FMO DATABASE

FMODB ID: 6738Z

Calculation Name: 2SN3-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: MPD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2SN3

Chain ID: A

ChEMBL ID:

UniProt ID: P01494

Base Structure: X-ray

Registration Date: 2025-10-04

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	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-358485.10678
FMO2-HF: Nuclear repulsion	331754.652257
FMO2-HF: Total energy	-26730.454524
FMO2-MP2: Total energy	-26801.821445

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:1:LYS)

Summations of interaction energy for fragment #1(A:1: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.
-328.296	-320.24	45.284	-24.519	-28.818	-0.308

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.619 / q_NPA : 1.803

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	3	GLY	0	0.039	0.020	2.919	-7.229	-4.325	0.236	-1.564	-1.576	-0.012
4	A	4	TYR	0	-0.044	-0.034	5.154	3.836	3.853	-0.001	-0.003	-0.012	0.000
47	A	50	GLY	0	0.027	0.000	4.436	5.610	5.747	-0.001	-0.018	-0.118	0.000
48	A	51	LEU	0	0.002	0.004	2.214	6.789	8.101	1.883	-1.015	-2.180	-0.001
49	A	52	PRO	0	0.004	0.002	1.858	-40.833	-41.115	8.582	-4.323	-3.976	-0.061
50	A	53	GLU	-1	-0.822	-0.932	1.934	-192.425	-185.464	11.867	-8.796	-10.032	-0.100
51	A	54	SER	0	-0.034	-0.012	1.853	-29.481	-32.204	8.671	-2.423	-3.525	-0.056
52	A	55	THR	0	-0.007	0.006	3.461	7.418	8.344	0.013	-0.326	-0.613	-0.001
53	A	56	PRO	0	-0.024	-0.001	1.739	-44.480	-47.455	11.823	-5.042	-3.806	-0.062
54	A	57	THR	0	0.058	0.019	2.429	-8.702	-7.003	2.212	-0.998	-2.912	-0.015
55	A	58	TYR	0	-0.068	-0.014	4.241	4.810	4.890	-0.001	-0.011	-0.068	0.000
5	A	5	LEU	0	0.046	0.031	6.445	-6.104	-6.104	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.045	-0.033	6.930	5.437	5.437	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.857	0.927	9.486	33.104	33.104	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.953	0.961	10.434	43.370	43.370	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.012	0.010	11.890	0.604	0.604	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.763	-0.872	15.054	-33.059	-33.059	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.066	0.052	12.307	1.161	1.161	0.000	0.000	0.000	0.000
12	A	65	CYS	-1	-0.991	-0.987	12.612	-30.197	-30.197	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.940	0.972	10.771	39.068	39.068	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.035	-0.010	11.172	2.543	2.543	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.015	0.018	14.195	-0.833	-0.833	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.092	-0.031	13.280	-1.701	-1.701	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.056	0.018	19.029	0.188	0.188	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.944	0.972	21.890	24.607	24.607	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.024	0.006	18.817	-1.441	-1.441	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.026	0.019	18.185	1.325	1.325	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.902	-0.951	17.730	-30.144	-30.144	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.053	-0.043	17.137	1.037	1.037	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.855	-0.925	17.268	-27.867	-27.867	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.015	0.028	18.090	-0.749	-0.749	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.060	-0.040	12.404	-0.390	-0.390	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.743	-0.849	13.161	-43.195	-43.195	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.025	-0.023	13.714	-1.367	-1.367	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.824	-0.906	11.604	-43.144	-43.144	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.093	-0.036	7.161	-0.923	-0.923	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.845	0.900	9.631	36.802	36.802	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.002	0.023	12.148	0.966	0.966	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.925	0.950	11.600	41.492	41.492	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.060	-0.027	11.757	0.105	0.105	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.052	-0.030	7.671	-8.162	-8.162	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.026	-0.023	7.013	-8.050	-8.050	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.012	0.013	6.633	-3.391	-3.391	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.053	-0.022	7.445	7.220	7.220	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.001	-0.011	9.271	5.415	5.415	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.023	0.006	10.000	-5.142	-5.142	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.103	-0.062	11.178	4.996	4.996	0.000	0.000	0.000	0.000
41	A	42	TYR	0	0.046	0.013	13.127	2.149	2.149	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.008	0.000	14.681	-1.233	-1.233	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.003	-0.009	17.039	-0.314	-0.314	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.003	0.000	13.175	0.351	0.351	0.000	0.000	0.000	0.000
45	A	47	TRP	0	-0.018	0.000	7.476	-3.655	-3.655	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.778	-0.875	5.920	-64.967	-64.967	0.000	0.000	0.000	0.000
56	A	59	PRO	0	-0.025	-0.014	6.899	-1.829	-1.829	0.000	0.000	0.000	0.000
57	A	60	LEU	0	0.049	0.010	7.583	-4.987	-4.987	0.000	0.000	0.000	0.000
58	A	61	PRO	0	0.012	0.001	7.099	4.418	4.418	0.000	0.000	0.000	0.000
59	A	62	ASN	0	-0.048	-0.031	9.766	0.203	0.203	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.850	0.912	12.009	34.944	34.944	0.000	0.000	0.000	0.000
61	A	64	SER	0	0.043	0.039	12.845	-2.270	-2.270	0.000	0.000	0.000	0.000

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