FMO DATABASE

FMODB ID: N875Q

Calculation Name: 4YF2-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YF2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9D9X8

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1180796.073989
FMO2-HF: Nuclear repulsion	1127045.184607
FMO2-HF: Total energy	-53750.889382
FMO2-MP2: Total energy	-53901.697576

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
-175.152	-174.07	15.262	-8.275	-8.069	-0.081

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.788 / q_NPA : 0.896

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

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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	2	VAL	0	0.020	0.026	3.879	-3.054	-1.077	-0.023	-1.073	-0.881	-0.002
40	A	39	ASN	0	0.012	0.002	3.904	-14.358	-14.265	-0.001	-0.070	-0.023	0.000
41	A	40	THR	0	0.005	-0.026	3.663	-4.416	-3.701	0.008	-0.387	-0.336	-0.002
42	A	41	ASN	0	-0.032	-0.030	1.874	-29.063	-30.991	11.907	-5.248	-4.731	-0.061
43	A	42	ALA	0	-0.001	0.016	4.016	3.267	3.441	0.000	-0.064	-0.109	0.000
84	A	84	ASN	0	-0.009	0.002	4.015	-12.386	-12.149	0.000	-0.049	-0.188	0.000
85	A	85	ASN	0	0.025	-0.010	2.475	-11.892	-12.080	3.372	-1.375	-1.809	-0.016
86	A	86	ASP	-1	-0.832	-0.900	4.778	-20.718	-20.716	-0.001	-0.009	0.008	0.000
4	A	3	PHE	0	0.039	0.015	6.390	1.542	1.542	0.000	0.000	0.000	0.000
5	A	4	SER	0	0.011	0.002	9.658	1.433	1.433	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.859	0.908	13.193	14.926	14.926	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.080	-0.038	15.825	-0.279	-0.279	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.829	-0.890	11.413	-27.981	-27.981	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.001	-0.013	11.417	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.030	0.015	14.109	0.591	0.591	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.855	0.932	16.863	16.535	16.535	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.896	-0.959	12.189	-21.699	-21.699	0.000	0.000	0.000	0.000
13	A	12	MET	0	-0.089	-0.046	14.305	0.827	0.827	0.000	0.000	0.000	0.000
14	A	13	HIS	0	-0.005	0.003	17.382	1.279	1.279	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.809	-0.883	17.734	-15.066	-15.066	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.080	-0.053	13.203	0.398	0.398	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.016	0.006	18.576	0.347	0.347	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.039	-0.038	17.420	0.388	0.388	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.851	-0.920	21.532	-12.227	-12.227	0.000	0.000	0.000	0.000
20	A	19	GLY	0	0.042	0.022	24.288	0.432	0.432	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.058	-0.026	23.273	0.525	0.525	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.812	0.879	25.556	10.831	10.831	0.000	0.000	0.000	0.000
23	A	22	GLY	0	-0.005	0.007	27.763	0.202	0.202	0.000	0.000	0.000	0.000
24	A	23	TYR	0	-0.030	0.000	24.354	0.158	0.158	0.000	0.000	0.000	0.000
25	A	24	ASN	0	0.049	0.024	25.305	-0.520	-0.520	0.000	0.000	0.000	0.000
26	A	25	LEU	0	0.000	-0.012	19.900	-0.553	-0.553	0.000	0.000	0.000	0.000
27	A	26	ALA	0	0.025	0.013	20.721	-0.879	-0.879	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.833	-0.915	21.351	-13.060	-13.060	0.000	0.000	0.000	0.000
29	A	28	TRP	0	-0.012	-0.015	18.184	-0.959	-0.959	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.038	0.017	16.454	-1.263	-1.263	0.000	0.000	0.000	0.000
31	A	30	CYS	0	-0.044	0.020	16.542	-1.223	-1.223	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.013	0.000	16.438	-0.405	-0.405	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.006	0.024	12.467	-0.700	-0.700	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.039	-0.006	12.771	-1.343	-1.343	0.000	0.000	0.000	0.000
35	A	34	TYR	0	0.005	-0.030	14.349	-0.455	-0.455	0.000	0.000	0.000	0.000
36	A	35	THR	0	-0.077	-0.048	14.009	0.095	0.095	0.000	0.000	0.000	0.000
37	A	36	SER	0	-0.007	-0.016	8.924	-1.041	-1.041	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.005	0.014	9.465	-2.848	-2.848	0.000	0.000	0.000	0.000
39	A	38	PHE	0	-0.040	-0.021	9.857	-0.821	-0.821	0.000	0.000	0.000	0.000
44	A	43	VAL	0	-0.020	-0.018	7.301	1.615	1.615	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.851	-0.913	10.210	-18.998	-18.998	0.000	0.000	0.000	0.000
46	A	45	HIS	0	-0.032	-0.028	12.418	1.088	1.088	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.770	-0.844	16.887	-14.384	-14.384	0.000	0.000	0.000	0.000
48	A	47	ALA	0	-0.012	-0.018	20.294	0.173	0.173	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.850	-0.906	22.908	-13.297	-13.297	0.000	0.000	0.000	0.000
50	A	49	GLY	0	-0.025	-0.010	21.097	0.274	0.274	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.135	-0.075	20.030	-0.701	-0.701	0.000	0.000	0.000	0.000
52	A	51	THR	0	0.014	0.004	14.454	-0.765	-0.765	0.000	0.000	0.000	0.000
53	A	52	ASN	0	-0.055	-0.043	14.823	0.974	0.974	0.000	0.000	0.000	0.000
54	A	53	ASN	0	-0.014	-0.031	11.035	-2.854	-2.854	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.071	0.050	8.024	1.684	1.684	0.000	0.000	0.000	0.000
56	A	55	ILE	0	-0.014	-0.004	8.290	1.247	1.247	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.021	0.016	9.622	1.447	1.447	0.000	0.000	0.000	0.000
58	A	57	GLN	0	-0.058	-0.037	10.336	2.900	2.900	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.002	0.002	13.466	1.944	1.944	0.000	0.000	0.000	0.000
60	A	59	SER	0	0.090	0.044	15.293	-0.517	-0.517	0.000	0.000	0.000	0.000
61	A	60	SER	0	0.011	-0.028	17.379	0.376	0.376	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.811	0.912	18.868	14.340	14.340	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.760	0.865	21.400	12.659	12.659	0.000	0.000	0.000	0.000
64	A	63	TRP	0	0.043	0.021	18.786	0.425	0.425	0.000	0.000	0.000	0.000
65	A	64	CYS	0	-0.003	0.020	13.494	-0.519	-0.519	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.944	0.977	17.743	14.640	14.640	0.000	0.000	0.000	0.000
67	A	66	THR	0	0.083	0.029	16.111	-0.904	-0.904	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.025	-0.025	18.600	0.948	0.948	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.017	0.015	21.241	-0.321	-0.321	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.051	0.017	20.921	0.415	0.415	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.063	-0.020	22.219	-0.477	-0.477	0.000	0.000	0.000	0.000
72	A	71	GLY	0	0.089	0.036	24.229	0.157	0.157	0.000	0.000	0.000	0.000
73	A	72	PRO	0	-0.078	-0.037	24.820	-0.064	-0.064	0.000	0.000	0.000	0.000
74	A	73	ASN	0	-0.007	0.005	19.937	-0.434	-0.434	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.052	0.029	22.244	0.009	0.009	0.000	0.000	0.000	0.000
76	A	75	CYS	0	-0.173	-0.078	15.686	1.610	1.610	0.000	0.000	0.000	0.000
77	A	76	ARG	1	0.861	0.932	19.751	12.841	12.841	0.000	0.000	0.000	0.000
78	A	77	ILE	0	0.035	0.031	13.583	0.175	0.175	0.000	0.000	0.000	0.000
79	A	78	TYR	0	0.014	0.008	14.471	0.983	0.983	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.049	0.013	9.140	-1.540	-1.540	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.904	-0.950	8.688	-25.895	-25.895	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.054	-0.029	9.202	-0.914	-0.914	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.050	-0.014	5.796	-0.762	-0.762	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.053	0.017	8.486	-0.447	-0.447	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.891	0.946	10.110	22.801	22.801	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.896	-0.949	11.780	-19.623	-19.623	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.015	-0.015	10.068	1.489	1.489	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.004	0.009	12.726	1.178	1.178	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.023	0.000	15.307	1.261	1.261	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.068	0.025	16.367	0.915	0.915	0.000	0.000	0.000	0.000
94	A	95	MET	0	0.011	0.000	18.169	0.653	0.653	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.904	0.960	20.009	15.217	15.217	0.000	0.000	0.000	0.000
96	A	97	ILE	0	0.005	0.012	18.538	0.614	0.614	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.018	0.008	21.838	0.636	0.636	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.004	-0.004	24.276	0.291	0.291	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.795	-0.878	26.033	-10.718	-10.718	0.000	0.000	0.000	0.000
100	A	101	PRO	0	-0.055	-0.050	28.114	-0.071	-0.071	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.005	0.008	27.463	0.173	0.173	0.000	0.000	0.000	0.000
102	A	103	GLY	0	0.011	0.027	26.309	-0.073	-0.073	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.045	0.011	20.880	-0.371	-0.371	0.000	0.000	0.000	0.000
104	A	105	GLY	0	-0.001	0.007	23.427	-0.321	-0.321	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.040	-0.017	21.780	0.082	0.082	0.000	0.000	0.000	0.000
106	A	107	TRP	0	0.002	-0.001	16.743	0.222	0.222	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.806	-0.885	21.212	-12.683	-12.683	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.010	-0.001	18.289	0.380	0.380	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.018	-0.004	20.257	0.380	0.380	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.815	0.870	22.076	12.750	12.750	0.000	0.000	0.000	0.000
111	A	112	HIS	0	-0.001	0.004	23.661	0.556	0.556	0.000	0.000	0.000	0.000
112	A	113	HIS	1	0.823	0.909	20.348	14.221	14.221	0.000	0.000	0.000	0.000
113	A	115	GLN	0	0.045	0.018	24.168	0.248	0.248	0.000	0.000	0.000	0.000
114	A	116	GLY	0	-0.028	-0.017	27.408	0.076	0.076	0.000	0.000	0.000	0.000
115	A	117	ARG	1	0.874	0.957	23.347	12.957	12.957	0.000	0.000	0.000	0.000
116	A	118	ASP	-1	-0.816	-0.880	29.484	-10.593	-10.593	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.055	-0.045	23.709	-0.441	-0.441	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.024	-0.002	24.775	-0.563	-0.563	0.000	0.000	0.000	0.000
119	A	121	ASP	-1	-0.849	-0.918	24.781	-12.242	-12.242	0.000	0.000	0.000	0.000
120	A	122	TRP	0	-0.079	-0.056	17.793	-0.975	-0.975	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.019	-0.018	20.632	-0.949	-0.949	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.836	-0.912	22.950	-11.517	-11.517	0.000	0.000	0.000	0.000
123	A	125	GLY	0	-0.038	-0.027	24.032	-0.548	-0.548	0.000	0.000	0.000	0.000
124	A	127	ASP	-1	-0.928	-0.973	22.402	-13.072	-13.072	0.000	0.000	0.000	0.000
125	A	128	PHE	0	-0.048	-0.026	20.443	0.101	0.101	0.000	0.000	0.000	0.000
126	A	129	LEU	-1	-0.932	-0.940	23.884	-11.224	-11.224	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)