FMO DATABASE

FMODB ID: 7J83K

Calculation Name: 3DSP-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DSP

Chain ID: A

ChEMBL ID:

UniProt ID: Q58AD3

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-381117.854344
FMO2-HF: Nuclear repulsion	353462.515566
FMO2-HF: Total energy	-27655.338778
FMO2-MP2: Total energy	-27730.771608

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:1:VAL )

Summations of interaction energy for fragment #1(A:1: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.
19.324	28.751	14.047	-8.492	-14.98	-0.094

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.788 / q_NPA : 0.892

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	3	MET	0	0.000	-0.027	2.357	-2.205	-1.336	6.474	-2.452	-4.891	-0.021
4	A	4	SER	0	-0.015	-0.023	3.649	6.447	6.714	0.019	-0.026	-0.260	-0.001
5	A	5	ASN	0	0.025	0.006	5.747	4.338	4.338	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.100	-0.037	2.963	0.355	1.060	0.295	-0.188	-0.812	-0.001
7	A	7	VAL	0	0.011	0.015	5.859	2.044	2.044	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.925	0.966	7.795	21.233	21.233	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.027	0.004	5.328	-5.537	-5.537	0.000	0.000	0.000	0.000
10	A	10	TYR	0	0.001	0.009	7.220	3.134	3.134	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.807	-0.894	8.786	-31.418	-31.418	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.025	0.017	10.370	2.469	2.469	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.033	0.004	12.842	-1.010	-1.010	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.914	-0.909	13.492	-21.517	-21.517	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.017	-0.026	12.737	-0.129	-0.129	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.104	-0.065	9.364	-2.906	-2.906	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.820	0.888	5.333	34.277	34.277	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.045	0.026	6.538	-2.911	-2.911	0.000	0.000	0.000	0.000
19	A	19	HIS	1	0.792	0.888	2.929	50.771	53.110	1.584	-0.863	-3.060	-0.006
20	A	20	VAL	0	0.064	0.038	4.884	0.993	1.054	0.000	-0.004	-0.056	0.000
21	A	21	PHE	0	-0.001	-0.015	2.181	-2.549	-3.286	3.327	-0.622	-1.968	-0.006
22	A	22	LYS	1	1.018	1.004	7.219	20.108	20.108	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.927	-0.966	9.951	-22.620	-22.620	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.017	0.007	10.874	1.128	1.128	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.909	0.975	8.027	22.282	22.282	0.000	0.000	0.000	0.000
26	A	26	MET	0	0.025	0.021	7.114	-1.439	-1.439	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.023	-0.015	4.388	-0.568	-0.517	0.000	-0.008	-0.043	0.000
28	A	28	MET	0	-0.018	0.015	5.359	0.628	0.668	0.000	-0.003	-0.036	0.000
29	A	29	GLU	-1	-0.843	-0.927	2.165	-105.912	-100.195	2.348	-4.315	-3.750	-0.059
30	A	30	ASN	0	0.069	0.017	5.951	1.974	1.974	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.982	0.991	7.689	16.736	16.736	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.043	-0.022	9.128	0.682	0.682	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.024	0.024	4.789	-0.730	-0.702	0.000	-0.003	-0.025	0.000
34	A	34	LYS	1	0.888	0.946	4.502	28.368	28.455	0.000	-0.008	-0.079	0.000
35	A	35	SER	0	0.024	0.009	5.993	1.308	1.308	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.018	-0.008	6.710	3.914	3.914	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.022	0.011	9.192	-2.239	-2.239	0.000	0.000	0.000	0.000
38	A	38	MET	0	-0.004	-0.004	8.943	0.651	0.651	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.031	-0.010	12.065	1.164	1.164	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.852	-0.932	15.645	-15.155	-15.155	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.069	-0.052	17.620	0.680	0.680	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.953	0.984	17.293	17.301	17.301	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.018	0.007	18.005	-0.581	-0.581	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.070	-0.040	13.041	-0.689	-0.689	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.899	-0.942	17.092	-13.919	-13.919	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.066	-0.072	14.371	-0.898	-0.898	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.952	0.942	10.984	23.100	23.100	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.919	-0.930	15.683	-16.464	-16.464	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.034	0.031	17.344	0.685	0.685	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.027	0.035	17.125	0.548	0.548	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.950	0.959	18.337	12.123	12.123	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.015	-0.007	12.618	0.185	0.185	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.016	0.004	17.020	0.159	0.159	0.000	0.000	0.000	0.000
54	A	54	MET	0	0.002	0.023	13.172	0.155	0.155	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.946	0.945	15.915	13.248	13.248	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.072	0.052	18.462	0.093	0.093	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.030	-0.031	12.685	-0.873	-0.873	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.877	-0.915	14.633	-14.513	-14.513	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.061	-0.047	11.178	-0.264	-0.264	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.004	0.021	15.169	0.519	0.519	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.939	0.938	16.382	14.517	14.517	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.022	-0.011	19.075	0.511	0.511	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.873	-0.937	22.357	-11.250	-11.250	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.905	-0.973	22.772	-12.102	-12.102	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.052	-0.004	25.576	0.354	0.354	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.097	-0.037	28.206	0.425	0.425	0.000	0.000	0.000	0.000
67	A	67	NME	0	-0.005	0.004	26.389	0.115	0.115	0.000	0.000	0.000	0.000

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