FMO DATABASE

FMODB ID: YZZQ2

Calculation Name: 4CVD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CVD

Chain ID: A

ChEMBL ID:

UniProt ID: P19385

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	48
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-214869.91204
FMO2-HF: Nuclear repulsion	196614.284536
FMO2-HF: Total energy	-18255.627504
FMO2-MP2: Total energy	-18309.932064

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:253:LEU)

Summations of interaction energy for fragment #1(A:253:LEU)

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.
-9.975	-2.854	3.73	-3.145	-7.706	-0.007

Interaction energy analysis for fragmet #1(A:253:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.011

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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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	255	THR	0	-0.001	0.008	3.797	-2.121	-0.488	-0.012	-0.673	-0.948	0.003
4	A	256	VAL	0	0.065	0.042	2.637	-2.243	-1.146	0.376	-0.384	-1.089	-0.001
5	A	257	ALA	0	0.023	0.013	3.590	-0.656	0.012	0.005	-0.287	-0.386	0.001
6	A	258	ASN	0	-0.033	-0.038	5.371	0.049	0.163	-0.001	-0.004	-0.109	0.000
7	A	259	GLU	-1	-0.832	-0.905	7.262	0.895	0.895	0.000	0.000	0.000	0.000
8	A	260	VAL	0	-0.039	-0.027	7.380	-0.031	-0.031	0.000	0.000	0.000	0.000
9	A	261	ILE	0	-0.047	-0.015	9.285	0.032	0.032	0.000	0.000	0.000	0.000
10	A	262	GLN	0	-0.072	-0.035	11.420	0.088	0.088	0.000	0.000	0.000	0.000
11	A	263	GLY	0	0.025	0.022	12.738	0.025	0.025	0.000	0.000	0.000	0.000
12	A	264	LEU	0	-0.068	-0.039	11.410	0.012	0.012	0.000	0.000	0.000	0.000
13	A	265	TRP	0	-0.047	-0.037	7.971	-0.098	-0.098	0.000	0.000	0.000	0.000
14	A	266	GLY	0	0.047	0.042	12.309	-0.040	-0.040	0.000	0.000	0.000	0.000
15	A	267	ASN	0	-0.034	-0.025	14.242	-0.056	-0.056	0.000	0.000	0.000	0.000
16	A	268	GLY	0	-0.009	-0.014	15.502	0.007	0.007	0.000	0.000	0.000	0.000
17	A	269	GLN	0	-0.039	-0.045	14.117	-0.049	-0.049	0.000	0.000	0.000	0.000
18	A	270	GLU	-1	-0.834	-0.912	14.637	-0.144	-0.144	0.000	0.000	0.000	0.000
19	A	271	ARG	1	0.902	0.963	8.854	0.675	0.675	0.000	0.000	0.000	0.000
20	A	272	TYR	0	-0.047	-0.035	9.976	-0.068	-0.068	0.000	0.000	0.000	0.000
21	A	273	ASP	-1	-0.835	-0.909	10.792	-0.311	-0.311	0.000	0.000	0.000	0.000
22	A	274	SER	0	-0.027	-0.027	12.179	0.033	0.033	0.000	0.000	0.000	0.000
23	A	275	LEU	0	-0.034	-0.018	5.727	0.014	0.014	0.000	0.000	0.000	0.000
24	A	276	ALA	0	0.010	0.006	8.564	0.016	0.016	0.000	0.000	0.000	0.000
25	A	277	ASN	0	-0.072	-0.027	10.054	0.037	0.037	0.000	0.000	0.000	0.000
26	A	278	ALA	0	-0.050	-0.024	9.011	0.052	0.052	0.000	0.000	0.000	0.000
27	A	279	GLY	0	-0.016	0.006	8.884	0.099	0.099	0.000	0.000	0.000	0.000
28	A	280	TYR	0	-0.058	-0.029	3.362	-0.708	-0.147	0.031	-0.135	-0.457	0.000
29	A	281	ASP	-1	-0.836	-0.915	3.852	-1.453	-1.332	0.000	-0.030	-0.092	0.000
30	A	282	PRO	0	-0.001	-0.022	4.304	-0.697	-0.532	-0.001	-0.016	-0.148	0.000
31	A	283	GLN	0	-0.025	-0.022	6.429	0.004	0.004	0.000	0.000	0.000	0.000
32	A	284	ALA	0	0.027	0.018	2.460	-0.468	-0.330	1.239	-0.329	-1.048	0.000
33	A	285	VAL	0	-0.015	-0.010	2.318	-3.331	-1.671	1.983	-1.162	-2.481	-0.010
34	A	286	GLN	0	0.027	0.037	3.532	0.467	0.548	0.018	0.047	-0.146	0.000
35	A	287	ASP	-1	-0.858	-0.929	5.199	-1.004	-1.004	0.000	0.000	0.000	0.000
36	A	288	LYS	1	0.802	0.882	3.213	0.294	1.131	0.093	-0.171	-0.759	0.000
37	A	289	VAL	0	-0.004	-0.014	5.232	0.409	0.455	-0.001	-0.001	-0.043	0.000
38	A	290	ASN	0	-0.039	-0.016	7.595	0.306	0.306	0.000	0.000	0.000	0.000
39	A	291	GLU	-1	-0.861	-0.902	7.556	-0.450	-0.450	0.000	0.000	0.000	0.000
40	A	292	ILE	0	-0.005	-0.010	6.482	0.136	0.136	0.000	0.000	0.000	0.000
41	A	293	LEU	0	-0.046	-0.032	10.301	0.118	0.118	0.000	0.000	0.000	0.000
42	A	294	ASN	0	-0.085	-0.033	12.905	0.060	0.060	0.000	0.000	0.000	0.000
43	A	295	ALA	0	0.014	0.013	13.379	0.039	0.039	0.000	0.000	0.000	0.000
44	A	296	ARG	1	0.885	0.963	14.800	0.169	0.169	0.000	0.000	0.000	0.000
45	A	297	GLU	-1	-0.871	-0.914	16.438	-0.053	-0.053	0.000	0.000	0.000	0.000
46	A	298	ILE	0	-0.060	-0.057	19.799	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	299	ALA	0	-0.046	-0.015	19.846	0.015	0.015	0.000	0.000	0.000	0.000
48	A	300	ASP	-1	-0.964	-0.980	21.902	-0.034	-0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:253:LEU)