FMO DATABASE

FMODB ID: 393KL

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	OptH
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	-463996.95717
FMO2-HF: Nuclear repulsion	434785.956173
FMO2-HF: Total energy	-29211.000997
FMO2-MP2: Total energy	-29297.159862

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.
-3.121	-2.267	-0.002	-0.361	-0.491	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 : -0.014 / 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

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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	-1	MET	0	-0.032	0.007	3.787	0.225	1.079	-0.002	-0.361	-0.491	0.001
4	A	4	HIS	0	-0.016	-0.025	6.483	0.231	0.231	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.013	0.011	9.597	-0.037	-0.037	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.007	0.028	12.815	0.089	0.089	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.019	0.001	15.745	0.025	0.025	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.844	0.915	18.872	0.206	0.206	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.887	0.924	21.630	0.076	0.076	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.049	0.016	25.177	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.011	-0.001	20.755	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.012	0.020	20.912	0.007	0.007	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.023	-0.023	15.890	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.902	-0.954	16.587	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.040	0.014	16.461	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.008	-0.002	19.094	0.023	0.023	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.018	0.005	21.626	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.060	-0.039	23.318	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.021	-0.012	21.834	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.857	-0.925	26.384	-0.081	-0.081	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.014	0.006	24.894	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.874	0.962	26.711	0.146	0.146	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.719	-0.862	27.108	-0.135	-0.135	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.877	0.898	23.615	0.216	0.216	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.059	-0.018	29.468	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.852	0.917	31.321	0.131	0.131	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.004	0.012	32.326	0.010	0.010	0.000	0.000	0.000	0.000
28	A	28	TRP	0	-0.016	-0.017	27.327	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.036	-0.006	30.468	0.013	0.013	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.022	0.002	29.683	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.031	-0.022	25.685	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.021	-0.021	24.478	0.015	0.015	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.023	0.010	17.799	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.896	-0.965	20.153	-0.104	-0.104	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.855	-0.924	14.219	-0.279	-0.279	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.105	-0.068	11.652	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.798	-0.886	8.896	-1.158	-1.158	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.029	-0.046	6.817	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.928	-0.947	4.848	-2.419	-2.419	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.902	-0.962	5.861	-1.294	-1.294	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.026	-0.017	8.809	0.236	0.236	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.843	0.910	10.562	0.898	0.898	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.021	0.007	13.364	0.008	0.008	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.005	0.017	16.121	0.011	0.011	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.025	-0.019	18.373	0.034	0.034	0.000	0.000	0.000	0.000
46	A	46	HIS	0	-0.036	-0.013	21.883	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.012	0.000	24.815	0.010	0.010	0.000	0.000	0.000	0.000
48	A	48	LYS	1	1.022	0.993	28.209	0.068	0.068	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.882	0.936	30.734	0.057	0.057	0.000	0.000	0.000	0.000
50	A	50	TRP	0	-0.008	0.019	29.441	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.011	-0.001	30.334	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	52	HIS	1	0.904	0.916	24.907	0.115	0.115	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.907	0.985	25.504	0.095	0.095	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.074	-0.061	26.630	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.734	-0.826	22.490	-0.152	-0.152	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.852	-0.914	22.082	-0.221	-0.221	0.000	0.000	0.000	0.000
57	A	57	TRP	0	0.043	0.028	14.096	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.054	-0.021	18.077	0.016	0.016	0.000	0.000	0.000	0.000
59	A	59	CYS	0	0.036	0.010	15.353	-0.041	-0.041	0.000	0.000	0.000	0.000
60	A	60	TRP	0	0.107	0.066	9.305	0.096	0.096	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.883	-0.938	15.264	-0.341	-0.341	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.075	-0.032	17.862	0.045	0.045	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.033	0.011	20.577	0.020	0.020	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.075	-0.043	23.654	0.029	0.029	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.055	0.034	19.620	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.818	0.905	23.972	0.100	0.100	0.000	0.000	0.000	0.000
67	A	67	PRO	0	0.036	0.023	26.196	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.009	0.019	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)