FMO DATABASE

FMODB ID: LZMQ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-463999.88865
FMO2-HF: Nuclear repulsion	434788.472712
FMO2-HF: Total energy	-29211.415938
FMO2-MP2: Total energy	-29297.585997

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.
-3.07	-2.211	-0.002	-0.364	-0.492	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 : -0.015 / q_NPA : -0.022

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	-0.020	0.014	3.787	0.176	1.035	-0.002	-0.364	-0.492	0.001
4	A	4	HIS	0	0.001	-0.023	6.483	0.258	0.258	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.004	0.007	9.599	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.006	0.028	12.815	0.085	0.085	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.006	-0.004	15.746	0.022	0.022	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.844	0.905	18.873	0.203	0.203	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.900	0.932	21.630	0.073	0.073	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.038	0.010	25.177	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.020	-0.004	20.807	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.014	0.024	20.927	0.000	0.000	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.025	-0.022	15.896	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.887	-0.954	16.609	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.030	0.011	16.444	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.002	0.001	19.113	0.023	0.023	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.014	0.009	21.570	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.060	-0.034	23.338	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.019	-0.009	21.846	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.826	-0.897	26.401	-0.079	-0.079	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.009	0.003	24.911	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.869	0.952	26.721	0.148	0.148	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.716	-0.856	27.105	-0.132	-0.132	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.857	0.889	23.718	0.215	0.215	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.057	-0.020	29.465	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.858	0.928	31.180	0.127	0.127	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.006	0.008	32.323	0.011	0.011	0.000	0.000	0.000	0.000
28	A	28	TRP	0	-0.011	-0.017	27.253	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.042	-0.014	30.480	0.012	0.012	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.020	-0.001	29.697	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.037	-0.022	25.643	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	HIS	0	0.019	0.000	24.482	0.015	0.015	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.019	0.010	17.890	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.874	-0.954	19.929	-0.098	-0.098	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.861	-0.943	14.377	-0.274	-0.274	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.096	-0.050	11.775	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.797	-0.885	9.082	-1.146	-1.146	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.017	-0.041	6.933	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.946	-0.952	4.872	-2.498	-2.498	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.812	-0.906	5.867	-1.206	-1.206	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.017	-0.007	8.806	0.226	0.226	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.733	0.847	10.562	0.979	0.979	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.016	0.000	13.377	0.010	0.010	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.007	0.016	16.134	0.011	0.011	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.034	-0.026	18.384	0.035	0.035	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.020	-0.003	21.895	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.006	-0.002	24.828	0.010	0.010	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.951	0.956	28.222	0.068	0.068	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.892	0.941	30.748	0.054	0.054	0.000	0.000	0.000	0.000
50	A	50	TRP	0	-0.013	0.014	29.246	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.003	-0.004	30.448	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	HIS	1	0.921	0.935	24.581	0.113	0.113	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.889	0.959	25.511	0.092	0.092	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.051	-0.034	26.634	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.762	-0.846	22.528	-0.148	-0.148	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.832	-0.897	22.047	-0.224	-0.224	0.000	0.000	0.000	0.000
57	A	57	TRP	0	0.031	0.026	14.082	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.057	-0.028	18.064	0.019	0.019	0.000	0.000	0.000	0.000
59	A	59	CYS	0	0.046	0.018	15.350	-0.037	-0.037	0.000	0.000	0.000	0.000
60	A	60	TRP	0	0.098	0.063	9.277	0.089	0.089	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.884	-0.936	14.928	-0.349	-0.349	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.065	-0.021	17.862	0.045	0.045	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.032	0.011	20.575	0.020	0.020	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.067	-0.044	23.646	0.027	0.027	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.057	0.036	19.608	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.798	0.881	23.972	0.096	0.096	0.000	0.000	0.000	0.000
67	A	67	PRO	0	0.038	0.025	26.196	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.003	0.016	27.564	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-3:GLY)