FMO DATABASE

FMODB ID: 1NV9Z

Calculation Name: 4RS8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RS8

Chain ID: A

ChEMBL ID:

UniProt ID: O93706

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	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	84
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-575362.382839
FMO2-HF: Nuclear repulsion	542025.929802
FMO2-HF: Total energy	-33336.453037
FMO2-MP2: Total energy	-33436.123331

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:9:TYR)

Summations of interaction energy for fragment #1(A:9:TYR)

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.
-16.385	-7.424	11.139	-6.558	-13.54	0.007

Interaction energy analysis for fragmet #1(A:9:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.035

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	11	PHE	0	0.043	0.026	3.819	-1.708	-0.194	-0.011	-0.644	-0.858	0.001
4	A	12	LEU	0	-0.002	0.012	3.332	-0.648	0.014	0.014	-0.155	-0.521	0.000
5	A	13	THR	0	0.041	0.014	2.343	-5.588	-3.951	3.864	-2.399	-3.102	-0.028
6	A	14	PRO	0	0.055	0.004	2.443	-4.220	-1.193	2.378	-1.555	-3.850	0.017
7	A	15	ARG	1	0.941	0.975	3.259	0.480	0.151	0.073	0.534	-0.277	0.002
8	A	16	ALA	0	0.015	0.027	5.634	0.101	0.101	0.000	0.000	0.000	0.000
9	A	17	TYR	0	0.051	0.020	2.649	-1.526	0.072	0.629	-0.468	-1.760	0.001
10	A	18	ILE	0	-0.017	-0.006	6.053	0.300	0.300	0.000	0.000	0.000	0.000
11	A	19	ILE	0	0.000	-0.012	8.054	0.172	0.172	0.000	0.000	0.000	0.000
12	A	20	VAL	0	0.020	0.004	9.706	0.098	0.098	0.000	0.000	0.000	0.000
13	A	21	HIS	0	0.001	0.004	9.885	0.060	0.060	0.000	0.000	0.000	0.000
14	A	22	LEU	0	0.002	-0.015	11.635	0.091	0.091	0.000	0.000	0.000	0.000
15	A	23	LEU	0	-0.043	-0.006	14.037	0.054	0.054	0.000	0.000	0.000	0.000
16	A	24	LYS	1	0.937	0.978	13.115	0.298	0.298	0.000	0.000	0.000	0.000
17	A	25	VAL	0	-0.015	0.004	15.095	0.028	0.028	0.000	0.000	0.000	0.000
18	A	26	GLY	0	-0.010	0.012	17.447	0.029	0.029	0.000	0.000	0.000	0.000
19	A	27	LYS	1	0.767	0.857	18.457	0.097	0.097	0.000	0.000	0.000	0.000
20	A	28	ALA	0	0.033	0.018	14.593	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	29	LYS	1	0.891	0.940	16.031	0.054	0.054	0.000	0.000	0.000	0.000
22	A	30	ALA	0	0.018	0.003	12.608	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	31	SER	0	0.038	0.007	11.453	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	32	GLU	-1	-0.785	-0.888	11.958	-0.151	-0.151	0.000	0.000	0.000	0.000
25	A	33	ILE	0	-0.024	-0.007	8.293	-0.051	-0.051	0.000	0.000	0.000	0.000
26	A	34	SER	0	-0.096	-0.054	7.347	-0.196	-0.196	0.000	0.000	0.000	0.000
27	A	35	GLU	-1	-0.877	-0.937	7.416	-0.179	-0.179	0.000	0.000	0.000	0.000
28	A	36	ASN	0	-0.039	-0.020	9.608	0.044	0.044	0.000	0.000	0.000	0.000
29	A	37	THR	0	-0.096	-0.063	5.258	-0.198	-0.198	0.000	0.000	0.000	0.000
30	A	38	GLN	0	-0.022	-0.011	4.540	-0.930	-0.872	-0.001	-0.009	-0.048	0.000
31	A	39	ILE	0	-0.058	0.005	1.686	-1.159	-0.987	4.186	-1.689	-2.668	0.013
32	A	40	PRO	0	0.046	0.031	3.688	-0.566	-0.042	0.008	-0.172	-0.360	0.001
33	A	41	TYR	0	0.081	0.023	6.875	-0.131	-0.131	0.000	0.000	0.000	0.000
34	A	42	GLN	0	0.056	0.016	9.895	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	43	THR	0	0.060	0.035	5.095	-0.403	-0.305	-0.001	-0.001	-0.096	0.000
36	A	44	VAL	0	-0.001	0.026	6.925	-0.145	-0.145	0.000	0.000	0.000	0.000
37	A	45	ILE	0	0.024	0.015	8.562	-0.078	-0.078	0.000	0.000	0.000	0.000
38	A	46	GLN	0	-0.046	-0.028	10.631	0.008	0.008	0.000	0.000	0.000	0.000
39	A	47	ASN	0	-0.038	-0.052	7.130	-0.214	-0.214	0.000	0.000	0.000	0.000
40	A	48	ILE	0	0.019	0.018	10.251	-0.080	-0.080	0.000	0.000	0.000	0.000
41	A	49	ARG	1	0.963	0.982	12.810	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	50	TRP	0	0.052	0.027	12.729	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	51	LEU	0	0.024	0.003	10.625	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	52	LEU	0	-0.088	-0.038	14.747	0.006	0.006	0.000	0.000	0.000	0.000
45	A	53	ALA	0	-0.024	-0.009	17.758	0.004	0.004	0.000	0.000	0.000	0.000
46	A	54	GLU	-1	-0.897	-0.945	16.325	-0.192	-0.192	0.000	0.000	0.000	0.000
47	A	55	GLY	0	-0.017	0.003	19.073	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	56	TYR	0	-0.006	0.002	15.327	0.004	0.004	0.000	0.000	0.000	0.000
49	A	57	VAL	0	0.001	0.000	14.186	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	58	VAL	0	0.003	-0.001	17.630	0.019	0.019	0.000	0.000	0.000	0.000
51	A	59	LYS	1	0.941	0.964	19.631	0.062	0.062	0.000	0.000	0.000	0.000
52	A	60	GLU	-1	-0.839	-0.926	21.205	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	61	GLN	0	-0.017	-0.004	22.996	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.902	0.955	24.065	0.064	0.064	0.000	0.000	0.000	0.000
55	A	63	GLY	0	0.039	0.024	25.990	0.002	0.002	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.858	-0.921	26.638	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	65	GLU	-1	-0.891	-0.932	21.605	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	66	ILE	0	-0.016	-0.022	19.469	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	67	TYR	0	-0.012	-0.003	18.630	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	68	TYR	0	-0.031	-0.022	15.635	0.012	0.012	0.000	0.000	0.000	0.000
61	A	69	LYS	1	1.000	1.001	17.634	0.102	0.102	0.000	0.000	0.000	0.000
62	A	70	LEU	0	0.013	0.007	14.302	0.009	0.009	0.000	0.000	0.000	0.000
63	A	71	THR	0	-0.040	-0.022	18.153	0.017	0.017	0.000	0.000	0.000	0.000
64	A	72	ASP	-1	-0.856	-0.940	20.789	-0.139	-0.139	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.913	0.956	20.439	0.170	0.170	0.000	0.000	0.000	0.000
66	A	74	GLY	0	0.016	-0.004	17.910	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	75	LYS	1	0.938	0.968	17.332	0.128	0.128	0.000	0.000	0.000	0.000
68	A	76	GLN	0	-0.002	0.008	19.247	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	77	MET	0	-0.010	0.021	13.762	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	78	ALA	0	0.031	0.008	14.499	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	79	THR	0	0.004	-0.001	15.486	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	80	ALA	0	0.012	0.001	18.199	0.006	0.006	0.000	0.000	0.000	0.000
73	A	81	GLU	-1	-0.925	-0.977	12.959	-0.467	-0.467	0.000	0.000	0.000	0.000
74	A	82	LEU	0	-0.011	-0.014	12.618	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	83	GLU	-1	-0.789	-0.864	15.085	-0.128	-0.128	0.000	0.000	0.000	0.000
76	A	84	LYS	1	0.822	0.908	16.194	0.354	0.354	0.000	0.000	0.000	0.000
77	A	85	ILE	0	-0.004	0.004	10.505	0.005	0.005	0.000	0.000	0.000	0.000
78	A	86	ARG	1	0.850	0.903	14.177	0.157	0.157	0.000	0.000	0.000	0.000
79	A	87	LYS	1	0.993	0.996	16.888	0.203	0.203	0.000	0.000	0.000	0.000
80	A	88	LEU	0	-0.020	-0.008	12.414	0.009	0.009	0.000	0.000	0.000	0.000
81	A	89	VAL	0	-0.058	-0.027	14.046	0.028	0.028	0.000	0.000	0.000	0.000
82	A	90	GLU	-1	-0.976	-0.986	16.318	-0.065	-0.065	0.000	0.000	0.000	0.000
83	A	91	VAL	0	-0.070	-0.026	19.089	0.011	0.011	0.000	0.000	0.000	0.000
84	A	92	VAL	0	-0.038	-0.003	15.164	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:TYR)