FMO DATABASE

FMODB ID: V5Y71

Calculation Name: 1BII-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BII

Chain ID: B

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2023-06-26

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

DOI:

IFIE MAP

IFIE Diagram

Modeling method

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-776750.993317
FMO2-HF: Nuclear repulsion	734767.738666
FMO2-HF: Total energy	-41983.254651
FMO2-MP2: Total energy	-42102.094224

3D Structure

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(B:301:ILE)

Summations of interaction energy for fragment #1(B:301:ILE)

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.
-2.879	0.394	1.036	-1.493	-2.816	-0.002

Interaction energy analysis for fragmet #1(B:301:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.012

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	B	303	LYS	1	0.876	0.947	3.790	-1.622	0.199	-0.023	-0.837	-0.961	0.002
4	B	304	THR	0	0.056	0.013	6.360	-0.490	-0.490	0.000	0.000	0.000	0.000
5	B	305	PRO	0	-0.004	0.020	10.083	0.067	0.067	0.000	0.000	0.000	0.000
6	B	306	GLN	0	-0.040	-0.010	12.234	-0.097	-0.097	0.000	0.000	0.000	0.000
7	B	307	ILE	0	-0.014	-0.025	15.146	-0.032	-0.032	0.000	0.000	0.000	0.000
8	B	308	GLN	0	0.003	0.013	18.297	0.006	0.006	0.000	0.000	0.000	0.000
9	B	309	VAL	0	0.005	-0.009	21.567	-0.011	-0.011	0.000	0.000	0.000	0.000
10	B	310	TYR	0	0.004	0.000	22.747	-0.002	-0.002	0.000	0.000	0.000	0.000
11	B	311	SER	0	0.023	0.011	27.506	-0.003	-0.003	0.000	0.000	0.000	0.000
12	B	312	ARG	1	0.898	0.956	28.284	-0.034	-0.034	0.000	0.000	0.000	0.000
13	B	313	HIS	0	0.027	0.023	30.780	0.005	0.005	0.000	0.000	0.000	0.000
14	B	314	PRO	0	0.058	0.026	34.204	0.001	0.001	0.000	0.000	0.000	0.000
15	B	315	PRO	0	-0.003	0.002	34.242	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	316	GLU	-1	-0.802	-0.888	36.714	0.030	0.030	0.000	0.000	0.000	0.000
17	B	317	ASN	0	-0.042	-0.017	40.117	0.000	0.000	0.000	0.000	0.000	0.000
18	B	318	GLY	0	-0.006	0.009	41.663	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	319	LYS	1	0.809	0.880	40.704	-0.029	-0.029	0.000	0.000	0.000	0.000
20	B	320	PRO	0	-0.001	0.004	38.841	0.002	0.002	0.000	0.000	0.000	0.000
21	B	321	ASN	0	-0.011	-0.003	33.890	0.004	0.004	0.000	0.000	0.000	0.000
22	B	322	ILE	0	-0.004	-0.007	29.308	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	323	LEU	0	0.000	0.016	27.797	0.006	0.006	0.000	0.000	0.000	0.000
24	B	324	ASN	0	-0.036	-0.038	24.634	-0.010	-0.010	0.000	0.000	0.000	0.000
25	B	325	CYS	0	-0.061	-0.020	21.179	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	326	TYR	0	-0.004	0.007	18.205	0.000	0.000	0.000	0.000	0.000	0.000
27	B	327	VAL	0	-0.001	-0.004	14.081	0.019	0.019	0.000	0.000	0.000	0.000
28	B	328	THR	0	0.037	0.006	13.434	0.006	0.006	0.000	0.000	0.000	0.000
29	B	329	GLN	0	-0.019	-0.026	10.386	0.040	0.040	0.000	0.000	0.000	0.000
30	B	330	PHE	0	-0.012	0.011	8.248	0.249	0.249	0.000	0.000	0.000	0.000
31	B	331	HIS	0	0.018	0.021	2.711	-1.781	-0.329	1.059	-0.656	-1.855	-0.004
32	B	332	PRO	0	0.026	0.006	5.455	0.092	0.092	0.000	0.000	0.000	0.000
33	B	333	PRO	0	0.046	0.006	6.177	0.254	0.254	0.000	0.000	0.000	0.000
34	B	334	HIS	0	0.006	0.024	9.350	0.103	0.103	0.000	0.000	0.000	0.000
35	B	335	ILE	0	0.022	0.009	11.240	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	336	GLU	-1	-0.842	-0.891	13.721	-0.066	-0.066	0.000	0.000	0.000	0.000
37	B	337	ILE	0	0.025	0.015	16.496	0.019	0.019	0.000	0.000	0.000	0.000
38	B	338	GLN	0	-0.058	-0.038	19.669	0.000	0.000	0.000	0.000	0.000	0.000
39	B	339	MET	0	0.034	0.037	23.328	0.009	0.009	0.000	0.000	0.000	0.000
40	B	340	LEU	0	-0.029	-0.017	25.985	-0.008	-0.008	0.000	0.000	0.000	0.000
41	B	341	LYS	1	0.914	0.950	28.771	-0.008	-0.008	0.000	0.000	0.000	0.000
42	B	342	ASN	0	-0.017	-0.018	32.369	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	343	GLY	0	0.014	0.010	30.948	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	344	LYS	1	0.924	0.967	31.216	0.002	0.002	0.000	0.000	0.000	0.000
45	B	345	LYS	1	0.917	0.960	24.687	0.043	0.043	0.000	0.000	0.000	0.000
46	B	346	ILE	0	-0.027	-0.020	29.136	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	347	PRO	0	-0.015	-0.012	29.214	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	348	LYS	1	0.831	0.912	30.067	-0.007	-0.007	0.000	0.000	0.000	0.000
49	B	349	VAL	0	-0.033	-0.005	24.868	0.006	0.006	0.000	0.000	0.000	0.000
50	B	350	GLU	-1	-0.862	-0.911	26.191	-0.004	-0.004	0.000	0.000	0.000	0.000
51	B	351	MET	0	-0.011	-0.013	18.766	0.012	0.012	0.000	0.000	0.000	0.000
52	B	352	SER	0	-0.035	-0.040	21.350	-0.008	-0.008	0.000	0.000	0.000	0.000
53	B	353	ASP	-1	-0.835	-0.894	19.338	0.058	0.058	0.000	0.000	0.000	0.000
54	B	354	MET	0	-0.003	0.006	15.410	0.006	0.006	0.000	0.000	0.000	0.000
55	B	355	SER	0	-0.007	-0.008	14.661	-0.021	-0.021	0.000	0.000	0.000	0.000
56	B	356	PHE	0	0.002	0.005	10.644	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	357	SER	0	0.027	0.015	11.670	-0.035	-0.035	0.000	0.000	0.000	0.000
58	B	358	LYS	1	0.958	0.968	12.020	-0.171	-0.171	0.000	0.000	0.000	0.000
59	B	359	ASP	-1	-0.798	-0.884	9.820	0.857	0.857	0.000	0.000	0.000	0.000
60	B	360	TRP	0	-0.028	-0.018	7.357	0.164	0.164	0.000	0.000	0.000	0.000
61	B	361	SER	0	-0.142	-0.051	7.298	-0.111	-0.111	0.000	0.000	0.000	0.000
62	B	362	PHE	0	0.068	0.008	6.772	-0.165	-0.165	0.000	0.000	0.000	0.000
63	B	363	TYR	0	-0.063	-0.031	10.319	0.072	0.072	0.000	0.000	0.000	0.000
64	B	364	ILE	0	-0.035	-0.013	13.693	-0.043	-0.043	0.000	0.000	0.000	0.000
65	B	365	LEU	0	0.001	0.007	16.842	0.022	0.022	0.000	0.000	0.000	0.000
66	B	366	ALA	0	0.014	0.005	20.525	-0.016	-0.016	0.000	0.000	0.000	0.000
67	B	367	HIS	0	-0.010	-0.024	22.543	0.013	0.013	0.000	0.000	0.000	0.000
68	B	368	THR	0	-0.008	-0.024	26.274	-0.008	-0.008	0.000	0.000	0.000	0.000
69	B	369	GLU	-1	-0.837	-0.908	29.699	0.014	0.014	0.000	0.000	0.000	0.000
70	B	370	PHE	0	-0.075	-0.044	32.579	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	371	THR	0	0.028	0.006	35.143	0.002	0.002	0.000	0.000	0.000	0.000
72	B	372	PRO	0	-0.030	0.015	35.670	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	373	THR	0	0.008	-0.030	37.551	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	374	GLU	-1	-0.839	-0.911	38.986	0.033	0.033	0.000	0.000	0.000	0.000
75	B	375	THR	0	0.004	-0.003	40.565	0.001	0.001	0.000	0.000	0.000	0.000
76	B	376	ASP	-1	-0.864	-0.892	36.343	0.015	0.015	0.000	0.000	0.000	0.000
77	B	377	THR	0	0.013	0.005	32.053	0.004	0.004	0.000	0.000	0.000	0.000
78	B	378	TYR	0	0.045	0.012	30.093	-0.006	-0.006	0.000	0.000	0.000	0.000
79	B	379	ALA	0	0.012	0.012	26.550	0.006	0.006	0.000	0.000	0.000	0.000
80	B	381	ARG	1	0.907	0.950	21.555	0.022	0.022	0.000	0.000	0.000	0.000
81	B	382	VAL	0	0.021	0.007	15.261	-0.010	-0.010	0.000	0.000	0.000	0.000
82	B	383	LYS	1	0.887	0.923	16.306	0.095	0.095	0.000	0.000	0.000	0.000
83	B	384	HIS	0	0.048	0.027	7.847	0.050	0.050	0.000	0.000	0.000	0.000
84	B	385	ASP	-1	-0.836	-0.916	8.597	-0.476	-0.476	0.000	0.000	0.000	0.000
85	B	386	SER	0	-0.092	-0.051	7.543	0.003	0.003	0.000	0.000	0.000	0.000
86	B	387	MET	0	-0.077	-0.037	8.463	0.106	0.106	0.000	0.000	0.000	0.000
87	B	388	ALA	0	0.010	0.011	11.939	-0.039	-0.039	0.000	0.000	0.000	0.000
88	B	389	GLU	-1	-0.925	-0.958	14.302	-0.042	-0.042	0.000	0.000	0.000	0.000
89	B	390	PRO	0	-0.047	-0.034	16.380	0.014	0.014	0.000	0.000	0.000	0.000
90	B	391	LYS	1	0.992	1.003	17.686	-0.123	-0.123	0.000	0.000	0.000	0.000
91	B	392	THR	0	-0.018	-0.023	19.392	-0.005	-0.005	0.000	0.000	0.000	0.000
92	B	393	VAL	0	-0.030	-0.008	20.916	0.008	0.008	0.000	0.000	0.000	0.000
93	B	394	TYR	0	0.016	-0.016	23.803	-0.010	-0.010	0.000	0.000	0.000	0.000
94	B	395	TRP	0	-0.021	-0.017	27.179	0.004	0.004	0.000	0.000	0.000	0.000
95	B	396	ASP	-1	-0.896	-0.940	28.796	0.069	0.069	0.000	0.000	0.000	0.000
96	B	397	ARG	1	0.834	0.897	30.159	-0.036	-0.036	0.000	0.000	0.000	0.000
97	B	398	ASP	-1	-0.900	-0.944	32.725	0.060	0.060	0.000	0.000	0.000	0.000
98	B	399	MET	0	-0.049	-0.016	26.221	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:301:ILE)