FMO DATABASE

FMODB ID: 5213Z

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:

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-425509.563404
FMO2-HF: Nuclear repulsion	394366.646673
FMO2-HF: Total energy	-31142.91673
FMO2-MP2: Total energy	-31235.022208

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.
-140.505	-133.244	14.882	-11.915	-10.23	-0.123

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 : 0.811 / q_NPA : 0.888

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	0.005	-0.007	3.668	-7.147	-4.728	-0.026	-1.013	-1.380	0.002
4	A	21	GLY	0	0.051	0.024	5.940	4.312	4.312	0.000	0.000	0.000	0.000
5	A	22	ILE	0	-0.040	-0.002	9.604	-0.678	-0.678	0.000	0.000	0.000	0.000
6	A	23	VAL	0	0.010	0.013	12.682	0.626	0.626	0.000	0.000	0.000	0.000
7	A	24	LYS	1	0.850	0.927	14.942	18.629	18.629	0.000	0.000	0.000	0.000
8	A	25	TRP	0	0.019	-0.009	17.818	0.985	0.985	0.000	0.000	0.000	0.000
9	A	26	PHE	0	0.029	-0.004	13.022	-1.108	-1.108	0.000	0.000	0.000	0.000
10	A	27	ASN	0	-0.012	0.011	18.627	0.877	0.877	0.000	0.000	0.000	0.000
11	A	28	ALA	0	0.042	-0.002	17.288	-0.046	-0.046	0.000	0.000	0.000	0.000
12	A	29	ASP	-1	-0.894	-0.935	18.407	-12.983	-12.983	0.000	0.000	0.000	0.000
13	A	30	LYS	1	0.860	0.921	21.428	12.565	12.565	0.000	0.000	0.000	0.000
14	A	31	GLY	0	0.008	0.032	17.649	0.175	0.175	0.000	0.000	0.000	0.000
15	A	32	PHE	0	-0.007	-0.014	16.971	-0.094	-0.094	0.000	0.000	0.000	0.000
16	A	33	GLY	0	-0.005	-0.006	16.062	0.201	0.201	0.000	0.000	0.000	0.000
17	A	34	PHE	0	-0.026	0.011	15.697	-0.108	-0.108	0.000	0.000	0.000	0.000
18	A	35	ILE	0	0.007	-0.002	10.208	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	36	THR	0	0.011	-0.028	13.587	1.274	1.274	0.000	0.000	0.000	0.000
20	A	37	PRO	0	-0.062	-0.036	8.438	-1.498	-1.498	0.000	0.000	0.000	0.000
21	A	38	ASP	-1	-0.754	-0.834	8.221	-32.240	-32.240	0.000	0.000	0.000	0.000
22	A	39	ASP	-1	-0.916	-0.935	7.093	-31.341	-31.341	0.000	0.000	0.000	0.000
23	A	40	GLY	0	-0.042	-0.033	10.058	0.372	0.372	0.000	0.000	0.000	0.000
24	A	41	SER	0	-0.003	-0.015	12.179	0.161	0.161	0.000	0.000	0.000	0.000
25	A	42	LYS	1	0.896	0.948	12.946	18.145	18.145	0.000	0.000	0.000	0.000
26	A	43	ASP	-1	-0.709	-0.816	12.601	-20.060	-20.060	0.000	0.000	0.000	0.000
27	A	44	VAL	0	-0.030	-0.023	9.796	0.408	0.408	0.000	0.000	0.000	0.000
28	A	45	PHE	0	0.029	0.015	12.984	-0.146	-0.146	0.000	0.000	0.000	0.000
29	A	46	VAL	0	-0.054	-0.026	10.831	-0.560	-0.560	0.000	0.000	0.000	0.000
30	A	47	HIS	0	0.037	0.005	13.895	0.686	0.686	0.000	0.000	0.000	0.000
31	A	48	PHE	0	-0.052	-0.021	13.537	-1.102	-1.102	0.000	0.000	0.000	0.000
32	A	49	SER	0	0.028	0.017	15.601	1.197	1.197	0.000	0.000	0.000	0.000
33	A	50	ALA	0	0.006	0.004	16.195	-1.071	-1.071	0.000	0.000	0.000	0.000
34	A	51	GLY	0	0.015	0.001	17.246	0.914	0.914	0.000	0.000	0.000	0.000
35	A	52	SER	0	-0.033	-0.014	17.271	-0.406	-0.406	0.000	0.000	0.000	0.000
36	A	53	SER	0	0.008	-0.006	12.468	0.462	0.462	0.000	0.000	0.000	0.000
37	A	54	GLY	0	0.018	0.006	14.657	-0.754	-0.754	0.000	0.000	0.000	0.000
38	A	55	ALA	0	-0.029	0.004	14.536	0.610	0.610	0.000	0.000	0.000	0.000
39	A	56	ALA	0	-0.003	-0.002	16.391	0.431	0.431	0.000	0.000	0.000	0.000
40	A	57	VAL	0	0.021	0.010	17.203	-0.973	-0.973	0.000	0.000	0.000	0.000
41	A	58	ARG	1	0.849	0.930	12.160	22.824	22.824	0.000	0.000	0.000	0.000
42	A	59	GLY	0	-0.001	0.006	17.574	0.533	0.533	0.000	0.000	0.000	0.000
43	A	60	ASN	0	0.048	-0.006	17.478	-1.690	-1.690	0.000	0.000	0.000	0.000
44	A	61	PRO	0	-0.017	0.008	14.483	0.578	0.578	0.000	0.000	0.000	0.000
45	A	62	GLN	0	-0.022	-0.011	16.940	1.215	1.215	0.000	0.000	0.000	0.000
46	A	63	GLN	0	-0.018	-0.018	17.240	-0.752	-0.752	0.000	0.000	0.000	0.000
47	A	64	GLY	0	-0.001	-0.005	16.870	0.641	0.641	0.000	0.000	0.000	0.000
48	A	65	ASP	-1	-0.812	-0.892	13.708	-20.810	-20.810	0.000	0.000	0.000	0.000
49	A	66	ARG	1	0.767	0.837	8.091	32.116	32.116	0.000	0.000	0.000	0.000
50	A	67	VAL	0	-0.035	-0.014	9.010	1.010	1.010	0.000	0.000	0.000	0.000
51	A	68	GLU	-1	-0.829	-0.909	1.686	-132.650	-132.446	14.029	-8.823	-5.411	-0.116
52	A	69	GLY	0	0.007	0.010	4.075	6.738	6.921	-0.001	-0.033	-0.150	0.000
53	A	70	LYS	1	0.916	0.959	2.774	21.061	24.784	0.850	-1.876	-2.697	-0.009
54	A	71	ILE	0	0.038	0.024	2.918	3.160	3.737	0.031	-0.151	-0.457	0.000
55	A	72	LYS	1	0.946	0.958	4.343	23.501	23.656	-0.001	-0.019	-0.135	0.000
56	A	73	SER	0	0.031	0.018	7.137	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	74	ILE	0	-0.002	0.000	10.024	0.020	0.020	0.000	0.000	0.000	0.000
58	A	75	THR	0	-0.038	-0.047	13.071	0.108	0.108	0.000	0.000	0.000	0.000
59	A	76	ASP	-1	-0.854	-0.881	15.442	-13.612	-13.612	0.000	0.000	0.000	0.000
60	A	77	PHE	0	-0.038	-0.037	17.478	-0.386	-0.386	0.000	0.000	0.000	0.000
61	A	78	GLY	0	0.022	0.023	19.782	0.495	0.495	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.031	-0.024	21.904	-0.409	-0.409	0.000	0.000	0.000	0.000
63	A	80	PHE	0	-0.023	-0.004	24.496	0.335	0.335	0.000	0.000	0.000	0.000
64	A	81	ILE	0	-0.029	-0.016	27.703	-0.144	-0.144	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.075	0.062	30.349	0.183	0.183	0.000	0.000	0.000	0.000
66	A	83	LEU	0	-0.046	-0.051	33.051	0.131	0.131	0.000	0.000	0.000	0.000
67	A	84	ASP	-1	-0.936	-0.965	34.387	-8.241	-8.241	0.000	0.000	0.000	0.000
68	A	85	GLY	0	-0.030	-0.008	33.741	0.051	0.051	0.000	0.000	0.000	0.000
69	A	86	GLY	0	-0.013	0.003	30.970	-0.206	-0.206	0.000	0.000	0.000	0.000
70	A	87	ILE	0	-0.053	-0.033	24.229	-0.101	-0.101	0.000	0.000	0.000	0.000
71	A	88	ASP	-1	-0.847	-0.927	27.592	-9.323	-9.323	0.000	0.000	0.000	0.000
72	A	89	GLY	0	-0.021	-0.019	24.657	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	90	LEU	0	-0.058	-0.032	17.718	0.083	0.083	0.000	0.000	0.000	0.000
74	A	91	VAL	0	-0.016	-0.002	20.427	-0.377	-0.377	0.000	0.000	0.000	0.000
75	A	92	HIS	0	-0.007	0.001	16.816	-0.117	-0.117	0.000	0.000	0.000	0.000
76	A	93	LEU	0	-0.032	-0.005	18.814	0.450	0.450	0.000	0.000	0.000	0.000
77	A	94	SER	0	-0.037	-0.032	19.506	-0.253	-0.253	0.000	0.000	0.000	0.000
78	A	95	ASP	-1	-0.947	-0.989	20.817	-10.948	-10.948	0.000	0.000	0.000	0.000
79	A	96	ILE	0	0.015	0.013	23.657	0.199	0.199	0.000	0.000	0.000	0.000
80	A	97	SER	0	-0.009	0.000	26.558	0.081	0.081	0.000	0.000	0.000	0.000
81	A	98	TRP	0	-0.027	-0.011	27.627	0.080	0.080	0.000	0.000	0.000	0.000
82	A	99	ALA	0	0.018	0.017	33.111	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	100	GLN	0	-0.042	-0.018	34.892	-0.138	-0.138	0.000	0.000	0.000	0.000
84	A	101	ALA	0	0.025	0.006	36.329	0.169	0.169	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.980	-0.985	39.379	-6.773	-6.773	0.000	0.000	0.000	0.000

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