FMO DATABASE

FMODB ID: JL9Q9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-181634.333239
FMO2-HF: Nuclear repulsion	163771.812448
FMO2-HF: Total energy	-17862.520791
FMO2-MP2: Total energy	-17910.030038

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.
-8.757	-3.333	5.855	-4.194	-7.084	-0.002

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 : 0.004 / q_NPA : -0.015

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	R	109	LEU	0	-0.007	0.005	3.383	-4.330	-1.554	0.025	-1.202	-1.599	0.003
4	R	110	ARG	1	0.982	0.991	1.671	-2.995	-3.663	5.432	-2.020	-2.745	0.000
5	R	111	LYS	1	0.994	0.993	3.583	0.638	0.990	0.006	-0.071	-0.287	0.000
6	R	112	TYR	0	-0.025	-0.015	3.178	-0.650	0.370	0.102	-0.288	-0.833	0.000
7	R	113	LYS	1	0.929	0.980	6.273	0.012	0.012	0.000	0.000	0.000	0.000
8	R	114	ASP	-1	-0.810	-0.923	8.079	0.123	0.123	0.000	0.000	0.000	0.000
9	R	115	PHE	0	-0.034	0.003	9.095	-0.061	-0.061	0.000	0.000	0.000	0.000
10	R	116	CYS	0	-0.048	-0.018	9.017	0.107	0.107	0.000	0.000	0.000	0.000
11	R	117	ILE	0	0.033	0.029	12.215	0.038	0.038	0.000	0.000	0.000	0.000
12	R	118	HIS	1	0.847	0.941	15.856	-0.119	-0.119	0.000	0.000	0.000	0.000
13	R	119	GLY	0	0.087	0.018	14.681	-0.034	-0.034	0.000	0.000	0.000	0.000
14	R	120	GLU	-1	-0.917	-0.935	11.672	0.760	0.760	0.000	0.000	0.000	0.000
15	R	122	LYS	1	0.933	0.960	6.646	-0.413	-0.413	0.000	0.000	0.000	0.000
16	R	123	TYR	0	-0.011	0.008	2.752	-2.591	-0.734	0.291	-0.606	-1.542	-0.005
17	R	124	VAL	0	0.045	0.033	4.865	0.006	0.093	-0.001	-0.007	-0.078	0.000
18	R	125	LYS	1	0.954	0.957	6.446	0.265	0.265	0.000	0.000	0.000	0.000
19	R	126	GLU	-1	-0.952	-0.989	7.271	-0.304	-0.304	0.000	0.000	0.000	0.000
20	R	127	LEU	0	0.041	0.019	10.383	0.008	0.008	0.000	0.000	0.000	0.000
21	R	128	ARG	1	0.882	0.955	6.441	0.867	0.867	0.000	0.000	0.000	0.000
22	R	129	ALA	0	0.033	0.021	7.223	-0.044	-0.044	0.000	0.000	0.000	0.000
23	R	130	PRO	0	-0.034	-0.011	5.298	-0.018	-0.018	0.000	0.000	0.000	0.000
24	R	131	SER	0	-0.004	-0.007	6.413	0.041	0.041	0.000	0.000	0.000	0.000
25	R	133	ILE	0	-0.003	0.002	11.744	-0.053	-0.053	0.000	0.000	0.000	0.000
26	R	134	CYS	0	-0.076	-0.018	14.108	0.074	0.074	0.000	0.000	0.000	0.000
27	R	135	HIS	0	0.000	0.004	15.881	-0.042	-0.042	0.000	0.000	0.000	0.000
28	R	136	PRO	0	0.021	-0.012	19.336	-0.024	-0.024	0.000	0.000	0.000	0.000
29	R	137	GLY	0	0.041	0.025	22.916	0.000	0.000	0.000	0.000	0.000	0.000
30	R	138	TYR	0	-0.026	-0.010	19.986	-0.015	-0.015	0.000	0.000	0.000	0.000
31	R	139	HIS	0	-0.001	-0.005	19.997	-0.007	-0.007	0.000	0.000	0.000	0.000
32	R	140	GLY	0	0.032	-0.003	18.768	0.002	0.002	0.000	0.000	0.000	0.000
33	R	141	GLU	-1	-0.898	-0.947	14.430	-0.021	-0.021	0.000	0.000	0.000	0.000
34	R	142	ARG	1	0.870	0.912	13.547	0.000	0.000	0.000	0.000	0.000	0.000
35	R	144	HIS	0	0.095	0.043	17.303	0.024	0.024	0.000	0.000	0.000	0.000
36	R	145	GLY	0	0.012	0.009	19.665	0.004	0.004	0.000	0.000	0.000	0.000
37	R	146	LEU	0	0.001	0.012	22.488	0.009	0.009	0.000	0.000	0.000	0.000
38	R	147	SER	0	-0.019	-0.009	24.998	-0.014	-0.014	0.000	0.000	0.000	0.000

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