FMO DATABASE

FMODB ID: G63V1

Calculation Name: 3ADG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ADG

Chain ID: A

ChEMBL ID:

UniProt ID: O04492

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-437240.543294
FMO2-HF: Nuclear repulsion	409375.526751
FMO2-HF: Total energy	-27865.016543
FMO2-MP2: Total energy	-27949.042573

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:13:SER)

Summations of interaction energy for fragment #1(A:13:SER)

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.
0.237	3.075	7.631	-4.198	-6.269	-0.006

Interaction energy analysis for fragmet #1(A:13:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.006

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	15	VAL	0	0.022	0.002	3.731	-0.405	0.952	-0.024	-0.503	-0.829	0.001
4	A	16	PHE	0	0.036	0.039	2.434	-2.055	-0.155	1.972	-1.474	-2.398	-0.005
5	A	17	LYS	1	0.852	0.916	5.453	1.964	1.964	0.000	0.000	0.000	0.000
6	A	18	SER	0	0.026	0.014	7.529	0.257	0.257	0.000	0.000	0.000	0.000
7	A	19	ARG	1	1.003	1.009	7.770	1.604	1.604	0.000	0.000	0.000	0.000
8	A	20	LEU	0	0.009	0.016	9.744	0.212	0.212	0.000	0.000	0.000	0.000
9	A	21	GLN	0	0.015	0.022	11.473	0.167	0.167	0.000	0.000	0.000	0.000
10	A	22	GLU	-1	-0.937	-0.970	13.161	-0.726	-0.726	0.000	0.000	0.000	0.000
11	A	23	TYR	0	0.023	0.007	14.428	0.081	0.081	0.000	0.000	0.000	0.000
12	A	24	ALA	0	0.011	-0.004	15.580	0.064	0.064	0.000	0.000	0.000	0.000
13	A	25	GLN	0	-0.022	-0.003	17.487	0.047	0.047	0.000	0.000	0.000	0.000
14	A	26	LYS	1	0.884	0.944	19.067	0.358	0.358	0.000	0.000	0.000	0.000
15	A	27	TYR	0	-0.009	-0.012	19.064	0.027	0.027	0.000	0.000	0.000	0.000
16	A	28	LYS	1	0.895	0.962	22.028	0.229	0.229	0.000	0.000	0.000	0.000
17	A	29	LEU	0	0.027	0.030	18.785	0.016	0.016	0.000	0.000	0.000	0.000
18	A	30	PRO	0	-0.006	-0.011	20.390	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	31	THR	0	-0.015	-0.027	15.389	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	32	PRO	0	-0.028	-0.005	12.754	0.030	0.030	0.000	0.000	0.000	0.000
21	A	33	VAL	0	0.001	0.011	14.628	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	34	TYR	0	0.011	-0.017	8.686	-0.138	-0.138	0.000	0.000	0.000	0.000
23	A	35	GLU	-1	-0.763	-0.829	13.548	-0.030	-0.030	0.000	0.000	0.000	0.000
24	A	36	ILE	0	-0.054	-0.037	12.147	0.009	0.009	0.000	0.000	0.000	0.000
25	A	37	VAL	0	0.064	0.038	14.489	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	38	LYS	1	0.897	0.949	15.023	-0.156	-0.156	0.000	0.000	0.000	0.000
27	A	39	GLU	-1	-0.906	-0.942	16.986	0.145	0.145	0.000	0.000	0.000	0.000
28	A	40	GLY	0	0.050	0.018	18.375	0.031	0.031	0.000	0.000	0.000	0.000
29	A	41	PRO	0	0.009	-0.005	20.424	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	42	SER	0	0.040	0.010	20.295	0.018	0.018	0.000	0.000	0.000	0.000
31	A	43	HIS	0	0.013	0.014	19.611	0.009	0.009	0.000	0.000	0.000	0.000
32	A	44	LYS	1	0.866	0.926	17.401	-0.284	-0.284	0.000	0.000	0.000	0.000
33	A	45	SER	0	-0.027	-0.007	16.204	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	46	LEU	0	0.000	0.011	13.757	0.057	0.057	0.000	0.000	0.000	0.000
35	A	47	PHE	0	-0.026	-0.028	10.881	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	48	GLN	0	-0.034	-0.014	11.489	0.065	0.065	0.000	0.000	0.000	0.000
37	A	49	SER	0	-0.053	-0.042	9.653	-0.109	-0.109	0.000	0.000	0.000	0.000
38	A	50	THR	0	0.041	0.018	11.725	0.041	0.041	0.000	0.000	0.000	0.000
39	A	51	VAL	0	-0.038	-0.008	10.646	-0.037	-0.037	0.000	0.000	0.000	0.000
40	A	52	ILE	0	-0.006	-0.008	12.883	0.039	0.039	0.000	0.000	0.000	0.000
41	A	53	LEU	0	0.003	-0.019	14.702	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	54	ASP	-1	-0.889	-0.945	17.186	-0.166	-0.166	0.000	0.000	0.000	0.000
43	A	55	GLY	0	0.021	0.015	20.797	0.016	0.016	0.000	0.000	0.000	0.000
44	A	56	VAL	0	-0.032	-0.002	18.005	0.022	0.022	0.000	0.000	0.000	0.000
45	A	57	ARG	1	0.807	0.861	16.793	0.026	0.026	0.000	0.000	0.000	0.000
46	A	58	TYR	0	0.037	0.014	12.662	0.019	0.019	0.000	0.000	0.000	0.000
47	A	59	ASN	0	0.010	0.007	12.881	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	60	SER	0	0.000	-0.013	8.345	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	61	LEU	0	0.023	0.014	8.257	-0.083	-0.083	0.000	0.000	0.000	0.000
50	A	62	PRO	0	0.061	0.033	10.507	0.015	0.015	0.000	0.000	0.000	0.000
51	A	63	GLY	0	0.009	0.001	11.553	0.073	0.073	0.000	0.000	0.000	0.000
52	A	64	PHE	0	0.036	0.029	5.757	0.131	0.131	0.000	0.000	0.000	0.000
53	A	65	PHE	0	0.052	0.008	8.807	-0.099	-0.099	0.000	0.000	0.000	0.000
54	A	66	ASN	0	-0.025	-0.013	6.747	-0.172	-0.172	0.000	0.000	0.000	0.000
55	A	67	ARG	1	0.969	0.967	8.479	0.185	0.185	0.000	0.000	0.000	0.000
56	A	68	LYS	1	0.962	0.988	5.634	-0.245	-0.245	0.000	0.000	0.000	0.000
57	A	69	ALA	0	-0.006	-0.004	3.530	-1.053	-0.887	0.003	-0.045	-0.124	0.000
58	A	70	ALA	0	0.045	0.037	4.613	0.501	0.548	-0.001	-0.003	-0.042	0.000
59	A	71	GLU	-1	-0.781	-0.887	7.141	-0.510	-0.510	0.000	0.000	0.000	0.000
60	A	72	GLN	0	-0.020	-0.014	1.678	-0.810	-1.810	5.681	-2.160	-2.521	-0.002
61	A	73	SER	0	0.031	0.036	3.731	0.246	0.577	0.001	-0.012	-0.320	0.000
62	A	74	ALA	0	0.046	0.011	5.255	-0.316	-0.279	-0.001	-0.001	-0.035	0.000
63	A	75	ALA	0	-0.027	-0.015	5.904	0.000	0.000	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.859	-0.907	4.988	1.048	1.048	0.000	0.000	0.000	0.000
65	A	77	VAL	0	-0.021	-0.012	6.928	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	78	ALA	0	0.033	0.014	10.118	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	79	LEU	0	-0.057	-0.032	7.980	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	80	ARG	1	0.809	0.884	7.987	0.104	0.104	0.000	0.000	0.000	0.000
69	A	81	GLU	-1	-0.801	-0.876	12.685	-0.063	-0.063	0.000	0.000	0.000	0.000
70	A	82	LEU	0	-0.034	-0.022	13.961	0.008	0.008	0.000	0.000	0.000	0.000
71	A	83	ALA	0	-0.047	-0.011	15.310	0.009	0.009	0.000	0.000	0.000	0.000
72	A	84	LYS	1	0.755	0.880	16.636	0.119	0.119	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:SER)