FMO DATABASE

FMODB ID: 2NGRR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1554794.513656
FMO2-HF: Nuclear repulsion	1489781.083658
FMO2-HF: Total energy	-65013.429998
FMO2-MP2: Total energy	-65201.454675

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.
-1.542	0.882	-0.007	-1.198	-1.219	0.004

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 : 0.016

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	310	THR	0	0.013	0.003	3.618	-1.476	0.820	-0.006	-1.195	-1.095	0.004
4	A	311	TYR	0	0.025	0.000	4.545	0.031	0.159	-0.001	-0.003	-0.124	0.000
5	A	312	ARG	1	0.948	0.983	8.991	0.556	0.556	0.000	0.000	0.000	0.000
6	A	313	TYR	0	0.088	0.045	12.695	0.047	0.047	0.000	0.000	0.000	0.000
7	A	314	PRO	0	0.005	-0.006	15.733	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	315	LEU	0	-0.028	0.006	11.274	0.026	0.026	0.000	0.000	0.000	0.000
9	A	316	GLU	-1	-0.858	-0.926	11.772	-0.391	-0.391	0.000	0.000	0.000	0.000
10	A	317	LEU	0	-0.028	-0.022	5.575	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	318	ASP	-1	-0.881	-0.957	9.030	-0.131	-0.131	0.000	0.000	0.000	0.000
12	A	319	THR	0	0.035	-0.010	7.877	0.048	0.048	0.000	0.000	0.000	0.000
13	A	320	ALA	0	-0.023	-0.005	9.389	0.071	0.071	0.000	0.000	0.000	0.000
14	A	321	ASN	0	-0.057	-0.044	11.090	0.062	0.062	0.000	0.000	0.000	0.000
15	A	322	ASN	0	-0.008	0.017	5.777	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	323	ARG	1	0.905	0.979	8.376	0.075	0.075	0.000	0.000	0.000	0.000
17	A	324	VAL	0	0.023	0.024	6.319	-0.091	-0.091	0.000	0.000	0.000	0.000
18	A	325	GLN	0	-0.039	-0.024	9.401	0.045	0.045	0.000	0.000	0.000	0.000
19	A	326	VAL	0	-0.006	-0.012	13.001	-0.065	-0.065	0.000	0.000	0.000	0.000
20	A	327	ALA	0	0.020	0.000	15.792	0.027	0.027	0.000	0.000	0.000	0.000
21	A	328	ASP	-1	-0.849	-0.927	17.666	-0.125	-0.125	0.000	0.000	0.000	0.000
22	A	329	ARG	1	0.814	0.910	17.478	0.292	0.292	0.000	0.000	0.000	0.000
23	A	330	PHE	0	-0.065	-0.019	19.955	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	331	GLY	0	0.106	0.065	22.038	0.005	0.005	0.000	0.000	0.000	0.000
25	A	332	MET	0	-0.066	-0.042	24.987	0.014	0.014	0.000	0.000	0.000	0.000
26	A	333	ARG	1	0.907	0.961	23.357	0.199	0.199	0.000	0.000	0.000	0.000
27	A	334	THR	0	0.057	0.023	27.652	0.002	0.002	0.000	0.000	0.000	0.000
28	A	335	GLY	0	0.017	0.020	30.634	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	336	THR	0	0.001	-0.018	33.261	0.006	0.006	0.000	0.000	0.000	0.000
30	A	337	TRP	0	-0.007	0.009	36.962	0.000	0.000	0.000	0.000	0.000	0.000
31	A	338	THR	0	-0.039	-0.029	38.923	0.006	0.006	0.000	0.000	0.000	0.000
32	A	339	GLY	0	0.047	0.020	42.261	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	340	GLN	0	-0.054	-0.030	44.660	0.003	0.003	0.000	0.000	0.000	0.000
34	A	341	LEU	0	0.033	0.029	45.542	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	342	GLN	0	-0.031	-0.024	46.564	0.002	0.002	0.000	0.000	0.000	0.000
36	A	343	TYR	0	0.026	0.031	49.241	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	344	GLN	0	-0.002	-0.038	49.052	0.001	0.001	0.000	0.000	0.000	0.000
38	A	345	HIS	0	0.087	0.043	52.918	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	346	PRO	0	0.004	-0.004	55.930	0.000	0.000	0.000	0.000	0.000	0.000
40	A	347	GLN	0	-0.038	-0.020	58.540	0.000	0.000	0.000	0.000	0.000	0.000
41	A	348	LEU	0	-0.035	-0.005	58.207	0.001	0.001	0.000	0.000	0.000	0.000
42	A	349	SER	0	0.015	0.001	55.161	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	350	TRP	0	-0.059	-0.011	51.911	0.000	0.000	0.000	0.000	0.000	0.000
44	A	351	ARG	1	0.953	0.962	49.084	0.061	0.061	0.000	0.000	0.000	0.000
45	A	352	ALA	0	-0.003	0.014	51.043	0.002	0.002	0.000	0.000	0.000	0.000
46	A	353	ASN	0	-0.034	-0.013	48.945	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	354	VAL	0	-0.001	0.003	44.822	0.002	0.002	0.000	0.000	0.000	0.000
48	A	355	THR	0	-0.025	-0.022	42.043	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	356	LEU	0	0.012	0.034	38.880	0.003	0.003	0.000	0.000	0.000	0.000
50	A	357	ASN	0	-0.009	-0.010	37.234	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	358	LEU	0	-0.016	-0.011	33.762	0.002	0.002	0.000	0.000	0.000	0.000
52	A	359	MET	0	-0.018	-0.025	31.491	0.001	0.001	0.000	0.000	0.000	0.000
53	A	360	LYS	1	0.888	0.975	26.522	0.180	0.180	0.000	0.000	0.000	0.000
54	A	361	VAL	0	-0.017	-0.017	27.356	0.001	0.001	0.000	0.000	0.000	0.000
55	A	362	ASP	-1	-0.870	-0.952	24.036	-0.133	-0.133	0.000	0.000	0.000	0.000
56	A	363	ASP	-1	-0.939	-0.970	23.638	-0.218	-0.218	0.000	0.000	0.000	0.000
57	A	364	TRP	0	-0.005	-0.003	26.445	0.011	0.011	0.000	0.000	0.000	0.000
58	A	365	LEU	0	-0.026	-0.010	29.607	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	366	VAL	0	-0.003	-0.006	32.111	0.008	0.008	0.000	0.000	0.000	0.000
60	A	367	LEU	0	0.013	0.004	34.871	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	368	SER	0	-0.031	-0.024	37.981	0.006	0.006	0.000	0.000	0.000	0.000
62	A	369	PHE	0	0.017	0.003	40.039	0.000	0.000	0.000	0.000	0.000	0.000
63	A	370	SER	0	0.025	0.009	43.683	0.003	0.003	0.000	0.000	0.000	0.000
64	A	371	GLN	0	0.002	-0.002	45.998	0.002	0.002	0.000	0.000	0.000	0.000
65	A	372	MET	0	-0.009	0.001	48.913	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	373	THR	0	-0.015	-0.013	51.778	0.002	0.002	0.000	0.000	0.000	0.000
67	A	374	THR	0	-0.017	0.002	52.541	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	375	ASN	0	0.007	-0.003	55.710	0.003	0.003	0.000	0.000	0.000	0.000
69	A	376	SER	0	0.067	0.025	57.639	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	377	ILE	0	-0.034	0.009	54.698	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	378	MET	0	0.029	0.027	57.717	0.002	0.002	0.000	0.000	0.000	0.000
72	A	379	ALA	0	0.005	-0.006	57.510	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	380	ASP	-1	-0.833	-0.896	54.669	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	381	GLY	0	-0.007	-0.003	53.580	0.000	0.000	0.000	0.000	0.000	0.000
75	A	382	LYS	1	0.903	0.964	48.305	0.065	0.065	0.000	0.000	0.000	0.000
76	A	383	PHE	0	-0.009	-0.018	46.691	0.002	0.002	0.000	0.000	0.000	0.000
77	A	384	VAL	0	-0.013	-0.001	44.617	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	385	ILE	0	-0.007	-0.012	40.419	0.003	0.003	0.000	0.000	0.000	0.000
79	A	386	ASN	0	0.029	0.020	41.313	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	387	PHE	0	0.050	0.007	36.337	0.001	0.001	0.000	0.000	0.000	0.000
81	A	388	VAL	0	-0.004	0.019	37.342	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	389	SER	0	-0.035	-0.024	38.195	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	390	GLY	0	0.039	0.022	39.318	0.003	0.003	0.000	0.000	0.000	0.000
84	A	391	LEU	0	-0.038	-0.005	33.281	0.003	0.003	0.000	0.000	0.000	0.000
85	A	392	SER	0	0.016	0.023	33.406	0.002	0.002	0.000	0.000	0.000	0.000
86	A	393	SER	0	0.023	-0.002	32.056	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	394	GLY	0	-0.032	-0.015	28.758	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	395	TRP	0	-0.073	-0.026	28.088	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	396	GLN	0	-0.039	-0.025	26.016	0.006	0.006	0.000	0.000	0.000	0.000
90	A	397	THR	0	0.021	0.002	30.707	0.000	0.000	0.000	0.000	0.000	0.000
91	A	398	GLY	0	0.048	0.024	30.095	0.005	0.005	0.000	0.000	0.000	0.000
92	A	399	ASP	-1	-0.900	-0.941	27.444	-0.200	-0.200	0.000	0.000	0.000	0.000
93	A	400	THR	0	-0.034	-0.035	29.432	0.005	0.005	0.000	0.000	0.000	0.000
94	A	401	GLU	-1	-0.896	-0.925	30.703	-0.152	-0.152	0.000	0.000	0.000	0.000
95	A	402	PRO	0	-0.012	-0.004	30.935	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	403	SER	0	-0.010	-0.004	28.791	0.000	0.000	0.000	0.000	0.000	0.000
97	A	404	SER	0	-0.057	-0.030	30.663	0.000	0.000	0.000	0.000	0.000	0.000
98	A	405	THR	0	0.054	0.014	33.890	0.001	0.001	0.000	0.000	0.000	0.000
99	A	406	ILE	0	-0.065	-0.024	36.012	0.005	0.005	0.000	0.000	0.000	0.000
100	A	407	ASP	-1	-0.800	-0.861	39.028	-0.075	-0.075	0.000	0.000	0.000	0.000
101	A	408	PRO	0	-0.070	-0.036	42.256	0.004	0.004	0.000	0.000	0.000	0.000
102	A	409	LEU	0	-0.014	-0.009	35.455	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	410	SER	0	-0.066	-0.075	37.930	0.002	0.002	0.000	0.000	0.000	0.000
104	A	411	THR	0	0.021	0.006	39.964	0.001	0.001	0.000	0.000	0.000	0.000
105	A	412	THR	0	-0.035	-0.012	42.480	0.002	0.002	0.000	0.000	0.000	0.000
106	A	413	PHE	0	0.009	0.005	44.474	0.001	0.001	0.000	0.000	0.000	0.000
107	A	414	ALA	0	0.017	0.026	46.954	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	415	ALA	0	-0.008	-0.006	49.051	0.002	0.002	0.000	0.000	0.000	0.000
109	A	416	VAL	0	0.014	-0.010	51.903	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	417	GLN	0	0.035	0.026	54.661	0.002	0.002	0.000	0.000	0.000	0.000
111	A	418	PHE	0	-0.007	-0.014	57.590	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	419	LEU	0	0.001	-0.004	59.406	0.002	0.002	0.000	0.000	0.000	0.000
113	A	420	ASN	0	0.045	0.023	62.803	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	421	ASN	0	-0.033	-0.016	66.186	0.000	0.000	0.000	0.000	0.000	0.000
115	A	422	GLY	0	0.050	0.030	68.127	0.000	0.000	0.000	0.000	0.000	0.000
116	A	423	GLN	0	-0.069	-0.039	66.848	0.000	0.000	0.000	0.000	0.000	0.000
117	A	424	ARG	1	0.931	0.956	58.088	0.033	0.033	0.000	0.000	0.000	0.000
118	A	425	ILE	0	-0.012	0.000	62.236	0.001	0.001	0.000	0.000	0.000	0.000
119	A	426	ASP	-1	-0.895	-0.927	58.226	-0.033	-0.033	0.000	0.000	0.000	0.000
120	A	427	ALA	0	-0.051	-0.026	57.356	0.001	0.001	0.000	0.000	0.000	0.000
121	A	428	PHE	0	0.004	0.007	52.505	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	429	ARG	1	0.749	0.846	51.576	0.044	0.044	0.000	0.000	0.000	0.000
123	A	430	ILE	0	-0.008	0.001	47.934	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	431	MET	0	-0.034	-0.017	45.560	0.001	0.001	0.000	0.000	0.000	0.000
125	A	432	GLY	0	0.054	0.009	44.026	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	433	VAL	0	-0.068	-0.029	38.258	0.000	0.000	0.000	0.000	0.000	0.000
127	A	434	SER	0	-0.064	-0.058	41.391	0.000	0.000	0.000	0.000	0.000	0.000
128	A	435	GLU	-1	-0.884	-0.932	40.569	-0.083	-0.083	0.000	0.000	0.000	0.000
129	A	436	TRP	0	-0.024	-0.043	34.108	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	437	THR	0	0.002	0.006	38.443	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	438	ASP	-1	-0.912	-0.942	37.289	-0.110	-0.110	0.000	0.000	0.000	0.000
132	A	439	GLY	0	-0.010	-0.023	36.789	0.002	0.002	0.000	0.000	0.000	0.000
133	A	440	GLU	-1	-0.973	-0.992	37.733	-0.080	-0.080	0.000	0.000	0.000	0.000
134	A	441	LEU	0	0.002	0.017	37.531	0.000	0.000	0.000	0.000	0.000	0.000
135	A	442	GLU	-1	-0.910	-0.965	40.517	-0.068	-0.068	0.000	0.000	0.000	0.000
136	A	443	ILE	0	0.006	-0.007	41.655	0.000	0.000	0.000	0.000	0.000	0.000
137	A	444	LYS	1	0.967	0.985	44.824	0.068	0.068	0.000	0.000	0.000	0.000
138	A	445	ASN	0	-0.035	0.001	47.861	0.001	0.001	0.000	0.000	0.000	0.000
139	A	446	TYR	0	0.021	-0.009	46.121	0.002	0.002	0.000	0.000	0.000	0.000
140	A	447	GLY	0	0.067	0.046	52.017	0.002	0.002	0.000	0.000	0.000	0.000
141	A	448	GLY	0	0.017	0.017	53.538	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	449	THR	0	0.000	-0.006	55.556	0.000	0.000	0.000	0.000	0.000	0.000
143	A	450	TYR	0	-0.035	-0.049	58.302	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	451	THR	0	-0.008	0.009	60.825	0.002	0.002	0.000	0.000	0.000	0.000
145	A	452	GLY	0	0.043	0.056	63.107	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	453	HIS	0	-0.063	-0.053	60.447	0.000	0.000	0.000	0.000	0.000	0.000
147	A	454	THR	0	-0.017	-0.015	64.274	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	455	GLN	0	0.014	0.004	60.226	0.000	0.000	0.000	0.000	0.000	0.000
149	A	456	VAL	0	-0.004	0.010	55.268	0.001	0.001	0.000	0.000	0.000	0.000
150	A	457	TYR	0	-0.044	-0.012	52.795	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	458	TRP	0	0.018	-0.011	50.274	0.000	0.000	0.000	0.000	0.000	0.000
152	A	459	ALA	0	0.037	0.019	50.553	0.000	0.000	0.000	0.000	0.000	0.000
153	A	460	PRO	0	-0.023	-0.034	45.657	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	461	TRP	0	0.001	0.000	44.122	0.001	0.001	0.000	0.000	0.000	0.000
155	A	462	THR	0	0.008	0.006	38.553	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	463	ILE	0	0.024	0.017	39.797	0.003	0.003	0.000	0.000	0.000	0.000
157	A	464	MET	0	-0.021	0.014	33.881	-0.004	-0.004	0.000	0.000	0.000	0.000
158	A	465	TYR	0	-0.053	-0.006	33.969	0.009	0.009	0.000	0.000	0.000	0.000
159	A	466	PRO	0	0.051	0.023	30.867	-0.005	-0.005	0.000	0.000	0.000	0.000
160	A	467	CYS	0	-0.031	-0.023	29.259	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	468	ASN	0	0.055	0.032	24.259	0.002	0.002	0.000	0.000	0.000	0.000
162	A	469	VAL	0	-0.025	-0.005	20.042	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:308:LEU)