FMO DATABASE

FMODB ID: RM778

Calculation Name: 6J5F-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6J5F

Chain ID: A

ChEMBL ID:

UniProt ID: A0A096

Base Structure: X-ray

Registration Date: 2025-10-04

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-648884.198091
FMO2-HF: Nuclear repulsion	611734.939638
FMO2-HF: Total energy	-37149.258453
FMO2-MP2: Total energy	-37254.481941

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:304:TYR)

Summations of interaction energy for fragment #1(A:304:TYR)

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.
-37.581	-20.966	9.762	-9.326	-17.048	-0.077

Interaction energy analysis for fragmet #1(A:304:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.914

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	306	MET	0	0.006	0.014	3.075	-6.286	-4.216	0.157	-1.098	-1.128	-0.005
4	A	307	CYS	0	-0.103	-0.042	2.472	-7.379	-4.076	1.935	-2.132	-3.106	-0.020
34	A	337	PRO	0	0.051	0.035	2.793	-0.207	1.606	4.390	-1.296	-4.906	0.006
35	A	339	ARG	1	0.882	0.938	2.695	44.316	46.703	0.828	-0.593	-2.623	-0.009
36	A	340	ILE	0	0.040	-0.003	4.114	3.496	3.673	0.002	-0.040	-0.138	0.000
59	A	363	THR	0	0.014	-0.011	2.181	-7.434	-6.805	1.507	-0.579	-1.557	-0.004
61	A	365	GLU	-1	-0.826	-0.940	2.612	-74.330	-68.094	0.943	-3.588	-3.590	-0.045
5	A	308	ASP	-1	-0.751	-0.852	7.404	-18.560	-18.560	0.000	0.000	0.000	0.000
6	A	309	LYS	1	0.886	0.919	11.021	17.587	17.587	0.000	0.000	0.000	0.000
7	A	310	THR	0	-0.010	-0.020	13.381	1.078	1.078	0.000	0.000	0.000	0.000
8	A	311	LYS	1	0.833	0.915	12.835	18.989	18.989	0.000	0.000	0.000	0.000
9	A	312	PHE	0	0.027	0.004	9.340	-0.869	-0.869	0.000	0.000	0.000	0.000
10	A	313	THR	0	0.025	0.006	14.882	1.094	1.094	0.000	0.000	0.000	0.000
11	A	314	TRP	0	0.025	-0.007	16.980	-1.035	-1.035	0.000	0.000	0.000	0.000
12	A	315	LYS	1	0.876	0.957	16.532	15.728	15.728	0.000	0.000	0.000	0.000
13	A	316	ARG	1	0.881	0.938	18.944	14.374	14.374	0.000	0.000	0.000	0.000
14	A	317	ALA	0	0.052	0.034	19.601	-0.705	-0.705	0.000	0.000	0.000	0.000
15	A	318	PRO	0	-0.028	-0.021	20.062	0.080	0.080	0.000	0.000	0.000	0.000
16	A	319	THR	0	-0.001	0.008	22.041	0.767	0.767	0.000	0.000	0.000	0.000
17	A	320	ASP	-1	-0.862	-0.932	23.762	-11.175	-11.175	0.000	0.000	0.000	0.000
18	A	321	SER	0	-0.020	-0.034	23.078	0.242	0.242	0.000	0.000	0.000	0.000
19	A	322	GLY	0	-0.017	-0.003	24.796	0.025	0.025	0.000	0.000	0.000	0.000
20	A	323	HIS	1	0.752	0.849	21.648	13.025	13.025	0.000	0.000	0.000	0.000
21	A	324	ASP	-1	-0.876	-0.930	25.984	-11.196	-11.196	0.000	0.000	0.000	0.000
22	A	325	THR	0	-0.040	-0.017	21.633	-0.180	-0.180	0.000	0.000	0.000	0.000
23	A	326	VAL	0	0.001	0.008	21.584	0.329	0.329	0.000	0.000	0.000	0.000
24	A	327	VAL	0	-0.021	-0.014	19.050	-0.861	-0.861	0.000	0.000	0.000	0.000
25	A	328	MET	0	-0.025	-0.002	16.189	0.483	0.483	0.000	0.000	0.000	0.000
26	A	329	GLU	-1	-0.863	-0.955	15.140	-17.103	-17.103	0.000	0.000	0.000	0.000
27	A	330	VAL	0	-0.038	-0.005	12.044	0.823	0.823	0.000	0.000	0.000	0.000
28	A	331	THR	0	0.010	0.002	13.302	-0.794	-0.794	0.000	0.000	0.000	0.000
29	A	332	PHE	0	-0.027	-0.016	8.430	-0.099	-0.099	0.000	0.000	0.000	0.000
30	A	333	SER	0	-0.013	-0.011	12.587	0.031	0.031	0.000	0.000	0.000	0.000
31	A	334	GLY	0	0.028	0.014	10.649	1.086	1.086	0.000	0.000	0.000	0.000
32	A	335	THR	0	-0.037	-0.025	6.076	0.099	0.099	0.000	0.000	0.000	0.000
33	A	336	LYS	1	0.892	0.968	5.758	22.150	22.150	0.000	0.000	0.000	0.000
37	A	341	PRO	0	-0.061	-0.013	7.795	0.117	0.117	0.000	0.000	0.000	0.000
38	A	342	VAL	0	0.015	-0.006	10.430	1.426	1.426	0.000	0.000	0.000	0.000
39	A	343	ARG	1	0.803	0.910	13.399	15.813	15.813	0.000	0.000	0.000	0.000
40	A	344	ALA	0	0.018	0.010	16.861	0.274	0.274	0.000	0.000	0.000	0.000
41	A	345	VAL	0	-0.023	0.011	20.523	-0.213	-0.213	0.000	0.000	0.000	0.000
42	A	346	ALA	0	0.095	0.048	23.720	0.212	0.212	0.000	0.000	0.000	0.000
43	A	347	HIS	0	0.036	0.000	27.401	-0.398	-0.398	0.000	0.000	0.000	0.000
44	A	348	GLY	0	-0.023	-0.015	29.294	0.233	0.233	0.000	0.000	0.000	0.000
45	A	349	SER	0	-0.034	-0.006	27.966	0.220	0.220	0.000	0.000	0.000	0.000
46	A	350	PRO	0	0.017	0.011	24.284	-0.452	-0.452	0.000	0.000	0.000	0.000
47	A	351	ASP	-1	-0.850	-0.931	22.688	-13.310	-13.310	0.000	0.000	0.000	0.000
48	A	352	VAL	0	-0.041	-0.025	21.582	-0.764	-0.764	0.000	0.000	0.000	0.000
49	A	353	ASN	0	0.010	0.001	16.717	0.367	0.367	0.000	0.000	0.000	0.000
50	A	354	VAL	0	0.001	-0.006	20.313	0.129	0.129	0.000	0.000	0.000	0.000
51	A	355	ALA	0	-0.010	-0.005	17.945	0.325	0.325	0.000	0.000	0.000	0.000
52	A	356	MET	0	-0.013	0.004	18.676	-0.651	-0.651	0.000	0.000	0.000	0.000
53	A	357	LEU	0	-0.038	-0.026	12.547	0.068	0.068	0.000	0.000	0.000	0.000
54	A	358	ILE	0	0.023	0.018	16.531	0.088	0.088	0.000	0.000	0.000	0.000
55	A	359	THR	0	-0.024	-0.007	10.658	-0.095	-0.095	0.000	0.000	0.000	0.000
56	A	360	PRO	0	0.037	0.021	10.693	-0.934	-0.934	0.000	0.000	0.000	0.000
57	A	361	ASN	0	-0.032	-0.028	6.744	-2.939	-2.939	0.000	0.000	0.000	0.000
58	A	362	PRO	0	0.065	0.059	6.493	-4.301	-4.301	0.000	0.000	0.000	0.000
60	A	364	ILE	0	-0.035	-0.003	4.887	5.169	5.169	0.000	0.000	0.000	0.000
62	A	366	ASN	0	-0.002	-0.027	5.593	2.204	2.204	0.000	0.000	0.000	0.000
63	A	367	ASN	0	-0.044	-0.026	8.179	2.253	2.253	0.000	0.000	0.000	0.000
64	A	368	GLY	0	0.047	0.033	9.316	1.186	1.186	0.000	0.000	0.000	0.000
65	A	369	GLY	0	0.024	0.020	7.577	-2.278	-2.278	0.000	0.000	0.000	0.000
66	A	370	GLY	0	0.011	-0.003	8.544	1.778	1.778	0.000	0.000	0.000	0.000
67	A	371	PHE	0	-0.009	0.003	10.804	1.428	1.428	0.000	0.000	0.000	0.000
68	A	372	ILE	0	-0.029	-0.029	11.754	-1.922	-1.922	0.000	0.000	0.000	0.000
69	A	373	GLU	-1	-0.770	-0.835	14.163	-13.741	-13.741	0.000	0.000	0.000	0.000
70	A	374	MET	0	-0.018	-0.012	16.499	-0.828	-0.828	0.000	0.000	0.000	0.000
71	A	375	GLN	0	0.024	0.015	18.969	0.408	0.408	0.000	0.000	0.000	0.000
72	A	376	LEU	0	-0.012	-0.012	21.391	-0.601	-0.601	0.000	0.000	0.000	0.000
73	A	377	PRO	0	0.029	0.025	24.439	0.359	0.359	0.000	0.000	0.000	0.000
74	A	378	PRO	0	0.019	-0.009	27.843	-0.059	-0.059	0.000	0.000	0.000	0.000
75	A	379	GLY	0	0.003	0.017	30.953	0.071	0.071	0.000	0.000	0.000	0.000
76	A	380	ASP	-1	-0.893	-0.935	30.247	-10.530	-10.530	0.000	0.000	0.000	0.000
77	A	381	ASN	0	-0.021	-0.013	25.081	-0.329	-0.329	0.000	0.000	0.000	0.000
78	A	382	ILE	0	-0.021	-0.004	22.965	0.151	0.151	0.000	0.000	0.000	0.000
79	A	383	ILE	0	0.013	0.006	18.492	-0.505	-0.505	0.000	0.000	0.000	0.000
80	A	384	TYR	0	0.002	-0.010	17.656	0.398	0.398	0.000	0.000	0.000	0.000
81	A	385	VAL	0	0.012	-0.010	12.546	-1.088	-1.088	0.000	0.000	0.000	0.000
82	A	386	GLY	0	-0.030	-0.017	13.512	0.038	0.038	0.000	0.000	0.000	0.000
83	A	387	GLU	-1	-0.835	-0.919	14.117	-15.456	-15.456	0.000	0.000	0.000	0.000
84	A	388	LEU	0	-0.050	0.008	16.731	0.968	0.968	0.000	0.000	0.000	0.000
85	A	389	SER	0	0.008	-0.002	18.247	-0.355	-0.355	0.000	0.000	0.000	0.000
86	A	390	HIS	0	-0.034	-0.031	20.997	0.364	0.364	0.000	0.000	0.000	0.000
87	A	391	GLN	0	-0.023	-0.010	23.433	-0.282	-0.282	0.000	0.000	0.000	0.000
88	A	392	TRP	0	-0.044	-0.042	24.660	-0.207	-0.207	0.000	0.000	0.000	0.000
89	A	393	PHE	0	0.042	0.019	26.738	0.032	0.032	0.000	0.000	0.000	0.000
90	A	394	GLN	0	0.007	0.036	27.399	-0.232	-0.232	0.000	0.000	0.000	0.000
91	A	395	LYS	1	0.934	0.968	29.430	10.177	10.177	0.000	0.000	0.000	0.000
92	A	396	GLY	0	-0.002	-0.014	32.023	-0.207	-0.207	0.000	0.000	0.000	0.000
93	A	397	SER	-1	-0.924	-0.951	32.726	-8.749	-8.749	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:304:TYR)