FMO DATABASE

FMODB ID: 15V2Z

Calculation Name: 1DFU-P-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DFU

Chain ID: P

ChEMBL ID:

UniProt ID: P68919

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-691928.832425
FMO2-HF: Nuclear repulsion	654651.825647
FMO2-HF: Total energy	-37277.006778
FMO2-MP2: Total energy	-37386.220212

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-54.528	-46.043	15.999	-11.327	-13.155	-0.097

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.915

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	3	THR	0	0.018	0.002	2.675	-0.078	2.896	0.665	-1.461	-2.179	-0.012
4	A	4	ILE	0	-0.014	0.000	4.664	3.389	3.460	-0.001	-0.011	-0.059	0.000
59	A	59	GLU	-1	-0.846	-0.947	2.108	-118.225	-112.164	5.611	-6.490	-5.182	-0.085
61	A	61	LEU	0	-0.058	-0.019	3.202	-13.163	-11.866	0.058	-0.562	-0.793	-0.005
62	A	62	THR	0	0.040	0.007	2.480	7.204	5.099	7.204	-1.937	-3.161	-0.001
63	A	63	ILE	0	-0.006	0.005	4.805	-0.567	-0.538	-0.001	-0.047	0.019	0.000
69	A	69	GLU	-1	-0.929	-0.964	5.819	-26.551	-26.444	-0.001	-0.005	-0.100	0.000
71	A	71	LYS	1	0.890	0.954	2.542	31.973	32.024	2.464	-0.814	-1.700	0.006
5	A	5	ASN	0	-0.012	0.001	8.068	1.543	1.543	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.018	-0.013	10.929	0.419	0.419	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.906	-0.945	13.735	-13.891	-13.891	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.022	-0.001	17.259	-0.214	-0.214	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.802	0.912	19.408	13.035	13.035	0.000	0.000	0.000	0.000
10	A	10	LYS	1	1.012	1.002	22.256	12.100	12.100	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.755	-0.838	25.662	-9.739	-9.739	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.022	-0.002	25.013	-0.647	-0.647	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.074	0.041	27.485	0.381	0.381	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.968	0.979	28.676	8.687	8.687	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.025	0.007	30.048	-0.183	-0.183	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.087	0.053	27.398	-0.097	-0.097	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.016	-0.018	25.478	-0.501	-0.501	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.889	0.943	26.031	9.357	9.357	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.856	0.895	28.182	9.617	9.617	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.019	0.016	21.926	-0.065	-0.065	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.845	0.915	23.263	12.513	12.513	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.054	-0.016	25.114	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.009	0.003	25.231	0.107	0.107	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.030	-0.012	22.372	-0.393	-0.393	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.911	0.961	19.245	13.557	13.557	0.000	0.000	0.000	0.000
26	A	26	PHE	0	-0.038	-0.031	15.410	0.722	0.722	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.047	-0.023	18.872	-0.414	-0.414	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.028	0.013	15.927	-0.246	-0.246	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.036	-0.005	17.497	0.722	0.722	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.025	0.025	12.739	-0.905	-0.905	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.041	-0.050	15.989	0.949	0.949	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.076	0.040	16.219	-0.909	-0.909	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.021	0.014	17.428	-0.435	-0.435	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.945	0.963	18.300	12.407	12.407	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.887	-0.935	17.540	-13.037	-13.037	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.042	0.033	20.178	-0.233	-0.233	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.008	-0.007	19.800	-0.629	-0.629	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.002	0.016	15.745	0.501	0.501	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.009	0.003	18.002	-0.676	-0.676	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.006	-0.002	13.870	0.227	0.227	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.861	-0.955	17.620	-12.865	-12.865	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.017	0.012	12.851	-0.729	-0.729	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.795	-0.888	14.933	-16.815	-16.815	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.001	-0.019	15.556	-0.766	-0.766	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.791	-0.884	16.909	-16.377	-16.377	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.874	0.927	12.524	17.693	17.693	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.021	0.009	11.476	-2.011	-2.011	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.045	-0.001	12.943	-1.322	-1.322	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.003	-0.016	13.426	-0.112	-0.112	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.050	-0.011	8.206	-2.920	-2.920	0.000	0.000	0.000	0.000
51	A	51	GLN	0	0.011	0.006	9.390	-1.160	-1.160	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.014	-0.003	11.591	1.322	1.322	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.856	0.940	7.155	36.978	36.978	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.055	0.025	9.974	-0.355	-0.355	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.810	-0.914	5.347	-36.794	-36.794	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.007	0.009	6.880	-1.940	-1.940	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.041	-0.036	7.743	1.411	1.411	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.077	-0.030	8.031	2.147	2.147	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.011	-0.001	4.801	4.779	4.779	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.025	0.009	7.443	0.735	0.735	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.002	-0.016	9.852	0.572	0.572	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.861	-0.915	13.573	-14.475	-14.475	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.012	0.009	15.286	-0.345	-0.345	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.839	0.911	11.830	15.601	15.601	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.071	-0.046	9.011	1.176	1.176	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.026	0.010	7.154	2.627	2.627	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.930	0.976	7.532	23.779	23.779	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.005	0.000	9.872	2.119	2.119	0.000	0.000	0.000	0.000
75	A	75	GLN	0	-0.034	-0.014	12.115	-0.477	-0.477	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.902	-0.955	15.688	-14.135	-14.135	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.002	-0.005	15.110	-0.914	-0.914	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.036	0.049	18.234	1.008	1.008	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.963	0.963	16.264	17.298	17.298	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.021	-0.015	22.289	0.485	0.485	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.011	-0.008	25.591	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	82	TYR	0	0.024	0.013	28.561	0.200	0.200	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.935	0.974	26.923	10.774	10.774	0.000	0.000	0.000	0.000
84	A	84	PRO	0	0.049	0.031	22.515	-0.316	-0.316	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.909	0.944	21.694	13.508	13.508	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.022	0.023	15.739	0.244	0.244	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.095	-0.061	20.215	0.843	0.843	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.024	-0.023	19.961	0.779	0.779	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.006	0.011	13.450	-0.362	-0.362	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.800	-0.873	16.973	-14.697	-14.697	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.013	-0.021	10.581	-1.163	-1.163	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.011	0.013	13.272	1.354	1.354	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.807	0.863	11.870	14.462	14.462	0.000	0.000	0.000	0.000
94	A	94	ALA	-1	-0.930	-0.949	9.106	-22.932	-22.932	0.000	0.000	0.000	0.000

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