FMO DATABASE

FMODB ID: VYNJ1

Calculation Name: 2KN9-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KN9

Chain ID: A

ChEMBL ID:

UniProt ID: O05893

Base Structure: SolutionNMR

Registration Date: 2025-10-05

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	-457409.814449
FMO2-HF: Nuclear repulsion	423695.5627
FMO2-HF: Total energy	-33714.251749
FMO2-MP2: Total energy	-33806.392451

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.
-54.819	-52.467	0.017	-0.887	-1.482	-0.001

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 : 0.865 / q_NPA : 0.923

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	HIS	0	0.012	0.003	3.421	4.676	6.883	0.018	-0.877	-1.349	-0.001
4	A	4	HIS	0	0.033	0.035	5.162	1.429	1.574	-0.001	-0.010	-0.133	0.000
5	A	5	HIS	0	-0.029	-0.027	7.880	0.967	0.967	0.000	0.000	0.000	0.000
6	A	6	HIS	0	0.000	0.006	11.606	0.740	0.740	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.019	0.005	15.311	0.580	0.580	0.000	0.000	0.000	0.000
8	A	8	HIS	0	0.014	0.005	18.246	0.442	0.442	0.000	0.000	0.000	0.000
9	A	9	MET	0	-0.009	-0.012	21.618	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.001	0.015	24.333	0.408	0.408	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.012	-0.008	26.969	-0.095	-0.095	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.010	0.006	29.383	0.139	0.139	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.917	-0.963	32.029	-8.421	-8.421	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.064	-0.040	35.121	0.197	0.197	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.010	0.018	36.956	0.292	0.292	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.020	-0.016	40.238	0.128	0.128	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.005	0.002	42.543	0.254	0.254	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.036	0.005	45.395	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.022	0.013	48.721	0.048	0.048	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.045	0.022	52.069	0.068	0.068	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.027	-0.007	54.661	0.100	0.100	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.041	-0.024	57.268	0.079	0.079	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.019	-0.010	60.113	0.146	0.146	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.798	-0.877	61.124	-5.174	-5.174	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.062	-0.026	59.023	0.067	0.067	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.792	0.882	60.028	5.193	5.193	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.013	0.015	53.564	-0.081	-0.081	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.032	0.008	55.960	0.132	0.132	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.760	0.858	52.013	5.823	5.823	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.025	0.004	52.406	0.146	0.146	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.013	-0.020	53.159	-0.107	-0.107	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.066	-0.049	53.452	-0.092	-0.092	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.134	-0.054	48.334	-0.049	-0.049	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.004	0.010	48.395	-0.129	-0.129	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.005	-0.017	48.005	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.902	-0.942	49.426	-6.185	-6.185	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.006	0.008	50.677	-0.120	-0.120	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.732	-0.870	53.013	-5.882	-5.882	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.716	-0.844	54.722	-5.278	-5.278	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.045	-0.016	55.623	0.035	0.035	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.078	-0.044	48.831	-0.066	-0.066	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.003	0.006	53.004	-0.035	-0.035	0.000	0.000	0.000	0.000
43	A	43	TRP	0	-0.023	-0.046	46.506	-0.127	-0.127	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.030	0.005	49.540	0.059	0.059	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.959	-0.977	45.931	-6.920	-6.920	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.905	-0.939	49.524	-5.896	-5.896	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.029	-0.007	52.977	0.119	0.119	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.034	-0.001	54.802	0.113	0.113	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.045	0.023	54.841	-0.122	-0.122	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.005	0.013	54.152	0.043	0.043	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.019	-0.011	56.091	0.073	0.073	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.047	-0.032	58.749	0.138	0.138	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.811	0.879	60.033	5.047	5.047	0.000	0.000	0.000	0.000
54	A	54	TRP	0	0.053	0.015	57.539	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.973	-0.988	62.650	-4.822	-4.822	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.973	-0.979	63.834	-5.014	-5.014	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.014	0.013	58.327	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.008	-0.005	60.883	0.072	0.072	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.928	-0.978	62.543	-4.970	-4.970	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.957	-0.977	62.213	-5.062	-5.062	0.000	0.000	0.000	0.000
61	A	61	TRP	0	-0.099	-0.042	54.497	-0.099	-0.099	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.014	-0.016	55.872	0.010	0.010	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.054	-0.012	51.914	-0.110	-0.110	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.008	-0.001	49.843	-0.065	-0.065	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.859	-0.907	46.322	-6.908	-6.908	0.000	0.000	0.000	0.000
66	A	66	CYS	0	-0.075	-0.053	47.726	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	67	GLY	0	-0.010	0.001	50.283	0.059	0.059	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.034	-0.011	53.707	0.120	0.120	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.072	0.034	55.873	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.893	0.937	58.941	5.093	5.093	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.011	-0.010	60.806	0.031	0.031	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.904	-0.933	57.188	-5.444	-5.444	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.021	-0.004	54.526	-0.150	-0.150	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.853	-0.879	56.067	-5.577	-5.577	0.000	0.000	0.000	0.000
75	A	75	MET	0	-0.026	-0.020	58.767	-0.053	-0.053	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.039	-0.021	55.833	0.038	0.038	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.951	-0.978	59.113	-5.161	-5.161	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.006	-0.014	56.321	-0.110	-0.110	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.010	0.014	56.644	0.054	0.054	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.750	0.848	51.907	5.919	5.919	0.000	0.000	0.000	0.000
81	A	81	SER	-1	-0.948	-0.960	56.483	-5.434	-5.434	0.000	0.000	0.000	0.000

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