FMO DATABASE

FMODB ID: 39VQL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-613099.435026
FMO2-HF: Nuclear repulsion	572940.335996
FMO2-HF: Total energy	-40159.09903
FMO2-MP2: Total energy	-40267.870177

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.
-0.552	1.757	0.271	-1.089	-1.492	-0.004

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 : -0.003 / q_NPA : -0.015

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	0.990	0.992	2.963	-1.308	0.895	0.272	-1.084	-1.391	-0.004
4	A	17	PHE	0	0.074	0.029	4.417	0.382	0.488	-0.001	-0.005	-0.101	0.000
5	A	18	MET	0	0.039	0.017	6.640	0.165	0.165	0.000	0.000	0.000	0.000
6	A	19	ASP	-1	-0.783	-0.850	7.330	-0.012	-0.012	0.000	0.000	0.000	0.000
7	A	20	VAL	0	-0.006	-0.009	5.825	0.167	0.167	0.000	0.000	0.000	0.000
8	A	21	TYR	0	0.033	0.029	8.630	0.113	0.113	0.000	0.000	0.000	0.000
9	A	22	GLN	0	-0.027	-0.026	11.750	0.012	0.012	0.000	0.000	0.000	0.000
10	A	23	ARG	1	0.788	0.855	8.677	-0.337	-0.337	0.000	0.000	0.000	0.000
11	A	24	SER	0	-0.032	-0.028	12.045	0.057	0.057	0.000	0.000	0.000	0.000
12	A	25	TYR	0	0.024	0.028	14.612	0.002	0.002	0.000	0.000	0.000	0.000
13	A	26	CYS	0	-0.095	-0.026	17.569	0.024	0.024	0.000	0.000	0.000	0.000
14	A	27	HIS	1	0.844	0.915	16.671	-0.115	-0.115	0.000	0.000	0.000	0.000
15	A	28	PRO	0	0.055	0.020	21.490	0.006	0.006	0.000	0.000	0.000	0.000
16	A	29	ILE	0	-0.070	-0.034	18.737	0.020	0.020	0.000	0.000	0.000	0.000
17	A	30	GLU	-1	-0.900	-0.953	21.376	0.185	0.185	0.000	0.000	0.000	0.000
18	A	31	THR	0	-0.037	-0.022	22.689	0.010	0.010	0.000	0.000	0.000	0.000
19	A	32	LEU	0	-0.016	-0.009	25.312	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	33	VAL	0	0.012	0.008	27.724	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	34	ASP	-1	-0.843	-0.929	31.064	0.085	0.085	0.000	0.000	0.000	0.000
22	A	35	ILE	0	0.010	-0.008	34.337	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	36	PHE	0	-0.026	-0.018	37.224	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	37	GLN	0	-0.059	-0.027	32.170	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	38	GLU	-1	-0.808	-0.870	34.294	0.059	0.059	0.000	0.000	0.000	0.000
26	A	39	TYR	0	-0.042	-0.041	37.966	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	40	PRO	0	0.027	0.023	40.732	0.001	0.001	0.000	0.000	0.000	0.000
28	A	41	ASP	-1	-0.925	-0.969	42.736	0.035	0.035	0.000	0.000	0.000	0.000
29	A	42	GLU	-1	-0.843	-0.911	44.182	0.044	0.044	0.000	0.000	0.000	0.000
30	A	43	ILE	0	-0.013	-0.013	42.119	0.002	0.002	0.000	0.000	0.000	0.000
31	A	44	GLU	-1	-0.896	-0.919	44.590	0.036	0.036	0.000	0.000	0.000	0.000
32	A	45	TYR	0	-0.091	-0.073	45.881	0.000	0.000	0.000	0.000	0.000	0.000
33	A	46	ILE	0	-0.002	-0.003	42.922	0.002	0.002	0.000	0.000	0.000	0.000
34	A	47	PHE	0	0.028	0.002	39.921	0.000	0.000	0.000	0.000	0.000	0.000
35	A	48	LYS	1	0.822	0.926	38.954	-0.062	-0.062	0.000	0.000	0.000	0.000
36	A	49	PRO	0	0.026	0.001	34.426	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	50	SER	0	0.006	-0.010	35.086	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	51	CYS	0	-0.032	0.005	31.716	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	52	VAL	0	0.023	0.002	31.748	0.003	0.003	0.000	0.000	0.000	0.000
40	A	53	PRO	0	-0.002	0.016	26.811	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.008	-0.014	27.765	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	55	MET	0	-0.027	-0.005	22.133	0.010	0.010	0.000	0.000	0.000	0.000
43	A	56	ARG	1	0.785	0.842	25.364	-0.082	-0.082	0.000	0.000	0.000	0.000
44	A	57	CYS	0	0.006	0.008	24.128	0.014	0.014	0.000	0.000	0.000	0.000
45	A	58	GLY	0	0.044	0.024	22.162	0.001	0.001	0.000	0.000	0.000	0.000
46	A	59	GLY	0	0.027	-0.011	19.349	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	60	CYS	0	-0.065	-0.027	16.230	0.013	0.013	0.000	0.000	0.000	0.000
48	A	61	ALA	0	0.055	0.039	19.468	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	62	ASN	0	-0.064	-0.048	21.295	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	63	ASP	-1	-0.890	-0.946	23.486	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	64	GLU	-1	-1.015	-1.006	22.145	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	65	GLY	0	-0.024	-0.003	26.639	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	66	LEU	0	-0.056	-0.021	23.143	0.001	0.001	0.000	0.000	0.000	0.000
54	A	67	GLU	-1	-0.840	-0.919	25.612	0.013	0.013	0.000	0.000	0.000	0.000
55	A	69	VAL	0	-0.001	0.013	25.796	0.008	0.008	0.000	0.000	0.000	0.000
56	A	70	PRO	0	0.035	0.002	27.809	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	71	THR	0	-0.057	-0.035	27.985	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	72	GLU	-1	-0.847	-0.905	29.987	0.033	0.033	0.000	0.000	0.000	0.000
59	A	73	GLU	-1	-0.839	-0.927	30.470	0.043	0.043	0.000	0.000	0.000	0.000
60	A	74	SER	0	-0.059	-0.046	31.675	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	75	ASN	0	0.023	0.000	34.263	0.002	0.002	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.023	0.002	31.747	0.001	0.001	0.000	0.000	0.000	0.000
63	A	77	THR	0	0.009	0.005	35.146	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	78	MET	0	-0.027	-0.008	31.541	0.004	0.004	0.000	0.000	0.000	0.000
65	A	79	GLN	0	-0.064	-0.035	37.593	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.007	0.006	36.641	0.005	0.005	0.000	0.000	0.000	0.000
67	A	81	MET	0	-0.017	-0.001	40.328	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	82	ARG	1	0.895	0.925	42.329	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	83	ILE	0	-0.061	-0.027	45.022	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	84	LYS	1	0.868	0.952	47.693	-0.040	-0.040	0.000	0.000	0.000	0.000
71	A	85	PRO	0	0.049	0.016	50.452	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	HIS	0	-0.024	-0.015	53.254	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	87	GLN	0	-0.010	0.008	52.806	0.000	0.000	0.000	0.000	0.000	0.000
74	A	88	GLY	0	0.040	0.018	52.579	0.001	0.001	0.000	0.000	0.000	0.000
75	A	89	GLN	0	-0.005	-0.016	46.168	0.003	0.003	0.000	0.000	0.000	0.000
76	A	90	HIS	0	-0.018	0.003	48.300	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	91	ILE	0	0.003	-0.014	42.922	0.003	0.003	0.000	0.000	0.000	0.000
78	A	92	GLY	0	-0.015	-0.002	44.070	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.893	-0.939	41.957	0.058	0.058	0.000	0.000	0.000	0.000
80	A	94	MET	0	-0.033	0.003	39.737	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	95	SER	0	-0.001	0.006	38.742	0.004	0.004	0.000	0.000	0.000	0.000
82	A	96	PHE	0	0.053	0.031	34.345	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	97	LEU	0	0.047	0.037	33.534	0.002	0.002	0.000	0.000	0.000	0.000
84	A	98	GLN	0	0.026	0.018	29.273	0.014	0.014	0.000	0.000	0.000	0.000
85	A	99	HIS	0	0.033	0.024	27.441	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	100	ASN	0	-0.020	0.002	27.227	0.009	0.009	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.784	0.864	25.807	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	103	GLU	-1	-0.859	-0.909	24.447	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	104	ALA	0	0.013	0.000	22.901	0.006	0.006	0.000	0.000	0.000	0.000
90	A	105	ARG	1	0.790	0.891	25.001	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.024	0.024	28.324	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:14:VAL)