FMO DATABASE

FMODB ID: LR549

Calculation Name: 2FYU-K-Xray549

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | (5s)-3-anilino-5-(2,4-difluorophenyl)-5-methyl-1,3-oxazolidine-2,4-dione | fe2/s2 (inorganic) cluster

Ligand 3-letter code: HEM | FDN | FES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FYU

Chain ID: K

ChEMBL ID:

UniProt ID: P00125

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	53
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-220791.812227
FMO2-HF: Nuclear repulsion	199776.36089
FMO2-HF: Total energy	-21015.451337
FMO2-MP2: Total energy	-21078.209071

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(K:1:MET)

Summations of interaction energy for fragment #1(K: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.
105.34	110.437	1.541	-2.982	-3.657	-0.029

Interaction energy analysis for fragmet #1(K:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.912 / q_NPA : 0.943

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	K	3	THR	0	0.070	0.028	2.264	-8.486	-3.785	1.542	-2.869	-3.374	-0.029
4	K	4	ARG	1	0.949	0.989	4.161	42.633	43.029	-0.001	-0.113	-0.283	0.000
5	K	5	PHE	0	0.001	-0.011	6.059	5.053	5.053	0.000	0.000	0.000	0.000
6	K	6	LEU	0	0.016	0.020	6.913	3.258	3.258	0.000	0.000	0.000	0.000
7	K	7	GLY	0	0.071	0.026	9.605	0.163	0.163	0.000	0.000	0.000	0.000
8	K	8	PRO	0	-0.029	-0.021	12.783	0.459	0.459	0.000	0.000	0.000	0.000
9	K	9	ARG	1	1.045	1.022	14.395	19.541	19.541	0.000	0.000	0.000	0.000
10	K	10	TYR	0	0.009	0.011	10.600	1.118	1.118	0.000	0.000	0.000	0.000
11	K	11	ARG	1	0.970	0.982	14.963	18.455	18.455	0.000	0.000	0.000	0.000
12	K	12	GLN	0	-0.001	0.004	17.003	0.535	0.535	0.000	0.000	0.000	0.000
13	K	13	LEU	0	0.027	0.005	16.762	0.529	0.529	0.000	0.000	0.000	0.000
14	K	14	ALA	0	0.007	0.004	17.091	0.508	0.508	0.000	0.000	0.000	0.000
15	K	15	ARG	1	0.921	0.956	19.006	14.917	14.917	0.000	0.000	0.000	0.000
16	K	16	ASN	0	0.015	0.002	22.237	0.751	0.751	0.000	0.000	0.000	0.000
17	K	17	TRP	0	0.025	0.021	20.008	0.548	0.548	0.000	0.000	0.000	0.000
18	K	18	VAL	0	0.004	0.016	22.039	0.270	0.270	0.000	0.000	0.000	0.000
19	K	19	PRO	0	0.031	0.023	23.439	0.275	0.275	0.000	0.000	0.000	0.000
20	K	20	THR	0	0.038	0.016	24.988	0.358	0.358	0.000	0.000	0.000	0.000
21	K	21	ALA	0	-0.008	-0.003	22.258	0.184	0.184	0.000	0.000	0.000	0.000
22	K	22	SER	0	-0.033	-0.023	24.243	0.274	0.274	0.000	0.000	0.000	0.000
23	K	23	LEU	0	0.014	0.012	26.817	0.321	0.321	0.000	0.000	0.000	0.000
24	K	24	TRP	0	0.018	0.002	25.644	0.342	0.342	0.000	0.000	0.000	0.000
25	K	25	GLY	0	-0.002	0.006	26.909	0.124	0.124	0.000	0.000	0.000	0.000
26	K	26	ALA	0	-0.008	-0.004	27.552	0.246	0.246	0.000	0.000	0.000	0.000
27	K	27	VAL	0	-0.002	-0.002	30.702	0.285	0.285	0.000	0.000	0.000	0.000
28	K	28	GLY	0	0.006	0.005	29.333	0.235	0.235	0.000	0.000	0.000	0.000
29	K	29	ALA	0	-0.021	-0.011	30.403	0.194	0.194	0.000	0.000	0.000	0.000
30	K	30	VAL	0	0.012	0.000	32.021	0.243	0.243	0.000	0.000	0.000	0.000
31	K	31	GLY	0	0.026	0.014	34.148	0.257	0.257	0.000	0.000	0.000	0.000
32	K	32	LEU	0	-0.009	-0.004	31.001	0.176	0.176	0.000	0.000	0.000	0.000
33	K	33	VAL	0	-0.002	-0.005	34.437	0.195	0.195	0.000	0.000	0.000	0.000
34	K	34	TRP	0	-0.020	0.001	37.235	0.134	0.134	0.000	0.000	0.000	0.000
35	K	35	ALA	0	-0.009	-0.003	36.631	0.172	0.172	0.000	0.000	0.000	0.000
36	K	36	THR	0	-0.072	-0.051	36.546	0.036	0.036	0.000	0.000	0.000	0.000
37	K	37	ASP	-1	-0.888	-0.936	39.546	-7.024	-7.024	0.000	0.000	0.000	0.000
38	K	38	TRP	0	-0.030	-0.016	33.871	0.058	0.058	0.000	0.000	0.000	0.000
39	K	39	ARG	1	0.923	0.944	40.621	7.411	7.411	0.000	0.000	0.000	0.000
40	K	40	LEU	0	0.022	0.009	38.703	0.071	0.071	0.000	0.000	0.000	0.000
41	K	41	ILE	0	-0.002	0.009	36.901	-0.010	-0.010	0.000	0.000	0.000	0.000
42	K	42	LEU	0	-0.022	-0.022	40.951	0.112	0.112	0.000	0.000	0.000	0.000
43	K	43	ASP	-1	-0.870	-0.908	43.793	-6.637	-6.637	0.000	0.000	0.000	0.000
44	K	44	TRP	0	-0.029	-0.019	43.572	0.136	0.136	0.000	0.000	0.000	0.000
45	K	45	VAL	0	-0.035	0.002	43.085	-0.071	-0.071	0.000	0.000	0.000	0.000
46	K	46	PRO	0	0.008	-0.003	45.761	0.131	0.131	0.000	0.000	0.000	0.000
47	K	47	TYR	0	-0.008	-0.003	48.610	0.143	0.143	0.000	0.000	0.000	0.000
48	K	48	ILE	0	0.035	0.002	45.290	-0.126	-0.126	0.000	0.000	0.000	0.000
49	K	49	ASN	0	0.011	0.017	48.432	-0.115	-0.115	0.000	0.000	0.000	0.000
50	K	50	GLY	0	-0.045	-0.017	50.211	0.140	0.140	0.000	0.000	0.000	0.000
51	K	51	LYS	1	0.858	0.904	46.245	6.713	6.713	0.000	0.000	0.000	0.000
52	K	52	PHE	0	-0.002	0.014	52.380	0.131	0.131	0.000	0.000	0.000	0.000
53	K	53	LYS	0	-0.006	0.004	54.669	-0.026	-0.026	0.000	0.000	0.000	0.000

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