FMO DATABASE

FMODB ID: G8M31

Calculation Name: 2KNB-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KNB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JK66

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	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-494300.519058
FMO2-HF: Nuclear repulsion	463906.815986
FMO2-HF: Total energy	-30393.703072
FMO2-MP2: Total energy	-30482.920401

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.
-170.779	-169.349	39.8	-18.358	-22.873	-0.226

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 : 0.682 / 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

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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	3	VAL	0	0.036	0.024	2.722	2.910	5.597	0.584	-1.232	-2.039	-0.004
4	A	4	PHE	0	-0.033	-0.020	4.973	1.630	1.662	-0.001	-0.008	-0.023	0.000
16	A	16	GLU	-1	-0.843	-0.911	1.693	-121.252	-127.003	16.824	-6.819	-4.255	-0.087
17	A	17	VAL	0	-0.021	-0.010	2.517	10.550	12.774	0.679	-0.963	-1.941	-0.005
18	A	18	ASP	-1	-0.807	-0.891	1.761	-84.523	-86.151	11.550	-5.977	-3.944	-0.077
19	A	19	SER	0	-0.015	-0.013	4.338	0.382	0.626	-0.001	-0.032	-0.210	0.000
56	A	56	VAL	0	0.003	0.006	2.379	1.242	1.108	1.926	-0.341	-1.451	-0.002
57	A	57	GLN	0	0.000	-0.014	5.173	0.274	0.366	-0.001	-0.003	-0.088	0.000
61	A	61	LEU	0	-0.027	-0.012	2.972	-0.356	0.104	0.062	-0.118	-0.404	0.000
62	A	62	GLU	-1	-0.848	-0.922	2.472	-33.175	-31.274	1.897	-1.597	-2.202	-0.023
63	A	63	GLN	0	0.077	0.024	2.269	-19.683	-17.705	6.208	-2.530	-5.656	-0.028
64	A	64	GLN	0	-0.079	-0.040	3.263	5.952	5.087	0.074	1.277	-0.486	0.000
65	A	65	SER	0	0.023	0.017	4.180	6.068	6.258	-0.001	-0.015	-0.174	0.000
5	A	5	VAL	0	0.027	0.007	8.670	1.327	1.327	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.891	0.958	11.076	18.101	18.101	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.017	0.010	14.391	0.312	0.312	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.036	-0.022	17.464	0.580	0.580	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.003	0.010	18.212	0.281	0.281	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.010	0.001	19.134	0.050	0.050	0.000	0.000	0.000	0.000
11	A	11	TYR	0	0.012	0.002	16.127	-0.417	-0.417	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.036	0.003	12.622	0.376	0.376	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.013	-0.012	13.236	0.151	0.151	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.009	-0.002	8.928	-0.916	-0.916	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.033	-0.014	7.193	2.681	2.681	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.861	-0.938	6.081	-21.477	-21.477	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.063	-0.040	6.125	0.533	0.533	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.019	-0.018	7.694	0.546	0.546	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.025	-0.027	8.449	-0.953	-0.953	0.000	0.000	0.000	0.000
24	A	24	PHE	0	0.000	0.003	10.909	0.517	0.517	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.137	0.091	10.787	0.577	0.577	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.005	0.000	6.972	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.802	0.904	10.385	17.512	17.512	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.910	-0.956	13.952	-17.960	-17.960	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.071	-0.034	10.401	1.008	1.008	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.010	-0.001	13.537	0.663	0.663	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.001	0.003	16.053	0.996	0.996	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.936	0.969	13.439	23.066	23.066	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.857	0.933	16.384	18.437	18.437	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.014	-0.002	19.214	-0.097	-0.097	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.034	0.036	21.804	0.670	0.670	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.060	-0.024	21.228	0.577	0.577	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.041	0.014	21.679	-0.634	-0.634	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.067	0.023	18.381	-0.186	-0.186	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.899	-0.959	19.235	-13.104	-13.104	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.004	-0.002	21.885	0.144	0.144	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.043	0.002	16.996	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.802	0.862	16.724	14.007	14.007	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.065	0.028	10.208	-0.209	-0.209	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.023	-0.007	13.616	0.610	0.610	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.036	0.012	7.832	-1.050	-1.050	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.026	0.018	11.407	1.005	1.005	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.010	0.004	13.131	0.702	0.702	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.802	0.900	11.546	19.020	19.020	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.778	-0.857	14.081	-14.618	-14.618	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.003	-0.001	8.825	0.454	0.454	0.000	0.000	0.000	0.000
51	A	51	GLN	0	0.013	0.000	12.984	0.534	0.534	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.031	0.002	13.454	-1.121	-1.121	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.011	-0.011	14.270	-0.190	-0.190	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.006	0.022	10.316	0.188	0.188	0.000	0.000	0.000	0.000
55	A	55	THR	0	0.056	0.032	8.938	-0.242	-0.242	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.077	-0.037	6.802	3.177	3.177	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.089	-0.037	6.881	1.354	1.354	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.790	-0.885	6.734	-21.573	-21.573	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.040	-0.020	5.785	-1.997	-1.997	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.005	0.007	7.417	1.779	1.779	0.000	0.000	0.000	0.000
68	A	68	HIS	0	0.013	0.007	10.057	-0.085	-0.085	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.006	0.004	10.819	0.380	0.380	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.009	-0.016	14.946	0.574	0.574	0.000	0.000	0.000	0.000
71	A	71	GLN	0	0.011	0.004	18.771	0.019	0.019	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.859	0.932	20.947	12.857	12.857	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.033	0.028	23.034	0.085	0.085	0.000	0.000	0.000	0.000
74	A	74	GLN	0	-0.053	-0.052	26.184	0.151	0.151	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.931	0.968	28.786	8.856	8.856	0.000	0.000	0.000	0.000
76	A	76	LYS	0	0.082	0.060	29.064	1.209	1.209	0.000	0.000	0.000	0.000

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