FMO DATABASE

FMODB ID: 4QYLN

Calculation Name: 1AM9-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AM9

Chain ID: A

ChEMBL ID:

UniProt ID: P36956

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-418668.405563
FMO2-HF: Nuclear repulsion	387086.265445
FMO2-HF: Total energy	-31582.140118
FMO2-MP2: Total energy	-31676.95958

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:319:GLN)

Summations of interaction energy for fragment #1(A:319:GLN)

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.
72.926	82.945	8.748	-7.369	-11.401	-0.031

Interaction energy analysis for fragmet #1(A:319:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.908

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	321	ARG	1	0.988	0.979	3.067	27.130	29.202	0.117	-1.008	-1.182	-0.003
5	A	323	GLU	-1	-0.774	-0.864	2.335	-87.439	-83.967	5.199	-4.164	-4.508	-0.042
6	A	324	LYS	0	0.045	0.024	2.402	1.866	5.537	2.311	-2.082	-3.900	0.006
7	A	325	ARG	1	0.889	0.950	3.338	29.307	28.960	0.097	0.643	-0.394	0.003
9	A	327	ALA	0	0.012	0.001	2.543	0.758	1.690	1.026	-0.744	-1.214	0.005
10	A	328	HIS	0	0.025	0.015	4.431	1.144	1.291	-0.001	-0.013	-0.133	0.000
13	A	331	ILE	0	-0.035	-0.019	4.565	1.260	1.332	-0.001	-0.001	-0.070	0.000
4	A	322	GLY	0	0.063	0.035	5.680	3.726	3.726	0.000	0.000	0.000	0.000
8	A	326	THR	0	-0.010	-0.008	6.231	4.043	4.043	0.000	0.000	0.000	0.000
11	A	329	ASN	0	0.026	0.002	6.792	1.787	1.787	0.000	0.000	0.000	0.000
12	A	330	ALA	0	-0.002	0.005	6.995	1.744	1.744	0.000	0.000	0.000	0.000
14	A	332	GLU	-1	-0.808	-0.894	8.607	-14.741	-14.741	0.000	0.000	0.000	0.000
15	A	333	LYS	1	0.919	0.968	11.473	16.332	16.332	0.000	0.000	0.000	0.000
16	A	334	ARG	1	0.968	0.995	7.561	22.482	22.482	0.000	0.000	0.000	0.000
17	A	335	TYR	0	0.018	0.022	12.793	0.958	0.958	0.000	0.000	0.000	0.000
18	A	336	ARG	1	0.940	0.958	14.633	16.407	16.407	0.000	0.000	0.000	0.000
19	A	337	SER	0	-0.057	-0.024	16.254	0.715	0.715	0.000	0.000	0.000	0.000
20	A	338	SER	0	-0.025	-0.023	16.667	0.598	0.598	0.000	0.000	0.000	0.000
21	A	339	ILE	0	0.054	0.037	18.621	0.516	0.516	0.000	0.000	0.000	0.000
22	A	340	ASN	0	-0.012	-0.024	20.335	0.926	0.926	0.000	0.000	0.000	0.000
23	A	341	ASP	-1	-0.846	-0.933	20.318	-11.899	-11.899	0.000	0.000	0.000	0.000
24	A	342	LYS	1	0.929	0.962	21.077	12.117	12.117	0.000	0.000	0.000	0.000
25	A	343	ILE	0	-0.045	-0.019	24.854	0.410	0.410	0.000	0.000	0.000	0.000
26	A	344	ILE	0	-0.017	-0.012	25.692	0.378	0.378	0.000	0.000	0.000	0.000
27	A	345	GLU	-1	-0.850	-0.916	26.286	-9.713	-9.713	0.000	0.000	0.000	0.000
28	A	346	LEU	0	-0.028	-0.023	28.927	0.345	0.345	0.000	0.000	0.000	0.000
29	A	347	LYS	1	0.783	0.888	30.929	8.599	8.599	0.000	0.000	0.000	0.000
30	A	348	ASP	-1	-0.823	-0.923	32.190	-8.269	-8.269	0.000	0.000	0.000	0.000
31	A	349	LEU	0	-0.036	-0.022	32.513	0.262	0.262	0.000	0.000	0.000	0.000
32	A	350	VAL	0	-0.062	-0.026	35.270	0.211	0.211	0.000	0.000	0.000	0.000
33	A	351	VAL	0	-0.081	-0.045	36.286	0.176	0.176	0.000	0.000	0.000	0.000
34	A	352	GLY	0	0.056	0.050	37.263	0.123	0.123	0.000	0.000	0.000	0.000
35	A	353	THR	0	-0.015	-0.022	34.338	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	354	GLU	-1	-0.922	-0.956	35.165	-7.152	-7.152	0.000	0.000	0.000	0.000
37	A	355	ALA	0	0.048	0.039	37.359	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	356	LYS	1	0.854	0.914	32.483	7.852	7.852	0.000	0.000	0.000	0.000
39	A	357	LEU	0	0.015	0.014	33.585	0.203	0.203	0.000	0.000	0.000	0.000
40	A	358	ASN	0	0.024	0.019	31.989	-0.148	-0.148	0.000	0.000	0.000	0.000
41	A	359	LYS	1	0.971	0.954	24.097	10.853	10.853	0.000	0.000	0.000	0.000
42	A	360	SER	0	0.039	0.023	30.219	0.028	0.028	0.000	0.000	0.000	0.000
43	A	361	ALA	0	0.026	0.013	32.415	0.134	0.134	0.000	0.000	0.000	0.000
44	A	362	VAL	0	-0.007	0.006	31.208	0.176	0.176	0.000	0.000	0.000	0.000
45	A	363	LEU	0	0.028	0.006	28.077	0.095	0.095	0.000	0.000	0.000	0.000
46	A	364	ARG	1	0.798	0.874	32.632	7.543	7.543	0.000	0.000	0.000	0.000
47	A	365	LYS	1	0.998	0.994	36.214	7.240	7.240	0.000	0.000	0.000	0.000
48	A	366	ALA	0	0.020	0.017	33.480	0.132	0.132	0.000	0.000	0.000	0.000
49	A	367	ILE	0	-0.017	-0.005	33.753	0.092	0.092	0.000	0.000	0.000	0.000
50	A	368	ASP	-1	-0.784	-0.861	36.702	-7.031	-7.031	0.000	0.000	0.000	0.000
51	A	369	TYR	0	0.011	0.008	37.722	0.246	0.246	0.000	0.000	0.000	0.000
52	A	370	ILE	0	0.035	0.014	34.275	0.116	0.116	0.000	0.000	0.000	0.000
53	A	371	ARG	1	0.884	0.936	38.893	7.203	7.203	0.000	0.000	0.000	0.000
54	A	372	PHE	0	0.005	0.007	41.962	0.141	0.141	0.000	0.000	0.000	0.000
55	A	373	LEU	0	0.023	0.009	39.252	0.149	0.149	0.000	0.000	0.000	0.000
56	A	374	GLN	0	0.006	0.011	39.118	0.162	0.162	0.000	0.000	0.000	0.000
57	A	375	HIS	0	0.026	0.008	43.605	0.136	0.136	0.000	0.000	0.000	0.000
58	A	376	SER	0	-0.019	0.000	46.167	0.184	0.184	0.000	0.000	0.000	0.000
59	A	377	ASN	0	0.032	0.012	44.669	0.124	0.124	0.000	0.000	0.000	0.000
60	A	378	GLN	0	-0.003	-0.002	46.798	0.142	0.142	0.000	0.000	0.000	0.000
61	A	379	LYS	1	0.970	0.980	49.207	5.727	5.727	0.000	0.000	0.000	0.000
62	A	380	LEU	0	0.071	0.036	48.094	0.092	0.092	0.000	0.000	0.000	0.000
63	A	381	LYS	1	0.878	0.945	46.018	6.316	6.316	0.000	0.000	0.000	0.000
64	A	382	GLN	0	0.008	0.010	52.036	0.133	0.133	0.000	0.000	0.000	0.000
65	A	383	GLU	-1	-0.904	-0.941	54.709	-5.299	-5.299	0.000	0.000	0.000	0.000
66	A	384	ASN	0	0.025	0.017	53.640	0.085	0.085	0.000	0.000	0.000	0.000
67	A	385	LEU	0	0.028	0.014	55.677	0.064	0.064	0.000	0.000	0.000	0.000
68	A	386	SER	0	0.005	0.002	57.516	0.120	0.120	0.000	0.000	0.000	0.000
69	A	387	LEU	0	0.000	0.000	57.422	0.099	0.099	0.000	0.000	0.000	0.000
70	A	388	ARG	1	0.896	0.939	54.180	5.447	5.447	0.000	0.000	0.000	0.000
71	A	389	THR	0	-0.004	-0.011	60.687	0.077	0.077	0.000	0.000	0.000	0.000
72	A	390	ALA	0	-0.017	-0.002	63.381	0.089	0.089	0.000	0.000	0.000	0.000
73	A	391	VAL	0	0.018	-0.001	62.581	0.077	0.077	0.000	0.000	0.000	0.000
74	A	392	HIS	0	-0.020	-0.008	64.363	0.018	0.018	0.000	0.000	0.000	0.000
75	A	393	LYS	1	1.004	0.987	66.194	4.343	4.343	0.000	0.000	0.000	0.000
76	A	394	SER	0	-0.063	-0.028	68.461	0.066	0.066	0.000	0.000	0.000	0.000
77	A	395	LYS	1	0.913	0.961	65.183	4.632	4.632	0.000	0.000	0.000	0.000
78	A	396	SER	0	-0.066	-0.026	69.586	0.035	0.035	0.000	0.000	0.000	0.000
79	A	397	LEU	0	-0.034	-0.008	71.629	0.001	0.001	0.000	0.000	0.000	0.000
80	A	398	LYS	0	0.049	0.034	75.049	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:319:GLN)