FMO DATABASE

FMODB ID: QMKYY

Calculation Name: 3RDY-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RDY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9S9F3

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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-388143.510785
FMO2-HF: Nuclear repulsion	361585.65873
FMO2-HF: Total energy	-26557.852056
FMO2-MP2: Total energy	-26634.198286

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:GLN)

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

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.
-116.745	-113.795	0.115	-1.535	-1.53	-0.01

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

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

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	5	SER	0	0.011	-0.006	3.055	-6.838	-3.888	0.115	-1.535	-1.530	-0.010
4	A	6	GLY	0	0.055	0.031	5.500	1.811	1.811	0.000	0.000	0.000	0.000
5	A	7	LYS	1	0.778	0.880	7.731	15.874	15.874	0.000	0.000	0.000	0.000
6	A	8	GLN	0	-0.004	-0.010	6.256	-3.859	-3.859	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.907	-0.958	9.546	-25.905	-25.905	0.000	0.000	0.000	0.000
8	A	10	TRP	0	0.003	-0.010	12.437	0.211	0.211	0.000	0.000	0.000	0.000
9	A	11	PRO	0	-0.002	-0.006	15.905	0.920	0.920	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.827	-0.916	18.073	-16.105	-16.105	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.050	-0.016	19.301	0.619	0.619	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.018	0.008	21.186	0.383	0.383	0.000	0.000	0.000	0.000
13	A	15	GLY	0	-0.003	0.002	23.671	0.392	0.392	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.824	-0.911	24.745	-12.201	-12.201	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.933	0.972	26.828	10.225	10.225	0.000	0.000	0.000	0.000
16	A	18	GLY	0	0.089	0.029	24.531	-0.264	-0.264	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.039	-0.030	24.101	-0.384	-0.384	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.767	0.887	25.700	11.728	11.728	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.089	0.042	21.722	-0.344	-0.344	0.000	0.000	0.000	0.000
20	A	22	ALA	0	0.027	0.005	20.297	-0.682	-0.682	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.833	0.918	20.246	14.427	14.427	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.009	-0.002	19.286	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.003	-0.007	15.405	-0.450	-0.450	0.000	0.000	0.000	0.000
24	A	26	GLU	-1	-0.834	-0.922	15.779	-17.138	-17.138	0.000	0.000	0.000	0.000
25	A	27	ASN	0	-0.046	-0.013	16.921	-0.314	-0.314	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.840	-0.894	15.264	-17.308	-17.308	0.000	0.000	0.000	0.000
27	A	29	ASN	0	-0.096	-0.074	8.868	-0.936	-0.936	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.874	-0.941	13.079	-17.828	-17.828	0.000	0.000	0.000	0.000
29	A	31	ASP	-1	-0.912	-0.916	9.379	-30.373	-30.373	0.000	0.000	0.000	0.000
30	A	32	VAL	0	-0.098	-0.044	10.912	-0.772	-0.772	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.902	0.958	13.490	18.861	18.861	0.000	0.000	0.000	0.000
32	A	34	ALA	0	-0.002	0.000	15.846	-0.820	-0.820	0.000	0.000	0.000	0.000
33	A	35	ILE	0	-0.076	-0.043	17.272	0.919	0.919	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.018	-0.005	20.028	-0.142	-0.142	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.051	-0.018	20.939	0.337	0.337	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.028	0.015	24.246	-0.089	-0.089	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.871	-0.925	24.768	-12.043	-12.043	0.000	0.000	0.000	0.000
38	A	40	GLY	0	-0.009	0.003	24.245	0.387	0.387	0.000	0.000	0.000	0.000
39	A	41	SER	0	-0.070	-0.049	23.530	0.295	0.295	0.000	0.000	0.000	0.000
40	A	42	ALA	0	-0.027	-0.012	22.441	-0.612	-0.612	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.019	0.016	17.625	0.082	0.082	0.000	0.000	0.000	0.000
42	A	44	PRO	0	-0.042	-0.023	15.821	0.107	0.107	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.891	0.935	14.157	19.556	19.556	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.820	-0.880	11.618	-22.686	-22.686	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.016	-0.011	7.147	0.167	0.167	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.746	0.831	7.699	23.538	23.538	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.734	-0.818	7.003	-25.719	-25.719	0.000	0.000	0.000	0.000
48	A	51	ARG	1	0.692	0.800	10.631	26.872	26.872	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.047	0.028	11.849	-1.543	-1.543	0.000	0.000	0.000	0.000
50	A	53	TRP	0	-0.013	-0.008	14.213	2.261	2.261	0.000	0.000	0.000	0.000
51	A	54	VAL	0	-0.005	-0.012	17.108	-0.166	-0.166	0.000	0.000	0.000	0.000
52	A	55	PHE	0	0.039	0.015	18.169	0.607	0.607	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.036	-0.023	22.421	0.131	0.131	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.726	-0.866	26.011	-10.350	-10.350	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.939	-0.978	29.459	-9.083	-9.083	0.000	0.000	0.000	0.000
56	A	59	ARG	1	0.850	0.929	32.211	9.516	9.516	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.021	-0.002	29.266	0.083	0.083	0.000	0.000	0.000	0.000
58	A	61	VAL	0	-0.094	-0.057	28.245	-0.275	-0.275	0.000	0.000	0.000	0.000
59	A	62	VAL	0	-0.003	0.001	21.840	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	VAL	0	0.002	0.003	24.456	0.220	0.220	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.879	-0.929	19.760	-14.426	-14.426	0.000	0.000	0.000	0.000
62	A	65	THR	0	-0.031	-0.040	16.032	0.273	0.273	0.000	0.000	0.000	0.000
63	A	66	PRO	0	-0.014	0.010	16.784	-0.761	-0.761	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.007	-0.012	11.573	-0.440	-0.440	0.000	0.000	0.000	0.000
65	A	68	VAL	0	-0.008	0.002	7.641	1.107	1.107	0.000	0.000	0.000	0.000
66	A	69	MET	-1	-0.799	-0.850	9.086	-27.795	-27.795	0.000	0.000	0.000	0.000

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