FMO DATABASE

FMODB ID: YYRN2

Calculation Name: 3D3R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3R

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EF93

Base Structure: X-ray

Registration Date: 2023-03-14

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	OptH
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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-454753.677093
FMO2-HF: Nuclear repulsion	421456.340216
FMO2-HF: Total energy	-33297.336877
FMO2-MP2: Total energy	-33392.671246

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:-6:GLU)

Summations of interaction energy for fragment #1(A:-6:GLU)

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.
42.936	47.176	0.108	-1.777	-2.571	0.005

Interaction energy analysis for fragmet #1(A:-6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.921 / q_NPA : -0.973

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	-4	LEU	0	-0.010	0.006	3.143	-9.256	-6.142	0.038	-1.392	-1.760	0.004
4	A	-3	TYR	0	-0.066	-0.019	3.148	-6.405	-5.309	0.071	-0.384	-0.784	0.001
5	A	-2	PHE	0	0.018	0.015	5.377	1.717	1.747	-0.001	-0.001	-0.027	0.000
6	A	-1	GLN	0	0.083	0.022	7.778	0.149	0.149	0.000	0.000	0.000	0.000
7	A	0	GLY	0	0.004	0.003	6.979	0.199	0.199	0.000	0.000	0.000	0.000
8	A	1	MET	0	-0.059	-0.035	8.054	-0.149	-0.149	0.000	0.000	0.000	0.000
9	A	2	CYS	0	-0.028	-0.012	9.311	-2.077	-2.077	0.000	0.000	0.000	0.000
10	A	3	LEU	0	0.035	0.020	7.406	1.770	1.770	0.000	0.000	0.000	0.000
11	A	4	SER	0	0.025	0.008	8.329	-1.858	-1.858	0.000	0.000	0.000	0.000
12	A	5	ILE	0	-0.047	-0.013	10.117	-0.237	-0.237	0.000	0.000	0.000	0.000
13	A	6	PRO	0	-0.013	-0.007	12.085	0.030	0.030	0.000	0.000	0.000	0.000
14	A	7	SER	0	-0.014	0.019	13.856	-1.381	-1.381	0.000	0.000	0.000	0.000
15	A	8	GLN	0	0.009	0.016	16.749	0.247	0.247	0.000	0.000	0.000	0.000
16	A	9	VAL	0	0.046	0.027	18.093	-0.271	-0.271	0.000	0.000	0.000	0.000
17	A	10	VAL	0	-0.056	-0.047	20.646	-0.554	-0.554	0.000	0.000	0.000	0.000
18	A	11	ALA	0	0.003	-0.005	23.632	-0.600	-0.600	0.000	0.000	0.000	0.000
19	A	12	VAL	0	0.004	0.007	22.147	0.572	0.572	0.000	0.000	0.000	0.000
20	A	13	ASP	-1	-0.877	-0.934	24.471	10.248	10.248	0.000	0.000	0.000	0.000
21	A	14	ASN	0	0.032	-0.010	23.226	0.652	0.652	0.000	0.000	0.000	0.000
22	A	15	GLU	-1	-0.969	-0.972	25.501	9.807	9.807	0.000	0.000	0.000	0.000
23	A	16	ARG	1	0.872	0.933	27.375	-9.919	-9.919	0.000	0.000	0.000	0.000
24	A	17	GLN	0	-0.031	0.004	22.159	0.728	0.728	0.000	0.000	0.000	0.000
25	A	18	SER	0	-0.017	0.002	21.816	0.341	0.341	0.000	0.000	0.000	0.000
26	A	19	VAL	0	0.025	0.012	18.261	-0.169	-0.169	0.000	0.000	0.000	0.000
27	A	20	THR	0	-0.028	-0.044	21.547	0.094	0.094	0.000	0.000	0.000	0.000
28	A	21	VAL	0	-0.011	-0.002	17.251	0.084	0.084	0.000	0.000	0.000	0.000
29	A	22	ASP	-1	-0.863	-0.937	20.474	11.921	11.921	0.000	0.000	0.000	0.000
30	A	23	THR	0	-0.023	-0.049	16.782	0.443	0.443	0.000	0.000	0.000	0.000
31	A	24	LEU	0	-0.035	-0.027	18.045	-0.384	-0.384	0.000	0.000	0.000	0.000
32	A	25	GLY	0	0.021	0.018	21.076	-0.427	-0.427	0.000	0.000	0.000	0.000
33	A	26	VAL	0	-0.065	-0.025	22.226	-0.449	-0.449	0.000	0.000	0.000	0.000
34	A	27	ARG	1	0.899	0.951	22.224	-10.630	-10.630	0.000	0.000	0.000	0.000
35	A	28	ARG	1	0.935	0.963	19.645	-14.374	-14.374	0.000	0.000	0.000	0.000
36	A	29	ASP	-1	-0.806	-0.848	21.884	11.977	11.977	0.000	0.000	0.000	0.000
37	A	30	VAL	0	-0.069	-0.052	17.406	0.124	0.124	0.000	0.000	0.000	0.000
38	A	31	SER	0	0.033	0.019	19.645	-0.225	-0.225	0.000	0.000	0.000	0.000
39	A	32	SER	0	0.043	-0.001	17.757	0.558	0.558	0.000	0.000	0.000	0.000
40	A	33	HIS	0	-0.042	-0.032	17.808	0.168	0.168	0.000	0.000	0.000	0.000
41	A	34	LEU	0	-0.033	-0.007	12.667	0.259	0.259	0.000	0.000	0.000	0.000
42	A	35	MET	0	-0.027	0.006	12.601	1.486	1.486	0.000	0.000	0.000	0.000
43	A	36	THR	0	0.000	-0.013	9.344	-0.132	-0.132	0.000	0.000	0.000	0.000
44	A	37	GLU	-1	-0.971	-0.975	12.794	19.720	19.720	0.000	0.000	0.000	0.000
45	A	38	PRO	0	-0.064	-0.039	15.919	-0.126	-0.126	0.000	0.000	0.000	0.000
46	A	39	LEU	0	0.044	0.033	15.431	0.153	0.153	0.000	0.000	0.000	0.000
47	A	40	ALA	0	-0.034	-0.024	19.498	-0.815	-0.815	0.000	0.000	0.000	0.000
48	A	41	ILE	0	-0.041	-0.039	21.599	0.360	0.360	0.000	0.000	0.000	0.000
49	A	42	GLY	0	-0.032	-0.012	22.967	-0.260	-0.260	0.000	0.000	0.000	0.000
50	A	43	ASP	-1	-0.826	-0.886	17.742	15.242	15.242	0.000	0.000	0.000	0.000
51	A	44	TYR	0	-0.050	-0.038	15.504	-0.382	-0.382	0.000	0.000	0.000	0.000
52	A	45	VAL	0	0.007	0.007	12.990	0.848	0.848	0.000	0.000	0.000	0.000
53	A	46	LEU	0	-0.034	-0.027	7.355	-0.822	-0.822	0.000	0.000	0.000	0.000
54	A	47	ILE	0	0.018	0.005	10.019	0.535	0.535	0.000	0.000	0.000	0.000
55	A	48	HIS	0	0.022	0.010	5.817	-1.345	-1.345	0.000	0.000	0.000	0.000
56	A	49	ILE	0	-0.044	-0.001	9.162	-1.241	-1.241	0.000	0.000	0.000	0.000
57	A	50	GLY	0	0.028	0.000	8.680	2.960	2.960	0.000	0.000	0.000	0.000
58	A	51	PHE	0	-0.063	-0.029	9.752	-2.566	-2.566	0.000	0.000	0.000	0.000
59	A	52	VAL	0	0.056	0.034	10.686	2.292	2.292	0.000	0.000	0.000	0.000
60	A	53	MET	0	-0.033	-0.024	11.956	-1.292	-1.292	0.000	0.000	0.000	0.000
61	A	54	ASN	0	0.038	0.030	15.409	0.185	0.185	0.000	0.000	0.000	0.000
62	A	55	LYS	1	0.928	0.960	18.949	-12.987	-12.987	0.000	0.000	0.000	0.000
63	A	56	ILE	0	0.052	0.023	21.652	-0.244	-0.244	0.000	0.000	0.000	0.000
64	A	57	ASP	-1	-0.887	-0.945	24.826	10.586	10.586	0.000	0.000	0.000	0.000
65	A	58	ARG	1	0.982	0.981	27.835	-10.991	-10.991	0.000	0.000	0.000	0.000
66	A	59	ASN	0	-0.023	-0.021	28.722	0.017	0.017	0.000	0.000	0.000	0.000
67	A	60	ASP	-1	-0.835	-0.903	29.758	10.041	10.041	0.000	0.000	0.000	0.000
68	A	61	ALA	0	-0.041	-0.028	26.610	0.035	0.035	0.000	0.000	0.000	0.000
69	A	62	LEU	0	-0.061	-0.047	28.416	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	63	GLN	0	0.004	0.011	30.814	-0.114	-0.114	0.000	0.000	0.000	0.000
71	A	64	SER	0	-0.033	-0.004	29.234	0.000	0.000	0.000	0.000	0.000	0.000
72	A	65	LEU	0	0.000	-0.018	25.756	0.024	0.024	0.000	0.000	0.000	0.000
73	A	66	GLU	-1	-0.928	-0.958	29.846	8.923	8.923	0.000	0.000	0.000	0.000
74	A	67	LEU	0	0.032	0.020	32.522	-0.076	-0.076	0.000	0.000	0.000	0.000
75	A	68	TYR	0	-0.039	-0.025	25.551	0.177	0.177	0.000	0.000	0.000	0.000
76	A	69	GLN	0	0.018	-0.003	29.385	0.142	0.142	0.000	0.000	0.000	0.000
77	A	70	GLU	-1	-0.914	-0.944	30.924	8.588	8.588	0.000	0.000	0.000	0.000
78	A	71	ILE	0	-0.041	-0.016	29.633	-0.166	-0.166	0.000	0.000	0.000	0.000
79	A	72	VAL	0	-0.020	-0.015	27.412	-0.068	-0.068	0.000	0.000	0.000	0.000
80	A	73	SER	0	-0.030	-0.020	30.174	-0.141	-0.141	0.000	0.000	0.000	0.000
81	A	74	LYS	1	0.866	0.943	33.643	-8.615	-8.615	0.000	0.000	0.000	0.000
82	A	75	LEU	0	-0.078	-0.059	30.496	-0.219	-0.219	0.000	0.000	0.000	0.000
83	A	76	GLU	-1	-0.984	-0.951	29.889	10.557	10.557	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-6:GLU)