FMO DATABASE

FMODB ID: 555VZ

Calculation Name: 2QIC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: n-trimethyllysine | zinc ion

Ligand 3-letter code: M3L | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2QIC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UK53

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	51
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-262680.084711
FMO2-HF: Nuclear repulsion	240080.746706
FMO2-HF: Total energy	-22599.338005
FMO2-MP2: Total energy	-22658.698489

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:209:GLU)

Summations of interaction energy for fragment #1(A:209: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.
-2.657	-1.269	-0.008	-0.602	-0.778	0

Interaction energy analysis for fragmet #1(A:209:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.047

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	211	THR	0	-0.025	-0.025	3.877	-2.868	-1.776	-0.012	-0.495	-0.584	0.001
10	A	218	VAL	0	0.041	0.016	3.423	-0.771	-0.475	0.004	-0.107	-0.194	-0.001
4	A	212	TYR	0	0.024	0.007	6.453	0.270	0.270	0.000	0.000	0.000	0.000
5	A	213	CYS	-1	-0.776	-0.749	9.983	-2.422	-2.422	0.000	0.000	0.000	0.000
6	A	214	LEU	0	-0.005	-0.003	13.380	0.040	0.040	0.000	0.000	0.000	0.000
7	A	215	CYS	0	-0.022	-0.005	13.044	0.069	0.069	0.000	0.000	0.000	0.000
8	A	216	ASN	0	-0.014	0.003	10.387	0.344	0.344	0.000	0.000	0.000	0.000
9	A	217	GLN	0	-0.010	-0.003	8.184	-0.661	-0.661	0.000	0.000	0.000	0.000
11	A	219	SER	0	-0.022	0.004	5.919	2.715	2.715	0.000	0.000	0.000	0.000
12	A	220	TYR	0	0.030	-0.006	8.344	-0.129	-0.129	0.000	0.000	0.000	0.000
13	A	221	GLY	0	-0.007	-0.001	11.117	0.309	0.309	0.000	0.000	0.000	0.000
14	A	222	GLU	-1	-0.907	-0.948	14.340	-1.877	-1.877	0.000	0.000	0.000	0.000
15	A	223	MET	0	-0.028	-0.003	11.356	-0.189	-0.189	0.000	0.000	0.000	0.000
16	A	224	ILE	0	-0.014	-0.014	15.547	0.192	0.192	0.000	0.000	0.000	0.000
17	A	225	GLY	0	0.051	0.040	17.376	-0.164	-0.164	0.000	0.000	0.000	0.000
18	A	226	CYS	0	-0.090	-0.029	18.329	0.248	0.248	0.000	0.000	0.000	0.000
19	A	227	ASP	-1	-0.776	-0.885	20.993	-1.112	-1.112	0.000	0.000	0.000	0.000
20	A	228	ASN	0	-0.033	-0.038	22.898	0.137	0.137	0.000	0.000	0.000	0.000
21	A	229	ASP	-1	-0.880	-0.944	21.380	-1.104	-1.104	0.000	0.000	0.000	0.000
22	A	230	GLU	-1	-0.931	-0.954	20.553	-0.855	-0.855	0.000	0.000	0.000	0.000
23	A	231	CYS	0	-0.109	-0.051	19.523	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	232	PRO	0	-0.007	-0.019	17.179	-0.170	-0.170	0.000	0.000	0.000	0.000
25	A	233	ILE	0	-0.041	-0.007	13.818	-0.117	-0.117	0.000	0.000	0.000	0.000
26	A	234	GLU	-1	-0.862	-0.927	13.910	-2.912	-2.912	0.000	0.000	0.000	0.000
27	A	235	TRP	0	-0.058	-0.022	12.657	0.119	0.119	0.000	0.000	0.000	0.000
28	A	236	PHE	0	0.066	-0.029	13.599	-0.262	-0.262	0.000	0.000	0.000	0.000
29	A	237	HIS	1	0.783	0.785	9.867	4.175	4.175	0.000	0.000	0.000	0.000
30	A	238	PHE	0	0.001	-0.009	15.086	0.236	0.236	0.000	0.000	0.000	0.000
31	A	239	SER	0	-0.001	0.001	17.545	0.201	0.201	0.000	0.000	0.000	0.000
32	A	240	CYS	0	-0.036	-0.048	15.079	0.148	0.148	0.000	0.000	0.000	0.000
33	A	241	VAL	0	-0.011	-0.005	18.593	0.107	0.107	0.000	0.000	0.000	0.000
34	A	242	GLY	0	-0.006	0.015	21.333	0.094	0.094	0.000	0.000	0.000	0.000
35	A	243	LEU	0	-0.041	-0.006	21.295	0.086	0.086	0.000	0.000	0.000	0.000
36	A	244	ASN	0	0.017	-0.001	22.246	-0.077	-0.077	0.000	0.000	0.000	0.000
37	A	245	HIS	0	-0.068	-0.041	24.126	0.026	0.026	0.000	0.000	0.000	0.000
38	A	246	LYS	1	1.037	1.024	22.758	1.232	1.232	0.000	0.000	0.000	0.000
39	A	247	PRO	0	-0.006	0.018	23.736	0.095	0.095	0.000	0.000	0.000	0.000
40	A	248	LYS	1	0.945	0.960	26.598	0.621	0.621	0.000	0.000	0.000	0.000
41	A	249	GLY	0	-0.016	-0.013	29.375	0.033	0.033	0.000	0.000	0.000	0.000
42	A	250	LYS	1	0.863	0.934	26.202	0.889	0.889	0.000	0.000	0.000	0.000
43	A	251	TRP	0	0.029	0.006	20.088	0.033	0.033	0.000	0.000	0.000	0.000
44	A	252	TYR	0	0.040	0.017	24.144	-0.067	-0.067	0.000	0.000	0.000	0.000
45	A	253	CYS	0	-0.017	-0.014	19.988	0.072	0.072	0.000	0.000	0.000	0.000
46	A	254	PRO	0	0.039	0.010	21.320	0.068	0.068	0.000	0.000	0.000	0.000
47	A	255	LYS	1	1.032	1.007	21.988	0.858	0.858	0.000	0.000	0.000	0.000
48	A	256	CYS	0	-0.044	-0.013	22.590	0.042	0.042	0.000	0.000	0.000	0.000
49	A	257	ARG	1	0.826	0.924	24.700	0.995	0.995	0.000	0.000	0.000	0.000
50	A	258	GLY	0	-0.054	-0.012	27.737	0.052	0.052	0.000	0.000	0.000	0.000
51	A	259	GLU	-2	-1.879	-1.934	26.267	-1.387	-1.387	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:209:GLU)