FMO DATABASE

FMODB ID: 9RK62

Calculation Name: 3OQ9-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3OQ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q13158

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-637388.135474
FMO2-HF: Nuclear repulsion	601180.310235
FMO2-HF: Total energy	-36207.825239
FMO2-MP2: Total energy	-36311.13754

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:223:LYS)

Summations of interaction energy for fragment #1(A:223: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.
-48.539	-43.472	1.178	-2.542	-3.704	-0.017

Interaction energy analysis for fragmet #1(A:223:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.845 / q_NPA : 1.896

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

Sort

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	225	ILE	0	0.020	0.025	2.141	2.363	5.402	1.107	-1.742	-2.405	-0.010
4	A	226	PRO	0	0.029	0.012	3.303	6.486	7.155	0.030	-0.182	-0.517	-0.002
52	A	274	TYR	0	-0.043	-0.035	3.523	-14.124	-12.952	0.042	-0.575	-0.639	-0.005
61	A	283	TYR	0	0.014	-0.001	3.935	-2.480	-2.293	-0.001	-0.043	-0.143	0.000
5	A	227	ARG	1	1.004	0.995	5.273	78.143	78.143	0.000	0.000	0.000	0.000
6	A	228	ILE	0	-0.006	0.014	7.251	5.119	5.119	0.000	0.000	0.000	0.000
7	A	229	ALA	0	0.045	0.015	9.000	5.140	5.140	0.000	0.000	0.000	0.000
8	A	230	GLU	-1	-0.947	-0.969	9.271	-50.507	-50.507	0.000	0.000	0.000	0.000
9	A	231	ASP	-1	-0.843	-0.930	12.431	-35.103	-35.103	0.000	0.000	0.000	0.000
10	A	232	MET	0	-0.113	-0.023	12.372	1.584	1.584	0.000	0.000	0.000	0.000
11	A	233	THR	0	0.012	0.000	15.363	1.045	1.045	0.000	0.000	0.000	0.000
12	A	234	ILE	0	0.078	0.023	16.788	-0.887	-0.887	0.000	0.000	0.000	0.000
13	A	235	GLN	0	-0.001	-0.004	18.347	-0.110	-0.110	0.000	0.000	0.000	0.000
14	A	236	GLU	-1	-0.847	-0.908	17.449	-30.686	-30.686	0.000	0.000	0.000	0.000
15	A	237	ALA	0	0.031	0.006	14.111	-0.471	-0.471	0.000	0.000	0.000	0.000
16	A	238	LYS	1	0.909	0.957	15.766	23.986	23.986	0.000	0.000	0.000	0.000
17	A	239	LYS	1	0.843	0.912	18.271	23.390	23.390	0.000	0.000	0.000	0.000
18	A	240	PHE	0	0.024	-0.004	11.369	0.272	0.272	0.000	0.000	0.000	0.000
19	A	241	ALA	0	0.053	0.033	13.631	0.317	0.317	0.000	0.000	0.000	0.000
20	A	242	ARG	1	0.871	0.936	15.226	25.100	25.100	0.000	0.000	0.000	0.000
21	A	243	GLU	-1	-0.935	-0.953	18.831	-24.077	-24.077	0.000	0.000	0.000	0.000
22	A	244	ASN	0	-0.076	-0.056	14.984	-1.856	-1.856	0.000	0.000	0.000	0.000
23	A	245	ASN	0	-0.002	-0.004	16.530	-0.168	-0.168	0.000	0.000	0.000	0.000
24	A	246	ILE	0	-0.024	0.001	13.558	-0.559	-0.559	0.000	0.000	0.000	0.000
25	A	247	LYS	1	0.964	0.972	16.933	27.214	27.214	0.000	0.000	0.000	0.000
26	A	248	GLU	-1	-0.833	-0.914	20.008	-23.714	-23.714	0.000	0.000	0.000	0.000
27	A	249	GLY	0	0.062	0.029	22.043	-0.409	-0.409	0.000	0.000	0.000	0.000
28	A	250	LYS	1	0.879	0.962	13.673	36.642	36.642	0.000	0.000	0.000	0.000
29	A	251	ILE	0	-0.025	-0.025	16.184	-0.790	-0.790	0.000	0.000	0.000	0.000
30	A	252	ASP	-1	-0.892	-0.967	19.547	-22.992	-22.992	0.000	0.000	0.000	0.000
31	A	253	GLU	-1	-0.955	-0.967	19.696	-27.966	-27.966	0.000	0.000	0.000	0.000
32	A	254	ILE	0	0.021	0.004	15.138	0.196	0.196	0.000	0.000	0.000	0.000
33	A	255	MET	0	-0.058	-0.012	19.368	0.040	0.040	0.000	0.000	0.000	0.000
34	A	256	HIS	0	-0.038	-0.028	21.897	0.715	0.715	0.000	0.000	0.000	0.000
35	A	257	ASP	-1	-0.929	-0.955	20.160	-27.639	-27.639	0.000	0.000	0.000	0.000
36	A	258	SER	0	0.019	-0.006	20.649	-0.155	-0.155	0.000	0.000	0.000	0.000
37	A	259	ILE	0	-0.029	0.004	22.381	-0.491	-0.491	0.000	0.000	0.000	0.000
38	A	260	GLN	0	-0.075	-0.042	24.756	0.215	0.215	0.000	0.000	0.000	0.000
39	A	261	ASP	-1	-0.773	-0.881	19.514	-29.424	-29.424	0.000	0.000	0.000	0.000
40	A	262	THR	0	-0.094	-0.064	17.981	-0.311	-0.311	0.000	0.000	0.000	0.000
41	A	263	ALA	0	0.004	0.002	16.864	-1.391	-1.391	0.000	0.000	0.000	0.000
42	A	264	GLU	-1	-0.860	-0.922	12.008	-44.221	-44.221	0.000	0.000	0.000	0.000
43	A	265	GLN	0	0.044	0.015	12.974	-4.015	-4.015	0.000	0.000	0.000	0.000
44	A	266	LYS	1	0.798	0.919	13.207	36.337	36.337	0.000	0.000	0.000	0.000
45	A	267	VAL	0	-0.011	-0.012	7.576	-2.706	-2.706	0.000	0.000	0.000	0.000
46	A	268	GLN	0	-0.001	0.010	9.632	-3.628	-3.628	0.000	0.000	0.000	0.000
47	A	269	LEU	0	0.025	0.015	11.822	-0.604	-0.604	0.000	0.000	0.000	0.000
48	A	270	LEU	0	-0.018	-0.008	8.469	-0.450	-0.450	0.000	0.000	0.000	0.000
49	A	271	LEU	0	-0.034	-0.027	5.668	-5.561	-5.561	0.000	0.000	0.000	0.000
50	A	272	CYS	0	-0.022	-0.011	7.895	0.492	0.492	0.000	0.000	0.000	0.000
51	A	273	TRP	0	0.020	0.005	8.346	-0.254	-0.254	0.000	0.000	0.000	0.000
53	A	275	GLN	0	-0.041	-0.036	7.708	1.953	1.953	0.000	0.000	0.000	0.000
54	A	276	SER	0	-0.051	0.001	9.871	3.187	3.187	0.000	0.000	0.000	0.000
55	A	277	HIS	0	0.004	0.008	11.091	1.781	1.781	0.000	0.000	0.000	0.000
56	A	278	GLY	0	0.008	0.005	8.448	0.207	0.207	0.000	0.000	0.000	0.000
57	A	279	LYS	1	0.943	0.977	9.397	34.367	34.367	0.000	0.000	0.000	0.000
58	A	280	SER	0	0.001	-0.003	11.364	-1.405	-1.405	0.000	0.000	0.000	0.000
59	A	281	ASP	-1	-0.890	-0.952	11.906	-38.639	-38.639	0.000	0.000	0.000	0.000
60	A	282	ALA	0	0.017	0.013	8.161	0.553	0.553	0.000	0.000	0.000	0.000
62	A	284	GLN	0	0.035	0.015	9.389	3.611	3.611	0.000	0.000	0.000	0.000
63	A	285	ASP	-1	-0.892	-0.941	12.465	-35.881	-35.881	0.000	0.000	0.000	0.000
64	A	286	LEU	0	-0.023	0.003	7.627	1.706	1.706	0.000	0.000	0.000	0.000
65	A	287	ILE	0	0.024	0.017	11.650	1.631	1.631	0.000	0.000	0.000	0.000
66	A	288	LYS	1	0.882	0.915	14.266	34.120	34.120	0.000	0.000	0.000	0.000
67	A	289	GLY	0	0.018	0.005	15.920	1.916	1.916	0.000	0.000	0.000	0.000
68	A	290	LEU	0	0.023	0.013	13.154	1.785	1.785	0.000	0.000	0.000	0.000
69	A	291	LYS	1	0.926	0.945	16.724	28.859	28.859	0.000	0.000	0.000	0.000
70	A	292	LYS	1	0.911	0.951	19.696	28.166	28.166	0.000	0.000	0.000	0.000
71	A	293	ALA	0	0.059	0.056	18.639	1.081	1.081	0.000	0.000	0.000	0.000
72	A	294	GLU	-1	-0.917	-0.964	20.703	-21.985	-21.985	0.000	0.000	0.000	0.000
73	A	295	CYS	0	-0.045	0.003	18.897	0.129	0.129	0.000	0.000	0.000	0.000
74	A	296	ARG	1	0.844	0.911	20.250	23.567	23.567	0.000	0.000	0.000	0.000
75	A	297	ARG	1	1.019	1.023	19.464	24.415	24.415	0.000	0.000	0.000	0.000
76	A	298	THR	0	0.030	-0.006	13.977	-0.215	-0.215	0.000	0.000	0.000	0.000
77	A	299	LEU	0	-0.032	-0.009	14.145	-2.204	-2.204	0.000	0.000	0.000	0.000
78	A	300	ASP	-1	-0.902	-0.953	14.924	-31.034	-31.034	0.000	0.000	0.000	0.000
79	A	301	LYS	1	0.972	0.990	15.024	31.551	31.551	0.000	0.000	0.000	0.000
80	A	302	PHE	0	-0.023	-0.022	7.080	-3.416	-3.416	0.000	0.000	0.000	0.000
81	A	303	GLN	0	-0.051	-0.027	11.431	-2.354	-2.354	0.000	0.000	0.000	0.000
82	A	304	ASP	-1	-0.860	-0.926	13.326	-35.229	-35.229	0.000	0.000	0.000	0.000
83	A	305	MET	0	-0.083	-0.051	8.796	-0.491	-0.491	0.000	0.000	0.000	0.000
84	A	306	VAL	0	-0.088	-0.052	7.715	-4.979	-4.979	0.000	0.000	0.000	0.000
85	A	307	GLN	0	-0.052	-0.025	9.650	0.184	0.184	0.000	0.000	0.000	0.000
86	A	308	LYS	0	-0.014	0.029	9.868	-12.523	-12.523	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:223:LYS)