FMO DATABASE

FMODB ID: 98KM2

Calculation Name: 3BF2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3BF2

Chain ID: A

ChEMBL ID:

UniProt ID: A1KSW9

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1048713.699844
FMO2-HF: Nuclear repulsion	997851.614091
FMO2-HF: Total energy	-50862.085753
FMO2-MP2: Total energy	-51011.543848

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:30:LEU)

Summations of interaction energy for fragment #1(A:30:LEU)

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.
-20.103	-10.388	15.409	-6.547	-18.578	-0.041

Interaction energy analysis for fragmet #1(A:30:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.047

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	32	TYR	0	-0.025	-0.020	2.917	-4.039	-0.164	0.258	-1.880	-2.253	0.000
4	A	33	ARG	1	0.867	0.919	2.176	-0.953	-0.196	4.150	-1.970	-2.936	0.009
5	A	34	SER	0	-0.005	0.023	3.028	1.351	-0.436	-0.047	2.291	-0.456	-0.001
6	A	35	TRP	0	0.013	-0.014	2.376	-1.439	-0.115	0.518	-0.477	-1.365	-0.004
7	A	36	HIS	0	0.078	0.058	6.643	-0.040	-0.040	0.000	0.000	0.000	0.000
8	A	37	ILE	0	-0.012	-0.013	9.350	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	38	GLU	-1	-0.882	-0.925	11.766	-0.177	-0.177	0.000	0.000	0.000	0.000
10	A	39	GLY	0	0.068	0.032	15.179	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	40	GLY	0	0.027	-0.009	15.755	-0.032	-0.032	0.000	0.000	0.000	0.000
12	A	41	GLN	0	0.036	0.012	16.127	-0.039	-0.039	0.000	0.000	0.000	0.000
13	A	42	ALA	0	-0.015	-0.014	17.873	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	43	LEU	0	-0.016	-0.019	13.810	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	44	GLN	0	-0.009	0.010	13.228	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	45	PHE	0	0.065	0.041	12.574	-0.064	-0.064	0.000	0.000	0.000	0.000
17	A	46	PRO	0	0.025	0.009	12.545	-0.082	-0.082	0.000	0.000	0.000	0.000
18	A	47	LEU	0	0.013	0.009	8.508	-0.147	-0.147	0.000	0.000	0.000	0.000
19	A	48	GLU	-1	-0.899	-0.949	7.914	-0.839	-0.839	0.000	0.000	0.000	0.000
20	A	49	THR	0	-0.028	-0.012	8.100	-0.190	-0.190	0.000	0.000	0.000	0.000
21	A	50	ALA	0	0.029	0.013	6.785	-0.149	-0.149	0.000	0.000	0.000	0.000
22	A	51	LEU	0	-0.006	-0.021	2.944	-1.555	-0.752	0.196	-0.166	-0.833	0.000
23	A	52	TYR	0	-0.017	-0.002	3.775	-1.341	-0.950	0.004	-0.163	-0.233	-0.001
24	A	53	GLN	0	-0.044	-0.007	6.304	0.007	0.007	0.000	0.000	0.000	0.000
25	A	54	ALA	0	-0.021	0.003	2.177	-0.871	-0.281	1.964	-0.896	-1.658	-0.002
26	A	55	SER	0	-0.028	-0.022	2.329	-5.193	-3.911	4.615	-2.579	-3.317	-0.030
27	A	56	GLY	0	-0.020	-0.016	2.331	0.484	0.918	1.870	-1.033	-1.272	-0.001
28	A	57	ARG	1	0.891	0.947	3.041	1.560	-0.063	0.176	1.741	-0.295	-0.001
29	A	58	VAL	0	0.031	0.007	6.197	0.049	0.049	0.000	0.000	0.000	0.000
30	A	59	ASP	-1	-0.954	-0.955	8.644	-0.171	-0.171	0.000	0.000	0.000	0.000
31	A	60	ASP	-1	-0.835	-0.936	11.412	-0.188	-0.188	0.000	0.000	0.000	0.000
32	A	61	ALA	0	-0.004	-0.007	13.062	0.003	0.003	0.000	0.000	0.000	0.000
33	A	62	ALA	0	-0.033	-0.022	14.104	0.020	0.020	0.000	0.000	0.000	0.000
34	A	63	GLY	0	-0.030	-0.016	14.059	0.028	0.028	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.029	0.023	9.258	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	65	GLN	0	-0.086	-0.046	8.003	0.053	0.053	0.000	0.000	0.000	0.000
37	A	66	MET	0	-0.056	-0.028	6.499	0.091	0.091	0.000	0.000	0.000	0.000
38	A	67	THR	0	0.021	0.008	8.435	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	68	LEU	0	-0.029	-0.005	7.405	0.015	0.015	0.000	0.000	0.000	0.000
40	A	69	ARG	1	0.870	0.909	9.982	0.150	0.150	0.000	0.000	0.000	0.000
41	A	70	ILE	0	-0.015	-0.007	12.261	0.004	0.004	0.000	0.000	0.000	0.000
42	A	71	ASP	-1	-0.823	-0.897	15.130	-0.154	-0.154	0.000	0.000	0.000	0.000
43	A	72	SER	0	-0.033	-0.015	17.937	0.016	0.016	0.000	0.000	0.000	0.000
44	A	73	VAL	0	0.009	-0.003	17.715	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	74	SER	0	-0.047	-0.013	20.173	0.017	0.017	0.000	0.000	0.000	0.000
46	A	75	GLN	0	0.013	-0.001	22.554	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	76	ASN	0	-0.054	-0.027	24.931	0.011	0.011	0.000	0.000	0.000	0.000
48	A	77	LYS	1	0.965	0.988	27.808	0.108	0.108	0.000	0.000	0.000	0.000
49	A	78	GLU	-1	-0.843	-0.912	30.301	-0.086	-0.086	0.000	0.000	0.000	0.000
50	A	79	THR	0	-0.026	-0.011	32.776	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	80	TYR	0	-0.022	-0.018	33.279	0.003	0.003	0.000	0.000	0.000	0.000
52	A	81	THR	0	-0.012	-0.012	35.492	0.006	0.006	0.000	0.000	0.000	0.000
53	A	82	VAL	0	0.039	0.012	38.383	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	83	THR	0	0.045	0.030	41.475	0.000	0.000	0.000	0.000	0.000	0.000
55	A	84	ARG	1	0.906	0.911	44.452	0.053	0.053	0.000	0.000	0.000	0.000
56	A	85	ALA	0	0.046	0.005	46.908	0.001	0.001	0.000	0.000	0.000	0.000
57	A	86	ALA	0	-0.050	0.005	45.788	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	87	VAL	0	-0.069	-0.045	44.101	0.000	0.000	0.000	0.000	0.000	0.000
59	A	88	ILE	0	-0.005	0.022	37.637	0.001	0.001	0.000	0.000	0.000	0.000
60	A	89	ASN	0	-0.038	-0.008	39.512	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	90	GLU	-1	-0.854	-0.914	34.268	-0.090	-0.090	0.000	0.000	0.000	0.000
62	A	91	TYR	0	-0.009	0.003	32.256	0.005	0.005	0.000	0.000	0.000	0.000
63	A	92	LEU	0	-0.023	-0.001	27.616	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	93	LEU	0	0.021	0.010	26.142	0.003	0.003	0.000	0.000	0.000	0.000
65	A	94	ILE	0	-0.026	-0.025	23.374	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	95	LEU	0	0.011	0.010	17.821	0.002	0.002	0.000	0.000	0.000	0.000
67	A	96	THR	0	-0.024	-0.028	19.462	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	97	VAL	0	-0.003	0.003	14.367	0.000	0.000	0.000	0.000	0.000	0.000
69	A	98	GLU	-1	-0.919	-0.956	16.078	-0.150	-0.150	0.000	0.000	0.000	0.000
70	A	99	ALA	0	0.021	0.007	11.833	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	100	GLN	0	-0.026	-0.009	13.208	0.029	0.029	0.000	0.000	0.000	0.000
72	A	101	VAL	0	0.008	0.015	7.937	-0.045	-0.045	0.000	0.000	0.000	0.000
73	A	102	LEU	0	-0.014	-0.011	10.502	0.065	0.065	0.000	0.000	0.000	0.000
74	A	103	LYS	1	0.976	0.967	10.169	-0.239	-0.239	0.000	0.000	0.000	0.000
75	A	104	ARG	1	0.851	0.933	12.417	0.071	0.071	0.000	0.000	0.000	0.000
76	A	105	GLY	0	0.028	0.018	14.810	0.013	0.013	0.000	0.000	0.000	0.000
77	A	106	GLU	-1	-0.882	-0.937	16.249	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	107	PRO	0	-0.026	-0.007	14.698	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	108	VAL	0	-0.012	0.001	10.915	0.039	0.039	0.000	0.000	0.000	0.000
80	A	109	GLY	0	-0.004	-0.004	12.403	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	110	LYS	1	0.931	0.956	13.839	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	111	PRO	0	0.049	0.038	13.993	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	112	MET	0	-0.063	-0.033	8.462	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	113	THR	0	0.037	0.018	13.960	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	114	VAL	0	-0.038	-0.024	12.403	0.005	0.005	0.000	0.000	0.000	0.000
86	A	115	SER	0	-0.019	-0.014	15.798	0.016	0.016	0.000	0.000	0.000	0.000
87	A	116	VAL	0	0.003	0.023	17.162	0.003	0.003	0.000	0.000	0.000	0.000
88	A	117	ARG	1	0.908	0.942	19.739	0.156	0.156	0.000	0.000	0.000	0.000
89	A	118	ARG	1	0.856	0.918	19.274	0.228	0.228	0.000	0.000	0.000	0.000
90	A	119	VAL	0	0.042	0.033	25.556	0.005	0.005	0.000	0.000	0.000	0.000
91	A	120	LEU	0	-0.012	-0.001	29.073	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	121	ALA	0	0.017	-0.009	30.807	0.008	0.008	0.000	0.000	0.000	0.000
93	A	122	TYR	0	-0.011	0.007	33.153	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	123	ALA	0	-0.007	-0.003	35.729	0.006	0.006	0.000	0.000	0.000	0.000
95	A	124	ASP	-1	-0.905	-0.977	37.971	-0.080	-0.080	0.000	0.000	0.000	0.000
96	A	125	ASN	0	-0.091	-0.059	40.051	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	126	GLU	-1	-0.879	-0.912	34.872	-0.104	-0.104	0.000	0.000	0.000	0.000
98	A	127	ILE	0	-0.073	-0.058	35.912	0.001	0.001	0.000	0.000	0.000	0.000
99	A	128	LEU	0	0.032	0.045	35.094	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	129	GLY	0	-0.015	0.008	34.610	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	130	LYS	1	0.959	0.958	33.871	0.087	0.087	0.000	0.000	0.000	0.000
102	A	131	GLN	0	0.003	-0.012	32.864	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	132	GLU	-1	-0.878	-0.941	30.822	-0.130	-0.130	0.000	0.000	0.000	0.000
104	A	133	GLU	-1	-0.860	-0.924	29.421	-0.140	-0.140	0.000	0.000	0.000	0.000
105	A	134	GLU	-1	-0.884	-0.928	28.370	-0.150	-0.150	0.000	0.000	0.000	0.000
106	A	135	ALA	0	-0.050	-0.028	26.695	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	136	ALA	0	0.023	0.014	24.865	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	137	LEU	0	0.059	0.027	23.609	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	138	TRP	0	-0.056	-0.066	22.582	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	139	ALA	0	-0.075	-0.036	20.569	-0.027	-0.027	0.000	0.000	0.000	0.000
111	A	140	GLU	-1	-0.810	-0.887	18.934	-0.271	-0.271	0.000	0.000	0.000	0.000
112	A	141	MET	0	-0.049	-0.025	18.134	-0.029	-0.029	0.000	0.000	0.000	0.000
113	A	142	ARG	1	0.909	0.956	16.921	0.251	0.251	0.000	0.000	0.000	0.000
114	A	143	GLN	0	-0.054	-0.030	13.976	-0.019	-0.019	0.000	0.000	0.000	0.000
115	A	144	ASP	-1	-0.851	-0.929	13.150	-0.430	-0.430	0.000	0.000	0.000	0.000
116	A	145	ALA	0	0.006	-0.009	13.224	-0.042	-0.042	0.000	0.000	0.000	0.000
117	A	146	ALA	0	-0.016	-0.005	10.451	-0.046	-0.046	0.000	0.000	0.000	0.000
118	A	147	GLU	-1	-0.849	-0.921	8.911	-0.815	-0.815	0.000	0.000	0.000	0.000
119	A	148	GLN	0	-0.056	-0.034	8.675	-0.080	-0.080	0.000	0.000	0.000	0.000
120	A	149	ILE	0	-0.010	-0.001	7.606	0.030	0.030	0.000	0.000	0.000	0.000
121	A	150	VAL	0	0.031	0.007	3.122	-0.369	-0.042	0.038	-0.064	-0.302	0.000
122	A	151	ARG	1	0.944	0.968	4.095	-0.237	0.025	0.001	-0.041	-0.223	0.000
123	A	152	ARG	1	0.942	0.970	5.871	0.425	0.425	0.000	0.000	0.000	0.000
124	A	153	LEU	0	-0.020	0.008	2.990	-0.296	0.210	0.104	-0.122	-0.487	0.000
125	A	154	THR	0	-0.081	-0.041	2.373	-3.824	-0.904	1.508	-1.799	-2.629	-0.010
126	A	155	PHE	0	-0.066	-0.035	3.095	1.699	1.353	0.054	0.611	-0.319	0.000
127	A	156	LEU	0	0.069	0.041	5.886	0.047	0.047	0.000	0.000	0.000	0.000
128	A	157	LYS	1	0.875	0.950	6.726	-1.473	-1.473	0.000	0.000	0.000	0.000
129	A	158	ALA	0	-0.047	-0.021	7.959	-0.043	-0.043	0.000	0.000	0.000	0.000
130	A	159	GLU	-1	-0.963	-0.968	9.909	0.039	0.039	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:LEU)