FMO DATABASE

FMODB ID: 7ML4K

Calculation Name: 3B09-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3B09

Chain ID: A

ChEMBL ID:

UniProt ID: Q765B0

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-285824.531996
FMO2-HF: Nuclear repulsion	260893.554423
FMO2-HF: Total energy	-24930.977573
FMO2-MP2: Total energy	-25001.629898

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:3:ASP)

Summations of interaction energy for fragment #1(A:3:ASP)

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.
-7.978	-6.987	8.585	-4.739	-4.839	-0.005

Interaction energy analysis for fragmet #1(A:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.160 / q_NPA : 0.040

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].
4	A	4	LEU	0	-0.082	0.089	4.188	0.115	0.363	-0.001	-0.088	-0.160	0.000
5	A	5	PHE	0	0.038	-0.084	2.479	-4.668	-2.314	0.663	-1.384	-1.633	0.013
6	A	5	PHE	0	-0.091	0.084	3.349	-1.321	-0.660	0.036	-0.362	-0.336	0.002
7	A	6	SER	0	0.113	-0.019	1.960	-0.835	-4.111	7.866	-2.391	-2.199	-0.023
8	A	6	SER	0	-0.014	0.080	5.851	0.090	0.090	0.000	0.000	0.000	0.000
9	A	7	THR	0	0.059	-0.088	3.175	-0.623	-0.078	0.008	-0.287	-0.266	0.001
10	A	7	THR	0	-0.079	0.046	2.996	-0.133	0.297	0.015	-0.226	-0.219	0.002
11	A	8	MET	0	0.028	-0.114	5.050	-0.115	-0.086	-0.002	-0.001	-0.026	0.000
12	A	8	MET	0	-0.036	0.118	5.436	-0.082	-0.082	0.000	0.000	0.000	0.000
13	A	9	GLU	0	0.059	-0.117	6.792	-0.056	-0.056	0.000	0.000	0.000	0.000
14	A	9	GLU	-1	-0.885	-0.813	5.696	0.175	0.175	0.000	0.000	0.000	0.000
15	A	10	GLN	0	0.092	-0.072	7.814	-0.125	-0.125	0.000	0.000	0.000	0.000
16	A	10	GLN	0	-0.097	0.094	8.136	0.011	0.011	0.000	0.000	0.000	0.000
17	A	11	HIS	0	0.094	-0.070	9.096	-0.091	-0.091	0.000	0.000	0.000	0.000
18	A	11	HIS	0	-0.099	0.076	9.198	-0.061	-0.061	0.000	0.000	0.000	0.000
19	A	12	ALA	0	0.153	-0.086	10.830	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	12	ALA	0	-0.074	0.108	11.796	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	13	SER	0	-0.024	-0.122	12.268	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	13	SER	0	-0.055	0.062	12.110	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	14	TYR	0	0.073	-0.072	13.571	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	14	TYR	0	-0.062	0.099	14.182	0.004	0.004	0.000	0.000	0.000	0.000
25	A	15	GLY	0	-0.018	-0.110	15.068	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	16	VAL	0	0.099	-0.004	16.824	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	16	VAL	0	-0.085	0.112	17.069	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	17	GLY	0	0.017	-0.104	18.056	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	18	ARG	0	0.047	-0.010	19.413	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	18	ARG	1	0.733	0.987	19.071	-0.206	-0.206	0.000	0.000	0.000	0.000
31	A	19	GLN	0	0.170	-0.049	21.203	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	19	GLN	0	-0.108	0.085	22.023	0.004	0.004	0.000	0.000	0.000	0.000
33	A	20	MET	0	0.011	-0.126	22.723	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	20	MET	0	-0.088	0.097	22.246	0.001	0.001	0.000	0.000	0.000	0.000
35	A	21	GLY	0	0.027	-0.096	23.872	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	22	GLU	0	0.101	0.001	25.350	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	22	GLU	-1	-0.920	-0.799	24.072	0.161	0.161	0.000	0.000	0.000	0.000
38	A	23	GLN	0	0.092	-0.101	27.035	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	23	GLN	0	-0.103	0.081	26.944	0.000	0.000	0.000	0.000	0.000	0.000
40	A	24	LEU	0	0.038	-0.107	28.436	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	24	LEU	0	-0.073	0.101	27.405	0.000	0.000	0.000	0.000	0.000	0.000
42	A	25	ALA	0	0.108	-0.086	29.608	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	25	ALA	0	-0.091	0.101	29.840	0.002	0.002	0.000	0.000	0.000	0.000
44	A	26	ALA	0	0.074	-0.093	31.447	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	26	ALA	0	-0.092	0.096	32.258	0.000	0.000	0.000	0.000	0.000	0.000
46	A	27	ASN	0	-0.044	-0.091	33.311	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	27	ASN	0	-0.169	0.029	34.967	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	28	SER	0	0.147	-0.023	34.015	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	28	SER	0	-0.097	0.017	32.993	0.001	0.001	0.000	0.000	0.000	0.000
50	A	29	PHE	0	0.010	-0.115	34.989	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	29	PHE	0	-0.056	0.089	35.329	0.000	0.000	0.000	0.000	0.000	0.000
52	A	30	GLU	0	0.133	-0.143	37.206	0.005	0.005	0.000	0.000	0.000	0.000
53	A	30	GLU	-1	-1.014	-0.816	40.815	0.055	0.055	0.000	0.000	0.000	0.000
54	A	31	GLY	0	-0.018	-0.115	38.305	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	32	ILE	0	0.032	-0.003	34.417	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	32	ILE	0	-0.070	0.109	32.017	0.000	0.000	0.000	0.000	0.000	0.000
57	A	33	ASP	0	0.090	-0.109	33.189	0.006	0.006	0.000	0.000	0.000	0.000
58	A	33	ASP	-1	-0.911	-0.813	32.251	0.084	0.084	0.000	0.000	0.000	0.000
59	A	34	ILE	0	0.040	-0.104	28.857	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	34	ILE	0	-0.079	0.097	26.785	0.002	0.002	0.000	0.000	0.000	0.000
61	A	35	PRO	0	0.052	-0.105	27.417	0.003	0.003	0.000	0.000	0.000	0.000
62	A	36	ALA	0	0.144	0.011	28.032	0.002	0.002	0.000	0.000	0.000	0.000
63	A	36	ALA	0	-0.077	0.117	32.117	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	37	VAL	0	0.041	-0.095	28.978	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	37	VAL	0	-0.108	0.082	27.249	0.000	0.000	0.000	0.000	0.000	0.000
66	A	38	GLN	0	0.091	-0.082	24.836	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	38	GLN	0	-0.092	0.064	22.470	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	39	ALA	0	0.060	-0.109	24.737	0.002	0.002	0.000	0.000	0.000	0.000
69	A	39	ALA	0	-0.076	0.114	27.923	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	40	GLY	0	0.007	-0.099	26.914	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	41	LEU	0	0.144	0.032	24.686	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	41	LEU	0	-0.121	0.081	21.465	0.003	0.003	0.000	0.000	0.000	0.000
73	A	42	ALA	0	0.087	-0.111	22.600	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	42	ALA	0	-0.100	0.095	22.835	0.002	0.002	0.000	0.000	0.000	0.000
75	A	43	ASP	0	0.072	-0.119	23.570	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	43	ASP	-1	-0.934	-0.819	27.832	0.043	0.043	0.000	0.000	0.000	0.000
77	A	44	ALA	0	0.120	-0.070	26.703	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	44	ALA	0	-0.083	0.093	26.689	0.000	0.000	0.000	0.000	0.000	0.000
79	A	45	PHE	0	0.063	-0.076	22.132	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	45	PHE	0	-0.133	0.053	17.581	0.003	0.003	0.000	0.000	0.000	0.000
81	A	46	ALA	0	0.022	-0.133	22.782	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	46	ALA	0	-0.094	0.101	22.959	0.002	0.002	0.000	0.000	0.000	0.000
83	A	47	GLY	0	-0.050	-0.120	23.664	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	48	LYS	0	0.059	0.013	27.014	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	48	LYS	1	0.693	0.960	27.213	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	49	GLU	0	0.103	-0.112	28.829	0.002	0.002	0.000	0.000	0.000	0.000
87	A	49	GLU	-1	-1.024	-0.847	33.083	0.008	0.008	0.000	0.000	0.000	0.000
88	A	50	SER	0	0.050	-0.090	31.579	0.004	0.004	0.000	0.000	0.000	0.000
89	A	50	SER	0	-0.075	0.033	33.204	0.002	0.002	0.000	0.000	0.000	0.000
90	A	51	ALA	0	0.070	-0.079	32.272	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	51	ALA	0	-0.085	0.092	32.208	0.001	0.001	0.000	0.000	0.000	0.000
92	A	52	VAL	0	0.022	-0.112	33.992	0.000	0.000	0.000	0.000	0.000	0.000
93	A	52	VAL	0	-0.090	0.107	35.267	0.000	0.000	0.000	0.000	0.000	0.000
94	A	53	SER	0	0.099	-0.053	36.618	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	53	SER	0	-0.052	0.038	40.665	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	54	MET	0	0.061	-0.115	38.827	0.003	0.003	0.000	0.000	0.000	0.000
97	A	54	MET	0	-0.063	0.107	35.191	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	55	GLU	0	0.108	-0.099	39.667	0.001	0.001	0.000	0.000	0.000	0.000
99	A	55	GLU	-1	-1.003	-0.843	44.043	0.015	0.015	0.000	0.000	0.000	0.000
100	A	56	GLU	0	0.076	-0.139	41.516	0.000	0.000	0.000	0.000	0.000	0.000
101	A	56	GLU	-1	-0.884	-0.767	40.666	0.027	0.027	0.000	0.000	0.000	0.000
102	A	57	LEU	0	0.060	-0.084	38.225	0.002	0.002	0.000	0.000	0.000	0.000
103	A	57	LEU	0	-0.090	0.093	35.317	0.000	0.000	0.000	0.000	0.000	0.000
104	A	58	GLN	0	0.132	-0.073	39.379	0.003	0.003	0.000	0.000	0.000	0.000
105	A	58	GLN	0	-0.090	0.096	42.006	0.001	0.001	0.000	0.000	0.000	0.000
106	A	59	VAL	0	0.067	-0.097	42.041	0.000	0.000	0.000	0.000	0.000	0.000
107	A	59	VAL	0	-0.066	0.111	44.273	0.000	0.000	0.000	0.000	0.000	0.000
108	A	60	ALA	0	0.170	-0.076	40.616	0.000	0.000	0.000	0.000	0.000	0.000
109	A	60	ALA	0	-0.073	0.108	39.948	0.001	0.001	0.000	0.000	0.000	0.000
110	A	61	PHE	0	-0.011	-0.137	40.470	0.003	0.003	0.000	0.000	0.000	0.000
111	A	61	PHE	0	-0.039	0.108	35.882	0.000	0.000	0.000	0.000	0.000	0.000
112	A	62	THR	0	0.082	-0.053	41.116	0.001	0.001	0.000	0.000	0.000	0.000
113	A	62	THR	0	-0.082	0.046	44.704	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	63	GLU	0	0.039	-0.130	44.589	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	63	GLU	-1	-0.998	-0.837	44.549	0.033	0.033	0.000	0.000	0.000	0.000
116	A	64	ILE	0	0.065	-0.086	41.119	0.000	0.000	0.000	0.000	0.000	0.000
117	A	64	ILE	0	-0.063	0.123	39.133	0.000	0.000	0.000	0.000	0.000	0.000
118	A	65	SER	0	0.060	-0.106	42.597	0.003	0.003	0.000	0.000	0.000	0.000
119	A	65	SER	0	-0.057	0.072	42.813	0.000	0.000	0.000	0.000	0.000	0.000
120	A	66	ARG	0	-0.046	-0.111	43.759	0.000	0.000	0.000	0.000	0.000	0.000
121	A	66	ARG	1	0.778	1.017	47.304	-0.027	-0.027	0.000	0.000	0.000	0.000
122	A	67	ARG	0	-0.027	-0.127	45.436	0.000	0.000	0.000	0.000	0.000	0.000
123	A	67	ARG	1	0.894	0.956	39.697	-0.044	-0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASP)