FMO DATABASE

FMODB ID: Y9762

Calculation Name: 1DH3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DH3

Chain ID: A

ChEMBL ID:

UniProt ID: Q01147

Base Structure: X-ray

Registration Date: 2025-09-02

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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-240141.634966
FMO2-HF: Nuclear repulsion	217079.45955
FMO2-HF: Total energy	-23062.175416
FMO2-MP2: Total energy	-23130.257851

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:285:LYS)

Summations of interaction energy for fragment #1(A:285:LYS)

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.
260.05	264.786	2.158	-2.318	-4.574	-0.025

Interaction energy analysis for fragmet #1(A:285:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.875 / q_NPA : 1.932

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	287	GLU	-1	-0.834	-0.905	3.395	-69.189	-67.110	0.006	-0.782	-1.302	-0.003
4	A	288	VAL	0	0.095	0.023	2.103	-2.093	0.240	2.152	-1.472	-3.013	-0.022
5	A	289	ARG	1	0.931	0.983	4.214	69.404	69.728	0.000	-0.064	-0.259	0.000
6	A	290	LEU	0	-0.003	-0.011	5.608	9.699	9.699	0.000	0.000	0.000	0.000
7	A	291	MET	0	-0.004	0.015	7.283	6.663	6.663	0.000	0.000	0.000	0.000
8	A	292	LYS	1	1.040	1.002	7.393	69.752	69.752	0.000	0.000	0.000	0.000
9	A	293	ASN	0	-0.052	-0.020	9.552	5.577	5.577	0.000	0.000	0.000	0.000
10	A	294	ARG	1	0.968	0.980	11.513	47.549	47.549	0.000	0.000	0.000	0.000
11	A	295	GLU	-1	-0.798	-0.886	13.150	-34.871	-34.871	0.000	0.000	0.000	0.000
12	A	296	ALA	0	0.011	0.012	13.946	2.529	2.529	0.000	0.000	0.000	0.000
13	A	297	ALA	0	0.000	-0.007	15.586	2.486	2.486	0.000	0.000	0.000	0.000
14	A	298	ARG	1	0.810	0.895	15.973	36.156	36.156	0.000	0.000	0.000	0.000
15	A	299	GLU	-1	-0.802	-0.891	18.815	-25.695	-25.695	0.000	0.000	0.000	0.000
16	A	300	SER	0	-0.005	0.000	19.811	1.577	1.577	0.000	0.000	0.000	0.000
17	A	301	ARG	1	0.904	0.944	19.697	29.643	29.643	0.000	0.000	0.000	0.000
18	A	302	ARG	1	0.876	0.947	23.500	25.386	25.386	0.000	0.000	0.000	0.000
19	A	303	LYS	1	0.998	0.992	22.752	26.526	26.526	0.000	0.000	0.000	0.000
20	A	304	LYS	1	0.962	0.987	25.895	21.554	21.554	0.000	0.000	0.000	0.000
21	A	305	LYS	1	0.979	0.985	27.804	20.842	20.842	0.000	0.000	0.000	0.000
22	A	306	GLU	-1	-0.870	-0.948	29.009	-20.612	-20.612	0.000	0.000	0.000	0.000
23	A	307	TYR	0	-0.006	0.011	30.263	0.661	0.661	0.000	0.000	0.000	0.000
24	A	308	VAL	0	0.009	0.002	31.982	0.547	0.547	0.000	0.000	0.000	0.000
25	A	309	LYS	1	1.002	1.012	33.981	18.235	18.235	0.000	0.000	0.000	0.000
26	A	310	SER	0	-0.071	-0.033	34.798	0.617	0.617	0.000	0.000	0.000	0.000
27	A	311	LEU	0	-0.017	-0.010	35.289	0.528	0.528	0.000	0.000	0.000	0.000
28	A	312	GLU	-1	-0.874	-0.944	37.773	-16.079	-16.079	0.000	0.000	0.000	0.000
29	A	313	ASN	0	0.005	0.003	39.649	0.410	0.410	0.000	0.000	0.000	0.000
30	A	314	ARG	1	0.930	0.944	38.355	16.037	16.037	0.000	0.000	0.000	0.000
31	A	315	VAL	0	0.032	0.021	42.477	0.371	0.371	0.000	0.000	0.000	0.000
32	A	316	ALA	0	0.023	0.025	44.433	0.375	0.375	0.000	0.000	0.000	0.000
33	A	317	VAL	0	-0.007	-0.010	44.597	0.318	0.318	0.000	0.000	0.000	0.000
34	A	318	LEU	0	-0.041	-0.018	44.708	0.274	0.274	0.000	0.000	0.000	0.000
35	A	319	GLU	0	0.020	0.003	47.888	0.341	0.341	0.000	0.000	0.000	0.000
36	A	320	ASN	0	-0.041	-0.014	49.970	0.402	0.402	0.000	0.000	0.000	0.000
37	A	321	GLN	0	0.044	0.019	49.601	0.373	0.373	0.000	0.000	0.000	0.000
38	A	322	ASN	0	-0.019	-0.013	51.091	0.353	0.353	0.000	0.000	0.000	0.000
39	A	323	LYS	1	0.985	0.998	54.044	11.287	11.287	0.000	0.000	0.000	0.000
40	A	324	THR	0	0.011	0.006	55.040	0.235	0.235	0.000	0.000	0.000	0.000
41	A	325	LEU	0	0.017	0.008	54.510	0.200	0.200	0.000	0.000	0.000	0.000
42	A	326	ILE	0	0.012	0.006	57.393	0.204	0.204	0.000	0.000	0.000	0.000
43	A	327	GLU	-1	-0.985	-0.985	60.224	-10.129	-10.129	0.000	0.000	0.000	0.000
44	A	328	GLU	0	-0.010	-0.022	59.745	0.200	0.200	0.000	0.000	0.000	0.000
45	A	329	LEU	0	-0.043	-0.028	61.418	0.171	0.171	0.000	0.000	0.000	0.000
46	A	330	LYS	1	0.962	0.982	63.539	9.804	9.804	0.000	0.000	0.000	0.000
47	A	331	ALA	0	-0.043	-0.009	66.011	0.155	0.155	0.000	0.000	0.000	0.000
48	A	332	LEU	0	0.023	0.004	65.088	0.124	0.124	0.000	0.000	0.000	0.000
49	A	333	LYS	1	0.937	0.984	68.046	9.365	9.365	0.000	0.000	0.000	0.000
50	A	334	ASP	-1	-0.887	-0.952	69.640	-8.563	-8.563	0.000	0.000	0.000	0.000
51	A	335	LEU	0	-0.048	-0.026	70.984	0.013	0.013	0.000	0.000	0.000	0.000
52	A	336	TYR	0	-0.015	0.005	71.647	0.061	0.061	0.000	0.000	0.000	0.000
53	A	337	SER	0	-0.021	-0.011	73.607	0.106	0.106	0.000	0.000	0.000	0.000
54	A	338	HIS	0	-0.119	-0.082	76.948	0.193	0.193	0.000	0.000	0.000	0.000
55	A	339	LYS	0	0.049	0.063	76.556	-0.022	-0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:285:LYS)