FMO DATABASE

FMODB ID: 94NL2

Calculation Name: 3SD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SD4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BVI0

Base Structure: X-ray

Registration Date: 2023-06-21

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

DOI:

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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-464023.409631
FMO2-HF: Nuclear repulsion	434811.849826
FMO2-HF: Total energy	-29211.559806
FMO2-MP2: Total energy	-29297.723437

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:-3:GLY)

Summations of interaction energy for fragment #1(A:-3:GLY)

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.
-2.737	-1.848	-0.005	-0.351	-0.535	0.001

Interaction energy analysis for fragmet #1(A:-3:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.021

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

Sort

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	-1	MET	0	-0.009	0.016	3.855	0.630	1.422	-0.004	-0.334	-0.455	0.001
4	A	4	HIS	0	0.017	-0.010	6.695	0.292	0.292	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.009	0.006	9.932	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	6	PRO	0	-0.003	0.028	13.154	0.081	0.081	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.020	-0.004	16.066	0.019	0.019	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.831	0.906	19.174	0.204	0.204	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.904	0.934	21.718	0.080	0.080	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.042	0.014	25.184	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.033	-0.015	20.924	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.007	-0.005	21.091	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.035	-0.022	15.846	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.856	-0.921	16.440	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.020	0.009	16.066	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.017	0.011	18.777	0.024	0.024	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.019	0.007	21.476	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.057	-0.027	23.206	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.006	-0.005	21.808	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.833	-0.897	26.232	-0.080	-0.080	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.019	0.017	24.946	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.878	0.951	26.720	0.153	0.153	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.703	-0.837	27.230	-0.130	-0.130	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.847	0.874	23.713	0.211	0.211	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.053	-0.016	29.524	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.880	0.942	31.572	0.121	0.121	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.022	0.000	32.635	0.009	0.009	0.000	0.000	0.000	0.000
28	A	28	TRP	0	-0.011	-0.021	27.602	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.037	-0.036	30.652	0.011	0.011	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.014	0.006	29.719	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.032	-0.011	25.756	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	HIS	0	0.016	0.004	24.138	0.016	0.016	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.003	0.021	17.699	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.900	-0.967	19.952	-0.107	-0.107	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.859	-0.936	14.173	-0.316	-0.316	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.078	-0.042	11.687	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.778	-0.869	9.282	-1.195	-1.195	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.013	-0.034	6.796	0.081	0.081	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.979	-0.968	4.667	-2.789	-2.692	-0.001	-0.017	-0.080	0.000
40	A	40	GLU	-1	-0.839	-0.926	6.108	-1.014	-1.014	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.006	0.002	8.924	0.207	0.207	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.749	0.860	10.801	0.948	0.948	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.019	-0.002	13.419	0.004	0.004	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.013	0.017	16.178	0.014	0.014	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.026	-0.021	18.484	0.031	0.031	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.014	-0.006	21.987	0.016	0.016	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.004	-0.007	24.948	0.011	0.011	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.885	0.927	28.219	0.075	0.075	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.911	0.951	30.363	0.064	0.064	0.000	0.000	0.000	0.000
50	A	50	TRP	0	-0.018	0.009	29.220	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.002	-0.009	30.450	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	HIS	1	0.927	0.939	24.593	0.120	0.120	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.880	0.956	25.550	0.092	0.092	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.030	-0.015	27.089	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.752	-0.851	22.728	-0.148	-0.148	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.852	-0.904	22.113	-0.228	-0.228	0.000	0.000	0.000	0.000
57	A	57	TRP	0	0.024	0.012	14.023	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.058	-0.024	18.763	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	CYS	0	0.060	0.019	15.362	-0.030	-0.030	0.000	0.000	0.000	0.000
60	A	60	TRP	0	0.068	0.040	9.342	0.085	0.085	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.877	-0.943	15.155	-0.350	-0.350	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.055	-0.011	18.087	0.047	0.047	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.034	0.007	20.804	0.018	0.018	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.073	-0.047	23.842	0.026	0.026	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.045	0.035	19.740	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.793	0.876	24.082	0.097	0.097	0.000	0.000	0.000	0.000
67	A	67	PRO	0	0.051	0.031	26.294	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.009	0.011	27.605	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:-3:GLY)