FMO DATABASE

FMODB ID: 6Y81Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-139331.91499
FMO2-HF: Nuclear repulsion	125106.772333
FMO2-HF: Total energy	-14225.142657
FMO2-MP2: Total energy	-14265.674047

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.
-32.878	-21.925	6.963	-6.616	-11.303	-0.016

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 : 0.071 / 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	0.941	0.965	3.903	-7.343	-4.750	0.018	-1.363	-1.248	0.006
4	A	4	GLU	-1	-0.855	-0.914	2.160	-9.195	-5.734	3.233	-2.866	-3.828	-0.018
5	A	34	CYS	0	-0.030	0.001	2.578	-8.376	-3.945	3.708	-2.308	-5.832	-0.004
6	A	6	LEU	0	0.029	0.016	5.874	-0.693	-0.693	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.116	-0.051	7.285	-0.394	-0.394	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.816	0.865	3.526	2.546	2.774	0.000	-0.024	-0.205	0.000
9	A	9	TYR	0	0.013	-0.021	7.665	-0.130	-0.130	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.852	0.926	11.304	-1.080	-1.080	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.832	-0.907	12.222	0.113	0.113	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.017	-0.010	13.087	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.036	-0.022	14.885	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.048	-0.035	16.561	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.771	-0.872	17.876	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.021	-0.013	19.735	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.073	-0.047	21.807	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.055	0.007	17.711	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.052	0.007	22.192	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.026	-0.003	22.342	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.027	0.018	21.516	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.054	0.022	20.050	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.891	0.968	17.771	0.014	0.014	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.003	-0.005	16.674	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.003	-0.003	16.181	-0.067	-0.067	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.791	0.882	13.319	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.024	-0.016	12.102	-0.085	-0.085	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.028	0.021	11.305	-0.141	-0.141	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.016	0.004	10.713	-0.121	-0.121	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.088	-0.038	6.750	-0.274	-0.274	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.868	-0.919	6.477	-1.709	-1.709	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.952	-0.965	7.446	-1.662	-1.662	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.861	-0.896	3.497	-3.983	-3.743	0.004	-0.055	-0.190	0.000

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