FMO DATABASE

FMODB ID: NN7RQ

Calculation Name: 2RB6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RB6

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EI81

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:

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-311403.257617
FMO2-HF: Nuclear repulsion	287054.982961
FMO2-HF: Total energy	-24348.274657
FMO2-MP2: Total energy	-24416.637244

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:25:SER)

Summations of interaction energy for fragment #1(A:25:SER)

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.
-14.314	-12.932	8.111	-4.513	-4.981	-0.048

Interaction energy analysis for fragmet #1(A:25:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.032

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	27	GLN	0	0.003	0.015	3.572	-1.694	-0.476	-0.002	-0.661	-0.555	0.001
4	A	28	TYR	0	-0.013	-0.028	5.257	1.093	1.093	0.000	0.000	0.000	0.000
5	A	29	ILE	0	0.042	0.015	8.656	0.027	0.027	0.000	0.000	0.000	0.000
6	A	30	MET	0	-0.068	-0.029	12.323	0.108	0.108	0.000	0.000	0.000	0.000
7	A	31	SER	0	0.006	0.015	15.264	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	32	THR	0	0.012	0.019	18.804	0.040	0.040	0.000	0.000	0.000	0.000
9	A	33	LYS	1	0.953	0.969	21.707	0.199	0.199	0.000	0.000	0.000	0.000
10	A	34	ASP	-1	-0.897	-0.966	24.689	-0.298	-0.298	0.000	0.000	0.000	0.000
11	A	35	GLY	0	-0.023	-0.013	24.667	0.013	0.013	0.000	0.000	0.000	0.000
12	A	36	LYS	1	0.888	0.954	21.544	0.291	0.291	0.000	0.000	0.000	0.000
13	A	37	MET	0	-0.025	-0.015	16.140	-0.033	-0.033	0.000	0.000	0.000	0.000
14	A	38	ILE	0	0.013	0.017	14.238	0.007	0.007	0.000	0.000	0.000	0.000
15	A	39	THR	0	0.027	0.014	11.021	0.006	0.006	0.000	0.000	0.000	0.000
16	A	40	SER	0	0.036	0.013	8.885	0.183	0.183	0.000	0.000	0.000	0.000
17	A	41	ASP	-1	-0.831	-0.907	4.628	-3.731	-3.685	-0.001	-0.003	-0.042	0.000
18	A	42	SER	0	-0.071	-0.029	3.763	-1.284	-1.104	0.001	-0.088	-0.092	-0.001
19	A	43	LYS	1	0.933	0.966	6.057	0.191	0.191	0.000	0.000	0.000	0.000
20	A	44	PRO	0	0.010	0.020	8.271	0.115	0.115	0.000	0.000	0.000	0.000
21	A	45	LYS	1	0.935	0.956	11.734	0.152	0.152	0.000	0.000	0.000	0.000
22	A	46	LEU	0	-0.044	-0.020	14.087	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	47	ASP	-1	-0.857	-0.925	17.633	-0.070	-0.070	0.000	0.000	0.000	0.000
24	A	48	LYS	1	0.950	0.939	20.566	0.031	0.031	0.000	0.000	0.000	0.000
25	A	49	THR	0	-0.035	0.010	23.586	0.008	0.008	0.000	0.000	0.000	0.000
26	A	50	THR	0	-0.008	-0.009	23.359	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	51	GLY	0	-0.010	0.010	23.491	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	52	MET	0	-0.015	0.003	20.888	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	53	TYR	0	0.028	-0.006	15.381	0.029	0.029	0.000	0.000	0.000	0.000
30	A	54	LEU	0	-0.006	0.001	15.296	-0.022	-0.022	0.000	0.000	0.000	0.000
31	A	55	TYR	0	-0.002	-0.020	11.663	0.032	0.032	0.000	0.000	0.000	0.000
32	A	56	TYR	0	0.000	-0.006	9.755	0.146	0.146	0.000	0.000	0.000	0.000
33	A	57	ASP	-1	-0.872	-0.930	11.017	-0.819	-0.819	0.000	0.000	0.000	0.000
34	A	58	GLU	-1	-0.932	-0.975	11.938	-0.945	-0.945	0.000	0.000	0.000	0.000
35	A	59	ASP	-1	-0.983	-0.972	12.656	-0.574	-0.574	0.000	0.000	0.000	0.000
36	A	60	GLY	0	0.007	0.001	13.715	0.110	0.110	0.000	0.000	0.000	0.000
37	A	61	ARG	1	0.854	0.943	14.005	0.278	0.278	0.000	0.000	0.000	0.000
38	A	62	GLU	-1	-0.927	-0.966	14.561	-0.341	-0.341	0.000	0.000	0.000	0.000
39	A	63	VAL	0	0.007	-0.001	15.512	0.062	0.062	0.000	0.000	0.000	0.000
40	A	64	MET	0	-0.051	-0.036	16.816	0.005	0.005	0.000	0.000	0.000	0.000
41	A	65	ILE	0	0.038	0.029	17.307	0.003	0.003	0.000	0.000	0.000	0.000
42	A	66	LYS	1	0.979	0.982	20.266	0.197	0.197	0.000	0.000	0.000	0.000
43	A	67	GLN	0	0.002	-0.019	20.669	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	68	GLU	-1	-0.984	-0.991	21.974	-0.173	-0.173	0.000	0.000	0.000	0.000
45	A	69	ASP	-1	-0.896	-0.938	23.052	-0.237	-0.237	0.000	0.000	0.000	0.000
46	A	70	VAL	0	-0.051	-0.015	17.539	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	71	THR	0	-0.052	-0.026	20.776	0.025	0.025	0.000	0.000	0.000	0.000
48	A	72	GLN	0	-0.024	-0.026	17.924	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	73	ILE	0	0.000	-0.002	12.320	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	74	ILE	0	-0.054	-0.027	12.710	0.075	0.075	0.000	0.000	0.000	0.000
51	A	75	GLU	-1	-0.848	-0.918	7.207	-0.185	-0.185	0.000	0.000	0.000	0.000
52	A	76	ARG	1	0.888	0.949	8.570	1.359	1.359	0.000	0.000	0.000	0.000
53	A	77	LEU	0	0.039	0.014	5.905	-0.907	-0.907	0.000	0.000	0.000	0.000
54	A	78	GLU	-1	-0.864	-0.918	2.082	-7.472	-7.698	8.115	-3.749	-4.141	-0.048
55	A	79	HIS	0	-0.029	-0.046	4.773	1.083	1.131	-0.001	-0.001	-0.046	0.000
56	A	80	HIS	0	-0.037	-0.006	7.131	0.324	0.324	0.000	0.000	0.000	0.000
57	A	81	HIS	1	0.966	0.998	4.324	-1.538	-1.422	-0.001	-0.011	-0.105	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:25:SER)