FMO DATABASE

FMODB ID: MRK5Z

Calculation Name: 2KRB-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KRB

Chain ID: A

ChEMBL ID:

UniProt ID: P55884

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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-524410.268387
FMO2-HF: Nuclear repulsion	493007.318482
FMO2-HF: Total energy	-31402.949905
FMO2-MP2: Total energy	-31497.305169

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:15:ASP)

Summations of interaction energy for fragment #1(A:15:ASP)

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.
-8.309	-3.287	0.104	-2.217	-2.908	-0.001

Interaction energy analysis for fragmet #1(A:15:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.035

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	17	VAL	0	-0.010	0.003	2.926	2.222	5.907	0.026	-1.759	-1.952	0.000
4	A	18	ILE	0	-0.016	0.001	4.015	-3.001	-2.804	-0.001	-0.101	-0.096	-0.001
57	A	71	PRO	0	0.016	0.008	3.493	-0.696	-0.475	0.017	-0.092	-0.146	0.000
58	A	72	ALA	0	0.000	-0.005	4.947	0.251	0.355	-0.001	-0.005	-0.097	0.000
60	A	74	ALA	0	0.002	0.020	4.363	0.615	0.671	-0.001	-0.033	-0.022	0.000
61	A	75	VAL	0	0.004	-0.011	3.196	0.494	1.253	0.064	-0.227	-0.595	0.000
5	A	19	VAL	0	-0.010	-0.008	6.735	0.545	0.545	0.000	0.000	0.000	0.000
6	A	20	VAL	0	-0.027	-0.010	9.395	0.446	0.446	0.000	0.000	0.000	0.000
7	A	21	ASP	-1	-0.854	-0.935	12.936	-0.914	-0.914	0.000	0.000	0.000	0.000
8	A	22	ASN	0	-0.041	-0.028	15.687	0.086	0.086	0.000	0.000	0.000	0.000
9	A	23	VAL	0	-0.045	-0.020	16.890	0.055	0.055	0.000	0.000	0.000	0.000
10	A	24	PRO	0	-0.001	0.022	19.764	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	25	GLN	0	-0.001	-0.007	23.052	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	26	VAL	0	-0.026	-0.019	24.628	0.070	0.070	0.000	0.000	0.000	0.000
13	A	27	GLY	0	0.057	0.029	27.669	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	28	PRO	0	0.044	0.004	30.116	-0.042	-0.042	0.000	0.000	0.000	0.000
15	A	29	ASP	-1	-0.906	-0.949	32.553	-0.487	-0.487	0.000	0.000	0.000	0.000
16	A	30	ARG	1	0.853	0.930	27.502	0.550	0.550	0.000	0.000	0.000	0.000
17	A	31	LEU	0	0.049	0.023	26.061	-0.050	-0.050	0.000	0.000	0.000	0.000
18	A	32	GLU	-1	-0.851	-0.924	24.797	-0.962	-0.962	0.000	0.000	0.000	0.000
19	A	33	LYS	1	0.906	0.945	24.702	0.547	0.547	0.000	0.000	0.000	0.000
20	A	34	LEU	0	0.014	0.026	20.398	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	35	LYS	1	0.896	0.956	18.244	1.720	1.720	0.000	0.000	0.000	0.000
22	A	36	ASN	0	0.008	-0.006	20.025	-0.084	-0.084	0.000	0.000	0.000	0.000
23	A	37	VAL	0	-0.035	-0.031	20.547	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	38	ILE	0	0.066	0.052	15.511	0.043	0.043	0.000	0.000	0.000	0.000
25	A	39	HIS	0	0.068	0.044	16.943	-0.076	-0.076	0.000	0.000	0.000	0.000
26	A	40	LYS	1	0.831	0.920	18.684	1.015	1.015	0.000	0.000	0.000	0.000
27	A	41	ILE	0	-0.058	-0.014	16.166	0.100	0.100	0.000	0.000	0.000	0.000
28	A	42	PHE	0	0.085	0.017	12.413	0.105	0.105	0.000	0.000	0.000	0.000
29	A	43	SER	0	-0.045	-0.035	15.199	-0.078	-0.078	0.000	0.000	0.000	0.000
30	A	44	LYS	1	0.822	0.927	16.904	0.867	0.867	0.000	0.000	0.000	0.000
31	A	45	PHE	0	0.052	0.035	12.506	0.124	0.124	0.000	0.000	0.000	0.000
32	A	46	GLY	0	0.019	0.018	13.278	-0.114	-0.114	0.000	0.000	0.000	0.000
33	A	47	LYS	1	0.917	0.959	14.303	1.574	1.574	0.000	0.000	0.000	0.000
34	A	48	ILE	0	-0.007	0.006	12.761	-0.269	-0.269	0.000	0.000	0.000	0.000
35	A	49	THR	0	-0.043	-0.023	11.992	0.482	0.482	0.000	0.000	0.000	0.000
36	A	50	ASN	0	-0.021	0.009	11.361	0.181	0.181	0.000	0.000	0.000	0.000
37	A	51	ASP	-1	-0.859	-0.944	12.347	-2.586	-2.586	0.000	0.000	0.000	0.000
38	A	52	PHE	0	0.034	0.017	11.836	0.341	0.341	0.000	0.000	0.000	0.000
39	A	53	TYR	0	-0.007	-0.023	15.021	-0.089	-0.089	0.000	0.000	0.000	0.000
40	A	54	PRO	0	0.009	0.016	15.714	0.181	0.181	0.000	0.000	0.000	0.000
41	A	55	GLU	-1	-0.849	-0.926	18.746	-0.904	-0.904	0.000	0.000	0.000	0.000
42	A	56	GLU	-1	-0.934	-0.960	21.995	-0.780	-0.780	0.000	0.000	0.000	0.000
43	A	57	ASP	-1	-0.941	-0.985	24.003	-0.527	-0.527	0.000	0.000	0.000	0.000
44	A	58	GLY	0	-0.001	0.017	25.836	0.035	0.035	0.000	0.000	0.000	0.000
45	A	59	LYS	1	0.907	0.955	26.530	0.548	0.548	0.000	0.000	0.000	0.000
46	A	60	THR	0	-0.040	-0.049	25.268	-0.051	-0.051	0.000	0.000	0.000	0.000
47	A	61	LYS	1	0.864	0.942	19.848	1.196	1.196	0.000	0.000	0.000	0.000
48	A	62	GLY	0	0.061	0.023	20.453	0.067	0.067	0.000	0.000	0.000	0.000
49	A	63	TYR	0	-0.010	-0.006	11.814	0.142	0.142	0.000	0.000	0.000	0.000
50	A	64	ILE	0	-0.062	-0.018	13.428	0.063	0.063	0.000	0.000	0.000	0.000
51	A	65	PHE	0	0.014	0.000	6.814	0.000	0.000	0.000	0.000	0.000	0.000
52	A	66	LEU	0	-0.020	-0.015	9.495	0.667	0.667	0.000	0.000	0.000	0.000
53	A	67	GLU	-1	-0.905	-0.955	7.745	-8.673	-8.673	0.000	0.000	0.000	0.000
54	A	68	TYR	0	0.007	-0.010	7.826	1.949	1.949	0.000	0.000	0.000	0.000
55	A	69	ALA	0	0.027	0.013	8.802	-0.871	-0.871	0.000	0.000	0.000	0.000
56	A	70	SER	0	0.019	-0.003	8.631	0.477	0.477	0.000	0.000	0.000	0.000
59	A	73	HIS	0	-0.010	-0.006	7.328	0.548	0.548	0.000	0.000	0.000	0.000
62	A	76	ASP	-1	-0.874	-0.933	5.541	0.722	0.722	0.000	0.000	0.000	0.000
63	A	77	ALA	0	-0.004	0.002	8.805	0.341	0.341	0.000	0.000	0.000	0.000
64	A	78	VAL	0	-0.006	-0.008	6.143	0.417	0.417	0.000	0.000	0.000	0.000
65	A	79	LYS	1	0.917	0.955	7.556	-3.160	-3.160	0.000	0.000	0.000	0.000
66	A	80	ASN	0	-0.084	-0.042	11.250	0.206	0.206	0.000	0.000	0.000	0.000
67	A	81	ALA	0	-0.069	-0.039	12.918	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	82	ASP	-1	-0.893	-0.940	13.070	-0.192	-0.192	0.000	0.000	0.000	0.000
69	A	83	GLY	0	0.012	0.019	14.504	0.134	0.134	0.000	0.000	0.000	0.000
70	A	84	TYR	0	-0.064	-0.034	14.162	0.026	0.026	0.000	0.000	0.000	0.000
71	A	85	LYS	1	0.976	0.972	19.538	0.374	0.374	0.000	0.000	0.000	0.000
72	A	86	LEU	0	-0.032	-0.028	22.914	0.005	0.005	0.000	0.000	0.000	0.000
73	A	87	ASP	-1	-0.945	-0.956	25.128	-0.276	-0.276	0.000	0.000	0.000	0.000
74	A	88	LYS	1	0.920	0.957	26.790	0.361	0.361	0.000	0.000	0.000	0.000
75	A	89	GLN	0	0.012	-0.002	27.243	0.009	0.009	0.000	0.000	0.000	0.000
76	A	90	HIS	0	0.030	0.022	23.984	0.054	0.054	0.000	0.000	0.000	0.000
77	A	91	THR	0	-0.026	-0.003	20.111	-0.060	-0.060	0.000	0.000	0.000	0.000
78	A	92	PHE	0	0.027	0.018	17.359	0.033	0.033	0.000	0.000	0.000	0.000
79	A	93	ARG	1	0.944	0.970	14.907	0.137	0.137	0.000	0.000	0.000	0.000
80	A	94	VAL	0	0.003	0.010	9.986	-0.281	-0.281	0.000	0.000	0.000	0.000
81	A	95	ASN	-1	-0.861	-0.927	6.612	-4.042	-4.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ASP)