FMO DATABASE

FMODB ID: YVQ72

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	-533963.56536
FMO2-HF: Nuclear repulsion	499545.517474
FMO2-HF: Total energy	-34418.047886
FMO2-MP2: Total energy	-34521.557589

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.
-1.597	1.887	0.903	-1.497	-2.892	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 : 0.052 / q_NPA : 0.015

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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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	0.016	0.006	3.488	-2.307	-0.612	0.005	-0.724	-0.977	0.002
4	A	541	VAL	0	0.027	0.016	2.345	-1.375	-0.086	0.899	-0.612	-1.577	-0.001
5	A	542	ARG	1	0.896	0.937	4.075	1.247	1.664	0.000	-0.145	-0.272	0.000
6	A	543	LYS	1	0.795	0.879	5.887	0.512	0.512	0.000	0.000	0.000	0.000
7	A	544	LEU	0	0.064	0.038	7.774	0.113	0.113	0.000	0.000	0.000	0.000
8	A	545	LEU	0	0.001	-0.006	6.639	0.135	0.135	0.000	0.000	0.000	0.000
9	A	546	SER	0	-0.005	0.004	9.773	0.077	0.077	0.000	0.000	0.000	0.000
10	A	547	GLY	0	0.035	0.031	11.993	0.062	0.062	0.000	0.000	0.000	0.000
11	A	548	ILE	0	0.009	0.003	11.200	0.048	0.048	0.000	0.000	0.000	0.000
12	A	549	VAL	0	-0.001	-0.004	13.624	0.036	0.036	0.000	0.000	0.000	0.000
13	A	550	GLN	0	-0.045	-0.025	15.846	0.020	0.020	0.000	0.000	0.000	0.000
14	A	551	GLN	0	0.016	-0.015	17.395	0.021	0.021	0.000	0.000	0.000	0.000
15	A	552	GLN	0	-0.021	-0.014	17.393	0.007	0.007	0.000	0.000	0.000	0.000
16	A	553	SER	0	-0.018	-0.004	20.232	0.015	0.015	0.000	0.000	0.000	0.000
17	A	554	ASN	0	-0.013	-0.006	21.182	0.009	0.009	0.000	0.000	0.000	0.000
18	A	555	LEU	0	0.034	0.011	21.974	0.009	0.009	0.000	0.000	0.000	0.000
19	A	556	LEU	0	-0.027	0.001	24.462	0.007	0.007	0.000	0.000	0.000	0.000
20	A	557	ARG	1	0.991	1.002	24.865	0.081	0.081	0.000	0.000	0.000	0.000
21	A	558	ALA	0	0.007	0.013	27.896	0.005	0.005	0.000	0.000	0.000	0.000
22	A	559	ILE	0	0.019	0.011	27.633	0.005	0.005	0.000	0.000	0.000	0.000
23	A	560	GLU	-1	-0.933	-0.974	29.171	-0.049	-0.049	0.000	0.000	0.000	0.000
24	A	561	ALA	0	-0.016	-0.013	32.375	0.004	0.004	0.000	0.000	0.000	0.000
25	A	562	GLN	0	0.021	0.000	32.671	0.003	0.003	0.000	0.000	0.000	0.000
26	A	563	GLN	0	-0.014	-0.002	34.985	0.003	0.003	0.000	0.000	0.000	0.000
27	A	564	HIS	0	0.048	0.033	35.601	0.005	0.005	0.000	0.000	0.000	0.000
28	A	565	LEU	0	0.038	0.030	38.064	0.002	0.002	0.000	0.000	0.000	0.000
29	A	566	LEU	0	0.002	0.007	37.674	0.002	0.002	0.000	0.000	0.000	0.000
30	A	567	LYS	1	0.853	0.922	40.079	0.029	0.029	0.000	0.000	0.000	0.000
31	A	568	LEU	0	0.029	0.028	42.552	0.002	0.002	0.000	0.000	0.000	0.000
32	A	569	THR	0	-0.016	-0.009	43.522	0.001	0.001	0.000	0.000	0.000	0.000
33	A	570	VAL	0	0.008	-0.002	44.892	0.001	0.001	0.000	0.000	0.000	0.000
34	A	571	TRP	0	-0.018	-0.007	47.225	0.001	0.001	0.000	0.000	0.000	0.000
35	A	572	GLY	0	0.027	0.013	48.831	0.001	0.001	0.000	0.000	0.000	0.000
36	A	573	ILE	0	0.010	-0.002	48.004	0.001	0.001	0.000	0.000	0.000	0.000
37	A	574	LYS	1	0.961	0.981	49.144	0.016	0.016	0.000	0.000	0.000	0.000
38	A	575	GLN	0	-0.010	0.020	53.150	0.001	0.001	0.000	0.000	0.000	0.000
39	A	576	LEU	0	0.004	0.004	53.720	0.001	0.001	0.000	0.000	0.000	0.000
40	A	577	GLN	0	0.020	0.004	54.660	0.000	0.000	0.000	0.000	0.000	0.000
41	A	578	ALA	0	-0.071	-0.029	57.378	0.000	0.000	0.000	0.000	0.000	0.000
42	A	579	ARG	1	0.813	0.902	58.226	0.012	0.012	0.000	0.000	0.000	0.000
43	A	580	VAL	0	0.019	0.019	60.025	0.000	0.000	0.000	0.000	0.000	0.000
44	A	628	TRP	0	-0.021	-0.025	52.131	0.000	0.000	0.000	0.000	0.000	0.000
45	A	629	LEU	0	0.021	0.007	52.335	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	630	GLN	0	0.007	0.003	49.645	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	631	TRP	0	0.035	0.014	47.714	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	632	ASP	-1	-0.795	-0.914	46.973	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	633	LYS	1	0.880	0.941	46.503	0.018	0.018	0.000	0.000	0.000	0.000
50	A	634	GLU	-1	-0.926	-0.964	43.813	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	635	ILE	0	0.032	0.011	42.301	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	636	SER	0	0.007	0.021	41.566	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	637	ASN	0	-0.003	0.002	40.552	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	638	TYR	0	0.017	-0.006	37.257	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	639	THR	0	-0.008	-0.020	36.432	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	640	HIS	0	-0.055	-0.034	36.313	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	641	ILE	0	0.017	0.019	32.328	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	642	ILE	0	-0.022	-0.010	31.916	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	643	TYR	0	-0.005	-0.014	31.449	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	644	GLU	-1	-0.925	-0.948	29.917	-0.050	-0.050	0.000	0.000	0.000	0.000
61	A	645	LEU	0	0.000	-0.009	26.989	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	646	ILE	0	-0.020	0.008	26.678	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	647	GLU	-1	-0.857	-0.910	26.878	-0.048	-0.048	0.000	0.000	0.000	0.000
64	A	648	GLU	-1	-0.837	-0.905	22.244	-0.084	-0.084	0.000	0.000	0.000	0.000
65	A	649	SER	0	-0.022	-0.035	22.765	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	650	GLN	0	-0.037	-0.006	22.154	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	651	LYS	1	0.920	0.949	21.944	0.054	0.054	0.000	0.000	0.000	0.000
68	A	652	GLN	0	-0.099	-0.042	15.790	0.004	0.004	0.000	0.000	0.000	0.000
69	A	653	GLN	0	-0.016	-0.016	17.464	-0.025	-0.025	0.000	0.000	0.000	0.000
70	A	654	GLU	-1	-0.905	-0.954	17.603	-0.055	-0.055	0.000	0.000	0.000	0.000
71	A	655	LYS	1	0.795	0.880	15.556	0.109	0.109	0.000	0.000	0.000	0.000
72	A	656	ASN	0	-0.015	-0.012	13.264	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	657	GLU	-1	-0.830	-0.913	12.855	-0.092	-0.092	0.000	0.000	0.000	0.000
74	A	658	GLN	0	-0.005	0.004	14.139	0.020	0.020	0.000	0.000	0.000	0.000
75	A	659	GLU	-1	-0.827	-0.905	9.130	-0.240	-0.240	0.000	0.000	0.000	0.000
76	A	660	LEU	0	0.008	0.004	9.179	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	661	LEU	0	0.032	0.017	10.413	0.016	0.016	0.000	0.000	0.000	0.000
78	A	662	GLU	-1	-0.870	-0.917	9.877	0.265	0.265	0.000	0.000	0.000	0.000
79	A	663	LEU	0	-0.032	-0.031	4.185	-0.061	0.022	-0.001	-0.016	-0.066	0.000
80	A	664	ASP	-1	-0.883	-0.927	7.340	0.045	0.045	0.000	0.000	0.000	0.000
81	A	665	LYS	1	0.903	0.966	10.014	-0.223	-0.223	0.000	0.000	0.000	0.000
82	A	666	TRP	0	-0.120	-0.085	6.640	0.076	0.076	0.000	0.000	0.000	0.000
83	A	667	ALA	0	-0.048	-0.006	7.249	0.034	0.034	0.000	0.000	0.000	0.000
84	A	668	ASN	0	-0.114	-0.054	8.376	0.006	0.006	0.000	0.000	0.000	0.000

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