FMO DATABASE

FMODB ID: Y9LY2

Calculation Name: 2BYE-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BYE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9P212

Base Structure: SolutionNMR

Registration Date: 2025-10-03

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	110
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-852053.441485
FMO2-HF: Nuclear repulsion	806842.44423
FMO2-HF: Total energy	-45210.997256
FMO2-MP2: Total energy	-45341.353395

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:GLY)

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

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.
-83.246	-86.637	22.286	-11.527	-7.369	-0.141

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.766 / q_NPA : 0.846

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	GLU	-1	-0.785	-0.868	1.799	-128.075	-131.590	22.287	-11.517	-7.256	-0.141
4	A	4	ARG	1	0.960	0.976	4.929	46.489	46.613	-0.001	-0.010	-0.113	0.000
5	A	5	LYS	1	0.948	0.973	8.332	27.100	27.100	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.001	0.015	6.674	-0.459	-0.459	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.028	0.003	8.095	3.610	3.610	0.000	0.000	0.000	0.000
8	A	8	GLN	0	-0.005	-0.001	10.553	-1.197	-1.197	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.013	-0.003	12.273	0.984	0.984	0.000	0.000	0.000	0.000
10	A	10	HIS	0	0.021	0.014	13.921	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.916	0.950	16.951	14.074	14.074	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.015	0.013	20.361	0.141	0.141	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.009	-0.013	23.410	0.082	0.082	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.015	-0.001	26.837	0.141	0.141	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.052	-0.009	29.779	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.049	-0.008	33.361	0.292	0.292	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.039	-0.010	30.859	-0.038	-0.038	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.024	0.015	32.149	0.262	0.262	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.001	0.007	33.516	0.151	0.151	0.000	0.000	0.000	0.000
20	A	20	PRO	0	-0.001	-0.013	34.457	0.136	0.136	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.901	-0.916	31.163	-10.265	-10.265	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.015	-0.020	35.185	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.017	-0.018	30.380	0.045	0.045	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.043	-0.030	29.091	-0.205	-0.205	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.010	-0.006	23.551	-0.111	-0.111	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.044	0.044	23.999	-0.340	-0.340	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.012	-0.022	17.533	-0.191	-0.191	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.000	0.015	17.339	0.177	0.177	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.014	-0.021	14.693	-1.263	-1.263	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.008	-0.002	13.213	0.812	0.812	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.037	0.017	14.226	-0.628	-0.628	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.058	-0.021	17.227	0.796	0.796	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.956	0.990	20.078	13.993	13.993	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.073	0.028	23.220	0.008	0.008	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.990	1.005	26.395	10.377	10.377	0.000	0.000	0.000	0.000
36	A	36	GLN	0	0.025	0.000	20.534	0.297	0.297	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.009	-0.002	21.397	-0.224	-0.224	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.033	0.034	24.877	0.090	0.090	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.017	-0.015	24.682	-0.265	-0.265	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.002	0.007	21.656	0.154	0.154	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.023	-0.009	25.069	0.063	0.063	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.046	-0.024	28.127	0.402	0.402	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.042	-0.031	24.440	0.174	0.174	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.002	-0.010	27.664	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.912	-0.973	23.807	-13.016	-13.016	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.044	-0.009	27.710	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.895	-0.954	29.093	-10.389	-10.389	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.055	-0.025	24.298	-0.151	-0.151	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.898	0.956	28.621	10.673	10.673	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.002	0.010	31.107	0.320	0.320	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.019	0.009	34.299	0.028	0.028	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.082	-0.035	31.529	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.020	0.011	34.557	0.035	0.035	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.852	-0.908	35.655	-8.401	-8.401	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.032	-0.041	34.261	0.159	0.159	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.012	-0.011	32.960	-0.242	-0.242	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.028	0.018	27.730	0.102	0.102	0.000	0.000	0.000	0.000
58	A	58	MET	0	-0.005	-0.003	31.982	0.293	0.293	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.849	-0.906	30.078	-10.527	-10.527	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.827	-0.904	32.029	-8.190	-8.190	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.808	0.893	29.781	10.154	10.154	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.074	-0.064	35.285	0.341	0.341	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.011	-0.003	36.443	-0.171	-0.171	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.013	-0.001	34.191	-0.062	-0.062	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.068	-0.037	38.791	0.111	0.111	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.822	0.905	42.155	6.989	6.989	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.763	-0.882	42.713	-6.856	-6.856	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.837	0.903	44.173	6.769	6.769	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.034	0.013	43.618	-0.265	-0.265	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.722	-0.821	40.574	-7.559	-7.559	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.020	-0.011	44.441	0.013	0.013	0.000	0.000	0.000	0.000
72	A	72	ARG	1	1.018	1.024	44.784	6.690	6.690	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.881	0.917	46.522	6.595	6.595	0.000	0.000	0.000	0.000
74	A	74	GLN	0	0.044	0.013	44.579	0.238	0.238	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.016	0.015	42.070	-0.097	-0.097	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.005	0.018	36.340	-0.077	-0.077	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.008	-0.001	36.148	-0.198	-0.198	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.841	0.893	32.118	9.531	9.531	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.009	-0.001	33.436	-0.210	-0.210	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.028	-0.010	28.296	-0.077	-0.077	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.051	0.030	31.443	0.052	0.052	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.055	-0.050	28.696	-0.408	-0.408	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.874	-0.956	27.088	-11.108	-11.108	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.819	-0.850	26.991	-10.242	-10.242	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.906	-0.972	21.548	-14.965	-14.965	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.060	0.018	22.145	-0.036	-0.036	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.019	-0.002	17.430	-0.047	-0.047	0.000	0.000	0.000	0.000
88	A	88	GLN	0	-0.038	-0.018	20.881	0.190	0.190	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.004	0.002	23.168	0.185	0.185	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.011	-0.021	21.603	0.177	0.177	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.075	-0.027	20.457	-0.061	-0.061	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.033	-0.020	22.032	0.212	0.212	0.000	0.000	0.000	0.000
93	A	93	TRP	0	-0.062	-0.006	24.844	0.564	0.564	0.000	0.000	0.000	0.000
94	A	94	PHE	0	-0.008	0.005	25.361	-0.397	-0.397	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.023	-0.024	24.806	0.087	0.087	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.904	-0.964	27.301	-10.400	-10.400	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.808	-0.897	29.723	-9.971	-9.971	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.006	0.009	28.186	0.237	0.237	0.000	0.000	0.000	0.000
99	A	99	TYR	0	-0.034	-0.013	28.401	-0.240	-0.240	0.000	0.000	0.000	0.000
100	A	100	MET	0	-0.061	-0.021	30.943	0.212	0.212	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.056	0.019	31.611	-0.084	-0.084	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.802	0.894	30.664	8.682	8.682	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.035	0.028	26.898	0.102	0.102	0.000	0.000	0.000	0.000
104	A	104	VAL	0	-0.027	-0.008	30.346	0.080	0.080	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.003	-0.007	31.376	-0.319	-0.319	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.869	0.935	34.271	8.584	8.584	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.053	0.020	36.778	-0.221	-0.221	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.094	-0.046	37.326	-0.174	-0.174	0.000	0.000	0.000	0.000
109	A	109	GLN	0	-0.116	-0.073	40.729	0.130	0.130	0.000	0.000	0.000	0.000
110	A	110	GLU	-2	-1.862	-1.905	43.629	-13.958	-13.958	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:GLY)