	-0.339	-0.339	0.000	0.000	0.000	0.000
122	A	567	LYS	1	0.930	0.973	19.687	11.163	11.163	0.000	0.000	0.000	0.000
123	A	568	ARG	1	0.765	0.855	20.990	13.266	13.266	0.000	0.000	0.000	0.000
124	A	569	HIS	0	-0.008	-0.022	12.862	-1.069	-1.069	0.000	0.000	0.000	0.000
125	A	570	ILE	0	-0.028	-0.021	16.874	-0.655	-0.655	0.000	0.000	0.000	0.000
126	A	571	ASP	-1	-0.838	-0.910	18.532	-12.429	-12.429	0.000	0.000	0.000	0.000
127	A	572	ILE	0	0.004	0.012	16.123	0.043	0.043	0.000	0.000	0.000	0.000
128	A	573	HIS	0	-0.064	-0.037	11.683	-0.109	-0.109	0.000	0.000	0.000	0.000
129	A	574	ARG	1	0.805	0.904	16.045	12.516	12.516	0.000	0.000	0.000	0.000
130	A	575	GLY	0	0.010	0.021	19.177	0.545	0.545	0.000	0.000	0.000	0.000
131	A	576	LYS	0	0.105	0.092	20.980	-0.931	-0.931	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:446:LYS)