FMO DATABASE

FMODB ID: 9Q5M2

Calculation Name: 2DK8-A-Other549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DK8

Chain ID: A

ChEMBL ID:

UniProt ID: Q921X6

Base Structure: SolutionNMR

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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) / 20230712

Total energy (hartree)

FMO2-HF: Electronic energy	-484803.949916
FMO2-HF: Nuclear repulsion	453621.517858
FMO2-HF: Total energy	-31182.432058
FMO2-MP2: Total energy	-31272.255471

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.
-59.033	-58.306	-0.003	-0.197	-0.527	0

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 : 0.853 / q_NPA : 0.911

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].
3	A	3	SER	0	0.003	0.008	3.833	4.241	4.968	-0.003	-0.197	-0.527
4	A	4	GLY	0	0.027	0.015	6.359	3.489	3.489	0.000	0.000	0.000
5	A	5	SER	0	-0.045	-0.029	8.747	-2.920	-2.920	0.000	0.000	0.000
6	A	6	SER	0	-0.053	-0.040	10.909	-1.062	-1.062	0.000	0.000	0.000
7	A	7	GLY	0	0.063	0.028	12.130	1.079	1.079	0.000	0.000	0.000
8	A	8	PRO	0	-0.053	-0.021	15.897	-0.275	-0.275	0.000	0.000	0.000
9	A	9	ASP	-1	-0.832	-0.902	13.989	-21.544	-21.544	0.000	0.000	0.000
10	A	10	ALA	0	0.008	-0.001	15.887	-0.899	-0.899	0.000	0.000	0.000
11	A	11	ASP	-1	-0.857	-0.933	16.403	-17.666	-17.666	0.000	0.000	0.000
12	A	12	PRO	0	-0.002	-0.002	13.393	-0.162	-0.162	0.000	0.000	0.000
13	A	13	VAL	0	0.026	0.009	15.157	-0.183	-0.183	0.000	0.000	0.000
14	A	14	GLU	-1	-0.907	-0.945	17.862	-13.990	-13.990	0.000	0.000	0.000
15	A	15	ILE	0	-0.016	-0.003	13.590	0.120	0.120	0.000	0.000	0.000
16	A	16	GLU	-1	-0.884	-0.964	13.342	-22.578	-22.578	0.000	0.000	0.000
17	A	17	ASN	0	0.014	-0.008	16.185	0.327	0.327	0.000	0.000	0.000
18	A	18	ARG	1	0.887	0.940	18.898	14.701	14.701	0.000	0.000	0.000
19	A	19	ILE	0	-0.015	-0.013	13.584	0.240	0.240	0.000	0.000	0.000
20	A	20	ILE	0	0.003	0.002	17.898	0.401	0.401	0.000	0.000	0.000
21	A	21	GLU	-1	-0.927	-0.965	20.273	-11.524	-11.524	0.000	0.000	0.000
22	A	22	LEU	0	-0.054	-0.025	19.423	0.439	0.439	0.000	0.000	0.000
23	A	23	CYS	0	-0.077	-0.048	18.752	0.018	0.018	0.000	0.000	0.000
24	A	24	HIS	0	0.011	0.008	21.445	0.537	0.537	0.000	0.000	0.000
25	A	25	GLN	0	-0.037	-0.013	24.966	0.555	0.555	0.000	0.000	0.000
26	A	26	PHE	0	-0.060	-0.018	22.794	0.408	0.408	0.000	0.000	0.000
27	A	27	PRO	0	0.039	0.027	23.371	-0.563	-0.563	0.000	0.000	0.000
28	A	28	HIS	0	-0.023	-0.028	24.498	-0.402	-0.402	0.000	0.000	0.000
29	A	29	GLY	0	0.016	0.006	20.755	-0.404	-0.404	0.000	0.000	0.000
30	A	30	ILE	0	-0.025	-0.007	17.188	0.447	0.447	0.000	0.000	0.000
31	A	31	THR	0	0.052	0.009	16.632	-0.825	-0.825	0.000	0.000	0.000
32	A	32	ASP	-1	-0.844	-0.927	11.355	-25.233	-25.233	0.000	0.000	0.000
33	A	33	GLN	0	0.007	-0.001	14.718	-0.348	-0.348	0.000	0.000	0.000
34	A	34	VAL	0	-0.003	0.012	17.980	0.616	0.616	0.000	0.000	0.000
35	A	35	ILE	0	0.032	0.009	14.385	0.318	0.318	0.000	0.000	0.000
36	A	36	GLN	0	-0.053	-0.028	15.484	0.813	0.813	0.000	0.000	0.000
37	A	37	ASN	0	-0.014	-0.016	17.438	0.523	0.523	0.000	0.000	0.000
38	A	38	GLU	-1	-0.856	-0.917	20.085	-12.701	-12.701	0.000	0.000	0.000
39	A	39	MET	0	-0.082	-0.037	16.527	0.522	0.522	0.000	0.000	0.000
40	A	40	PRO	0	0.011	0.019	17.579	-1.121	-1.121	0.000	0.000	0.000
41	A	41	HIS	0	-0.018	-0.010	18.328	-0.269	-0.269	0.000	0.000	0.000
42	A	42	ILE	0	-0.024	-0.005	12.967	-0.462	-0.462	0.000	0.000	0.000
43	A	43	GLU	-1	-0.828	-0.926	11.608	-25.273	-25.273	0.000	0.000	0.000
44	A	44	ALA	0	-0.036	-0.012	9.420	-1.089	-1.089	0.000	0.000	0.000
45	A	45	GLN	0	-0.028	-0.024	5.765	-6.055	-6.055	0.000	0.000	0.000
46	A	46	GLN	0	0.046	0.027	7.457	-4.836	-4.836	0.000	0.000	0.000
47	A	47	ARG	1	0.903	0.944	10.201	24.332	24.332	0.000	0.000	0.000
48	A	48	ALA	0	-0.010	0.006	5.280	0.056	0.056	0.000	0.000	0.000
49	A	49	VAL	0	-0.036	-0.023	6.068	-1.791	-1.791	0.000	0.000	0.000
50	A	50	ALA	0	0.068	0.036	7.453	1.166	1.166	0.000	0.000	0.000
51	A	51	ILE	0	0.031	0.017	9.409	1.288	1.288	0.000	0.000	0.000
52	A	52	ASN	0	-0.049	-0.037	5.703	2.182	2.182	0.000	0.000	0.000
53	A	53	ARG	1	0.870	0.938	6.964	34.095	34.095	0.000	0.000	0.000
54	A	54	LEU	0	0.038	0.030	10.839	1.464	1.464	0.000	0.000	0.000
55	A	55	LEU	0	-0.044	-0.011	10.052	1.166	1.166	0.000	0.000	0.000
56	A	56	SER	0	-0.089	-0.035	10.439	1.929	1.929	0.000	0.000	0.000
57	A	57	MET	0	-0.048	-0.034	12.546	1.687	1.687	0.000	0.000	0.000
58	A	58	GLY	0	-0.018	0.005	15.507	1.238	1.238	0.000	0.000	0.000
59	A	59	GLN	0	-0.010	-0.012	17.021	1.609	1.609	0.000	0.000	0.000
60	A	60	LEU	0	-0.031	-0.006	13.215	0.467	0.467	0.000	0.000	0.000
61	A	61	ASP	-1	-0.795	-0.899	16.417	-17.059	-17.059	0.000	0.000	0.000
62	A	62	LEU	0	-0.050	-0.020	10.999	-0.183	-0.183	0.000	0.000	0.000
63	A	63	LEU	0	0.017	0.015	15.503	0.820	0.820	0.000	0.000	0.000
64	A	64	ARG	1	0.957	0.977	14.093	18.319	18.319	0.000	0.000	0.000
65	A	65	SER	0	-0.001	-0.020	17.315	1.253	1.253	0.000	0.000	0.000
66	A	66	ASN	0	-0.005	0.009	20.116	-0.257	-0.257	0.000	0.000	0.000
67	A	67	THR	0	-0.017	-0.002	18.929	-0.547	-0.547	0.000	0.000	0.000
68	A	68	GLY	0	0.009	0.011	14.938	0.050	0.050	0.000	0.000	0.000
69	A	69	LEU	0	-0.063	-0.041	10.667	0.290	0.290	0.000	0.000	0.000
70	A	70	LEU	0	-0.020	0.005	14.889	0.031	0.031	0.000	0.000	0.000
71	A	71	TYR	0	0.010	-0.013	11.499	-1.370	-1.370	0.000	0.000	0.000
72	A	72	ARG	1	0.837	0.902	16.616	14.947	14.947	0.000	0.000	0.000
73	A	73	ILE	0	0.030	0.017	19.026	-0.847	-0.847	0.000	0.000	0.000
74	A	74	LYS	1	0.825	0.934	16.863	17.666	17.666	0.000	0.000	0.000
75	A	75	ASP	-1	-0.816	-0.882	21.371	-12.270	-12.270	0.000	0.000	0.000
76	A	76	SER	0	-0.030	-0.041	24.258	-0.409	-0.409	0.000	0.000	0.000
77	A	77	GLY	0	-0.015	0.010	26.967	0.301	0.301	0.000	0.000	0.000
78	A	78	PRO	0	-0.005	-0.003	30.301	-0.055	-0.055	0.000	0.000	0.000
79	A	79	SER	0	-0.050	-0.037	33.588	-0.090	-0.090	0.000	0.000	0.000
80	A	80	SER	0	-0.039	-0.034	35.549	0.047	0.047	0.000	0.000	0.000
81	A	81	GLY	-1	-0.898	-0.918	38.715	-7.968	-7.968	0.000	0.000	0.000

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