FMO DATABASE

FMODB ID: KK6R3

Calculation Name: 2EBP-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EBP

Chain ID: A

ChEMBL ID:

UniProt ID: O94885

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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-381459.808784
FMO2-HF: Nuclear repulsion	354050.56041
FMO2-HF: Total energy	-27409.248373
FMO2-MP2: Total energy	-27488.029739

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.
23.864	24.591	0	-0.29	-0.437	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 : 0.874 / q_NPA : 0.924

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].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].
3	A	3	SER	0	0.040	0.008	3.823	-5.828	-5.101	-0.290	-0.437
4	A	4	GLY	0	0.012	0.024	6.297	4.453	4.453	0.000	0.000
5	A	5	SER	0	-0.019	-0.005	8.259	2.694	2.694	0.000	0.000
6	A	6	SER	0	-0.008	-0.014	9.762	-3.324	-3.324	0.000	0.000
7	A	7	GLY	0	0.004	0.014	11.761	1.901	1.901	0.000	0.000
8	A	8	PHE	0	-0.026	-0.022	10.496	0.032	0.032	0.000	0.000
9	A	9	CYS	0	-0.035	0.000	15.911	0.812	0.812	0.000	0.000
10	A	10	GLY	0	0.043	0.010	18.340	0.766	0.766	0.000	0.000
11	A	11	ARG	1	0.872	0.937	13.447	19.354	19.354	0.000	0.000
12	A	12	ALA	0	-0.015	0.000	18.453	0.912	0.912	0.000	0.000
13	A	13	ARG	1	0.991	1.003	19.217	12.334	12.334	0.000	0.000
14	A	14	VAL	0	0.013	0.012	20.531	0.769	0.769	0.000	0.000
15	A	15	HIS	1	0.874	0.934	22.799	10.752	10.752	0.000	0.000
16	A	16	THR	0	-0.049	-0.034	25.951	0.591	0.591	0.000	0.000
17	A	17	ASP	-1	-0.813	-0.899	25.808	-12.142	-12.142	0.000	0.000
18	A	18	PHE	0	-0.001	-0.001	25.862	0.465	0.465	0.000	0.000
19	A	19	THR	0	-0.017	-0.024	25.436	-0.767	-0.767	0.000	0.000
20	A	20	PRO	0	0.002	0.017	24.902	0.430	0.430	0.000	0.000
21	A	21	SER	0	0.040	0.010	28.017	0.100	0.100	0.000	0.000
22	A	22	PRO	0	-0.032	-0.012	28.236	-0.393	-0.393	0.000	0.000
23	A	23	TYR	0	-0.034	-0.030	29.280	0.097	0.097	0.000	0.000
24	A	24	ASP	-1	-0.859	-0.907	28.144	-10.584	-10.584	0.000	0.000
25	A	25	THR	0	0.000	-0.005	22.857	-0.669	-0.669	0.000	0.000
26	A	26	ASP	-1	-0.875	-0.941	22.717	-13.006	-13.006	0.000	0.000
27	A	27	SER	0	-0.025	-0.014	23.437	-0.214	-0.214	0.000	0.000
28	A	28	LEU	0	-0.026	-0.003	18.512	-0.254	-0.254	0.000	0.000
29	A	29	LYS	1	0.944	0.969	20.972	13.965	13.965	0.000	0.000
30	A	30	LEU	0	-0.022	-0.001	20.657	-0.698	-0.698	0.000	0.000
31	A	31	LYS	1	0.851	0.917	21.161	13.348	13.348	0.000	0.000
32	A	32	LYS	1	0.934	0.969	21.943	10.297	10.297	0.000	0.000
33	A	33	GLY	0	-0.015	-0.016	21.390	0.227	0.227	0.000	0.000
34	A	34	ASP	-1	-0.868	-0.915	17.788	-16.510	-16.510	0.000	0.000
35	A	35	ILE	0	-0.034	-0.031	14.619	0.852	0.852	0.000	0.000
36	A	36	ILE	0	0.003	0.009	15.399	-0.774	-0.774	0.000	0.000
37	A	37	ASP	-1	-0.826	-0.895	12.017	-22.708	-22.708	0.000	0.000
38	A	38	ILE	0	-0.041	-0.036	15.052	0.265	0.265	0.000	0.000
39	A	39	ILE	0	0.012	0.010	15.522	-0.159	-0.159	0.000	0.000
40	A	40	SER	0	-0.002	-0.012	18.081	0.566	0.566	0.000	0.000
41	A	41	LYS	1	0.917	0.963	21.913	12.779	12.779	0.000	0.000
42	A	42	PRO	0	0.016	0.030	25.102	0.171	0.171	0.000	0.000
43	A	43	PRO	0	0.010	0.006	28.545	-0.004	-0.004	0.000	0.000
44	A	44	MET	0	0.023	0.002	31.595	0.200	0.200	0.000	0.000
45	A	45	GLY	0	0.023	0.012	30.681	-0.034	-0.034	0.000	0.000
46	A	46	THR	0	-0.085	-0.038	26.247	0.134	0.134	0.000	0.000
47	A	47	TRP	0	0.027	0.008	23.380	-0.232	-0.232	0.000	0.000
48	A	48	MET	0	0.060	0.039	19.871	-0.011	-0.011	0.000	0.000
49	A	49	GLY	0	-0.010	-0.016	17.696	-0.312	-0.312	0.000	0.000
50	A	50	LEU	0	0.011	0.000	10.517	0.324	0.324	0.000	0.000
51	A	51	LEU	0	0.023	0.002	14.007	-0.270	-0.270	0.000	0.000
52	A	52	ASN	0	0.002	-0.002	12.185	-0.692	-0.692	0.000	0.000
53	A	53	ASN	0	-0.026	-0.013	8.661	-0.996	-0.996	0.000	0.000
54	A	54	LYS	1	0.900	0.964	11.873	16.180	16.180	0.000	0.000
55	A	55	VAL	0	0.002	-0.002	15.543	-0.084	-0.084	0.000	0.000
56	A	56	GLY	0	0.045	0.025	17.165	0.554	0.554	0.000	0.000
57	A	57	THR	0	-0.026	-0.015	20.835	-0.082	-0.082	0.000	0.000
58	A	58	PHE	0	0.009	0.000	20.599	0.231	0.231	0.000	0.000
59	A	59	LYS	1	0.941	0.971	24.504	10.276	10.276	0.000	0.000
60	A	60	PHE	0	0.088	0.020	26.510	-0.122	-0.122	0.000	0.000
61	A	61	ILE	0	0.030	0.021	27.554	-0.095	-0.095	0.000	0.000
62	A	62	TYR	0	-0.007	0.003	26.270	0.291	0.291	0.000	0.000
63	A	63	VAL	0	-0.043	-0.029	22.397	-0.296	-0.296	0.000	0.000
64	A	64	ASP	-1	-0.865	-0.926	24.619	-10.659	-10.659	0.000	0.000
65	A	65	VAL	0	-0.034	-0.042	23.952	-0.657	-0.657	0.000	0.000
66	A	66	LEU	0	-0.006	0.003	20.278	0.349	0.349	0.000	0.000
67	A	67	SER	0	-0.034	-0.019	23.133	-0.385	-0.385	0.000	0.000
68	A	68	SER	0	0.020	0.001	23.117	0.280	0.280	0.000	0.000
69	A	69	GLY	0	0.026	0.033	25.872	0.331	0.331	0.000	0.000
70	A	70	PRO	0	-0.031	-0.020	28.271	-0.311	-0.311	0.000	0.000
71	A	71	SER	0	-0.008	-0.003	30.762	-0.011	-0.011	0.000	0.000
72	A	72	SER	0	-0.052	-0.040	28.027	-0.407	-0.407	0.000	0.000
73	A	73	GLY	-1	-0.918	-0.935	29.163	-10.528	-10.528	0.000	0.000

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