FMO DATABASE

FMODB ID: VYK71

Calculation Name: 2D8D-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D8D

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLA5

Base Structure: X-ray

Registration Date: 2025-10-05

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-494772.404036
FMO2-HF: Nuclear repulsion	462178.628857
FMO2-HF: Total energy	-32593.775179
FMO2-MP2: Total energy	-32690.635965

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
-34.636	-25.662	10.086	-8.116	-10.944	0.029

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.014

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	5	ILE	0	0.074	0.038	2.050	-25.146	-19.219	5.410	-5.069	-6.268	0.054
4	A	6	GLN	0	-0.025	-0.027	1.998	-15.560	-13.116	4.666	-2.877	-4.233	-0.025
5	A	7	ALA	0	0.016	0.011	3.767	1.008	1.611	0.010	-0.170	-0.443	0.000
6	A	8	LEU	0	0.054	0.017	5.507	1.962	1.962	0.000	0.000	0.000	0.000
7	A	9	ARG	1	0.965	0.983	6.209	-4.264	-4.264	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.962	0.987	6.551	7.679	7.679	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.898	-0.939	9.572	-3.064	-3.064	0.000	0.000	0.000	0.000
10	A	12	VAL	0	0.000	0.005	11.444	0.401	0.401	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.851	-0.919	11.795	-2.021	-2.021	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.748	0.852	13.786	1.723	1.723	0.000	0.000	0.000	0.000
13	A	15	VAL	0	0.057	0.030	15.594	0.142	0.142	0.000	0.000	0.000	0.000
14	A	16	ASN	0	0.017	-0.003	15.309	0.279	0.279	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.826	0.897	14.727	1.972	1.972	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.831	-0.881	20.447	-0.932	-0.932	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.033	0.017	20.011	0.074	0.074	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.027	0.019	22.788	0.045	0.045	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.952	0.988	24.636	0.749	0.749	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.034	0.003	26.171	0.029	0.029	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.000	0.008	25.699	0.047	0.047	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.015	-0.026	28.280	0.022	0.022	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-1.020	-1.016	30.602	-0.386	-0.386	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.957	0.978	31.975	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.053	0.032	33.221	0.023	0.023	0.000	0.000	0.000	0.000
26	A	28	ARG	1	0.900	0.957	31.722	0.372	0.372	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.017	-0.006	35.400	0.009	0.009	0.000	0.000	0.000	0.000
28	A	30	VAL	0	0.021	0.011	37.502	0.011	0.011	0.000	0.000	0.000	0.000
29	A	31	GLN	0	-0.009	-0.006	38.489	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.867	-0.905	41.195	-0.169	-0.169	0.000	0.000	0.000	0.000
31	A	33	ILE	0	-0.018	-0.006	40.929	0.009	0.009	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.108	0.056	43.621	0.009	0.009	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.803	0.893	41.801	0.171	0.171	0.000	0.000	0.000	0.000
34	A	36	LEU	0	0.032	0.011	46.529	0.007	0.007	0.000	0.000	0.000	0.000
35	A	37	GLN	0	0.004	-0.002	45.795	0.002	0.002	0.000	0.000	0.000	0.000
36	A	38	THR	0	-0.064	-0.036	48.799	0.012	0.012	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.996	-0.988	51.279	-0.093	-0.093	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.041	-0.023	52.068	0.004	0.004	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.019	0.003	54.361	0.008	0.008	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.055	-0.024	51.010	0.012	0.012	0.000	0.000	0.000	0.000
41	A	43	PRO	0	-0.018	-0.015	49.382	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	44	HIS	0	-0.007	-0.010	45.066	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.023	-0.006	41.927	0.005	0.005	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.786	-0.902	43.942	0.095	0.095	0.000	0.000	0.000	0.000
45	A	47	PRO	0	0.012	-0.001	43.098	0.006	0.006	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.898	0.954	43.548	-0.137	-0.137	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.998	1.009	40.185	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.909	-0.973	39.128	0.167	0.167	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.815	-0.914	38.944	0.329	0.329	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.908	-0.960	40.215	0.108	0.108	0.000	0.000	0.000	0.000
51	A	53	MET	0	-0.071	-0.026	36.664	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.022	-0.008	34.341	0.019	0.019	0.000	0.000	0.000	0.000
53	A	55	ALA	0	-0.024	0.012	35.906	0.035	0.035	0.000	0.000	0.000	0.000
54	A	56	TYR	0	0.006	0.008	35.199	0.018	0.018	0.000	0.000	0.000	0.000
55	A	57	LEU	0	0.006	0.002	31.468	0.011	0.011	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.064	-0.049	32.127	0.057	0.057	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.023	-0.015	33.237	0.032	0.032	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.929	-0.968	32.605	0.123	0.123	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.060	-0.040	27.614	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	62	PRO	0	-0.029	-0.003	25.485	0.023	0.023	0.000	0.000	0.000	0.000
61	A	63	GLY	0	-0.005	0.024	24.794	0.073	0.073	0.000	0.000	0.000	0.000
62	A	64	PRO	0	-0.053	-0.052	19.179	-0.062	-0.062	0.000	0.000	0.000	0.000
63	A	65	PHE	0	-0.020	-0.017	19.939	0.112	0.112	0.000	0.000	0.000	0.000
64	A	66	PRO	0	0.056	0.023	24.079	-0.098	-0.098	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.766	-0.868	27.462	0.559	0.559	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.845	-0.926	30.706	0.569	0.569	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.053	-0.030	24.485	0.033	0.033	0.000	0.000	0.000	0.000
68	A	70	ILE	0	0.028	0.022	26.026	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.870	0.916	28.887	-0.440	-0.440	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.820	0.907	29.780	-0.678	-0.678	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.004	0.003	24.496	-0.033	-0.033	0.000	0.000	0.000	0.000
72	A	74	PHE	0	0.024	0.006	28.680	-0.060	-0.060	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.896	0.956	31.493	-0.404	-0.404	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.871	-0.910	29.840	0.394	0.394	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.027	-0.011	27.617	-0.051	-0.051	0.000	0.000	0.000	0.000
76	A	78	PHE	0	-0.049	-0.027	31.681	-0.050	-0.050	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.891	0.918	34.062	-0.393	-0.393	0.000	0.000	0.000	0.000
78	A	80	ALA	0	-0.048	-0.015	32.666	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.113	-0.070	34.600	-0.048	-0.048	0.000	0.000	0.000	0.000
80	A	82	LEU	-1	-0.942	-0.945	36.786	0.038	0.038	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)