FMO DATABASE

FMODB ID: 853RY

Calculation Name: 2DYQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DYQ

Chain ID: A

ChEMBL ID:

UniProt ID: O95704

Base Structure: X-ray

Registration Date: 2023-09-20

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1057278.021349
FMO2-HF: Nuclear repulsion	1005900.283343
FMO2-HF: Total energy	-51377.738005
FMO2-MP2: Total energy	-51520.480404

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:288:ALA)

Summations of interaction energy for fragment #1(A:288: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.
-8.273	-7.669	8.809	-5.513	-3.899	-0.034

Interaction energy analysis for fragmet #1(A:288:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : 0.003

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

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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	290	LYS	1	0.924	0.960	3.882	1.540	3.814	-0.019	-1.323	-0.932	0.005
4	A	291	TYR	0	0.009	-0.009	7.044	-0.013	-0.013	0.000	0.000	0.000	0.000
5	A	292	GLU	-1	-0.892	-0.929	10.195	-0.293	-0.293	0.000	0.000	0.000	0.000
6	A	293	ALA	0	-0.005	-0.010	13.303	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	294	LEU	0	-0.015	0.004	15.413	0.043	0.043	0.000	0.000	0.000	0.000
8	A	295	TYR	0	0.015	0.007	16.622	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	296	MET	0	-0.006	-0.011	18.276	0.015	0.015	0.000	0.000	0.000	0.000
10	A	297	GLY	0	0.005	0.015	20.347	0.016	0.016	0.000	0.000	0.000	0.000
11	A	298	THR	0	-0.060	-0.062	20.005	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	299	LEU	0	0.000	0.009	21.981	0.013	0.013	0.000	0.000	0.000	0.000
13	A	300	PRO	0	0.030	0.022	24.150	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	301	VAL	0	0.010	0.002	24.393	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	302	THR	0	0.005	-0.008	27.175	0.005	0.005	0.000	0.000	0.000	0.000
16	A	303	LYS	1	0.907	0.955	27.559	0.075	0.075	0.000	0.000	0.000	0.000
17	A	304	ALA	0	0.019	0.020	23.310	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	305	MET	0	-0.007	0.003	22.524	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	306	GLY	0	0.072	0.031	24.172	0.014	0.014	0.000	0.000	0.000	0.000
20	A	307	MET	0	0.024	0.023	21.822	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	308	ASP	-1	-0.843	-0.923	25.596	-0.105	-0.105	0.000	0.000	0.000	0.000
22	A	309	VAL	0	-0.003	-0.004	25.916	0.001	0.001	0.000	0.000	0.000	0.000
23	A	310	LEU	0	0.012	0.010	20.136	0.005	0.005	0.000	0.000	0.000	0.000
24	A	311	ASN	0	-0.001	-0.005	24.117	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	312	GLU	-1	-0.892	-0.919	26.460	-0.074	-0.074	0.000	0.000	0.000	0.000
26	A	313	ALA	0	0.081	0.046	24.397	0.000	0.000	0.000	0.000	0.000	0.000
27	A	314	ILE	0	0.012	0.001	20.805	0.001	0.001	0.000	0.000	0.000	0.000
28	A	315	GLY	0	-0.039	-0.002	24.431	0.000	0.000	0.000	0.000	0.000	0.000
29	A	316	THR	0	-0.024	-0.037	28.158	0.001	0.001	0.000	0.000	0.000	0.000
30	A	317	LEU	0	-0.042	-0.009	22.515	0.007	0.007	0.000	0.000	0.000	0.000
31	A	318	THR	0	-0.040	-0.042	25.847	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	319	ALA	0	-0.057	-0.013	27.427	0.003	0.003	0.000	0.000	0.000	0.000
33	A	320	ARG	1	0.811	0.889	27.324	0.082	0.082	0.000	0.000	0.000	0.000
34	A	321	GLY	0	0.019	0.006	30.624	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	322	ASP	-1	-0.765	-0.866	29.794	-0.064	-0.064	0.000	0.000	0.000	0.000
36	A	323	ARG	1	0.880	0.939	25.834	0.066	0.066	0.000	0.000	0.000	0.000
37	A	324	ASN	0	-0.001	-0.004	25.845	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	325	ALA	0	-0.066	-0.035	26.424	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	326	TRP	0	0.041	0.032	21.901	0.003	0.003	0.000	0.000	0.000	0.000
40	A	327	VAL	0	0.018	0.006	18.790	0.000	0.000	0.000	0.000	0.000	0.000
41	A	328	PRO	0	-0.030	-0.013	17.937	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	329	THR	0	-0.042	-0.025	13.376	0.036	0.036	0.000	0.000	0.000	0.000
43	A	330	MET	0	0.020	0.016	8.369	-0.189	-0.189	0.000	0.000	0.000	0.000
44	A	331	LEU	0	-0.015	-0.020	8.999	0.117	0.117	0.000	0.000	0.000	0.000
45	A	332	SER	0	0.017	0.023	4.304	-0.705	-0.661	-0.001	-0.009	-0.033	0.000
46	A	333	VAL	0	-0.022	-0.024	3.669	0.352	0.911	0.000	-0.261	-0.297	0.000
47	A	334	SER	0	0.045	0.021	1.908	-8.337	-10.584	8.791	-3.999	-2.546	-0.039
48	A	335	ASP	-1	-0.839	-0.932	3.344	-0.474	-0.500	0.038	0.079	-0.091	0.000
49	A	336	SER	0	-0.079	-0.047	6.584	-0.073	-0.073	0.000	0.000	0.000	0.000
50	A	337	LEU	0	-0.047	-0.013	6.712	-0.234	-0.234	0.000	0.000	0.000	0.000
51	A	338	MET	0	0.016	0.025	6.009	0.011	0.011	0.000	0.000	0.000	0.000
52	A	339	THR	0	0.007	-0.011	7.458	0.259	0.259	0.000	0.000	0.000	0.000
53	A	340	ALA	0	0.005	0.005	8.815	-0.168	-0.168	0.000	0.000	0.000	0.000
54	A	341	HIS	0	0.030	0.014	9.095	0.183	0.183	0.000	0.000	0.000	0.000
55	A	342	PRO	0	0.038	0.010	12.403	-0.095	-0.095	0.000	0.000	0.000	0.000
56	A	343	ILE	0	0.011	0.009	14.073	0.004	0.004	0.000	0.000	0.000	0.000
57	A	344	GLN	0	-0.019	-0.004	15.050	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	345	ALA	0	-0.027	-0.015	16.605	0.031	0.031	0.000	0.000	0.000	0.000
59	A	346	GLU	-1	-0.930	-0.987	11.008	0.220	0.220	0.000	0.000	0.000	0.000
60	A	347	ALA	0	0.000	-0.005	12.156	0.000	0.000	0.000	0.000	0.000	0.000
61	A	348	SER	0	-0.027	-0.037	13.241	0.041	0.041	0.000	0.000	0.000	0.000
62	A	349	THR	0	-0.114	-0.042	16.694	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	350	GLU	-1	-0.853	-0.889	19.415	0.148	0.148	0.000	0.000	0.000	0.000
64	A	351	GLH	0	-0.071	-0.035	16.014	0.048	0.048	0.000	0.000	0.000	0.000
65	A	352	GLU	-1	-0.869	-0.926	14.279	0.250	0.250	0.000	0.000	0.000	0.000
66	A	353	PRO	0	-0.077	-0.044	11.531	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	354	LEU	0	0.007	0.012	13.899	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	355	TRP	0	-0.015	-0.015	11.123	-0.024	-0.024	0.000	0.000	0.000	0.000
69	A	356	GLN	0	0.013	-0.003	11.760	0.086	0.086	0.000	0.000	0.000	0.000
70	A	357	CYS	0	-0.009	-0.001	11.387	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	358	PRO	0	0.006	0.001	10.908	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	359	VAL	0	0.037	0.018	7.893	-0.061	-0.061	0.000	0.000	0.000	0.000
73	A	360	ARG	1	0.946	0.963	11.176	-0.387	-0.387	0.000	0.000	0.000	0.000
74	A	361	LEU	0	-0.041	-0.007	14.246	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	362	VAL	0	-0.022	-0.006	12.814	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	363	THR	0	-0.044	-0.040	15.917	0.004	0.004	0.000	0.000	0.000	0.000
77	A	364	PHE	0	-0.028	-0.025	18.402	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	365	ILE	0	0.008	0.004	13.970	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	366	GLY	0	0.019	0.010	17.295	0.018	0.018	0.000	0.000	0.000	0.000
80	A	367	VAL	0	0.013	0.011	17.957	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	368	GLY	0	0.000	0.014	19.726	0.026	0.026	0.000	0.000	0.000	0.000
82	A	369	ARG	1	0.813	0.868	23.015	0.127	0.127	0.000	0.000	0.000	0.000
83	A	370	ASP	-1	-0.835	-0.885	25.122	-0.196	-0.196	0.000	0.000	0.000	0.000
84	A	371	PRO	0	0.060	0.018	22.421	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	372	HIS	0	-0.028	-0.012	20.818	-0.043	-0.043	0.000	0.000	0.000	0.000
86	A	373	THR	0	-0.051	-0.031	19.895	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	374	PHE	0	0.030	0.000	13.277	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	375	GLY	0	0.023	0.006	17.312	0.025	0.025	0.000	0.000	0.000	0.000
89	A	376	LEU	0	-0.052	-0.018	13.305	-0.033	-0.033	0.000	0.000	0.000	0.000
90	A	377	ILE	0	0.005	-0.003	17.287	0.028	0.028	0.000	0.000	0.000	0.000
91	A	378	ALA	0	0.051	0.021	16.855	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	379	ASP	-1	-0.882	-0.939	18.920	0.026	0.026	0.000	0.000	0.000	0.000
93	A	380	LEU	0	0.007	-0.001	19.731	0.017	0.017	0.000	0.000	0.000	0.000
94	A	381	GLY	0	-0.005	0.002	21.846	0.015	0.015	0.000	0.000	0.000	0.000
95	A	382	ARG	1	0.898	0.950	24.318	-0.055	-0.055	0.000	0.000	0.000	0.000
96	A	383	GLN	0	-0.049	-0.040	25.687	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	384	SER	0	-0.004	0.005	25.921	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	385	PHE	0	0.044	0.024	23.205	0.009	0.009	0.000	0.000	0.000	0.000
99	A	386	GLN	0	0.005	0.016	20.622	0.000	0.000	0.000	0.000	0.000	0.000
100	A	387	CYS	0	0.013	0.012	20.467	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	388	ALA	0	-0.029	0.006	17.024	0.021	0.021	0.000	0.000	0.000	0.000
102	A	389	ALA	0	0.025	0.014	18.354	-0.029	-0.029	0.000	0.000	0.000	0.000
103	A	390	PHE	0	-0.013	-0.013	14.345	0.007	0.007	0.000	0.000	0.000	0.000
104	A	391	TRP	0	0.050	0.026	17.674	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	392	CYS	0	-0.040	-0.029	15.217	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	393	GLN	0	0.041	0.010	18.072	0.016	0.016	0.000	0.000	0.000	0.000
107	A	394	PRO	0	-0.037	-0.010	16.673	0.026	0.026	0.000	0.000	0.000	0.000
108	A	395	HIS	0	0.019	0.018	18.438	-0.026	-0.026	0.000	0.000	0.000	0.000
109	A	396	ALA	0	0.044	0.016	16.272	-0.058	-0.058	0.000	0.000	0.000	0.000
110	A	397	GLY	0	0.014	-0.003	15.156	-0.062	-0.062	0.000	0.000	0.000	0.000
111	A	398	GLY	0	-0.011	-0.006	13.717	-0.052	-0.052	0.000	0.000	0.000	0.000
112	A	399	LEU	0	0.007	0.014	9.463	-0.221	-0.221	0.000	0.000	0.000	0.000
113	A	400	SER	0	-0.029	-0.017	10.701	-0.095	-0.095	0.000	0.000	0.000	0.000
114	A	401	GLU	-1	-0.810	-0.901	12.389	-0.593	-0.593	0.000	0.000	0.000	0.000
115	A	402	ALA	0	-0.040	-0.006	6.883	-0.079	-0.079	0.000	0.000	0.000	0.000
116	A	403	VAL	0	0.012	-0.002	7.839	-0.108	-0.108	0.000	0.000	0.000	0.000
117	A	404	GLN	0	-0.020	-0.017	9.545	0.191	0.191	0.000	0.000	0.000	0.000
118	A	405	ALA	0	-0.009	-0.002	8.919	0.118	0.118	0.000	0.000	0.000	0.000
119	A	406	ALA	0	0.032	0.020	6.374	0.172	0.172	0.000	0.000	0.000	0.000
120	A	407	CYS	0	-0.050	-0.035	8.276	0.303	0.303	0.000	0.000	0.000	0.000
121	A	408	MET	0	-0.012	0.001	11.801	0.128	0.128	0.000	0.000	0.000	0.000
122	A	409	VAL	0	0.011	0.011	8.973	0.108	0.108	0.000	0.000	0.000	0.000
123	A	410	GLN	0	-0.024	-0.022	10.474	0.219	0.219	0.000	0.000	0.000	0.000
124	A	411	TYR	0	0.015	0.005	12.126	0.057	0.057	0.000	0.000	0.000	0.000
125	A	412	GLN	0	0.015	-0.001	14.752	0.038	0.038	0.000	0.000	0.000	0.000
126	A	413	LYS	1	0.836	0.924	10.030	-0.369	-0.369	0.000	0.000	0.000	0.000
127	A	414	CYS	0	-0.065	-0.033	15.296	0.055	0.055	0.000	0.000	0.000	0.000
128	A	415	LEU	0	-0.053	-0.003	18.184	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	416	VAL	0	-0.024	-0.012	19.640	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	417	ALA	0	-0.003	0.008	19.834	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:288:ALA)