FMO DATABASE

FMODB ID: 76GVK

Calculation Name: 1XHM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XHM

Chain ID: B

ChEMBL ID:

UniProt ID: P62871

Base Structure: X-ray

Registration Date: 2023-09-21

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	46
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-159782.616188
FMO2-HF: Nuclear repulsion	141614.050062
FMO2-HF: Total energy	-18168.566126
FMO2-MP2: Total energy	-18219.790356

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(B:7:ALA)

Summations of interaction energy for fragment #1(B:7:ALA)

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.
-5.42	-1.759	0.648	-1.663	-2.646	0.012

Interaction energy analysis for fragmet #1(B:7:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / 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

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	B	9	ILE	0	0.053	0.006	3.048	-3.784	-0.304	0.649	-1.638	-2.490	0.012
4	B	10	ALA	0	0.021	0.014	4.731	-0.778	-0.597	-0.001	-0.025	-0.156	0.000
5	B	11	GLN	0	0.029	0.000	6.554	0.008	0.008	0.000	0.000	0.000	0.000
6	B	12	ALA	0	0.022	0.025	7.278	-0.012	-0.012	0.000	0.000	0.000	0.000
7	B	13	ARG	1	0.839	0.894	8.005	-0.320	-0.320	0.000	0.000	0.000	0.000
8	B	14	LYS	1	0.860	0.920	10.207	-0.132	-0.132	0.000	0.000	0.000	0.000
9	B	15	LEU	0	0.039	0.031	12.301	-0.031	-0.031	0.000	0.000	0.000	0.000
10	B	16	VAL	0	0.044	0.020	13.185	-0.047	-0.047	0.000	0.000	0.000	0.000
11	B	17	GLU	-1	-0.808	-0.875	14.293	0.079	0.079	0.000	0.000	0.000	0.000
12	B	18	GLN	0	0.032	0.005	16.081	-0.037	-0.037	0.000	0.000	0.000	0.000
13	B	19	LEU	0	0.043	0.016	16.649	-0.011	-0.011	0.000	0.000	0.000	0.000
14	B	20	LYS	1	0.880	0.940	17.037	-0.307	-0.307	0.000	0.000	0.000	0.000
15	B	21	MET	0	-0.038	-0.013	19.643	-0.021	-0.021	0.000	0.000	0.000	0.000
16	B	22	GLU	-1	-0.904	-0.937	22.191	0.099	0.099	0.000	0.000	0.000	0.000
17	B	23	ALA	0	-0.019	-0.011	23.378	-0.009	-0.009	0.000	0.000	0.000	0.000
18	B	24	ASN	0	-0.064	-0.029	24.900	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	25	ILE	0	0.023	0.018	26.805	-0.008	-0.008	0.000	0.000	0.000	0.000
20	B	26	ASP	-1	-0.901	-0.933	29.850	0.067	0.067	0.000	0.000	0.000	0.000
21	B	27	ARG	1	0.831	0.909	27.466	-0.099	-0.099	0.000	0.000	0.000	0.000
22	B	28	ILE	0	0.032	0.012	34.859	0.000	0.000	0.000	0.000	0.000	0.000
23	B	29	LYS	1	0.886	0.941	37.626	-0.057	-0.057	0.000	0.000	0.000	0.000
24	B	30	VAL	0	0.109	0.035	37.617	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	31	SER	0	0.019	0.015	40.149	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	32	LYS	1	0.865	0.916	42.766	-0.036	-0.036	0.000	0.000	0.000	0.000
27	B	33	ALA	0	0.029	0.026	40.064	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	34	ALA	0	0.018	-0.002	42.127	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	35	ALA	0	0.006	0.005	44.299	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	36	ASP	-1	-0.818	-0.908	43.664	0.030	0.030	0.000	0.000	0.000	0.000
31	B	37	LEU	0	-0.022	-0.007	41.234	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	38	MET	0	-0.005	0.004	45.654	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	39	ALA	0	0.051	0.037	49.100	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	40	TYR	0	-0.027	-0.017	47.437	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	41	CYS	0	-0.034	-0.031	47.975	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	42	GLU	-1	-0.900	-0.960	50.719	0.019	0.019	0.000	0.000	0.000	0.000
37	B	43	ALA	0	-0.058	-0.023	52.600	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	44	HIS	1	0.804	0.879	50.495	-0.014	-0.014	0.000	0.000	0.000	0.000
39	B	45	ALA	0	0.078	0.058	53.830	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	46	LYS	1	0.815	0.897	55.455	-0.011	-0.011	0.000	0.000	0.000	0.000
41	B	47	GLU	-1	-0.846	-0.898	54.916	0.009	0.009	0.000	0.000	0.000	0.000
42	B	48	ASP	-1	-0.843	-0.911	52.333	0.009	0.009	0.000	0.000	0.000	0.000
43	B	49	PRO	0	0.004	-0.005	55.114	0.000	0.000	0.000	0.000	0.000	0.000
44	B	50	LEU	0	-0.107	-0.030	52.023	0.000	0.000	0.000	0.000	0.000	0.000
45	B	51	LEU	0	-0.048	-0.032	53.426	0.001	0.001	0.000	0.000	0.000	0.000
46	B	52	THR	0	-0.065	-0.030	57.582	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:7:ALA)