FMO DATABASE

FMODB ID: V5521

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	OptAll
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	-215253.607321
FMO2-HF: Nuclear repulsion	196997.902465
FMO2-HF: Total energy	-18255.704856
FMO2-MP2: Total energy	-18309.992605

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.
-8.292	-1.772	3.737	-2.669	-7.587	-0.011

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 : 0.041 / q_NPA : 0.009

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	255	THR	0	-0.010	0.010	3.886	-1.707	-0.301	-0.009	-0.586	-0.811	0.002
4	A	256	VAL	0	0.090	0.057	3.090	-1.687	-0.763	0.120	-0.215	-0.828	-0.001
5	A	257	ALA	0	0.020	0.011	3.853	-0.139	0.281	0.001	-0.167	-0.253	0.000
6	A	258	ASN	0	-0.033	-0.026	5.417	0.299	0.299	0.000	0.000	0.000	0.000
7	A	259	GLU	-1	-0.835	-0.918	7.272	0.413	0.413	0.000	0.000	0.000	0.000
8	A	260	VAL	0	-0.034	-0.023	7.382	0.049	0.049	0.000	0.000	0.000	0.000
9	A	261	ILE	0	-0.041	-0.011	9.463	0.083	0.083	0.000	0.000	0.000	0.000
10	A	262	GLN	0	-0.075	-0.040	11.606	0.086	0.086	0.000	0.000	0.000	0.000
11	A	263	GLY	0	0.026	0.018	13.095	0.044	0.044	0.000	0.000	0.000	0.000
12	A	264	LEU	0	-0.068	-0.037	11.784	0.012	0.012	0.000	0.000	0.000	0.000
13	A	265	TRP	0	-0.038	-0.040	8.212	-0.063	-0.063	0.000	0.000	0.000	0.000
14	A	266	GLY	0	0.037	0.035	12.267	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	267	ASN	0	-0.058	-0.050	14.394	-0.061	-0.061	0.000	0.000	0.000	0.000
16	A	268	GLY	0	-0.008	-0.012	15.517	0.014	0.014	0.000	0.000	0.000	0.000
17	A	269	GLN	0	-0.039	-0.044	14.095	-0.058	-0.058	0.000	0.000	0.000	0.000
18	A	270	GLU	-1	-0.826	-0.896	14.605	-0.245	-0.245	0.000	0.000	0.000	0.000
19	A	271	ARG	1	0.911	0.974	9.012	0.784	0.784	0.000	0.000	0.000	0.000
20	A	272	TYR	0	-0.063	-0.050	10.209	-0.104	-0.104	0.000	0.000	0.000	0.000
21	A	273	ASP	-1	-0.833	-0.909	10.687	-0.394	-0.394	0.000	0.000	0.000	0.000
22	A	274	SER	0	-0.029	-0.030	11.932	0.035	0.035	0.000	0.000	0.000	0.000
23	A	275	LEU	0	-0.047	-0.022	5.387	0.015	0.015	0.000	0.000	0.000	0.000
24	A	276	ALA	0	0.028	0.017	8.379	0.030	0.030	0.000	0.000	0.000	0.000
25	A	277	ASN	0	-0.071	-0.029	10.150	0.067	0.067	0.000	0.000	0.000	0.000
26	A	278	ALA	0	-0.046	-0.020	8.890	0.065	0.065	0.000	0.000	0.000	0.000
27	A	279	GLY	0	-0.025	-0.003	8.848	0.082	0.082	0.000	0.000	0.000	0.000
28	A	280	TYR	0	-0.054	-0.026	3.467	-0.581	0.061	0.034	-0.149	-0.528	0.000
29	A	281	ASP	-1	-0.837	-0.917	4.125	-1.505	-1.351	0.000	-0.031	-0.123	0.000
30	A	282	PRO	0	-0.011	-0.022	4.577	-0.703	-0.580	-0.001	-0.007	-0.115	0.000
31	A	283	GLN	0	-0.034	-0.009	6.774	0.001	0.001	0.000	0.000	0.000	0.000
32	A	284	ALA	0	0.042	0.016	2.677	-0.429	-0.264	1.211	-0.371	-1.005	-0.001
33	A	285	VAL	0	-0.005	-0.004	2.387	-2.941	-1.268	2.145	-0.967	-2.851	-0.011
34	A	286	GLN	0	0.036	0.038	3.691	0.597	0.697	0.008	0.023	-0.131	0.000
35	A	287	ASP	-1	-0.847	-0.922	5.541	-0.848	-0.848	0.000	0.000	0.000	0.000
36	A	288	LYS	1	0.778	0.871	2.718	-0.194	0.719	0.228	-0.199	-0.942	0.000
37	A	289	VAL	0	0.005	-0.004	5.407	0.341	0.341	0.000	0.000	0.000	0.000
38	A	290	ASN	0	-0.037	-0.018	7.682	0.272	0.272	0.000	0.000	0.000	0.000
39	A	291	GLU	-1	-0.836	-0.893	7.265	-0.295	-0.295	0.000	0.000	0.000	0.000
40	A	292	ILE	0	0.002	-0.007	6.504	0.140	0.140	0.000	0.000	0.000	0.000
41	A	293	LEU	0	-0.039	-0.033	10.277	0.105	0.105	0.000	0.000	0.000	0.000
42	A	294	ASN	0	-0.092	-0.028	12.879	0.055	0.055	0.000	0.000	0.000	0.000
43	A	295	ALA	0	0.010	0.006	12.802	0.040	0.040	0.000	0.000	0.000	0.000
44	A	296	ARG	1	0.828	0.922	14.574	0.186	0.186	0.000	0.000	0.000	0.000
45	A	297	GLU	-1	-0.852	-0.907	16.144	-0.051	-0.051	0.000	0.000	0.000	0.000
46	A	298	ILE	0	-0.035	-0.032	19.674	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	299	ALA	0	-0.001	0.003	20.543	0.015	0.015	0.000	0.000	0.000	0.000
48	A	300	ASP	-1	-1.009	-0.999	22.483	-0.070	-0.070	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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