FMO DATABASE

FMODB ID: KG913

Calculation Name: 3KVQ-A-Xray372

Preferred Name: Vascular endothelial growth factor receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3KVQ

Chain ID: A

ChEMBL ID: CHEMBL279

UniProt ID: P35968

Base Structure: X-ray

Registration Date: 2023-09-21

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	OptH
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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-593077.397813
FMO2-HF: Nuclear repulsion	557768.50839
FMO2-HF: Total energy	-35308.889424
FMO2-MP2: Total energy	-35409.087448

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: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.
-9.931	-2.305	9.969	-6.336	-11.256	-0.025

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 : 0 / q_Mulliken : 0.013 / q_NPA : -0.022

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	-0.042	-0.002	3.791	-1.247	1.584	-0.034	-1.357	-1.441	-0.003
4	A	670	THR	0	-0.020	-0.003	5.933	-0.640	-0.640	0.000	0.000	0.000	0.000
5	A	671	GLY	0	0.046	0.004	9.650	0.178	0.178	0.000	0.000	0.000	0.000
6	A	672	ASN	0	0.071	0.041	12.680	0.086	0.086	0.000	0.000	0.000	0.000
7	A	673	LEU	0	-0.008	0.001	12.323	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	674	GLU	-1	-0.931	-0.962	14.513	0.204	0.204	0.000	0.000	0.000	0.000
9	A	675	ASN	0	-0.012	-0.027	17.242	0.021	0.021	0.000	0.000	0.000	0.000
10	A	676	GLN	0	-0.062	-0.037	19.853	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	677	THR	0	0.047	0.038	23.011	0.010	0.010	0.000	0.000	0.000	0.000
12	A	678	THR	0	0.009	0.019	25.881	0.004	0.004	0.000	0.000	0.000	0.000
13	A	679	SER	0	-0.007	0.015	28.278	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	680	ILE	0	0.031	-0.011	31.202	0.006	0.006	0.000	0.000	0.000	0.000
15	A	681	GLY	0	-0.075	-0.033	32.254	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	682	GLU	-1	-0.957	-0.971	30.161	0.115	0.115	0.000	0.000	0.000	0.000
17	A	683	SER	0	-0.036	-0.029	26.414	0.004	0.004	0.000	0.000	0.000	0.000
18	A	684	ILE	0	0.014	0.032	21.089	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	685	GLU	-1	-0.989	-1.006	21.395	0.217	0.217	0.000	0.000	0.000	0.000
20	A	686	VAL	0	0.002	0.011	16.404	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	687	SER	0	-0.041	-0.039	14.457	0.003	0.003	0.000	0.000	0.000	0.000
22	A	688	CYS	0	-0.069	0.013	9.046	0.030	0.030	0.000	0.000	0.000	0.000
23	A	689	THR	0	0.016	-0.010	8.946	0.061	0.061	0.000	0.000	0.000	0.000
24	A	690	ALA	0	0.038	0.019	3.974	-0.217	0.115	0.007	-0.153	-0.185	0.001
25	A	691	SER	0	0.012	0.005	3.711	-1.839	-1.396	0.004	-0.214	-0.233	0.000
26	A	692	GLY	0	0.029	-0.006	2.560	-1.251	0.174	0.972	-1.069	-1.328	-0.011
27	A	693	ASN	0	-0.038	-0.022	4.554	0.198	0.253	-0.001	-0.010	-0.044	0.000
28	A	694	PRO	0	0.008	0.027	6.405	0.141	0.141	0.000	0.000	0.000	0.000
29	A	695	PRO	0	0.007	-0.010	5.412	-0.194	-0.194	0.000	0.000	0.000	0.000
30	A	696	PRO	0	-0.041	-0.005	2.403	-0.955	-0.324	0.595	-0.283	-0.942	0.001
31	A	697	GLN	0	-0.033	-0.026	5.732	0.158	0.158	0.000	0.000	0.000	0.000
32	A	698	ILE	0	0.005	0.007	7.132	0.329	0.329	0.000	0.000	0.000	0.000
33	A	699	MET	0	-0.043	-0.016	8.982	-0.319	-0.319	0.000	0.000	0.000	0.000
34	A	700	TRP	0	0.032	0.009	11.208	0.117	0.117	0.000	0.000	0.000	0.000
35	A	701	PHE	0	-0.041	-0.035	11.617	-0.051	-0.051	0.000	0.000	0.000	0.000
36	A	702	LYS	1	0.905	0.963	15.889	-0.191	-0.191	0.000	0.000	0.000	0.000
37	A	703	ASP	-1	-0.859	-0.938	18.985	0.187	0.187	0.000	0.000	0.000	0.000
38	A	704	ASN	0	-0.095	-0.044	15.755	0.023	0.023	0.000	0.000	0.000	0.000
39	A	705	GLU	-1	-0.859	-0.922	17.753	0.172	0.172	0.000	0.000	0.000	0.000
40	A	706	THR	0	-0.069	-0.029	16.792	0.040	0.040	0.000	0.000	0.000	0.000
41	A	707	LEU	0	0.014	0.009	17.688	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	708	VAL	0	-0.016	-0.011	19.501	0.002	0.002	0.000	0.000	0.000	0.000
43	A	709	GLU	-1	-0.909	-0.955	20.607	0.288	0.288	0.000	0.000	0.000	0.000
44	A	710	ASP	-1	-0.849	-0.936	23.428	0.158	0.158	0.000	0.000	0.000	0.000
45	A	711	SER	0	-0.049	-0.031	26.577	0.009	0.009	0.000	0.000	0.000	0.000
46	A	712	GLY	0	-0.018	0.004	27.874	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	713	ILE	0	-0.026	-0.001	21.679	0.012	0.012	0.000	0.000	0.000	0.000
48	A	714	VAL	0	-0.013	-0.011	22.687	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	715	LEU	0	0.032	0.032	16.369	0.026	0.026	0.000	0.000	0.000	0.000
50	A	716	LYS	1	0.910	0.934	18.403	-0.329	-0.329	0.000	0.000	0.000	0.000
51	A	717	ASP	-1	-0.958	-0.971	16.336	0.491	0.491	0.000	0.000	0.000	0.000
52	A	718	GLY	0	0.047	0.011	13.904	0.074	0.074	0.000	0.000	0.000	0.000
53	A	719	ASN	0	-0.005	-0.011	12.764	0.067	0.067	0.000	0.000	0.000	0.000
54	A	720	ARG	1	0.938	0.996	10.160	-0.755	-0.755	0.000	0.000	0.000	0.000
55	A	721	ASN	0	-0.036	-0.022	13.582	0.006	0.006	0.000	0.000	0.000	0.000
56	A	722	LEU	0	0.032	0.017	16.925	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	723	THR	0	-0.044	-0.025	18.391	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	724	ILE	0	0.044	0.030	21.379	0.000	0.000	0.000	0.000	0.000	0.000
59	A	725	ARG	1	0.920	0.960	24.531	-0.202	-0.202	0.000	0.000	0.000	0.000
60	A	726	ARG	1	0.878	0.944	28.175	-0.114	-0.114	0.000	0.000	0.000	0.000
61	A	727	VAL	0	0.040	0.039	26.338	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	728	ARG	1	0.970	0.972	28.671	-0.164	-0.164	0.000	0.000	0.000	0.000
63	A	729	LYS	1	0.900	0.926	29.159	-0.103	-0.103	0.000	0.000	0.000	0.000
64	A	730	GLU	-1	-0.914	-0.973	28.877	0.126	0.126	0.000	0.000	0.000	0.000
65	A	731	ASP	-1	-0.845	-0.904	24.980	0.188	0.188	0.000	0.000	0.000	0.000
66	A	732	GLU	-1	-0.917	-0.949	24.082	0.148	0.148	0.000	0.000	0.000	0.000
67	A	733	GLY	0	0.004	0.000	22.788	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	734	LEU	0	-0.050	-0.017	16.691	0.003	0.003	0.000	0.000	0.000	0.000
69	A	735	TYR	0	-0.043	-0.047	16.452	0.019	0.019	0.000	0.000	0.000	0.000
70	A	736	THR	0	-0.011	-0.012	10.715	0.004	0.004	0.000	0.000	0.000	0.000
71	A	738	GLN	0	0.040	-0.012	7.259	0.058	0.058	0.000	0.000	0.000	0.000
72	A	739	ALA	0	-0.007	0.016	3.497	-0.152	0.182	0.013	-0.075	-0.271	0.000
73	A	740	CYS	0	0.060	0.021	4.247	-0.526	-0.228	0.001	-0.063	-0.236	0.000
74	A	741	SER	0	-0.017	-0.003	4.768	-0.163	-0.065	-0.001	-0.016	-0.080	0.000
75	A	742	VAL	0	-0.007	-0.016	2.443	-2.962	-0.936	0.634	-0.785	-1.875	-0.004
76	A	743	LEU	0	-0.037	-0.021	3.586	-1.166	-0.631	0.013	-0.211	-0.337	-0.001
77	A	744	GLY	0	0.030	0.026	2.470	0.109	-0.056	1.808	-0.728	-0.915	0.001
78	A	745	CYS	0	-0.026	-0.037	2.764	-0.317	-0.604	1.286	0.562	-1.561	-0.007
79	A	746	ALA	0	-0.055	0.008	2.152	0.190	-0.883	4.661	-1.944	-1.644	-0.002
80	A	747	LYS	1	0.955	0.945	3.601	-0.494	-0.351	0.011	0.010	-0.164	0.000
81	A	748	VAL	0	0.002	0.022	6.992	-0.155	-0.155	0.000	0.000	0.000	0.000
82	A	749	GLU	-1	-0.937	-0.974	9.853	0.375	0.375	0.000	0.000	0.000	0.000
83	A	750	ALA	0	0.020	0.018	13.404	-0.030	-0.030	0.000	0.000	0.000	0.000
84	A	751	PHE	0	-0.003	0.008	16.678	0.010	0.010	0.000	0.000	0.000	0.000
85	A	752	PHE	0	-0.022	-0.011	18.226	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	753	ILE	0	0.014	0.004	22.640	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	754	ILE	0	0.018	0.012	25.973	0.001	0.001	0.000	0.000	0.000	0.000
88	A	755	GLU	-1	-0.912	-0.955	28.964	0.089	0.089	0.000	0.000	0.000	0.000
89	A	756	GLY	0	-0.030	-0.015	32.162	0.003	0.003	0.000	0.000	0.000	0.000

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