FMO DATABASE

FMODB ID: 2JJ8R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1109550.307284
FMO2-HF: Nuclear repulsion	1058403.78872
FMO2-HF: Total energy	-51146.518564
FMO2-MP2: Total energy	-51295.923882

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.
-11.885	-17.115	19.188	-7.32	-6.639	0.016

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 : 0.001 / q_NPA : 0.005

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	0.006	0.022	3.878	-0.629	1.065	-0.018	-0.844	-0.833	-0.001
4	A	402	SER	0	-0.001	-0.041	1.852	-7.454	-15.656	16.126	-5.291	-2.633	0.021
5	A	403	LEU	0	-0.041	-0.004	4.037	-1.377	-1.215	0.000	-0.032	-0.130	0.000
6	A	404	GLU	-1	-0.801	-0.896	6.878	1.073	1.073	0.000	0.000	0.000	0.000
7	A	405	PRO	0	-0.016	-0.008	9.890	-0.076	-0.076	0.000	0.000	0.000	0.000
8	A	406	GLU	-1	-0.783	-0.873	12.818	0.449	0.449	0.000	0.000	0.000	0.000
9	A	407	ALA	0	0.056	0.029	13.653	-0.046	-0.046	0.000	0.000	0.000	0.000
10	A	408	LEU	0	-0.059	-0.023	14.697	-0.036	-0.036	0.000	0.000	0.000	0.000
11	A	409	GLN	0	0.029	0.009	16.491	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	410	ILE	0	0.025	0.021	18.048	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	411	ALA	0	-0.065	-0.036	19.259	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	412	ASP	-1	-0.945	-0.960	21.032	0.203	0.203	0.000	0.000	0.000	0.000
15	A	413	ASN	0	-0.131	-0.075	22.740	-0.036	-0.036	0.000	0.000	0.000	0.000
16	A	414	GLU	-1	-0.914	-0.950	23.807	0.198	0.198	0.000	0.000	0.000	0.000
17	A	415	GLY	0	0.003	0.008	25.334	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	416	THR	0	0.028	-0.021	21.330	0.019	0.019	0.000	0.000	0.000	0.000
19	A	417	GLU	-1	-0.979	-0.983	21.274	0.232	0.232	0.000	0.000	0.000	0.000
20	A	418	ALA	0	0.057	0.039	21.861	0.022	0.022	0.000	0.000	0.000	0.000
21	A	419	ALA	0	0.031	0.026	18.059	0.025	0.025	0.000	0.000	0.000	0.000
22	A	420	LEU	0	-0.046	-0.028	16.902	0.069	0.069	0.000	0.000	0.000	0.000
23	A	421	SER	0	0.015	0.006	17.227	0.048	0.048	0.000	0.000	0.000	0.000
24	A	422	TRP	0	-0.005	-0.019	16.432	0.019	0.019	0.000	0.000	0.000	0.000
25	A	423	LEU	0	-0.033	-0.010	11.782	0.059	0.059	0.000	0.000	0.000	0.000
26	A	424	GLN	0	-0.048	-0.051	13.531	0.053	0.053	0.000	0.000	0.000	0.000
27	A	425	ALA	0	-0.016	0.014	15.792	-0.035	-0.035	0.000	0.000	0.000	0.000
28	A	426	ARG	1	0.751	0.839	10.509	-0.742	-0.742	0.000	0.000	0.000	0.000
29	A	427	PRO	0	0.000	0.007	11.936	-0.060	-0.060	0.000	0.000	0.000	0.000
30	A	428	GLY	0	0.027	0.019	12.418	0.073	0.073	0.000	0.000	0.000	0.000
31	A	429	ILE	0	-0.049	-0.030	8.036	-0.051	-0.051	0.000	0.000	0.000	0.000
32	A	430	GLN	0	0.029	0.005	10.769	0.017	0.017	0.000	0.000	0.000	0.000
33	A	431	SER	0	-0.020	0.001	7.851	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	432	ASP	-1	-0.773	-0.881	8.720	0.596	0.596	0.000	0.000	0.000	0.000
35	A	433	ARG	1	0.853	0.907	3.033	-0.469	0.459	0.917	-0.515	-1.330	-0.004
36	A	434	SER	0	0.000	-0.019	4.925	0.291	0.291	0.000	0.000	0.000	0.000
37	A	435	ASN	0	0.016	0.026	5.820	0.181	0.181	0.000	0.000	0.000	0.000
38	A	436	TRP	0	0.015	-0.004	7.405	0.068	0.068	0.000	0.000	0.000	0.000
39	A	437	LEU	0	-0.005	-0.010	2.426	-0.419	-0.495	2.164	-0.577	-1.511	0.000
40	A	438	LEU	0	0.014	0.017	6.508	0.036	0.036	0.000	0.000	0.000	0.000
41	A	439	ARG	1	0.860	0.890	8.794	-0.652	-0.652	0.000	0.000	0.000	0.000
42	A	440	LEU	0	0.018	0.005	7.178	-0.161	-0.161	0.000	0.000	0.000	0.000
43	A	441	LEU	0	-0.059	-0.020	7.580	-0.177	-0.177	0.000	0.000	0.000	0.000
44	A	442	MET	0	-0.021	0.003	10.738	-0.189	-0.189	0.000	0.000	0.000	0.000
45	A	443	ALA	0	0.012	0.000	13.235	-0.096	-0.096	0.000	0.000	0.000	0.000
46	A	444	ARG	1	0.787	0.861	6.664	-1.106	-1.106	0.000	0.000	0.000	0.000
47	A	445	VAL	0	0.072	0.049	13.834	-0.085	-0.085	0.000	0.000	0.000	0.000
48	A	446	ALA	0	-0.014	-0.001	16.157	-0.068	-0.068	0.000	0.000	0.000	0.000
49	A	447	GLU	-1	-0.857	-0.906	16.772	0.212	0.212	0.000	0.000	0.000	0.000
50	A	448	GLN	0	-0.043	-0.025	16.066	0.015	0.015	0.000	0.000	0.000	0.000
51	A	449	THR	0	0.063	0.034	20.205	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	450	GLY	0	-0.020	-0.016	23.362	0.009	0.009	0.000	0.000	0.000	0.000
53	A	451	LYN	0	-0.024	-0.013	20.312	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	452	ASN	0	-0.022	-0.023	22.908	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	453	ASP	-1	-0.744	-0.845	22.654	0.159	0.159	0.000	0.000	0.000	0.000
56	A	454	LEU	0	0.007	0.005	20.663	0.006	0.006	0.000	0.000	0.000	0.000
57	A	455	ALA	0	0.058	0.024	18.502	0.025	0.025	0.000	0.000	0.000	0.000
58	A	456	LEU	0	-0.034	-0.014	18.730	0.016	0.016	0.000	0.000	0.000	0.000
59	A	457	HIS	0	-0.031	-0.016	20.561	0.006	0.006	0.000	0.000	0.000	0.000
60	A	458	LEU	0	-0.003	0.000	16.266	0.005	0.005	0.000	0.000	0.000	0.000
61	A	459	LEU	0	-0.008	-0.004	14.474	0.030	0.030	0.000	0.000	0.000	0.000
62	A	460	ALA	0	-0.004	-0.002	16.816	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	461	GLU	-1	-0.823	-0.875	15.770	0.383	0.383	0.000	0.000	0.000	0.000
64	A	462	LEU	0	-0.009	-0.003	11.272	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	463	ASP	-1	-0.747	-0.855	14.025	0.124	0.124	0.000	0.000	0.000	0.000
66	A	464	GLU	-1	-0.844	-0.884	16.300	0.102	0.102	0.000	0.000	0.000	0.000
67	A	465	ARG	1	0.743	0.839	12.171	-0.476	-0.476	0.000	0.000	0.000	0.000
68	A	466	ALA	0	0.015	0.007	12.522	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	467	THR	0	-0.044	-0.033	13.694	-0.050	-0.050	0.000	0.000	0.000	0.000
70	A	468	ARG	1	0.843	0.901	17.260	-0.180	-0.180	0.000	0.000	0.000	0.000
71	A	469	LEU	0	-0.040	-0.015	11.350	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	470	THR	0	-0.008	-0.002	14.175	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	471	LEU	0	0.012	0.022	8.336	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	472	SER	0	-0.022	-0.017	12.036	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	473	GLN	0	-0.029	-0.023	14.454	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	474	TRP	0	-0.030	-0.020	8.651	-0.058	-0.058	0.000	0.000	0.000	0.000
77	A	475	GLU	-1	-0.814	-0.882	4.224	-1.352	-1.088	-0.001	-0.061	-0.202	0.000
78	A	476	PRO	0	0.063	0.034	8.626	0.060	0.060	0.000	0.000	0.000	0.000
79	A	477	GLU	-1	-0.803	-0.868	8.605	-0.182	-0.182	0.000	0.000	0.000	0.000
80	A	478	LEU	0	-0.008	0.006	4.894	0.149	0.149	0.000	0.000	0.000	0.000
81	A	479	VAL	0	0.039	0.013	9.005	0.112	0.112	0.000	0.000	0.000	0.000
82	A	480	PHE	0	0.013	0.006	12.633	0.028	0.028	0.000	0.000	0.000	0.000
83	A	481	GLU	-1	-0.750	-0.831	9.221	0.491	0.491	0.000	0.000	0.000	0.000
84	A	482	VAL	0	0.000	0.000	11.461	0.023	0.023	0.000	0.000	0.000	0.000
85	A	483	LYS	1	0.903	0.927	13.952	-0.108	-0.108	0.000	0.000	0.000	0.000
86	A	484	ALA	0	0.013	0.021	16.209	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	485	ARG	1	0.752	0.844	11.947	-0.360	-0.360	0.000	0.000	0.000	0.000
88	A	486	ARG	1	0.851	0.905	17.563	-0.156	-0.156	0.000	0.000	0.000	0.000
89	A	487	LEU	0	0.021	0.017	19.666	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	488	LYS	1	0.869	0.925	18.509	-0.171	-0.171	0.000	0.000	0.000	0.000
91	A	489	LEU	0	0.022	-0.002	19.864	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	490	LEU	0	-0.016	0.004	23.302	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	491	ARG	1	0.897	0.941	25.512	-0.062	-0.062	0.000	0.000	0.000	0.000
94	A	492	MET	0	-0.045	-0.024	24.394	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	493	LYS	1	0.849	0.916	27.394	-0.127	-0.127	0.000	0.000	0.000	0.000
96	A	494	SER	0	0.025	-0.005	29.108	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	495	ALA	0	-0.047	-0.018	30.847	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	496	LYS	1	0.889	0.961	28.135	-0.118	-0.118	0.000	0.000	0.000	0.000
99	A	497	THR	0	-0.039	-0.039	33.651	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	498	GLU	-1	-0.749	-0.866	35.057	0.055	0.055	0.000	0.000	0.000	0.000
101	A	499	SER	0	-0.068	-0.029	37.296	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	500	ASP	-1	-0.802	-0.891	32.417	0.083	0.083	0.000	0.000	0.000	0.000
103	A	501	ARG	1	0.897	0.953	33.037	-0.051	-0.051	0.000	0.000	0.000	0.000
104	A	502	VAL	0	-0.015	-0.012	33.429	0.000	0.000	0.000	0.000	0.000	0.000
105	A	503	ARG	1	0.827	0.915	33.249	-0.075	-0.075	0.000	0.000	0.000	0.000
106	A	504	LEU	0	0.000	-0.004	28.258	0.005	0.005	0.000	0.000	0.000	0.000
107	A	505	GLN	0	-0.073	-0.051	29.117	0.004	0.004	0.000	0.000	0.000	0.000
108	A	506	PRO	0	0.027	0.010	29.989	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	507	ASP	-1	-0.819	-0.897	24.883	0.112	0.112	0.000	0.000	0.000	0.000
110	A	508	MET	0	-0.036	-0.024	25.196	0.004	0.004	0.000	0.000	0.000	0.000
111	A	509	GLU	-1	-0.810	-0.895	25.660	0.042	0.042	0.000	0.000	0.000	0.000
112	A	510	HIS	0	-0.028	0.000	23.360	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	511	LEU	0	-0.024	-0.023	20.491	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	512	LEU	0	0.005	0.004	21.620	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	513	ALA	0	0.006	-0.002	23.438	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	514	GLY	0	0.002	-0.004	20.880	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	515	LEU	0	-0.040	-0.022	17.483	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	516	ILE	0	-0.011	-0.024	19.897	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	517	ALA	0	-0.052	-0.023	21.218	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	518	ILE	0	-0.065	-0.012	15.009	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	519	ASP	-1	-0.839	-0.933	17.709	-0.125	-0.125	0.000	0.000	0.000	0.000
122	A	520	ALA	0	0.061	0.024	19.603	0.013	0.013	0.000	0.000	0.000	0.000
123	A	521	ALA	0	-0.036	-0.004	22.248	0.009	0.009	0.000	0.000	0.000	0.000
124	A	522	ARG	1	0.768	0.842	12.957	0.156	0.156	0.000	0.000	0.000	0.000
125	A	523	ALA	0	0.019	0.007	20.585	0.014	0.014	0.000	0.000	0.000	0.000
126	A	524	ALA	0	0.027	0.018	22.131	0.011	0.011	0.000	0.000	0.000	0.000
127	A	525	VAL	0	-0.018	-0.013	22.952	0.006	0.006	0.000	0.000	0.000	0.000
128	A	526	LEU	0	-0.021	0.002	20.953	0.009	0.009	0.000	0.000	0.000	0.000
129	A	527	CYS	0	-0.027	0.000	25.079	0.007	0.007	0.000	0.000	0.000	0.000
130	A	528	ASN	0	-0.030	0.007	28.119	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	529	SER	0	-0.005	-0.010	28.504	0.005	0.005	0.000	0.000	0.000	0.000

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