FMO DATABASE

FMODB ID: 67RLZ

Calculation Name: 4QUF-C-Xray547

Preferred Name:

Target Type:

Ligand Name: n-trimethyllysine

Ligand 3-letter code: M3L

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4QUF

Chain ID: C

ChEMBL ID:

UniProt ID: Q7JXA8

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	-343482.973401
FMO2-HF: Nuclear repulsion	318431.657476
FMO2-HF: Total energy	-25051.315924
FMO2-MP2: Total energy	-25124.547668

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:22:GLU)

Summations of interaction energy for fragment #1(A:22: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.
-5.688	-1.044	2.681	-2.805	-4.52	0.009

Interaction energy analysis for fragmet #1(A:22:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.075 / q_NPA : -0.061

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	24	TYR	0	0.007	0.009	3.558	2.513	4.511	-0.014	-0.908	-1.076	-0.001
4	A	25	VAL	0	-0.001	-0.003	4.809	-2.176	-2.142	-0.001	-0.009	-0.024	0.000
40	A	61	VAL	0	-0.011	0.011	4.399	-3.578	-3.515	-0.001	-0.011	-0.051	0.000
41	A	62	GLY	0	0.038	0.006	4.781	1.141	1.276	-0.001	-0.002	-0.132	0.000
42	A	63	ASN	0	-0.019	-0.028	2.451	-8.488	-6.119	2.699	-1.872	-3.196	0.010
43	A	64	CYS	0	-0.004	0.010	5.145	-1.378	-1.333	-0.001	-0.003	-0.041	0.000
5	A	26	VAL	0	0.003	0.001	6.092	0.981	0.981	0.000	0.000	0.000	0.000
6	A	27	GLU	-1	-0.893	-0.937	8.731	-1.605	-1.605	0.000	0.000	0.000	0.000
7	A	28	LYS	1	0.924	0.946	12.394	1.419	1.419	0.000	0.000	0.000	0.000
8	A	29	ILE	0	0.011	0.018	9.898	-0.178	-0.178	0.000	0.000	0.000	0.000
9	A	30	LEU	0	-0.007	-0.021	13.816	0.168	0.168	0.000	0.000	0.000	0.000
10	A	31	GLY	0	0.012	0.001	16.157	0.133	0.133	0.000	0.000	0.000	0.000
11	A	32	LYS	1	0.835	0.902	15.971	-0.078	-0.078	0.000	0.000	0.000	0.000
12	A	33	ARG	1	0.879	0.949	16.924	0.118	0.118	0.000	0.000	0.000	0.000
13	A	34	PHE	0	0.018	0.002	18.168	0.051	0.051	0.000	0.000	0.000	0.000
14	A	35	VAL	0	0.004	0.004	18.555	-0.068	-0.068	0.000	0.000	0.000	0.000
15	A	36	ASN	0	0.001	-0.003	19.892	0.045	0.045	0.000	0.000	0.000	0.000
16	A	37	GLY	0	0.036	0.023	21.810	0.070	0.070	0.000	0.000	0.000	0.000
17	A	38	ARG	1	0.871	0.929	14.967	-1.245	-1.245	0.000	0.000	0.000	0.000
18	A	39	PRO	0	-0.003	0.012	14.988	-0.126	-0.126	0.000	0.000	0.000	0.000
19	A	40	GLN	0	0.065	0.020	13.510	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	41	VAL	0	0.017	-0.007	10.854	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	42	LEU	0	-0.034	-0.005	12.461	-0.101	-0.101	0.000	0.000	0.000	0.000
22	A	43	VAL	0	-0.001	-0.005	8.146	0.006	0.006	0.000	0.000	0.000	0.000
23	A	44	LYS	1	0.860	0.947	11.469	1.952	1.952	0.000	0.000	0.000	0.000
24	A	45	TRP	0	0.041	-0.004	5.352	-0.725	-0.725	0.000	0.000	0.000	0.000
25	A	46	SER	0	0.007	-0.009	10.707	0.498	0.498	0.000	0.000	0.000	0.000
26	A	47	GLY	0	-0.010	0.002	12.687	-0.109	-0.109	0.000	0.000	0.000	0.000
27	A	48	PHE	0	-0.033	0.003	11.754	0.234	0.234	0.000	0.000	0.000	0.000
28	A	49	PRO	0	0.002	-0.002	15.801	0.008	0.008	0.000	0.000	0.000	0.000
29	A	50	ASN	0	0.048	0.002	17.189	-0.183	-0.183	0.000	0.000	0.000	0.000
30	A	51	GLU	-1	-0.905	-0.954	18.261	-0.791	-0.791	0.000	0.000	0.000	0.000
31	A	52	ASN	0	-0.039	-0.021	14.519	0.126	0.126	0.000	0.000	0.000	0.000
32	A	53	ASN	0	-0.012	-0.005	13.762	-0.393	-0.393	0.000	0.000	0.000	0.000
33	A	54	THR	0	-0.010	-0.018	10.173	0.139	0.139	0.000	0.000	0.000	0.000
34	A	55	TRP	0	-0.045	-0.029	12.317	-0.136	-0.136	0.000	0.000	0.000	0.000
35	A	56	GLU	-1	-0.760	-0.841	7.765	-0.803	-0.803	0.000	0.000	0.000	0.000
36	A	57	PRO	0	-0.018	-0.017	9.765	-0.079	-0.079	0.000	0.000	0.000	0.000
37	A	58	LEU	0	-0.004	-0.008	9.458	-0.242	-0.242	0.000	0.000	0.000	0.000
38	A	59	GLU	-1	-0.867	-0.934	8.774	1.751	1.751	0.000	0.000	0.000	0.000
39	A	60	ASN	0	-0.025	-0.015	5.707	3.515	3.515	0.000	0.000	0.000	0.000
44	A	65	MET	0	-0.004	0.025	7.659	0.441	0.441	0.000	0.000	0.000	0.000
45	A	66	LYS	1	0.814	0.885	10.646	1.447	1.447	0.000	0.000	0.000	0.000
46	A	67	LEU	0	0.033	0.019	10.630	0.200	0.200	0.000	0.000	0.000	0.000
47	A	68	VAL	0	0.025	0.014	10.446	0.179	0.179	0.000	0.000	0.000	0.000
48	A	69	SER	0	0.005	-0.002	13.202	0.136	0.136	0.000	0.000	0.000	0.000
49	A	70	ASP	-1	-0.810	-0.889	15.978	-1.024	-1.024	0.000	0.000	0.000	0.000
50	A	71	PHE	0	-0.014	0.007	15.962	0.106	0.106	0.000	0.000	0.000	0.000
51	A	72	GLU	-1	-0.843	-0.908	16.591	-0.036	-0.036	0.000	0.000	0.000	0.000
52	A	73	SER	0	-0.024	-0.002	19.143	0.097	0.097	0.000	0.000	0.000	0.000
53	A	74	GLU	-1	-0.764	-0.847	21.112	-0.422	-0.422	0.000	0.000	0.000	0.000
54	A	75	VAL	0	-0.006	-0.004	20.914	0.048	0.048	0.000	0.000	0.000	0.000
55	A	76	PHE	0	0.003	-0.002	23.296	0.055	0.055	0.000	0.000	0.000	0.000
56	A	77	ARG	1	0.810	0.859	25.274	0.419	0.419	0.000	0.000	0.000	0.000
57	A	78	LEU	0	-0.069	-0.044	25.192	0.021	0.021	0.000	0.000	0.000	0.000
58	A	79	HIS	0	-0.008	0.003	27.402	0.013	0.013	0.000	0.000	0.000	0.000
59	A	80	ARG	1	0.915	0.950	29.160	0.127	0.127	0.000	0.000	0.000	0.000
60	A	81	LYS	1	0.864	0.948	31.226	0.250	0.250	0.000	0.000	0.000	0.000
61	A	82	ALA	-1	-0.933	-0.942	32.438	-0.109	-0.109	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:GLU)