FMO DATABASE

FMODB ID: Q1ZLY

Calculation Name: 3FXD-A-Xray372

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: 2023-06-19

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-229936.891255
FMO2-HF: Nuclear repulsion	210778.761386
FMO2-HF: Total energy	-19158.129869
FMO2-MP2: Total energy	-19215.901554

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:4:GLN)

Summations of interaction energy for fragment #1(A:4:GLN)

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.
-0.142	1.532	-0.015	-0.811	-0.848	0.002

Interaction energy analysis for fragmet #1(A:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.022

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	6	SER	0	0.045	0.019	3.811	-0.312	1.362	-0.015	-0.811	-0.848	0.002
4	A	7	ASP	-1	-0.811	-0.924	6.037	0.698	0.698	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.898	-0.937	9.152	0.348	0.348	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.026	0.010	5.726	-0.470	-0.470	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.828	0.894	5.764	-1.281	-1.281	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.937	-0.966	9.809	0.169	0.169	0.000	0.000	0.000	0.000
9	A	12	THR	0	-0.010	0.008	11.824	-0.032	-0.032	0.000	0.000	0.000	0.000
10	A	13	ILE	0	-0.031	-0.017	8.912	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.007	-0.003	13.115	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.961	0.975	14.891	-0.114	-0.114	0.000	0.000	0.000	0.000
13	A	16	ALA	0	0.036	0.028	16.033	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.003	-0.008	14.198	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	18	ASN	0	0.020	-0.002	18.253	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	19	ASP	-1	-0.835	-0.893	20.756	0.065	0.065	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.047	0.027	21.302	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.079	-0.041	20.439	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.937	-0.963	24.110	0.053	0.053	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.841	0.908	25.184	-0.060	-0.060	0.000	0.000	0.000	0.000
21	A	24	GLY	0	-0.007	0.018	26.980	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	25	PRO	0	-0.009	-0.016	28.195	0.000	0.000	0.000	0.000	0.000	0.000
23	A	26	TRP	0	-0.051	-0.049	24.986	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	27	ASP	-1	-0.848	-0.916	30.428	0.008	0.008	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.862	0.931	33.821	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	29	SER	0	0.041	0.018	34.893	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.060	0.025	34.448	0.000	0.000	0.000	0.000	0.000	0.000
28	A	31	PHE	0	0.034	0.020	30.276	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.055	0.017	29.931	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.953	0.988	29.610	0.015	0.015	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.041	-0.019	28.172	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.007	0.001	25.259	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	36	GLY	0	0.084	0.038	24.816	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.914	0.952	24.502	0.018	0.018	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.952	0.990	19.537	0.117	0.117	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.046	0.021	19.581	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.046	0.025	19.612	0.005	0.005	0.000	0.000	0.000	0.000
38	A	41	ALA	0	-0.002	0.010	19.904	0.005	0.005	0.000	0.000	0.000	0.000
39	A	42	ILE	0	-0.069	-0.038	15.199	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	43	ARG	1	0.836	0.900	15.245	-0.043	-0.043	0.000	0.000	0.000	0.000
41	A	44	ASP	-1	-0.802	-0.900	15.779	0.046	0.046	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.863	0.936	12.498	0.193	0.193	0.000	0.000	0.000	0.000
43	A	46	PHE	0	-0.013	-0.011	8.243	0.016	0.016	0.000	0.000	0.000	0.000
44	A	47	LEU	0	0.060	0.030	11.361	0.083	0.083	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.952	0.976	13.417	0.061	0.061	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.893	0.943	7.857	0.299	0.299	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.006	0.002	7.940	0.136	0.136	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.018	0.028	9.896	0.029	0.029	0.000	0.000	0.000	0.000
49	A	52	ALA	0	-0.059	-0.017	10.861	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLN)