FMO DATABASE

FMODB ID: G69J1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1055860.441802
FMO2-HF: Nuclear repulsion	1004483.241883
FMO2-HF: Total energy	-51377.19992
FMO2-MP2: Total energy	-51520.000032

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.
-7.397	-2.955	2.295	-3.48	-3.256	-0.011

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 : 0.016 / q_NPA : 0.012

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	290	LYS	1	0.948	0.973	3.851	1.015	3.637	-0.028	-1.529	-1.064	0.006
4	A	291	TYR	0	-0.012	-0.020	7.006	-0.082	-0.082	0.000	0.000	0.000	0.000
5	A	292	GLU	-1	-0.902	-0.926	10.284	-0.300	-0.300	0.000	0.000	0.000	0.000
6	A	293	ALA	0	-0.008	-0.007	13.483	-0.002	-0.002	0.000	0.000	0.000	0.000
7	A	294	LEU	0	-0.025	0.002	15.241	0.042	0.042	0.000	0.000	0.000	0.000
8	A	295	TYR	0	0.018	0.017	16.561	0.000	0.000	0.000	0.000	0.000	0.000
9	A	296	MET	0	-0.022	-0.017	18.222	0.007	0.007	0.000	0.000	0.000	0.000
10	A	297	GLY	0	-0.003	0.010	20.710	0.008	0.008	0.000	0.000	0.000	0.000
11	A	298	THR	0	-0.051	-0.052	20.166	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	299	LEU	0	0.005	0.012	22.174	0.011	0.011	0.000	0.000	0.000	0.000
13	A	300	PRO	0	0.004	0.003	24.459	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	301	VAL	0	0.023	0.005	24.369	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	302	THR	0	0.011	-0.003	27.228	0.006	0.006	0.000	0.000	0.000	0.000
16	A	303	LYS	1	0.928	0.974	27.789	0.028	0.028	0.000	0.000	0.000	0.000
17	A	304	ALA	0	0.041	0.021	23.612	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	305	MET	0	-0.021	-0.016	23.017	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	306	GLY	0	0.057	0.037	24.264	0.008	0.008	0.000	0.000	0.000	0.000
20	A	307	MET	0	0.021	0.011	21.922	0.002	0.002	0.000	0.000	0.000	0.000
21	A	308	ASP	-1	-0.849	-0.926	25.756	-0.069	-0.069	0.000	0.000	0.000	0.000
22	A	309	VAL	0	0.000	0.001	26.337	0.002	0.002	0.000	0.000	0.000	0.000
23	A	310	LEU	0	0.014	0.016	20.438	0.005	0.005	0.000	0.000	0.000	0.000
24	A	311	ASN	0	0.007	-0.002	24.498	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	312	GLU	-1	-0.924	-0.941	26.614	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	313	ALA	0	0.079	0.044	24.643	0.003	0.003	0.000	0.000	0.000	0.000
27	A	314	ILE	0	0.012	-0.004	21.250	0.002	0.002	0.000	0.000	0.000	0.000
28	A	315	GLY	0	-0.041	-0.025	24.555	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	316	THR	0	-0.039	-0.027	28.084	0.000	0.000	0.000	0.000	0.000	0.000
30	A	317	LEU	0	-0.029	0.006	22.882	0.007	0.007	0.000	0.000	0.000	0.000
31	A	318	THR	0	-0.072	-0.049	26.033	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	319	ALA	0	-0.037	-0.017	27.481	0.001	0.001	0.000	0.000	0.000	0.000
33	A	320	ARG	1	0.863	0.933	27.677	0.051	0.051	0.000	0.000	0.000	0.000
34	A	321	GLY	0	0.009	0.011	31.157	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	322	ASP	-1	-0.793	-0.915	29.701	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	323	ARG	1	0.891	0.953	25.872	0.053	0.053	0.000	0.000	0.000	0.000
37	A	324	ASN	0	-0.008	0.001	26.186	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	325	ALA	0	-0.071	-0.044	26.227	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	326	TRP	0	0.034	0.027	21.724	0.008	0.008	0.000	0.000	0.000	0.000
40	A	327	VAL	0	0.029	0.013	18.332	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	328	PRO	0	-0.003	-0.003	17.931	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	329	THR	0	-0.067	-0.038	13.313	0.035	0.035	0.000	0.000	0.000	0.000
43	A	330	MET	0	0.038	0.017	8.431	-0.192	-0.192	0.000	0.000	0.000	0.000
44	A	331	LEU	0	-0.039	-0.034	8.759	0.117	0.117	0.000	0.000	0.000	0.000
45	A	332	SER	0	-0.010	0.011	3.983	-0.783	-0.708	0.000	-0.024	-0.051	0.000
46	A	333	VAL	0	-0.011	-0.023	3.659	0.535	0.849	0.000	-0.091	-0.223	0.000
47	A	334	SER	0	-0.003	-0.003	2.264	-6.385	-4.432	2.253	-2.373	-1.833	-0.018
48	A	335	ASP	-1	-0.845	-0.942	3.114	-0.374	-0.896	0.070	0.537	-0.085	0.001
49	A	336	SER	0	-0.087	-0.036	6.301	-0.463	-0.463	0.000	0.000	0.000	0.000
50	A	337	LEU	0	-0.045	-0.024	6.563	-0.410	-0.410	0.000	0.000	0.000	0.000
51	A	338	MET	0	0.028	0.034	5.980	0.168	0.168	0.000	0.000	0.000	0.000
52	A	339	THR	0	-0.024	-0.026	7.763	0.184	0.184	0.000	0.000	0.000	0.000
53	A	340	ALA	0	0.037	0.025	8.917	-0.177	-0.177	0.000	0.000	0.000	0.000
54	A	341	HIS	0	0.033	0.015	8.648	0.199	0.199	0.000	0.000	0.000	0.000
55	A	342	PRO	0	0.038	0.008	12.057	-0.094	-0.094	0.000	0.000	0.000	0.000
56	A	343	ILE	0	0.016	0.008	13.981	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	344	GLN	0	0.003	0.018	14.976	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	345	ALA	0	-0.021	-0.034	16.552	0.029	0.029	0.000	0.000	0.000	0.000
59	A	346	GLU	-1	-0.937	-0.978	10.805	0.200	0.200	0.000	0.000	0.000	0.000
60	A	347	ALA	0	-0.012	-0.008	12.048	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	348	SER	0	-0.033	-0.039	13.239	0.047	0.047	0.000	0.000	0.000	0.000
62	A	349	THR	0	-0.094	-0.030	16.641	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	350	GLU	-1	-0.835	-0.878	18.946	0.149	0.149	0.000	0.000	0.000	0.000
64	A	351	GLH	0	-0.124	-0.048	15.675	0.036	0.036	0.000	0.000	0.000	0.000
65	A	352	GLU	-1	-0.874	-0.952	14.073	0.303	0.303	0.000	0.000	0.000	0.000
66	A	353	PRO	0	-0.072	-0.050	11.495	-0.053	-0.053	0.000	0.000	0.000	0.000
67	A	354	LEU	0	0.024	0.029	13.886	-0.024	-0.024	0.000	0.000	0.000	0.000
68	A	355	TRP	0	-0.010	-0.021	11.535	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	356	GLN	0	0.002	0.001	11.934	0.107	0.107	0.000	0.000	0.000	0.000
70	A	357	CYS	0	-0.001	-0.001	11.587	-0.061	-0.061	0.000	0.000	0.000	0.000
71	A	358	PRO	0	0.003	0.001	10.978	0.047	0.047	0.000	0.000	0.000	0.000
72	A	359	VAL	0	0.056	0.025	7.899	-0.105	-0.105	0.000	0.000	0.000	0.000
73	A	360	ARG	1	0.945	0.963	11.212	-0.505	-0.505	0.000	0.000	0.000	0.000
74	A	361	LEU	0	-0.046	-0.019	14.351	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	362	VAL	0	-0.014	0.000	12.695	-0.029	-0.029	0.000	0.000	0.000	0.000
76	A	363	THR	0	-0.044	-0.029	15.843	0.003	0.003	0.000	0.000	0.000	0.000
77	A	364	PHE	0	-0.018	-0.013	18.911	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	365	ILE	0	-0.001	0.000	14.066	0.003	0.003	0.000	0.000	0.000	0.000
79	A	366	GLY	0	0.029	0.014	17.306	0.007	0.007	0.000	0.000	0.000	0.000
80	A	367	VAL	0	0.012	0.028	18.114	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	368	GLY	0	0.015	0.014	19.990	0.021	0.021	0.000	0.000	0.000	0.000
82	A	369	ARG	1	0.824	0.885	23.341	0.091	0.091	0.000	0.000	0.000	0.000
83	A	370	ASP	-1	-0.825	-0.891	25.249	-0.175	-0.175	0.000	0.000	0.000	0.000
84	A	371	PRO	0	0.040	0.000	22.373	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	372	HIS	0	-0.022	-0.010	20.760	-0.043	-0.043	0.000	0.000	0.000	0.000
86	A	373	THR	0	-0.053	-0.034	19.711	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	374	PHE	0	0.017	-0.001	13.164	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	375	GLY	0	0.019	-0.001	17.725	0.024	0.024	0.000	0.000	0.000	0.000
89	A	376	LEU	0	-0.060	-0.027	13.343	-0.022	-0.022	0.000	0.000	0.000	0.000
90	A	377	ILE	0	0.022	0.008	17.434	0.025	0.025	0.000	0.000	0.000	0.000
91	A	378	ALA	0	0.021	0.009	16.864	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	379	ASP	-1	-0.877	-0.943	18.885	0.077	0.077	0.000	0.000	0.000	0.000
93	A	380	LEU	0	0.012	0.012	20.176	0.025	0.025	0.000	0.000	0.000	0.000
94	A	381	GLY	0	0.018	0.014	21.879	0.013	0.013	0.000	0.000	0.000	0.000
95	A	382	ARG	1	0.905	0.951	24.430	-0.100	-0.100	0.000	0.000	0.000	0.000
96	A	383	GLN	0	-0.072	-0.060	26.055	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	384	SER	0	-0.006	0.001	26.282	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	385	PHE	0	0.027	0.023	23.377	0.011	0.011	0.000	0.000	0.000	0.000
99	A	386	GLN	0	0.002	0.021	20.900	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	387	CYS	0	0.033	0.010	20.408	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	388	ALA	0	-0.043	0.003	16.888	0.008	0.008	0.000	0.000	0.000	0.000
102	A	389	ALA	0	0.037	0.017	18.218	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	390	PHE	0	-0.016	-0.016	14.472	0.007	0.007	0.000	0.000	0.000	0.000
104	A	391	TRP	0	0.040	0.027	17.839	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	392	CYS	0	-0.013	-0.011	15.792	-0.040	-0.040	0.000	0.000	0.000	0.000
106	A	393	GLN	0	0.031	-0.001	18.168	0.018	0.018	0.000	0.000	0.000	0.000
107	A	394	PRO	0	-0.018	0.005	16.556	0.018	0.018	0.000	0.000	0.000	0.000
108	A	395	HIS	0	0.051	0.034	18.150	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	396	ALA	0	0.006	-0.010	16.187	-0.062	-0.062	0.000	0.000	0.000	0.000
110	A	397	GLY	0	0.020	0.013	15.398	-0.033	-0.033	0.000	0.000	0.000	0.000
111	A	398	GLY	0	0.007	0.001	13.638	-0.037	-0.037	0.000	0.000	0.000	0.000
112	A	399	LEU	0	0.020	0.017	9.619	-0.176	-0.176	0.000	0.000	0.000	0.000
113	A	400	SER	0	0.022	0.006	10.807	-0.065	-0.065	0.000	0.000	0.000	0.000
114	A	401	GLU	-1	-0.902	-0.961	12.447	-0.510	-0.510	0.000	0.000	0.000	0.000
115	A	402	ALA	0	-0.038	-0.006	6.981	-0.047	-0.047	0.000	0.000	0.000	0.000
116	A	403	VAL	0	0.002	-0.011	8.290	0.002	0.002	0.000	0.000	0.000	0.000
117	A	404	GLN	0	-0.003	0.004	9.787	0.195	0.195	0.000	0.000	0.000	0.000
118	A	405	ALA	0	0.002	0.001	9.247	0.109	0.109	0.000	0.000	0.000	0.000
119	A	406	ALA	0	0.016	0.014	6.865	0.128	0.128	0.000	0.000	0.000	0.000
120	A	407	CYS	0	-0.034	-0.033	8.586	0.247	0.247	0.000	0.000	0.000	0.000
121	A	408	MET	0	-0.025	-0.007	12.052	0.099	0.099	0.000	0.000	0.000	0.000
122	A	409	VAL	0	0.012	0.013	9.139	0.086	0.086	0.000	0.000	0.000	0.000
123	A	410	GLN	0	0.004	0.001	10.750	0.194	0.194	0.000	0.000	0.000	0.000
124	A	411	TYR	0	0.013	0.002	12.390	0.039	0.039	0.000	0.000	0.000	0.000
125	A	412	GLN	0	0.007	-0.002	15.199	0.031	0.031	0.000	0.000	0.000	0.000
126	A	413	LYS	1	0.873	0.933	10.663	-0.505	-0.505	0.000	0.000	0.000	0.000
127	A	414	CYS	0	-0.084	-0.043	15.766	0.033	0.033	0.000	0.000	0.000	0.000
128	A	415	LEU	0	-0.053	0.008	18.387	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	416	VAL	0	-0.009	-0.005	19.720	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	417	ALA	0	-0.001	0.003	20.532	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)