FMO DATABASE

FMODB ID: 6Y84Z

Calculation Name: 3E0E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E0E

Chain ID: A

ChEMBL ID:

UniProt ID: Q6LYF9

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-679310.462795
FMO2-HF: Nuclear repulsion	642058.21185
FMO2-HF: Total energy	-37252.250944
FMO2-MP2: Total energy	-37361.749925

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:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

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.
-22.292	-13.838	8.548	-5.973	-11.029	-0.036

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / 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

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	2	TYR	0	-0.014	-0.021	2.541	-11.094	-5.329	6.866	-4.175	-8.457	-0.010
4	A	3	LYS	1	0.860	0.906	3.562	3.921	4.180	0.006	0.049	-0.313	0.000
5	A	4	ILE	0	-0.020	-0.035	5.878	0.030	0.030	0.000	0.000	0.000	0.000
6	A	5	SER	0	-0.061	-0.036	8.390	0.167	0.167	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.863	-0.930	2.692	-12.577	-10.147	1.676	-1.847	-2.259	-0.026
8	A	7	LEU	0	-0.061	-0.016	6.054	0.603	0.603	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.005	0.000	7.800	0.421	0.421	0.000	0.000	0.000	0.000
10	A	9	PRO	0	-0.009	-0.029	10.422	-0.116	-0.116	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.064	-0.026	13.170	0.074	0.074	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.026	0.052	5.993	0.132	0.132	0.000	0.000	0.000	0.000
13	A	12	SER	0	0.024	-0.003	8.956	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	13	GLY	0	-0.004	0.000	6.001	-0.219	-0.219	0.000	0.000	0.000	0.000
15	A	14	THR	0	0.028	0.022	5.625	1.015	1.015	0.000	0.000	0.000	0.000
16	A	15	ILE	0	0.010	0.028	5.926	-1.188	-1.188	0.000	0.000	0.000	0.000
17	A	16	ASN	0	0.021	0.008	8.360	0.431	0.431	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.027	-0.019	10.983	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.770	-0.861	13.260	-0.585	-0.585	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.003	0.001	16.891	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.001	0.004	18.544	0.080	0.080	0.000	0.000	0.000	0.000
22	A	21	THR	0	-0.052	-0.047	21.181	0.078	0.078	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.068	0.043	22.303	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	23	TYR	0	-0.047	-0.024	23.086	0.032	0.032	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.019	0.000	27.127	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.812	0.894	28.396	0.272	0.272	0.000	0.000	0.000	0.000
27	A	26	LYS	1	0.868	0.936	28.566	0.342	0.342	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.830	-0.916	30.273	-0.239	-0.239	0.000	0.000	0.000	0.000
29	A	28	PHE	0	-0.025	-0.011	28.078	0.011	0.011	0.000	0.000	0.000	0.000
30	A	29	SER	0	0.038	0.009	33.868	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.814	0.903	28.601	0.201	0.201	0.000	0.000	0.000	0.000
32	A	31	LYS	1	0.921	0.958	29.524	0.186	0.186	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.797	-0.904	30.169	-0.182	-0.182	0.000	0.000	0.000	0.000
34	A	33	GLY	0	0.065	0.054	33.571	0.012	0.012	0.000	0.000	0.000	0.000
35	A	34	THR	0	0.007	-0.025	32.715	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	35	DLY	1	0.818	0.924	33.044	0.204	0.204	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.021	0.011	29.796	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	37	GLN	0	-0.052	-0.031	27.989	0.030	0.030	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.011	0.013	23.650	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	39	LYS	1	0.887	0.951	23.694	0.474	0.474	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.029	-0.005	22.294	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.045	0.029	18.703	0.043	0.043	0.000	0.000	0.000	0.000
43	A	42	PHE	0	-0.023	-0.006	19.026	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	43	LEU	0	0.015	0.008	14.206	0.043	0.043	0.000	0.000	0.000	0.000
45	A	44	LYS	1	0.841	0.898	14.527	0.749	0.749	0.000	0.000	0.000	0.000
46	A	45	ASP	-1	-0.698	-0.826	9.110	-2.107	-2.107	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.861	-0.916	10.768	-1.465	-1.465	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.079	-0.036	8.674	0.000	0.000	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.037	0.017	11.617	0.119	0.119	0.000	0.000	0.000	0.000
50	A	49	SER	0	-0.023	-0.016	13.360	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.021	0.002	12.175	0.046	0.046	0.000	0.000	0.000	0.000
52	A	51	ARG	1	0.830	0.909	15.201	0.493	0.493	0.000	0.000	0.000	0.000
53	A	52	GLY	0	0.065	0.038	16.577	-0.066	-0.066	0.000	0.000	0.000	0.000
54	A	53	THR	0	-0.075	-0.048	17.518	0.088	0.088	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.038	0.029	18.889	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	55	TRP	0	0.042	-0.006	20.037	0.084	0.084	0.000	0.000	0.000	0.000
57	A	56	ASN	0	0.019	-0.014	23.478	0.003	0.003	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.802	-0.893	23.752	-0.322	-0.322	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.043	0.031	18.883	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	59	ALA	0	-0.075	-0.037	23.005	-0.029	-0.029	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.811	-0.892	25.333	-0.294	-0.294	0.000	0.000	0.000	0.000
62	A	61	PHE	0	-0.009	0.015	19.994	0.013	0.013	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.864	-0.923	24.299	-0.375	-0.375	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.004	-0.005	20.390	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.793	0.886	23.635	0.469	0.469	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.871	0.928	23.188	0.448	0.448	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.003	-0.006	22.201	0.037	0.037	0.000	0.000	0.000	0.000
68	A	67	ASP	-1	-0.799	-0.893	20.633	-0.546	-0.546	0.000	0.000	0.000	0.000
69	A	68	ILE	0	-0.007	0.006	15.248	-0.071	-0.071	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.020	-0.024	15.922	0.063	0.063	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.892	-0.938	9.646	-1.777	-1.777	0.000	0.000	0.000	0.000
72	A	71	VAL	0	-0.062	-0.048	11.641	0.237	0.237	0.000	0.000	0.000	0.000
73	A	72	SER	0	0.035	-0.001	9.277	-0.265	-0.265	0.000	0.000	0.000	0.000
74	A	73	GLY	0	0.026	0.008	10.454	0.314	0.314	0.000	0.000	0.000	0.000
75	A	74	TYR	0	-0.021	-0.002	10.812	-0.178	-0.178	0.000	0.000	0.000	0.000
76	A	75	VAL	0	0.007	0.008	9.971	0.051	0.051	0.000	0.000	0.000	0.000
77	A	76	LYS	1	0.869	0.924	12.925	0.606	0.606	0.000	0.000	0.000	0.000
78	A	77	GLN	0	0.031	0.005	16.327	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	78	GLY	0	-0.051	-0.029	18.634	0.026	0.026	0.000	0.000	0.000	0.000
80	A	79	TYR	0	-0.054	-0.035	21.230	0.013	0.013	0.000	0.000	0.000	0.000
81	A	80	SER	0	-0.011	-0.013	20.525	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.052	0.031	18.468	0.029	0.029	0.000	0.000	0.000	0.000
83	A	82	LEU	0	0.005	0.026	12.298	0.053	0.053	0.000	0.000	0.000	0.000
84	A	83	GLU	-1	-0.780	-0.892	15.896	-0.488	-0.488	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.035	0.026	10.543	0.026	0.026	0.000	0.000	0.000	0.000
86	A	85	SER	0	-0.037	-0.019	14.509	0.082	0.082	0.000	0.000	0.000	0.000
87	A	86	VAL	0	-0.052	-0.032	15.102	-0.062	-0.062	0.000	0.000	0.000	0.000
88	A	87	ASP	-1	-0.894	-0.946	13.518	-0.716	-0.716	0.000	0.000	0.000	0.000
89	A	88	ASN	0	-0.029	-0.035	12.852	0.222	0.222	0.000	0.000	0.000	0.000
90	A	89	ILE	0	-0.021	-0.011	14.317	-0.143	-0.143	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.029	0.031	15.486	0.126	0.126	0.000	0.000	0.000	0.000
92	A	91	ILE	0	-0.068	-0.037	16.288	-0.089	-0.089	0.000	0.000	0.000	0.000
93	A	92	ILE	0	-0.020	0.001	12.558	0.051	0.051	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.929	-0.969	16.367	-0.491	-0.491	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.906	0.951	19.393	0.394	0.394	0.000	0.000	0.000	0.000
96	A	95	SER	0	0.013	0.003	22.690	0.015	0.015	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.042	-0.005	24.370	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)