FMO DATABASE

FMODB ID: V2421

Calculation Name: 3FXD-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FXD

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZYC9

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	51
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-233035.292188
FMO2-HF: Nuclear repulsion	213706.647417
FMO2-HF: Total energy	-19328.64477
FMO2-MP2: Total energy	-19386.995925

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:ACE )

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

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.
1.169	2.184	-0.006	-0.468	-0.541	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.001

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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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	LEU	0	0.008	0.010	3.837	0.703	1.652	-0.006	-0.464	-0.479	-0.001
4	A	6	SER	0	0.044	0.026	5.129	0.383	0.449	0.000	-0.004	-0.062	0.000
5	A	7	ASP	-1	-0.868	-0.956	7.368	0.469	0.469	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.898	-0.940	9.974	-0.118	-0.118	0.000	0.000	0.000	0.000
7	A	9	GLN	0	0.022	-0.012	9.059	-0.122	-0.122	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.903	0.941	5.398	-0.764	-0.764	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.924	-0.955	11.484	0.078	0.078	0.000	0.000	0.000	0.000
10	A	12	THR	0	-0.038	0.009	14.462	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.011	-0.014	12.421	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.008	-0.006	15.382	0.005	0.005	0.000	0.000	0.000	0.000
13	A	15	LYS	1	1.006	1.000	16.953	0.007	0.007	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.037	0.032	19.376	0.001	0.001	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.003	-0.010	17.113	0.003	0.003	0.000	0.000	0.000	0.000
16	A	18	ASN	0	0.005	-0.007	20.007	0.003	0.003	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.826	-0.896	22.965	-0.023	-0.023	0.000	0.000	0.000	0.000
18	A	20	ALA	0	-0.003	0.005	24.407	0.000	0.000	0.000	0.000	0.000	0.000
19	A	21	ILE	0	-0.068	-0.032	23.085	0.002	0.002	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.969	-0.983	26.724	0.003	0.003	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.894	0.948	27.897	0.031	0.031	0.000	0.000	0.000	0.000
22	A	24	GLY	0	-0.024	-0.005	29.863	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	PRO	0	-0.027	-0.026	31.300	0.004	0.004	0.000	0.000	0.000	0.000
24	A	26	TRP	0	-0.058	-0.052	28.756	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.850	-0.914	33.323	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.870	0.933	36.497	0.013	0.013	0.000	0.000	0.000	0.000
27	A	29	SER	0	0.047	0.019	37.883	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	30	ASN	0	0.075	0.026	37.397	0.001	0.001	0.000	0.000	0.000	0.000
29	A	31	PHE	0	0.027	0.017	34.540	0.000	0.000	0.000	0.000	0.000	0.000
30	A	32	LEU	0	0.048	0.015	33.600	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.965	1.005	32.669	0.007	0.007	0.000	0.000	0.000	0.000
32	A	34	VAL	0	-0.051	-0.025	31.379	0.001	0.001	0.000	0.000	0.000	0.000
33	A	35	ILE	0	0.005	0.007	28.878	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	36	GLY	0	0.081	0.034	27.926	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.909	0.952	27.162	0.004	0.004	0.000	0.000	0.000	0.000
36	A	38	LYS	1	0.956	0.993	22.529	0.053	0.053	0.000	0.000	0.000	0.000
37	A	39	LEU	0	0.064	0.020	23.387	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	40	ILE	0	0.040	0.029	22.263	0.000	0.000	0.000	0.000	0.000	0.000
39	A	41	ALA	0	-0.001	0.010	21.921	0.006	0.006	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.075	-0.041	18.358	0.001	0.001	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.851	0.908	17.709	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.816	-0.908	17.508	0.040	0.040	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.847	0.924	12.980	0.042	0.042	0.000	0.000	0.000	0.000
44	A	46	PHE	0	-0.017	-0.010	10.725	0.015	0.015	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.072	0.032	12.536	0.030	0.030	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.961	0.984	13.493	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.892	0.938	9.395	0.112	0.112	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.035	-0.007	8.609	0.091	0.091	0.000	0.000	0.000	0.000
49	A	51	GLY	0	0.030	0.028	9.696	0.076	0.076	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.079	-0.027	9.417	0.001	0.001	0.000	0.000	0.000	0.000
51	A	53	NME	0	0.020	0.015	8.329	0.096	0.096	0.000	0.000	0.000	0.000

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