FMO DATABASE

FMODB ID: 52MMZ

Calculation Name: 2J8B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J8B

Chain ID: A

ChEMBL ID:

UniProt ID: P13987

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	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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-542424.175513
FMO2-HF: Nuclear repulsion	507926.009455
FMO2-HF: Total energy	-34498.166059
FMO2-MP2: Total energy	-34589.700717

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:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

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.
-11.807	-6.673	6.187	-4.095	-7.223	-0.011

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.008

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	2	GLN	0	0.030	0.013	3.720	-0.424	1.928	-0.003	-1.096	-1.254	0.004
4	A	3	CYS	0	-0.040	-0.003	5.602	-0.005	-0.005	0.000	0.000	0.000	0.000
5	A	4	TYR	0	0.043	0.016	8.735	0.198	0.198	0.000	0.000	0.000	0.000
6	A	5	ASN	0	0.022	0.001	9.991	-0.121	-0.121	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.088	-0.009	11.969	0.114	0.114	0.000	0.000	0.000	0.000
8	A	7	PRO	0	-0.001	-0.001	14.919	-0.029	-0.029	0.000	0.000	0.000	0.000
9	A	8	ASN	0	0.007	-0.010	16.432	0.004	0.004	0.000	0.000	0.000	0.000
10	A	9	PRO	0	0.026	0.031	19.463	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	10	THR	0	-0.063	-0.039	19.860	0.040	0.040	0.000	0.000	0.000	0.000
12	A	11	ALA	0	-0.005	-0.003	21.886	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.905	-0.960	21.187	-0.360	-0.360	0.000	0.000	0.000	0.000
14	A	14	LYS	1	1.027	1.004	16.336	0.177	0.177	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.036	-0.020	11.972	0.035	0.035	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.020	0.028	9.454	-0.124	-0.124	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.008	-0.009	6.486	0.270	0.270	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.025	0.002	2.226	-3.827	-3.740	3.980	-1.225	-2.841	0.004
19	A	19	CYS	0	-0.019	0.002	3.284	-1.383	-0.312	0.173	-0.341	-0.903	-0.002
20	A	20	SER	0	0.047	0.015	2.424	-4.323	-2.870	2.038	-1.443	-2.046	-0.017
21	A	21	SER	0	0.028	-0.004	4.089	-0.121	0.050	-0.001	0.010	-0.179	0.000
22	A	22	ASP	-1	-0.943	-0.945	5.571	-0.259	-0.259	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.124	-0.062	7.328	0.172	0.172	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.847	-0.919	7.139	-1.183	-1.183	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.037	-0.024	8.597	-0.092	-0.092	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.025	0.006	11.201	0.103	0.103	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.019	-0.006	14.753	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.007	-0.014	17.505	0.020	0.020	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.833	0.927	20.874	0.353	0.353	0.000	0.000	0.000	0.000
30	A	31	ALA	0	0.074	0.035	24.196	0.004	0.004	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.027	0.017	26.925	0.013	0.013	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.027	-0.024	28.525	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.035	0.003	24.847	0.004	0.004	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.016	0.012	20.272	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.082	-0.078	18.630	0.003	0.003	0.000	0.000	0.000	0.000
36	A	37	ASN	0	0.000	-0.013	14.688	0.032	0.032	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.871	0.944	12.669	0.494	0.494	0.000	0.000	0.000	0.000
38	A	40	TRP	0	-0.011	-0.034	9.926	0.216	0.216	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.968	0.977	11.019	0.360	0.360	0.000	0.000	0.000	0.000
40	A	42	PHE	0	0.012	-0.022	11.372	0.064	0.064	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.901	-0.939	15.042	-0.351	-0.351	0.000	0.000	0.000	0.000
42	A	44	HIS	0	-0.047	-0.022	16.472	0.050	0.050	0.000	0.000	0.000	0.000
43	A	45	CYS	0	-0.088	-0.021	14.692	-0.056	-0.056	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.025	-0.020	18.669	0.036	0.036	0.000	0.000	0.000	0.000
45	A	47	PHE	0	0.064	0.030	22.463	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.029	0.013	25.258	0.014	0.014	0.000	0.000	0.000	0.000
47	A	49	ASP	-1	-0.817	-0.912	21.200	-0.311	-0.311	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.009	-0.008	19.587	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	51	THR	0	0.004	0.004	21.971	0.014	0.014	0.000	0.000	0.000	0.000
50	A	52	THR	0	-0.047	-0.023	24.449	0.012	0.012	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.844	0.938	18.391	0.366	0.366	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.052	-0.032	18.627	0.002	0.002	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.889	0.956	22.391	0.222	0.222	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.813	-0.865	25.013	-0.215	-0.215	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.012	-0.018	27.405	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.953	-0.976	29.907	-0.193	-0.193	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.036	-0.018	23.861	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	60	THR	0	0.004	0.009	25.375	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	61	TYR	0	0.012	-0.013	19.792	0.005	0.005	0.000	0.000	0.000	0.000
60	A	62	TYR	0	0.050	0.025	16.588	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	64	CYS	0	-0.022	0.032	11.173	0.224	0.224	0.000	0.000	0.000	0.000
62	A	65	LYS	1	1.011	1.000	8.953	1.305	1.305	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.885	0.928	8.829	1.424	1.424	0.000	0.000	0.000	0.000
64	A	67	ASP	-1	-0.767	-0.899	6.017	-4.582	-4.582	0.000	0.000	0.000	0.000
65	A	68	LEU	0	-0.072	-0.039	8.817	0.398	0.398	0.000	0.000	0.000	0.000
66	A	70	ASN	0	-0.015	-0.020	12.345	0.042	0.042	0.000	0.000	0.000	0.000
67	A	71	PHE	0	0.037	0.014	14.699	0.045	0.045	0.000	0.000	0.000	0.000
68	A	72	ASN	0	0.062	0.013	17.504	0.017	0.017	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.866	-0.959	21.129	-0.386	-0.386	0.000	0.000	0.000	0.000
70	A	74	GLN	0	-0.082	-0.017	16.601	0.065	0.065	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.073	-0.026	21.211	0.008	0.008	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.921	-0.946	23.567	-0.273	-0.273	0.000	0.000	0.000	0.000
73	A	77	ASN	0	-0.023	-0.011	26.498	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)