FMO DATABASE

FMODB ID: 2NQ8R

Calculation Name: 3TYS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TYS

Chain ID: A

ChEMBL ID:

UniProt ID: Q6WRY9

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-462503.212475
FMO2-HF: Nuclear repulsion	432013.956596
FMO2-HF: Total energy	-30489.25588
FMO2-MP2: Total energy	-30576.699245

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:ARG)

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

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.
24.967	26.352	0.01	-0.516	-0.879	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.887 / q_NPA : 0.906

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	-5	ASN	0	-0.016	-0.013	3.520	7.425	8.810	0.010	-0.516	-0.879	0.001
4	A	-4	LEU	0	0.006	0.007	6.229	1.351	1.351	0.000	0.000	0.000	0.000
5	A	-3	TYR	0	0.017	0.001	8.781	1.858	1.858	0.000	0.000	0.000	0.000
6	A	-2	PHE	0	-0.003	-0.002	11.673	1.692	1.692	0.000	0.000	0.000	0.000
7	A	-1	GLN	0	-0.055	-0.045	9.711	-0.566	-0.566	0.000	0.000	0.000	0.000
8	A	0	GLY	0	0.067	0.057	12.496	0.434	0.434	0.000	0.000	0.000	0.000
9	A	1	MET	0	-0.059	-0.023	15.146	0.849	0.849	0.000	0.000	0.000	0.000
10	A	2	ARG	1	0.861	0.927	14.951	13.255	13.255	0.000	0.000	0.000	0.000
11	A	3	VAL	0	0.005	0.015	16.186	0.439	0.439	0.000	0.000	0.000	0.000
12	A	4	SER	0	0.002	-0.004	17.961	0.568	0.568	0.000	0.000	0.000	0.000
13	A	5	TYR	0	0.037	-0.019	17.131	-0.297	-0.297	0.000	0.000	0.000	0.000
14	A	6	ASN	0	-0.025	-0.017	23.216	0.421	0.421	0.000	0.000	0.000	0.000
15	A	7	LYS	1	0.859	0.938	25.211	12.046	12.046	0.000	0.000	0.000	0.000
16	A	8	LEU	0	0.070	0.049	23.749	0.267	0.267	0.000	0.000	0.000	0.000
17	A	9	TRP	0	-0.058	-0.033	24.663	0.337	0.337	0.000	0.000	0.000	0.000
18	A	10	LYS	1	0.951	0.970	29.521	9.850	9.850	0.000	0.000	0.000	0.000
19	A	11	LEU	0	0.066	0.052	28.375	0.242	0.242	0.000	0.000	0.000	0.000
20	A	12	LEU	0	-0.046	-0.034	28.706	0.158	0.158	0.000	0.000	0.000	0.000
21	A	13	ILE	0	-0.010	0.000	32.242	0.233	0.233	0.000	0.000	0.000	0.000
22	A	14	ASP	-1	-0.894	-0.939	34.465	-8.514	-8.514	0.000	0.000	0.000	0.000
23	A	15	ARG	1	0.787	0.894	31.439	9.550	9.550	0.000	0.000	0.000	0.000
24	A	16	ASP	-1	-0.914	-0.947	36.168	-7.530	-7.530	0.000	0.000	0.000	0.000
25	A	17	MET	0	-0.072	-0.030	32.283	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	18	LYS	1	0.848	0.906	33.848	7.989	7.989	0.000	0.000	0.000	0.000
27	A	19	LYS	1	1.006	0.983	28.136	9.885	9.885	0.000	0.000	0.000	0.000
28	A	20	GLY	0	-0.058	-0.034	29.252	-0.306	-0.306	0.000	0.000	0.000	0.000
29	A	21	GLU	-1	-0.742	-0.867	30.892	-8.595	-8.595	0.000	0.000	0.000	0.000
30	A	22	LEU	0	0.044	0.040	25.630	-0.119	-0.119	0.000	0.000	0.000	0.000
31	A	23	ARG	1	0.769	0.866	25.696	9.882	9.882	0.000	0.000	0.000	0.000
32	A	24	GLU	-1	-0.881	-0.943	26.775	-9.718	-9.718	0.000	0.000	0.000	0.000
33	A	25	ALA	0	-0.009	0.018	29.351	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	26	VAL	0	-0.004	-0.001	23.327	-0.145	-0.145	0.000	0.000	0.000	0.000
35	A	27	GLY	0	0.032	0.035	24.628	-0.339	-0.339	0.000	0.000	0.000	0.000
36	A	28	VAL	0	-0.076	-0.031	20.592	-0.510	-0.510	0.000	0.000	0.000	0.000
37	A	29	SER	0	0.057	0.029	20.054	0.372	0.372	0.000	0.000	0.000	0.000
38	A	30	LYS	1	1.022	0.986	22.698	10.290	10.290	0.000	0.000	0.000	0.000
39	A	31	SER	0	0.017	0.008	19.315	0.062	0.062	0.000	0.000	0.000	0.000
40	A	32	THR	0	-0.002	-0.013	17.107	-0.548	-0.548	0.000	0.000	0.000	0.000
41	A	33	PHE	0	0.058	0.026	19.282	-0.108	-0.108	0.000	0.000	0.000	0.000
42	A	34	ALA	0	-0.010	-0.012	21.693	0.168	0.168	0.000	0.000	0.000	0.000
43	A	35	LYS	1	0.908	0.965	13.293	18.134	18.134	0.000	0.000	0.000	0.000
44	A	36	LEU	0	0.038	0.033	19.418	-0.087	-0.087	0.000	0.000	0.000	0.000
45	A	37	GLY	0	-0.053	-0.016	21.480	0.260	0.260	0.000	0.000	0.000	0.000
46	A	38	LYS	1	0.788	0.886	19.244	13.607	13.607	0.000	0.000	0.000	0.000
47	A	39	ASN	0	0.027	0.025	20.052	-0.331	-0.331	0.000	0.000	0.000	0.000
48	A	40	GLU	-1	-0.776	-0.870	15.734	-14.868	-14.868	0.000	0.000	0.000	0.000
49	A	41	ASN	0	0.049	0.027	10.877	1.302	1.302	0.000	0.000	0.000	0.000
50	A	42	VAL	0	-0.006	-0.003	14.158	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	43	SER	0	-0.001	-0.002	12.223	-0.448	-0.448	0.000	0.000	0.000	0.000
52	A	44	LEU	0	0.117	0.040	11.557	1.079	1.079	0.000	0.000	0.000	0.000
53	A	45	THR	0	0.015	0.007	13.871	0.513	0.513	0.000	0.000	0.000	0.000
54	A	46	VAL	0	-0.016	-0.005	15.836	1.005	1.005	0.000	0.000	0.000	0.000
55	A	47	LEU	0	-0.011	-0.010	16.274	0.773	0.773	0.000	0.000	0.000	0.000
56	A	48	LEU	0	0.036	0.019	16.424	0.538	0.538	0.000	0.000	0.000	0.000
57	A	49	ALA	0	0.036	0.029	19.751	0.652	0.652	0.000	0.000	0.000	0.000
58	A	50	ILE	0	-0.030	-0.017	21.475	0.657	0.657	0.000	0.000	0.000	0.000
59	A	51	CYS	0	-0.036	-0.014	22.479	0.351	0.351	0.000	0.000	0.000	0.000
60	A	52	GLU	-1	-0.939	-0.963	23.892	-11.645	-11.645	0.000	0.000	0.000	0.000
61	A	53	TYR	0	-0.017	-0.011	25.729	0.488	0.488	0.000	0.000	0.000	0.000
62	A	54	LEU	0	-0.029	-0.028	26.985	0.459	0.459	0.000	0.000	0.000	0.000
63	A	55	ASN	0	-0.050	-0.012	28.462	0.418	0.418	0.000	0.000	0.000	0.000
64	A	56	CYS	0	-0.070	-0.014	25.569	0.209	0.209	0.000	0.000	0.000	0.000
65	A	57	ASP	-1	-0.788	-0.899	23.125	-13.401	-13.401	0.000	0.000	0.000	0.000
66	A	58	PHE	0	0.005	-0.025	17.197	-0.137	-0.137	0.000	0.000	0.000	0.000
67	A	59	GLY	0	-0.030	-0.017	21.895	-0.040	-0.040	0.000	0.000	0.000	0.000
68	A	60	ASP	-1	-0.839	-0.909	24.169	-10.544	-10.544	0.000	0.000	0.000	0.000
69	A	61	ILE	0	-0.067	-0.057	21.403	0.262	0.262	0.000	0.000	0.000	0.000
70	A	62	ILE	0	-0.064	-0.030	17.911	-0.222	-0.222	0.000	0.000	0.000	0.000
71	A	63	GLU	-1	-0.890	-0.943	21.439	-11.313	-11.313	0.000	0.000	0.000	0.000
72	A	64	ALA	0	-0.006	0.001	18.506	-0.395	-0.395	0.000	0.000	0.000	0.000
73	A	65	LEU	0	-0.011	-0.017	19.864	0.622	0.622	0.000	0.000	0.000	0.000
74	A	66	PRO	0	0.036	0.015	19.622	-0.674	-0.674	0.000	0.000	0.000	0.000
75	A	67	GLU	-1	-0.987	-0.987	17.006	-14.543	-14.543	0.000	0.000	0.000	0.000

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