FMO DATABASE

FMODB ID: QL6KY

Calculation Name: 4ID3-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4ID3

Chain ID: A

ChEMBL ID:

UniProt ID: P12689

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-641445.586013
FMO2-HF: Nuclear repulsion	606736.436498
FMO2-HF: Total energy	-34709.149515
FMO2-MP2: Total energy	-34812.36269

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:164:LYS)

Summations of interaction energy for fragment #1(A:164: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.
124.242	125.304	13.574	-5.023	-9.614	-0.073

Interaction energy analysis for fragmet #1(A:164:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.795 / q_NPA : 1.891

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	166	PHE	0	0.036	0.030	3.845	8.346	10.026	-0.018	-0.681	-0.981	-0.002
4	A	167	LYS	1	0.979	1.001	3.154	82.188	82.827	0.031	-0.112	-0.558	0.000
5	A	168	ASN	0	-0.025	-0.032	4.683	5.357	5.432	-0.001	-0.009	-0.065	0.000
27	A	190	LEU	0	-0.001	0.019	3.611	-23.981	-23.378	0.004	-0.264	-0.343	-0.002
28	A	191	HIS	0	-0.043	-0.027	2.769	-21.822	-19.717	0.229	-1.011	-1.324	-0.008
29	A	192	GLY	0	-0.093	-0.076	2.009	-27.474	-28.235	13.245	-7.075	-5.409	-0.052
30	A	193	GLY	0	0.046	0.034	2.761	9.933	6.654	0.084	4.129	-0.934	-0.009
6	A	169	CYS	0	-0.031	0.012	7.563	6.675	6.675	0.000	0.000	0.000	0.000
7	A	170	VAL	0	-0.022	-0.019	9.092	-4.157	-4.157	0.000	0.000	0.000	0.000
8	A	171	ILE	0	0.033	0.012	10.409	3.345	3.345	0.000	0.000	0.000	0.000
9	A	172	TYR	0	0.006	0.011	13.834	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	173	ILE	0	0.013	0.012	14.580	0.671	0.671	0.000	0.000	0.000	0.000
11	A	174	ASN	0	0.042	0.017	18.507	1.431	1.431	0.000	0.000	0.000	0.000
12	A	175	GLY	0	0.004	0.002	22.260	0.392	0.392	0.000	0.000	0.000	0.000
13	A	176	TYR	0	0.034	0.011	23.057	-0.886	-0.886	0.000	0.000	0.000	0.000
14	A	177	THR	0	-0.019	-0.016	19.132	0.186	0.186	0.000	0.000	0.000	0.000
15	A	178	LYS	1	0.931	0.976	20.890	24.966	24.966	0.000	0.000	0.000	0.000
16	A	179	PRO	0	0.106	0.047	15.822	0.179	0.179	0.000	0.000	0.000	0.000
17	A	180	GLY	0	0.061	0.051	18.545	0.204	0.204	0.000	0.000	0.000	0.000
18	A	181	ARG	1	0.885	0.921	17.519	29.752	29.752	0.000	0.000	0.000	0.000
19	A	182	LEU	0	0.032	0.030	14.978	-1.976	-1.976	0.000	0.000	0.000	0.000
20	A	183	GLN	0	0.109	0.054	14.097	-1.027	-1.027	0.000	0.000	0.000	0.000
21	A	184	LEU	0	-0.004	-0.003	12.873	-3.487	-3.487	0.000	0.000	0.000	0.000
22	A	185	HIS	0	-0.012	-0.016	11.518	-1.669	-1.669	0.000	0.000	0.000	0.000
23	A	186	GLU	-1	-0.884	-0.942	9.838	-47.978	-47.978	0.000	0.000	0.000	0.000
24	A	187	MET	0	-0.025	-0.010	8.241	-6.132	-6.132	0.000	0.000	0.000	0.000
25	A	188	ILE	0	0.012	0.011	6.975	-9.169	-9.169	0.000	0.000	0.000	0.000
26	A	189	VAL	0	-0.012	-0.005	5.333	-11.984	-11.984	0.000	0.000	0.000	0.000
31	A	194	LYS	1	0.920	0.945	5.890	60.574	60.574	0.000	0.000	0.000	0.000
32	A	195	PHE	0	0.027	0.019	8.677	1.797	1.797	0.000	0.000	0.000	0.000
33	A	196	LEU	0	-0.021	-0.006	12.032	0.572	0.572	0.000	0.000	0.000	0.000
34	A	197	HIS	0	0.023	-0.002	15.357	0.686	0.686	0.000	0.000	0.000	0.000
35	A	198	TYR	0	0.009	0.004	18.278	1.271	1.271	0.000	0.000	0.000	0.000
36	A	199	LEU	0	-0.012	-0.001	19.497	-1.471	-1.471	0.000	0.000	0.000	0.000
37	A	200	SER	0	0.026	0.021	18.831	1.123	1.123	0.000	0.000	0.000	0.000
38	A	201	SER	0	0.044	0.009	20.586	1.182	1.182	0.000	0.000	0.000	0.000
39	A	202	LYS	1	0.931	0.975	19.803	23.966	23.966	0.000	0.000	0.000	0.000
40	A	203	LYS	1	0.954	0.997	19.594	26.061	26.061	0.000	0.000	0.000	0.000
41	A	204	THR	0	-0.062	-0.033	15.644	-1.101	-1.101	0.000	0.000	0.000	0.000
42	A	205	VAL	0	-0.011	-0.001	15.013	-2.284	-2.284	0.000	0.000	0.000	0.000
43	A	206	THR	0	-0.006	-0.018	12.567	0.748	0.748	0.000	0.000	0.000	0.000
44	A	207	HIS	0	-0.001	0.011	12.403	0.754	0.754	0.000	0.000	0.000	0.000
45	A	208	ILE	0	-0.021	-0.004	16.111	-0.609	-0.609	0.000	0.000	0.000	0.000
46	A	209	VAL	0	-0.009	0.010	14.814	-0.080	-0.080	0.000	0.000	0.000	0.000
47	A	210	ALA	0	0.012	-0.003	18.179	0.732	0.732	0.000	0.000	0.000	0.000
48	A	211	SER	0	0.013	-0.020	21.530	-0.497	-0.497	0.000	0.000	0.000	0.000
49	A	212	ASN	0	-0.021	-0.012	23.519	0.196	0.196	0.000	0.000	0.000	0.000
50	A	213	LEU	0	0.029	0.009	24.565	-0.499	-0.499	0.000	0.000	0.000	0.000
51	A	214	PRO	0	0.033	0.027	28.088	0.656	0.656	0.000	0.000	0.000	0.000
52	A	215	LEU	0	0.075	0.023	31.103	-0.494	-0.494	0.000	0.000	0.000	0.000
53	A	216	LYS	1	0.992	0.994	31.814	18.924	18.924	0.000	0.000	0.000	0.000
54	A	217	LYS	1	0.795	0.886	27.281	22.408	22.408	0.000	0.000	0.000	0.000
55	A	218	ARG	1	0.937	0.981	27.880	19.804	19.804	0.000	0.000	0.000	0.000
56	A	219	ILE	0	0.015	0.021	29.657	-0.137	-0.137	0.000	0.000	0.000	0.000
57	A	220	GLU	-1	-0.831	-0.914	27.655	-22.428	-22.428	0.000	0.000	0.000	0.000
58	A	221	PHE	0	-0.023	-0.026	23.980	-0.746	-0.746	0.000	0.000	0.000	0.000
59	A	222	ALA	0	0.075	0.045	25.011	-0.804	-0.804	0.000	0.000	0.000	0.000
60	A	223	ASN	0	-0.033	-0.030	24.876	-0.424	-0.424	0.000	0.000	0.000	0.000
61	A	224	TYR	0	0.027	0.013	19.940	-1.059	-1.059	0.000	0.000	0.000	0.000
62	A	225	LYS	1	0.912	0.975	16.366	34.324	34.324	0.000	0.000	0.000	0.000
63	A	226	VAL	0	0.003	-0.004	18.731	-1.466	-1.466	0.000	0.000	0.000	0.000
64	A	227	VAL	0	0.013	0.009	15.624	0.701	0.701	0.000	0.000	0.000	0.000
65	A	228	SER	0	0.036	-0.003	19.034	-0.489	-0.489	0.000	0.000	0.000	0.000
66	A	229	PRO	0	-0.029	-0.041	16.407	-1.873	-1.873	0.000	0.000	0.000	0.000
67	A	230	ASP	-1	-0.804	-0.887	15.042	-32.828	-32.828	0.000	0.000	0.000	0.000
68	A	231	TRP	0	-0.014	0.011	11.406	-2.728	-2.728	0.000	0.000	0.000	0.000
69	A	232	ILE	0	-0.045	-0.023	9.802	-3.643	-3.643	0.000	0.000	0.000	0.000
70	A	233	VAL	0	0.009	-0.011	10.439	-3.805	-3.805	0.000	0.000	0.000	0.000
71	A	234	ASP	-1	-0.784	-0.867	12.127	-37.065	-37.065	0.000	0.000	0.000	0.000
72	A	235	SER	0	-0.027	-0.028	8.658	-1.251	-1.251	0.000	0.000	0.000	0.000
73	A	236	VAL	0	-0.056	-0.035	6.879	-4.989	-4.989	0.000	0.000	0.000	0.000
74	A	237	LYS	1	0.891	0.944	8.450	36.550	36.550	0.000	0.000	0.000	0.000
75	A	238	GLU	-1	-0.854	-0.918	10.583	-37.914	-37.914	0.000	0.000	0.000	0.000
76	A	239	ALA	0	-0.045	-0.008	6.122	-0.877	-0.877	0.000	0.000	0.000	0.000
77	A	240	ARG	1	0.876	0.930	5.801	37.272	37.272	0.000	0.000	0.000	0.000
78	A	241	LEU	0	-0.053	-0.027	7.306	1.254	1.254	0.000	0.000	0.000	0.000
79	A	242	LEU	0	0.055	0.037	8.693	2.947	2.947	0.000	0.000	0.000	0.000
80	A	243	PRO	0	0.013	0.004	12.314	-0.880	-0.880	0.000	0.000	0.000	0.000
81	A	244	TRP	0	0.022	0.005	14.974	1.020	1.020	0.000	0.000	0.000	0.000
82	A	245	GLN	0	0.048	0.004	16.311	-0.200	-0.200	0.000	0.000	0.000	0.000
83	A	246	ASN	0	0.007	0.005	17.851	1.971	1.971	0.000	0.000	0.000	0.000
84	A	247	TYR	0	-0.041	-0.050	15.711	-0.075	-0.075	0.000	0.000	0.000	0.000
85	A	248	SER	0	-0.052	-0.047	19.547	-0.483	-0.483	0.000	0.000	0.000	0.000
86	A	249	LEU	0	-0.032	-0.010	21.666	0.875	0.875	0.000	0.000	0.000	0.000
87	A	250	THR	-1	-0.946	-0.935	24.433	-22.788	-22.788	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:164:LYS)