FMO DATABASE

FMODB ID: V5LY1

Calculation Name: 5F67-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F67

Chain ID: A

ChEMBL ID:

UniProt ID: Q24008

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:

Apendix: None

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-693423.995752
FMO2-HF: Nuclear repulsion	655982.300423
FMO2-HF: Total energy	-37441.69533
FMO2-MP2: Total energy	-37550.92502

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:351:SER)

Summations of interaction energy for fragment #1(A:351: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.
-32.615	-33.968	14.413	-7.878	-5.182	-0.07

Interaction energy analysis for fragmet #1(A:351:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.040

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	353	GLU	-1	-0.827	-0.902	1.662	-36.026	-37.530	14.414	-7.861	-5.050	-0.070
4	A	354	THR	0	-0.055	-0.047	4.379	2.444	2.595	-0.001	-0.017	-0.132	0.000
5	A	355	LYS	1	0.854	0.920	5.900	2.770	2.770	0.000	0.000	0.000	0.000
6	A	356	PHE	0	0.056	0.025	6.964	0.777	0.777	0.000	0.000	0.000	0.000
7	A	357	ILE	0	0.037	0.022	8.730	0.477	0.477	0.000	0.000	0.000	0.000
8	A	358	PHE	0	-0.077	-0.038	10.575	0.282	0.282	0.000	0.000	0.000	0.000
9	A	359	ASP	-1	-0.905	-0.943	11.764	-0.724	-0.724	0.000	0.000	0.000	0.000
10	A	360	GLN	0	-0.062	-0.025	13.400	0.007	0.007	0.000	0.000	0.000	0.000
11	A	361	PHE	0	-0.020	-0.032	15.105	0.147	0.147	0.000	0.000	0.000	0.000
12	A	362	PRO	0	0.034	0.023	16.536	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	363	LYS	1	0.874	0.939	17.545	0.473	0.473	0.000	0.000	0.000	0.000
14	A	364	ALA	0	-0.017	0.004	15.987	0.041	0.041	0.000	0.000	0.000	0.000
15	A	365	ARG	1	0.777	0.866	17.526	0.553	0.553	0.000	0.000	0.000	0.000
16	A	366	THR	0	0.040	0.003	13.851	-0.083	-0.083	0.000	0.000	0.000	0.000
17	A	367	VAL	0	-0.033	-0.002	16.750	0.105	0.105	0.000	0.000	0.000	0.000
18	A	368	GLN	0	0.034	0.021	14.559	-0.082	-0.082	0.000	0.000	0.000	0.000
19	A	369	VAL	0	0.001	0.000	19.424	0.073	0.073	0.000	0.000	0.000	0.000
20	A	370	ARG	1	0.942	0.986	21.465	0.227	0.227	0.000	0.000	0.000	0.000
21	A	371	LYS	1	0.807	0.894	22.818	0.488	0.488	0.000	0.000	0.000	0.000
22	A	372	GLU	-1	-0.870	-0.929	24.622	-0.219	-0.219	0.000	0.000	0.000	0.000
23	A	373	GLY	0	-0.008	0.010	28.086	0.011	0.011	0.000	0.000	0.000	0.000
24	A	374	PHE	0	-0.031	-0.044	27.534	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	375	LEU	0	0.046	0.018	21.770	0.013	0.013	0.000	0.000	0.000	0.000
26	A	376	GLY	0	-0.008	-0.014	26.081	0.017	0.017	0.000	0.000	0.000	0.000
27	A	377	ILE	0	0.010	0.017	23.291	0.007	0.007	0.000	0.000	0.000	0.000
28	A	378	MET	0	-0.039	-0.006	27.960	0.006	0.006	0.000	0.000	0.000	0.000
29	A	379	VAL	0	0.024	0.016	23.318	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	380	ILE	0	0.020	0.010	26.543	0.030	0.030	0.000	0.000	0.000	0.000
31	A	381	TYR	0	0.022	0.012	22.126	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	382	GLY	0	0.001	-0.003	25.811	0.042	0.042	0.000	0.000	0.000	0.000
33	A	383	LYS	1	0.911	0.945	26.284	0.349	0.349	0.000	0.000	0.000	0.000
34	A	384	HIS	0	0.054	0.037	26.345	0.017	0.017	0.000	0.000	0.000	0.000
35	A	385	ALA	0	-0.007	-0.012	27.544	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	386	GLU	-1	-0.934	-0.975	25.963	-0.376	-0.376	0.000	0.000	0.000	0.000
37	A	387	VAL	0	-0.020	-0.012	21.272	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	388	GLY	0	0.002	0.025	22.892	-0.035	-0.035	0.000	0.000	0.000	0.000
39	A	389	SER	0	-0.043	-0.050	24.361	0.025	0.025	0.000	0.000	0.000	0.000
40	A	390	GLY	0	0.084	0.044	21.555	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	391	ILE	0	0.002	0.012	20.325	0.070	0.070	0.000	0.000	0.000	0.000
42	A	392	PHE	0	-0.022	-0.006	22.133	-0.037	-0.037	0.000	0.000	0.000	0.000
43	A	393	ILE	0	-0.006	-0.006	23.024	0.019	0.019	0.000	0.000	0.000	0.000
44	A	394	SER	0	-0.008	-0.018	26.259	0.014	0.014	0.000	0.000	0.000	0.000
45	A	395	ASP	-1	-0.884	-0.945	29.566	-0.254	-0.254	0.000	0.000	0.000	0.000
46	A	396	LEU	0	-0.054	-0.035	28.447	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	397	ARG	1	0.908	0.971	31.307	0.251	0.251	0.000	0.000	0.000	0.000
48	A	398	GLU	-1	-0.867	-0.928	32.983	-0.193	-0.193	0.000	0.000	0.000	0.000
49	A	399	GLY	0	-0.020	-0.016	34.734	0.006	0.006	0.000	0.000	0.000	0.000
50	A	400	SER	0	-0.100	-0.047	30.038	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	401	ASN	0	0.033	-0.024	26.278	0.013	0.013	0.000	0.000	0.000	0.000
52	A	402	ALA	0	-0.008	-0.005	25.774	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	403	GLU	-1	-0.883	-0.938	26.779	-0.259	-0.259	0.000	0.000	0.000	0.000
54	A	404	LEU	0	-0.019	-0.014	29.004	0.002	0.002	0.000	0.000	0.000	0.000
55	A	405	ALA	0	-0.039	0.000	23.917	0.007	0.007	0.000	0.000	0.000	0.000
56	A	406	GLY	0	-0.025	-0.012	24.936	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	407	VAL	0	-0.012	0.003	23.431	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	408	LYS	1	0.852	0.921	25.681	0.374	0.374	0.000	0.000	0.000	0.000
59	A	409	VAL	0	0.050	0.024	27.059	-0.032	-0.032	0.000	0.000	0.000	0.000
60	A	410	GLY	0	-0.003	-0.005	28.317	0.016	0.016	0.000	0.000	0.000	0.000
61	A	411	ASP	-1	-0.731	-0.817	23.099	-0.511	-0.511	0.000	0.000	0.000	0.000
62	A	412	MET	0	-0.018	0.003	19.979	0.000	0.000	0.000	0.000	0.000	0.000
63	A	413	LEU	0	-0.022	-0.023	18.272	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	414	LEU	0	-0.015	-0.014	14.989	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	415	ALA	0	0.061	0.031	12.037	-0.203	-0.203	0.000	0.000	0.000	0.000
66	A	416	VAL	0	-0.006	-0.004	13.760	0.235	0.235	0.000	0.000	0.000	0.000
67	A	417	ASN	0	0.004	-0.016	12.347	-0.043	-0.043	0.000	0.000	0.000	0.000
68	A	418	GLN	0	-0.021	-0.028	5.919	-1.518	-1.518	0.000	0.000	0.000	0.000
69	A	419	ASP	-1	-0.892	-0.929	8.561	-2.210	-2.210	0.000	0.000	0.000	0.000
70	A	420	VAL	0	0.010	-0.003	8.759	0.285	0.285	0.000	0.000	0.000	0.000
71	A	421	THR	0	-0.034	-0.043	11.546	0.142	0.142	0.000	0.000	0.000	0.000
72	A	422	LEU	0	-0.057	-0.026	13.274	0.154	0.154	0.000	0.000	0.000	0.000
73	A	423	GLU	-1	-0.913	-0.949	14.919	-0.826	-0.826	0.000	0.000	0.000	0.000
74	A	424	SER	0	-0.052	-0.006	16.552	0.027	0.027	0.000	0.000	0.000	0.000
75	A	425	ASN	0	-0.006	-0.014	18.267	0.080	0.080	0.000	0.000	0.000	0.000
76	A	426	TYR	0	0.007	-0.016	21.547	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	427	ASP	-1	-0.866	-0.930	23.758	-0.431	-0.431	0.000	0.000	0.000	0.000
78	A	428	ASP	-1	-0.876	-0.931	18.491	-0.697	-0.697	0.000	0.000	0.000	0.000
79	A	429	ALA	0	-0.010	-0.001	19.013	-0.050	-0.050	0.000	0.000	0.000	0.000
80	A	430	THR	0	-0.031	-0.031	20.063	0.001	0.001	0.000	0.000	0.000	0.000
81	A	431	GLY	0	-0.001	-0.001	21.685	0.027	0.027	0.000	0.000	0.000	0.000
82	A	432	LEU	0	-0.012	-0.006	15.195	0.055	0.055	0.000	0.000	0.000	0.000
83	A	433	LEU	0	0.001	0.008	18.793	0.019	0.019	0.000	0.000	0.000	0.000
84	A	434	LYS	1	0.894	0.942	21.092	0.425	0.425	0.000	0.000	0.000	0.000
85	A	435	ARG	1	0.955	0.975	17.637	0.729	0.729	0.000	0.000	0.000	0.000
86	A	436	ALA	0	0.005	0.041	18.171	0.020	0.020	0.000	0.000	0.000	0.000
87	A	437	GLU	-1	-0.912	-0.949	18.904	-0.283	-0.283	0.000	0.000	0.000	0.000
88	A	438	GLY	0	0.010	0.003	19.131	-0.032	-0.032	0.000	0.000	0.000	0.000
89	A	439	VAL	0	-0.052	-0.040	18.121	0.007	0.007	0.000	0.000	0.000	0.000
90	A	440	VAL	0	0.017	0.019	17.273	-0.055	-0.055	0.000	0.000	0.000	0.000
91	A	441	THR	0	0.006	-0.015	13.275	0.033	0.033	0.000	0.000	0.000	0.000
92	A	442	MET	0	-0.028	-0.001	15.811	-0.081	-0.081	0.000	0.000	0.000	0.000
93	A	443	ILE	0	0.011	0.025	11.422	0.094	0.094	0.000	0.000	0.000	0.000
94	A	444	LEU	0	-0.004	0.002	15.969	0.021	0.021	0.000	0.000	0.000	0.000
95	A	445	LEU	0	0.024	0.011	19.251	0.016	0.016	0.000	0.000	0.000	0.000
96	A	446	THR	0	-0.048	-0.043	20.903	0.037	0.037	0.000	0.000	0.000	0.000
97	A	447	LEU	0	-0.032	-0.010	23.415	0.004	0.004	0.000	0.000	0.000	0.000
98	A	448	LYS	1	0.945	0.985	26.362	0.389	0.389	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:351:SER)