FMO DATABASE

FMODB ID: GR511

Calculation Name: 3KVQ-A-Xray547

Preferred Name: Vascular endothelial growth factor receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KVQ

Chain ID: A

ChEMBL ID: CHEMBL279

UniProt ID: P35968

Base Structure: X-ray

Registration Date: 2025-10-04

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-595710.8114
FMO2-HF: Nuclear repulsion	560401.577303
FMO2-HF: Total energy	-35309.234097
FMO2-MP2: Total energy	-35409.346919

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:667:PRO)

Summations of interaction energy for fragment #1(A:667:PRO)

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.
-164.533	-180.767	50.194	-10.742	-23.221	-0.16

Interaction energy analysis for fragmet #1(A:667:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.736 / q_NPA : 0.857

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

Sort

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	669	ILE	0	-0.009	0.020	3.904	1.180	3.226	-0.020	-0.996	-1.030	0.000
24	A	690	ALA	0	0.031	0.006	3.724	-1.313	-1.162	-0.001	-0.048	-0.102	0.000
25	A	691	SER	0	-0.024	-0.029	4.494	0.839	1.097	-0.001	-0.044	-0.214	0.000
26	A	692	GLY	0	0.043	0.019	2.214	10.193	7.171	2.905	1.896	-1.779	-0.007
27	A	693	ASN	0	-0.036	-0.041	1.874	-39.821	-55.402	34.248	-7.840	-10.827	-0.102
28	A	694	PRO	0	0.044	0.012	2.674	13.670	9.755	0.524	3.961	-0.570	-0.001
72	A	739	ALA	0	-0.001	-0.001	3.857	2.524	2.654	-0.001	-0.040	-0.090	0.000
73	A	740	CYS	-1	-0.825	-0.851	3.031	-58.825	-56.973	0.138	-0.949	-1.041	-0.009
74	A	741	SER	0	-0.005	-0.035	2.674	-2.982	-2.002	0.160	-0.315	-0.824	-0.001
75	A	742	VAL	0	-0.031	-0.038	4.372	3.214	3.267	-0.001	-0.014	-0.038	0.000
77	A	744	GLY	0	-0.007	0.007	3.168	0.999	1.272	0.056	-0.078	-0.251	0.000
78	A	745	CYS	0	-0.047	-0.017	2.526	-21.431	-19.224	3.091	-1.974	-3.325	-0.028
79	A	746	ALA	0	-0.035	-0.003	1.900	-5.750	-7.653	9.067	-4.306	-2.858	-0.011
80	A	747	LYS	1	0.861	0.911	3.373	27.786	28.023	0.029	0.005	-0.272	-0.001
4	A	670	THR	0	-0.040	-0.007	6.113	4.028	4.028	0.000	0.000	0.000	0.000
5	A	671	GLY	0	0.048	0.009	9.660	-0.395	-0.395	0.000	0.000	0.000	0.000
6	A	672	ASN	0	0.040	0.036	12.739	-1.400	-1.400	0.000	0.000	0.000	0.000
7	A	673	LEU	0	-0.015	-0.003	12.057	1.059	1.059	0.000	0.000	0.000	0.000
8	A	674	GLU	-1	-0.922	-0.959	14.508	-18.030	-18.030	0.000	0.000	0.000	0.000
9	A	675	ASN	0	0.004	-0.011	17.294	0.090	0.090	0.000	0.000	0.000	0.000
10	A	676	GLN	0	-0.051	-0.025	19.765	0.667	0.667	0.000	0.000	0.000	0.000
11	A	677	THR	0	0.039	0.028	23.107	-0.204	-0.204	0.000	0.000	0.000	0.000
12	A	678	THR	0	-0.049	-0.028	26.204	-0.300	-0.300	0.000	0.000	0.000	0.000
13	A	679	SER	0	0.019	0.020	28.415	0.136	0.136	0.000	0.000	0.000	0.000
14	A	680	ILE	0	0.008	0.002	31.323	-0.194	-0.194	0.000	0.000	0.000	0.000
15	A	681	GLY	0	-0.061	-0.029	32.299	0.277	0.277	0.000	0.000	0.000	0.000
16	A	682	GLU	-1	-0.926	-0.956	30.374	-9.864	-9.864	0.000	0.000	0.000	0.000
17	A	683	SER	0	-0.047	-0.045	26.251	-0.075	-0.075	0.000	0.000	0.000	0.000
18	A	684	ILE	0	0.026	0.036	21.019	0.037	0.037	0.000	0.000	0.000	0.000
19	A	685	GLU	-1	-0.913	-0.968	21.068	-12.988	-12.988	0.000	0.000	0.000	0.000
20	A	686	VAL	0	-0.007	0.011	16.473	-0.186	-0.186	0.000	0.000	0.000	0.000
21	A	687	SER	0	-0.016	-0.023	14.317	-0.299	-0.299	0.000	0.000	0.000	0.000
22	A	688	CYS	0	-0.045	0.003	8.873	-0.849	-0.849	0.000	0.000	0.000	0.000
23	A	689	THR	0	-0.006	0.010	9.031	-1.197	-1.197	0.000	0.000	0.000	0.000
29	A	695	PRO	0	0.029	0.018	5.997	-1.935	-1.935	0.000	0.000	0.000	0.000
30	A	696	PRO	0	-0.024	-0.017	7.970	1.143	1.143	0.000	0.000	0.000	0.000
31	A	697	GLN	0	-0.063	-0.029	6.292	4.492	4.492	0.000	0.000	0.000	0.000
32	A	698	ILE	0	0.007	-0.007	6.521	-6.599	-6.599	0.000	0.000	0.000	0.000
33	A	699	MET	0	-0.020	-0.009	8.514	3.566	3.566	0.000	0.000	0.000	0.000
34	A	700	TRP	0	0.045	0.002	10.900	-1.603	-1.603	0.000	0.000	0.000	0.000
35	A	701	PHE	0	-0.022	-0.021	11.084	0.251	0.251	0.000	0.000	0.000	0.000
36	A	702	LYS	1	0.843	0.925	15.828	12.912	12.912	0.000	0.000	0.000	0.000
37	A	703	ASP	-1	-0.802	-0.896	19.056	-13.752	-13.752	0.000	0.000	0.000	0.000
38	A	704	ASN	0	-0.096	-0.051	15.562	-0.701	-0.701	0.000	0.000	0.000	0.000
39	A	705	GLU	-1	-0.902	-0.935	17.501	-13.786	-13.786	0.000	0.000	0.000	0.000
40	A	706	THR	0	-0.049	-0.043	16.475	-0.838	-0.838	0.000	0.000	0.000	0.000
41	A	707	LEU	0	-0.005	0.003	17.176	0.821	0.821	0.000	0.000	0.000	0.000
42	A	708	VAL	0	-0.021	-0.006	19.086	0.008	0.008	0.000	0.000	0.000	0.000
43	A	709	GLU	-1	-0.861	-0.934	20.653	-14.799	-14.799	0.000	0.000	0.000	0.000
44	A	710	ASP	-1	-0.812	-0.907	23.344	-10.916	-10.916	0.000	0.000	0.000	0.000
45	A	711	SER	0	-0.060	-0.033	26.420	-0.222	-0.222	0.000	0.000	0.000	0.000
46	A	712	GLY	0	0.002	0.010	27.809	0.105	0.105	0.000	0.000	0.000	0.000
47	A	713	ILE	0	-0.052	-0.015	21.588	-0.316	-0.316	0.000	0.000	0.000	0.000
48	A	714	VAL	0	-0.001	-0.003	22.029	0.103	0.103	0.000	0.000	0.000	0.000
49	A	715	LEU	0	0.013	0.024	15.847	-0.690	-0.690	0.000	0.000	0.000	0.000
50	A	716	LYS	1	0.919	0.939	17.454	15.574	15.574	0.000	0.000	0.000	0.000
51	A	717	ASP	-1	-0.900	-0.950	15.553	-20.557	-20.557	0.000	0.000	0.000	0.000
52	A	718	GLY	0	0.020	0.006	13.558	-1.108	-1.108	0.000	0.000	0.000	0.000
53	A	719	ASN	0	0.010	0.003	12.237	-0.888	-0.888	0.000	0.000	0.000	0.000
54	A	720	ARG	1	0.876	0.961	10.097	24.457	24.457	0.000	0.000	0.000	0.000
55	A	721	ASN	0	-0.046	-0.031	12.607	-0.080	-0.080	0.000	0.000	0.000	0.000
56	A	722	LEU	0	0.030	0.024	16.016	0.287	0.287	0.000	0.000	0.000	0.000
57	A	723	THR	0	-0.070	-0.035	17.773	0.144	0.144	0.000	0.000	0.000	0.000
58	A	724	ILE	0	0.040	0.029	21.134	0.097	0.097	0.000	0.000	0.000	0.000
59	A	725	ARG	1	0.853	0.916	24.049	12.211	12.211	0.000	0.000	0.000	0.000
60	A	726	ARG	1	0.891	0.948	27.795	9.204	9.204	0.000	0.000	0.000	0.000
61	A	727	VAL	0	0.014	0.033	26.397	0.139	0.139	0.000	0.000	0.000	0.000
62	A	728	ARG	1	0.854	0.912	27.741	11.387	11.387	0.000	0.000	0.000	0.000
63	A	729	LYS	1	0.860	0.906	29.485	9.791	9.791	0.000	0.000	0.000	0.000
64	A	730	GLU	-1	-0.895	-0.964	29.313	-10.106	-10.106	0.000	0.000	0.000	0.000
65	A	731	ASP	-1	-0.817	-0.900	25.348	-11.954	-11.954	0.000	0.000	0.000	0.000
66	A	732	GLU	-1	-0.812	-0.871	24.435	-11.456	-11.456	0.000	0.000	0.000	0.000
67	A	733	GLY	0	0.007	0.007	22.940	0.159	0.159	0.000	0.000	0.000	0.000
68	A	734	LEU	0	-0.051	-0.020	16.524	-0.148	-0.148	0.000	0.000	0.000	0.000
69	A	735	TYR	0	-0.020	-0.030	16.825	-0.233	-0.233	0.000	0.000	0.000	0.000
70	A	736	THR	0	-0.015	-0.012	11.077	-0.323	-0.323	0.000	0.000	0.000	0.000
71	A	738	GLN	0	-0.011	-0.021	7.249	-3.028	-3.028	0.000	0.000	0.000	0.000
76	A	743	LEU	0	-0.012	-0.007	6.595	3.496	3.496	0.000	0.000	0.000	0.000
81	A	748	VAL	0	0.002	0.004	6.933	-0.409	-0.409	0.000	0.000	0.000	0.000
82	A	749	GLU	-1	-0.823	-0.920	9.711	-21.143	-21.143	0.000	0.000	0.000	0.000
83	A	750	ALA	0	0.014	0.022	13.371	0.297	0.297	0.000	0.000	0.000	0.000
84	A	751	PHE	0	-0.019	-0.006	16.831	0.129	0.129	0.000	0.000	0.000	0.000
85	A	752	PHE	0	-0.020	-0.008	18.162	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	753	ILE	0	-0.008	-0.012	22.748	0.247	0.247	0.000	0.000	0.000	0.000
87	A	754	ILE	0	-0.006	-0.010	26.445	0.000	0.000	0.000	0.000	0.000	0.000
88	A	755	GLU	-1	-0.950	-0.982	29.299	-9.752	-9.752	0.000	0.000	0.000	0.000
89	A	756	GLY	-1	-0.929	-0.962	32.382	-8.800	-8.800	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:667:PRO)