FMO DATABASE

FMODB ID: MVVJZ

Calculation Name: 4YO5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YO5

Chain ID: A

ChEMBL ID:

UniProt ID: D3GUX1

Base Structure: X-ray

Registration Date: 2023-06-21

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1102900.475764
FMO2-HF: Nuclear repulsion	1051755.431408
FMO2-HF: Total energy	-51145.044356
FMO2-MP2: Total energy	-51294.534982

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:399:ALA)

Summations of interaction energy for fragment #1(A:399:ALA)

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.
-6.188	-2.719	5.55	-3.072	-5.946	-0.007

Interaction energy analysis for fragmet #1(A:399:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.013

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	401	LEU	0	-0.028	-0.001	3.843	-0.815	0.840	-0.016	-0.788	-0.851	-0.001
4	A	402	SER	0	0.051	0.023	2.446	-0.262	0.344	1.812	-0.941	-1.477	-0.008
5	A	403	LEU	0	-0.056	-0.018	4.511	-0.900	-0.801	-0.001	-0.013	-0.085	0.000
6	A	404	GLU	-1	-0.843	-0.940	6.828	0.635	0.635	0.000	0.000	0.000	0.000
7	A	405	PRO	0	-0.029	-0.023	10.040	0.039	0.039	0.000	0.000	0.000	0.000
8	A	406	GLU	-1	-0.899	-0.955	12.774	0.057	0.057	0.000	0.000	0.000	0.000
9	A	407	ALA	0	0.009	-0.011	13.564	0.008	0.008	0.000	0.000	0.000	0.000
10	A	408	LEU	0	-0.018	-0.017	14.541	0.004	0.004	0.000	0.000	0.000	0.000
11	A	409	GLN	0	0.002	0.013	16.739	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	410	ILE	0	-0.005	0.006	17.631	0.003	0.003	0.000	0.000	0.000	0.000
13	A	411	ALA	0	-0.041	-0.018	19.298	0.002	0.002	0.000	0.000	0.000	0.000
14	A	412	ASP	-1	-0.965	-0.965	21.199	0.038	0.038	0.000	0.000	0.000	0.000
15	A	413	ASN	0	-0.088	-0.041	22.652	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	414	GLU	-1	-0.945	-0.969	23.972	0.085	0.085	0.000	0.000	0.000	0.000
17	A	415	GLY	0	0.029	0.016	25.410	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	416	THR	0	0.007	-0.016	21.453	0.010	0.010	0.000	0.000	0.000	0.000
19	A	417	GLU	-1	-0.928	-0.974	21.506	0.154	0.154	0.000	0.000	0.000	0.000
20	A	418	ALA	0	0.056	0.029	22.190	0.021	0.021	0.000	0.000	0.000	0.000
21	A	419	ALA	0	0.027	0.024	18.302	0.013	0.013	0.000	0.000	0.000	0.000
22	A	420	LEU	0	-0.043	-0.033	17.389	0.044	0.044	0.000	0.000	0.000	0.000
23	A	421	SER	0	0.028	0.000	17.518	0.046	0.046	0.000	0.000	0.000	0.000
24	A	422	TRP	0	-0.028	0.004	16.998	0.026	0.026	0.000	0.000	0.000	0.000
25	A	423	LEU	0	-0.056	-0.039	11.964	0.028	0.028	0.000	0.000	0.000	0.000
26	A	424	GLN	0	-0.039	-0.038	13.808	0.038	0.038	0.000	0.000	0.000	0.000
27	A	425	ALA	0	-0.023	0.013	16.060	0.006	0.006	0.000	0.000	0.000	0.000
28	A	426	ARG	1	0.956	1.004	11.630	-0.325	-0.325	0.000	0.000	0.000	0.000
29	A	427	PRO	0	-0.011	-0.013	11.507	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	428	GLY	0	0.037	0.027	12.487	0.081	0.081	0.000	0.000	0.000	0.000
31	A	429	ILE	0	-0.060	-0.024	8.656	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	430	GLN	0	0.044	-0.003	10.700	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	431	SER	0	-0.030	-0.002	7.220	0.083	0.083	0.000	0.000	0.000	0.000
34	A	432	ASP	-1	-0.812	-0.923	9.057	0.782	0.782	0.000	0.000	0.000	0.000
35	A	433	ARG	1	0.965	0.989	2.476	-2.924	-2.687	2.765	-0.828	-2.173	-0.001
36	A	434	SER	0	0.006	-0.013	5.066	0.274	0.274	0.000	0.000	0.000	0.000
37	A	435	ASN	0	0.037	0.029	5.954	-0.045	-0.045	0.000	0.000	0.000	0.000
38	A	436	TRP	0	0.021	0.000	7.511	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	437	LEU	0	-0.016	-0.013	2.762	-1.053	-0.339	0.992	-0.499	-1.208	0.003
40	A	438	LEU	0	0.014	0.011	6.901	-0.288	-0.288	0.000	0.000	0.000	0.000
41	A	439	ARG	1	0.912	0.939	9.284	-0.693	-0.693	0.000	0.000	0.000	0.000
42	A	440	LEU	0	-0.011	0.004	7.292	-0.154	-0.154	0.000	0.000	0.000	0.000
43	A	441	LEU	0	-0.033	-0.008	7.775	-0.208	-0.208	0.000	0.000	0.000	0.000
44	A	442	MET	0	-0.016	-0.002	11.139	-0.123	-0.123	0.000	0.000	0.000	0.000
45	A	443	ALA	0	0.006	0.004	13.810	-0.074	-0.074	0.000	0.000	0.000	0.000
46	A	444	ARG	1	0.779	0.865	7.574	-0.194	-0.194	0.000	0.000	0.000	0.000
47	A	445	VAL	0	0.055	0.038	14.341	-0.052	-0.052	0.000	0.000	0.000	0.000
48	A	446	ALA	0	-0.023	-0.006	16.404	-0.036	-0.036	0.000	0.000	0.000	0.000
49	A	447	GLU	-1	-0.895	-0.963	17.307	0.096	0.096	0.000	0.000	0.000	0.000
50	A	448	GLN	0	-0.055	-0.009	16.742	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	449	THR	0	0.066	0.011	20.542	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	450	GLY	0	-0.018	-0.030	23.526	0.007	0.007	0.000	0.000	0.000	0.000
53	A	451	LYN	0	-0.023	0.010	20.493	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	452	ASN	0	0.015	0.021	22.910	0.002	0.002	0.000	0.000	0.000	0.000
55	A	453	ASP	-1	-0.890	-0.947	22.921	0.129	0.129	0.000	0.000	0.000	0.000
56	A	454	LEU	0	-0.003	0.003	20.694	0.011	0.011	0.000	0.000	0.000	0.000
57	A	455	ALA	0	0.064	0.022	18.853	0.026	0.026	0.000	0.000	0.000	0.000
58	A	456	LEU	0	-0.034	-0.025	18.934	0.023	0.023	0.000	0.000	0.000	0.000
59	A	457	HIS	0	-0.021	-0.002	20.902	0.021	0.021	0.000	0.000	0.000	0.000
60	A	458	LEU	0	-0.002	-0.003	16.585	0.020	0.020	0.000	0.000	0.000	0.000
61	A	459	LEU	0	-0.011	-0.014	14.755	0.047	0.047	0.000	0.000	0.000	0.000
62	A	460	ALA	0	-0.025	-0.006	17.057	0.010	0.010	0.000	0.000	0.000	0.000
63	A	461	GLU	-1	-0.862	-0.925	16.462	0.392	0.392	0.000	0.000	0.000	0.000
64	A	462	LEU	0	-0.041	-0.023	11.575	0.016	0.016	0.000	0.000	0.000	0.000
65	A	463	ASP	-1	-0.788	-0.910	14.262	0.236	0.236	0.000	0.000	0.000	0.000
66	A	464	GLU	-1	-0.935	-0.949	16.457	0.203	0.203	0.000	0.000	0.000	0.000
67	A	465	ARG	1	0.823	0.901	11.984	-0.640	-0.640	0.000	0.000	0.000	0.000
68	A	466	ALA	0	0.016	0.021	12.969	0.017	0.017	0.000	0.000	0.000	0.000
69	A	467	THR	0	-0.038	-0.024	13.974	-0.034	-0.034	0.000	0.000	0.000	0.000
70	A	468	ARG	1	0.918	0.967	17.340	-0.304	-0.304	0.000	0.000	0.000	0.000
71	A	469	LEU	0	-0.028	-0.023	11.451	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	470	THR	0	-0.007	0.008	14.128	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	471	LEU	0	0.001	-0.006	8.372	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	472	SER	0	-0.041	-0.012	11.868	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	473	GLN	0	-0.035	-0.016	14.470	-0.054	-0.054	0.000	0.000	0.000	0.000
76	A	474	TRP	0	0.008	0.007	8.039	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	475	GLU	-1	-0.918	-0.966	5.099	0.223	0.328	-0.001	-0.002	-0.101	0.000
78	A	476	PRO	0	0.059	0.023	8.872	0.034	0.034	0.000	0.000	0.000	0.000
79	A	477	GLU	-1	-0.950	-0.973	8.868	-0.403	-0.403	0.000	0.000	0.000	0.000
80	A	478	LEU	0	0.007	0.006	4.765	0.032	0.085	-0.001	-0.001	-0.051	0.000
81	A	479	VAL	0	0.034	0.014	9.032	0.046	0.046	0.000	0.000	0.000	0.000
82	A	480	PHE	0	-0.005	-0.007	12.510	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	481	GLU	-1	-0.790	-0.864	9.545	0.134	0.134	0.000	0.000	0.000	0.000
84	A	482	VAL	0	0.008	0.005	11.512	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	483	LYS	1	0.945	0.971	14.100	-0.177	-0.177	0.000	0.000	0.000	0.000
86	A	484	ALA	0	0.015	0.012	16.545	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	485	ARG	1	0.792	0.883	12.398	-0.131	-0.131	0.000	0.000	0.000	0.000
88	A	486	ARG	1	0.936	0.965	17.750	-0.182	-0.182	0.000	0.000	0.000	0.000
89	A	487	LEU	0	0.009	0.010	19.824	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	488	LYS	1	0.947	0.968	19.293	-0.031	-0.031	0.000	0.000	0.000	0.000
91	A	489	LEU	0	0.038	0.009	20.051	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	490	LEU	0	-0.014	0.002	23.544	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	491	ARG	1	0.897	0.945	25.663	-0.041	-0.041	0.000	0.000	0.000	0.000
94	A	492	MET	0	-0.027	-0.015	24.740	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	493	LYS	1	0.905	0.961	27.752	-0.103	-0.103	0.000	0.000	0.000	0.000
96	A	494	SER	0	-0.009	-0.011	29.511	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	495	ALA	0	-0.002	0.008	31.150	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	496	LYS	1	0.931	0.974	29.829	-0.065	-0.065	0.000	0.000	0.000	0.000
99	A	497	THR	0	0.001	0.005	34.153	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	498	GLU	-1	-0.824	-0.923	35.276	0.040	0.040	0.000	0.000	0.000	0.000
101	A	499	SER	0	-0.074	-0.038	37.587	0.002	0.002	0.000	0.000	0.000	0.000
102	A	500	ASP	-1	-0.936	-0.992	33.039	0.067	0.067	0.000	0.000	0.000	0.000
103	A	501	ARG	1	0.978	1.006	33.172	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	502	VAL	0	0.002	0.005	33.768	0.001	0.001	0.000	0.000	0.000	0.000
105	A	503	ARG	1	0.912	0.959	32.871	-0.066	-0.066	0.000	0.000	0.000	0.000
106	A	504	LEU	0	0.003	-0.002	28.525	0.006	0.006	0.000	0.000	0.000	0.000
107	A	505	GLN	0	-0.051	-0.016	29.455	0.003	0.003	0.000	0.000	0.000	0.000
108	A	506	PRO	0	0.010	0.007	30.474	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	507	ASP	-1	-0.912	-0.958	26.032	0.110	0.110	0.000	0.000	0.000	0.000
110	A	508	MET	0	-0.037	-0.029	25.505	0.006	0.006	0.000	0.000	0.000	0.000
111	A	509	GLU	-1	-0.837	-0.920	26.028	0.047	0.047	0.000	0.000	0.000	0.000
112	A	510	HIS	0	-0.004	0.006	23.156	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	511	LEU	0	-0.040	-0.026	20.775	0.005	0.005	0.000	0.000	0.000	0.000
114	A	512	LEU	0	0.001	0.008	21.799	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	513	ALA	0	0.011	0.007	23.626	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	514	GLY	0	-0.005	-0.004	21.134	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	515	LEU	0	-0.045	-0.030	17.678	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	516	ILE	0	-0.017	-0.024	20.014	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	517	ALA	0	-0.051	-0.024	21.328	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	518	ILE	0	-0.078	-0.018	15.076	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	519	ASP	-1	-0.853	-0.935	17.285	-0.092	-0.092	0.000	0.000	0.000	0.000
122	A	520	ALA	0	0.076	0.035	19.332	0.001	0.001	0.000	0.000	0.000	0.000
123	A	521	ALA	0	-0.019	-0.004	21.887	0.002	0.002	0.000	0.000	0.000	0.000
124	A	522	ARG	1	0.919	0.958	13.273	0.105	0.105	0.000	0.000	0.000	0.000
125	A	523	ALA	0	-0.002	-0.003	20.586	0.004	0.004	0.000	0.000	0.000	0.000
126	A	524	ALA	0	0.015	0.013	22.159	0.007	0.007	0.000	0.000	0.000	0.000
127	A	525	VAL	0	-0.015	-0.012	23.099	0.005	0.005	0.000	0.000	0.000	0.000
128	A	526	LEU	0	-0.056	-0.013	20.617	0.004	0.004	0.000	0.000	0.000	0.000
129	A	527	CYS	0	0.021	0.012	25.172	0.010	0.010	0.000	0.000	0.000	0.000
130	A	528	ASN	0	-0.030	0.011	28.289	0.003	0.003	0.000	0.000	0.000	0.000
131	A	529	SER	0	-0.021	-0.013	29.225	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:399:ALA)