FMO DATABASE

FMODB ID: 463NN

Calculation Name: 2X9B-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2X9B

Chain ID: A

ChEMBL ID:

UniProt ID: O80297

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	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-334262.692417
FMO2-HF: Nuclear repulsion	309977.032206
FMO2-HF: Total energy	-24285.660211
FMO2-MP2: Total energy	-24355.909827

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:ALA)

Summations of interaction energy for fragment #1(A:1:ALA)

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.
-139.585	-138.088	-0.01	-0.664	-0.824	-0.001

Interaction energy analysis for fragmet #1(A:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.898

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	THR	0	0.012	0.004	3.767	3.315	4.641	-0.009	-0.624	-0.694	-0.001
33	A	33	ASN	0	-0.066	-0.036	4.054	-0.671	-0.500	-0.001	-0.040	-0.130	0.000
4	A	4	ASP	-1	-0.770	-0.891	6.398	-26.458	-26.458	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.018	-0.007	9.797	1.499	1.499	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.862	-0.923	6.473	-45.651	-45.651	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.012	0.017	6.289	-3.289	-3.289	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.020	-0.006	10.866	1.722	1.722	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.057	-0.029	13.560	2.048	2.048	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.840	0.926	8.053	35.638	35.638	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.018	-0.006	14.899	0.769	0.769	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.020	0.005	17.593	-0.574	-0.574	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.066	-0.024	16.637	0.740	0.740	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.864	-0.918	21.509	-12.233	-12.233	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.010	-0.001	23.127	0.020	0.020	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.040	-0.032	22.528	0.250	0.250	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.017	0.018	15.971	-0.701	-0.701	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.012	-0.017	18.544	0.798	0.798	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.082	-0.041	16.657	-0.619	-0.619	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.044	-0.016	17.631	-0.678	-0.678	0.000	0.000	0.000	0.000
21	A	21	TRP	0	-0.054	-0.030	13.173	0.452	0.452	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.856	0.919	20.289	11.199	11.199	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.787	-0.871	17.317	-17.317	-17.317	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.005	0.000	22.228	0.164	0.164	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.927	-0.974	25.850	-10.431	-10.431	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.006	0.035	22.965	0.246	0.246	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.795	0.849	21.680	11.708	11.708	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.012	-0.026	16.363	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.032	0.020	15.866	0.537	0.537	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.017	0.007	8.387	-1.207	-1.207	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.005	-0.007	11.285	0.655	0.655	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.924	-0.970	8.598	-27.786	-27.786	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.039	0.028	9.093	1.942	1.942	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.022	-0.017	12.009	0.085	0.085	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.840	-0.910	15.390	-14.479	-14.479	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.043	-0.012	18.881	0.232	0.232	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.033	-0.027	22.013	0.528	0.528	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.013	-0.003	25.075	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.036	-0.027	28.372	0.176	0.176	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.031	0.030	27.574	-0.246	-0.246	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.048	-0.041	27.985	0.473	0.473	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.043	0.027	27.238	-0.424	-0.424	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.050	-0.044	25.251	0.515	0.515	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.791	-0.869	25.214	-12.425	-12.425	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.055	-0.019	26.301	0.027	0.027	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.764	-0.850	26.521	-11.752	-11.752	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.010	-0.005	22.020	-0.514	-0.514	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.002	-0.016	21.726	-1.160	-1.160	0.000	0.000	0.000	0.000
50	A	51	TRP	0	-0.062	-0.021	22.659	0.869	0.869	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.024	0.013	23.019	-0.875	-0.875	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.035	0.009	24.611	0.486	0.486	0.000	0.000	0.000	0.000
53	A	54	HIS	1	0.840	0.918	23.028	12.920	12.920	0.000	0.000	0.000	0.000
54	A	55	TRP	0	0.002	0.016	18.463	-0.258	-0.258	0.000	0.000	0.000	0.000
55	A	56	THR	0	0.017	-0.014	18.836	-0.075	-0.075	0.000	0.000	0.000	0.000
56	A	57	PRO	0	-0.013	0.019	13.633	0.046	0.046	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.015	-0.025	14.264	0.757	0.757	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.851	0.923	11.436	21.103	21.103	0.000	0.000	0.000	0.000
59	A	60	ALA	0	0.013	-0.016	6.062	-0.563	-0.563	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.072	-0.038	5.577	3.200	3.200	0.000	0.000	0.000	0.000
61	A	62	ASP	-2	-1.904	-1.935	5.944	-64.289	-64.289	0.000	0.000	0.000	0.000

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