FMO DATABASE

FMODB ID: NN3GQ

Calculation Name: 4FDX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FDX

Chain ID: A

ChEMBL ID:

UniProt ID: A2SL37

Base Structure: X-ray

Registration Date: 2023-09-20

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-293328.376569
FMO2-HF: Nuclear repulsion	269584.906063
FMO2-HF: Total energy	-23743.470506
FMO2-MP2: Total energy	-23812.597253

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:PRO)

Summations of interaction energy for fragment #1(A:1:PRO)

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.
-11.246	-5.836	10.577	-5.641	-10.346	-0.033

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.005

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	ILE	0	0.005	0.005	3.457	-0.330	1.539	0.001	-0.601	-1.269	0.003
4	A	4	GLN	0	-0.009	0.001	5.888	0.025	0.025	0.000	0.000	0.000	0.000
5	A	5	MET	0	0.002	0.000	9.580	0.065	0.065	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.014	0.012	11.875	0.006	0.006	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.043	-0.016	15.404	0.003	0.003	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.014	0.006	17.989	0.006	0.006	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.828	-0.902	21.427	-0.119	-0.119	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.029	0.007	23.310	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.851	0.940	19.789	0.178	0.178	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.052	0.012	22.598	0.002	0.002	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.014	-0.001	20.590	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.807	-0.921	19.745	-0.271	-0.271	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.020	0.026	19.595	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.832	0.911	16.498	0.198	0.198	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.911	0.953	15.045	0.232	0.232	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.019	-0.005	15.095	-0.065	-0.065	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.001	0.019	13.768	-0.037	-0.037	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.001	-0.010	10.616	-0.064	-0.064	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.008	0.026	10.077	-0.186	-0.186	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.080	0.038	11.330	-0.077	-0.077	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.031	-0.024	6.784	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.038	-0.038	6.486	-0.284	-0.284	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.926	-0.957	7.448	-0.756	-0.756	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.050	-0.022	8.966	0.049	0.049	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.009	0.016	2.520	-0.831	-0.120	0.868	-0.315	-1.264	-0.001
28	A	28	VAL	0	-0.004	-0.003	5.193	-0.121	-0.014	-0.001	-0.003	-0.103	0.000
29	A	29	ARG	1	0.957	0.979	6.703	0.644	0.644	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.093	-0.074	7.327	0.132	0.132	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.042	-0.023	2.332	-0.245	0.063	0.870	-0.225	-0.953	-0.001
32	A	32	ASP	-1	-0.946	-0.948	5.893	-0.241	-0.241	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.049	-0.007	2.392	-1.089	-0.236	1.090	-0.408	-1.536	0.000
34	A	34	ARG	1	0.886	0.886	5.542	0.291	0.291	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.077	0.018	5.168	-0.702	-0.644	-0.001	0.000	-0.056	0.000
36	A	36	ASP	-1	-0.822	-0.856	6.520	-1.074	-1.074	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.014	-0.009	3.364	-0.593	0.179	0.046	-0.239	-0.578	0.000
38	A	38	VAL	0	0.004	0.015	1.951	-9.132	-9.013	7.700	-3.690	-4.129	-0.034
39	A	39	ARG	1	0.841	0.921	3.710	3.297	3.910	0.004	-0.160	-0.458	0.000
40	A	40	ILE	0	0.037	0.019	5.417	-0.199	-0.199	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.030	-0.013	7.785	0.194	0.194	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.004	-0.008	10.914	0.033	0.033	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.036	-0.018	13.665	0.035	0.035	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.800	-0.913	16.387	-0.202	-0.202	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.046	-0.012	19.093	0.019	0.019	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.110	0.051	21.909	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.012	-0.021	25.470	0.006	0.006	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.826	-0.907	27.471	-0.035	-0.035	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.087	-0.047	24.356	0.002	0.002	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.057	0.022	21.311	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.011	-0.003	24.286	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.034	-0.017	24.071	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.026	0.002	26.560	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.021	-0.002	28.792	0.000	0.000	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.016	0.010	30.140	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.003	-0.047	28.437	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.025	-0.026	26.144	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.004	0.011	28.278	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	MET	0	0.019	0.027	31.430	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.803	0.929	25.126	0.055	0.055	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.037	0.003	28.657	-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:1:PRO)