FMO DATABASE

FMODB ID: 92832

Calculation Name: 4HDD-A-Xray549

Preferred Name: Rhomboid protease GlpG

Target Type: SINGLE PROTEIN

Ligand Name: acetate ion

Ligand 3-letter code: ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4HDD

Chain ID: A

ChEMBL ID: CHEMBL4296282

UniProt ID: P09391

Base Structure: X-ray

Registration Date: 2025-10-12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-299334.752191
FMO2-HF: Nuclear repulsion	273193.711372
FMO2-HF: Total energy	-26141.04082
FMO2-MP2: Total energy	-26217.086316

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:2:LEU)

Summations of interaction energy for fragment #1(A:2:LEU)

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.
-39.618	-37.409	2.669	-1.238	-3.641	-0.008

Interaction energy analysis for fragmet #1(A:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.924

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	4	ILE	0	0.024	0.014	2.438	0.139	2.266	2.660	-1.377	-3.410	-0.008
4	A	5	THR	0	0.044	0.018	3.531	4.511	4.593	0.009	0.139	-0.231	0.000
5	A	6	SER	0	-0.024	-0.019	6.977	-1.765	-1.765	0.000	0.000	0.000	0.000
6	A	7	PHE	0	0.012	0.007	10.207	1.337	1.337	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.058	0.032	13.691	-0.100	-0.100	0.000	0.000	0.000	0.000
8	A	9	ASN	0	0.007	0.008	17.006	0.500	0.500	0.000	0.000	0.000	0.000
9	A	10	PRO	0	0.077	0.031	16.299	-0.683	-0.683	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.985	0.980	16.907	12.900	12.900	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.013	0.003	15.142	0.163	0.163	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.000	0.001	12.590	-0.620	-0.620	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.060	-0.043	13.397	-1.588	-1.588	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.054	0.032	15.870	-0.267	-0.267	0.000	0.000	0.000	0.000
15	A	16	PHE	0	-0.021	-0.007	8.520	0.057	0.057	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.017	-0.012	10.608	-0.869	-0.869	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.829	-0.906	12.973	-17.725	-17.725	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.006	-0.002	14.853	0.242	0.242	0.000	0.000	0.000	0.000
19	A	20	MET	0	0.002	0.007	10.578	0.823	0.823	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.016	0.017	13.684	0.021	0.021	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.088	-0.060	14.747	1.086	1.086	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.073	-0.034	14.934	1.092	1.092	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.002	0.006	15.288	-0.343	-0.343	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.059	-0.027	9.174	-1.397	-1.397	0.000	0.000	0.000	0.000
25	A	26	ILE	0	0.009	0.000	10.314	-0.067	-0.067	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.026	-0.008	6.361	-4.763	-4.763	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.013	-0.014	7.508	1.916	1.916	0.000	0.000	0.000	0.000
28	A	29	ILE	0	0.030	0.010	8.437	-2.604	-2.604	0.000	0.000	0.000	0.000
29	A	30	GLN	0	0.009	0.003	8.658	1.864	1.864	0.000	0.000	0.000	0.000
30	A	31	GLN	0	-0.022	-0.016	10.591	0.976	0.976	0.000	0.000	0.000	0.000
31	A	32	HIS	0	-0.036	-0.009	11.881	1.753	1.753	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.024	-0.007	15.985	0.213	0.213	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.017	-0.028	19.691	-0.498	-0.498	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.057	-0.041	22.422	0.040	0.040	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.853	-0.892	25.586	-12.223	-12.223	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.009	-0.011	28.037	0.199	0.199	0.000	0.000	0.000	0.000
37	A	38	TRP	0	-0.019	-0.005	28.699	0.272	0.272	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.034	-0.018	33.666	0.136	0.136	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.020	0.017	37.456	-0.082	-0.082	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.902	-0.951	39.533	-7.327	-7.327	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.898	-0.958	39.221	-8.079	-8.079	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.046	-0.021	42.418	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	44	GLN	0	0.022	0.001	42.929	0.131	0.131	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.030	0.025	40.107	-0.089	-0.089	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.837	-0.946	40.845	-7.880	-7.880	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.891	0.959	42.868	6.959	6.959	0.000	0.000	0.000	0.000
47	A	48	VAL	0	0.020	0.006	37.948	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.901	0.953	34.962	8.485	8.485	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.002	0.007	39.527	-0.082	-0.082	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.787	-0.846	40.499	-7.513	-7.513	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.000	0.004	33.435	-0.100	-0.100	0.000	0.000	0.000	0.000
52	A	53	ALA	0	-0.005	-0.009	36.698	-0.181	-0.181	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.814	0.880	38.544	7.278	7.278	0.000	0.000	0.000	0.000
54	A	55	PHE	0	-0.010	-0.007	32.500	-0.075	-0.075	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.031	-0.038	31.766	-0.211	-0.211	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-1.008	-0.979	34.682	-8.083	-8.083	0.000	0.000	0.000	0.000
57	A	58	ASN	0	0.033	0.008	36.786	-0.280	-0.280	0.000	0.000	0.000	0.000
58	A	59	PRO	0	0.005	0.001	32.523	0.136	0.136	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.029	-0.011	35.336	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.828	-0.902	37.012	-7.241	-7.241	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.014	-0.011	40.627	-0.064	-0.064	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.806	0.903	42.031	7.504	7.504	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.050	-0.053	38.116	0.025	0.025	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.060	-0.021	36.735	-0.136	-0.136	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.078	-0.032	39.871	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	67	ALA	-1	-0.952	-0.952	41.467	-7.354	-7.354	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LEU)