FMO DATABASE

FMODB ID: 6Y57Z

Calculation Name: 4ODB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ODB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y624

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1555098.756167
FMO2-HF: Nuclear repulsion	1490084.085743
FMO2-HF: Total energy	-65014.670423
FMO2-MP2: Total energy	-65202.626025

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:308:LEU)

Summations of interaction energy for fragment #1(A:308:LEU)

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.
-1.425	0.964	-0.011	-1.186	-1.191	0.005

Interaction energy analysis for fragmet #1(A:308:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.015

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	310	THR	0	0.006	-0.006	3.680	-1.406	0.862	-0.010	-1.184	-1.074	0.005
4	A	311	TYR	0	0.027	0.003	4.796	0.063	0.184	-0.001	-0.002	-0.117	0.000
5	A	312	ARG	1	0.942	0.980	9.052	0.536	0.536	0.000	0.000	0.000	0.000
6	A	313	TYR	0	0.087	0.048	12.775	0.041	0.041	0.000	0.000	0.000	0.000
7	A	314	PRO	0	0.011	-0.001	15.791	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	315	LEU	0	-0.021	0.009	11.817	0.026	0.026	0.000	0.000	0.000	0.000
9	A	316	GLU	-1	-0.811	-0.878	11.773	-0.379	-0.379	0.000	0.000	0.000	0.000
10	A	317	LEU	0	-0.020	-0.011	5.976	0.004	0.004	0.000	0.000	0.000	0.000
11	A	318	ASP	-1	-0.845	-0.931	9.463	-0.086	-0.086	0.000	0.000	0.000	0.000
12	A	319	THR	0	0.027	-0.015	8.267	0.045	0.045	0.000	0.000	0.000	0.000
13	A	320	ALA	0	-0.032	-0.010	9.605	0.070	0.070	0.000	0.000	0.000	0.000
14	A	321	ASN	0	-0.085	-0.059	11.357	0.062	0.062	0.000	0.000	0.000	0.000
15	A	322	ASN	0	-0.026	0.007	6.028	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	323	ARG	1	0.935	0.986	8.459	0.048	0.048	0.000	0.000	0.000	0.000
17	A	324	VAL	0	0.026	0.031	6.712	-0.088	-0.088	0.000	0.000	0.000	0.000
18	A	325	GLN	0	-0.057	-0.037	9.761	0.036	0.036	0.000	0.000	0.000	0.000
19	A	326	VAL	0	0.006	-0.002	13.455	-0.061	-0.061	0.000	0.000	0.000	0.000
20	A	327	ALA	0	0.021	-0.004	16.271	0.028	0.028	0.000	0.000	0.000	0.000
21	A	328	ASP	-1	-0.873	-0.940	18.163	-0.122	-0.122	0.000	0.000	0.000	0.000
22	A	329	ARG	1	0.766	0.851	17.170	0.278	0.278	0.000	0.000	0.000	0.000
23	A	330	PHE	0	-0.056	-0.010	20.336	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	331	GLY	0	0.099	0.059	22.402	0.005	0.005	0.000	0.000	0.000	0.000
25	A	332	MET	0	-0.077	-0.047	25.391	0.014	0.014	0.000	0.000	0.000	0.000
26	A	333	ARG	1	0.896	0.948	23.877	0.181	0.181	0.000	0.000	0.000	0.000
27	A	334	THR	0	0.037	0.018	27.713	0.001	0.001	0.000	0.000	0.000	0.000
28	A	335	GLY	0	0.035	0.026	30.699	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	336	THR	0	0.006	-0.006	33.330	0.005	0.005	0.000	0.000	0.000	0.000
30	A	337	TRP	0	-0.024	0.001	37.037	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	338	THR	0	-0.032	-0.027	39.010	0.004	0.004	0.000	0.000	0.000	0.000
32	A	339	GLY	0	0.047	0.015	42.353	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	340	GLN	0	-0.065	-0.030	44.758	0.003	0.003	0.000	0.000	0.000	0.000
34	A	341	LEU	0	0.024	0.022	45.835	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	342	GLN	0	-0.017	-0.010	46.650	0.005	0.005	0.000	0.000	0.000	0.000
36	A	343	TYR	0	0.006	0.012	49.322	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	344	GLN	0	0.022	-0.014	49.163	0.001	0.001	0.000	0.000	0.000	0.000
38	A	345	HIS	0	0.047	0.009	53.001	0.000	0.000	0.000	0.000	0.000	0.000
39	A	346	PRO	0	0.000	-0.005	56.007	0.000	0.000	0.000	0.000	0.000	0.000
40	A	347	GLN	0	-0.037	-0.010	58.625	0.001	0.001	0.000	0.000	0.000	0.000
41	A	348	LEU	0	-0.041	-0.013	58.541	0.001	0.001	0.000	0.000	0.000	0.000
42	A	349	SER	0	0.004	0.006	55.022	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	350	TRP	0	-0.033	-0.017	52.035	0.000	0.000	0.000	0.000	0.000	0.000
44	A	351	ARG	1	0.879	0.925	49.196	0.059	0.059	0.000	0.000	0.000	0.000
45	A	352	ALA	0	0.003	0.015	51.126	0.002	0.002	0.000	0.000	0.000	0.000
46	A	353	ASN	0	0.000	0.004	49.039	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	354	VAL	0	0.012	0.009	44.832	0.002	0.002	0.000	0.000	0.000	0.000
48	A	355	THR	0	0.016	-0.003	42.384	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	356	LEU	0	-0.023	0.020	38.847	0.003	0.003	0.000	0.000	0.000	0.000
50	A	357	ASN	0	-0.012	-0.009	37.358	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	358	LEU	0	-0.006	-0.008	33.696	0.001	0.001	0.000	0.000	0.000	0.000
52	A	359	MET	0	-0.026	-0.029	31.615	0.001	0.001	0.000	0.000	0.000	0.000
53	A	360	LYS	1	0.811	0.927	26.533	0.169	0.169	0.000	0.000	0.000	0.000
54	A	361	VAL	0	-0.017	-0.013	27.796	0.001	0.001	0.000	0.000	0.000	0.000
55	A	362	ASP	-1	-0.873	-0.957	24.476	-0.125	-0.125	0.000	0.000	0.000	0.000
56	A	363	ASP	-1	-0.906	-0.941	23.913	-0.209	-0.209	0.000	0.000	0.000	0.000
57	A	364	TRP	0	0.000	-0.002	26.703	0.010	0.010	0.000	0.000	0.000	0.000
58	A	365	LEU	0	-0.036	-0.003	29.787	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	366	VAL	0	0.006	-0.005	32.194	0.007	0.007	0.000	0.000	0.000	0.000
60	A	367	LEU	0	0.015	0.005	35.067	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	368	SER	0	-0.026	-0.022	38.060	0.005	0.005	0.000	0.000	0.000	0.000
62	A	369	PHE	0	0.019	0.004	40.218	0.000	0.000	0.000	0.000	0.000	0.000
63	A	370	SER	0	0.019	0.007	43.801	0.003	0.003	0.000	0.000	0.000	0.000
64	A	371	GLN	0	-0.003	0.012	46.146	0.001	0.001	0.000	0.000	0.000	0.000
65	A	372	MET	0	-0.004	-0.002	49.106	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	373	THR	0	-0.005	-0.005	51.824	0.002	0.002	0.000	0.000	0.000	0.000
67	A	374	THR	0	-0.015	0.002	52.558	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	375	ASN	0	0.008	-0.001	55.771	0.003	0.003	0.000	0.000	0.000	0.000
69	A	376	SER	0	0.047	0.016	57.699	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	377	ILE	0	-0.022	0.011	54.815	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	378	MET	0	0.029	0.021	57.762	0.002	0.002	0.000	0.000	0.000	0.000
72	A	379	ALA	0	-0.002	-0.007	57.559	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	380	ASP	-1	-0.785	-0.888	54.711	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	381	GLY	0	0.020	0.031	53.642	0.000	0.000	0.000	0.000	0.000	0.000
75	A	382	LYS	1	0.792	0.883	48.365	0.063	0.063	0.000	0.000	0.000	0.000
76	A	383	PHE	0	-0.021	-0.015	46.870	0.002	0.002	0.000	0.000	0.000	0.000
77	A	384	VAL	0	-0.015	-0.001	44.590	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	385	ILE	0	-0.033	-0.019	40.327	0.003	0.003	0.000	0.000	0.000	0.000
79	A	386	ASN	0	-0.018	-0.018	41.407	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	387	PHE	0	0.065	0.010	36.434	0.001	0.001	0.000	0.000	0.000	0.000
81	A	388	VAL	0	-0.009	0.006	37.457	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	389	SER	0	-0.058	-0.028	38.327	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	390	GLY	0	0.064	0.029	39.436	0.003	0.003	0.000	0.000	0.000	0.000
84	A	391	LEU	0	-0.041	-0.003	33.460	0.003	0.003	0.000	0.000	0.000	0.000
85	A	392	SER	0	-0.005	-0.002	33.205	0.001	0.001	0.000	0.000	0.000	0.000
86	A	393	SER	0	-0.005	0.001	32.591	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	394	GLY	0	0.001	-0.006	28.873	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	395	TRP	0	-0.075	-0.035	28.202	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	396	GLN	0	-0.006	0.007	25.830	0.004	0.004	0.000	0.000	0.000	0.000
90	A	397	THR	0	0.045	0.020	30.829	0.000	0.000	0.000	0.000	0.000	0.000
91	A	398	GLY	0	0.053	0.032	30.216	0.004	0.004	0.000	0.000	0.000	0.000
92	A	399	ASP	-1	-0.834	-0.928	27.146	-0.196	-0.196	0.000	0.000	0.000	0.000
93	A	400	THR	0	0.003	-0.014	29.528	0.005	0.005	0.000	0.000	0.000	0.000
94	A	401	GLU	-1	-0.888	-0.918	30.666	-0.149	-0.149	0.000	0.000	0.000	0.000
95	A	402	PRO	0	-0.004	0.000	31.009	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	403	SER	0	-0.021	-0.001	29.029	0.000	0.000	0.000	0.000	0.000	0.000
97	A	404	SER	0	-0.041	-0.024	30.718	0.000	0.000	0.000	0.000	0.000	0.000
98	A	405	THR	0	0.049	0.014	33.913	0.001	0.001	0.000	0.000	0.000	0.000
99	A	406	ILE	0	-0.060	-0.022	35.991	0.005	0.005	0.000	0.000	0.000	0.000
100	A	407	ASP	-1	-0.771	-0.843	39.038	-0.071	-0.071	0.000	0.000	0.000	0.000
101	A	408	PRO	0	-0.051	-0.031	42.296	0.004	0.004	0.000	0.000	0.000	0.000
102	A	409	LEU	0	-0.033	-0.014	35.701	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	410	SER	0	-0.047	-0.063	38.249	0.002	0.002	0.000	0.000	0.000	0.000
104	A	411	THR	0	0.016	0.001	40.242	0.001	0.001	0.000	0.000	0.000	0.000
105	A	412	THR	0	-0.043	-0.013	42.902	0.002	0.002	0.000	0.000	0.000	0.000
106	A	413	PHE	0	0.010	0.006	44.873	0.001	0.001	0.000	0.000	0.000	0.000
107	A	414	ALA	0	0.009	0.016	47.376	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	415	ALA	0	-0.013	-0.004	49.390	0.002	0.002	0.000	0.000	0.000	0.000
109	A	416	VAL	0	0.027	-0.001	52.311	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	417	GLN	0	-0.027	-0.027	54.963	0.001	0.001	0.000	0.000	0.000	0.000
111	A	418	PHE	0	-0.007	-0.016	57.605	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	419	LEU	0	0.000	-0.002	59.603	0.002	0.002	0.000	0.000	0.000	0.000
113	A	420	ASN	0	0.028	0.013	62.960	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	421	ASN	0	-0.040	-0.020	66.316	0.000	0.000	0.000	0.000	0.000	0.000
115	A	422	GLY	0	0.054	0.031	68.257	0.000	0.000	0.000	0.000	0.000	0.000
116	A	423	GLN	0	-0.048	-0.024	67.196	0.000	0.000	0.000	0.000	0.000	0.000
117	A	424	ARG	1	0.934	0.956	58.291	0.032	0.032	0.000	0.000	0.000	0.000
118	A	425	ILE	0	-0.009	0.007	62.490	0.001	0.001	0.000	0.000	0.000	0.000
119	A	426	ASP	-1	-0.830	-0.880	58.768	-0.032	-0.032	0.000	0.000	0.000	0.000
120	A	427	ALA	0	-0.056	-0.029	57.761	0.001	0.001	0.000	0.000	0.000	0.000
121	A	428	PHE	0	0.010	0.013	53.003	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	429	ARG	1	0.762	0.870	51.669	0.042	0.042	0.000	0.000	0.000	0.000
123	A	430	ILE	0	-0.007	-0.002	48.358	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	431	MET	0	-0.048	-0.016	45.800	0.000	0.000	0.000	0.000	0.000	0.000
125	A	432	GLY	0	0.057	0.018	44.204	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	433	VAL	0	-0.063	-0.026	38.384	0.000	0.000	0.000	0.000	0.000	0.000
127	A	434	SER	0	-0.069	-0.058	41.433	0.000	0.000	0.000	0.000	0.000	0.000
128	A	435	GLU	-1	-0.855	-0.917	40.620	-0.077	-0.077	0.000	0.000	0.000	0.000
129	A	436	TRP	0	0.004	-0.026	34.098	0.000	0.000	0.000	0.000	0.000	0.000
130	A	437	THR	0	0.001	0.004	38.537	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	438	ASP	-1	-0.908	-0.942	37.405	-0.107	-0.107	0.000	0.000	0.000	0.000
132	A	439	GLY	0	-0.004	-0.018	36.897	0.002	0.002	0.000	0.000	0.000	0.000
133	A	440	GLU	-1	-0.890	-0.944	37.845	-0.075	-0.075	0.000	0.000	0.000	0.000
134	A	441	LEU	0	0.001	0.012	37.767	0.000	0.000	0.000	0.000	0.000	0.000
135	A	442	GLU	-1	-0.801	-0.895	40.599	-0.063	-0.063	0.000	0.000	0.000	0.000
136	A	443	ILE	0	-0.011	-0.016	41.663	0.000	0.000	0.000	0.000	0.000	0.000
137	A	444	LYS	1	0.865	0.930	44.881	0.070	0.070	0.000	0.000	0.000	0.000
138	A	445	ASN	0	-0.035	-0.006	47.907	0.001	0.001	0.000	0.000	0.000	0.000
139	A	446	TYR	0	0.039	-0.002	46.116	0.002	0.002	0.000	0.000	0.000	0.000
140	A	447	GLY	0	0.042	0.033	52.116	0.002	0.002	0.000	0.000	0.000	0.000
141	A	448	GLY	0	0.016	0.011	53.764	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	449	THR	0	-0.005	-0.006	55.862	0.000	0.000	0.000	0.000	0.000	0.000
143	A	450	TYR	0	-0.030	-0.037	58.577	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	451	THR	0	-0.003	0.006	61.062	0.002	0.002	0.000	0.000	0.000	0.000
145	A	452	GLY	0	0.021	0.038	63.242	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	453	HIS	0	-0.058	-0.044	60.389	0.000	0.000	0.000	0.000	0.000	0.000
147	A	454	THR	0	-0.007	-0.006	64.329	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	455	GLN	0	-0.011	-0.008	60.268	0.000	0.000	0.000	0.000	0.000	0.000
149	A	456	VAL	0	0.000	0.006	55.632	0.001	0.001	0.000	0.000	0.000	0.000
150	A	457	TYR	0	-0.032	-0.017	53.504	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	458	TRP	0	0.019	-0.016	50.446	0.000	0.000	0.000	0.000	0.000	0.000
152	A	459	ALA	0	0.031	0.017	51.054	0.000	0.000	0.000	0.000	0.000	0.000
153	A	460	PRO	0	-0.016	-0.029	45.964	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	461	TRP	0	0.016	0.006	44.809	0.001	0.001	0.000	0.000	0.000	0.000
155	A	462	THR	0	-0.007	-0.008	38.768	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	463	ILE	0	0.016	0.014	40.042	0.003	0.003	0.000	0.000	0.000	0.000
157	A	464	MET	0	-0.014	0.014	34.458	-0.004	-0.004	0.000	0.000	0.000	0.000
158	A	465	TYR	0	-0.042	-0.010	33.998	0.009	0.009	0.000	0.000	0.000	0.000
159	A	466	PRO	0	0.055	0.025	30.983	-0.005	-0.005	0.000	0.000	0.000	0.000
160	A	467	CYS	0	-0.066	-0.043	29.522	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	468	ASN	0	0.003	-0.004	24.351	-0.001	-0.001	0.000	0.000	0.000	0.000
162	A	469	VAL	0	-0.032	-0.009	20.067	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:308:LEU)