FMO DATABASE

FMODB ID: M26KZ

Calculation Name: 2NR5-C-Xray549

Preferred Name:

Target Type:

Ligand Name: (4s)-2-methyl-2,4-pentanediol | acetate ion

Ligand 3-letter code: MPD | ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NR5

Chain ID: C

ChEMBL ID:

UniProt ID: Q8EDS4

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	64
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-335037.004515
FMO2-HF: Nuclear repulsion	308283.174014
FMO2-HF: Total energy	-26753.830501
FMO2-MP2: Total energy	-26828.458065

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(C:1:MET)

Summations of interaction energy for fragment #1(C:1:MET)

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.
-31.379	-28.881	0.114	-1.42	-1.192	-0.008

Interaction energy analysis for fragmet #1(C:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.913

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	C	3	THR	0	-0.027	-0.044	3.082	-12.025	-9.527	0.114	-1.420	-1.192	-0.008
4	C	4	LYS	1	0.977	0.974	5.474	26.119	26.119	0.000	0.000	0.000	0.000
5	C	5	LYS	1	1.010	1.008	8.614	24.374	24.374	0.000	0.000	0.000	0.000
6	C	6	GLU	-1	-0.777	-0.859	6.666	-42.385	-42.385	0.000	0.000	0.000	0.000
7	C	7	ARG	1	0.937	0.953	7.913	28.505	28.505	0.000	0.000	0.000	0.000
8	C	8	ILE	0	-0.014	-0.004	9.797	1.716	1.716	0.000	0.000	0.000	0.000
9	C	9	ALA	0	0.010	0.008	12.852	1.529	1.529	0.000	0.000	0.000	0.000
10	C	10	ILE	0	0.011	0.002	9.618	1.138	1.138	0.000	0.000	0.000	0.000
11	C	11	GLN	0	0.035	0.017	13.446	0.732	0.732	0.000	0.000	0.000	0.000
12	C	12	ARG	1	0.869	0.919	15.697	16.855	16.855	0.000	0.000	0.000	0.000
13	C	13	SER	0	0.027	0.018	16.892	0.949	0.949	0.000	0.000	0.000	0.000
14	C	14	MET	0	-0.029	-0.025	15.852	0.174	0.174	0.000	0.000	0.000	0.000
15	C	15	ALA	0	-0.002	0.009	19.163	0.762	0.762	0.000	0.000	0.000	0.000
16	C	16	GLU	-1	-0.858	-0.936	21.717	-12.063	-12.063	0.000	0.000	0.000	0.000
17	C	17	GLU	-1	-0.976	-0.979	20.245	-14.114	-14.114	0.000	0.000	0.000	0.000
18	C	18	ALA	0	-0.054	-0.024	23.327	0.622	0.622	0.000	0.000	0.000	0.000
19	C	19	LEU	0	0.013	0.008	25.083	0.633	0.633	0.000	0.000	0.000	0.000
20	C	20	GLY	0	0.014	0.010	26.835	0.529	0.529	0.000	0.000	0.000	0.000
21	C	21	LYS	1	0.895	0.943	27.403	11.175	11.175	0.000	0.000	0.000	0.000
22	C	22	LEU	0	0.019	0.000	28.852	0.399	0.399	0.000	0.000	0.000	0.000
23	C	23	LYS	1	0.851	0.898	30.024	10.877	10.877	0.000	0.000	0.000	0.000
24	C	24	ALA	0	-0.033	-0.013	32.227	0.311	0.311	0.000	0.000	0.000	0.000
25	C	25	ILE	0	-0.017	-0.005	32.388	0.232	0.232	0.000	0.000	0.000	0.000
26	C	26	ARG	1	0.909	0.946	35.580	8.537	8.537	0.000	0.000	0.000	0.000
27	C	27	GLN	0	-0.056	-0.028	36.798	0.377	0.377	0.000	0.000	0.000	0.000
28	C	28	LEU	0	-0.062	-0.029	37.273	0.127	0.127	0.000	0.000	0.000	0.000
29	C	29	CYS	0	-0.054	-0.013	40.832	0.048	0.048	0.000	0.000	0.000	0.000
30	C	30	GLY	0	0.079	0.050	43.315	0.024	0.024	0.000	0.000	0.000	0.000
31	C	31	ALA	0	-0.099	-0.032	43.585	0.038	0.038	0.000	0.000	0.000	0.000
32	C	32	GLU	-1	-0.963	-0.991	45.740	-6.821	-6.821	0.000	0.000	0.000	0.000
33	C	33	ASP	-1	-1.002	-0.996	48.640	-5.812	-5.812	0.000	0.000	0.000	0.000
34	C	34	SER	0	0.004	-0.029	49.539	0.022	0.022	0.000	0.000	0.000	0.000
35	C	35	SER	0	-0.021	-0.008	51.892	0.119	0.119	0.000	0.000	0.000	0.000
36	C	36	ASP	-1	-0.824	-0.919	50.902	-6.217	-6.217	0.000	0.000	0.000	0.000
37	C	37	SER	0	-0.113	-0.062	50.504	-0.090	-0.090	0.000	0.000	0.000	0.000
38	C	38	SER	0	-0.005	0.000	49.908	-0.026	-0.026	0.000	0.000	0.000	0.000
39	C	39	ASP	-1	-0.741	-0.848	46.792	-6.770	-6.770	0.000	0.000	0.000	0.000
40	C	40	MET	0	-0.044	-0.038	45.668	-0.241	-0.241	0.000	0.000	0.000	0.000
41	C	41	GLN	0	0.003	0.020	45.948	-0.064	-0.064	0.000	0.000	0.000	0.000
42	C	42	GLU	-1	-0.896	-0.956	43.000	-7.513	-7.513	0.000	0.000	0.000	0.000
43	C	43	VAL	0	0.010	0.001	41.444	-0.279	-0.279	0.000	0.000	0.000	0.000
44	C	44	GLU	-1	-0.965	-0.947	41.051	-7.322	-7.322	0.000	0.000	0.000	0.000
45	C	45	ILE	0	-0.003	0.001	39.986	-0.240	-0.240	0.000	0.000	0.000	0.000
46	C	46	TRP	0	0.014	-0.010	34.514	-0.483	-0.483	0.000	0.000	0.000	0.000
47	C	47	THR	0	-0.053	-0.046	36.406	-0.341	-0.341	0.000	0.000	0.000	0.000
48	C	48	ASN	0	0.002	0.001	36.438	-0.343	-0.343	0.000	0.000	0.000	0.000
49	C	49	ARG	1	0.832	0.906	32.069	9.331	9.331	0.000	0.000	0.000	0.000
50	C	50	ILE	0	-0.028	-0.008	31.245	-0.366	-0.366	0.000	0.000	0.000	0.000
51	C	51	LYS	1	0.846	0.905	31.601	8.970	8.970	0.000	0.000	0.000	0.000
52	C	52	GLU	-1	-0.844	-0.911	32.256	-9.649	-9.649	0.000	0.000	0.000	0.000
53	C	53	LEU	0	-0.009	-0.004	26.328	-0.319	-0.319	0.000	0.000	0.000	0.000
54	C	54	GLU	-1	-0.834	-0.911	27.571	-11.018	-11.018	0.000	0.000	0.000	0.000
55	C	55	ASP	-1	-0.826	-0.889	27.807	-10.045	-10.045	0.000	0.000	0.000	0.000
56	C	56	TRP	0	-0.022	-0.007	22.638	-0.737	-0.737	0.000	0.000	0.000	0.000
57	C	57	LEU	0	-0.032	-0.031	22.346	-0.587	-0.587	0.000	0.000	0.000	0.000
58	C	58	TRP	0	-0.047	-0.025	21.030	-1.083	-1.083	0.000	0.000	0.000	0.000
59	C	59	GLY	0	-0.001	0.017	25.093	0.010	0.010	0.000	0.000	0.000	0.000
60	C	60	GLU	-1	-0.941	-0.973	25.726	-11.114	-11.114	0.000	0.000	0.000	0.000
61	C	61	SER	0	-0.033	-0.008	21.545	-0.676	-0.676	0.000	0.000	0.000	0.000
62	C	62	PRO	0	-0.060	-0.051	17.828	-0.434	-0.434	0.000	0.000	0.000	0.000
63	C	63	ILE	0	-0.124	-0.063	15.835	-1.645	-1.645	0.000	0.000	0.000	0.000
64	C	64	ALA	-1	-0.831	-0.873	18.075	-15.791	-15.791	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1:MET)