FMO DATABASE

FMODB ID: 4Y41N

Calculation Name: 6AGB-E-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6AGB

Chain ID: E

ChEMBL ID:

UniProt ID: P41812

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1285442.599544
FMO2-HF: Nuclear repulsion	1227388.842617
FMO2-HF: Total energy	-58053.756927
FMO2-MP2: Total energy	-58219.564435

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:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
143.849	146.957	0.409	-1.48	-2.036	-0.008

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.892 / q_NPA : 0.942

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	4	LEU	0	0.097	0.045	2.798	-1.950	0.827	0.406	-1.432	-1.751	-0.008
4	A	5	LYS	1	0.908	0.961	3.689	42.422	42.753	0.003	-0.048	-0.285	0.000
5	A	6	SER	0	0.028	0.032	6.184	1.121	1.121	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.895	0.947	9.509	20.006	20.006	0.000	0.000	0.000	0.000
7	A	8	TYR	0	0.004	-0.002	12.643	0.481	0.481	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.061	0.009	16.027	0.003	0.003	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.064	-0.026	19.294	0.166	0.166	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.024	0.003	22.700	0.001	0.001	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.787	-0.891	25.650	-9.320	-9.320	0.000	0.000	0.000	0.000
12	A	13	ILE	0	0.001	0.010	29.397	-0.072	-0.072	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.035	-0.015	32.233	0.077	0.077	0.000	0.000	0.000	0.000
14	A	15	PHE	0	0.053	0.014	35.380	-0.090	-0.090	0.000	0.000	0.000	0.000
15	A	16	PRO	0	0.011	0.008	38.142	0.089	0.089	0.000	0.000	0.000	0.000
16	A	17	PRO	0	-0.009	-0.008	40.979	0.065	0.065	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.057	-0.021	43.381	0.075	0.075	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.875	-0.952	45.983	-5.892	-5.892	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.020	-0.007	49.747	-0.038	-0.038	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.062	-0.030	52.336	0.130	0.130	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.033	0.003	52.969	0.121	0.121	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.935	-0.956	53.220	-5.433	-5.433	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.932	-0.977	46.650	-6.607	-6.607	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.020	-0.010	50.007	0.105	0.105	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.009	-0.006	48.268	-0.167	-0.167	0.000	0.000	0.000	0.000
26	A	27	SER	0	0.020	-0.012	47.469	0.017	0.017	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.935	0.958	40.273	7.208	7.208	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.023	0.006	42.519	-0.187	-0.187	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.802	-0.879	43.587	-6.540	-6.540	0.000	0.000	0.000	0.000
30	A	31	ILE	0	0.039	0.028	41.845	-0.083	-0.083	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.061	-0.034	37.950	-0.225	-0.225	0.000	0.000	0.000	0.000
32	A	33	LEU	0	0.003	-0.006	40.288	-0.189	-0.189	0.000	0.000	0.000	0.000
33	A	34	SER	0	0.035	0.022	42.566	-0.051	-0.051	0.000	0.000	0.000	0.000
34	A	35	HIS	0	0.031	0.029	38.305	-0.071	-0.071	0.000	0.000	0.000	0.000
35	A	36	HIS	1	0.739	0.862	33.874	8.323	8.323	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.908	0.961	38.134	6.874	6.874	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.040	0.013	38.953	0.056	0.056	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.053	-0.031	35.589	-0.124	-0.124	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.043	0.025	37.201	0.115	0.115	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.018	0.003	38.233	-0.173	-0.173	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.905	-0.934	36.822	-8.355	-8.355	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.014	0.002	32.897	-0.272	-0.272	0.000	0.000	0.000	0.000
43	A	44	SER	0	0.036	-0.009	32.096	-0.164	-0.164	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.015	-0.009	25.638	-0.106	-0.106	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.976	0.975	27.556	9.706	9.706	0.000	0.000	0.000	0.000
46	A	47	SER	0	0.023	0.041	29.380	-0.161	-0.161	0.000	0.000	0.000	0.000
47	A	48	ILE	0	0.046	0.016	26.601	-0.078	-0.078	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.033	-0.032	22.546	-0.274	-0.274	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.020	-0.009	26.315	-0.236	-0.236	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.859	-0.916	29.015	-9.464	-9.464	0.000	0.000	0.000	0.000
51	A	52	ILE	0	0.034	0.014	23.332	-0.109	-0.109	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.914	0.949	21.275	12.390	12.390	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.908	0.971	25.950	8.824	8.824	0.000	0.000	0.000	0.000
54	A	55	SER	0	0.025	0.015	27.862	0.098	0.098	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.012	-0.016	21.542	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.028	-0.034	25.688	-0.111	-0.111	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.044	-0.023	27.577	0.120	0.120	0.000	0.000	0.000	0.000
58	A	59	ASN	0	-0.036	-0.005	28.170	0.363	0.363	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.043	-0.022	23.107	-0.126	-0.126	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.027	0.030	25.349	-0.268	-0.268	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.895	-0.956	25.553	-11.744	-11.744	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.034	0.004	17.779	-0.584	-0.584	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.028	0.015	20.577	-0.717	-0.717	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.023	0.003	20.387	-0.773	-0.773	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.014	-0.008	20.158	-0.566	-0.566	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.852	0.928	15.766	15.167	15.167	0.000	0.000	0.000	0.000
67	A	68	CYS	0	-0.014	0.008	15.525	-1.060	-1.060	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.009	-0.022	16.631	-0.693	-0.693	0.000	0.000	0.000	0.000
69	A	70	SER	0	0.006	0.036	13.281	-0.628	-0.628	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.078	-0.056	10.354	-1.072	-1.072	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.007	0.026	14.313	-0.115	-0.115	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.029	-0.023	17.274	0.264	0.264	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.027	0.027	19.005	-0.339	-0.339	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.863	0.935	17.082	16.164	16.164	0.000	0.000	0.000	0.000
75	A	76	TYR	0	0.022	0.010	20.742	0.096	0.096	0.000	0.000	0.000	0.000
76	A	77	PHE	0	0.049	0.007	23.913	-0.152	-0.152	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.017	0.007	27.168	0.187	0.187	0.000	0.000	0.000	0.000
78	A	79	ASN	0	0.100	0.044	30.841	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.974	0.992	33.884	8.283	8.283	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.011	0.016	31.310	0.027	0.027	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.006	0.003	31.984	0.053	0.053	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.008	0.001	27.774	-0.256	-0.256	0.000	0.000	0.000	0.000
83	A	84	GLY	0	0.003	-0.009	25.587	0.063	0.063	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.061	-0.026	19.224	-0.250	-0.250	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.057	0.030	18.339	-0.203	-0.203	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.872	0.929	10.322	21.820	21.820	0.000	0.000	0.000	0.000
87	A	88	CYS	0	0.051	0.033	14.105	0.488	0.488	0.000	0.000	0.000	0.000
88	A	89	HIS	0	0.101	0.026	9.727	-2.784	-2.784	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.871	0.913	5.072	32.888	32.888	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.924	-0.949	8.321	-25.187	-25.187	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.774	-0.883	12.053	-16.578	-16.578	0.000	0.000	0.000	0.000
92	A	93	CYS	0	-0.053	-0.037	14.086	0.731	0.731	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.905	-0.939	15.859	-12.891	-12.891	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.043	0.031	18.216	0.578	0.578	0.000	0.000	0.000	0.000
95	A	96	VAL	0	-0.014	-0.021	17.345	0.487	0.487	0.000	0.000	0.000	0.000
96	A	97	ILE	0	-0.036	-0.025	19.106	0.460	0.460	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.042	0.022	21.974	0.594	0.594	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.013	0.002	22.920	0.417	0.417	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.068	-0.052	22.155	0.345	0.345	0.000	0.000	0.000	0.000
100	A	101	MET	0	-0.032	-0.013	25.647	0.328	0.328	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.025	0.023	27.829	0.334	0.334	0.000	0.000	0.000	0.000
102	A	103	MET	0	-0.081	-0.025	27.717	0.027	0.027	0.000	0.000	0.000	0.000
103	A	104	SER	0	0.002	0.009	30.604	0.188	0.188	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.924	0.953	34.383	7.932	7.932	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.007	0.016	33.766	-0.214	-0.214	0.000	0.000	0.000	0.000
106	A	107	GLY	0	-0.082	-0.055	35.554	0.158	0.158	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.907	-0.943	37.613	-7.256	-7.256	0.000	0.000	0.000	0.000
108	A	109	VAL	0	0.012	0.007	38.647	0.144	0.144	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.920	-0.968	38.084	-7.445	-7.445	0.000	0.000	0.000	0.000
110	A	111	GLY	0	0.050	0.026	39.811	0.031	0.031	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.066	-0.034	34.379	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	113	ILE	0	0.037	0.021	33.842	-0.061	-0.061	0.000	0.000	0.000	0.000
113	A	114	VAL	0	0.001	-0.004	27.708	-0.083	-0.083	0.000	0.000	0.000	0.000
114	A	115	ASN	0	0.004	0.005	29.211	-0.267	-0.267	0.000	0.000	0.000	0.000
115	A	116	PRO	0	0.026	0.006	23.760	-0.230	-0.230	0.000	0.000	0.000	0.000
116	A	117	VAL	0	-0.001	0.011	25.299	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.883	0.940	20.021	13.536	13.536	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.096	0.062	16.243	-0.363	-0.363	0.000	0.000	0.000	0.000
119	A	120	SER	0	-0.105	-0.066	15.753	0.274	0.274	0.000	0.000	0.000	0.000
120	A	121	GLY	0	0.015	0.012	11.710	-0.333	-0.333	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.032	-0.029	11.971	-0.781	-0.781	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.102	0.060	14.673	0.564	0.564	0.000	0.000	0.000	0.000
123	A	124	LYS	1	1.041	1.035	17.924	15.000	15.000	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.873	0.912	17.639	14.778	14.778	0.000	0.000	0.000	0.000
125	A	126	ILE	0	-0.033	0.000	17.849	0.502	0.502	0.000	0.000	0.000	0.000
126	A	127	GLU	-1	-0.817	-0.912	21.347	-12.845	-12.845	0.000	0.000	0.000	0.000
127	A	128	GLN	0	0.044	0.029	23.232	-0.026	-0.026	0.000	0.000	0.000	0.000
128	A	129	PHE	0	-0.065	-0.033	23.627	0.308	0.308	0.000	0.000	0.000	0.000
129	A	130	ALA	0	0.069	0.031	25.384	0.435	0.435	0.000	0.000	0.000	0.000
130	A	131	MET	0	0.031	0.016	26.586	0.461	0.461	0.000	0.000	0.000	0.000
131	A	132	ARG	1	0.908	0.945	24.985	11.490	11.490	0.000	0.000	0.000	0.000
132	A	133	ARG	1	0.828	0.909	28.791	10.053	10.053	0.000	0.000	0.000	0.000
133	A	134	ASN	0	0.068	0.021	30.683	0.309	0.309	0.000	0.000	0.000	0.000
134	A	135	SER	0	0.029	0.025	33.022	0.355	0.355	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.941	0.971	31.261	9.557	9.557	0.000	0.000	0.000	0.000
136	A	137	ILE	0	0.022	0.018	33.785	0.199	0.199	0.000	0.000	0.000	0.000
137	A	138	LEU	0	0.037	0.007	36.858	0.196	0.196	0.000	0.000	0.000	0.000
138	A	139	ASN	0	-0.058	-0.031	37.631	0.343	0.343	0.000	0.000	0.000	0.000
139	A	140	ILE	0	-0.001	0.007	37.863	0.161	0.161	0.000	0.000	0.000	0.000
140	A	141	ILE	0	0.017	0.012	40.928	0.160	0.160	0.000	0.000	0.000	0.000
141	A	142	LYS	1	0.982	0.986	42.856	7.137	7.137	0.000	0.000	0.000	0.000
142	A	143	CYS	0	-0.095	-0.060	43.494	0.131	0.131	0.000	0.000	0.000	0.000
143	A	144	SER	0	0.021	0.001	45.138	0.115	0.115	0.000	0.000	0.000	0.000
144	A	145	GLN	0	-0.038	0.000	46.917	-0.043	-0.043	0.000	0.000	0.000	0.000
145	A	146	SER	0	-0.105	-0.056	48.869	0.092	0.092	0.000	0.000	0.000	0.000
146	A	147	SER	-1	-0.915	-0.937	50.481	-5.917	-5.917	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)