FMO DATABASE

FMODB ID: 4J9MN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-594663.400444
FMO2-HF: Nuclear repulsion	559353.568337
FMO2-HF: Total energy	-35309.832106
FMO2-MP2: Total energy	-35409.993069

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.
-8.97	-1.112	9.123	-6.006	-10.969	-0.023

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 : 0.008 / 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

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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	669	ILE	0	-0.040	0.000	3.791	-1.422	1.501	-0.037	-1.386	-1.499	-0.003
4	A	670	THR	0	-0.014	-0.004	5.885	-0.681	-0.681	0.000	0.000	0.000	0.000
5	A	671	GLY	0	0.032	-0.001	9.603	0.163	0.163	0.000	0.000	0.000	0.000
6	A	672	ASN	0	0.060	0.034	12.637	0.078	0.078	0.000	0.000	0.000	0.000
7	A	673	LEU	0	-0.033	-0.009	11.994	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	674	GLU	-1	-0.915	-0.959	14.486	0.223	0.223	0.000	0.000	0.000	0.000
9	A	675	ASN	0	0.006	-0.013	17.216	0.017	0.017	0.000	0.000	0.000	0.000
10	A	676	GLN	0	-0.059	-0.036	19.467	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	677	THR	0	0.026	0.025	22.985	0.006	0.006	0.000	0.000	0.000	0.000
12	A	678	THR	0	-0.016	-0.003	26.028	0.006	0.006	0.000	0.000	0.000	0.000
13	A	679	SER	0	-0.006	-0.006	28.244	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	680	ILE	0	0.009	-0.008	31.163	0.006	0.006	0.000	0.000	0.000	0.000
15	A	681	GLY	0	-0.052	-0.025	32.231	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	682	GLU	-1	-0.909	-0.931	30.210	0.115	0.115	0.000	0.000	0.000	0.000
17	A	683	SER	0	-0.053	-0.038	26.474	0.006	0.006	0.000	0.000	0.000	0.000
18	A	684	ILE	0	0.017	0.033	21.043	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	685	GLU	-1	-0.816	-0.890	21.328	0.245	0.245	0.000	0.000	0.000	0.000
20	A	686	VAL	0	-0.012	0.009	16.364	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	687	SER	0	-0.028	-0.024	14.574	0.016	0.016	0.000	0.000	0.000	0.000
22	A	688	CYS	0	-0.044	0.022	9.054	0.000	0.000	0.000	0.000	0.000	0.000
23	A	689	THR	0	0.012	-0.005	9.361	0.095	0.095	0.000	0.000	0.000	0.000
24	A	690	ALA	0	0.043	0.024	4.037	-0.112	0.174	0.005	-0.126	-0.165	0.001
25	A	691	SER	0	0.002	0.000	3.863	-1.858	-1.480	0.002	-0.169	-0.211	0.000
26	A	692	GLY	0	0.042	0.002	2.619	-0.387	0.862	0.829	-0.906	-1.172	-0.009
27	A	693	ASN	0	-0.040	-0.024	4.813	0.147	0.194	-0.001	-0.006	-0.040	0.000
28	A	694	PRO	0	0.004	0.025	6.605	0.123	0.123	0.000	0.000	0.000	0.000
29	A	695	PRO	0	0.011	-0.009	5.509	-0.152	-0.152	0.000	0.000	0.000	0.000
30	A	696	PRO	0	-0.050	-0.009	2.606	-0.993	-0.350	0.482	-0.232	-0.892	0.001
31	A	697	GLN	0	-0.028	-0.025	5.802	0.156	0.156	0.000	0.000	0.000	0.000
32	A	698	ILE	0	-0.009	-0.003	7.138	0.271	0.271	0.000	0.000	0.000	0.000
33	A	699	MET	0	-0.031	-0.009	8.922	-0.294	-0.294	0.000	0.000	0.000	0.000
34	A	700	TRP	0	0.014	-0.007	11.133	0.096	0.096	0.000	0.000	0.000	0.000
35	A	701	PHE	0	-0.037	-0.033	11.242	-0.053	-0.053	0.000	0.000	0.000	0.000
36	A	702	LYS	1	0.833	0.911	15.868	-0.171	-0.171	0.000	0.000	0.000	0.000
37	A	703	ASP	-1	-0.814	-0.905	18.967	0.167	0.167	0.000	0.000	0.000	0.000
38	A	704	ASN	0	-0.102	-0.050	15.803	0.003	0.003	0.000	0.000	0.000	0.000
39	A	705	GLU	-1	-0.858	-0.912	17.752	0.140	0.140	0.000	0.000	0.000	0.000
40	A	706	THR	0	-0.053	-0.026	16.837	0.038	0.038	0.000	0.000	0.000	0.000
41	A	707	LEU	0	0.013	0.009	17.535	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	708	VAL	0	-0.010	-0.009	19.339	0.003	0.003	0.000	0.000	0.000	0.000
43	A	709	GLU	-1	-0.880	-0.939	20.652	0.290	0.290	0.000	0.000	0.000	0.000
44	A	710	ASP	-1	-0.781	-0.899	23.260	0.143	0.143	0.000	0.000	0.000	0.000
45	A	711	SER	0	-0.063	-0.020	26.423	0.006	0.006	0.000	0.000	0.000	0.000
46	A	712	GLY	0	-0.026	-0.008	27.826	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	713	ILE	0	-0.040	-0.011	21.700	0.011	0.011	0.000	0.000	0.000	0.000
48	A	714	VAL	0	-0.001	-0.004	22.837	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	715	LEU	0	0.024	0.024	16.320	0.030	0.030	0.000	0.000	0.000	0.000
50	A	716	LYS	1	0.838	0.910	18.359	-0.346	-0.346	0.000	0.000	0.000	0.000
51	A	717	ASP	-1	-0.929	-0.970	16.037	0.563	0.563	0.000	0.000	0.000	0.000
52	A	718	GLY	0	0.059	0.022	14.085	0.072	0.072	0.000	0.000	0.000	0.000
53	A	719	ASN	0	-0.017	-0.016	12.862	0.082	0.082	0.000	0.000	0.000	0.000
54	A	720	ARG	1	0.945	1.002	10.594	-0.792	-0.792	0.000	0.000	0.000	0.000
55	A	721	ASN	0	-0.047	-0.034	13.582	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	722	LEU	0	0.029	0.023	16.808	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	723	THR	0	-0.065	-0.062	18.336	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	724	ILE	0	0.042	0.029	21.290	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	725	ARG	1	0.832	0.900	24.483	-0.200	-0.200	0.000	0.000	0.000	0.000
60	A	726	ARG	1	0.883	0.948	28.125	-0.112	-0.112	0.000	0.000	0.000	0.000
61	A	727	VAL	0	0.036	0.037	26.290	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	728	ARG	1	0.839	0.887	27.068	-0.169	-0.169	0.000	0.000	0.000	0.000
63	A	729	LYS	1	0.841	0.883	29.128	-0.100	-0.100	0.000	0.000	0.000	0.000
64	A	730	GLU	-1	-0.902	-0.966	28.853	0.118	0.118	0.000	0.000	0.000	0.000
65	A	731	ASP	-1	-0.792	-0.868	25.005	0.175	0.175	0.000	0.000	0.000	0.000
66	A	732	GLU	-1	-0.810	-0.860	24.055	0.135	0.135	0.000	0.000	0.000	0.000
67	A	733	GLY	0	0.010	0.005	22.769	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	734	LEU	0	-0.052	-0.021	17.024	0.004	0.004	0.000	0.000	0.000	0.000
69	A	735	TYR	0	-0.035	-0.043	16.415	0.014	0.014	0.000	0.000	0.000	0.000
70	A	736	THR	0	-0.043	-0.041	10.868	0.006	0.006	0.000	0.000	0.000	0.000
71	A	738	GLN	0	0.040	-0.017	7.108	0.082	0.082	0.000	0.000	0.000	0.000
72	A	739	ALA	0	0.000	0.018	3.440	-0.139	0.223	0.018	-0.085	-0.295	0.000
73	A	740	CYS	0	0.054	0.038	3.819	-0.998	-0.535	0.008	-0.179	-0.291	-0.001
74	A	741	SER	0	0.002	-0.006	4.714	-0.005	0.101	-0.001	-0.016	-0.089	0.000
75	A	742	VAL	0	-0.011	-0.019	2.491	-2.962	-0.955	0.559	-0.702	-1.864	-0.003
76	A	743	LEU	0	-0.036	-0.019	3.712	-0.863	-0.415	0.009	-0.141	-0.315	-0.001
77	A	744	GLY	0	0.033	0.023	2.308	0.277	0.042	1.626	-0.603	-0.787	0.000
78	A	745	CYS	0	-0.060	-0.044	2.819	-0.189	-0.274	0.952	0.586	-1.452	-0.006
79	A	746	ALA	0	-0.041	0.008	2.187	0.145	-0.749	4.660	-2.041	-1.725	-0.002
80	A	747	LYS	1	0.841	0.897	3.622	-0.361	-0.201	0.012	0.000	-0.172	0.000
81	A	748	VAL	0	0.017	0.023	6.992	-0.134	-0.134	0.000	0.000	0.000	0.000
82	A	749	GLU	-1	-0.808	-0.899	9.841	0.334	0.334	0.000	0.000	0.000	0.000
83	A	750	ALA	0	0.013	0.020	13.396	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	751	PHE	0	-0.008	-0.001	16.662	0.006	0.006	0.000	0.000	0.000	0.000
85	A	752	PHE	0	-0.025	-0.017	17.986	0.001	0.001	0.000	0.000	0.000	0.000
86	A	753	ILE	0	-0.009	-0.008	22.616	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	754	ILE	0	0.022	0.004	26.045	0.002	0.002	0.000	0.000	0.000	0.000
88	A	755	GLU	-1	-0.937	-0.968	28.937	0.086	0.086	0.000	0.000	0.000	0.000
89	A	756	GLY	0	-0.012	-0.013	32.136	0.002	0.002	0.000	0.000	0.000	0.000

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