FMO DATABASE

FMODB ID: N9G1Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-612886.973667
FMO2-HF: Nuclear repulsion	572728.285855
FMO2-HF: Total energy	-40158.687811
FMO2-MP2: Total energy	-40267.370577

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.
-0.183	2.12	0.705	-1.212	-1.795	-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 : 0.007 / q_NPA : -0.013

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	0.978	0.986	2.710	-0.968	1.234	0.706	-1.207	-1.700	-0.007
4	A	17	PHE	0	0.084	0.039	4.431	0.393	0.494	-0.001	-0.005	-0.095	0.000
5	A	18	MET	0	0.050	0.012	6.705	0.180	0.180	0.000	0.000	0.000	0.000
6	A	19	ASP	-1	-0.797	-0.859	7.151	-0.254	-0.254	0.000	0.000	0.000	0.000
7	A	20	VAL	0	-0.007	-0.012	5.724	0.181	0.181	0.000	0.000	0.000	0.000
8	A	21	TYR	0	-0.016	-0.009	8.569	0.129	0.129	0.000	0.000	0.000	0.000
9	A	22	GLN	0	-0.003	-0.008	11.580	0.034	0.034	0.000	0.000	0.000	0.000
10	A	23	ARG	1	0.799	0.866	8.001	-0.110	-0.110	0.000	0.000	0.000	0.000
11	A	24	SER	0	-0.018	-0.016	12.311	0.070	0.070	0.000	0.000	0.000	0.000
12	A	25	TYR	0	0.014	0.031	14.573	0.014	0.014	0.000	0.000	0.000	0.000
13	A	26	CYS	0	-0.110	-0.034	17.454	0.016	0.016	0.000	0.000	0.000	0.000
14	A	27	HIS	1	0.860	0.926	16.828	-0.061	-0.061	0.000	0.000	0.000	0.000
15	A	28	PRO	0	0.053	0.018	21.345	0.008	0.008	0.000	0.000	0.000	0.000
16	A	29	ILE	0	-0.061	-0.030	18.908	0.014	0.014	0.000	0.000	0.000	0.000
17	A	30	GLU	-1	-0.904	-0.941	21.423	0.175	0.175	0.000	0.000	0.000	0.000
18	A	31	THR	0	-0.041	-0.034	22.706	0.009	0.009	0.000	0.000	0.000	0.000
19	A	32	LEU	0	-0.011	-0.008	25.412	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	33	VAL	0	0.005	0.011	27.965	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	34	ASP	-1	-0.879	-0.940	31.256	0.079	0.079	0.000	0.000	0.000	0.000
22	A	35	ILE	0	0.007	-0.019	34.425	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	36	PHE	0	-0.038	-0.017	37.345	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	37	GLN	0	-0.043	-0.010	32.226	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	38	GLU	-1	-0.844	-0.926	34.572	0.047	0.047	0.000	0.000	0.000	0.000
26	A	39	TYR	0	-0.058	-0.045	37.825	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	40	PRO	0	0.027	0.017	40.502	0.001	0.001	0.000	0.000	0.000	0.000
28	A	41	ASP	-1	-0.945	-0.971	42.701	0.028	0.028	0.000	0.000	0.000	0.000
29	A	42	GLU	-1	-0.899	-0.959	44.060	0.040	0.040	0.000	0.000	0.000	0.000
30	A	43	ILE	0	-0.007	-0.013	42.455	0.002	0.002	0.000	0.000	0.000	0.000
31	A	44	GLU	-1	-0.961	-0.970	44.606	0.035	0.035	0.000	0.000	0.000	0.000
32	A	45	TYR	0	-0.060	-0.038	45.732	0.000	0.000	0.000	0.000	0.000	0.000
33	A	46	ILE	0	0.012	-0.002	42.986	0.003	0.003	0.000	0.000	0.000	0.000
34	A	47	PHE	0	0.014	-0.004	39.977	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	48	LYS	1	0.839	0.953	38.807	-0.061	-0.061	0.000	0.000	0.000	0.000
36	A	49	PRO	0	0.060	0.005	34.413	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	50	SER	0	0.044	0.006	35.432	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	51	CYS	0	-0.022	0.012	31.070	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	52	VAL	0	0.005	-0.003	31.701	0.004	0.004	0.000	0.000	0.000	0.000
40	A	53	PRO	0	0.013	0.015	26.874	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.011	-0.007	27.951	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	55	MET	0	-0.037	-0.013	22.181	0.010	0.010	0.000	0.000	0.000	0.000
43	A	56	ARG	1	0.811	0.884	25.330	-0.066	-0.066	0.000	0.000	0.000	0.000
44	A	57	CYS	0	-0.027	0.001	23.903	0.013	0.013	0.000	0.000	0.000	0.000
45	A	58	GLY	0	0.040	0.023	22.267	0.003	0.003	0.000	0.000	0.000	0.000
46	A	59	GLY	0	0.027	-0.010	19.876	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	60	CYS	0	-0.068	-0.029	16.095	0.016	0.016	0.000	0.000	0.000	0.000
48	A	61	ALA	0	0.054	0.035	19.495	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	62	ASN	0	-0.076	-0.048	21.172	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	63	ASP	-1	-0.877	-0.935	23.430	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	64	GLU	-1	-1.016	-1.013	22.828	-0.090	-0.090	0.000	0.000	0.000	0.000
52	A	65	GLY	0	-0.024	-0.007	26.782	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	66	LEU	0	-0.058	-0.019	23.000	0.001	0.001	0.000	0.000	0.000	0.000
54	A	67	GLU	-1	-0.888	-0.942	26.063	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	69	VAL	0	0.023	0.014	25.836	0.008	0.008	0.000	0.000	0.000	0.000
56	A	70	PRO	0	0.043	0.003	27.982	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	71	THR	0	-0.069	-0.045	28.571	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	72	GLU	-1	-0.857	-0.927	30.187	0.006	0.006	0.000	0.000	0.000	0.000
59	A	73	GLU	-1	-0.896	-0.950	30.763	0.025	0.025	0.000	0.000	0.000	0.000
60	A	74	SER	0	-0.049	-0.035	32.097	0.000	0.000	0.000	0.000	0.000	0.000
61	A	75	ASN	0	0.010	0.006	34.421	0.002	0.002	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.028	-0.006	31.837	0.001	0.001	0.000	0.000	0.000	0.000
63	A	77	THR	0	0.000	0.001	35.318	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	78	MET	0	-0.038	-0.018	31.728	0.004	0.004	0.000	0.000	0.000	0.000
65	A	79	GLN	0	-0.004	-0.003	37.589	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	80	ILE	0	0.013	0.016	36.894	0.005	0.005	0.000	0.000	0.000	0.000
67	A	81	MET	0	-0.017	-0.004	40.374	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	82	ARG	1	0.910	0.949	42.423	-0.041	-0.041	0.000	0.000	0.000	0.000
69	A	83	ILE	0	-0.066	-0.033	45.086	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	84	LYS	1	0.957	0.997	47.840	-0.035	-0.035	0.000	0.000	0.000	0.000
71	A	85	PRO	0	0.047	0.016	50.493	0.001	0.001	0.000	0.000	0.000	0.000
72	A	86	HIS	0	-0.015	-0.011	53.061	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	87	GLN	0	-0.017	0.004	52.727	0.000	0.000	0.000	0.000	0.000	0.000
74	A	88	GLY	0	0.033	0.014	52.294	0.001	0.001	0.000	0.000	0.000	0.000
75	A	89	GLN	0	-0.027	-0.026	46.144	0.000	0.000	0.000	0.000	0.000	0.000
76	A	90	HIS	0	-0.046	-0.011	47.825	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	91	ILE	0	0.012	-0.007	42.901	0.002	0.002	0.000	0.000	0.000	0.000
78	A	92	GLY	0	-0.013	-0.006	43.959	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	93	GLU	-1	-0.948	-0.967	41.956	0.048	0.048	0.000	0.000	0.000	0.000
80	A	94	MET	0	-0.021	0.003	39.724	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	95	SER	0	0.008	0.011	38.772	0.004	0.004	0.000	0.000	0.000	0.000
82	A	96	PHE	0	0.078	0.045	34.444	0.000	0.000	0.000	0.000	0.000	0.000
83	A	97	LEU	0	0.047	0.037	33.654	0.001	0.001	0.000	0.000	0.000	0.000
84	A	98	GLN	0	0.030	0.008	29.274	0.013	0.013	0.000	0.000	0.000	0.000
85	A	99	HIS	0	0.077	0.042	27.648	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	100	ASN	0	-0.006	-0.003	27.420	0.005	0.005	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.823	0.902	25.817	0.001	0.001	0.000	0.000	0.000	0.000
88	A	103	GLU	-1	-0.831	-0.879	24.635	-0.044	-0.044	0.000	0.000	0.000	0.000
89	A	104	ALA	0	-0.020	-0.015	22.837	0.007	0.007	0.000	0.000	0.000	0.000
90	A	105	ARG	1	0.813	0.877	24.948	0.017	0.017	0.000	0.000	0.000	0.000
91	A	106	PRO	0	0.051	0.048	28.271	0.005	0.005	0.000	0.000	0.000	0.000

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