FMO DATABASE

FMODB ID: 3GJLL

Calculation Name: 3J7R-m-Other547

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: 3J7R

Chain ID: m

ChEMBL ID:

UniProt ID: P63246

Base Structure: ElectronMicroscopy

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	52
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-267972.943061
FMO2-HF: Nuclear repulsion	245328.721808
FMO2-HF: Total energy	-22644.221253
FMO2-MP2: Total energy	-22706.266021

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:77:ILE)

Summations of interaction energy for fragment #1(A:77:ILE)

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.
163.496	166.297	0.07	-1.084	-1.788	-0.002

Interaction energy analysis for fragmet #1(A:77:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.907 / q_NPA : 0.937

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	79	GLU	-1	-0.735	-0.833	3.408	-32.768	-30.422	0.021	-0.986	-1.382	-0.002
7	A	83	ARG	1	0.900	0.955	2.894	41.922	42.377	0.049	-0.098	-0.406	0.000
4	A	80	PRO	0	0.040	0.006	5.644	3.470	3.470	0.000	0.000	0.000	0.000
5	A	81	SER	0	-0.011	-0.031	7.634	2.829	2.829	0.000	0.000	0.000	0.000
6	A	82	LEU	0	0.080	0.033	8.068	1.544	1.544	0.000	0.000	0.000	0.000
8	A	84	GLN	0	-0.028	-0.028	8.318	2.344	2.344	0.000	0.000	0.000	0.000
9	A	85	LEU	0	0.043	0.035	11.620	1.962	1.962	0.000	0.000	0.000	0.000
10	A	86	ALA	0	0.027	0.009	10.215	1.571	1.571	0.000	0.000	0.000	0.000
11	A	87	GLN	0	-0.029	-0.030	9.670	2.817	2.817	0.000	0.000	0.000	0.000
12	A	88	LYS	1	1.012	1.036	13.340	16.840	16.840	0.000	0.000	0.000	0.000
13	A	89	TYR	0	-0.001	-0.005	15.699	1.667	1.667	0.000	0.000	0.000	0.000
14	A	90	ASN	0	-0.006	-0.010	12.431	1.850	1.850	0.000	0.000	0.000	0.000
15	A	91	CYS	0	-0.058	-0.027	12.442	0.725	0.725	0.000	0.000	0.000	0.000
16	A	92	ASP	-1	-0.880	-0.933	16.075	-15.619	-15.619	0.000	0.000	0.000	0.000
17	A	93	LYS	1	0.813	0.903	18.856	14.578	14.578	0.000	0.000	0.000	0.000
18	A	94	MET	0	0.035	0.056	21.967	-0.248	-0.248	0.000	0.000	0.000	0.000
19	A	95	ILE	0	-0.058	-0.052	21.962	-0.227	-0.227	0.000	0.000	0.000	0.000
20	A	96	CYS	-1	-0.776	-0.738	26.312	-8.982	-8.982	0.000	0.000	0.000	0.000
21	A	97	ARG	1	0.897	0.937	29.360	8.946	8.946	0.000	0.000	0.000	0.000
22	A	98	LYS	1	1.006	1.000	31.211	7.937	7.937	0.000	0.000	0.000	0.000
23	A	99	CYS	0	-0.087	-0.112	32.343	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	100	TYR	0	0.044	0.025	27.082	-0.272	-0.272	0.000	0.000	0.000	0.000
25	A	101	ALA	0	-0.011	-0.004	26.703	-0.390	-0.390	0.000	0.000	0.000	0.000
26	A	102	ARG	1	0.980	0.987	18.987	13.803	13.803	0.000	0.000	0.000	0.000
27	A	103	LEU	0	-0.042	-0.018	25.188	0.274	0.274	0.000	0.000	0.000	0.000
28	A	104	HIS	0	0.088	0.037	24.222	-0.760	-0.760	0.000	0.000	0.000	0.000
29	A	105	PRO	0	0.025	-0.013	22.201	0.363	0.363	0.000	0.000	0.000	0.000
30	A	106	ARG	1	0.989	0.993	24.730	11.505	11.505	0.000	0.000	0.000	0.000
31	A	107	ALA	0	-0.070	-0.014	28.165	0.365	0.365	0.000	0.000	0.000	0.000
32	A	108	VAL	0	0.101	0.054	30.162	-0.112	-0.112	0.000	0.000	0.000	0.000
33	A	109	ASN	0	0.077	0.034	33.309	0.129	0.129	0.000	0.000	0.000	0.000
34	A	110	CYS	0	-0.118	-0.061	32.067	-0.376	-0.376	0.000	0.000	0.000	0.000
35	A	111	ARG	1	0.981	0.962	27.601	10.340	10.340	0.000	0.000	0.000	0.000
36	A	112	LYS	1	0.934	0.965	30.426	9.695	9.695	0.000	0.000	0.000	0.000
37	A	113	LYS	1	1.110	1.041	35.065	7.135	7.135	0.000	0.000	0.000	0.000
38	A	114	LYS	1	0.972	0.985	33.290	8.801	8.801	0.000	0.000	0.000	0.000
39	A	115	CYS	0	-0.043	-0.028	34.250	0.014	0.014	0.000	0.000	0.000	0.000
40	A	116	GLY	0	0.047	0.033	37.540	0.043	0.043	0.000	0.000	0.000	0.000
41	A	117	HIS	0	-0.059	-0.046	36.418	0.169	0.169	0.000	0.000	0.000	0.000
42	A	118	THR	0	0.022	-0.033	34.409	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	119	ASN	0	0.075	0.059	34.971	0.005	0.005	0.000	0.000	0.000	0.000
44	A	120	ASN	0	0.000	0.005	34.066	-0.296	-0.296	0.000	0.000	0.000	0.000
45	A	121	LEU	0	-0.038	-0.002	29.184	-0.173	-0.173	0.000	0.000	0.000	0.000
46	A	122	ARG	1	0.931	0.968	24.556	11.423	11.423	0.000	0.000	0.000	0.000
47	A	123	PRO	0	0.106	0.039	23.179	-0.151	-0.151	0.000	0.000	0.000	0.000
48	A	124	LYS	1	0.831	0.922	17.309	15.442	15.442	0.000	0.000	0.000	0.000
49	A	125	LYS	1	0.946	0.965	19.864	11.873	11.873	0.000	0.000	0.000	0.000
50	A	126	LYS	1	0.900	0.949	15.535	16.282	16.282	0.000	0.000	0.000	0.000
51	A	127	VAL	0	-0.024	-0.011	11.148	0.775	0.775	0.000	0.000	0.000	0.000
52	A	128	LYS	0	0.103	0.068	12.024	-5.538	-5.538	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:77:ILE)