FMO DATABASE

FMODB ID: 4JNKN

Calculation Name: 3P30-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P30

Chain ID: A

ChEMBL ID:

UniProt ID:

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	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-529910.618662
FMO2-HF: Nuclear repulsion	495493.034172
FMO2-HF: Total energy	-34417.584491
FMO2-MP2: Total energy	-34521.029269

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:538:THR)

Summations of interaction energy for fragment #1(A:538:THR)

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.
-3.136	-0.193	2.272	-1.844	-3.372	0.001

Interaction energy analysis for fragmet #1(A:538:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.009

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	540	GLN	0	0.026	0.004	3.636	-3.476	-1.559	0.005	-0.874	-1.049	0.003
4	A	541	VAL	0	0.033	0.024	2.039	-2.339	-1.771	2.267	-0.849	-1.987	-0.002
5	A	542	ARG	1	0.946	0.982	3.956	0.855	1.203	0.000	-0.098	-0.249	0.000
6	A	543	LYS	1	0.841	0.908	5.820	-0.636	-0.636	0.000	0.000	0.000	0.000
7	A	544	LEU	0	0.092	0.063	7.594	-0.033	-0.033	0.000	0.000	0.000	0.000
8	A	545	LEU	0	-0.025	-0.031	6.280	-0.049	-0.049	0.000	0.000	0.000	0.000
9	A	546	SER	0	-0.050	-0.029	9.551	0.006	0.006	0.000	0.000	0.000	0.000
10	A	547	GLY	0	0.035	0.031	11.749	0.018	0.018	0.000	0.000	0.000	0.000
11	A	548	ILE	0	0.006	0.000	11.178	0.011	0.011	0.000	0.000	0.000	0.000
12	A	549	VAL	0	-0.005	-0.005	13.323	0.004	0.004	0.000	0.000	0.000	0.000
13	A	550	GLN	0	-0.016	-0.001	15.646	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	551	GLN	0	0.018	-0.020	17.319	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	552	GLN	0	-0.034	-0.019	17.873	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	553	SER	0	-0.042	-0.007	20.123	0.003	0.003	0.000	0.000	0.000	0.000
17	A	554	ASN	0	0.026	0.005	21.404	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	555	LEU	0	0.028	0.010	22.256	0.004	0.004	0.000	0.000	0.000	0.000
19	A	556	LEU	0	-0.011	0.014	24.425	0.002	0.002	0.000	0.000	0.000	0.000
20	A	557	ARG	1	1.003	1.000	25.554	0.051	0.051	0.000	0.000	0.000	0.000
21	A	558	ALA	0	0.020	0.021	27.791	0.003	0.003	0.000	0.000	0.000	0.000
22	A	559	ILE	0	0.009	0.000	27.541	0.002	0.002	0.000	0.000	0.000	0.000
23	A	560	GLU	-1	-0.957	-0.986	29.205	-0.051	-0.051	0.000	0.000	0.000	0.000
24	A	561	ALA	0	-0.033	-0.023	32.150	0.001	0.001	0.000	0.000	0.000	0.000
25	A	562	GLN	0	0.014	-0.007	33.393	0.001	0.001	0.000	0.000	0.000	0.000
26	A	563	GLN	0	0.024	0.026	34.984	0.003	0.003	0.000	0.000	0.000	0.000
27	A	564	HIS	0	0.028	0.010	36.006	0.002	0.002	0.000	0.000	0.000	0.000
28	A	565	LEU	0	0.041	0.030	38.063	0.001	0.001	0.000	0.000	0.000	0.000
29	A	566	LEU	0	0.037	0.025	37.521	0.001	0.001	0.000	0.000	0.000	0.000
30	A	567	LYS	1	0.839	0.919	40.206	0.021	0.021	0.000	0.000	0.000	0.000
31	A	568	LEU	0	0.037	0.023	42.598	0.000	0.000	0.000	0.000	0.000	0.000
32	A	569	THR	0	-0.027	-0.003	43.747	0.001	0.001	0.000	0.000	0.000	0.000
33	A	570	VAL	0	-0.006	-0.007	44.912	0.001	0.001	0.000	0.000	0.000	0.000
34	A	571	TRP	0	-0.024	-0.010	47.149	0.001	0.001	0.000	0.000	0.000	0.000
35	A	572	GLY	0	0.047	0.017	48.852	0.000	0.000	0.000	0.000	0.000	0.000
36	A	573	ILE	0	0.011	0.004	48.256	0.000	0.000	0.000	0.000	0.000	0.000
37	A	574	LYS	1	0.969	0.975	49.639	0.010	0.010	0.000	0.000	0.000	0.000
38	A	575	GLN	0	-0.062	-0.011	53.199	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	576	LEU	0	-0.015	-0.014	53.817	0.000	0.000	0.000	0.000	0.000	0.000
40	A	577	GLN	0	-0.016	-0.003	54.808	0.000	0.000	0.000	0.000	0.000	0.000
41	A	578	ALA	0	-0.023	-0.004	57.492	0.000	0.000	0.000	0.000	0.000	0.000
42	A	579	ARG	1	0.850	0.941	58.726	0.002	0.002	0.000	0.000	0.000	0.000
43	A	580	VAL	0	0.031	0.021	60.184	0.000	0.000	0.000	0.000	0.000	0.000
44	A	628	TRP	0	0.031	-0.001	53.184	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	629	LEU	0	0.061	0.030	52.576	0.001	0.001	0.000	0.000	0.000	0.000
46	A	630	GLN	0	0.017	-0.018	49.745	0.002	0.002	0.000	0.000	0.000	0.000
47	A	631	TRP	0	0.019	0.014	47.492	0.000	0.000	0.000	0.000	0.000	0.000
48	A	632	ASP	-1	-0.841	-0.929	47.102	0.004	0.004	0.000	0.000	0.000	0.000
49	A	633	LYS	1	0.840	0.926	46.630	0.005	0.005	0.000	0.000	0.000	0.000
50	A	634	GLU	-1	-0.940	-0.971	43.891	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	635	ILE	0	0.035	0.020	42.383	0.000	0.000	0.000	0.000	0.000	0.000
52	A	636	SER	0	-0.019	0.011	41.677	0.002	0.002	0.000	0.000	0.000	0.000
53	A	637	ASN	0	0.000	-0.012	40.652	0.003	0.003	0.000	0.000	0.000	0.000
54	A	638	TYR	0	0.025	0.005	37.073	0.000	0.000	0.000	0.000	0.000	0.000
55	A	639	THR	0	-0.026	-0.031	36.428	0.001	0.001	0.000	0.000	0.000	0.000
56	A	640	HIS	0	-0.037	-0.019	36.269	0.005	0.005	0.000	0.000	0.000	0.000
57	A	641	ILE	0	0.010	0.016	32.444	0.001	0.001	0.000	0.000	0.000	0.000
58	A	642	ILE	0	-0.014	-0.011	31.996	0.001	0.001	0.000	0.000	0.000	0.000
59	A	643	TYR	0	-0.003	-0.020	31.343	0.002	0.002	0.000	0.000	0.000	0.000
60	A	644	GLU	-1	-0.910	-0.928	29.980	0.005	0.005	0.000	0.000	0.000	0.000
61	A	645	LEU	0	0.000	-0.010	26.959	0.002	0.002	0.000	0.000	0.000	0.000
62	A	646	ILE	0	-0.040	-0.010	26.761	0.005	0.005	0.000	0.000	0.000	0.000
63	A	647	GLU	-1	-0.918	-0.952	27.069	0.057	0.057	0.000	0.000	0.000	0.000
64	A	648	GLU	-1	-0.956	-0.978	22.804	0.048	0.048	0.000	0.000	0.000	0.000
65	A	649	SER	0	-0.019	-0.033	22.868	0.005	0.005	0.000	0.000	0.000	0.000
66	A	650	GLN	0	-0.034	-0.012	22.446	0.016	0.016	0.000	0.000	0.000	0.000
67	A	651	LYS	1	0.980	0.997	22.651	-0.051	-0.051	0.000	0.000	0.000	0.000
68	A	652	GLN	0	-0.086	-0.040	16.032	0.011	0.011	0.000	0.000	0.000	0.000
69	A	653	GLN	0	-0.037	-0.019	17.810	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	654	GLU	-1	-0.896	-0.946	18.163	0.187	0.187	0.000	0.000	0.000	0.000
71	A	655	LYS	1	0.901	0.953	15.843	-0.076	-0.076	0.000	0.000	0.000	0.000
72	A	656	ASN	0	0.008	-0.003	13.473	0.065	0.065	0.000	0.000	0.000	0.000
73	A	657	GLU	-1	-0.879	-0.944	13.183	0.267	0.267	0.000	0.000	0.000	0.000
74	A	658	GLN	0	-0.012	0.003	14.875	0.071	0.071	0.000	0.000	0.000	0.000
75	A	659	GLU	-1	-0.864	-0.931	9.870	0.565	0.565	0.000	0.000	0.000	0.000
76	A	660	LEU	0	0.006	0.001	9.605	0.235	0.235	0.000	0.000	0.000	0.000
77	A	661	LEU	0	0.040	0.020	10.717	0.085	0.085	0.000	0.000	0.000	0.000
78	A	662	GLU	-1	-0.923	-0.950	10.059	1.224	1.224	0.000	0.000	0.000	0.000
79	A	663	LEU	0	-0.059	-0.056	3.882	0.237	0.347	0.000	-0.023	-0.087	0.000
80	A	664	ASP	-1	-0.891	-0.949	7.566	0.829	0.829	0.000	0.000	0.000	0.000
81	A	665	LYS	1	0.884	0.953	10.172	-1.169	-1.169	0.000	0.000	0.000	0.000
82	A	666	TRP	0	-0.104	-0.063	7.343	-0.082	-0.082	0.000	0.000	0.000	0.000
83	A	667	ALA	0	-0.026	0.014	7.405	0.128	0.128	0.000	0.000	0.000	0.000
84	A	668	ASN	0	-0.054	-0.006	8.627	-0.195	-0.195	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:538:THR)