FMO DATABASE

FMODB ID: Q5NNY

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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-490597.44058
FMO2-HF: Nuclear repulsion	460819.663313
FMO2-HF: Total energy	-29777.777267
FMO2-MP2: Total energy	-29866.802797

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
200.922	208.097	1.672	-3.833	-5.015	-0.031

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.902

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	4	GLU	-1	-0.827	-0.892	3.848	-29.267	-27.558	-0.018	-0.756	-0.935	-0.002
48	A	49	TYR	0	-0.007	-0.011	3.353	-5.450	-4.734	0.040	-0.173	-0.583	-0.001
49	A	50	LEU	0	0.013	0.016	2.423	5.323	6.837	0.723	-0.715	-1.522	-0.004
50	A	51	TYR	0	0.033	0.008	2.736	-17.919	-14.820	0.928	-2.185	-1.843	-0.024
51	A	52	THR	0	-0.030	-0.018	4.349	3.561	3.698	-0.001	-0.004	-0.132	0.000
4	A	5	ILE	0	-0.023	-0.009	6.651	0.240	0.240	0.000	0.000	0.000	0.000
5	A	6	THR	0	0.035	0.023	10.412	0.425	0.425	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.771	-0.886	13.561	-18.111	-18.111	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.041	0.006	15.207	-0.866	-0.866	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.943	0.977	16.565	13.380	13.380	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.869	0.925	12.907	19.024	19.024	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.004	-0.004	9.896	-1.070	-1.070	0.000	0.000	0.000	0.000
11	A	12	MET	0	0.036	0.019	13.214	-0.236	-0.236	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.965	0.979	16.209	17.431	17.431	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.089	-0.036	9.619	-0.675	-0.675	0.000	0.000	0.000	0.000
14	A	15	TRP	0	0.041	0.019	13.409	-0.273	-0.273	0.000	0.000	0.000	0.000
15	A	16	GLN	0	0.003	0.016	15.188	0.919	0.919	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.004	0.002	17.325	-0.807	-0.807	0.000	0.000	0.000	0.000
17	A	18	ASN	0	-0.048	-0.038	19.841	0.353	0.353	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.893	0.914	21.481	12.403	12.403	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.865	-0.928	20.086	-14.295	-14.295	0.000	0.000	0.000	0.000
20	A	21	THR	0	-0.001	0.002	21.633	0.282	0.282	0.000	0.000	0.000	0.000
21	A	22	PRO	0	0.024	0.035	23.588	0.006	0.006	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.091	0.048	20.091	-0.574	-0.574	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.056	-0.027	15.336	0.850	0.850	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.027	0.014	18.298	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.000	-0.021	16.266	-1.140	-1.140	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.015	-0.001	17.281	0.452	0.452	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.965	0.977	16.681	15.850	15.850	0.000	0.000	0.000	0.000
28	A	29	LYS	0	-0.040	-0.006	11.872	-1.467	-1.467	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.009	0.008	13.627	0.986	0.986	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.020	-0.004	12.514	-1.775	-1.775	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.005	-0.006	10.414	0.377	0.377	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.029	-0.023	11.627	-1.529	-1.529	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.928	0.965	11.891	19.814	19.814	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.061	0.035	13.892	-0.439	-0.439	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.046	-0.027	13.065	-0.407	-0.407	0.000	0.000	0.000	0.000
36	A	37	LYS	1	1.014	0.996	16.883	12.994	12.994	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.987	1.006	18.792	14.427	14.427	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.016	-0.014	13.517	-0.277	-0.277	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.022	0.030	15.338	0.068	0.068	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.904	0.944	8.356	26.342	26.342	0.000	0.000	0.000	0.000
41	A	42	PHE	0	0.072	0.047	11.165	0.629	0.629	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.861	0.922	5.595	32.870	32.870	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.093	0.064	7.685	1.921	1.921	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.895	0.946	6.255	31.752	31.752	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.111	0.073	7.284	2.974	2.974	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.974	0.969	7.972	18.950	18.950	0.000	0.000	0.000	0.000
47	A	48	LYS	1	1.016	1.002	6.980	27.420	27.420	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.067	0.037	6.659	-0.473	-0.473	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.849	0.900	9.966	25.835	25.835	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.062	0.029	12.407	0.448	0.448	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.016	-0.006	16.230	-0.051	-0.051	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.804	-0.888	18.823	-12.882	-12.882	0.000	0.000	0.000	0.000
57	A	58	PRO	0	0.051	-0.010	21.132	-0.428	-0.428	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.940	0.984	23.384	10.787	10.787	0.000	0.000	0.000	0.000
59	A	60	ILE	0	0.028	0.007	18.640	-0.124	-0.124	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.009	0.003	18.667	-0.370	-0.370	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.943	0.958	19.719	10.840	10.840	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.067	0.038	22.484	0.099	0.099	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.042	-0.027	15.482	-0.191	-0.191	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.870	0.928	18.754	13.918	13.918	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.951	-0.955	20.359	-11.666	-11.666	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.005	-0.002	19.656	0.009	0.009	0.000	0.000	0.000	0.000
67	A	68	ILE	0	-0.052	-0.016	17.668	-0.574	-0.574	0.000	0.000	0.000	0.000
68	A	69	PRO	0	0.012	0.015	18.815	0.596	0.596	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.063	0.012	21.325	-0.362	-0.362	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.039	-0.013	20.026	0.112	0.112	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.057	-0.029	14.177	-1.128	-1.128	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.040	0.034	18.548	0.562	0.562	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.973	0.981	16.940	12.081	12.081	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.002	-0.002	15.050	0.537	0.537	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.952	-0.986	15.593	-15.520	-15.520	0.000	0.000	0.000	0.000
76	A	77	ILE	-1	-0.895	-0.945	12.541	-16.576	-16.576	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)