FMO DATABASE

FMODB ID: 1V65Z

Calculation Name: 4V8P-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q245F2

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-778635.803082
FMO2-HF: Nuclear repulsion	738831.930145
FMO2-HF: Total energy	-39803.872938
FMO2-MP2: Total energy	-39922.680064

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:12:LYS)

Summations of interaction energy for fragment #1(A:12: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.
190.09	194.572	1.55	-2.509	-3.525	-0.022

Interaction energy analysis for fragmet #1(A:12:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.821 / 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

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	14	ASN	0	0.033	0.033	3.865	1.687	2.978	-0.016	-0.488	-0.788	0.000
59	A	70	THR	0	0.001	0.006	2.578	-4.575	-4.003	0.745	-0.400	-0.917	-0.004
60	A	71	ILE	0	0.007	-0.002	2.570	-25.709	-23.181	0.822	-1.594	-1.757	-0.018
61	A	72	PRO	0	-0.019	-0.005	3.996	3.843	3.934	-0.001	-0.027	-0.063	0.000
4	A	15	LEU	0	-0.006	-0.001	6.636	4.231	4.231	0.000	0.000	0.000	0.000
5	A	16	GLY	0	0.045	0.011	8.767	0.562	0.562	0.000	0.000	0.000	0.000
6	A	17	PHE	0	-0.068	-0.034	11.371	1.141	1.141	0.000	0.000	0.000	0.000
7	A	18	LYS	1	0.974	0.994	15.283	30.485	30.485	0.000	0.000	0.000	0.000
8	A	19	ILE	0	-0.014	-0.016	18.941	0.228	0.228	0.000	0.000	0.000	0.000
9	A	20	ASP	-1	-0.816	-0.911	21.884	-21.179	-21.179	0.000	0.000	0.000	0.000
10	A	21	CYS	0	-0.029	-0.028	25.185	0.234	0.234	0.000	0.000	0.000	0.000
11	A	22	SER	0	0.053	0.030	27.602	0.564	0.564	0.000	0.000	0.000	0.000
12	A	23	GLN	0	0.000	0.008	30.570	0.711	0.711	0.000	0.000	0.000	0.000
13	A	24	PRO	0	0.040	0.013	30.953	0.314	0.314	0.000	0.000	0.000	0.000
14	A	25	VAL	0	-0.031	-0.012	30.317	0.213	0.213	0.000	0.000	0.000	0.000
15	A	26	GLU	-1	-0.882	-0.933	33.462	-17.042	-17.042	0.000	0.000	0.000	0.000
16	A	27	ASP	-1	-0.812	-0.883	36.547	-15.334	-15.334	0.000	0.000	0.000	0.000
17	A	28	LYS	1	0.868	0.930	36.432	15.314	15.314	0.000	0.000	0.000	0.000
18	A	29	VAL	0	0.023	0.029	34.268	0.092	0.092	0.000	0.000	0.000	0.000
19	A	30	ILE	0	-0.083	-0.052	28.070	-0.346	-0.346	0.000	0.000	0.000	0.000
20	A	31	LEU	0	0.060	0.037	31.593	0.017	0.017	0.000	0.000	0.000	0.000
21	A	32	ILE	0	0.005	-0.007	25.853	-0.561	-0.561	0.000	0.000	0.000	0.000
22	A	33	GLY	0	0.032	0.013	26.426	-0.838	-0.838	0.000	0.000	0.000	0.000
23	A	34	GLU	-1	-0.866	-0.932	26.875	-19.007	-19.007	0.000	0.000	0.000	0.000
24	A	35	PHE	0	-0.037	-0.026	22.422	-0.632	-0.632	0.000	0.000	0.000	0.000
25	A	36	ALA	0	0.010	0.000	22.489	-1.030	-1.030	0.000	0.000	0.000	0.000
26	A	37	GLU	-1	-0.763	-0.859	22.224	-24.672	-24.672	0.000	0.000	0.000	0.000
27	A	38	PHE	0	-0.050	-0.006	23.798	-0.341	-0.341	0.000	0.000	0.000	0.000
28	A	39	LEU	0	-0.039	-0.033	19.189	-0.703	-0.703	0.000	0.000	0.000	0.000
29	A	40	LYS	1	0.873	0.907	19.098	23.089	23.089	0.000	0.000	0.000	0.000
30	A	41	SER	0	-0.014	-0.008	19.993	-0.326	-0.326	0.000	0.000	0.000	0.000
31	A	42	LYS	1	0.863	0.922	20.993	24.547	24.547	0.000	0.000	0.000	0.000
32	A	43	ILE	0	0.003	0.014	14.393	-0.378	-0.378	0.000	0.000	0.000	0.000
33	A	44	LYS	1	0.914	0.961	15.732	28.216	28.216	0.000	0.000	0.000	0.000
34	A	45	VAL	0	0.037	0.026	10.882	-2.284	-2.284	0.000	0.000	0.000	0.000
35	A	46	GLY	0	0.020	0.011	12.885	1.438	1.438	0.000	0.000	0.000	0.000
36	A	47	GLY	0	-0.009	-0.003	14.425	1.630	1.630	0.000	0.000	0.000	0.000
37	A	48	LYS	1	0.937	0.969	16.734	34.923	34.923	0.000	0.000	0.000	0.000
38	A	49	LEU	0	-0.034	-0.032	17.469	-1.066	-1.066	0.000	0.000	0.000	0.000
39	A	50	GLY	0	0.086	0.053	19.573	0.218	0.218	0.000	0.000	0.000	0.000
40	A	51	ASN	0	-0.025	-0.016	13.582	0.935	0.935	0.000	0.000	0.000	0.000
41	A	52	LEU	0	0.007	0.008	14.325	-2.337	-2.337	0.000	0.000	0.000	0.000
42	A	53	GLY	0	0.015	0.005	12.983	-0.190	-0.190	0.000	0.000	0.000	0.000
43	A	54	GLU	-1	-0.840	-0.939	10.842	-42.582	-42.582	0.000	0.000	0.000	0.000
44	A	55	ASN	0	-0.084	-0.023	5.987	-0.878	-0.878	0.000	0.000	0.000	0.000
45	A	56	ILE	0	-0.043	-0.009	8.100	-3.138	-3.138	0.000	0.000	0.000	0.000
46	A	57	THR	0	0.032	0.014	10.744	1.649	1.649	0.000	0.000	0.000	0.000
47	A	58	ILE	0	-0.026	-0.012	13.751	-0.432	-0.432	0.000	0.000	0.000	0.000
48	A	59	SER	0	-0.012	-0.002	17.011	0.545	0.545	0.000	0.000	0.000	0.000
49	A	60	ASN	0	-0.013	-0.031	19.630	-0.520	-0.520	0.000	0.000	0.000	0.000
50	A	61	ASP	-1	-0.804	-0.880	23.206	-22.834	-22.834	0.000	0.000	0.000	0.000
51	A	62	ASP	-1	-0.822	-0.902	25.821	-19.718	-19.718	0.000	0.000	0.000	0.000
52	A	63	LYS	1	0.852	0.916	28.297	18.795	18.795	0.000	0.000	0.000	0.000
53	A	64	LYS	1	0.837	0.897	23.386	23.079	23.079	0.000	0.000	0.000	0.000
54	A	65	ILE	0	0.018	0.021	19.564	-0.093	-0.093	0.000	0.000	0.000	0.000
55	A	66	ASN	0	-0.068	-0.049	15.913	-0.761	-0.761	0.000	0.000	0.000	0.000
56	A	67	VAL	0	0.016	0.018	12.986	0.128	0.128	0.000	0.000	0.000	0.000
57	A	68	GLN	0	0.058	0.041	10.882	1.593	1.593	0.000	0.000	0.000	0.000
58	A	69	SER	0	-0.035	-0.035	7.367	1.644	1.644	0.000	0.000	0.000	0.000
62	A	73	PHE	0	0.091	0.039	6.309	5.790	5.790	0.000	0.000	0.000	0.000
63	A	74	SER	0	0.006	-0.015	9.686	1.090	1.090	0.000	0.000	0.000	0.000
64	A	75	LYS	1	0.836	0.920	13.006	30.560	30.560	0.000	0.000	0.000	0.000
65	A	76	ARG	1	0.953	0.968	16.193	28.402	28.402	0.000	0.000	0.000	0.000
66	A	77	TYR	0	-0.027	-0.001	14.316	1.701	1.701	0.000	0.000	0.000	0.000
67	A	78	LEU	0	0.100	0.049	15.729	1.409	1.409	0.000	0.000	0.000	0.000
68	A	79	LYS	1	0.931	0.994	18.771	24.475	24.475	0.000	0.000	0.000	0.000
69	A	80	TYR	0	-0.045	-0.019	20.664	1.274	1.274	0.000	0.000	0.000	0.000
70	A	81	LEU	0	-0.005	-0.004	18.860	1.234	1.234	0.000	0.000	0.000	0.000
71	A	82	THR	0	0.042	0.001	22.295	0.904	0.904	0.000	0.000	0.000	0.000
72	A	83	LYS	1	0.917	0.964	24.557	22.981	22.981	0.000	0.000	0.000	0.000
73	A	84	LYS	1	0.942	0.973	25.697	21.970	21.970	0.000	0.000	0.000	0.000
74	A	85	TYR	0	0.040	0.026	26.286	0.441	0.441	0.000	0.000	0.000	0.000
75	A	86	LEU	0	0.036	0.004	28.147	0.521	0.521	0.000	0.000	0.000	0.000
76	A	87	LYS	1	0.922	0.963	30.269	17.102	17.102	0.000	0.000	0.000	0.000
77	A	88	LYS	1	0.905	0.944	28.841	20.237	20.237	0.000	0.000	0.000	0.000
78	A	89	GLN	0	0.027	0.020	31.012	0.735	0.735	0.000	0.000	0.000	0.000
79	A	90	ASP	-1	-0.905	-0.949	34.181	-15.348	-15.348	0.000	0.000	0.000	0.000
80	A	91	LEU	0	0.078	0.039	32.393	0.129	0.129	0.000	0.000	0.000	0.000
81	A	92	ARG	1	0.878	0.934	31.063	18.419	18.419	0.000	0.000	0.000	0.000
82	A	93	ASN	0	-0.051	-0.018	33.897	-0.228	-0.228	0.000	0.000	0.000	0.000
83	A	94	TYR	0	0.050	0.046	36.217	0.219	0.219	0.000	0.000	0.000	0.000
84	A	95	LEU	0	-0.004	0.004	31.707	-0.252	-0.252	0.000	0.000	0.000	0.000
85	A	96	TYR	0	-0.058	-0.032	30.722	-0.557	-0.557	0.000	0.000	0.000	0.000
86	A	97	VAL	0	-0.022	-0.014	24.163	-0.429	-0.429	0.000	0.000	0.000	0.000
87	A	98	THR	0	-0.004	-0.007	26.844	0.033	0.033	0.000	0.000	0.000	0.000
88	A	99	SER	0	-0.063	-0.042	22.345	-1.092	-1.092	0.000	0.000	0.000	0.000
89	A	100	SER	0	0.012	0.013	23.596	0.835	0.835	0.000	0.000	0.000	0.000
90	A	101	ASP	-1	-0.751	-0.842	21.103	-25.184	-25.184	0.000	0.000	0.000	0.000
91	A	102	LYS	1	0.971	0.972	14.621	36.008	36.008	0.000	0.000	0.000	0.000
92	A	103	ASN	0	0.007	-0.009	14.344	-0.473	-0.473	0.000	0.000	0.000	0.000
93	A	104	SER	0	0.010	-0.003	17.235	-0.473	-0.473	0.000	0.000	0.000	0.000
94	A	105	TYR	0	-0.070	-0.036	19.599	0.399	0.399	0.000	0.000	0.000	0.000
95	A	106	GLN	0	0.058	0.035	22.541	-0.105	-0.105	0.000	0.000	0.000	0.000
96	A	107	LEU	0	-0.028	-0.015	26.100	0.172	0.172	0.000	0.000	0.000	0.000
97	A	108	ARG	1	0.883	0.935	28.706	19.608	19.608	0.000	0.000	0.000	0.000
98	A	109	TYR	0	0.072	0.002	32.151	-0.347	-0.347	0.000	0.000	0.000	0.000
99	A	110	PHE	0	-0.112	-0.056	35.463	-0.259	-0.259	0.000	0.000	0.000	0.000
100	A	111	ASN	-1	-0.890	-0.921	37.937	-14.370	-14.370	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:LYS)