FMO DATABASE

FMODB ID: 2N8VR

Calculation Name: 3S1B-A-Xray372

Preferred Name: Vascular endothelial growth factor A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3S1B

Chain ID: A

ChEMBL ID: CHEMBL1783

UniProt ID: P15692

Base Structure: X-ray

Registration Date: 2023-09-23

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	33
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-139079.835021
FMO2-HF: Nuclear repulsion	124854.902315
FMO2-HF: Total energy	-14224.932706
FMO2-MP2: Total energy	-14265.43307

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:1:PHE)

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

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.
-36.374	-22.766	5.089	-7.048	-11.648	-0.017

Interaction energy analysis for fragmet #1(A:1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.016

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	3	LYS	1	0.926	0.948	3.447	-8.023	-4.229	0.026	-1.876	-1.944	0.010
4	A	4	GLU	-1	-0.867	-0.948	2.365	-11.343	-6.801	1.972	-2.725	-3.788	-0.020
5	A	34	CYS	0	-0.026	0.002	2.648	-9.842	-5.039	3.087	-2.366	-5.524	-0.007
6	A	6	LEU	0	0.020	0.013	5.777	-0.800	-0.800	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.105	-0.059	7.027	-0.430	-0.430	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.827	0.900	3.238	3.075	3.372	0.004	-0.044	-0.257	0.000
9	A	9	TYR	0	-0.005	-0.024	7.851	-0.081	-0.081	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.869	0.931	11.351	-1.002	-1.002	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.823	-0.904	12.556	0.046	0.046	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.017	0.003	13.255	-0.061	-0.061	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.059	-0.037	15.047	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.048	-0.036	16.266	0.006	0.006	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.818	-0.897	17.859	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.042	-0.022	19.751	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.063	-0.038	21.964	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.029	0.021	17.170	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.048	0.009	21.611	0.005	0.005	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.011	-0.012	22.205	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.031	0.018	21.564	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.004	-0.006	20.036	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.935	0.976	17.612	0.034	0.034	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.018	-0.016	16.786	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.018	0.006	16.242	-0.060	-0.060	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.877	0.933	12.811	0.071	0.071	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.027	-0.016	11.982	-0.105	-0.105	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.024	0.020	11.123	-0.138	-0.138	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.020	0.010	10.671	-0.092	-0.092	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.089	-0.044	6.826	-0.319	-0.319	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.843	-0.924	6.287	-1.691	-1.691	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.969	-0.956	7.070	-1.757	-1.757	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.879	-0.918	3.842	-3.673	-3.501	0.000	-0.037	-0.135	0.000

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