FMO DATABASE

FMODB ID: 34N6L

Calculation Name: 2VGH-A-Other549

Preferred Name: Vascular endothelial growth factor A

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2VGH

Chain ID: A

ChEMBL ID: CHEMBL1783

UniProt ID: P15692

Base Structure: SolutionNMR

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	51
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-271897.619476
FMO2-HF: Nuclear repulsion	247215.616589
FMO2-HF: Total energy	-24682.002887
FMO2-MP2: Total energy	-24747.036984

3D Structure Molmil

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:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-27.048	-22.714	11.889	-7.713	-8.509	-0.085

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.904

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	A	3	GLN	0	0.007	0.000	3.902	-0.572	0.571	-0.009	-0.567	-0.566	0.000
4	A	4	GLU	-1	-0.873	-0.927	4.775	-34.572	-34.438	-0.001	-0.032	-0.101	0.000
5	A	5	ASN	0	-0.033	-0.036	2.533	-11.458	-8.987	1.596	-1.787	-2.280	-0.021
6	A	6	PRO	0	0.011	0.010	4.005	3.756	3.807	0.003	-0.044	-0.010	0.000
22	A	22	PRO	0	-0.012	0.009	4.677	-0.387	-0.305	-0.001	-0.019	-0.062	0.000
23	A	23	GLN	0	-0.036	-0.041	1.971	-50.104	-49.329	10.292	-5.790	-5.277	-0.063
24	A	24	THR	0	-0.022	-0.042	3.142	4.049	3.727	0.009	0.526	-0.213	-0.001
7	A	7	CYS	0	0.026	0.043	6.519	2.876	2.876	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.064	0.033	9.749	1.478	1.478	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.050	-0.025	13.291	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	10	CYS	0	0.013	0.016	11.124	0.074	0.074	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.006	0.017	17.027	0.741	0.741	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.744	-0.864	19.331	-12.637	-12.637	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.833	0.900	20.781	11.391	11.391	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.956	0.974	21.198	10.179	10.179	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.901	0.955	16.377	16.107	16.107	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.058	0.016	19.231	-0.740	-0.740	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.032	-0.010	20.851	-0.213	-0.213	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.017	0.010	16.902	0.157	0.157	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.019	-0.008	13.372	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.031	-0.052	9.392	1.097	1.097	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.777	-0.861	6.628	-41.764	-41.764	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.994	1.005	8.520	27.063	27.063	0.000	0.000	0.000	0.000
26	A	28	SER	0	0.003	-0.003	13.741	0.533	0.533	0.000	0.000	0.000	0.000
27	A	29	CYS	0	-0.008	0.008	16.270	-0.240	-0.240	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.939	0.978	18.096	15.853	15.853	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.056	-0.045	19.630	0.419	0.419	0.000	0.000	0.000	0.000
30	A	32	THR	0	0.075	0.032	20.737	0.267	0.267	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.778	-0.903	23.594	-10.427	-10.427	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.011	-0.006	25.104	0.470	0.470	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.874	0.920	23.645	12.878	12.878	0.000	0.000	0.000	0.000
34	A	36	CYS	0	-0.086	0.012	27.763	0.051	0.051	0.000	0.000	0.000	0.000
35	A	37	LYS	1	1.083	1.047	29.473	10.823	10.823	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.021	-0.010	30.609	0.319	0.319	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.867	0.920	27.981	10.723	10.723	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.042	-0.015	34.328	0.372	0.372	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.062	-0.026	32.993	0.195	0.195	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.862	-0.926	31.697	-9.227	-9.227	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.037	-0.035	24.412	-0.075	-0.075	0.000	0.000	0.000	0.000
42	A	44	ASN	0	0.058	0.038	29.108	-0.258	-0.258	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.912	-0.982	25.024	-12.129	-12.129	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.939	0.978	24.671	9.727	9.727	0.000	0.000	0.000	0.000
45	A	47	THR	0	-0.061	-0.025	25.768	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.939	0.965	25.227	10.083	10.083	0.000	0.000	0.000	0.000
47	A	51	ASP	-1	-0.857	-0.941	30.854	-9.136	-9.136	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.886	0.927	34.286	7.659	7.659	0.000	0.000	0.000	0.000
49	A	53	PRO	0	0.009	0.023	35.907	0.021	0.021	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.971	0.975	36.946	7.697	7.697	0.000	0.000	0.000	0.000
51	A	55	ARG	0	0.075	0.066	40.092	-0.094	-0.094	0.000	0.000	0.000	0.000

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