FMO DATABASE

FMODB ID: R9248

Calculation Name: 5FM4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FM4

Chain ID: A

ChEMBL ID:

UniProt ID: P52179

Base Structure: X-ray

Registration Date: 2023-09-19

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-702912.733086
FMO2-HF: Nuclear repulsion	664323.204738
FMO2-HF: Total energy	-38589.528348
FMO2-MP2: Total energy	-38701.302495

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:508:SER)

Summations of interaction energy for fragment #1(A:508: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.
-5.119	-5.387	12.953	-6.986	-5.697	-0.034

Interaction energy analysis for fragmet #1(A:508:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : 0.003

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	510	PRO	0	-0.040	-0.018	3.711	0.382	3.091	0.005	-1.600	-1.114	0.008
4	A	511	ALA	0	-0.018	0.001	6.396	0.706	0.706	0.000	0.000	0.000	0.000
5	A	512	ALA	0	0.023	0.008	8.211	-0.268	-0.268	0.000	0.000	0.000	0.000
6	A	513	PRO	0	-0.032	-0.022	11.758	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	514	LEU	0	-0.014	-0.013	14.656	0.071	0.071	0.000	0.000	0.000	0.000
8	A	515	ASP	-1	-0.857	-0.920	17.459	-0.036	-0.036	0.000	0.000	0.000	0.000
9	A	516	VAL	0	0.010	0.014	19.795	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	517	LYS	1	0.950	0.980	22.291	0.069	0.069	0.000	0.000	0.000	0.000
11	A	518	CYS	0	0.000	0.008	25.995	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	519	LEU	0	-0.118	-0.063	27.836	0.004	0.004	0.000	0.000	0.000	0.000
13	A	520	GLU	-1	-0.832	-0.927	30.837	-0.072	-0.072	0.000	0.000	0.000	0.000
14	A	521	ALA	0	-0.009	-0.007	32.838	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	522	ASN	0	0.016	0.005	35.095	0.000	0.000	0.000	0.000	0.000	0.000
16	A	523	LYS	1	0.776	0.882	36.651	0.037	0.037	0.000	0.000	0.000	0.000
17	A	524	ASP	-1	-0.909	-0.951	37.702	-0.065	-0.065	0.000	0.000	0.000	0.000
18	A	525	TYR	0	-0.122	-0.062	32.994	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	526	ILE	0	0.018	0.006	30.001	0.005	0.005	0.000	0.000	0.000	0.000
20	A	527	ILE	0	-0.027	0.004	28.807	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	528	ILE	0	0.006	0.003	23.319	0.009	0.009	0.000	0.000	0.000	0.000
22	A	529	SER	0	0.004	-0.014	23.846	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	530	TRP	0	-0.060	-0.024	17.543	0.035	0.035	0.000	0.000	0.000	0.000
24	A	531	LYS	1	0.870	0.928	18.748	0.032	0.032	0.000	0.000	0.000	0.000
25	A	532	GLN	0	0.007	-0.003	14.311	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	533	PRO	0	0.005	0.001	10.324	0.048	0.048	0.000	0.000	0.000	0.000
27	A	534	ALA	0	-0.011	-0.006	11.911	-0.089	-0.089	0.000	0.000	0.000	0.000
28	A	535	VAL	0	0.002	-0.004	5.506	-0.048	-0.048	0.000	0.000	0.000	0.000
29	A	536	ASP	-1	-0.838	-0.934	6.849	-1.954	-1.954	0.000	0.000	0.000	0.000
30	A	537	GLY	0	0.013	0.014	2.948	-0.764	-0.135	0.100	-0.298	-0.431	0.001
31	A	538	GLY	0	0.006	0.006	1.895	-8.397	-13.259	12.605	-4.673	-3.069	-0.044
32	A	539	SER	0	-0.074	-0.041	4.406	1.356	1.501	-0.001	-0.018	-0.126	0.000
33	A	540	PRO	0	0.054	0.033	6.087	0.051	0.051	0.000	0.000	0.000	0.000
34	A	541	ILE	0	0.006	0.002	8.464	-0.137	-0.137	0.000	0.000	0.000	0.000
35	A	542	LEU	0	-0.035	-0.036	10.629	0.213	0.213	0.000	0.000	0.000	0.000
36	A	543	GLY	0	-0.011	-0.008	12.835	0.140	0.140	0.000	0.000	0.000	0.000
37	A	544	TYR	0	-0.007	0.006	13.801	-0.089	-0.089	0.000	0.000	0.000	0.000
38	A	545	PHE	0	0.008	-0.001	14.554	0.005	0.005	0.000	0.000	0.000	0.000
39	A	546	ILE	0	0.025	0.016	17.797	0.021	0.021	0.000	0.000	0.000	0.000
40	A	547	ASP	-1	-0.779	-0.872	18.901	-0.105	-0.105	0.000	0.000	0.000	0.000
41	A	548	LYS	1	0.932	0.950	21.841	0.087	0.087	0.000	0.000	0.000	0.000
42	A	549	CYS	0	0.004	0.000	25.188	0.002	0.002	0.000	0.000	0.000	0.000
43	A	550	GLU	-1	-0.774	-0.852	27.045	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	551	VAL	0	0.025	0.001	30.368	0.006	0.006	0.000	0.000	0.000	0.000
45	A	552	GLY	0	-0.029	0.005	31.471	0.006	0.006	0.000	0.000	0.000	0.000
46	A	553	THR	0	-0.098	-0.054	30.510	0.000	0.000	0.000	0.000	0.000	0.000
47	A	554	ASP	-1	-0.855	-0.943	25.315	0.054	0.054	0.000	0.000	0.000	0.000
48	A	555	SER	0	-0.050	-0.019	26.187	0.000	0.000	0.000	0.000	0.000	0.000
49	A	556	TRP	0	0.010	-0.004	22.197	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	557	SER	0	0.008	0.009	24.273	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	558	GLN	0	0.018	0.011	18.972	0.001	0.001	0.000	0.000	0.000	0.000
52	A	559	CYS	0	-0.072	-0.024	22.604	0.012	0.012	0.000	0.000	0.000	0.000
53	A	560	ASN	0	0.006	0.007	19.887	0.022	0.022	0.000	0.000	0.000	0.000
54	A	561	ASP	-1	-0.861	-0.920	22.061	-0.187	-0.187	0.000	0.000	0.000	0.000
55	A	562	THR	0	0.012	-0.003	20.503	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	563	PRO	0	-0.041	-0.010	16.400	0.022	0.022	0.000	0.000	0.000	0.000
57	A	564	VAL	0	0.015	0.022	18.619	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	565	LYS	1	0.890	0.934	14.553	0.678	0.678	0.000	0.000	0.000	0.000
59	A	566	PHE	0	-0.012	-0.019	18.372	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	567	ALA	0	0.022	0.014	20.558	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	568	ARG	1	0.942	0.963	21.638	0.163	0.163	0.000	0.000	0.000	0.000
62	A	569	PHE	0	0.022	0.003	23.818	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	570	PRO	0	0.018	0.033	25.890	0.013	0.013	0.000	0.000	0.000	0.000
64	A	571	VAL	0	-0.010	-0.007	26.397	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	572	THR	0	0.073	0.028	29.102	0.008	0.008	0.000	0.000	0.000	0.000
66	A	573	GLY	0	-0.016	-0.011	30.904	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	574	LEU	0	-0.037	-0.012	30.902	0.004	0.004	0.000	0.000	0.000	0.000
68	A	575	ILE	0	0.003	0.006	34.439	0.000	0.000	0.000	0.000	0.000	0.000
69	A	576	GLU	-1	-0.780	-0.893	37.418	-0.031	-0.031	0.000	0.000	0.000	0.000
70	A	577	GLY	0	-0.009	-0.005	39.401	0.003	0.003	0.000	0.000	0.000	0.000
71	A	578	ARG	1	0.800	0.905	35.521	0.020	0.020	0.000	0.000	0.000	0.000
72	A	579	SER	0	0.015	-0.003	33.688	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	580	TYR	0	-0.034	-0.044	29.161	0.000	0.000	0.000	0.000	0.000	0.000
74	A	581	ILE	0	0.015	0.035	25.212	0.001	0.001	0.000	0.000	0.000	0.000
75	A	582	PHE	0	0.034	0.000	23.831	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	583	ARG	1	0.837	0.915	18.198	0.027	0.027	0.000	0.000	0.000	0.000
77	A	584	VAL	0	0.006	0.007	16.808	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	585	ARG	1	0.863	0.910	13.285	0.250	0.250	0.000	0.000	0.000	0.000
79	A	586	ALA	0	0.032	0.019	10.911	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	587	VAL	0	-0.009	-0.001	9.740	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	588	ASN	0	0.037	0.009	4.341	0.535	0.606	-0.001	-0.038	-0.031	0.000
82	A	589	LYS	1	0.975	0.972	6.430	1.889	1.889	0.000	0.000	0.000	0.000
83	A	590	MET	0	-0.052	-0.005	2.535	0.277	1.317	0.245	-0.359	-0.926	0.001
84	A	591	GLY	0	0.043	0.024	5.453	0.608	0.608	0.000	0.000	0.000	0.000
85	A	592	ILE	0	-0.035	-0.023	7.423	-0.211	-0.211	0.000	0.000	0.000	0.000
86	A	593	GLY	0	0.037	0.034	7.258	0.098	0.098	0.000	0.000	0.000	0.000
87	A	594	PHE	0	-0.018	-0.014	7.078	-0.080	-0.080	0.000	0.000	0.000	0.000
88	A	595	PRO	0	0.002	-0.005	10.537	-0.078	-0.078	0.000	0.000	0.000	0.000
89	A	596	SER	0	-0.009	0.002	14.059	0.058	0.058	0.000	0.000	0.000	0.000
90	A	597	ARG	1	0.929	0.961	16.181	-0.186	-0.186	0.000	0.000	0.000	0.000
91	A	598	VAL	0	0.001	0.001	19.037	-0.024	-0.024	0.000	0.000	0.000	0.000
92	A	599	SER	0	-0.013	-0.003	22.100	0.004	0.004	0.000	0.000	0.000	0.000
93	A	600	GLU	-1	-0.901	-0.951	24.809	0.030	0.030	0.000	0.000	0.000	0.000
94	A	601	PRO	0	-0.030	-0.018	28.462	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	602	VAL	0	-0.033	-0.021	29.852	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	603	ALA	0	0.022	0.016	32.446	0.000	0.000	0.000	0.000	0.000	0.000
97	A	604	ALA	0	0.000	0.009	35.250	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	605	LEU	0	0.003	-0.020	36.674	0.003	0.003	0.000	0.000	0.000	0.000
99	A	606	ASP	-1	-0.807	-0.887	39.368	-0.047	-0.047	0.000	0.000	0.000	0.000
100	A	607	PRO	0	0.007	0.006	39.624	0.004	0.004	0.000	0.000	0.000	0.000
101	A	608	ALA	0	-0.061	-0.022	42.273	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:508:SER)