FMO DATABASE

FMODB ID: 4KRRN

Calculation Name: 2HD3-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HD3

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEJ8

Base Structure: X-ray

Registration Date: 2025-10-12

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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-602653.610284
FMO2-HF: Nuclear repulsion	566443.023377
FMO2-HF: Total energy	-36210.586907
FMO2-MP2: Total energy	-36312.907164

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.
-133.31	-125.274	4.428	-5.123	-7.34	-0.044

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 : 0.803 / q_NPA : 0.892

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	LEU	0	0.033	0.034	3.851	-1.204	0.607	-0.017	-0.832	-0.963	-0.002
56	A	56	LEU	0	0.005	0.005	2.429	-4.828	-3.912	0.477	-0.295	-1.097	-0.002
57	A	57	LEU	0	0.026	0.015	4.037	2.290	2.682	0.000	-0.093	-0.299	0.000
58	A	58	VAL	0	-0.030	-0.024	2.324	-29.317	-25.343	3.134	-3.548	-3.560	-0.038
59	A	59	SER	0	0.038	0.004	3.753	6.421	6.583	0.005	-0.045	-0.121	0.000
79	A	79	ILE	0	-0.044	-0.034	3.090	-0.132	0.649	0.829	-0.310	-1.300	-0.002
4	A	4	ALA	0	0.027	0.013	6.172	1.084	1.084	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.023	0.024	9.244	0.403	0.403	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.010	0.001	12.586	-0.068	-0.068	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.015	-0.003	14.466	1.070	1.070	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.011	0.004	17.574	1.114	1.114	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.045	-0.023	18.222	-0.585	-0.585	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.015	0.010	18.187	0.660	0.660	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.014	-0.007	21.390	-0.165	-0.165	0.000	0.000	0.000	0.000
12	A	12	CYS	0	0.003	0.006	21.867	0.338	0.338	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.021	0.005	24.382	-0.269	-0.269	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.002	0.003	27.469	0.079	0.079	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.806	0.896	20.257	13.519	13.519	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.075	0.033	21.733	0.532	0.532	0.000	0.000	0.000	0.000
17	A	17	HIS	0	0.074	0.023	22.431	-0.724	-0.724	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.000	0.010	20.663	-0.089	-0.089	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.016	-0.021	17.106	-0.679	-0.679	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.000	0.003	18.864	-0.279	-0.279	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.009	-0.007	21.203	0.166	0.166	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.826	-0.889	16.481	-16.068	-16.068	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.961	0.980	17.383	13.844	13.844	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.034	0.022	16.221	-1.014	-1.014	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.009	0.006	12.449	0.998	0.998	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.014	-0.008	14.510	-0.858	-0.858	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.009	-0.008	10.457	-0.198	-0.198	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.842	-0.921	12.964	-18.149	-18.149	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.048	-0.021	8.088	-2.768	-2.768	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.010	0.012	9.799	2.482	2.482	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.674	-0.808	9.526	-24.784	-24.784	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.041	-0.045	9.559	0.454	0.454	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.130	-0.086	11.134	2.070	2.070	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.007	0.013	13.630	1.322	1.322	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.100	-0.058	14.962	1.738	1.738	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.015	0.012	14.312	-1.640	-1.640	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.920	-0.963	11.648	-25.307	-25.307	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.029	-0.019	14.725	0.631	0.631	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.065	-0.026	12.372	0.330	0.330	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.025	-0.014	13.001	-1.458	-1.458	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.023	-0.011	11.652	0.098	0.098	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.003	-0.009	13.676	0.848	0.848	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.011	0.003	10.121	-1.389	-1.389	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.044	-0.017	11.639	1.682	1.682	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.742	-0.883	11.521	-21.502	-21.502	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.035	-0.022	12.133	0.628	0.628	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.061	-0.022	9.606	0.491	0.491	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.037	-0.026	14.241	1.114	1.114	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.024	-0.010	13.150	0.099	0.099	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.008	-0.005	15.291	0.657	0.657	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.064	-0.053	16.457	-1.025	-1.025	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.020	0.006	17.488	0.577	0.577	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.843	-0.917	14.104	-17.501	-17.501	0.000	0.000	0.000	0.000
54	A	54	TRP	0	0.035	0.019	10.627	-1.385	-1.385	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.011	-0.002	8.517	0.319	0.319	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.005	0.007	6.373	-2.674	-2.674	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.052	-0.029	9.392	0.476	0.476	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.041	-0.004	6.674	2.843	2.843	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.002	0.013	7.932	-0.430	-0.430	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.834	0.910	8.812	22.118	22.118	0.000	0.000	0.000	0.000
65	A	65	GLN	0	0.005	-0.012	10.416	1.835	1.835	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.026	-0.006	7.368	0.992	0.992	0.000	0.000	0.000	0.000
67	A	67	HIS	0	-0.004	0.016	9.442	1.039	1.039	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.809	0.886	12.166	18.596	18.596	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.032	0.044	15.036	0.950	0.950	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.736	-0.872	14.491	-20.933	-20.933	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.074	-0.033	16.746	0.373	0.373	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.008	-0.002	14.981	0.864	0.864	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.067	-0.027	16.120	-0.911	-0.911	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.002	-0.008	12.289	0.297	0.297	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.906	-0.948	11.321	-23.429	-23.429	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.004	-0.018	6.768	-4.692	-4.692	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.036	-0.006	7.518	3.795	3.795	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.006	0.015	6.600	-5.658	-5.658	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.018	0.007	6.488	1.694	1.694	0.000	0.000	0.000	0.000
81	A	81	ILE	0	0.007	0.010	8.131	-2.156	-2.156	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.030	-0.012	8.407	-0.221	-0.221	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.827	-0.912	10.770	-17.501	-17.501	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.921	-0.964	13.239	-14.626	-14.626	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.027	-0.002	11.093	-1.699	-1.699	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.020	0.008	13.657	1.283	1.283	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.006	-0.007	14.875	-0.933	-0.933	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.005	-0.002	17.426	0.766	0.766	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.017	-0.006	19.237	0.669	0.669	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.033	-0.005	20.862	0.752	0.752	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.004	-0.005	18.189	-0.768	-0.768	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.029	-0.004	15.425	0.602	0.602	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.013	0.003	13.846	0.214	0.214	0.000	0.000	0.000	0.000
94	A	94	HIS	1	0.799	0.874	16.369	14.776	14.776	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.859	0.952	14.934	17.013	17.013	0.000	0.000	0.000	0.000
96	A	96	LEU	-1	-0.895	-0.936	17.254	-13.299	-13.299	0.000	0.000	0.000	0.000

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