FMO DATABASE

FMODB ID: VRGV1

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	OptAll
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	-118089.052395
FMO2-HF: Nuclear repulsion	104265.197759
FMO2-HF: Total energy	-13823.854636
FMO2-MP2: Total energy	-13863.186147

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.
-21.072	-21.252	13.034	-7.046	-5.808	-0.053

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 : 0.020 / q_NPA : -0.002

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	0.799	0.884	2.928	-2.551	0.283	0.097	-1.376	-1.555	0.006
4	A	759	ASP	-1	-0.766	-0.885	1.787	-20.276	-23.583	12.938	-5.561	-4.070	-0.059
5	A	760	PHE	0	0.002	0.016	4.208	1.718	2.011	-0.001	-0.109	-0.183	0.000
6	A	761	ILE	0	0.004	0.002	6.133	0.771	0.771	0.000	0.000	0.000	0.000
7	A	762	ASP	-1	-0.802	-0.862	7.395	-1.602	-1.602	0.000	0.000	0.000	0.000
8	A	763	THR	0	-0.017	-0.030	7.672	0.425	0.425	0.000	0.000	0.000	0.000
9	A	764	MET	0	0.013	0.019	9.992	0.347	0.347	0.000	0.000	0.000	0.000
10	A	765	THR	0	-0.041	-0.034	11.805	0.235	0.235	0.000	0.000	0.000	0.000
11	A	766	ARG	1	0.816	0.889	13.148	0.707	0.707	0.000	0.000	0.000	0.000
12	A	767	GLU	-1	-0.887	-0.947	13.224	-0.761	-0.761	0.000	0.000	0.000	0.000
13	A	768	LEU	0	-0.013	-0.009	15.611	0.093	0.093	0.000	0.000	0.000	0.000
14	A	769	TYR	0	-0.037	-0.012	17.634	0.055	0.055	0.000	0.000	0.000	0.000
15	A	770	ASP	-1	-0.788	-0.901	18.738	-0.483	-0.483	0.000	0.000	0.000	0.000
16	A	771	ALA	0	-0.020	0.003	20.179	0.038	0.038	0.000	0.000	0.000	0.000
17	A	772	PHE	0	-0.022	-0.013	20.987	0.039	0.039	0.000	0.000	0.000	0.000
18	A	773	LEU	0	-0.007	-0.006	23.021	0.026	0.026	0.000	0.000	0.000	0.000
19	A	774	HIS	0	-0.032	-0.006	24.520	0.023	0.023	0.000	0.000	0.000	0.000
20	A	775	GLU	-1	-0.790	-0.870	26.095	-0.119	-0.119	0.000	0.000	0.000	0.000
21	A	776	ARG	1	0.863	0.901	27.973	0.146	0.146	0.000	0.000	0.000	0.000
22	A	777	LEU	0	-0.004	-0.006	27.735	0.013	0.013	0.000	0.000	0.000	0.000
23	A	778	TYR	0	-0.010	-0.002	30.339	0.012	0.012	0.000	0.000	0.000	0.000
24	A	779	LEU	0	-0.035	-0.025	31.970	0.012	0.012	0.000	0.000	0.000	0.000
25	A	780	ILE	0	0.007	0.007	32.846	0.009	0.009	0.000	0.000	0.000	0.000
26	A	781	TYR	0	-0.019	-0.005	34.857	0.010	0.010	0.000	0.000	0.000	0.000
27	A	782	MET	0	-0.048	-0.029	35.886	0.008	0.008	0.000	0.000	0.000	0.000
28	A	783	ASP	-1	-0.919	-0.950	38.166	-0.082	-0.082	0.000	0.000	0.000	0.000
29	A	784	SER	0	-0.045	-0.026	39.437	0.004	0.004	0.000	0.000	0.000	0.000
30	A	785	ARG	1	0.848	0.926	40.676	0.106	0.106	0.000	0.000	0.000	0.000
31	A	786	ALA	0	-0.038	0.000	43.127	0.005	0.005	0.000	0.000	0.000	0.000

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