FMO DATABASE

FMODB ID: Z9LKN

Calculation Name: 6R6P-l-Other547

Preferred Name: X-box-binding protein 1

Target Type: SINGLE PROTEIN

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6R6P

Chain ID: l

ChEMBL ID: CHEMBL1741176

UniProt ID: P17861

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	50
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-248729.58781
FMO2-HF: Nuclear repulsion	227288.059611
FMO2-HF: Total energy	-21441.528199
FMO2-MP2: Total energy	-21505.36262

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:SER)

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

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.
319.116	324.392	0.03	-2.425	-2.88	-0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.892 / q_NPA : 0.916

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	HIS	0	0.116	0.089	2.934	3.859	8.602	0.029	-2.296	-2.475	-0.009
4	A	5	LYS	1	0.894	0.949	3.973	54.583	55.099	0.002	-0.128	-0.390	-0.001
5	A	6	THR	0	0.153	0.077	5.394	4.550	4.567	-0.001	-0.001	-0.015	0.000
6	A	7	PHE	0	0.077	0.017	8.636	-1.501	-1.501	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.981	0.988	11.664	19.533	19.533	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.087	0.047	6.399	0.558	0.558	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.967	0.976	8.396	27.147	27.147	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.973	0.998	9.172	20.038	20.038	0.000	0.000	0.000	0.000
11	A	12	PHE	0	0.051	0.028	10.799	1.382	1.382	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.013	-0.005	5.946	0.937	0.937	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.036	0.021	10.383	1.298	1.298	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.941	0.972	12.967	17.225	17.225	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.891	0.942	12.221	20.063	20.063	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.019	0.000	10.482	1.547	1.547	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.989	0.992	14.457	17.973	17.973	0.000	0.000	0.000	0.000
18	A	19	GLN	0	0.032	0.020	17.448	0.304	0.304	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.058	-0.010	15.807	1.738	1.738	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.987	1.000	18.566	12.494	12.494	0.000	0.000	0.000	0.000
21	A	22	PRO	0	0.006	-0.003	21.634	0.284	0.284	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.022	0.006	25.079	-0.056	-0.056	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.009	0.010	28.207	0.047	0.047	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.085	0.015	30.459	0.318	0.318	0.000	0.000	0.000	0.000
25	A	26	TRP	0	0.100	0.046	31.648	0.203	0.203	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.051	-0.026	31.509	0.184	0.184	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.904	0.942	34.177	9.084	9.084	0.000	0.000	0.000	0.000
28	A	29	MET	0	0.054	0.048	37.055	0.072	0.072	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.911	0.974	35.597	8.780	8.780	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.083	0.035	40.402	-0.084	-0.084	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.042	0.029	41.773	0.080	0.080	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.040	-0.021	35.180	-0.269	-0.269	0.000	0.000	0.000	0.000
33	A	34	LYS	1	1.053	1.019	37.144	7.858	7.858	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.050	-0.015	31.059	-0.149	-0.149	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.945	0.971	33.646	8.816	8.816	0.000	0.000	0.000	0.000
36	A	37	TYR	0	0.052	0.006	27.509	-0.288	-0.288	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.011	-0.015	23.471	0.151	0.151	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.013	0.010	26.401	-0.076	-0.076	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.995	0.998	21.951	12.208	12.208	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.896	0.951	20.135	13.862	13.862	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.943	0.971	11.468	23.008	23.008	0.000	0.000	0.000	0.000
42	A	43	HIS	0	0.079	0.028	16.073	-0.692	-0.692	0.000	0.000	0.000	0.000
43	A	44	TRP	0	0.056	0.021	10.720	-0.768	-0.768	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.955	0.972	11.701	18.099	18.099	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.976	1.006	14.327	15.563	15.563	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.026	0.007	15.007	0.455	0.455	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.894	0.930	8.854	27.801	27.801	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.091	-0.042	9.774	-2.118	-2.118	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.050	0.036	9.968	-2.423	-2.423	0.000	0.000	0.000	0.000
50	A	51	LEU	-1	-0.922	-0.948	8.917	-24.562	-24.562	0.000	0.000	0.000	0.000

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