FMO DATABASE

FMODB ID: 53VYZ

Calculation Name: 4C31-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C31

Chain ID: A

ChEMBL ID:

UniProt ID: P20676

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	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	31
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-117940.375928
FMO2-HF: Nuclear repulsion	104116.765855
FMO2-HF: Total energy	-13823.610074
FMO2-MP2: Total energy	-13862.936066

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:756:SER)

Summations of interaction energy for fragment #1(A:756:SER)

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.
-13.656	-7.159	0.392	-3.301	-3.588	-0.003

Interaction energy analysis for fragmet #1(A:756:SER)

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 : 0.025

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	758	LYS	1	0.827	0.900	3.037	-5.434	-1.966	0.107	-1.783	-1.792	0.010
4	A	759	ASP	-1	-0.826	-0.916	2.548	-9.148	-6.423	0.286	-1.413	-1.598	-0.013
5	A	760	PHE	0	-0.032	-0.012	4.330	0.974	1.278	-0.001	-0.105	-0.198	0.000
6	A	761	ILE	0	0.024	0.001	6.173	0.353	0.353	0.000	0.000	0.000	0.000
7	A	762	ASP	-1	-0.806	-0.859	7.287	-0.894	-0.894	0.000	0.000	0.000	0.000
8	A	763	THR	0	-0.023	-0.013	8.418	0.215	0.215	0.000	0.000	0.000	0.000
9	A	764	MET	0	0.017	0.015	10.259	0.206	0.206	0.000	0.000	0.000	0.000
10	A	765	THR	0	-0.054	-0.044	11.742	0.129	0.129	0.000	0.000	0.000	0.000
11	A	766	ARG	1	0.916	0.950	13.366	0.361	0.361	0.000	0.000	0.000	0.000
12	A	767	GLU	-1	-0.871	-0.930	14.223	-0.363	-0.363	0.000	0.000	0.000	0.000
13	A	768	LEU	0	-0.006	-0.004	15.964	0.046	0.046	0.000	0.000	0.000	0.000
14	A	769	TYR	0	-0.076	-0.030	17.753	0.029	0.029	0.000	0.000	0.000	0.000
15	A	770	ASP	-1	-0.858	-0.945	18.778	-0.260	-0.260	0.000	0.000	0.000	0.000
16	A	771	ALA	0	-0.021	-0.001	20.563	0.017	0.017	0.000	0.000	0.000	0.000
17	A	772	PHE	0	-0.003	-0.005	21.282	0.016	0.016	0.000	0.000	0.000	0.000
18	A	773	LEU	0	-0.010	-0.012	23.830	0.010	0.010	0.000	0.000	0.000	0.000
19	A	774	HIS	0	-0.038	-0.012	24.723	0.012	0.012	0.000	0.000	0.000	0.000
20	A	775	GLU	-1	-0.902	-0.959	26.461	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	776	ARG	1	0.915	0.960	28.257	0.033	0.033	0.000	0.000	0.000	0.000
22	A	777	LEU	0	0.001	-0.005	28.337	0.004	0.004	0.000	0.000	0.000	0.000
23	A	778	TYR	0	0.011	0.012	30.816	0.004	0.004	0.000	0.000	0.000	0.000
24	A	779	LEU	0	-0.010	-0.019	32.245	0.005	0.005	0.000	0.000	0.000	0.000
25	A	780	ILE	0	0.007	0.016	33.275	0.004	0.004	0.000	0.000	0.000	0.000
26	A	781	TYR	0	-0.022	-0.020	35.346	0.002	0.002	0.000	0.000	0.000	0.000
27	A	782	MET	0	-0.051	-0.041	36.553	0.002	0.002	0.000	0.000	0.000	0.000
28	A	783	ASP	-1	-0.963	-0.972	38.452	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	784	SER	0	-0.029	-0.001	39.847	0.002	0.002	0.000	0.000	0.000	0.000
30	A	785	ARG	1	0.858	0.936	40.809	0.047	0.047	0.000	0.000	0.000	0.000
31	A	786	ALA	0	-0.023	0.008	43.416	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:756:SER)