FMO DATABASE

FMODB ID: 89JVY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-293194.323535
FMO2-HF: Nuclear repulsion	269451.242798
FMO2-HF: Total energy	-23743.080738
FMO2-MP2: Total energy	-23812.286156

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.
-11.101	-5.527	10.601	-5.565	-10.606	-0.034

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 : 0.027 / q_NPA : -0.001

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	0.016	0.009	3.419	-0.288	1.611	0.004	-0.621	-1.282	0.003
4	A	4	GLN	0	-0.012	0.000	5.885	0.017	0.017	0.000	0.000	0.000	0.000
5	A	5	MET	0	-0.002	-0.006	9.680	0.077	0.077	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.008	0.002	11.839	-0.005	-0.005	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.046	-0.018	15.521	0.005	0.005	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.017	0.005	17.940	0.004	0.004	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.840	-0.927	21.377	-0.115	-0.115	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.034	0.010	23.258	0.008	0.008	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.855	0.948	19.359	0.174	0.174	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.073	0.022	22.548	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.003	-0.012	20.365	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.849	-0.941	19.698	-0.251	-0.251	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.015	0.026	19.553	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.877	0.936	16.443	0.210	0.210	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.950	0.978	14.999	0.256	0.256	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.042	0.009	15.055	-0.067	-0.067	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.013	0.013	13.644	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.003	-0.016	10.533	-0.057	-0.057	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.006	0.025	10.042	-0.183	-0.183	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.084	0.040	11.308	-0.077	-0.077	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.035	-0.023	6.703	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.037	-0.042	6.465	-0.271	-0.271	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.922	-0.956	7.310	-0.767	-0.767	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.045	-0.018	8.891	0.050	0.050	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.011	0.008	2.544	-0.732	-0.165	1.071	-0.335	-1.302	0.000
28	A	28	VAL	0	-0.001	-0.002	5.116	-0.110	0.002	-0.001	-0.004	-0.107	0.000
29	A	29	ARG	1	0.967	0.978	6.493	0.605	0.605	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.101	-0.068	7.399	0.146	0.146	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.037	-0.017	2.385	-0.207	0.112	0.906	-0.231	-0.993	-0.001
32	A	32	ASP	-1	-0.961	-0.960	5.992	-0.315	-0.315	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.036	0.004	2.608	-1.288	-0.258	0.854	-0.379	-1.505	-0.001
34	A	34	ARG	1	0.879	0.886	5.487	0.525	0.525	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.081	0.018	5.016	-0.790	-0.726	-0.001	0.000	-0.063	0.000
36	A	36	ASP	-1	-0.836	-0.869	6.379	-1.224	-1.224	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.023	-0.019	3.053	-0.635	0.210	0.127	-0.263	-0.708	0.000
38	A	38	VAL	0	-0.002	0.016	1.974	-8.896	-8.764	7.636	-3.577	-4.190	-0.035
39	A	39	ARG	1	0.877	0.941	3.725	3.253	3.859	0.005	-0.155	-0.456	0.000
40	A	40	ILE	0	0.039	0.022	5.365	-0.173	-0.173	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.045	-0.020	7.731	0.183	0.183	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.007	-0.008	10.860	0.041	0.041	0.000	0.000	0.000	0.000
43	A	43	ASN	0	-0.025	-0.006	13.610	0.029	0.029	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.860	-0.941	16.334	-0.184	-0.184	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.050	-0.012	19.235	0.018	0.018	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.120	0.055	21.896	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.020	-0.014	25.543	0.007	0.007	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.822	-0.927	27.523	-0.030	-0.030	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.090	-0.048	24.374	0.003	0.003	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.022	0.009	20.967	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.023	-0.003	24.441	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.008	-0.005	24.328	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.005	-0.008	26.695	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.020	-0.003	28.935	0.000	0.000	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.045	0.028	30.284	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.012	-0.043	28.585	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.018	-0.038	26.309	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.009	0.011	28.421	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	MET	0	0.012	0.025	31.576	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.838	0.951	25.440	0.048	0.048	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.034	0.004	28.742	-0.004	-0.004	0.000	0.000	0.000	0.000

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