FMO DATABASE

FMODB ID: QKQYY

Calculation Name: 2BYK-B-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BYK

Chain ID: B

ChEMBL ID:

UniProt ID: Q9V452

Base Structure: X-ray

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-507474.149468
FMO2-HF: Nuclear repulsion	474315.459495
FMO2-HF: Total energy	-33158.689973
FMO2-MP2: Total energy	-33258.158095

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:11:PRO)

Summations of interaction energy for fragment #1(A:11:PRO)

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.
72.737	77.114	2.033	-2.19	-4.222	-0.016

Interaction energy analysis for fragmet #1(A:11:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.927 / q_NPA : 0.944

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	13	ALA	0	0.046	0.031	3.760	4.466	6.239	0.003	-0.717	-1.060	-0.001
4	A	14	VAL	0	0.007	0.005	2.082	1.502	2.475	1.471	-0.805	-1.639	-0.011
5	A	15	ILE	0	0.064	0.030	2.756	3.863	5.217	0.562	-0.642	-1.273	-0.004
6	A	16	GLY	0	0.004	0.001	5.142	6.112	6.202	-0.001	-0.007	-0.083	0.000
28	A	38	ALA	0	-0.018	-0.010	4.109	-2.141	-2.044	-0.001	-0.015	-0.082	0.000
32	A	42	SER	0	-0.048	-0.031	4.881	-2.140	-2.050	-0.001	-0.004	-0.085	0.000
7	A	17	ARG	1	0.924	0.962	7.731	34.537	34.537	0.000	0.000	0.000	0.000
8	A	18	LEU	0	0.088	0.035	6.348	1.610	1.610	0.000	0.000	0.000	0.000
9	A	19	ILE	0	-0.025	-0.016	8.465	2.306	2.306	0.000	0.000	0.000	0.000
10	A	20	LYS	1	0.879	0.929	11.114	25.266	25.266	0.000	0.000	0.000	0.000
11	A	21	GLU	-1	-0.948	-0.952	12.766	-21.620	-21.620	0.000	0.000	0.000	0.000
12	A	22	ALA	0	0.008	0.006	13.533	1.113	1.113	0.000	0.000	0.000	0.000
13	A	23	LEU	0	-0.065	-0.022	15.062	1.008	1.008	0.000	0.000	0.000	0.000
14	A	24	PRO	0	0.044	0.011	17.330	0.013	0.013	0.000	0.000	0.000	0.000
15	A	25	GLU	-1	-0.915	-0.953	19.513	-13.733	-13.733	0.000	0.000	0.000	0.000
16	A	26	SER	0	-0.023	-0.006	20.557	-0.252	-0.252	0.000	0.000	0.000	0.000
17	A	27	ALA	0	-0.016	0.009	18.927	0.346	0.346	0.000	0.000	0.000	0.000
18	A	28	SER	0	-0.035	-0.024	17.723	-0.609	-0.609	0.000	0.000	0.000	0.000
19	A	29	VAL	0	0.061	0.023	13.303	0.000	0.000	0.000	0.000	0.000	0.000
20	A	30	SER	0	0.048	0.025	15.234	-0.990	-0.990	0.000	0.000	0.000	0.000
21	A	31	LYS	1	0.975	0.960	12.395	17.375	17.375	0.000	0.000	0.000	0.000
22	A	32	GLU	-1	-0.859	-0.922	11.374	-21.657	-21.657	0.000	0.000	0.000	0.000
23	A	33	ALA	0	0.044	0.022	12.167	-1.103	-1.103	0.000	0.000	0.000	0.000
24	A	34	ARG	1	0.886	0.943	8.987	22.985	22.985	0.000	0.000	0.000	0.000
25	A	35	ALA	0	0.012	0.014	7.619	-3.325	-3.325	0.000	0.000	0.000	0.000
26	A	36	ALA	0	-0.023	-0.018	8.337	-1.455	-1.455	0.000	0.000	0.000	0.000
27	A	37	ILE	0	0.050	0.024	8.126	-0.571	-0.571	0.000	0.000	0.000	0.000
29	A	39	ARG	1	0.927	0.975	5.555	21.104	21.104	0.000	0.000	0.000	0.000
30	A	40	ALA	0	0.033	0.019	7.979	0.330	0.330	0.000	0.000	0.000	0.000
31	A	41	ALA	0	0.017	0.005	6.087	0.916	0.916	0.000	0.000	0.000	0.000
33	A	43	VAL	0	0.003	-0.002	6.786	1.818	1.818	0.000	0.000	0.000	0.000
34	A	44	PHE	0	0.011	0.018	10.376	1.175	1.175	0.000	0.000	0.000	0.000
35	A	45	ALA	0	0.026	0.015	8.455	1.367	1.367	0.000	0.000	0.000	0.000
36	A	46	ILE	0	-0.014	0.003	9.716	1.632	1.632	0.000	0.000	0.000	0.000
37	A	47	PHE	0	0.018	0.012	12.210	1.364	1.364	0.000	0.000	0.000	0.000
38	A	48	VAL	0	0.068	0.042	14.158	1.305	1.305	0.000	0.000	0.000	0.000
39	A	49	THR	0	-0.009	-0.002	13.061	1.047	1.047	0.000	0.000	0.000	0.000
40	A	50	SER	0	-0.032	-0.007	15.793	1.333	1.333	0.000	0.000	0.000	0.000
41	A	51	SER	0	0.034	0.004	18.071	1.064	1.064	0.000	0.000	0.000	0.000
42	A	52	SER	0	0.001	-0.017	18.360	0.747	0.747	0.000	0.000	0.000	0.000
43	A	53	THR	0	-0.059	-0.039	19.191	0.538	0.538	0.000	0.000	0.000	0.000
44	A	54	ALA	0	-0.003	0.003	21.727	0.666	0.666	0.000	0.000	0.000	0.000
45	A	55	LEU	0	-0.013	-0.001	23.610	0.670	0.670	0.000	0.000	0.000	0.000
46	A	56	ALA	0	0.000	-0.006	24.191	0.501	0.501	0.000	0.000	0.000	0.000
47	A	57	HIS	0	-0.005	-0.008	25.966	0.528	0.528	0.000	0.000	0.000	0.000
48	A	58	LYS	1	0.872	0.947	27.878	11.330	11.330	0.000	0.000	0.000	0.000
49	A	59	GLN	0	-0.045	-0.017	27.582	0.609	0.609	0.000	0.000	0.000	0.000
50	A	60	ASN	0	-0.033	-0.009	30.782	0.282	0.282	0.000	0.000	0.000	0.000
51	A	61	HIS	0	-0.091	-0.043	26.182	0.550	0.550	0.000	0.000	0.000	0.000
52	A	62	LYS	1	0.954	0.955	27.544	10.394	10.394	0.000	0.000	0.000	0.000
53	A	63	THR	0	-0.047	-0.020	22.517	-0.151	-0.151	0.000	0.000	0.000	0.000
54	A	64	ILE	0	0.038	0.034	18.750	0.365	0.365	0.000	0.000	0.000	0.000
55	A	65	THR	0	-0.062	-0.043	21.825	-0.331	-0.331	0.000	0.000	0.000	0.000
56	A	66	ALA	0	0.017	-0.012	20.458	-0.306	-0.306	0.000	0.000	0.000	0.000
57	A	67	LYS	1	0.941	0.968	21.474	11.008	11.008	0.000	0.000	0.000	0.000
58	A	68	ASP	-1	-0.643	-0.792	22.701	-12.544	-12.544	0.000	0.000	0.000	0.000
59	A	69	ILE	0	0.010	0.021	16.818	-0.113	-0.113	0.000	0.000	0.000	0.000
60	A	70	LEU	0	-0.025	-0.007	20.006	-0.226	-0.226	0.000	0.000	0.000	0.000
61	A	71	GLN	0	0.019	0.008	21.722	-0.091	-0.091	0.000	0.000	0.000	0.000
62	A	72	THR	0	0.024	0.002	19.413	0.256	0.256	0.000	0.000	0.000	0.000
63	A	73	LEU	0	-0.056	-0.028	16.113	-0.303	-0.303	0.000	0.000	0.000	0.000
64	A	74	THR	0	-0.067	-0.048	20.260	0.215	0.215	0.000	0.000	0.000	0.000
65	A	75	GLU	-1	-0.954	-0.976	23.678	-11.678	-11.678	0.000	0.000	0.000	0.000
66	A	76	LEU	0	-0.063	-0.034	18.484	0.008	0.008	0.000	0.000	0.000	0.000
67	A	77	ASP	-1	-0.868	-0.926	20.943	-12.710	-12.710	0.000	0.000	0.000	0.000
68	A	78	PHE	0	-0.070	-0.031	16.803	-0.427	-0.427	0.000	0.000	0.000	0.000
69	A	79	GLU	-1	-0.865	-0.943	20.065	-11.915	-11.915	0.000	0.000	0.000	0.000
70	A	80	SER	0	-0.027	-0.020	20.663	-0.114	-0.114	0.000	0.000	0.000	0.000
71	A	81	PHE	0	-0.014	-0.015	14.721	-0.382	-0.382	0.000	0.000	0.000	0.000
72	A	82	VAL	0	0.020	0.019	18.999	-0.321	-0.321	0.000	0.000	0.000	0.000
73	A	83	PRO	0	0.007	0.012	21.522	0.082	0.082	0.000	0.000	0.000	0.000
74	A	84	SER	0	0.041	0.025	18.764	0.206	0.206	0.000	0.000	0.000	0.000
75	A	85	LEU	0	0.038	0.024	15.082	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	86	THR	0	-0.059	-0.043	19.128	0.183	0.183	0.000	0.000	0.000	0.000
77	A	87	GLN	0	-0.012	-0.006	22.321	0.022	0.022	0.000	0.000	0.000	0.000
78	A	88	ASP	-1	-0.870	-0.940	17.309	-17.275	-17.275	0.000	0.000	0.000	0.000
79	A	89	LEU	0	-0.036	-0.036	19.491	0.144	0.144	0.000	0.000	0.000	0.000
80	A	90	GLU	-1	-0.899	-0.929	21.054	-11.143	-11.143	0.000	0.000	0.000	0.000
81	A	91	VAL	0	-0.001	-0.013	21.214	0.432	0.432	0.000	0.000	0.000	0.000
82	A	92	TYR	0	-0.008	0.004	17.984	0.332	0.332	0.000	0.000	0.000	0.000
83	A	93	ARG	1	0.914	0.939	20.935	13.341	13.341	0.000	0.000	0.000	0.000
84	A	94	LYS	1	0.820	0.919	24.236	12.155	12.155	0.000	0.000	0.000	0.000
85	A	95	VAL	0	0.055	0.031	21.031	0.188	0.188	0.000	0.000	0.000	0.000
86	A	96	VAL	0	-0.012	-0.006	21.340	0.153	0.153	0.000	0.000	0.000	0.000
87	A	97	LYS	1	0.833	0.919	24.158	11.030	11.030	0.000	0.000	0.000	0.000
88	A	98	GLU	-1	-0.955	-0.971	26.929	-10.849	-10.849	0.000	0.000	0.000	0.000
89	A	99	LYS	0	0.000	0.014	24.680	-0.653	-0.653	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:PRO)