FMO DATABASE

FMODB ID: 6YV5Z

Calculation Name: 2H8E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H8E

Chain ID: A

ChEMBL ID:

UniProt ID: P0AG74

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	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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1027748.162743
FMO2-HF: Nuclear repulsion	978386.882815
FMO2-HF: Total energy	-49361.279928
FMO2-MP2: Total energy	-49502.41458

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-4.716	-0.646	3.778	-2.475	-5.373	-0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.009

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	3	THR	0	-0.029	-0.023	3.442	-0.786	1.298	0.012	-0.931	-1.165	0.005
4	A	4	TYR	0	-0.003	-0.017	5.770	0.443	0.443	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.036	-0.012	9.490	0.067	0.067	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.012	-0.011	11.962	0.079	0.079	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.014	-0.021	15.240	0.040	0.040	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.017	-0.002	18.430	0.029	0.029	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.036	0.006	20.959	0.020	0.020	0.000	0.000	0.000	0.000
10	A	10	TRP	0	0.026	0.014	24.005	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.004	0.018	24.373	0.013	0.013	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.017	-0.018	27.007	0.017	0.017	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.003	-0.015	29.434	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.076	0.041	29.562	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.015	0.004	31.112	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.894	0.954	33.808	0.153	0.153	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.020	-0.007	25.812	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.031	0.024	27.001	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.802	0.889	33.485	0.142	0.142	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.057	0.035	35.762	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.014	0.010	38.813	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.953	0.963	40.797	0.068	0.068	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.045	0.023	41.405	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.962	1.005	36.342	0.095	0.095	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.026	-0.007	32.989	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	HIS	0	-0.036	-0.021	33.256	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.008	0.013	28.901	0.001	0.001	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.041	-0.036	32.269	0.007	0.007	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.081	0.025	33.514	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.788	-0.874	33.846	-0.160	-0.160	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.011	0.000	29.933	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.011	-0.015	29.009	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.046	0.031	29.933	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.033	-0.027	23.180	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.809	0.860	25.290	0.210	0.210	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.822	-0.896	25.529	-0.245	-0.245	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.089	-0.057	26.963	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.030	0.020	20.627	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.042	0.014	22.070	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.849	0.929	23.590	0.264	0.264	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.033	-0.017	20.021	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.015	0.007	16.898	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.960	0.991	19.890	0.283	0.283	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.067	-0.040	22.517	0.012	0.012	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.032	-0.003	18.026	0.008	0.008	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.033	-0.010	18.129	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.015	0.005	13.752	-0.058	-0.058	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.906	-0.968	16.518	-0.451	-0.451	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.031	-0.025	12.738	0.043	0.043	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.004	0.013	16.419	0.022	0.022	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.010	-0.008	9.891	0.038	0.038	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.045	0.016	12.716	0.027	0.027	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.030	0.015	7.374	0.082	0.082	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.069	0.034	7.665	-0.079	-0.079	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.035	-0.012	6.808	-0.314	-0.314	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.929	0.976	4.668	1.033	1.141	-0.001	-0.001	-0.105	0.000
57	A	57	ILE	0	-0.005	-0.005	7.977	-0.215	-0.215	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.845	0.912	10.652	0.764	0.764	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.026	-0.001	12.564	-0.033	-0.033	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.780	-0.853	15.643	-0.443	-0.443	0.000	0.000	0.000	0.000
61	A	61	CYS	0	-0.031	-0.016	18.171	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	HIS	0	0.016	0.006	19.061	0.065	0.065	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.005	0.009	23.616	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.022	0.019	27.137	0.005	0.005	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.784	-0.865	29.935	-0.156	-0.156	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.990	0.978	31.288	0.116	0.116	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.904	0.972	33.541	0.156	0.156	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.904	0.929	32.392	0.122	0.122	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.783	0.868	29.461	0.191	0.191	0.000	0.000	0.000	0.000
70	A	70	ASN	0	0.058	0.041	27.813	0.010	0.010	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.063	0.014	22.283	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.741	-0.859	22.594	-0.220	-0.220	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.102	-0.075	23.341	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.028	-0.007	22.770	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	GLN	0	0.042	0.042	18.177	0.010	0.010	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.912	0.955	20.107	0.176	0.176	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.030	-0.013	22.486	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.022	0.003	18.850	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.102	0.039	14.898	-0.033	-0.033	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.741	-0.802	18.979	-0.258	-0.258	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.026	-0.021	21.971	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.019	0.007	15.469	0.006	0.006	0.000	0.000	0.000	0.000
83	A	83	THR	0	0.022	0.007	18.710	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.849	0.918	19.677	0.285	0.285	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.057	-0.026	20.139	0.021	0.021	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.030	0.030	19.871	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.035	-0.012	11.093	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	88	TRP	0	-0.027	-0.018	12.970	-0.110	-0.110	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.034	-0.013	15.335	0.050	0.050	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.890	-0.946	16.589	-0.224	-0.224	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.958	-0.979	15.928	-0.360	-0.360	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.011	-0.011	15.997	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.046	-0.039	11.923	0.063	0.063	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.064	-0.033	11.175	-0.110	-0.110	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.010	0.013	8.606	0.079	0.079	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.921	-0.962	8.975	-0.415	-0.415	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.007	-0.019	10.902	-0.130	-0.130	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.945	0.982	13.065	0.377	0.377	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.012	0.003	14.947	-0.048	-0.048	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.031	-0.017	17.168	0.043	0.043	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.944	0.973	19.896	0.163	0.163	0.000	0.000	0.000	0.000
102	A	102	MET	0	0.001	0.010	18.812	0.019	0.019	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.025	-0.006	22.826	0.016	0.016	0.000	0.000	0.000	0.000
104	A	104	VAL	0	-0.045	-0.016	25.688	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	105	THR	0	0.007	0.020	25.207	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.981	0.978	28.271	0.176	0.176	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.016	0.009	29.805	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	108	GLY	0	-0.035	-0.020	26.938	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.790	0.858	20.465	0.386	0.386	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.030	-0.017	19.512	0.022	0.022	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.724	-0.814	16.184	-0.544	-0.544	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.009	-0.004	13.667	0.013	0.013	0.000	0.000	0.000	0.000
113	A	113	THR	0	-0.022	-0.016	8.361	-0.032	-0.032	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.006	0.011	8.196	0.101	0.101	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.011	-0.013	2.472	-0.951	-0.387	1.119	-0.391	-1.292	0.000
116	A	116	GLU	-1	-0.768	-0.866	4.275	-1.204	-0.843	-0.001	-0.049	-0.312	0.000
117	A	117	MET	0	-0.035	-0.024	2.482	-4.143	-3.262	2.650	-1.115	-2.416	-0.015
118	A	118	GLY	0	0.026	0.014	4.002	0.643	0.715	-0.001	0.012	-0.083	0.000
119	A	119	ASN	0	-0.022	-0.018	4.828	-0.113	-0.113	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.991	-0.980	6.244	0.124	0.124	0.000	0.000	0.000	0.000

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