FMO DATABASE

FMODB ID: 5J9QZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-530866.492058
FMO2-HF: Nuclear repulsion	496448.568286
FMO2-HF: Total energy	-34417.923772
FMO2-MP2: Total energy	-34521.414125

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.
-2.55	0.606	1.95	-1.816	-3.291	0

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 : 0.040 / q_NPA : 0.006

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

Sort

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	0.038	0.012	3.637	-3.335	-1.450	0.004	-0.841	-1.049	0.003
4	A	541	VAL	0	0.028	0.020	2.088	-2.110	-1.284	1.947	-0.857	-1.916	-0.003
5	A	542	ARG	1	0.916	0.959	3.979	1.025	1.366	0.000	-0.095	-0.246	0.000
6	A	543	LYS	1	0.816	0.897	5.839	-0.398	-0.398	0.000	0.000	0.000	0.000
7	A	544	LEU	0	0.061	0.047	7.560	0.012	0.012	0.000	0.000	0.000	0.000
8	A	545	LEU	0	-0.014	-0.022	6.454	0.003	0.003	0.000	0.000	0.000	0.000
9	A	546	SER	0	-0.008	-0.010	9.561	0.005	0.005	0.000	0.000	0.000	0.000
10	A	547	GLY	0	0.029	0.034	11.757	0.032	0.032	0.000	0.000	0.000	0.000
11	A	548	ILE	0	0.007	0.000	11.290	0.022	0.022	0.000	0.000	0.000	0.000
12	A	549	VAL	0	0.002	-0.001	13.400	0.013	0.013	0.000	0.000	0.000	0.000
13	A	550	GLN	0	-0.034	-0.016	15.659	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	551	GLN	0	0.012	-0.020	17.327	0.001	0.001	0.000	0.000	0.000	0.000
15	A	552	GLN	0	-0.025	-0.016	17.510	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	553	SER	0	-0.040	-0.007	20.135	0.006	0.006	0.000	0.000	0.000	0.000
17	A	554	ASN	0	0.015	0.005	21.355	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	555	LEU	0	0.027	0.011	22.002	0.005	0.005	0.000	0.000	0.000	0.000
19	A	556	LEU	0	-0.020	0.007	24.436	0.003	0.003	0.000	0.000	0.000	0.000
20	A	557	ARG	1	1.017	1.013	25.659	0.064	0.064	0.000	0.000	0.000	0.000
21	A	558	ALA	0	0.001	0.010	27.802	0.004	0.004	0.000	0.000	0.000	0.000
22	A	559	ILE	0	0.011	0.001	27.491	0.003	0.003	0.000	0.000	0.000	0.000
23	A	560	GLU	-1	-0.937	-0.979	29.045	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	561	ALA	0	-0.041	-0.027	32.161	0.002	0.002	0.000	0.000	0.000	0.000
25	A	562	GLN	0	0.018	-0.004	33.017	0.001	0.001	0.000	0.000	0.000	0.000
26	A	563	GLN	0	-0.003	0.011	35.000	0.002	0.002	0.000	0.000	0.000	0.000
27	A	564	HIS	0	0.060	0.030	35.849	0.003	0.003	0.000	0.000	0.000	0.000
28	A	565	LEU	0	0.043	0.031	37.914	0.001	0.001	0.000	0.000	0.000	0.000
29	A	566	LEU	0	0.027	0.019	37.692	0.001	0.001	0.000	0.000	0.000	0.000
30	A	567	LYS	1	0.838	0.912	40.121	0.026	0.026	0.000	0.000	0.000	0.000
31	A	568	LEU	0	0.027	0.019	42.434	0.000	0.000	0.000	0.000	0.000	0.000
32	A	569	THR	0	-0.019	0.002	43.761	0.002	0.002	0.000	0.000	0.000	0.000
33	A	570	VAL	0	-0.005	-0.008	44.960	0.001	0.001	0.000	0.000	0.000	0.000
34	A	571	TRP	0	-0.027	-0.012	47.160	0.001	0.001	0.000	0.000	0.000	0.000
35	A	572	GLY	0	0.042	0.017	48.861	0.000	0.000	0.000	0.000	0.000	0.000
36	A	573	ILE	0	0.012	0.002	48.240	0.001	0.001	0.000	0.000	0.000	0.000
37	A	574	LYS	1	0.971	0.978	49.280	0.013	0.013	0.000	0.000	0.000	0.000
38	A	575	GLN	0	-0.013	0.022	53.206	0.000	0.000	0.000	0.000	0.000	0.000
39	A	576	LEU	0	-0.007	-0.011	53.755	0.000	0.000	0.000	0.000	0.000	0.000
40	A	577	GLN	0	-0.022	-0.006	54.789	0.000	0.000	0.000	0.000	0.000	0.000
41	A	578	ALA	0	-0.027	-0.006	57.500	0.000	0.000	0.000	0.000	0.000	0.000
42	A	579	ARG	1	0.809	0.907	58.299	0.005	0.005	0.000	0.000	0.000	0.000
43	A	580	VAL	0	0.042	0.030	60.577	0.000	0.000	0.000	0.000	0.000	0.000
44	A	628	TRP	0	0.028	-0.005	52.969	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	629	LEU	0	0.050	0.029	52.587	0.000	0.000	0.000	0.000	0.000	0.000
46	A	630	GLN	0	0.011	-0.016	49.728	0.001	0.001	0.000	0.000	0.000	0.000
47	A	631	TRP	0	0.015	0.011	47.585	0.000	0.000	0.000	0.000	0.000	0.000
48	A	632	ASP	-1	-0.830	-0.923	47.113	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	633	LYS	1	0.843	0.919	46.620	0.008	0.008	0.000	0.000	0.000	0.000
50	A	634	GLU	-1	-0.923	-0.962	43.908	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	635	ILE	0	0.025	0.013	42.395	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	636	SER	0	0.000	0.011	41.687	0.001	0.001	0.000	0.000	0.000	0.000
53	A	637	ASN	0	-0.008	-0.004	40.685	0.002	0.002	0.000	0.000	0.000	0.000
54	A	638	TYR	0	0.023	0.004	37.085	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	639	THR	0	-0.013	-0.015	36.439	0.000	0.000	0.000	0.000	0.000	0.000
56	A	640	HIS	0	-0.040	-0.031	36.279	0.004	0.004	0.000	0.000	0.000	0.000
57	A	641	ILE	0	0.011	0.017	32.519	0.001	0.001	0.000	0.000	0.000	0.000
58	A	642	ILE	0	-0.016	-0.012	32.008	0.000	0.000	0.000	0.000	0.000	0.000
59	A	643	TYR	0	0.002	-0.016	31.352	0.001	0.001	0.000	0.000	0.000	0.000
60	A	644	GLU	-1	-0.923	-0.935	30.070	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	645	LEU	0	-0.001	-0.009	26.975	0.000	0.000	0.000	0.000	0.000	0.000
62	A	646	ILE	0	-0.040	-0.001	26.769	0.002	0.002	0.000	0.000	0.000	0.000
63	A	647	GLU	-1	-0.847	-0.909	26.932	0.039	0.039	0.000	0.000	0.000	0.000
64	A	648	GLU	-1	-0.834	-0.910	22.613	0.037	0.037	0.000	0.000	0.000	0.000
65	A	649	SER	0	-0.031	-0.042	22.855	0.001	0.001	0.000	0.000	0.000	0.000
66	A	650	GLN	0	-0.030	-0.011	22.313	0.010	0.010	0.000	0.000	0.000	0.000
67	A	651	LYS	1	0.895	0.942	22.437	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	652	GLN	0	-0.074	-0.037	15.924	0.013	0.013	0.000	0.000	0.000	0.000
69	A	653	GLN	0	-0.030	-0.033	17.665	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	654	GLU	-1	-0.904	-0.949	18.030	0.146	0.146	0.000	0.000	0.000	0.000
71	A	655	LYS	1	0.778	0.886	15.701	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	656	ASN	0	-0.013	-0.015	13.327	0.043	0.043	0.000	0.000	0.000	0.000
73	A	657	GLU	-1	-0.838	-0.909	13.052	0.196	0.196	0.000	0.000	0.000	0.000
74	A	658	GLN	0	-0.008	0.005	14.746	0.065	0.065	0.000	0.000	0.000	0.000
75	A	659	GLU	-1	-0.823	-0.913	9.589	0.467	0.467	0.000	0.000	0.000	0.000
76	A	660	LEU	0	-0.008	-0.004	9.457	0.182	0.182	0.000	0.000	0.000	0.000
77	A	661	LEU	0	0.043	0.020	10.624	0.078	0.078	0.000	0.000	0.000	0.000
78	A	662	GLU	-1	-0.883	-0.926	9.855	1.195	1.195	0.000	0.000	0.000	0.000
79	A	663	LEU	0	-0.061	-0.050	3.956	0.153	0.257	-0.001	-0.023	-0.080	0.000
80	A	664	ASP	-1	-0.904	-0.950	7.462	0.749	0.749	0.000	0.000	0.000	0.000
81	A	665	LYS	1	0.902	0.965	10.120	-1.095	-1.095	0.000	0.000	0.000	0.000
82	A	666	TRP	0	-0.114	-0.084	7.193	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	667	ALA	0	-0.041	0.006	7.439	0.144	0.144	0.000	0.000	0.000	0.000
84	A	668	ASN	0	-0.079	-0.019	8.640	-0.220	-0.220	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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