FMO DATABASE

FMODB ID: 7654K

Calculation Name: 3FIF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FIF

Chain ID: A

ChEMBL ID:

UniProt ID: P65294

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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-279333.988912
FMO2-HF: Nuclear repulsion	256658.405028
FMO2-HF: Total energy	-22675.583885
FMO2-MP2: Total energy	-22739.70141

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-6.147	1.183	3.017	-4.205	-6.141	-0.01

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.034

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

Sort

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	TYR	0	-0.086	-0.057	2.587	2.446	4.139	0.472	-0.824	-1.340	0.000
4	A	6	VAL	0	-0.051	-0.024	6.312	-0.621	-0.621	0.000	0.000	0.000	0.000
5	A	7	MET	0	-0.009	-0.003	9.847	0.241	0.241	0.000	0.000	0.000	0.000
6	A	8	ALA	0	0.009	0.002	12.815	-0.072	-0.072	0.000	0.000	0.000	0.000
7	A	9	THR	0	0.016	-0.004	15.791	0.008	0.008	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.914	0.959	19.163	-0.076	-0.076	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.892	-0.943	22.296	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.040	-0.019	21.673	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.899	0.958	19.730	0.049	0.049	0.000	0.000	0.000	0.000
12	A	14	MET	0	0.001	0.003	14.306	0.054	0.054	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.013	0.004	13.925	-0.051	-0.051	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.011	-0.005	11.105	0.064	0.064	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.101	-0.080	8.070	0.130	0.130	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.918	-0.926	8.245	-2.055	-2.055	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.068	0.028	5.756	0.271	0.271	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.895	0.938	5.313	-0.260	-0.260	0.000	0.000	0.000	0.000
19	A	21	PRO	0	-0.033	-0.016	6.685	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.953	-0.980	10.319	0.020	0.020	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.079	-0.039	13.025	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.742	-0.858	15.680	0.012	0.012	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.974	-1.003	18.806	0.117	0.117	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.951	-0.967	21.461	0.024	0.024	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.127	-0.071	21.574	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	28	GLY	0	-0.048	-0.015	22.301	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	29	LEU	0	-0.048	-0.028	20.229	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	30	VAL	0	-0.017	-0.006	14.344	0.017	0.017	0.000	0.000	0.000	0.000
29	A	31	SER	0	0.031	0.004	15.325	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	32	TYR	0	-0.043	-0.038	11.992	0.045	0.045	0.000	0.000	0.000	0.000
31	A	33	HIS	0	0.111	0.071	11.615	0.114	0.114	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.871	-0.929	12.075	-0.507	-0.507	0.000	0.000	0.000	0.000
33	A	35	GLN	0	0.069	0.022	10.760	-0.188	-0.188	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.104	-0.046	14.200	-0.057	-0.057	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.018	0.017	15.352	0.043	0.043	0.000	0.000	0.000	0.000
36	A	38	ASN	0	-0.033	-0.013	16.398	0.055	0.055	0.000	0.000	0.000	0.000
37	A	39	ALA	0	0.010	0.016	16.324	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	40	MET	0	-0.064	-0.033	16.604	0.053	0.053	0.000	0.000	0.000	0.000
39	A	41	GLN	0	0.027	0.005	17.140	0.015	0.015	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.033	-0.011	17.214	0.001	0.001	0.000	0.000	0.000	0.000
41	A	43	ASN	0	0.069	0.030	19.686	0.009	0.009	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.986	0.995	18.717	-0.120	-0.120	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.946	-0.966	20.282	0.073	0.073	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.929	-0.967	22.032	0.020	0.020	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.048	-0.028	15.584	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.075	-0.051	17.997	0.016	0.016	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.053	-0.033	14.047	0.031	0.031	0.000	0.000	0.000	0.000
48	A	50	ILE	0	0.023	0.021	9.269	-0.060	-0.060	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.038	-0.020	8.162	0.092	0.092	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.842	-0.919	2.894	-0.604	1.802	0.709	-1.446	-1.669	-0.006
51	A	53	ARG	1	0.873	0.938	4.323	-1.320	-1.073	0.001	-0.070	-0.178	0.000
52	A	54	LEU	0	0.010	0.000	2.548	-2.093	-0.723	1.365	-1.265	-1.469	-0.009
53	A	55	GLU	-1	-0.894	-0.937	2.773	-1.056	0.429	0.471	-0.584	-1.373	0.005
54	A	56	HIS	0	-0.037	-0.027	4.624	-0.556	-0.427	-0.001	-0.016	-0.112	0.000
55	A	57	HIS	0	-0.036	-0.005	7.130	-0.373	-0.373	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)