FMO DATABASE

FMODB ID: LGJZ9

Calculation Name: 2Y1S-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2Y1S

Chain ID: A

ChEMBL ID:

UniProt ID: Q2MDE2

Base Structure: SolutionNMR

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-797965.907627
FMO2-HF: Nuclear repulsion	753275.509229
FMO2-HF: Total energy	-44690.398398
FMO2-MP2: Total energy	-44814.411808

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:MET)

Summations of interaction energy for fragment #1(A: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.
-352.69	-348.016	0.2	-2.226	-2.65	-0.018

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.830 / q_NPA : 0.905

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	ASN	0	0.032	0.017	3.619	-0.348	0.710	-0.005	-0.446	-0.608	-0.001
94	A	97	GLN	0	-0.095	-0.045	2.806	-22.844	-20.881	0.164	-1.117	-1.010	-0.012
95	A	98	ILE	0	0.065	0.034	4.476	7.173	7.281	-0.001	-0.007	-0.100	0.000
96	A	99	ASP	-1	-0.924	-0.951	3.522	-63.712	-62.320	0.043	-0.649	-0.786	-0.005
105	A	108	GLY	-1	-0.951	-0.955	4.351	-43.833	-43.680	-0.001	-0.007	-0.146	0.000
4	A	4	PHE	0	0.032	0.020	6.490	2.890	2.890	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.052	-0.036	9.769	3.229	3.229	0.000	0.000	0.000	0.000
6	A	6	HIS	0	-0.051	-0.044	10.579	0.324	0.324	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.049	-0.031	8.651	2.285	2.285	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.019	-0.011	11.770	0.254	0.254	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.022	0.019	14.429	-0.099	-0.099	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.046	-0.040	17.615	0.126	0.126	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.021	0.020	14.185	0.332	0.332	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.038	-0.016	18.044	0.707	0.707	0.000	0.000	0.000	0.000
13	A	13	TYR	0	0.016	-0.010	18.571	-1.059	-1.059	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.882	-0.916	20.575	-12.379	-12.379	0.000	0.000	0.000	0.000
15	A	15	PRO	0	-0.042	-0.032	23.371	-0.222	-0.222	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.933	-0.963	24.471	-10.948	-10.948	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.024	-0.020	24.728	-0.088	-0.088	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.018	0.013	20.530	-0.129	-0.129	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.044	-0.006	19.877	-0.791	-0.791	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.006	0.004	13.770	0.257	0.257	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.033	-0.022	17.849	0.178	0.178	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.020	0.012	15.824	-0.280	-0.280	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.960	-0.976	17.964	-13.749	-13.749	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.002	0.007	15.260	1.955	1.955	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.037	0.025	14.863	-1.269	-1.269	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.818	0.887	10.728	22.432	22.432	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.884	-0.941	16.890	-14.382	-14.382	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.047	-0.014	19.114	0.634	0.634	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-1.009	-0.999	20.350	-11.958	-11.958	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.051	-0.026	18.438	-1.086	-1.086	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.007	0.000	18.710	0.778	0.778	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.004	0.013	19.055	-0.737	-0.737	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.050	-0.037	15.435	-0.360	-0.360	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.927	-0.966	18.487	-13.752	-13.752	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.011	-0.001	12.747	-0.499	-0.499	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.839	0.928	17.040	14.361	14.361	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.059	0.017	13.659	-0.709	-0.709	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.016	-0.018	16.903	-0.208	-0.208	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.903	-0.953	17.402	-15.523	-15.523	0.000	0.000	0.000	0.000
40	A	41	HIS	0	-0.043	-0.016	13.781	-0.736	-0.736	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.038	0.023	14.425	-1.078	-1.078	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.021	0.010	17.448	0.783	0.783	0.000	0.000	0.000	0.000
43	A	44	ASN	0	0.001	-0.021	20.674	-0.835	-0.835	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.005	0.005	21.378	0.432	0.432	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.921	-0.968	24.277	-11.164	-11.164	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.012	0.002	26.238	0.373	0.373	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.959	-0.962	21.612	-13.193	-13.193	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.004	-0.008	18.460	0.205	0.205	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.081	-0.051	16.604	-0.552	-0.552	0.000	0.000	0.000	0.000
50	A	51	PHE	0	0.017	-0.007	11.087	-0.043	-0.043	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.057	-0.025	14.627	0.254	0.254	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.883	-0.910	16.135	-14.501	-14.501	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.017	-0.023	18.613	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.078	-0.038	21.191	0.277	0.277	0.000	0.000	0.000	0.000
55	A	56	PHE	0	0.066	0.035	19.594	0.184	0.184	0.000	0.000	0.000	0.000
56	A	57	GLN	0	0.052	0.007	23.184	0.011	0.011	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.938	-0.962	25.306	-11.124	-11.124	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.077	-0.035	26.430	0.452	0.452	0.000	0.000	0.000	0.000
59	A	60	CYS	0	-0.075	-0.014	23.878	-0.097	-0.097	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.003	-0.003	26.688	0.299	0.299	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.936	-0.976	26.246	-11.124	-11.124	0.000	0.000	0.000	0.000
62	A	63	CYS	0	-0.055	-0.007	20.529	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.922	0.962	22.183	12.747	12.747	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.039	0.017	16.573	-0.617	-0.617	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.956	-0.980	18.571	-13.166	-13.166	0.000	0.000	0.000	0.000
66	A	67	PHE	0	0.022	0.010	17.650	-1.025	-1.025	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.030	0.014	17.154	0.739	0.739	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.975	-0.997	18.280	-14.909	-14.909	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.050	-0.021	17.052	0.545	0.545	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.953	-0.987	16.363	-15.627	-15.627	0.000	0.000	0.000	0.000
71	A	72	GLN	0	-0.049	-0.024	13.126	-0.887	-0.887	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.037	0.037	10.559	-1.906	-1.906	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.021	-0.004	12.885	1.823	1.823	0.000	0.000	0.000	0.000
74	A	75	TRP	0	-0.051	-0.025	13.313	-0.907	-0.907	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.036	0.026	15.539	1.071	1.071	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.013	-0.007	17.248	-0.156	-0.156	0.000	0.000	0.000	0.000
77	A	79	THR	0	0.019	0.011	22.997	-0.068	-0.068	0.000	0.000	0.000	0.000
78	A	81	GLN	0	-0.045	-0.025	26.528	0.165	0.165	0.000	0.000	0.000	0.000
79	A	82	THR	0	0.021	0.001	28.621	-0.263	-0.263	0.000	0.000	0.000	0.000
80	A	83	MET	0	0.020	0.003	30.483	0.139	0.139	0.000	0.000	0.000	0.000
81	A	84	ASP	-1	-0.977	-0.976	32.686	-8.721	-8.721	0.000	0.000	0.000	0.000
82	A	85	GLY	0	-0.043	-0.022	34.139	0.284	0.284	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.985	-0.982	33.213	-9.045	-9.045	0.000	0.000	0.000	0.000
84	A	87	TRP	0	-0.001	-0.011	29.491	-0.301	-0.301	0.000	0.000	0.000	0.000
85	A	88	LYS	1	0.852	0.915	26.099	12.107	12.107	0.000	0.000	0.000	0.000
86	A	89	SER	0	-0.025	-0.005	25.430	-0.104	-0.104	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.022	0.002	21.208	-0.075	-0.075	0.000	0.000	0.000	0.000
88	A	91	GLN	0	-0.007	-0.013	17.435	0.728	0.728	0.000	0.000	0.000	0.000
89	A	92	ILE	0	0.000	0.005	13.253	-0.312	-0.312	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.023	-0.005	9.318	0.860	0.860	0.000	0.000	0.000	0.000
91	A	94	LEU	0	0.049	0.018	10.084	-1.069	-1.069	0.000	0.000	0.000	0.000
92	A	95	ASP	-1	-0.834	-0.904	6.893	-35.497	-35.497	0.000	0.000	0.000	0.000
93	A	96	SER	0	-0.052	-0.047	5.000	1.292	1.292	0.000	0.000	0.000	0.000
97	A	100	ASN	0	0.053	0.027	5.762	3.614	3.614	0.000	0.000	0.000	0.000
98	A	101	ASN	0	-0.088	-0.037	7.610	-2.965	-2.965	0.000	0.000	0.000	0.000
99	A	102	ASP	-1	-0.851	-0.939	9.427	-23.133	-23.133	0.000	0.000	0.000	0.000
100	A	103	SER	0	-0.011	-0.025	12.121	0.772	0.772	0.000	0.000	0.000	0.000
101	A	104	GLN	0	-0.059	-0.006	12.650	1.713	1.713	0.000	0.000	0.000	0.000
102	A	105	LEU	0	0.022	0.012	10.586	-1.992	-1.992	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.947	-0.967	9.514	-22.567	-22.567	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.037	-0.017	7.726	-1.696	-1.696	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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