FMO DATABASE

FMODB ID: 4913N

Calculation Name: 2BH8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BH8

Chain ID: A

ChEMBL ID:

UniProt ID: P0A9X9

Base Structure: X-ray

Registration Date: 2023-09-20

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-425132.365943
FMO2-HF: Nuclear repulsion	393990.052332
FMO2-HF: Total energy	-31142.313611
FMO2-MP2: Total energy	-31234.409597

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(A:18:LYS)

Summations of interaction energy for fragment #1(A:18:LYS)

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.
-30.48	-24.699	0.751	-2.57	-3.963	-0.005

Interaction energy analysis for fragmet #1(A:18:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.911 / q_NPA : 0.948

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	20	THR	0	0.058	0.038	3.772	-1.445	0.598	-0.030	-0.883	-1.131	0.002
4	A	21	GLY	0	0.044	0.029	6.026	1.518	1.518	0.000	0.000	0.000	0.000
5	A	22	ILE	0	-0.037	-0.004	9.759	0.066	0.066	0.000	0.000	0.000	0.000
6	A	23	VAL	0	-0.002	0.009	13.287	0.271	0.271	0.000	0.000	0.000	0.000
7	A	24	LYS	1	0.935	0.976	15.530	15.428	15.428	0.000	0.000	0.000	0.000
8	A	25	TRP	0	0.032	-0.004	18.033	0.740	0.740	0.000	0.000	0.000	0.000
9	A	26	PHE	0	0.016	-0.011	13.556	-0.848	-0.848	0.000	0.000	0.000	0.000
10	A	27	ASN	0	0.001	0.012	19.027	0.675	0.675	0.000	0.000	0.000	0.000
11	A	28	ALA	0	0.039	0.004	18.243	-0.106	-0.106	0.000	0.000	0.000	0.000
12	A	29	ASP	-1	-0.879	-0.937	19.179	-11.805	-11.805	0.000	0.000	0.000	0.000
13	A	30	LYS	1	0.828	0.915	22.007	11.394	11.394	0.000	0.000	0.000	0.000
14	A	31	GLY	0	0.010	0.031	17.998	0.072	0.072	0.000	0.000	0.000	0.000
15	A	32	PHE	0	-0.027	-0.019	16.985	-0.168	-0.168	0.000	0.000	0.000	0.000
16	A	33	GLY	0	0.000	-0.004	16.143	0.286	0.286	0.000	0.000	0.000	0.000
17	A	34	PHE	0	-0.023	0.012	15.735	-0.220	-0.220	0.000	0.000	0.000	0.000
18	A	35	ILE	0	-0.004	-0.007	10.219	0.179	0.179	0.000	0.000	0.000	0.000
19	A	36	THR	0	0.011	-0.007	13.605	0.685	0.685	0.000	0.000	0.000	0.000
20	A	37	PRO	0	-0.071	-0.041	8.436	-0.828	-0.828	0.000	0.000	0.000	0.000
21	A	38	ASP	-1	-0.813	-0.905	8.370	-24.162	-24.162	0.000	0.000	0.000	0.000
22	A	39	ASP	-1	-0.920	-0.941	6.927	-29.519	-29.519	0.000	0.000	0.000	0.000
23	A	40	GLY	0	-0.048	-0.036	9.759	0.322	0.322	0.000	0.000	0.000	0.000
24	A	41	SER	0	-0.004	-0.014	12.178	0.292	0.292	0.000	0.000	0.000	0.000
25	A	42	LYS	1	0.885	0.939	12.997	17.728	17.728	0.000	0.000	0.000	0.000
26	A	43	ASP	-1	-0.771	-0.871	12.582	-17.537	-17.537	0.000	0.000	0.000	0.000
27	A	44	VAL	0	-0.035	-0.027	9.834	0.078	0.078	0.000	0.000	0.000	0.000
28	A	45	PHE	0	0.017	0.013	12.972	0.139	0.139	0.000	0.000	0.000	0.000
29	A	46	VAL	0	-0.050	-0.025	10.897	-0.623	-0.623	0.000	0.000	0.000	0.000
30	A	47	HIS	0	0.045	0.010	13.893	0.542	0.542	0.000	0.000	0.000	0.000
31	A	48	PHE	0	-0.056	-0.033	13.535	-0.989	-0.989	0.000	0.000	0.000	0.000
32	A	49	SER	0	0.023	0.015	15.633	1.015	1.015	0.000	0.000	0.000	0.000
33	A	50	ALA	0	0.022	0.012	16.938	-0.859	-0.859	0.000	0.000	0.000	0.000
34	A	51	GLY	0	0.005	-0.004	18.585	0.690	0.690	0.000	0.000	0.000	0.000
35	A	52	SER	0	-0.035	-0.015	18.856	-0.306	-0.306	0.000	0.000	0.000	0.000
36	A	53	SER	0	0.008	-0.006	13.712	0.342	0.342	0.000	0.000	0.000	0.000
37	A	54	GLY	0	0.018	0.007	15.445	-0.821	-0.821	0.000	0.000	0.000	0.000
38	A	55	ALA	0	-0.027	0.004	15.997	0.504	0.504	0.000	0.000	0.000	0.000
39	A	56	ALA	0	0.000	0.000	17.803	0.358	0.358	0.000	0.000	0.000	0.000
40	A	57	VAL	0	0.028	0.015	19.093	-0.697	-0.697	0.000	0.000	0.000	0.000
41	A	58	ARG	1	0.945	0.983	13.925	18.743	18.743	0.000	0.000	0.000	0.000
42	A	59	GLY	0	0.006	0.006	19.480	0.367	0.367	0.000	0.000	0.000	0.000
43	A	60	ASN	0	0.066	0.005	19.321	-1.307	-1.307	0.000	0.000	0.000	0.000
44	A	61	PRO	0	-0.038	0.001	15.586	0.417	0.417	0.000	0.000	0.000	0.000
45	A	62	GLN	0	-0.062	-0.044	18.500	0.996	0.996	0.000	0.000	0.000	0.000
46	A	63	GLN	0	-0.015	-0.014	18.719	-0.640	-0.640	0.000	0.000	0.000	0.000
47	A	64	GLY	0	-0.018	-0.010	17.886	0.480	0.480	0.000	0.000	0.000	0.000
48	A	65	ASP	-1	-0.837	-0.906	15.950	-16.325	-16.325	0.000	0.000	0.000	0.000
49	A	66	ARG	1	0.829	0.898	9.847	24.079	24.079	0.000	0.000	0.000	0.000
50	A	67	VAL	0	-0.051	-0.023	9.585	0.754	0.754	0.000	0.000	0.000	0.000
51	A	68	GLU	-1	-0.932	-0.970	5.678	-40.657	-40.657	0.000	0.000	0.000	0.000
52	A	69	GLY	0	0.013	0.009	4.600	3.478	3.562	-0.001	-0.019	-0.064	0.000
53	A	70	LYS	1	0.910	0.959	2.801	36.140	39.062	0.748	-1.489	-2.181	-0.007
54	A	71	ILE	0	0.048	0.021	2.934	2.684	3.261	0.035	-0.162	-0.450	0.000
55	A	72	LYS	1	0.916	0.945	4.362	27.352	27.507	-0.001	-0.017	-0.137	0.000
56	A	73	SER	0	0.046	0.027	7.155	0.500	0.500	0.000	0.000	0.000	0.000
57	A	74	ILE	0	0.000	0.002	10.037	-0.183	-0.183	0.000	0.000	0.000	0.000
58	A	75	THR	0	-0.055	-0.048	12.902	0.136	0.136	0.000	0.000	0.000	0.000
59	A	76	ASP	-1	-0.851	-0.887	15.458	-14.486	-14.486	0.000	0.000	0.000	0.000
60	A	77	PHE	0	-0.042	-0.035	17.602	-0.306	-0.306	0.000	0.000	0.000	0.000
61	A	78	GLY	0	0.019	0.019	19.799	0.467	0.467	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.030	-0.025	21.973	-0.354	-0.354	0.000	0.000	0.000	0.000
63	A	80	PHE	0	-0.029	-0.005	24.508	0.302	0.302	0.000	0.000	0.000	0.000
64	A	81	ILE	0	-0.027	-0.012	27.716	-0.120	-0.120	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.089	0.061	30.359	0.171	0.171	0.000	0.000	0.000	0.000
66	A	83	LEU	0	-0.051	-0.053	33.060	0.109	0.109	0.000	0.000	0.000	0.000
67	A	84	ASP	-1	-0.950	-0.970	34.485	-8.088	-8.088	0.000	0.000	0.000	0.000
68	A	85	GLY	0	-0.029	-0.010	33.749	0.051	0.051	0.000	0.000	0.000	0.000
69	A	86	GLY	0	-0.008	0.007	30.975	-0.213	-0.213	0.000	0.000	0.000	0.000
70	A	87	ILE	0	-0.049	-0.032	24.204	-0.118	-0.118	0.000	0.000	0.000	0.000
71	A	88	ASP	-1	-0.849	-0.920	27.599	-9.147	-9.147	0.000	0.000	0.000	0.000
72	A	89	GLY	0	-0.027	-0.023	24.668	0.010	0.010	0.000	0.000	0.000	0.000
73	A	90	LEU	0	-0.054	-0.031	17.580	0.043	0.043	0.000	0.000	0.000	0.000
74	A	91	VAL	0	-0.019	-0.001	20.457	-0.306	-0.306	0.000	0.000	0.000	0.000
75	A	92	HIS	0	-0.001	-0.002	15.539	0.056	0.056	0.000	0.000	0.000	0.000
76	A	93	LEU	0	-0.034	-0.008	18.832	0.520	0.520	0.000	0.000	0.000	0.000
77	A	94	SER	0	-0.012	-0.020	19.642	-0.292	-0.292	0.000	0.000	0.000	0.000
78	A	95	ASP	-1	-0.950	-0.993	20.840	-11.816	-11.816	0.000	0.000	0.000	0.000
79	A	96	ILE	0	0.007	0.017	23.680	0.303	0.303	0.000	0.000	0.000	0.000
80	A	97	SER	0	-0.018	-0.004	26.580	0.047	0.047	0.000	0.000	0.000	0.000
81	A	98	TRP	0	-0.012	-0.007	27.714	0.126	0.126	0.000	0.000	0.000	0.000
82	A	99	ALA	0	0.024	0.020	33.132	-0.067	-0.067	0.000	0.000	0.000	0.000
83	A	100	GLN	0	-0.048	-0.027	34.869	0.188	0.188	0.000	0.000	0.000	0.000
84	A	101	ALA	0	0.021	0.005	36.349	0.173	0.173	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.978	-0.978	39.398	-7.138	-7.138	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:LYS)