FMO DATABASE

FMODB ID: YVZG2

Calculation Name: 3DGP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DGP

Chain ID: B

ChEMBL ID:

UniProt ID: Q02939

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:

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	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-343075.491811
FMO2-HF: Nuclear repulsion	318176.556806
FMO2-HF: Total energy	-24898.935005
FMO2-MP2: Total energy	-24971.694451

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(B:2:ALA)

Summations of interaction energy for fragment #1(B:2:ALA)

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.
0.97	2.361	-0.017	-0.75	-0.625	0.002

Interaction energy analysis for fragmet #1(B:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.003

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	B	4	ALA	0	0.037	0.024	3.892	0.284	1.675	-0.017	-0.750	-0.625	0.002
4	B	5	ARG	1	0.859	0.912	6.548	-0.546	-0.546	0.000	0.000	0.000	0.000
5	B	6	LYS	1	0.965	0.977	10.248	0.172	0.172	0.000	0.000	0.000	0.000
6	B	7	GLY	0	0.034	0.004	13.339	0.032	0.032	0.000	0.000	0.000	0.000
7	B	8	ALA	0	-0.015	0.012	15.760	-0.030	-0.030	0.000	0.000	0.000	0.000
8	B	9	LEU	0	0.006	0.015	15.544	0.025	0.025	0.000	0.000	0.000	0.000
9	B	10	VAL	0	-0.018	-0.009	17.700	-0.029	-0.029	0.000	0.000	0.000	0.000
10	B	11	GLN	0	0.043	0.029	20.745	0.033	0.033	0.000	0.000	0.000	0.000
11	B	12	CYS	0	-0.061	-0.022	22.322	-0.014	-0.014	0.000	0.000	0.000	0.000
12	B	13	ASP	-1	-0.760	-0.855	25.382	0.101	0.101	0.000	0.000	0.000	0.000
13	B	14	PRO	0	0.077	0.016	27.105	0.002	0.002	0.000	0.000	0.000	0.000
14	B	15	SER	0	-0.069	-0.042	28.171	0.002	0.002	0.000	0.000	0.000	0.000
15	B	16	ILE	0	0.029	0.001	27.661	-0.001	-0.001	0.000	0.000	0.000	0.000
16	B	17	LYS	1	0.831	0.914	21.920	-0.219	-0.219	0.000	0.000	0.000	0.000
17	B	18	ALA	0	0.009	-0.001	26.485	0.004	0.004	0.000	0.000	0.000	0.000
18	B	19	LEU	0	0.004	0.004	29.045	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	20	ILE	0	-0.005	-0.009	24.747	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.012	0.010	23.445	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	22	GLN	0	-0.038	-0.014	27.173	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	23	ILE	0	-0.014	-0.008	29.166	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	24	ASP	-1	-0.822	-0.925	25.048	0.138	0.138	0.000	0.000	0.000	0.000
24	B	25	ALA	0	0.004	0.014	27.672	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	26	LYS	1	0.866	0.940	29.545	-0.076	-0.076	0.000	0.000	0.000	0.000
26	B	27	MET	0	-0.027	-0.011	29.821	-0.006	-0.006	0.000	0.000	0.000	0.000
27	B	28	SER	0	-0.038	-0.007	26.825	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	29	ASP	-1	-0.843	-0.923	23.422	0.080	0.080	0.000	0.000	0.000	0.000
29	B	30	ILE	0	-0.009	-0.004	24.184	-0.009	-0.009	0.000	0.000	0.000	0.000
30	B	31	VAL	0	-0.021	-0.020	20.570	0.004	0.004	0.000	0.000	0.000	0.000
31	B	32	LEU	0	-0.082	-0.039	16.330	0.003	0.003	0.000	0.000	0.000	0.000
32	B	33	GLU	-1	-0.853	-0.926	12.496	0.742	0.742	0.000	0.000	0.000	0.000
33	B	34	GLU	-1	-0.851	-0.927	17.007	0.195	0.195	0.000	0.000	0.000	0.000
34	B	35	LEU	0	-0.075	-0.036	13.405	0.038	0.038	0.000	0.000	0.000	0.000
35	B	36	ASP	-1	-0.744	-0.852	16.573	0.277	0.277	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.893	-0.939	19.306	0.181	0.181	0.000	0.000	0.000	0.000
37	B	38	THR	0	-0.105	-0.051	21.745	-0.024	-0.024	0.000	0.000	0.000	0.000
38	B	39	HIS	1	0.797	0.853	17.951	-0.220	-0.220	0.000	0.000	0.000	0.000
39	B	40	LEU	0	0.034	0.033	18.845	0.025	0.025	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.007	0.004	13.136	-0.021	-0.021	0.000	0.000	0.000	0.000
41	B	42	VAL	0	0.017	0.004	17.080	0.000	0.000	0.000	0.000	0.000	0.000
42	B	43	ASN	0	0.046	0.024	18.990	-0.019	-0.019	0.000	0.000	0.000	0.000
43	B	44	PRO	0	0.016	-0.001	18.402	-0.009	-0.009	0.000	0.000	0.000	0.000
44	B	45	SER	0	-0.075	-0.044	21.138	-0.009	-0.009	0.000	0.000	0.000	0.000
45	B	46	LYS	1	0.870	0.933	23.936	-0.073	-0.073	0.000	0.000	0.000	0.000
46	B	47	VAL	0	0.007	0.013	22.427	0.003	0.003	0.000	0.000	0.000	0.000
47	B	48	GLU	-1	-0.790	-0.892	25.381	0.038	0.038	0.000	0.000	0.000	0.000
48	B	49	PHE	0	0.007	0.011	28.855	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	50	VAL	0	0.044	0.021	25.858	-0.001	-0.001	0.000	0.000	0.000	0.000
50	B	51	LYS	1	0.847	0.911	26.504	-0.044	-0.044	0.000	0.000	0.000	0.000
51	B	52	HIS	0	-0.018	-0.016	30.335	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.906	-0.953	31.986	0.055	0.055	0.000	0.000	0.000	0.000
53	B	54	LEU	0	-0.004	-0.001	28.678	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	55	ASN	0	0.020	0.008	33.140	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	56	ARG	1	0.916	0.987	35.875	-0.038	-0.038	0.000	0.000	0.000	0.000
56	B	57	LEU	0	0.018	0.001	33.743	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	58	LEU	0	0.007	0.017	34.642	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	59	SER	0	-0.058	-0.059	38.213	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	60	LYS	1	0.851	0.911	40.901	-0.035	-0.035	0.000	0.000	0.000	0.000
60	B	61	ASN	0	0.017	0.025	41.301	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	62	ILE	0	-0.005	-0.009	43.169	-0.002	-0.002	0.000	0.000	0.000	0.000
62	B	63	TYR	0	-0.055	-0.012	45.231	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	64	ASN	0	0.002	0.011	42.404	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:ALA)