FMO DATABASE

FMODB ID: 39VJL

Calculation Name: 1XDT-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XDT

Chain ID: R

ChEMBL ID:

UniProt ID: P00588

Base Structure: X-ray

Registration Date: 2023-09-19

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	38
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-181424.19001
FMO2-HF: Nuclear repulsion	163561.403099
FMO2-HF: Total energy	-17862.786911
FMO2-MP2: Total energy	-17910.277877

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(R:107:PRO)

Summations of interaction energy for fragment #1(R:107:PRO)

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.
-13.633	-4.796	1.794	-3.367	-7.262	-0.004

Interaction energy analysis for fragmet #1(R:107:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.014

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	R	109	LEU	0	-0.008	0.007	3.361	-4.004	-1.187	0.030	-1.250	-1.597	0.004
4	R	110	ARG	1	0.990	0.989	2.385	-7.416	-5.412	0.412	-0.773	-1.643	0.004
5	R	111	LYS	1	0.967	0.981	3.579	0.337	0.686	0.006	-0.069	-0.285	0.000
6	R	112	TYR	0	0.004	-0.002	2.615	-0.597	0.485	0.298	-0.324	-1.056	0.000
7	R	113	LYS	1	0.911	0.959	5.969	-0.229	-0.229	0.000	0.000	0.000	0.000
8	R	114	ASP	-1	-0.810	-0.900	8.079	0.215	0.215	0.000	0.000	0.000	0.000
9	R	115	PHE	0	-0.005	0.004	8.791	-0.071	-0.071	0.000	0.000	0.000	0.000
10	R	116	CYS	0	-0.054	-0.010	9.051	0.020	0.020	0.000	0.000	0.000	0.000
11	R	117	ILE	0	0.031	0.020	12.089	0.058	0.058	0.000	0.000	0.000	0.000
12	R	118	HIS	1	0.850	0.946	15.728	-0.060	-0.060	0.000	0.000	0.000	0.000
13	R	119	GLY	0	0.091	0.028	14.378	-0.033	-0.033	0.000	0.000	0.000	0.000
14	R	120	GLU	-1	-0.914	-0.924	10.673	0.588	0.588	0.000	0.000	0.000	0.000
15	R	122	LYS	1	0.924	0.958	5.725	-0.128	-0.128	0.000	0.000	0.000	0.000
16	R	123	TYR	0	-0.002	0.004	2.991	-3.413	-0.939	1.049	-0.942	-2.581	-0.012
17	R	124	VAL	0	0.032	0.027	4.788	0.030	0.141	-0.001	-0.009	-0.100	0.000
18	R	125	LYS	1	0.873	0.904	6.101	0.555	0.555	0.000	0.000	0.000	0.000
19	R	126	GLU	-1	-0.849	-0.921	6.890	-0.552	-0.552	0.000	0.000	0.000	0.000
20	R	127	LEU	0	0.037	0.017	9.890	0.043	0.043	0.000	0.000	0.000	0.000
21	R	128	ARG	1	0.873	0.958	6.518	1.070	1.070	0.000	0.000	0.000	0.000
22	R	129	ALA	0	0.031	0.020	7.051	0.028	0.028	0.000	0.000	0.000	0.000
23	R	130	PRO	0	-0.041	-0.017	5.007	-0.185	-0.185	0.000	0.000	0.000	0.000
24	R	131	SER	0	-0.002	-0.006	6.328	0.170	0.170	0.000	0.000	0.000	0.000
25	R	133	ILE	0	0.007	0.006	11.084	-0.024	-0.024	0.000	0.000	0.000	0.000
26	R	134	CYS	0	-0.085	-0.020	13.567	0.088	0.088	0.000	0.000	0.000	0.000
27	R	135	HIS	0	-0.003	-0.013	15.166	-0.035	-0.035	0.000	0.000	0.000	0.000
28	R	136	PRO	0	0.027	-0.009	18.656	-0.022	-0.022	0.000	0.000	0.000	0.000
29	R	137	GLY	0	0.034	0.024	22.203	0.005	0.005	0.000	0.000	0.000	0.000
30	R	138	TYR	0	-0.027	-0.014	19.823	-0.007	-0.007	0.000	0.000	0.000	0.000
31	R	139	HIS	0	-0.019	-0.009	19.995	-0.013	-0.013	0.000	0.000	0.000	0.000
32	R	140	GLY	0	0.034	0.008	18.663	0.010	0.010	0.000	0.000	0.000	0.000
33	R	141	GLU	-1	-0.870	-0.939	14.275	-0.117	-0.117	0.000	0.000	0.000	0.000
34	R	142	ARG	1	0.855	0.895	13.030	0.021	0.021	0.000	0.000	0.000	0.000
35	R	144	HIS	0	0.078	0.033	17.222	0.031	0.031	0.000	0.000	0.000	0.000
36	R	145	GLY	0	0.018	0.011	19.514	0.013	0.013	0.000	0.000	0.000	0.000
37	R	146	LEU	0	0.006	0.013	22.424	0.001	0.001	0.000	0.000	0.000	0.000
38	R	147	SER	0	-0.008	-0.005	24.947	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(R:107:PRO)