FMO DATABASE

FMODB ID: QY65Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-707267.987864
FMO2-HF: Nuclear repulsion	668678.415905
FMO2-HF: Total energy	-38589.571959
FMO2-MP2: Total energy	-38701.448718

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.
-14.778	-14.7	16.78	-8.208	-8.648	-0.038

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 : 0.005 / q_NPA : 0.002

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	-0.045	-0.016	3.789	0.915	3.188	0.005	-1.318	-0.959	0.005
4	A	511	ALA	0	-0.014	-0.002	6.383	0.423	0.423	0.000	0.000	0.000	0.000
5	A	512	ALA	0	0.017	0.009	8.004	-0.308	-0.308	0.000	0.000	0.000	0.000
6	A	513	PRO	0	-0.045	-0.025	11.537	0.017	0.017	0.000	0.000	0.000	0.000
7	A	514	LEU	0	-0.005	-0.014	14.360	0.064	0.064	0.000	0.000	0.000	0.000
8	A	515	ASP	-1	-0.855	-0.920	17.221	-0.029	-0.029	0.000	0.000	0.000	0.000
9	A	516	VAL	0	-0.007	0.007	19.630	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	517	LYS	1	0.964	0.987	22.104	0.074	0.074	0.000	0.000	0.000	0.000
11	A	518	CYS	0	-0.006	0.011	25.750	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	519	LEU	0	-0.127	-0.074	27.380	0.005	0.005	0.000	0.000	0.000	0.000
13	A	520	GLU	-1	-0.831	-0.904	30.731	-0.082	-0.082	0.000	0.000	0.000	0.000
14	A	521	ALA	0	-0.018	-0.018	32.631	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	522	ASN	0	0.015	0.001	34.931	0.002	0.002	0.000	0.000	0.000	0.000
16	A	523	LYS	1	0.779	0.884	36.437	0.046	0.046	0.000	0.000	0.000	0.000
17	A	524	ASP	-1	-0.903	-0.945	37.297	-0.078	-0.078	0.000	0.000	0.000	0.000
18	A	525	TYR	0	-0.133	-0.085	32.792	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	526	ILE	0	0.032	0.007	29.905	0.007	0.007	0.000	0.000	0.000	0.000
20	A	527	ILE	0	-0.047	-0.001	28.630	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	528	ILE	0	0.016	0.006	23.042	0.012	0.012	0.000	0.000	0.000	0.000
22	A	529	SER	0	-0.038	-0.030	23.495	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	530	TRP	0	-0.009	0.003	17.242	0.028	0.028	0.000	0.000	0.000	0.000
24	A	531	LYS	1	0.852	0.917	18.098	0.017	0.017	0.000	0.000	0.000	0.000
25	A	532	GLN	0	0.019	0.005	13.992	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	533	PRO	0	0.002	0.003	9.843	0.057	0.057	0.000	0.000	0.000	0.000
27	A	534	ALA	0	-0.016	-0.013	11.670	-0.084	-0.084	0.000	0.000	0.000	0.000
28	A	535	VAL	0	0.006	0.001	5.166	-0.066	0.005	-0.001	-0.003	-0.067	0.000
29	A	536	ASP	-1	-0.807	-0.917	6.487	-2.180	-2.180	0.000	0.000	0.000	0.000
30	A	537	GLY	0	0.051	0.039	2.662	-0.380	0.873	0.908	-1.084	-1.076	0.007
31	A	538	GLY	0	-0.005	0.009	1.891	-18.393	-23.000	13.127	-4.382	-4.139	-0.059
32	A	539	SER	0	-0.069	-0.067	4.374	0.723	0.905	-0.001	-0.012	-0.169	0.000
33	A	540	PRO	0	0.021	0.031	6.001	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	541	ILE	0	0.006	0.007	8.923	-0.126	-0.126	0.000	0.000	0.000	0.000
35	A	542	LEU	0	-0.008	-0.007	10.363	0.216	0.216	0.000	0.000	0.000	0.000
36	A	543	GLY	0	0.001	-0.005	12.641	0.156	0.156	0.000	0.000	0.000	0.000
37	A	544	TYR	0	-0.009	-0.003	13.697	-0.093	-0.093	0.000	0.000	0.000	0.000
38	A	545	PHE	0	0.013	0.010	14.306	0.011	0.011	0.000	0.000	0.000	0.000
39	A	546	ILE	0	0.030	0.018	17.712	0.013	0.013	0.000	0.000	0.000	0.000
40	A	547	ASP	-1	-0.793	-0.875	18.988	-0.175	-0.175	0.000	0.000	0.000	0.000
41	A	548	LYS	1	0.920	0.932	21.803	0.125	0.125	0.000	0.000	0.000	0.000
42	A	549	CYS	0	0.006	0.017	25.242	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	550	GLU	-1	-0.763	-0.846	27.226	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	551	VAL	0	0.004	-0.013	30.222	0.005	0.005	0.000	0.000	0.000	0.000
45	A	552	GLY	0	-0.023	0.008	31.507	0.006	0.006	0.000	0.000	0.000	0.000
46	A	553	THR	0	-0.088	-0.055	30.595	0.000	0.000	0.000	0.000	0.000	0.000
47	A	554	ASP	-1	-0.816	-0.918	25.129	0.004	0.004	0.000	0.000	0.000	0.000
48	A	555	SER	0	-0.037	-0.019	26.138	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	556	TRP	0	-0.040	-0.040	22.456	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	557	SER	0	0.010	0.012	24.230	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	558	GLN	0	0.011	0.014	19.006	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	559	CYS	0	-0.074	-0.019	22.604	0.021	0.021	0.000	0.000	0.000	0.000
53	A	560	ASN	0	0.017	0.005	19.598	0.023	0.023	0.000	0.000	0.000	0.000
54	A	561	ASP	-1	-0.846	-0.909	21.569	-0.229	-0.229	0.000	0.000	0.000	0.000
55	A	562	THR	0	0.002	-0.001	20.043	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	563	PRO	0	-0.049	-0.016	15.800	0.025	0.025	0.000	0.000	0.000	0.000
57	A	564	VAL	0	0.027	0.027	18.138	0.008	0.008	0.000	0.000	0.000	0.000
58	A	565	LYS	1	0.856	0.914	14.700	0.696	0.696	0.000	0.000	0.000	0.000
59	A	566	PHE	0	-0.005	-0.016	18.512	-0.026	-0.026	0.000	0.000	0.000	0.000
60	A	567	ALA	0	0.024	0.021	20.316	0.004	0.004	0.000	0.000	0.000	0.000
61	A	568	ARG	1	0.939	0.951	21.208	0.174	0.174	0.000	0.000	0.000	0.000
62	A	569	PHE	0	0.016	0.004	23.520	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	570	PRO	0	0.024	0.026	25.574	0.013	0.013	0.000	0.000	0.000	0.000
64	A	571	VAL	0	0.003	0.002	25.950	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	572	THR	0	0.058	0.019	28.579	0.010	0.010	0.000	0.000	0.000	0.000
66	A	573	GLY	0	-0.029	-0.011	30.488	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	574	LEU	0	-0.027	-0.007	30.672	0.002	0.002	0.000	0.000	0.000	0.000
68	A	575	ILE	0	0.002	-0.004	34.341	0.001	0.001	0.000	0.000	0.000	0.000
69	A	576	GLU	-1	-0.761	-0.880	37.655	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	577	GLY	0	-0.021	-0.012	39.783	0.003	0.003	0.000	0.000	0.000	0.000
71	A	578	ARG	1	0.807	0.906	35.765	0.039	0.039	0.000	0.000	0.000	0.000
72	A	579	SER	0	0.021	0.003	34.022	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	580	TYR	0	-0.035	-0.034	29.351	0.001	0.001	0.000	0.000	0.000	0.000
74	A	581	ILE	0	0.014	0.027	25.495	0.004	0.004	0.000	0.000	0.000	0.000
75	A	582	PHE	0	0.037	0.005	23.840	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	583	ARG	1	0.838	0.916	18.286	0.098	0.098	0.000	0.000	0.000	0.000
77	A	584	VAL	0	0.020	0.010	16.412	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	585	ARG	1	0.849	0.897	13.559	0.331	0.331	0.000	0.000	0.000	0.000
79	A	586	ALA	0	0.039	0.024	10.685	-0.034	-0.034	0.000	0.000	0.000	0.000
80	A	587	VAL	0	0.000	0.005	9.629	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	588	ASN	0	0.022	-0.003	4.108	0.550	0.835	-0.001	-0.185	-0.099	0.000
82	A	589	LYS	1	0.947	0.953	5.586	2.187	2.187	0.000	0.000	0.000	0.000
83	A	590	MET	0	-0.055	0.000	1.883	0.673	1.182	2.744	-1.221	-2.032	0.009
84	A	591	GLY	0	0.036	0.021	5.170	0.566	0.678	-0.001	-0.003	-0.107	0.000
85	A	592	ILE	0	-0.035	-0.027	7.334	-0.265	-0.265	0.000	0.000	0.000	0.000
86	A	593	GLY	0	0.027	0.024	7.227	-0.045	-0.045	0.000	0.000	0.000	0.000
87	A	594	PHE	0	-0.011	-0.010	6.762	0.022	0.022	0.000	0.000	0.000	0.000
88	A	595	PRO	0	-0.011	-0.010	10.317	-0.064	-0.064	0.000	0.000	0.000	0.000
89	A	596	SER	0	-0.020	-0.017	13.970	0.054	0.054	0.000	0.000	0.000	0.000
90	A	597	ARG	1	0.936	0.966	15.887	-0.141	-0.141	0.000	0.000	0.000	0.000
91	A	598	VAL	0	0.014	0.016	18.783	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	599	SER	0	-0.033	-0.025	21.826	0.006	0.006	0.000	0.000	0.000	0.000
93	A	600	GLU	-1	-0.886	-0.943	24.570	0.010	0.010	0.000	0.000	0.000	0.000
94	A	601	PRO	0	-0.032	-0.009	28.143	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	602	VAL	0	-0.041	-0.025	29.859	0.000	0.000	0.000	0.000	0.000	0.000
96	A	603	ALA	0	0.027	0.016	32.465	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	604	ALA	0	0.004	0.008	35.034	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	605	LEU	0	-0.017	-0.022	36.440	0.003	0.003	0.000	0.000	0.000	0.000
99	A	606	ASP	-1	-0.785	-0.873	38.878	-0.058	-0.058	0.000	0.000	0.000	0.000
100	A	607	PRO	0	-0.001	0.004	39.298	0.004	0.004	0.000	0.000	0.000	0.000
101	A	608	ALA	0	-0.067	-0.027	41.830	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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