FMO DATABASE

FMODB ID: 241NR

Calculation Name: 2ES2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ES2

Chain ID: A

ChEMBL ID:

UniProt ID: P32081

Base Structure: X-ray

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-375047.903423
FMO2-HF: Nuclear repulsion	349413.99544
FMO2-HF: Total energy	-25633.907984
FMO2-MP2: Total energy	-25709.512748

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.
-241.145	-230.699	12.469	-8.4	-14.513	-0.085

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 : 0.749 / q_NPA : 0.889

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	GLU	-1	-0.866	-0.951	2.567	-73.144	-69.365	1.281	-2.360	-2.700	-0.022
4	A	4	GLY	0	0.015	0.005	5.238	3.378	3.394	-0.001	-0.001	-0.014	0.000
48	A	48	SER	0	-0.011	-0.015	2.215	-5.633	-4.716	1.583	-0.931	-1.569	-0.004
49	A	49	PHE	0	-0.028	-0.018	2.544	3.752	5.889	0.912	-0.742	-2.307	-0.008
50	A	50	GLU	-1	-0.858	-0.926	2.332	-77.173	-74.864	8.658	-4.059	-6.907	-0.050
51	A	51	ILE	0	0.024	0.011	4.355	5.702	5.869	0.003	-0.062	-0.108	0.000
62	A	62	ASN	0	-0.057	-0.053	3.642	0.123	0.567	0.015	-0.098	-0.361	0.000
63	A	63	VAL	0	0.015	0.010	4.481	-2.928	-2.367	0.019	-0.133	-0.446	-0.001
64	A	64	THR	0	0.003	0.003	4.786	4.870	4.986	-0.001	-0.014	-0.101	0.000
5	A	5	LYS	1	0.851	0.926	8.373	21.125	21.125	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.021	0.005	11.247	-0.148	-0.148	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.836	0.924	13.278	17.279	17.279	0.000	0.000	0.000	0.000
8	A	8	TRP	0	-0.036	-0.028	16.150	1.309	1.309	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.006	-0.015	15.427	-1.066	-1.066	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.010	0.018	18.442	0.826	0.826	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.059	0.014	21.145	-0.048	-0.048	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.955	-0.968	22.075	-10.422	-10.422	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.866	0.922	23.310	11.096	11.096	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.016	0.023	19.376	-0.145	-0.145	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.053	-0.039	17.273	-0.395	-0.395	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.012	0.002	16.815	0.786	0.786	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.032	-0.015	14.625	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	ILE	0	0.008	0.009	8.296	0.471	0.471	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.895	-0.945	11.782	-17.822	-17.822	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.013	-0.022	8.634	-1.972	-1.972	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.890	-0.938	11.210	-16.984	-16.984	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.037	-0.029	13.584	-1.117	-1.117	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.103	-0.041	11.128	-0.137	-0.137	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.919	-0.952	14.489	-16.889	-16.889	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.851	-0.907	13.619	-18.652	-18.652	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.009	-0.010	9.686	0.305	0.305	0.000	0.000	0.000	0.000
27	A	27	PHE	0	-0.021	0.000	12.686	0.340	0.340	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.046	0.018	11.551	-1.390	-1.390	0.000	0.000	0.000	0.000
29	A	29	HIS	0	0.042	0.044	13.486	0.873	0.873	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.047	0.001	13.574	-1.024	-1.024	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.079	-0.061	14.213	-0.752	-0.752	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.014	0.019	9.563	-0.344	-0.344	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.048	0.006	9.084	-2.066	-2.066	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.020	-0.006	6.958	2.073	2.073	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.019	0.016	10.170	0.533	0.533	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.944	-0.979	13.384	-16.347	-16.347	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.021	-0.006	17.069	0.188	0.188	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.029	-0.025	18.966	-0.291	-0.291	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.869	0.942	13.017	18.265	18.265	0.000	0.000	0.000	0.000
40	A	40	THR	0	0.020	0.003	16.437	0.212	0.212	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.032	-0.024	11.826	-0.943	-0.943	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.883	-0.941	15.770	-12.830	-12.830	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.787	-0.900	15.876	-15.586	-15.586	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.028	-0.004	15.741	0.409	0.409	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.073	-0.040	11.330	0.543	0.543	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.000	0.008	9.643	-0.650	-0.650	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.002	-0.001	7.045	1.117	1.117	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.020	-0.014	7.694	-0.475	-0.475	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.871	-0.936	10.336	-17.905	-17.905	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.003	0.001	14.129	0.332	0.332	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.067	-0.059	15.842	0.645	0.645	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.889	0.936	18.771	13.529	13.529	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.075	0.069	17.665	0.270	0.270	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.016	0.016	12.538	-0.299	-0.299	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.057	-0.033	12.392	1.805	1.805	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.003	0.005	8.692	-1.984	-1.984	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.036	-0.028	6.663	2.818	2.818	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.852	0.925	6.757	17.760	17.760	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.857	-0.905	5.489	-36.173	-36.173	0.000	0.000	0.000	0.000
67	A	67	ALA	-1	-0.946	-0.977	9.172	-20.131	-20.131	0.000	0.000	0.000	0.000

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