FMO DATABASE

FMODB ID: 89GZY

Calculation Name: 2H3R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H3R

Chain ID: A

ChEMBL ID:

UniProt ID: P88989

Base Structure: X-ray

Registration Date: 2023-09-22

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-526108.0045
FMO2-HF: Nuclear repulsion	490526.001853
FMO2-HF: Total energy	-35582.002647
FMO2-MP2: Total energy	-35685.054225

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:7:ASP)

Summations of interaction energy for fragment #1(A:7:ASP)

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.
-35.483	-25.367	4.938	-6.815	-8.239	0.033

Interaction energy analysis for fragmet #1(A:7:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.935 / q_NPA : -0.969

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	9	THR	0	-0.022	-0.001	3.846	-9.657	-6.908	-0.026	-1.437	-1.286	0.003
4	A	10	TYR	0	0.082	0.014	4.744	4.483	4.554	-0.001	-0.004	-0.066	0.000
5	A	11	GLU	-1	-0.793	-0.877	6.858	27.950	27.950	0.000	0.000	0.000	0.000
6	A	12	GLU	-1	-0.791	-0.878	2.496	49.634	53.389	2.347	-3.105	-2.997	0.018
7	A	13	MET	0	0.054	0.028	2.738	2.714	4.822	2.503	-1.764	-2.848	0.008
8	A	14	VAL	0	-0.029	-0.016	3.639	-5.406	-5.298	0.013	0.028	-0.149	0.000
9	A	15	LYS	1	0.850	0.921	5.754	-34.408	-34.408	0.000	0.000	0.000	0.000
10	A	16	GLU	-1	-0.725	-0.827	3.254	38.547	39.850	0.103	-0.532	-0.873	0.004
11	A	17	VAL	0	-0.012	-0.012	5.144	-8.134	-8.112	-0.001	-0.001	-0.020	0.000
12	A	18	GLU	-1	-0.850	-0.914	7.825	18.904	18.904	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.751	0.836	7.405	-38.238	-38.238	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.016	0.008	7.503	-3.680	-3.680	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.789	0.882	10.557	-25.878	-25.878	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.003	0.003	13.022	-2.132	-2.132	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.852	-0.895	12.001	24.225	24.225	0.000	0.000	0.000	0.000
18	A	24	ASN	0	0.017	-0.002	14.456	-2.285	-2.285	0.000	0.000	0.000	0.000
19	A	25	LYS	1	0.953	0.963	16.360	-16.178	-16.178	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.031	-0.028	17.749	-1.321	-1.321	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.047	-0.028	17.279	-0.915	-0.915	0.000	0.000	0.000	0.000
22	A	28	LYS	1	0.801	0.891	19.412	-16.208	-16.208	0.000	0.000	0.000	0.000
23	A	29	GLN	0	0.001	0.002	22.376	-0.236	-0.236	0.000	0.000	0.000	0.000
24	A	30	LYS	1	0.912	0.979	21.934	-14.176	-14.176	0.000	0.000	0.000	0.000
25	A	31	VAL	0	-0.050	-0.007	24.756	-0.814	-0.814	0.000	0.000	0.000	0.000
26	A	39	SER	0	-0.014	-0.023	27.643	0.010	0.010	0.000	0.000	0.000	0.000
27	A	40	ASP	-1	-0.851	-0.912	22.789	13.753	13.753	0.000	0.000	0.000	0.000
28	A	41	ASP	-1	-0.858	-0.934	22.595	14.361	14.361	0.000	0.000	0.000	0.000
29	A	42	SER	0	-0.077	-0.047	22.753	-0.520	-0.520	0.000	0.000	0.000	0.000
30	A	43	ILE	0	0.005	0.010	23.623	0.384	0.384	0.000	0.000	0.000	0.000
31	A	44	LEU	0	-0.004	0.003	19.157	0.187	0.187	0.000	0.000	0.000	0.000
32	A	45	THR	0	0.030	0.010	22.439	-0.220	-0.220	0.000	0.000	0.000	0.000
33	A	46	ALA	0	0.008	0.001	22.239	0.504	0.504	0.000	0.000	0.000	0.000
34	A	47	ALA	0	0.066	0.027	20.609	0.360	0.360	0.000	0.000	0.000	0.000
35	A	48	LYS	1	0.957	0.981	15.644	-17.548	-17.548	0.000	0.000	0.000	0.000
36	A	49	ARG	1	0.930	0.959	17.589	-11.793	-11.793	0.000	0.000	0.000	0.000
37	A	50	GLU	-1	-0.780	-0.890	18.230	14.395	14.395	0.000	0.000	0.000	0.000
38	A	51	SER	0	0.001	0.006	13.841	0.563	0.563	0.000	0.000	0.000	0.000
39	A	52	ILE	0	-0.010	0.006	12.904	1.610	1.610	0.000	0.000	0.000	0.000
40	A	53	ILE	0	0.042	0.034	14.522	1.018	1.018	0.000	0.000	0.000	0.000
41	A	54	VAL	0	0.012	0.015	14.612	0.340	0.340	0.000	0.000	0.000	0.000
42	A	55	SER	0	-0.037	-0.032	10.346	0.891	0.891	0.000	0.000	0.000	0.000
43	A	56	SER	0	0.004	-0.017	11.583	1.687	1.687	0.000	0.000	0.000	0.000
44	A	57	SER	0	-0.031	-0.025	13.336	-0.230	-0.230	0.000	0.000	0.000	0.000
45	A	58	ARG	1	0.888	0.949	11.881	-20.120	-20.120	0.000	0.000	0.000	0.000
46	A	59	ALA	0	-0.003	0.011	9.666	0.270	0.270	0.000	0.000	0.000	0.000
47	A	60	LEU	0	0.049	0.007	11.137	-0.184	-0.184	0.000	0.000	0.000	0.000
48	A	61	GLY	0	0.010	0.009	14.659	-0.951	-0.951	0.000	0.000	0.000	0.000
49	A	62	ALA	0	-0.001	0.008	11.648	-0.891	-0.891	0.000	0.000	0.000	0.000
50	A	63	VAL	0	-0.007	0.002	13.205	-0.785	-0.785	0.000	0.000	0.000	0.000
51	A	64	ALA	0	0.004	-0.005	15.087	-1.052	-1.052	0.000	0.000	0.000	0.000
52	A	65	MET	0	-0.002	0.001	16.226	-1.136	-1.136	0.000	0.000	0.000	0.000
53	A	66	ARG	1	0.814	0.874	11.929	-24.911	-24.911	0.000	0.000	0.000	0.000
54	A	67	LYS	1	0.780	0.855	16.843	-17.391	-17.391	0.000	0.000	0.000	0.000
55	A	68	ILE	0	-0.012	-0.007	19.832	-0.910	-0.910	0.000	0.000	0.000	0.000
56	A	69	GLU	-1	-0.796	-0.882	18.799	14.707	14.707	0.000	0.000	0.000	0.000
57	A	70	ALA	0	-0.007	0.006	20.510	-0.565	-0.565	0.000	0.000	0.000	0.000
58	A	71	LYS	1	0.883	0.925	22.290	-13.450	-13.450	0.000	0.000	0.000	0.000
59	A	72	VAL	0	0.001	-0.005	24.859	-0.586	-0.586	0.000	0.000	0.000	0.000
60	A	73	ARG	1	0.851	0.907	21.270	-14.011	-14.011	0.000	0.000	0.000	0.000
61	A	74	SER	0	-0.045	-0.018	26.272	-0.439	-0.439	0.000	0.000	0.000	0.000
62	A	75	ARG	1	0.903	0.941	28.064	-10.670	-10.670	0.000	0.000	0.000	0.000
63	A	76	ALA	0	0.034	0.002	29.453	-0.379	-0.379	0.000	0.000	0.000	0.000
64	A	77	ALA	0	-0.021	-0.009	30.021	-0.279	-0.279	0.000	0.000	0.000	0.000
65	A	78	LYS	1	0.929	0.980	31.859	-8.841	-8.841	0.000	0.000	0.000	0.000
66	A	79	ALA	0	-0.035	-0.002	34.838	-0.265	-0.265	0.000	0.000	0.000	0.000
67	A	80	VAL	0	0.001	0.001	35.963	0.151	0.151	0.000	0.000	0.000	0.000
68	A	81	THR	0	-0.038	-0.042	38.458	-0.074	-0.074	0.000	0.000	0.000	0.000
69	A	82	GLU	-1	-0.882	-0.953	36.560	8.276	8.276	0.000	0.000	0.000	0.000
70	A	83	GLN	0	0.009	0.019	37.523	0.219	0.219	0.000	0.000	0.000	0.000
71	A	84	GLU	-1	-0.822	-0.885	38.732	7.871	7.871	0.000	0.000	0.000	0.000
72	A	85	LEU	0	0.014	0.003	31.356	0.152	0.152	0.000	0.000	0.000	0.000
73	A	86	THR	0	-0.006	-0.016	34.398	0.291	0.291	0.000	0.000	0.000	0.000
74	A	87	SER	0	-0.015	-0.006	35.878	0.118	0.118	0.000	0.000	0.000	0.000
75	A	88	LEU	0	-0.034	0.006	32.746	0.064	0.064	0.000	0.000	0.000	0.000
76	A	89	LEU	0	-0.011	-0.022	29.399	0.223	0.223	0.000	0.000	0.000	0.000
77	A	90	GLN	0	-0.030	-0.017	32.475	0.205	0.205	0.000	0.000	0.000	0.000
78	A	91	SER	0	-0.044	-0.025	34.980	-0.109	-0.109	0.000	0.000	0.000	0.000
79	A	92	LEU	0	-0.059	-0.010	29.198	0.088	0.088	0.000	0.000	0.000	0.000
80	A	93	THR	0	0.009	-0.003	31.203	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	94	LEU	0	-0.044	-0.030	25.827	-0.044	-0.044	0.000	0.000	0.000	0.000
82	A	95	ARG	1	0.988	1.014	27.094	-10.543	-10.543	0.000	0.000	0.000	0.000
83	A	96	VAL	0	-0.042	-0.028	21.232	0.074	0.074	0.000	0.000	0.000	0.000
84	A	97	ASP	-1	-0.845	-0.914	22.642	12.862	12.862	0.000	0.000	0.000	0.000
85	A	98	VAL	0	-0.036	-0.012	17.276	0.541	0.541	0.000	0.000	0.000	0.000
86	A	99	SER	0	0.004	-0.030	16.891	-0.349	-0.349	0.000	0.000	0.000	0.000
87	A	100	MET	0	0.051	0.017	11.925	1.126	1.126	0.000	0.000	0.000	0.000
88	A	101	GLU	-1	-0.871	-0.896	11.963	19.686	19.686	0.000	0.000	0.000	0.000
89	A	102	GLU	-1	-0.786	-0.875	13.140	18.648	18.648	0.000	0.000	0.000	0.000
90	A	103	LEU	0	-0.074	-0.004	8.560	1.356	1.356	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ASP)