FMO DATABASE

FMODB ID: JL939

Calculation Name: 1MKK-A-Xray372

Preferred Name: Vascular endothelial growth factor A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1MKK

Chain ID: A

ChEMBL ID: CHEMBL1783

UniProt ID: P15692

Base Structure: X-ray

Registration Date: 2023-09-19

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	91
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-613240.409878
FMO2-HF: Nuclear repulsion	573081.407565
FMO2-HF: Total energy	-40159.002313
FMO2-MP2: Total energy	-40267.713891

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:14:VAL)

Summations of interaction energy for fragment #1(A:14:VAL)

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.
-0.646	1.766	0.539	-1.228	-1.722	-0.007

Interaction energy analysis for fragmet #1(A:14:VAL)

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 : -0.016

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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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	16	LYS	1	0.980	0.988	2.759	-1.357	0.956	0.540	-1.223	-1.629	-0.007
4	A	17	PHE	0	0.089	0.038	4.529	0.354	0.453	-0.001	-0.005	-0.093	0.000
5	A	18	MET	0	0.041	0.012	6.744	0.161	0.161	0.000	0.000	0.000	0.000
6	A	19	ASP	-1	-0.796	-0.856	7.274	-0.108	-0.108	0.000	0.000	0.000	0.000
7	A	20	VAL	0	0.007	-0.008	5.798	0.160	0.160	0.000	0.000	0.000	0.000
8	A	21	TYR	0	-0.004	0.003	8.600	0.117	0.117	0.000	0.000	0.000	0.000
9	A	22	GLN	0	-0.001	-0.009	11.607	0.026	0.026	0.000	0.000	0.000	0.000
10	A	23	ARG	1	0.793	0.861	8.455	-0.218	-0.218	0.000	0.000	0.000	0.000
11	A	24	SER	0	-0.036	-0.027	12.051	0.062	0.062	0.000	0.000	0.000	0.000
12	A	25	TYR	0	0.017	0.030	14.584	0.006	0.006	0.000	0.000	0.000	0.000
13	A	26	CYS	0	-0.100	-0.029	17.480	0.018	0.018	0.000	0.000	0.000	0.000
14	A	27	HIS	1	0.850	0.921	16.638	-0.078	-0.078	0.000	0.000	0.000	0.000
15	A	28	PRO	0	0.050	0.020	21.379	0.005	0.005	0.000	0.000	0.000	0.000
16	A	29	ILE	0	-0.064	-0.033	18.962	0.017	0.017	0.000	0.000	0.000	0.000
17	A	30	GLU	-1	-0.895	-0.943	21.431	0.168	0.168	0.000	0.000	0.000	0.000
18	A	31	THR	0	-0.035	-0.025	22.707	0.007	0.007	0.000	0.000	0.000	0.000
19	A	32	LEU	0	-0.021	-0.009	25.414	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	33	VAL	0	0.008	0.008	27.965	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	34	ASP	-1	-0.863	-0.936	31.257	0.075	0.075	0.000	0.000	0.000	0.000
22	A	35	ILE	0	0.002	-0.018	34.426	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	36	PHE	0	-0.029	-0.017	37.345	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	37	GLN	0	-0.054	-0.018	32.356	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	38	GLU	-1	-0.806	-0.880	34.392	0.049	0.049	0.000	0.000	0.000	0.000
26	A	39	TYR	0	-0.057	-0.046	37.828	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	40	PRO	0	0.036	0.023	40.606	0.001	0.001	0.000	0.000	0.000	0.000
28	A	41	ASP	-1	-0.952	-0.974	42.705	0.029	0.029	0.000	0.000	0.000	0.000
29	A	42	GLU	-1	-0.882	-0.937	44.122	0.040	0.040	0.000	0.000	0.000	0.000
30	A	43	ILE	0	-0.013	-0.013	42.345	0.002	0.002	0.000	0.000	0.000	0.000
31	A	44	GLU	-1	-0.907	-0.939	44.608	0.034	0.034	0.000	0.000	0.000	0.000
32	A	45	TYR	0	-0.078	-0.054	45.842	0.000	0.000	0.000	0.000	0.000	0.000
33	A	46	ILE	0	0.002	-0.002	42.966	0.002	0.002	0.000	0.000	0.000	0.000
34	A	47	PHE	0	0.024	0.001	40.025	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	48	LYS	1	0.839	0.947	38.797	-0.058	-0.058	0.000	0.000	0.000	0.000
36	A	49	PRO	0	0.051	0.000	34.399	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	50	SER	0	0.048	0.010	35.274	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	51	CYS	0	-0.042	0.001	31.490	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	52	VAL	0	0.016	0.001	31.692	0.004	0.004	0.000	0.000	0.000	0.000
40	A	53	PRO	0	0.005	0.017	26.794	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.014	-0.013	27.945	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	55	MET	0	-0.032	-0.010	22.118	0.009	0.009	0.000	0.000	0.000	0.000
43	A	56	ARG	1	0.784	0.841	25.330	-0.068	-0.068	0.000	0.000	0.000	0.000
44	A	57	CYS	0	-0.032	0.002	24.011	0.012	0.012	0.000	0.000	0.000	0.000
45	A	58	GLY	0	0.048	0.025	22.392	0.001	0.001	0.000	0.000	0.000	0.000
46	A	59	GLY	0	0.027	-0.009	19.877	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	60	CYS	0	-0.070	-0.027	16.200	0.014	0.014	0.000	0.000	0.000	0.000
48	A	61	ALA	0	0.050	0.032	19.586	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	62	ASN	0	-0.069	-0.048	21.235	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	63	ASP	-1	-0.887	-0.943	23.492	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	64	GLU	-1	-1.004	-1.005	22.563	-0.081	-0.081	0.000	0.000	0.000	0.000
52	A	65	GLY	0	-0.026	-0.009	26.755	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	66	LEU	0	-0.061	-0.019	23.094	0.002	0.002	0.000	0.000	0.000	0.000
54	A	67	GLU	-1	-0.886	-0.942	26.050	0.002	0.002	0.000	0.000	0.000	0.000
55	A	69	VAL	0	0.033	0.020	25.845	0.007	0.007	0.000	0.000	0.000	0.000
56	A	70	PRO	0	0.038	0.001	28.010	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	71	THR	0	-0.062	-0.041	28.551	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	72	GLU	-1	-0.835	-0.901	30.215	0.020	0.020	0.000	0.000	0.000	0.000
59	A	73	GLU	-1	-0.855	-0.934	30.808	0.032	0.032	0.000	0.000	0.000	0.000
60	A	74	SER	0	-0.053	-0.041	32.100	0.000	0.000	0.000	0.000	0.000	0.000
61	A	75	ASN	0	0.014	0.004	34.424	0.002	0.002	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.027	-0.004	31.755	0.001	0.001	0.000	0.000	0.000	0.000
63	A	77	THR	0	0.008	0.003	35.316	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	78	MET	0	-0.037	-0.014	31.579	0.004	0.004	0.000	0.000	0.000	0.000
65	A	79	GLN	0	-0.009	-0.005	37.584	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.013	0.013	36.762	0.005	0.005	0.000	0.000	0.000	0.000
67	A	81	MET	0	-0.001	0.011	40.368	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	82	ARG	1	0.882	0.918	42.418	-0.041	-0.041	0.000	0.000	0.000	0.000
69	A	83	ILE	0	-0.077	-0.041	45.081	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	84	LYS	1	0.943	0.997	47.836	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	85	PRO	0	0.043	0.012	50.490	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	HIS	0	-0.019	-0.014	53.058	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	87	GLN	0	-0.014	0.007	52.777	0.000	0.000	0.000	0.000	0.000	0.000
74	A	88	GLY	0	0.037	0.017	52.288	0.001	0.001	0.000	0.000	0.000	0.000
75	A	89	GLN	0	-0.030	-0.029	46.637	0.001	0.001	0.000	0.000	0.000	0.000
76	A	90	HIS	0	-0.036	-0.008	47.819	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	91	ILE	0	0.001	-0.011	42.803	0.002	0.002	0.000	0.000	0.000	0.000
78	A	92	GLY	0	-0.003	-0.002	43.950	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.941	-0.965	41.948	0.051	0.051	0.000	0.000	0.000	0.000
80	A	94	MET	0	-0.030	0.003	39.755	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	95	SER	0	0.026	0.018	38.771	0.004	0.004	0.000	0.000	0.000	0.000
82	A	96	PHE	0	0.041	0.027	34.506	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	97	LEU	0	0.037	0.035	33.792	0.001	0.001	0.000	0.000	0.000	0.000
84	A	98	GLN	0	0.044	0.020	29.235	0.012	0.012	0.000	0.000	0.000	0.000
85	A	99	HIS	0	0.042	0.024	27.682	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	100	ASN	0	-0.014	0.000	27.424	0.006	0.006	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.785	0.868	25.871	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	103	GLU	-1	-0.864	-0.907	24.664	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	104	ALA	0	0.000	-0.007	22.836	0.006	0.006	0.000	0.000	0.000	0.000
90	A	105	ARG	1	0.832	0.902	24.969	0.006	0.006	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.041	0.043	28.288	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:VAL)