FMO DATABASE

FMODB ID: Z689N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-702085.253196
FMO2-HF: Nuclear repulsion	663495.979746
FMO2-HF: Total energy	-38589.27345
FMO2-MP2: Total energy	-38700.991545

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.
-12.52	-8.831	9.309	-6.527	-6.472	-0.042

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 : 0.029 / q_NPA : 0.016

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	-0.006	-0.006	2.382	-9.973	-5.249	0.857	-3.185	-2.397	-0.018
4	A	511	ALA	0	-0.006	0.011	5.088	0.383	0.459	-0.001	-0.003	-0.071	0.000
5	A	512	ALA	0	0.018	0.002	7.054	0.028	0.028	0.000	0.000	0.000	0.000
6	A	513	PRO	0	-0.038	-0.023	10.568	0.093	0.093	0.000	0.000	0.000	0.000
7	A	514	LEU	0	-0.005	-0.010	13.421	0.084	0.084	0.000	0.000	0.000	0.000
8	A	515	ASP	-1	-0.880	-0.948	16.323	-0.393	-0.393	0.000	0.000	0.000	0.000
9	A	516	VAL	0	0.007	0.012	18.520	0.001	0.001	0.000	0.000	0.000	0.000
10	A	517	LYS	1	0.952	0.983	21.057	0.293	0.293	0.000	0.000	0.000	0.000
11	A	518	CYS	0	0.006	0.008	24.760	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	519	LEU	0	-0.130	-0.071	26.692	0.014	0.014	0.000	0.000	0.000	0.000
13	A	520	GLU	-1	-0.872	-0.947	29.559	-0.191	-0.191	0.000	0.000	0.000	0.000
14	A	521	ALA	0	-0.020	-0.007	31.523	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	522	ASN	0	0.032	0.025	33.785	0.004	0.004	0.000	0.000	0.000	0.000
16	A	523	LYS	1	0.875	0.941	35.556	0.125	0.125	0.000	0.000	0.000	0.000
17	A	524	ASP	-1	-0.901	-0.948	36.739	-0.182	-0.182	0.000	0.000	0.000	0.000
18	A	525	TYR	0	-0.072	-0.045	31.884	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	526	ILE	0	0.027	0.015	28.552	0.006	0.006	0.000	0.000	0.000	0.000
20	A	527	ILE	0	-0.043	-0.002	27.709	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	528	ILE	0	0.010	0.005	21.949	0.006	0.006	0.000	0.000	0.000	0.000
22	A	529	SER	0	-0.041	-0.032	22.548	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	530	TRP	0	-0.020	-0.011	16.411	0.027	0.027	0.000	0.000	0.000	0.000
24	A	531	LYS	1	0.900	0.960	17.688	0.393	0.393	0.000	0.000	0.000	0.000
25	A	532	GLN	0	0.010	0.001	13.537	-0.090	-0.090	0.000	0.000	0.000	0.000
26	A	533	PRO	0	0.005	0.002	9.222	0.132	0.132	0.000	0.000	0.000	0.000
27	A	534	ALA	0	-0.010	-0.007	11.101	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	535	VAL	0	0.003	-0.004	5.187	0.190	0.190	0.000	0.000	0.000	0.000
29	A	536	ASP	-1	-0.859	-0.943	6.621	-2.563	-2.563	0.000	0.000	0.000	0.000
30	A	537	GLY	0	0.005	0.004	3.047	-2.012	-1.231	0.085	-0.412	-0.454	0.002
31	A	538	GLY	0	0.009	0.010	2.151	-3.395	-6.329	8.245	-2.651	-2.660	-0.026
32	A	539	SER	0	-0.069	-0.038	4.287	1.394	1.526	-0.001	-0.011	-0.121	0.000
33	A	540	PRO	0	0.047	0.035	5.877	-0.372	-0.372	0.000	0.000	0.000	0.000
34	A	541	ILE	0	-0.011	-0.014	8.058	-0.185	-0.185	0.000	0.000	0.000	0.000
35	A	542	LEU	0	-0.075	-0.044	10.307	0.333	0.333	0.000	0.000	0.000	0.000
36	A	543	GLY	0	-0.025	-0.014	12.608	0.227	0.227	0.000	0.000	0.000	0.000
37	A	544	TYR	0	-0.015	-0.002	13.014	-0.286	-0.286	0.000	0.000	0.000	0.000
38	A	545	PHE	0	0.006	-0.001	14.644	0.084	0.084	0.000	0.000	0.000	0.000
39	A	546	ILE	0	0.017	0.015	16.960	-0.047	-0.047	0.000	0.000	0.000	0.000
40	A	547	ASP	-1	-0.793	-0.885	18.364	-0.586	-0.586	0.000	0.000	0.000	0.000
41	A	548	LYS	1	0.963	0.973	21.263	0.306	0.306	0.000	0.000	0.000	0.000
42	A	549	CYS	0	0.005	-0.004	24.627	0.004	0.004	0.000	0.000	0.000	0.000
43	A	550	GLU	-1	-0.861	-0.913	26.594	-0.172	-0.172	0.000	0.000	0.000	0.000
44	A	551	VAL	0	0.025	-0.005	29.913	0.002	0.002	0.000	0.000	0.000	0.000
45	A	552	GLY	0	-0.026	0.004	30.937	0.004	0.004	0.000	0.000	0.000	0.000
46	A	553	THR	0	-0.091	-0.047	30.285	0.007	0.007	0.000	0.000	0.000	0.000
47	A	554	ASP	-1	-0.873	-0.947	25.457	-0.251	-0.251	0.000	0.000	0.000	0.000
48	A	555	SER	0	-0.051	-0.018	26.190	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	556	TRP	0	0.008	-0.003	22.046	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	557	SER	0	-0.020	-0.012	24.178	0.009	0.009	0.000	0.000	0.000	0.000
51	A	558	GLN	0	0.003	-0.010	19.213	-0.041	-0.041	0.000	0.000	0.000	0.000
52	A	559	CYS	0	-0.090	-0.039	22.355	0.046	0.046	0.000	0.000	0.000	0.000
53	A	560	ASN	0	0.001	0.003	19.499	0.027	0.027	0.000	0.000	0.000	0.000
54	A	561	ASP	-1	-0.844	-0.913	21.803	-0.382	-0.382	0.000	0.000	0.000	0.000
55	A	562	THR	0	-0.028	-0.023	20.494	-0.038	-0.038	0.000	0.000	0.000	0.000
56	A	563	PRO	0	-0.020	0.004	16.338	0.004	0.004	0.000	0.000	0.000	0.000
57	A	564	VAL	0	0.014	0.016	18.449	0.043	0.043	0.000	0.000	0.000	0.000
58	A	565	LYS	1	0.969	0.970	15.511	0.652	0.652	0.000	0.000	0.000	0.000
59	A	566	PHE	0	-0.011	-0.020	18.061	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	567	ALA	0	0.024	0.017	19.792	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	568	ARG	1	0.941	0.958	20.745	0.347	0.347	0.000	0.000	0.000	0.000
62	A	569	PHE	0	0.015	0.005	22.804	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	570	PRO	0	0.041	0.037	24.798	0.007	0.007	0.000	0.000	0.000	0.000
64	A	571	VAL	0	-0.015	-0.007	25.473	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	572	THR	0	0.069	0.030	28.139	0.017	0.017	0.000	0.000	0.000	0.000
66	A	573	GLY	0	-0.026	-0.016	30.240	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	574	LEU	0	-0.038	-0.016	30.226	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	575	ILE	0	0.003	0.002	33.785	0.011	0.011	0.000	0.000	0.000	0.000
69	A	576	GLU	-1	-0.879	-0.953	36.712	-0.137	-0.137	0.000	0.000	0.000	0.000
70	A	577	GLY	0	-0.005	0.000	38.568	0.007	0.007	0.000	0.000	0.000	0.000
71	A	578	ARG	1	0.830	0.930	35.054	0.151	0.151	0.000	0.000	0.000	0.000
72	A	579	SER	0	0.018	-0.001	32.865	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	580	TYR	0	0.011	-0.007	28.372	0.002	0.002	0.000	0.000	0.000	0.000
74	A	581	ILE	0	0.015	0.032	24.254	0.002	0.002	0.000	0.000	0.000	0.000
75	A	582	PHE	0	0.030	0.001	22.774	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	583	ARG	1	0.896	0.961	17.605	0.512	0.512	0.000	0.000	0.000	0.000
77	A	584	VAL	0	0.009	0.014	15.357	0.000	0.000	0.000	0.000	0.000	0.000
78	A	585	ARG	1	0.881	0.927	12.695	0.770	0.770	0.000	0.000	0.000	0.000
79	A	586	ALA	0	0.035	0.023	9.592	0.127	0.127	0.000	0.000	0.000	0.000
80	A	587	VAL	0	-0.014	-0.004	9.505	-0.308	-0.308	0.000	0.000	0.000	0.000
81	A	588	ASN	0	0.050	0.026	4.097	1.295	1.406	-0.001	-0.052	-0.058	0.000
82	A	589	LYS	1	0.973	0.968	6.895	0.533	0.533	0.000	0.000	0.000	0.000
83	A	590	MET	0	-0.045	-0.014	2.839	0.305	1.104	0.125	-0.213	-0.711	0.000
84	A	591	GLY	0	0.040	0.021	5.483	0.491	0.491	0.000	0.000	0.000	0.000
85	A	592	ILE	0	-0.032	-0.019	7.428	-0.424	-0.424	0.000	0.000	0.000	0.000
86	A	593	GLY	0	0.025	0.026	7.012	-0.157	-0.157	0.000	0.000	0.000	0.000
87	A	594	PHE	0	-0.016	-0.012	7.620	0.452	0.452	0.000	0.000	0.000	0.000
88	A	595	PRO	0	0.004	-0.012	10.088	-0.108	-0.108	0.000	0.000	0.000	0.000
89	A	596	SER	0	-0.016	-0.001	13.325	0.019	0.019	0.000	0.000	0.000	0.000
90	A	597	ARG	1	0.925	0.959	15.009	0.421	0.421	0.000	0.000	0.000	0.000
91	A	598	VAL	0	0.003	0.003	17.958	-0.024	-0.024	0.000	0.000	0.000	0.000
92	A	599	SER	0	-0.007	0.000	21.109	0.009	0.009	0.000	0.000	0.000	0.000
93	A	600	GLU	-1	-0.917	-0.960	23.625	-0.209	-0.209	0.000	0.000	0.000	0.000
94	A	601	PRO	0	-0.021	-0.014	27.302	-0.015	-0.015	0.000	0.000	0.000	0.000
95	A	602	VAL	0	-0.022	-0.017	28.851	0.009	0.009	0.000	0.000	0.000	0.000
96	A	603	ALA	0	0.019	0.013	31.325	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	604	ALA	0	-0.007	0.007	34.405	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	605	LEU	0	-0.002	-0.025	35.680	0.012	0.012	0.000	0.000	0.000	0.000
99	A	606	ASP	-1	-0.822	-0.902	38.146	-0.158	-0.158	0.000	0.000	0.000	0.000
100	A	607	PRO	0	-0.020	-0.010	38.377	0.006	0.006	0.000	0.000	0.000	0.000
101	A	608	ALA	0	-0.022	0.001	40.978	0.008	0.008	0.000	0.000	0.000	0.000

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