FMO DATABASE

FMODB ID: 5J2LZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-594094.31307
FMO2-HF: Nuclear repulsion	558784.047827
FMO2-HF: Total energy	-35310.265243
FMO2-MP2: Total energy	-35410.380741

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.
-12.382	-3.34	7.638	-5.659	-11.023	-0.022

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 : -0.024

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	-0.029	-0.007	3.886	-0.068	1.776	-0.019	-0.841	-0.985	0.001
4	A	670	THR	0	-0.032	-0.013	6.231	-0.708	-0.708	0.000	0.000	0.000	0.000
5	A	671	GLY	0	0.040	0.009	9.892	0.195	0.195	0.000	0.000	0.000	0.000
6	A	672	ASN	0	0.025	0.029	13.205	0.014	0.014	0.000	0.000	0.000	0.000
7	A	673	LEU	0	-0.030	-0.008	12.229	-0.023	-0.023	0.000	0.000	0.000	0.000
8	A	674	GLU	-1	-0.902	-0.956	14.875	0.181	0.181	0.000	0.000	0.000	0.000
9	A	675	ASN	0	-0.002	-0.010	17.653	0.019	0.019	0.000	0.000	0.000	0.000
10	A	676	GLN	0	-0.053	-0.024	19.757	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	677	THR	0	0.029	0.015	23.345	0.004	0.004	0.000	0.000	0.000	0.000
12	A	678	THR	0	-0.039	-0.014	26.641	0.008	0.008	0.000	0.000	0.000	0.000
13	A	679	SER	0	-0.010	-0.009	28.809	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	680	ILE	0	-0.013	-0.015	31.688	0.007	0.007	0.000	0.000	0.000	0.000
15	A	681	GLY	0	-0.050	-0.023	32.599	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	682	GLU	-1	-0.883	-0.922	30.768	0.112	0.112	0.000	0.000	0.000	0.000
17	A	683	SER	0	-0.058	-0.054	27.187	0.005	0.005	0.000	0.000	0.000	0.000
18	A	684	ILE	0	0.019	0.032	21.528	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	685	GLU	-1	-0.784	-0.855	21.902	0.249	0.249	0.000	0.000	0.000	0.000
20	A	686	VAL	0	-0.007	0.012	17.017	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	687	SER	0	-0.002	-0.013	14.752	0.037	0.037	0.000	0.000	0.000	0.000
22	A	688	CYS	0	-0.080	-0.010	9.615	0.003	0.003	0.000	0.000	0.000	0.000
23	A	689	THR	0	0.013	0.006	9.211	0.142	0.142	0.000	0.000	0.000	0.000
24	A	690	ALA	0	0.041	0.021	3.751	-0.296	0.241	0.021	-0.275	-0.283	0.002
25	A	691	SER	0	-0.027	-0.019	3.465	-1.623	-1.206	0.004	-0.158	-0.264	0.000
26	A	692	GLY	0	0.056	0.008	2.282	-3.582	-2.666	2.048	-1.391	-1.572	-0.018
27	A	693	ASN	0	-0.039	-0.020	4.760	0.264	0.325	-0.001	-0.009	-0.051	0.000
28	A	694	PRO	0	0.004	0.026	6.331	0.102	0.102	0.000	0.000	0.000	0.000
29	A	695	PRO	0	0.013	-0.007	5.415	-0.141	-0.141	0.000	0.000	0.000	0.000
30	A	696	PRO	0	-0.034	-0.009	2.301	-1.267	-0.797	1.541	-0.494	-1.518	0.001
31	A	697	GLN	0	-0.056	-0.040	5.350	0.221	0.199	-0.001	-0.001	0.025	0.000
32	A	698	ILE	0	-0.010	-0.005	7.003	0.440	0.440	0.000	0.000	0.000	0.000
33	A	699	MET	0	-0.035	-0.010	9.000	-0.339	-0.339	0.000	0.000	0.000	0.000
34	A	700	TRP	0	0.049	-0.003	11.334	0.097	0.097	0.000	0.000	0.000	0.000
35	A	701	PHE	0	-0.036	-0.022	11.531	-0.050	-0.050	0.000	0.000	0.000	0.000
36	A	702	LYS	1	0.833	0.911	16.239	-0.168	-0.168	0.000	0.000	0.000	0.000
37	A	703	ASP	-1	-0.811	-0.902	19.311	0.162	0.162	0.000	0.000	0.000	0.000
38	A	704	ASN	0	-0.093	-0.048	16.150	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	705	GLU	-1	-0.907	-0.936	17.919	0.156	0.156	0.000	0.000	0.000	0.000
40	A	706	THR	0	-0.044	-0.042	17.088	0.036	0.036	0.000	0.000	0.000	0.000
41	A	707	LEU	0	-0.001	0.002	17.572	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	708	VAL	0	-0.029	-0.011	19.406	0.010	0.010	0.000	0.000	0.000	0.000
43	A	709	GLU	-1	-0.843	-0.921	20.605	0.329	0.329	0.000	0.000	0.000	0.000
44	A	710	ASP	-1	-0.809	-0.895	23.326	0.151	0.151	0.000	0.000	0.000	0.000
45	A	711	SER	0	-0.096	-0.051	26.929	0.003	0.003	0.000	0.000	0.000	0.000
46	A	712	GLY	0	0.008	0.006	28.391	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	713	ILE	0	-0.041	-0.007	22.066	0.008	0.008	0.000	0.000	0.000	0.000
48	A	714	VAL	0	0.021	0.004	22.931	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	715	LEU	0	0.021	0.016	16.238	0.029	0.029	0.000	0.000	0.000	0.000
50	A	716	LYS	1	0.840	0.910	18.163	-0.381	-0.381	0.000	0.000	0.000	0.000
51	A	717	ASP	-1	-0.856	-0.928	15.519	0.637	0.637	0.000	0.000	0.000	0.000
52	A	718	GLY	0	0.048	0.024	13.941	0.082	0.082	0.000	0.000	0.000	0.000
53	A	719	ASN	0	0.009	0.008	12.790	0.099	0.099	0.000	0.000	0.000	0.000
54	A	720	ARG	1	0.884	0.952	10.249	-0.841	-0.841	0.000	0.000	0.000	0.000
55	A	721	ASN	0	-0.049	-0.030	13.112	-0.050	-0.050	0.000	0.000	0.000	0.000
56	A	722	LEU	0	0.013	0.015	16.576	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	723	THR	0	-0.067	-0.061	18.582	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	724	ILE	0	0.033	0.023	21.428	0.002	0.002	0.000	0.000	0.000	0.000
59	A	725	ARG	1	0.808	0.879	24.691	-0.204	-0.204	0.000	0.000	0.000	0.000
60	A	726	ARG	1	0.890	0.950	28.461	-0.113	-0.113	0.000	0.000	0.000	0.000
61	A	727	VAL	0	0.008	0.031	26.857	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	728	ARG	1	0.825	0.876	26.998	-0.178	-0.178	0.000	0.000	0.000	0.000
63	A	729	LYS	1	0.832	0.882	29.723	-0.093	-0.093	0.000	0.000	0.000	0.000
64	A	730	GLU	-1	-0.870	-0.955	29.532	0.115	0.115	0.000	0.000	0.000	0.000
65	A	731	ASP	-1	-0.803	-0.871	25.524	0.181	0.181	0.000	0.000	0.000	0.000
66	A	732	GLU	-1	-0.806	-0.863	24.642	0.124	0.124	0.000	0.000	0.000	0.000
67	A	733	GLY	0	0.013	0.009	23.268	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	734	LEU	0	-0.052	-0.017	16.901	0.002	0.002	0.000	0.000	0.000	0.000
69	A	735	TYR	0	-0.030	-0.031	17.027	0.017	0.017	0.000	0.000	0.000	0.000
70	A	736	THR	0	-0.013	-0.032	11.622	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	738	GLN	0	0.021	-0.024	7.366	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	739	ALA	0	0.026	0.026	3.819	-0.038	0.236	0.005	-0.060	-0.219	0.000
73	A	740	CYS	0	-0.002	-0.009	4.121	-0.834	-0.536	0.002	-0.078	-0.221	0.000
74	A	741	SER	0	0.036	0.022	4.313	0.008	0.162	-0.001	-0.029	-0.124	0.000
75	A	742	VAL	0	-0.019	-0.022	2.477	-3.372	-1.098	1.146	-0.916	-2.504	-0.003
76	A	743	LEU	0	-0.029	-0.017	3.549	-0.909	-0.308	0.023	-0.211	-0.413	-0.001
77	A	744	GLY	0	0.027	0.023	2.654	-0.196	0.159	0.396	-0.248	-0.503	0.001
78	A	745	CYS	0	-0.085	-0.035	3.183	-0.363	0.258	0.180	0.089	-0.891	-0.002
79	A	746	ALA	0	-0.003	0.019	2.326	-0.926	-0.834	2.289	-1.029	-1.352	-0.003
80	A	747	LYS	1	0.861	0.906	3.793	0.140	0.290	0.005	-0.008	-0.148	0.000
81	A	748	VAL	0	0.008	0.012	7.290	-0.197	-0.197	0.000	0.000	0.000	0.000
82	A	749	GLU	-1	-0.790	-0.886	10.056	0.328	0.328	0.000	0.000	0.000	0.000
83	A	750	ALA	0	-0.006	0.015	13.700	-0.040	-0.040	0.000	0.000	0.000	0.000
84	A	751	PHE	0	-0.013	-0.002	17.189	0.013	0.013	0.000	0.000	0.000	0.000
85	A	752	PHE	0	-0.019	-0.009	18.211	0.000	0.000	0.000	0.000	0.000	0.000
86	A	753	ILE	0	0.007	-0.003	23.008	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	754	ILE	0	0.007	-0.003	26.607	0.002	0.002	0.000	0.000	0.000	0.000
88	A	755	GLU	-1	-0.910	-0.955	29.600	0.076	0.076	0.000	0.000	0.000	0.000
89	A	756	GLY	0	-0.021	-0.013	32.760	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)